7,172 Matching Annotations
  1. Jun 2026
    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study investigates the impact of Pink1 loss on glial function and neuronal health in a Drosophila model, highlighting the role of mitochondria-organelle contacts and key genes such as Ccz1, Vps13, Mon1, and Rab7. The work provides insights into cellular processes underlying neurodegenerative diseases, with a focus on glia-neuron interactions. While the findings are promising, the study lacks critical controls, detailed mechanistic evidence, and explanatory figures to strengthen its claims.

      Strengths:

      (1) The study addresses an important topic in neuroscience, exploring the mechanisms of Pink1 loss, which has implications for Parkinson's disease and neurodegeneration.

      (2) The focus on mitochondria-organelle contacts and their regulation by Rab7-mediated pathways is novel and provides a potential mechanism for neuronal dysfunction.

      (3) The identification of key genes (Ccz1, Vps13, Mon1, Rab7) and their potential roles in Pink1-related pathways adds valuable knowledge to the field.

      (4) The manuscript uses a combination of genetic tools, Drosophila models, and functional assays to approach the problem from multiple angles.

      Weaknesses:

      (1) Specificity of Mz-Gal4: The study lacks validation of Mz-Gal4 specificity, as it may also drive expression in a few neurons or other types of glia. Additional control experiments using nls-GFP with Elav, Repo, or Draper antibody staining or alternative glial drivers would be helpful.

      We have addressed this issue of Gal4 driver specificity based on new experiments in the revised manuscript.

      (2) DLG staining is central to the story but is not well-supported by high-resolution Z-stack imaging, which should be included in the supplementary figures.

      We have included these in the supplement.

      (3) The manuscript does not confirm whether the candidate RNAi (Ccz1, Vps13, Mon1, Rab7) directly influence Rab7-mediated membrane trafficking or mitochondria-lysosome contacts in Pink1 mutants.

      This is indeed the case. These more mechanistic experiments were not yet performed.

      (4) Using ERG as a readout for EG effects in the antenna is not a direct or appropriate assay. Alternative functional assays relevant to antenna glia should be considered.

      We made the assumption that ensheating glial function is conserved across brain regions and now make this explicit in the reworded manuscript.

      (5) A graphical explanation of the interactions and functions of the candidate genes in Pink1 KO mutants is missing. This would greatly enhance the manuscript's clarity.

      We have included such a scheme in the new manuscript.

      (6) The study lacks details on sample sizes, effect sizes, and reproducibility, which are necessary for robust conclusions.

      We have included these essential data in the reworked document.

      (7) There are repeated words on page 3 ("olfactory Olfactory Receptor Neurons") and a lack of explanation in Figure 3C regarding the most up-regulated and down-regulated genes and the significance of large red dots.

      We have included the requested information.

      Reviewer #2 (Public review):

      Summary:

      This study proposes a novel role for ensheathing glia (EG) in a Pink1-model of Parkinson's disease and shows that this cell population exibits the highest number of DEG in a pre-symptomatic stage. In the olfactory system, there seems to be morphological changes in this cell-type that resembles an 'activated' state and the authors further show that the neuronal loss of Pink1 is responsible for this defect. The authors go on to show that manipulation of Pink1 in EG also leads to some defects in the visual system and in the dopaminergic neurons (DAN) that innervate the mushroom body (MB), and performed a screen based on the 'on-transient' defect of the ERG to identify potential genes that may modulate the function of EG in synaptic regulation. They focus on several genes related to Rab7/Vps13, and performed some additional experiments in the visual system and MB to propose the role of vesicle/lipid trafficking in EG as a important factor for PD pathogenesis.

      Strengths:

      The study proposes functional and mechanistic connections between several genes that have been linked to PD (PINK1, VPS13A/C). I feel that the data presented in Figure 1 and Fig3A-C are performed with rigor and are convincing/novel. The selection of Drosophila to study the questions is also a strength and the lab has extensive experiences in this field and model organism.

      Weaknesses:

      There is one fundamental concern I have with the genetic experiments performed in this paper (especially in Fig 3D and Fig4, see major issue #1), and I feel that there is a bit of a disconnect between the EG 'activation' phenotype the author show in the olfactory system and the other two neuronal systems (visual system, MB DAN) that the authors investigate see major issue #2). Also, there are quite a bit of information that is not provided in the manuscript (see major issues #3 and #4), which makes me difficult to judge the rigor and interpretation of several experiments.

      Major Concern #1: A number of lines used in this study are referred to as "RNAi" lines but when I look at the actual genotypes of reagents listed in the table in the METHODS section, many are actually NOT RNAi lines. Quite a few lines, including lines that the authors use as RNAi against Ccz1, Rab7 and Mon1, are gRNA lines for the TKO (TRiP-CRISPR knockout) system. While these reagents can theoretically knock-out these genes in somatic cells if used in combination with UAS-Cas9, there is no mention that UAS-Cas9 was used in this work throughout the manuscript. Hence, when these lines are just crossed to GAL4 with or without the Pink1 mutant, they shouldn't be having any effects. Similarly, the strongest hit from their screen was a TOE (TRiP-CRISPR Over Expression) gRNA against PIG-A, which could allow overexpression of PIG-A if there is a UAS-dCas9::VP64. However, I also do not see any mention that such activator was introduced into the crossing scheme. Considering that 3 of the 4 'hits' from their screen are not RNAi lines, I am quite skeptical of the study. Similarly, except for Vps13, all reagents used in Fig4 are TKO gRNA lines. Therefore, if this experiment was conducted without an UAS-Cas9, most of the data shown here are problematic. Also, note that several of the 'RNAi' lines listed in the Table in the METHODS section are actually MiMIC alleles. While some MiMIC lines could function as strong LOF alleles (if they are inserted in the exon or in an intron of the gene in the same orientation as the gene), some of the lines are not expected to affect gene function (e.g. FASN2 and CG17712, MiMICs are in introns and face the opposite orientation). Hence, the rationale of including these reagents in the screen doesn't make much sense. The description of the modifier screen should be much more detailed in the RESULTS and METHODS section and if the UAS-Cas9/dCas9::VP64 transgenes were not introduced when the TKO/TOE reagents were utilized, what can be concluded?

      In addition, for the 4 genes that the authors further study in Fig4, there are many other reagents that the authors can use, including mutant alleles, previously characterized RNAi lines (e.g. Vps13) and dominant negative/constitute active lines (e.g. especially for Rab7). The authors should validate their results with independent reagents to really convincingly show that the same conclusions can be drawn for the Vps13/Rab7 related genes since this is the key takeaway message of this paper.

      Also, they do not show whether the manipulation of these genes in a wild-type background (they only show what happens in Pink1 mutants) affect ERG and MB DAN synapse morphology. If these manipulations alone dramatically affect these phenotypes, it would be very difficult to interpret their data.

      We sincerely thank the reviewer for spotting this major oversight regarding the use of the TKO (TRiP-CRISPR knockout) and TOE (TRiP-CRISPR Over Expression) systems and the MiMIC alleles. As the reviewer pointed out, these lines were not used as intended, therefore our results and conclusions regarding the genetic interactions between Pink1 and several genes (PIG-A, Rab7, Ccz1, CG10646, Mon1, FASN2, CG17712), are incorrect and based on a technical mistake. These results were removed from the manuscript. While our mistake compromises the data regarding PIG-A, Rab7, Ccz1, CG10646, Mon1, FASN2, CG17712, it does not affect the results and conclusions for most of the genes of the screening and for Vps13 where we did use RNAi lines.

      Also, in the reworked manuscript, we provide additional evidence that modulation of vesicle trafficking proteins involved in mitochondria–endoplasmic reticulum (ER) membrane interactions, such as Vps13 and Vps35, influences neuronal function and rescues Pink1 mutant phenotypes when selectively downregulated in EG.

      Major Concern #2: In Figure 1, the authors show some morphological evidence that EG are 'activated' in Pink1 mutants, but whether the same phenomenon occurs in the visual system and in the MB is not shown. Since all of the studies in Fig3D and Fig4 are done in the visual system and MB, it is not clear whether the visual system and MB phenotypes are related to 'activation' of EG.

      Also, in the RNA-seq data in Fig1A and Fig3C, is there any molecular evidence that EG are indeed 'activated'? The only evidence that the authors show to state that EG are 'activated' in young Pink1 null animals is based on increased CD8::GFP staining in the olfactory system.

      The authors cannot draw a strong conclusion that indeed EG are 'activated' based on these data (e.g. perhaps the expression level of CD8::GFP is just increased). Additional evidence that the EG are 'activated' could be provided by looking at the increase in Draper intensity (as reported by Doherty et al. and MacDonald et al. that the authors cite), not only in the olfactory system, but also in the visual system and in the MB. It would also be informative if the authors can look at morphology of the EG in the visual system and MB to convincingly that the data shown in Fig4 is relevant to EG 'activation'.

      In line with the identification of DEG across the ensheating glia cluster in our single cell sequencing (where we did not distinguish between EG of different brain regions) we made the assumption that EG-(dys) function is consistent in the Pink1 mutant and conserved across brain regions. Nonetheless, to make clear that we did not consistently analyze EG morphology in the different brain regions that we probed in functional assays, we added a note in the manuscript. Furthermore, we also toned down our conclusion that the EG in Pink1 mutants are in an activated state: we note the similarity in phenotype in Pink1 mutants and situations of neuronal damage (where EG are activated) but added that the phenotype in Pink1 mutants may also be the result of the mere upregulation of GFP expression/fluorescence.

      Major Concern #3: In Fig3, there is no clear explanation why they focus on the ON transients and ignore the OFF transients, and also why the difference in the depolarization is not quantified in Fig4.

      We included this explanation in the reworked manuscript: In the Drosophila ERG, the sustained depolarization primarily reflects phototransduction in photoreceptors (and is defective when photoreceptors degenerate), whereas the ON and OFF transients arise from second-order lamina neurons and are widely used as readouts of signal transfer. We wanted to assess function and focused on the ON transient because in general it provides an onset-locked, more robust readout of function (Vilinsky & Johnson, 2012).

      Major Concern #4: While the authors claim that mz709-GAL4 is a EG specific driver, do the authors know that this is indeed true in the tissues and stages that are studied here? The Ito et al,. paper that is cited in the METHOD section has only looked at the expression of this reporter in embryonic and larval stages. The authors need to that the authors should validate their findings with an additional EG specific driver and/or provide additional data that mz709-GAL4 is indeed specific to EG in the adult fly brain and eye. If mz709-GAL4 is expressed in other cell-types, the interpretation of many of the data in this paper becomes quite questionable. I believe the data in Fig3B is suggesting that mz709-GAL4 is indeed specific to glia cells and not expressed in neurons, but whether this driver is truly specific to EG (and not in other glial types), especially in the visual system (including the lamina as well as in the eye), is not obvious.

      We labelled animals that express UAS-HisTag-eGFP (used also in our paper) under control of MZ709-Gal4 with anti-Elav (a neuronal marker) and find no significant overlap (see below “recommendation for authors”), consistent with MZ709-Gal4 not driving expression in neurons. This is consistent with previous published work: Indeed, MZ709-Gal4 has been amply used in adult flies and shown to be ensheating glia-specific (Doherty et al., 2009; Li et al., 2023; Sehgal et al.,2018). In the lamina neuropil of the Drosophila eye, MZ709-Gal4 is expressed in the marginal glia (Stenesen et al., 2019) which are neuropil-associated glia and are equivalent to generic ensheathing glia (Kremer et al., 2017). MZ709-Gal4 is also expressed also in satellite glia (Stenesen et al., 2019), but these glia enwrap the cell bodies of the lamina neurons and not the neuropil where synapses reside.

      Recommendations for the authors:

      Reviewing Editor Comments:

      We strongly encourage you to very carefully edit this manuscript. The reviewers made many probing comments that you should consider carefully.

      Reviewer #1 (Recommendations for the authors):

      (1) Validate the specificity of Mz-Gal4 by performing experiments with nls-GFP and Elav antibody staining to ensure there is no neuronal overlap. Additionally, consider using alternative glial-specific drivers, such as Repo-Gal4 or WG-Gal4, to confirm the findings.

      We expressed HisTag-eGFP (used also in our paper) under control of MZ709-Gal4 and labelled fly brains with anti-Elav (a neuronal marker). We do not observe significant overlap between the labels indicating MZ709-Gal4 does not express Gal4 in neurons (Supplementary figure 1).

      As indicated, these observations are consistent with previous published work. MZ709-Gal4 has been amply used in adult flies and shown to be ensheating glia-specific (Doherty et al., 2009; Li et al., 2023; Sehgal et al., 2018; Stahl et al., 2018). In the lamina neuropil of the Drosophila eye, MZ709-Gal4 is expressed in the marginal glia (Stenesen et al., 2019) which are neuropil-associated glia and are equivalent to generic ensheathing glia (Kremer et al., 2017). MZ709-Gal4 is also expressed also in satellite glia (Stenesen et al., 2019), but these glia enwrap the cell bodies of the lamina neurons and not the neuropil where synapses reside.

      (2) Include high-resolution Z-stack imaging of DLG staining to strengthen the assessment of synaptic integrity and ensure the robustness of the conclusions. These images should be added to either the main or supplementary figures.

      We included 2 supplementary figures (2 and 3) showing Z stacks that were used to delineate regions of interest at the MBs for the quantification of dopaminergic neuron afferents invasion. Our approach is identical to the one we used in Kaempf et al. 2026 (Kaempf et al., 2026).

      (3) Demonstrate whether the candidate RNAi (Ccz1, Vps13, Mon1, Rab7) directly influence Rab7-mediated membrane trafficking or mitochondria-lysosome contacts in Pink1 mutants. Use an appropriate method to confirm changes in organelle contacts in response to the RNAi treatments.

      Ccz1, Mon1 and Rab 7 were removed due to the technical mistake we made. We did confirm and maintain that Vps35 and Vps13 downregulation in EG rescues neuronal defects in Pink1 mutants. In the reworked manuscript we present a possible mechanism that involves the role of Vps35 and Vps13 in regulating ER-mitochondrial contacts, in line with our previous work (Valadas et al., 2018), while not ruling out possible other mechanisms.

      (4) Provide an alternative functional assay or evidence to support the use of ERG as a readout for EG effects in the antenna. Consider using a more direct assay relevant to antenna glia function.

      We agree that a more direct functional assay of antennal glia would be a nice addition (e.g., single-sensillum recordings or glial/ORN Ca<sup>2+</sup> imaging). However, implementing such assays would require new experimental pipelines and substantial additional data generation that is beyond our current ability and the scope of this revision.

      (5) Add a graphical illustration explaining the proposed mechanism of how Ccz1, Vps13, Mon1, and Rab7 function in Pink1 KO mutants, highlighting their interactions and roles within specific cell types.

      We included a schematic of our working model in Figure 5.

      (6) Clarify Figure 3C by explaining the most up-regulated and down-regulated genes and the significance of the large red dots. This will enhance the interpretability of the data.

      We expanded the legend to this figure: The large red dots represent the genes that rescue Pink1<sup>KO-WS</sup> phenotype when downregulated, the dark green dots are the 50 top most deregulated genes (magnitude of deregulation) in EG in Pink1<sup>KO-WS</sup> compared to controls, while the light green dots represent whole the genes detected in our cell-type specific transcriptomic experiment.

      (7) Correct repeated words on page 3 ("olfactory Olfactory Receptor Neurons") for clarity and consistency.

      Of course, sorry for this.

      (8) Ensure that sample sizes, effect sizes, and the number of replicates are explicitly stated for all experiments. This information is essential for evaluating the robustness and reproducibility of the findings.

      We made sure we consistently added all this information in the revised manuscript.

      (9) Verify and ensure that all data, reagents, and code used in the study are accessible and appropriately documented, in adherence with eLife's publishing policies.

      We made sure all data, reagents and code are available and/or properly described.

      By addressing these recommendations, the authors will significantly improve the clarity, rigor, and reproducibility of the manuscript.

      Reviewer #2 (Recommendations for the authors):

      Minor Points.

      (1) All figures seem to lack titles.

      We fixed this error.

      (2) In the abstract, the authors say that Rab7 and Vps13 are mutated in PD patients but I couldn't find the reference/information for Rab7 (the authors do refer to papers that linked VPS13A/C variants to PD but no mention about RAB7A/B being linked to PD). Please discuss this in the paper or modify the abstract accordingly.

      We removed this statement for rab7 from the paper.

      (3) When referring to the human gene, Pink1 should be written as PINK1 according to the HGNC nomenclature rules.

      We made this change.

      (4) The authors say Vps13 has two mammalian orthologs but actually it has four (VPS13A/B/C/D). I guess two of the four is linked to PD so the authors should modify there statement to reflect this.

      This is a misinterpretation of what we meant and we have clarified our intention: Drosophila possesses 3 paralogues of Vps13 - Vps13, Vps13B, and Vps13D - which we also detected in our screening (Neuman et al., 2025; Velayos-Baeza et al., 2004; Vonk et al., 2017). Among these Vps13 is most similar to human VPS13A and VPS13C (Hanna et al., 2023; McEwan & Ryan, 2022).

      (5) The abbreviation 'CNS' is used in the first page of the intro but I don't see it being spelled out as "central nervous system".

      We have spelled out central nervous system in the first page of the introduction.

      (6) On the top of page 5, the authors state that they confirmed that the 'synaptic area of DAN show a decrease in aged (25 days) animals' but data is not shown. If they want to make a statement like this, I believe such data should be included in supplemental data. Since the phenotype in the aged animal is not relevant to this study, one could remove this statement regarding the aged animals if they prefer not to show the data.

      The decreased synaptic area of DAN in 25-day old Pink1 mutants is shown in figure 2C-D of the manuscript and is consistent with data shown in (Kaempf et al., 2026).

    1. Author response:

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

      (1) We bioinformatically examined the repeat compositions of MLSs (Figure 3B), which clearly indicated that all MLSs are composed of repetitive sequences to a much greater extent than the rest of the genome.

      (2) We confirmed the blockage of chromosome breakage by the 4R-CBS mutations using a telomere-anchored PCR assay (Figure 5C-E).

      (3) We examined the effect of the 4R-CBS mutations on the expression of genes encoded in 4R-MDS by RNA-seq (Figure 9). This analysis unexpectedly revealed that gene expression from 4R-MDS is not significantly affected in the mutants, allowing us to extend our discussion.

      (4) We added two authors, Alix Lemoine and Tomoko Noto, who performed the experiments for these revisions.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this study, Nagao and Mochizuki examine the fate of germline chromosome ends during somatic genome differentiation in the ciliate Tetrahymena thermophila. During sexual reproduction, a new somatic genome is created from a zygotic, germline-derived genome by extensive programmed DNA elimination events. It has been known for some time that the termini of the germline chromosomes are eliminated, but the exact process and kinetics of the elimination events have not been thoroughly investigated. The authors first use germline-specific telomere probes to show that the loss of these chromosome ends occurs with similar timing as other DNA elimination events. By comparative analysis of the assembled germline and somatic genomes, the authors find that the ends of each of the germline chromosomes are composed of a few hundred kilobases of micronuclear limited sequences (MLS) that are removed starting around 14 hours after the start of conjugation, which initiates sexual development. They then develop an in situ hybridization assay to track the fate of one end of chromosome 4 while simultaneously following the adjacent macronuclear destined sequence (MDS) retained in the new somatic genome. This allows the authors to more clearly show that these adjacent chromosomal segments are initially amplified in the developing genome before the terminal MLS is eliminated. Finally, they mutate the chromosome breakage sequence (CBS) that normally separates the MLS terminus from the adjacent MDS region, to show that strains that develop with only one mutant chromosome can produce viable sexual progeny, but it appears that both the MLS and the MDS from the mutant chromosome are lost. If both chromosome copies have the CBS mutation, the cells arrest during development and do not eliminate many germline-limited sequences and fail to produce viable progeny. Overall, this study provides many new insights into the fate of germline chromosome ends during somatic genome remodeling and suggests extensive coordination of different DNA elimination events in Tetrahymena.

      Strengths:

      Overall, the experiments were well executed with appropriate controls. The findings are generally robust. Importantly, the study provides several novel findings. First, the authors provide a fairly comprehensive characterization of the size of the MLS at the end of each germline chromosome. I'm not sure whether this has been published elsewhere. Second, the authors develop a novel method to study the fate of chromosome termini during development and use it to conclusively track the elimination of these termini. Third, the authors show that the elimination of these termini appears to occur concurrently with most other DNA elimination events during somatic genome differentiation. And fourth, the authors show that failure to separate these eliminated sequences from the normally retained chromosome alters the fate of these adjacent MDS and the loss of the cells' ability to produce viable progeny.

      Weaknesses:

      It appears the authors did extensive analysis of the MLS chromosome ends, but did not provide too much information related to their composition. If this has not been published elsewhere, it would be useful to describe the proportion of unique and repetitive sequences and provide more information about the general composition of the chromosome ends. Such information would help the reader understand the nature of these MLS and how they may or may not differ from other eliminated sequences.

      We now calculated the proportions of unique and repetitive sequences for each MLS, and these data are included in Figure 3B and described in the main text of the revised manuscript. A more comprehensive analysis of chromosome-end composition, including detailed characterization in the context of the complete MIC genome assembly, is beyond the scope of the current study and will be presented in a future publication.

      Although the development of the novel FISH probes for large chromosome ends allowed for these novel discoveries, the signal in several images was visible, but often quite faint. I'm not sure there is anything the authors could do to improve the signal-to-noise ratio, but one needs to stare at the images carefully to understand the findings.

      We have submitted higher-resolution images for the revised manuscript, which we believe much improve the visibility of faint signals.

      One main weakness in the opinion of this reviewer is that the authors did very little to understand why, when a terminal MLS and the adjacent MDS fail to get separated because of failure in chromosome breakage, both segments are eliminated. The authors propose that possibly essential genes in the MDS get silenced, and the resulting lack of gene expression is the issue, but this and other possibilities were not tested. The study would provide more mechanistic insight if they had tried to assess whether the MDS on the CBS mutant chromosome becomes enriched in silencing modifications (e.g., H3K9me3). Alternatively, the authors could have examined changes in gene expression for some of the loci on the neighbouring MDS.

      The 4R-CBS mutation causes two distinct defects that should be considered separately: (1) co-elimination of 4R-MLS and the adjacent 4R-MDS during uniparental transmission of the 4R-CBS mutation; and (2) a global block of DNA elimination during biparental transmission of the 4R-CBS mutation.

      For the first defect, 4R-MLS and 4R-MDS may simply co-segregate into the nuclear compartment where DNA elimination occurs when the chromosome break that normally separates 4R-MLS from 4R-MDS is blocked. In this scenario, no additional process, such as spreading of scnRNA production, heterochromatin formation, or gene silencing, would be required to induce co-elimination. This point was not clearly stated in the previous manuscript, and we have now added a discussion of it to the revised manuscript.

      The possibility of gene silencing within 4R-MDS was raised as a potential explanation for the second defect. To test this possibility, we performed RNA-seq analysis of wild-type and 4R-CBS mutant cells to determine whether gene expression from 4R-MDS is affected by mutations at 4R-CBS. Contrary to our expectations, we found that genes in 4R-MDS are not significantly down-regulated in 4R-CBS mutant cells compared with other genes. This result suggests that the DNA elimination defect in these cells cannot be explained by silencing of genes located within 4R-MDS. We have added these RNA-seq data to Figure 9 and described them in the Results section. We have also revised the Discussion to propose alternative possibilities that may guide future investigations.

      The other main weakness is that since the authors only mutated the end of one germline chromosome, it is not clear whether the elimination of the MDS adjacent to the terminal MLS on chromosome 4 when the CBS is mutated is a general phenomenon, i.e., would happen at all chromosome ends, or is unique to the situation at Chromosome 4R. Knowing whether it is a general phenomenon or not would provide important insight into the authors' findings.

      As was described in the manuscript, the short (CBS = 15 nt) target within AT-rich and repetitive regions prevent designing gRNAs specifically targeting some of the chromosome end CBSs. We tried to mutate the CBS sequences of the left end of the chromosome 3 (3L) and the left end of the chromosome 5 (5L) by the strategy we used to mutate 4R-CBS but failed. Therefore, to systematically mutate other chromosome-end CBSs, we need to establish a different strategy, such as combining template-based repairing to CRISPR-induced DSB. We have explained this technical limitation and stated that “Our data support a critical role for 4R-CBS in separating 4R-MLS from 4R-MDS, but it remains unclear whether all MIC chromosome ends are strictly CBS-dependent for their elimination.” in Discussion (Page 12).

      Reviewer #2 (Public review):

      Summary:

      Nagao and Mochizuki investigated how the germline (MIC) telomere was removed during programmed genome rearrangement in the developing somatic nucleus (MAC). Using an optimized oligo-FISH procedure, the authors demonstrated that MIC telomeres were co-eliminated with a large region of MIC-limited sequences (MLS) demarcated on the opposite side by a sub-telomeric chromosome breakage site (CBS). This conclusion was corroborated by the latest assembly of the Tetrahymena MIC genome. They further employed CRISPR-Cas9 mutagenesis to disrupt a specific sub-telomeric CBS (4R-CBS). In uniparental progeny (mutant X WT), DNA elimination of the sub-telomeric MLS was not affected, but the adjacent MAC-destined sequence (MDS) may be co-eliminated. However, in biparental progeny (mutant X mutant), global DNA elimination was arrested, revealing previously unrecognized connections between chromosome breakage and DNA elimination. It also paves the way for future studies into the underlying molecular mechanisms. The work is rigorous, well-controlled, and offers important insights into how eukaryotic genomes demarcate genic regions (retained DNA) and regions derived from transposable elements (TE; eliminated DNA) during differentiation. The identification of chromosome breakage sequences as barriers preventing the spread of silencing (and ultimately, DNA elimination) from TE-derived regions into functional somatic genes is a key conceptual contribution.

      Strengths:

      New method development: Oligo-FISH in Tetrahymena. This allows high-resolution visualization of critical genome rearrangement events during MIC-to-MAC differentiation. This method will be a very powerful tool in this area of study.

      Integration of cytological and genomic data. The conclusion is strongly supported by both analyses.

      Rigorous genetic analysis of the role played by 4R-CBS in separating the fate of sub-telomeric MLS (elimination) and MDS (retention). DNA elimination in ciliates has long been regarded as an extreme form of gene silencing. Now, chromosome breakage sequences can be viewed as an extreme form of gene insulators.

      Weaknesses:

      The finding of global disruption of DNA elimination in 4R-CBS mutant progeny is highly intriguing, but it's mostly presented as a hypothesis in the Discussion. The authors propose that the failure to separate MLS from MDS allows aberrant heterochromatin spreading from the former into the latter, potentially silencing genes required for DNA elimination itself. While supported by prior literature on heterochromatin feedback loops, the specific targets silenced are not identified. While results from ChIP-seq and small RNA-seq can greatly strengthen the paper, the reviewer understands that direct molecular characterization may be beyond the scope of the current work.

      As mentioned in our reply to Reviewer #1’s comment above, we performed RNA-seq on wild-type and 4R-CBS mutant cells at 13.5 hpm and 15 hpm and found that genes in 4R-MDS are not significantly downregulated in 4R-CBS mutant cells (Figure 9), suggesting that the DNA elimination defect in these cells cannot be explained by aberrant heterochromatin spreading. Therefore, the link between the chromosome break at 4R-CBS and general DNA elimination remains elusive and will be a very interesting subject for our future research. We have added these results and revised the discussion in the manuscript.

      Reviewer #3 (Public review):

      Programmed DNA elimination (PDE) is a process that removes a substantial amount of genomic DNA during development. While it contradicts the genome constancy rule, an increasing number of organisms have been found to undergo PDE, indicating its potential biological function. Single-cell ciliates have been used as a prominent model system for studying PDE, providing important mechanistic insights into this process. Many of those studies have focused on the excision of internally eliminated sequences (IES) and the subsequent repair using non-homologous end joining (NHEJ). These studies have led to the identification of small RNAs that mark retained or eliminated regions and the transposons that generate double-strand breaks.

      In this manuscript, Nagao and Mochizuki examined the other type of breaks in ciliates that were healed with telomere addition. They specifically focused on the sequences at the ends of the germline (MIC) chromosomes, which have received relatively less attention due to the technical challenges associated with the highly repetitive nature of the sequences. The authors used the Tetrahymena model and developed a set of new tools. They used a novel FISH strategy that enables the distinction between germline and somatic telomeres, as well as the retained and eliminated DNA near the chromosome ends. This allows them to track these sequences at the cellular level throughout the development process, where PDE occurs. They also analyzed the more comprehensive germline and somatic genomes and determined at the sequence level the loss of subtelomeric and telomere sequences at all chromosome ends. Their result is reminiscent of the PDE observed in nematodes, where all germline chromosome ends are removed and remodeled. Thus, the finding connects two independent PDE systems, a protozoan and a metazoan, and suggests the convergent evolution of chromosome end removal and remodeling in PDE.

      The majority of sites (8/10) at the junctions of retained and eliminated DNA at the chromosome ends contain a chromosome breakage sequence (CBS). The authors created a set of mutants that modify the CBS at the ends of chromosome 4R. CBS regions are challenging for CRISPR due to their AT-rich sequences, making the creation of the 4R-CBS mutants a significant breakthrough. They used the FISH assay to determine if PDE still occurs in these mutant strains with compromised CBS. Surprisingly, they found that instead of blocking PDE, its adjacent retained DNA is now eliminated, suggesting a co-elimination event when the breakage is impaired. Furthermore, in biparental mutant crosses, no PDE occurred, and no viable progeny were produced, indicating that the removal of chromosome ends is crucial for proper PDE and sexual progeny development. Overall, the work demonstrates a critical role for 4R-CBS in separating retained and eliminated DNA.

      We appreciate Reviewer 3’s assessment.

      Recommendations for the authors:

      Reviewing Editor Comments:

      All reviewers agree that this study makes an important contribution to the field; however, they also offered several suggestions for how the manuscript could be improved. In particular, we draw your attention to the comments from Reviewer #1, who suggests that the manuscript could benefit from additional information on the general composition of germline chromosome ends, where available.

      As noted in our response to Reviewer #1 in the Public Reviews above, we have included an analysis of the fraction of repetitive sequences for each MLS as Figure 3B in the revised manuscript, highlighting the highly repetitive nature of MLSs compared with the rest of the genome.

      Reviewer #1 (Recommendations for the authors):

      As mentioned in the weaknesses section, the authors could provide more information regarding the nature of the sequences that make up the terminal MLS. There have been reports that these are highly repetitive; is that the case? Also, did the authors identify common repeats that are not internal to mic chromosomes that could be used to track all terminal segments of the five chromosomes? This would complement their mic-telomere probe.

      As noted in our response to Reviewer #1’s Public Review above, we have added an analysis of the fraction of repetitive sequences for each MLS as Figure 3B in the revised manuscript, which confirms that MLSs are highly repetitive.

      Apart from the moderately conserved Telomere Associated Sequence (TAS), described by Kirk and Blackburn (1995) and of unknown function, we were unable to identify any obvious shared repeats unique to MLSs that could support the development of pan-MLS-specific probes.

      One major weakness is that the authors did little to determine the cause of the elimination of the adjacent MDS along the 4R-MLS when the CBS was mutated. It would really improve the study if the authors could show that:

      (1) Gene expression of genes on the MDS is reduced in 4r-CBS mutant progeny.

      (2) Heterochromatin modifications are unexpectedly acquired on the MDS in mutants relative to wild-type chromosomes.

      (3) Do scnRNA specific to the MDS region appear in the mutant progeny during development, but not in wild-type crosses?

      Any data that would help support the authors' hypothesis regarding how the MDS region is eliminated when the CBS is mutant would definitely strengthen the conclusions of the study.

      As noted in our response to Reviewer #1’s Public Review above, we performed RNA-seq on wild-type and 4R-CBS mutant cells at 13.5 hpm and 15 hpm. Our analysis showed that genes within the 4R-MDS are not significantly downregulated in 4R-CBS mutant cells (Figure 9), suggesting that the DNA elimination defect in these cells cannot be attributed to aberrant heterochromatin spreading. Therefore, the connection between the chromosome break at 4R-CBS and general DNA elimination remains unclear and represents an important avenue for future investigation. We have incorporated these results and revised the discussion accordingly in the updated manuscript.

      The other main weakness is that by mutating the CBS of only one chromosome arm, one can't know whether the loss of the MDS with the MLS in the mutants is generalizable for all chromosome arms or is unique to 4R. The authors noted that they were unable to make any other mutated CBSs. Another way to try to get to this question is to try to rescue the mutant by inserting a new CBS into the 4R arm such that some MLS remains linked to the 4R-MDS and see whether removing the mic telomere is the issue, or would a block of MLS attached to the 4R-MDS be sufficient to cause its elimination. I'm not sure where to exactly put the new CBS, but worth thinking about.

      To introduce a new CBS into 4R-MLS, we would need to insert a CBS-containing construct into the MIC by homologous recombination during conjugation and then select engineered transformants using a drug resistance marker expressed from the derived MAC. However, because 4R-MLS is still eliminated in the progeny of 4R-CBS mutants, the introduced marker would be lost from the MAC even if homologous recombination were successful. Therefore, although the strategy suggested by this reviewer is very interesting, several technical innovations are required to make such experiments feasible, leaving this approach for a future project.

      It seems somewhat curious that the mutation of the CBS completely blocks nuclear development. In Paramecium, the failure to complete internal DNA elimination events can lead to alternative telomere addition. The caveat being that, in Paramecium, telomere addition appears more promiscuous than in Tetrahymena. It would be helpful to know how absolute the failure to produce progeny is in these mutants. Is it zero progeny in 10<sup>6</sup>, 10<sup>7</sup>, 10<sup>8</sup> ..... mated cells? Can the authors provide a possible lowest possible frequency?

      The viability tests were performed using bulk mating of 2.5 × 10<sup>4</sup> cells for each cross. Because ~70-80% of mating pairs complete the conjugation process and produce exconjugants under our standard culture conditions, and because we did not detect any 6-mp-resistant progeny from MUT x MUT crosses, we estimate that the probability of obtaining viable progeny in these crosses was less than 1 progeny per ~2 × 10<sup>4</sup> mating pairs. The number of cells used for the viability assay is described in the “Viability Test of Sexual Progeny” section of Materials and Methods and the estimated frequency of progeny production from the mutants has been mentioned in Results section in the revised manuscript.

      The one implication of the study is that chromosome breakage and DNA elimination, two different events, are coupled. In most mutants that block scnRNA-directed DNA elimination, both IES excision and chromosome breakage occur. In the study by McDaniel, SL. et al (2016). DRH1, a p68-related RNA helicase, is required for chromosome breakage in Tetrahymena. Biology Open pii: bio.021576. doi: 10.1242/bio.021576, germline knockouts of DRH1 could complete IES excision, but not chromosome breakage, indicating that the processes can be uncoupled. It may be useful for the authors to discuss this previous work in relation to their finding that failure in chromosome breakage can lead to DNA elimination of neighboring sequences.

      So far, DRH1 is the only gene reported to be required for chromosome breakage without affecting DNA elimination in Tetrahymena. However, McDaniel SL et al. (2016) examined chromosome breakage at only two CBSs (distinct from 4R-CBS), and thus it remains unclear how broadly chromosome breakage, including that at 4R-CBS, is affected in the absence of DRH1. In addition, McDaniel SL et al. (2016) assessed DNA elimination at three different IESs using PCR, whereas our study examined elimination of the repetitive Tlr1 transposon using FISH. Therefore, without further analysis of the similarities and differences in chromosome breakage and DNA elimination phenotypes between DRH1 knockout cells and 4R-CBS mutants, it is difficult to draw meaningful conclusions. Accordingly, we have limited ourselves to stating the following in the Discussion of the revised manuscript: “Moreover, chromosome breakage can be inhibited without disrupting DNA elimination, as shown in cells lacking zygotic expression of the p68-like RNA helicase Drh1 (McDaniel et al., 2016).”

      Minor corrections:

      Page 7, line 3: the text "......inducing chromosome break" should either be "......inducing chromosome breaks" or "......inducing a chromosome break".

      Corrected as “inducing a chromosome break”.

      Page 13, line 13: "......large block...." should be "......large blocks......".

      Corrected as suggested.

      Reviewer #2 (Recommendations for the authors):

      The authors can experimentally validate that chromosome breakage at 4R-CBS is indeed disrupted by the mutations. A PCR-based assay testing de novo telomere addition is a standard tool. In addition, MLS-linked telomere should only appear transiently during conjugation in WT cells.

      Because it was previously unknown whether de novo telomere addition occurs at the ends of MLSs upon chromosome breakage, we tested this using a PCR-based assay. We detected telomere-added chromosome ends of 4R-MLS and 3L-MLS, which were undetectable until 10.5 hpm, appeared at 12 hpm, and gradually decreased by 18 hpm in wild-type cells (WT × WT cross). Importantly, the appearance of the telomere-added 4R-MLS end, but not the 3L-MLS end, was blocked in 4R-CBS mutants (Mut x Mut crosses), strongly supporting that the 4R-CBS mutations specifically disrupt chromosome breakage at 4R-CBS. These new data are shown in Figure 5C–E and described in the Results section.

      The high FISH background during conjugation may be caused by the abundant presence of dsRNA, which is resistant to RNase A treatment but may be degraded by RNase III.

      The high FISH background was observed in the parental MAC at 9 and 12 hpm (Figure 2, 4, and S2) where dsRNA accumulation was not detected in the previous studies (Woo et al. 2016; Shehzada et al. 2024). In contrast, the MIC at 3 hpm and the new MAC at 9 and 12 hpm, where strong dsRNA accumulation was detected, showed much weaker background FISH signals (Figure 2, 4, and S2). Therefore, we believe that dsRNA is not the main cause of the high FISH background.

      It is likely that the long MIC telomere is treated as IES and targeted for DNA elimination. Indeed, telomere-specific scnRNA is abundantly produced during conjugation (http://www.ncbi.nlm.nih.gov/pubmed/19460867).

      We have cited the suggested literature and the following description has been added in Discussion to relate the reported telomere-derived scnRNAs to the abundant scnRNAs produced from MIC chromosomal ends: “In addition, telomere-complementary scnRNAs were reported to be produced specifically during conjugation (Cao et al. 2009).”

      Global disruption of DNA elimination may be a direct effect (DNA excision machinery affected) or indirect (unrepaired DSB and checkpoint activation).

      It has been reported that unrepaired DSBs caused by loss of Ku80 (Tku80) do not block DNA elimination in Tetrahymena (Lin et al. 2012). Therefore, checkpoint activation by unrepaired DSBs, if it occurs, is unlikely to explain the DNA elimination defect observed in the progeny of 4R-CBS mutants. Nonetheless, this direct-versus-indirect issue would be relevant when considering whether disruption of specific 4R-MDS-encoded genes in 4R-CBS mutants could cause the DNA elimination defect. Our new RNA-seq analysis, however, suggests that this possibility is unlikely. Therefore, we did not add further discussion of this direct-versus-indirect issue.

      Minor points:

      The zoom-in boxes in most images are barely visible.

      We have modified the zoom-in boxes to make them clearer.

      Page 13: scnRNA precursors (Cai et al., 2025) (Cai et al., in press). Is it one paper or two?

      They are two papers and the latter was published reacently. We have updated the citation.

      Reviewer #3 (Recommendations for the authors):

      The manuscript is well-written, with clear data, thoughtful discussion, and concise presentation. I have only a few minor comments below.

      For Figure 4 and others, the right panel shows the stats and percentages, with positive and negative labels. It's a bit confusing at first glance. I think it can be clarified what positive and negative mean in the legend.

      The legends of Figure 4, Figure 6 and Supplementary Figure S2, have been modified as “The presence (Positive) or absence (Negative) of the 4R-MLS FISH signal in new MAC (An) in 50 cells per time point was examined.”

      The quality of the FISH images is low at their current resolution. It is difficult to get a clear view.

      In the initial version, some images were in low resolution when we combined them into a single pdf file for review. In the revised manuscript, the images have been replaced with high-resolution images.

      The co-elimination of neighboring 4R-MDS when 4R-CBS is mutated, can this be viewed as a fail-safe mechanism to ensure the elimination of the chromosome ends? Regardless, the result begs the question of the significance of end removal and remodeling of PDE. Some speculations in the discussion might be helpful.

      Because the neighboring 4R-MDS contains approximately 100 predicted genes, its co-elimination would likely be too risky to evolve as a fail-safe mechanism for ensuring chromosome-end elimination in every generation. Instead, we interpret this as an erroneous process that can still be compensated for through endoreplication of the remaining, normally processed 4R-MDS from the non-mutated copy.

      We further speculate that the connection between chromosome breakage at 4R-CBS and the essential PDE process may serve as an evolutionary pressure to preserve the 4R-CBS locus in a chromosome breakage-competent state. We have added the following discussion to the revised manuscript (Page 15): “The observed link between chromosome breakage at 4R-CBS and the essential DNA elimination process may reflect the biological significance of MLSs and the importance of their removal from the MAC. Coupling these processes may have evolved as a mechanism to ensure that only functional chromosome-end CBS loci are preferentially transmitted to future generations.”

      Figure 1, legend, line 3, "the sexual reproduction process", do you mean "the sexual reproduction proceeds or initiates"?

      We meant “conjugation” = “the sexual reproduction process”. To make this clearer, we have revised the legend as “conjugation, which is the sexual reproduction process of Tetrahymena”.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this study, the authors propose that HSV-1 infection degrades the class I histone deacetylases HDAC1 and HDAC2. The MDM2 E3 ubiquitin ligase from the DNA damage response pathway is responsible for ubiquitinating these HDACs that are subsequently degraded via proteasomes. The authors hypothesize that HDAC degradation will cause hyperacetylation of viral chromatin and enable viral gene transcription.

      Strengths:

      The ubiquitination of HDAC1 & HDAC2 by Mdm2 and the mapping studies are clear.

      Comments on revised version:

      The authors enhanced their manuscript by more supportive data and providing clarification and the necessary corrections. However, a few more issues pertain:

      (1) In Figure 4j at 2 h post-infection we typically see the input virus and not progeny virus production. The input seems to have about 1-log difference that is expected to impact the results.

      We sincerely appreciate the reviewer's valuable comments regarding the timing notation. It should be noted that the "2 h" indicated in Figure 4j does not refer to two hours after the start of viral infection, but rather to two hours following medium replacement—after the virus has completed adsorption and internalization at 37°C (typically taking 2 hours), with this moment defined as the new time zero point (t = 0 h). Thus, this corresponds to approximately 4 hours post-infection (4 hpi). All subsequent sampling time points (4, 6, 12, and 24 h) are consistently defined according to this same system. This temporal framework aligns with previous studies: Nobe et al. (mBio 2025; DOI: 10.1128/mbio.00280-25) have clearly demonstrated that newly generated viral particles can be detected as early as 4 hours after HSV-1 infection, supporting the possibility of early progeny virus production at this time point in our experiment. We have accordingly revised the figure legend for Figure 4j to explicitly state the time reference ("t = 0 h defined as time of medium replacement post-adsorption") and added detailed procedural descriptions in the Methods section regarding adsorption, medium change, and sample collection time points to ensure clarity and reproducibility of the timing protocol.

      (2) Figs 1A, 1E, 2H it seems unclear why ICP4 becomes detectable at 12 h post-infection in HeLa cells? How about other a-genes? How about other cells? ICP4 is typically detectable within 2-3 h post-infection.

      We sincerely appreciate the valuable comments provided by the reviewers. Regarding the observation that ICP4 was detected only after 12 hours post-infection in HeLa cells, we re-evaluated our experimental conditions and reviewed relevant literature. The results indicate that at a higher multiplicity of infection (MOI = 5), ICP4 can indeed be reliably detected in HeLa cells as early as 2 hours post-infection (Author response image 1). Notably, Fouad S. El-Mayet et al. reported that under MOI = 1, ICP4 could not be detected until 8 hours after HSV-1 infection of mouse neuroblastoma Neuro-2A cells Figure 5A (Fouad S. El-Mayet et al., Antiviral Research, 2024, DOI: 10.1016/j.antiviral.2024.105870), although their early protein VP16 showed positive expression as early as 4 hours post-infection. This time difference is closely related to cell type: Neuro-2A is a highly susceptible neuronal cell line for HSV-1, exhibiting significantly faster viral gene expression kinetics compared to epithelial-derived HeLa cells. In contrast, HeLa cells are human cervical cancer epithelial cells with relatively low efficiency in initial transcriptional activation of HSV-1 and higher baseline expression levels of endogenous antiviral factors (such as interferon-stimulated genes), which may lead to a marked delay in the expression of early immediate-early genes like ICP4.

      Author response image 1.

      (3) In responses 2-2, Fig 5K: An infection without transfection has not been included. This is important to understand kinetics of infection in transfected cells.

      We sincerely appreciate the reviewer's insightful identification of this critical oversight. In all relevant experiments, we have strictly included empty vector transfection controls—serving as a baseline reference for each transfection group to eliminate potential influences from the transfection procedure itself and the vector background on viral replication, gene expression, and signaling pathways. The failure to clearly label this control in previous figure legends and main figures was indeed an omission in our presentation; we have now fully addressed this in the revised manuscript: all figures involving transfections (including Figures 3L, 3M, 5K, etc.) now explicitly indicate the "empty vector" control, and we have added detailed explanations in the figure legends and methods section regarding its role as an internal transfection control and procedural comparator. Once again, we thank the reviewer for their high level of professionalism in helping us enhance the completeness and scientific rigor of our data presentation.

      (4) Why HDAC1 with deleted NES does not accumulate or looks like it is degraded? Why then ICP4 does not accumulate?

      We sincerely apologize for the lack of clear labeling of the FLAG-HDAC1 ΔNES protein band in Author response image 2. This omission may have led reviewers to misinterpret its expression level as abnormal. After re-evaluation and improved annotation, Author response image 2 now clearly indicates the FLAG-HDAC1 ΔNES band its migration position corresponds to the expected molecular weight (slightly smaller than wild-type FLAG-HDAC1), and the band intensity is comparable to that of the empty vector and wild-type groups, indicating stable intracellular expression of this mutant protein without significant degradation. Therefore, its inhibitory effect on HSV-1 replication is not due to protein instability, but rather results from subcellular localization defects caused by the loss of nuclear export signal (NES): the ΔNES mutation causes HDAC1 to abnormally retain within the nucleus, ultimately leading to significant downregulation of ICP4 transcription and impaired protein accumulation.

      Author response image 2.

      Reviewer #2 (Public review):

      Summary:

      The authors discovered that HDAC1/2 are degraded in HSV-1 and PRV infections. They attempted to establish a new mechanism by which HDAC1/2 are translocated to the cytoplasm to be degraded in HSV-1 infection, and the degradation causes changes in histone acetylation to affect the DDR pathway.

      Strengths:

      (1) Interesting findings of HDAC1/2 degradation during HSV-1 and PRV infection, and it may impact more than the virology field.

      (2) Significant work to identify the ubiquitin site in HDAC1/2 and K63 linkage.

      Comments on revised version:

      The authors added experiments to address the previous comments. The added knockdown and overexpression experiments provided sufficient support for the proposed mechanism. The conclusions are now strengthened. However, a few essential controls are still missing.

      (1) Figure 3K: How does the expression level of Flag-HDAC1 variants compare to the endogenous HDAC1 level? The stripe probed by Flag antibody should be reprobed by HDAC1 antibody. Also, how does the K74R mutant affect histone acetylation? Moreover, the numbers between the panels are hard to read and have not been explained.

      We sincerely thank the reviewers for their insightful and constructive feedback. In response to the comment on Figure 3K, we performed antibody re-probing of the Flag-immunoprecipitated or Flag-immunoblotted membranes with a validated HDAC1-specific antibody. Consistent with robust transfection and expression, both wild-type Flag-HDAC1 and its mutants including K74R exhibited markedly elevated total HDAC1 protein levels relative to vector control, confirming efficient exogenous expression and protein stability. To directly assess functional consequences, we evaluated global histone acetylation status in parallel samples and found that the K74R mutant induces significantly greater deacetylation than wild-type Flag-HDAC1, as demonstrated by pronounced reductions in H3K56ac and H4K8 acetylation levels. Finally, to improve clarity and readability, we have revised the lane annotations in Figure 3K—increasing font size, enhancing contrast, and ensuring consistent alignment—and fully documented these modifications in the updated figure legend.

      (2) Figure 3M and 3L: DNA transfection per se frequently stimulates cell reactions that inhibit HSV-1 replication. Is the HSV-1 only sample transfected by empty vector or untransfected?

      We sincerely appreciate the reviewer's insightful identification of this critical oversight. In all relevant experiments, we have strictly included empty vector transfection controls serving as a baseline reference for each transfection group to eliminate potential influences from the transfection procedure itself and the vector background on viral replication, gene expression, and signaling pathways. The failure to clearly label this control in previous figure legends and main figures was indeed an omission in our presentation; we have now fully addressed this in the revised manuscript: all figures involving transfections (including Figures 3L, 3M, 5K, etc.) now explicitly indicate the "empty vector" control, and we have added detailed explanations in the figure legends and methods section regarding its role as an internal transfection control and procedural comparator. Once again, we thank the reviewer for their high level of professionalism in helping us enhance the completeness and scientific rigor of our data presentation.

      (3) Figure 4G-4J: What is the MDM2 knockdown efficiency?

      During the construction of the MDM2 knockdown cell lines, we first systematically validated the knockdown efficiency by qRT-PCR. As shown in Figure 4A, compared to the control group (shCtrl), MDM2 mRNA levels were reduced by approximately 60% in shMDM2 cells, and protein expression also showed a corresponding significant decrease, confirming that the cell line had been successfully established and exhibited stable gene silencing effects.

      (4) Figure 5F and line 400-401: "thereby preventing HDAC1 degradation-markedly impaired HSV-1 replication (Fig. 5F)." However, viral replication is not demonstrated in Figure 5F.

      We sincerely appreciate the reviewer for pointing out the error in the figure legend numbering. Upon verification, the experimental data referred to in lines 400–401 of the original text and in Figure 5F actually correspond to the revised new Figure 5J. We apologize for failing to update the figure references in the main text during the revision process due to an oversight. We have now uniformly corrected all relevant descriptions in the text to "Figure 5J" and conducted a comprehensive review of all figure numbers, table numbers, and cross-references throughout the manuscript to confirm there are no other similar errors.

      (5) Figure 5K: also need a control of empty vector. Furthermore, how does the HDAC1 ΔNES expression affect histone acetylation and DDR responses?

      We sincerely thank the reviewers for their thoughtful and constructive feedback on Figure 5K. With regard to the empty vector control: all pertinent experiments in this study were performed with rigorous inclusion of an appropriate empty vector control (pCMV-Flag or its isogenic backbone), serving as the definitive negative control. The prior absence of this control in the figure representation was unintentional and reflects an oversight in data presentation—not in experimental design—and we offer our sincere apologies. We have now incorporated the empty vector control bands into Figure 5K and revised the figure legend to explicitly identify and describe this control. In addition, per the reviewers’ recommendation, we conducted a comprehensive assessment of HDAC1 ΔNES function, specifically examining its impact on global histone acetylation and canonical DNA damage response (DDR) activation. Quantitative immunoblotting and immunofluorescence analyses revealed that HDAC1 ΔNES expression leads to significantly greater reduction in H3K56ac and H4K8 acetylation compared with wild-type HDAC1. Moreover, upon induction of DNA damage, HDAC1 ΔNES-expressing cells exhibit attenuated DDR signaling, evidenced by diminished γH2AX focus formation, reduced CHK2 phosphorylation (p-CHK2), and blunted p53 stabilization and activation consistent with impaired DDR initiation or propagation (see Author response image 3). Collectively, these data indicate that nuclear retention of HDAC1 due to NES deletion not only potentiates its chromatin-targeted deacetylase activity but also contributes to suppression of DDR signaling, likely through epigenetic modulation of damage-sensing chromatin domains.

      Author response image 3.

      (6) Statements listed below are better moved to discussion after all data being presented. They are quite a stretch when looking at each figure by itself.

      (i) Line 268-270: "Together, these findings indicate that HSV-1 selectively degrades class I HDACs, resulting in widespread histone hyperacetylation that fosters a chromatin state conducive to viral replication". ----may be okay for a statement.

      (ii) Line 291-292: "providing initial evidence that HSV-1 infection promotes DDR activation through downregulation of HDAC1 expression"

      (iii) Line 331-333: "Together, these results indicate that HSV-1 infection promotes K63-linked polyubiquitination of HDAC1/2 at conserved lysine residues, ultimately leading to their proteasomal degradation."

      (iv) Line 334-336 is a repeated sentence.

      We sincerely thank the reviewers for their thoughtful and constructive feedback. As noted, statements of mechanistic interpretation are not appropriate in the Results section; accordingly, we have relocated all such statements to the Discussion section. Furthermore, we have conducted a comprehensive line-by-line review of the manuscript to ensure that (i) every mechanistic inference is directly supported by experimental data presented in the Results, and (ii) integrative interpretations particularly those linking molecular observations to broader biological implications are confined exclusively to the Discussion.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) The central concept of geomapping as a broadly applicable strategy is wonderfully supported by the 17 successes documented in the paper. While this is actually, of course, a strength, the study does not include a comparative analysis across multiple sites with varying sampling outcomes for different bacterial types, which would be necessary to validate this claim more generally.

      We thank the reviewer for the point, and it is well taken. We addressed this below, where we give a full discussion.

      (2) Some elements, such as beta diversity comparisons and the metagenomics analysis of viral dark matter, would benefit from additional statistical analysis and clearer context.

      The reviewer is quite correct as to the importance of bringing statistical analysis to our metagenomic analysis. To that end, we performed statistical analysis on our metagenomic datasets. We performed statistical analysis on our metagenomic datasets. We approached this using MetaPop to analyze viral metagenomic sequence data at the interpopulation (macrodiversity) level. MetaPop's macrodiversity analysis includes raw population abundance, normalized population abundance, and α-diversity calculations. With normalized population abundance tables, we were able to generate heatmaps to view feature-level distinction between samples and biomes. Furthermore, we were able to calculate β-diversity based on Bray-Curtis dissimilarity. PCoA was performed, and to assess robustness, 2,000 features were randomly subsampled and analysis repeated across 1,000 bootstrap iterations. Resulting ordinations were aligned to a reference with Procrustes alignment. Mean coordinates and standard deviations were calculated for each sample, and scatter plots were generated. Supplementary Tables 6 and 8 and Supplementary Figure 4 have been added.

      (3) Claims about therapeutic cocktails would be better framed as speculative and/or moved to the discussion section.

      We thank the reviewer for their point, and it is well taken. Please see our more detailed response to this earlier in this reply.

      (4) The manuscript could be strengthened by elaborating on the scope and composition of the phage and bacterial isolate collections, which are important for interpreting the broader significance of the findings.

      We thank the reviewer for their point. We have added further details on the bacterial and phage isolate collections so the readers may draw the proper conclusions.

      Reviewer #2 (Public review):

      Weaknesses:
>

      While the authors acknowledge several limitations, some aspects require clearer framing or additional clarification. The proposed workflow focuses exclusively on aquatic environments as sources of phages, which may limit the diversity of hosts and phage types recoverable using this approach. Some interpretations, particularly regarding taxonomic classification and sampling saturation, would benefit from more cautious wording given current limitations in viral taxonomy and the observed data.

      The reviewer makes an excellent point. To try and address this, we made several edits to the main text of the discussion section to reframe and add clarification to our limitations. We also mention the limitation of our strategy to aquatic environments. Lastly, we addressed the final sentence below.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) To really demonstrate geomapping success would require more comparisons: choosing a variety of locations with and without high host levels and then analyzing the yes or no outcomes in terms of whether phages were found. This manuscript demonstrates 17 substantial and significant successes, very much worth sharing, but I am not sure it answers the central question posed in the title and abstract. This could potentially be accomplished through analysis of existing data related to the attempts, or it may be important to state this limitation in the discussion.

      We thank the reviewer for their insightful comment on the generalizability of our geomapping strategy and their emphasis on adding more comparisons to support the claim. While we did not test the 17 bacterial isolates (XΦROs) across multiple sites with varied host levels, we did incorporate an initial, broad preliminary screening panel designed to assess the presence and diversity of phage against multiple pathogens and laboratory strains across different sampled environments after site comparisons with the geomap (Fig. 2G). In another instance, we did without the guidance of the geomap (Supp. Fig. 2I). In each case, highly polluted waters located in densely populated areas (wastewater, Brays Bayou, and Buffalo Bayou) had higher success rates in phage recovery compared to other less polluted sites (Clear Creek, Galveston seawater, Hamilton Pool Preserve, and Pedernales Falls). This trend is consistent with previous reports [16,51]. The screening step functioned as an initial comparison and allowed us to gauge phage availability across different genera of bacteria prior to a focused geomap-guided phage hunt. In the geomap-guided experiment, we compared a low host-availability control site (Clear Creek) with two high host-availability sites (wastewater and Brays Bayou). More comparisons, especially incorporating even more sites with varied host availability, would strengthen the claim but not be invalid without it.

      In an ideal situation, we would perform the exact additional experiments proposed by the reviewer. However, we ran into logistical issues. As it turns out, phage quantities in various sites vary with weather, specifically rainfall (a finding that we intend to touch on in a future manuscript). As such, this variable must be matched. Even with the long summers of Texas, we were unable to perform multiple, serial PhiHD runs at multiple sites with similar weather conditions. As such we rely on the strength of preliminary screening (16S and plating for phage) to provide a clear guide as to where to place PhiHD experiments.

      We would still contend that the consistency between preliminary screening results and subsequent successful geomapping-guided discoveries (finding phages against 17 different isolates) gives sufficient evidence that geomapping is an effective strategy for identifying productive sampling sites. However, we acknowledge the excellent point of the reviewer and we have edited the main text to include this in the limitations, so that the reader may make their own evaluation.

      (2) Line 44: 24% of infections >> perhaps better to describe as isolates, as many infections contain multiple isolates of different types. More background in terms of the number of infections in general, comprising the 24% on the bacterial side, and also a description of the 350 phages in terms of known hosts, would be very interesting to add.

      This is an excellent suggestion that would add valuable background to the introduction and provide context for phage laboratories interested in the volume of cases handled by TAILΦR and the isolates they receive. We changed the main text to include information regarding this suggestion. We also provided a three extra tables to show 1) TAILΦR’s number of distinct case counts with number of bacterial isolates received, 2) TAILΦR’s phage library, and 3) number of isolates with NO phage. Please see Supp. Tables 1-3.

      (3) Line 92: To add a statistical test to the beta diversity comparisons beyond visual inspection of the location of the points on an ordination, I suggest adding a PERMANOVA.

      The reviewer makes an excellent point, and we agree that visual inspection should be backed up by rigorous statistics where possible. As such, we performed an analysis of molecular variance (AMOVA, done in Mothur) to compare samples derived from brackish, sea, fresh, and sewage. AMOVA showed statistical significance between the samples and confirms our visual inspection of the β-analysis. The text has been altered to reflect AMOVA data.

      (4) Line 112 (related to point 2 and Fig 1A): How many isolates in the collection for which 24% did not have a phage, and 35% were Pseudomonas?

      Related to changes in point 2, we added a supplementary table to provide insight into the number of bacterial isolates without a phage. In total, 104 (24% of 435 isolates in the TAILOR library) have no phage, and 35 belong to Pseudomonas aeruginosa.

      (5) Line 141: How is it known that Pseudomonas phage concentration increased by 95x? There could be unknowns / difficult to cultivate or phages without the right host. Consider describing as yields rather than the absolute concentrations.

      We appreciate the reviewer’s point that not all Pseudomonas phages are accounted for due to host specificity and potential unknowns. We agree completely that all we have are surrogates. We tracked the concentration of phages that infected our indicator strain Pseudomonas aeruginosa PAO1. We selected PAO1 because of its broad susceptibility profile and its role as a permissive host for isolating a wide range of Pseudomonas phages. While we acknowledge that not all Pseudomonas phages will be detected, PAO1 captures a wide breadth of Pseudomonas phages, enabling consistent comparisons between samples. Our concentration changes reflect a within-sample comparison between unprocessed material and the processed material. Aligned with reviewer’s concern, the values should not be taken as an estimate of absolute phage concentration in the samples. Rather, the values are method-dependent estimates of enrichment efficiency for PAO1-infecting phages. In tandem with PAO1-infecting phages, the concentration of other viral-like particles infecting other organisms is most likely increased with each concentration step. We have revised the entire manuscript to mention “phage yield,” rather than associate an increase to a concentration.

      (6) Line 224: 39.1% viruses> I believe this refers to vOTUs rather than viruses.

      The reviewer is correct; we appreciate the catch! We corrected the text to “vOTUs.”

      (7) Lines 224-230: How does this relate to the expected ~70% Dark Matter?

      As observed in many viral metagenomic studies, our dataset is also dominated by viral dark matter. Between 60.9% (outlier/singles from vCONTact2) and 66.5% (unclassified from PhaGCN) of vOTUs are in this group. To proceed with caution, we edited the main text to draw attention to the large percentage of viral dark matter in our metagenomic dataset. Although a substantial fraction of vOTUs is unknown, the remaining identifiable sequences provide some biological context, enable validation of sampling strategies and comparative analyses between samples.

      (8) Line 241: there are many perspectives on whether phage treatment should involve cocktails. If a phage is immunogenic and leads to antibody production that can neutralize other phages, one phage could ruin the game for others. Consider presenting this as a perspective, rather than a ground truth, and consider moving to discussion

      This is a very insightful input on this perspective. Our intent was not to present this as a definitive conclusion, but rather to highlight a broader need for a more diverse phage library. This is not limited to phage cocktail generation. We changed the introductory sentence to this paragraph to encompass a broader need for phage diversity and succinctly lead into the next sentence.

      (9) Figure 2b contains an R2 value of 0.7, and 2c has R2=0.76. Where does this come from? Maybe a PERMANOVA? Please describe in legend and/or methods+results.

      Thank you for catching this! β-diversity calculations were based on Bray-Curtis dissimilarity. We have adjusted the methods and results to incorporate this information.

      (10) The Rphi library is mentioned in several places, would be wonderful to have a bit more description of this collection.

      We thank the reviewer for their sharp eye, we definitely wanted to ensure the reader understands the significance of this. We added some descriptor sentences to better highlight and introduce the RΦ-library.

      (11) Consider adding a central success to the abstract, the fact that phages were found for 17 recalcitrant strains of various ESKAPE pathogens, yielding 35 phages after standard phage hunting and experimental evolution approaches had failed.

      We appreciate the reviewer for their emphasis on highlighting the success of our manuscript and made the appropriate changes. We added altered the last sentence to the abstract, and added another sentence to summarize our success.

      Reviewer #2 (Recommendations for the authors):

      (1) Figures 1C and 1D require a more detailed description.

      We thank the reviewer for noticing this. We have altered the figure legend to be more descriptive.

      (2) Raw and assembled sequencing data should be submitted to a public repository, and the accession numbers should be provided.

      We have uploaded the raw and assembled sequencing data to a public repository, and the accession numbers are provided in Supp. Table 9 and 12. For raw metagenomic shotgun sequences, BioProject accession is PRJNA1308632 (Supp. Table 2).

      (3) Line 89: The text states that the rarefaction curves plateaued; however, by definition, a plateau implies that the curve no longer increases. In the presented data, all curves continue to rise at the final sampling point. This does not affect the conclusions but suggests that sampling saturation has not been fully reached.

      This is a great observation by our reviewer. We agree with this point as the curves do not reach a complete plateau. We have revised the text to use more accurate language and clarify sampling depth.

      (4) Figure 2D: The heatmap normalized by Z-score within the selected taxa may give a biased impression of enrichment of certain taxa in specific environments, when in fact it only indicates enrichment relative to the other pathogenic taxa included in the analysis.

      The reviewer raises a great point, and we should have pointed this out directly. To avoid potential misinterpretations, we have revised main text to explicitly state that the heatmap displays relative enrichment to the other pathogenic taxa.

      (5) Given the variable taxonomic resolution achieved by 16S rRNA sequencing (genus or family level), it would be important to highlight that some detected taxa include non-pathogenic members. For example, Vibrio is common in seawater, yet only a few species are pathogenic to humans.

      We agree with this! We added a sentence to emphasize this point.

      (6) Figure 2G: The color scale bar is uniform across all panels; please adjust for accurate comparison.

      For more accurate comparisons between different samples and phage concentrations, we added a second color to assist with visualization.

      (7) The PCoA figures should specify which distance metric was used.

      We want to thank the reviewer for the catch, we should have mentioned that. Our PCoA was calculated based on Bray-Curtis dissimilarity. We have adjusted the main text and methods section to mention it.

      (8) Figure 3: The meaning of the colors in panels A and B should be clarified.

      We thank the reviewer for their keen eye. We changed the figure and figure legend to clarify. The colors on the map and PCoA represent influents from various wastewater treatment plants around Texas.

      (9) The manuscript jumps from Supplementary Figure 2 to Figure 6. In general, the order and referencing of supplementary materials are confusing. Supplementary tables and figures should not be intercalated within the same file.

      We thank the reviewer for their patience and apologize for the confusion. This occurred as we had multiple revisions to the manuscript and we did not update the sequence of the figures. To address the reviewer’s comment, we separated the supplementary tables and figures into apart. We also ensured that each main and supplementary figures and table were mentioned sequentially in the main text.

      (10) It is unclear why some vOTUs were observed in the 5 L collection but not in the concentrated sample (10/24; Supplementary Figure 3E). One would expect that the most abundant vOTUs in the 5 L sample should also be easily detected in the concentrate.

      The reviewer brings up a fantastic point. One would certainly expect that the most abundant vOTUs in the 5L samples would also be detected in the concentrated sample.

      We have several suspicions as to why several vOTUS were not detected in our concentrated samples. Because we used shallow shotgun metagenomic sequencing, as compared to deep sequencing, we may have obscured our ability to detect and quantify low-abundance taxa. Consequently, dominant taxa occupying a large portion of sequencing reads may have masked the detection of rarer species/vOTUs. Lower sequencing depth results in fewer total reads per sample and reduced sensitivity for rare, infrequent species/vOTUs to be detected. When their abundance falls below detecting limits, they may appear absent from a data set.

      Furthermore, we reached out to Novogene, who we outsourced for library preparation and shotgun metagenomic sequencing. According to Novogene, not all genetic material in a sample is used during their library preparation. The maximum amount of DNA to build a PCR-free metagenomic library at each time is approximately 1.5 µg of DNA. Although we submitted 184.4 µg of DNA (from the 400L-concentrate) and 25.6 µg of DNA (from the 5L-sample), we suspect only a fraction of the material was used for library preparation and subsequently sequenced. This may have limited the representation of low abundance vOTUs.

      (11) Line 227: The statement that "but only 33.5% of viruses could be classified to the family-level" requires caution. Since the traditional Siphoviridae, Podoviridae, and Myoviridae families were abolished, many viruses currently lack family-level classification. Therefore, this taxonomic level may not be ideal for assessing novelty, as many viruses closely related to known types remain unassigned.

      We appreciate the reviewer for bringing up this topic. We recognize the current limitation in the viral metagenomic landscape. Many viruses lack-family level classification due to ICTV taxonomic restructuring and the lack of reference genomes present in a database. A large fraction of viral sequences constitute “viral dark matter.” From a single metagenomic dataset, viral dark matter ranges from 60-90% of vOTUs. Within our own dataset, it is also dominated by viral dark matter. Between 60.9% (outlier/singles from vCONTact2) and 66.5% (unclassified from PhaGCN) of vOTUs are in this group. Although a substantial fraction of vOTUs is unknown, the remaining identifiable sequences provide some biological context, enable validation of sampling strategies and comparative analyses between samples. To complement vCONTact2 results, we utilized PhaGCN to classify each vOTU as a means to compare taxa derived from each sampled biome from one another and not to assess novelty of the metagenomic dataset. We aimed to provide measurable and interpretable context to our metagenomes. However, due to the substantial variability and uncertainty in the field and our dataset, we revised the text to highlight the large fraction of unclassified sequences and their implications.

      (12) Supplementary Figure 5: The legend does not clearly explain the two inner rings. One may correspond to GC skew, but this should be explicitly stated.

      Well spotted! We have made the appropriate corrections.

      (13) Line 325: The reference to "50 mL samples" is unclear-please specify which samples this refers to.

    1. Author response:

      We thank the reviewers for such positive and constructive feedback, and for their enthusiasm about our use of controllability and dynamical systems perspectives to understand learning variability. We are glad to see that they believe this work will be “highly impactful” and “directly motivate new learning experiments”. We agree that these findings suggest new experimental tests of dynamical constraints on learning, in BCIs and motor control as well as other computations that depend on neural dynamics, such as decision-making tasks. Combined with new tools for data-driven identification of latent dynamics, we are excited to see how dynamical constraints can help understand learning outcomes across different tasks, brain areas, and individuals.

      Based on reviewer comments, we identified three sets of analyses that will improve the clarity and strength of evidence for our primary conclusions.

      (1) As the reviewers identified, a central contribution of this study is to show that continuous within-class variability becomes explainable by considering underlying dynamical structure. We realize this was insufficiently emphasized in Figure 6. All regression models included group-specific intercepts, so improvements from dynamical features reflect prediction beyond class-level differences. To quantify this directly, we compared against an intercept-only model and evaluated prediction of within-class residual variability (mean-subtracted). Geometric features did not improve performance beyond class means, whereas dynamical features significantly improved prediction (p<10<sup>-5</sup> for both behavioral measures). Moreover, only dynamical features predicted within-class residual variability (cross-validated R<sup>²</sup> = 0.19 and 0.30 for learning speed and hit-rate change, respectively; p < 10<sup-8</sup>). We will add these analyses and revise the text to clarify this point.

      Author response image 1.

      Cross-validated R<sup>2</sup> for (left) learning speed and (right) change in hit rate, for true behavioral outcomes (total variability, blue) and after subtracting class means for OMPs and WMPs (residual variability, orange).

      (2) We appreciate the reviewers’ comments to clarify what changes in neural structure are small, and to provide a quantitative comparison to changes observed in the primate BCI experiments.

      We referred to published analyses of within-manifold perturbations (WMPs) in the primate BCI experiments, which reported <10% reduction in fractional variance within the intrinsic manifold for most sessions (Golub et al., 2017). (No comparable analysis was reported for OMP sessions.) For adaptation to WMPs, changes in variance within the intrinsic manifold in RNN models with input plasticity closely matched experimental observations (75th percentile: 94% of pre-learning variance in the model versus 90% in data), whereas recurrent plasticity RNN models produced substantially larger departures (78%). In fact, the entire distribution with recurrent plasticity was shifted to larger changes than those observed in most primate WMP sessions. A second comparison based on covariance changes along BCI dimensions (Figure 5 in [1]) yielded a similar conclusion. The authors estimated ~5-20% changes in covariance along both the intuitive and perturbed decoder dimensions during WMP sessions. For our RNN models trained with input plasticity, we observed similar changes: changes along the perturbed decoder were <10% although changes along the intuitive decoder were ~40%. We borrowed the terminology of “small” from the experimental findings in [1], where comparisons were made to alternative learning hypotheses (with predicted changes as >10-fold higher). These analyses now provide more quantitative evidence that neural reorganization under input plasticity is largely consistent with primate neural data. We will add these comparisons as a supplementary figure in the revised manuscript.

      Author response image 2.

      Proportion of maps with normalized variance in intrinsic manifold (IM) above a certain minimum value. Results with training RNNs on WMPs, with either input plasticity (blue) or recurrent plasticity (orange), overlaid on primate data from Golub et al, 2017 (black). Dashed lines indicate the 75th percentile value.

      We agree with reviewers that under input plasticity, both statistical and dynamical changes are relatively modest, particularly when compared to the behavioral changes. Rather than focusing on the magnitude of these changes, our regression analyses in Figure 6 highlight that the dynamical changes are a better predictor of continuous variability of behavioral outcomes. Moreover, OMPs are misaligned with both the intrinsic manifold and the controllable subspace. Thus, mean OMP learning performance alone cannot disentangle the contribution of these different sources of misalignment. By showing that variability within each class is explained by considering dynamics (Figure 4, Figure 6), and using the dissociation between task manifold and controllable subspace by varying controller architecture (Figure 8), we provide evidence that dynamical constraints provide a more comprehensive picture of learning variability, beyond categorical differences.

      (3) Finally, we tested whether the same dynamical features explain learning variability across the alternative controller architectures in Figure 8. They remained predictive of learning speed (cross-validated R<sup>2</sup> of 0.35 and 0.33 for low-D and high-D controller networks respectively), supporting the generality of the proposed dynamical constraints. We will add this analysis to the revised manuscript.

      As per reviewer suggestions, we will also perform additional analyses to examine the relationship of learning outcomes to initial behavioral metrics for different decoders, assess flowfield changes during the preparatory phase, report the relevant statistics for stated comparisons, and clarify that learning with only one set of inputs (either feedforward or feedback) was poorer.  We will also clarify several points raised by the reviewers, including:

      (i) the compatibility of overlapping confidence intervals of WMP/OMP learning outcomes with prior experimental data in Sadtler et al, 2014;

      (ii) the distinction between flow-field changes in the full neural state space (Figure 5D) and along behavioral readout dimensions (Figure 5E);

      (iii) that autonomous dynamics contribute to controllability and how differences in pre-trained autonomous dynamics across controller architectures could indirectly vary feedforward controllability (Figure 8); and

      (iv) the relationship between controllability and reachable manifolds in position-decoder BCIs.

      References:

      (1) [Golub et al, 2017]   Golub, M.D., Sadtler, P.T., Oby, E.R., Quick, K.M., Ryu, S.I., Tyler-Kabara, E.C., Batista, A.P., Chase, S.M. and Yu, B.M., 2018. Learning by neural reassociation. Nature neuroscience, 21(4), pp.607-616.

      (2) [Sadtler et al, 2014]   Sadtler, P.T., Quick, K.M., Golub, M.D., Chase, S.M., Ryu, S.I., Tyler-Kabara, E.C., Yu, B.M. and Batista, A.P., 2014. Neural constraints on learning. Nature, 512(7515), pp.423-426.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The authors conclude that mPFC is not required for avoidance, based on the minimal behavioral effects of optogenetic inhibition. While this interpretation is supported by the data, the choice of viral constructs could lead to an underestimation of the mPFC's role for other reasons. First, the choice of viral constructs could lead to an underestimation of the mPFC's role for several reasons. Specifically, the efficacy of eArch3.0 inhibition was not verified beyond histology, and its non-cell-type-specific nature could lead to disinhibition or compensatory activity in downstream regions. Although the authors' use of visual cortex (VI) inhibition as a control suggests that broad cortical inhibition does not impair avoidance, subcortical compensation cannot be ruled out. Additionally, Vgat-ChR2 targets only GABAergic neurons, potentially missing glutamatergic contributions. Addressing these limitations in the Discussion section would strengthen the manuscript.

      We thank the reviewer for these points. First, although we did not perform direct electrophysiological verification of eArch3.0 efficacy in mPFC in the present study, this construct has been extensively validated in prior work and is widely used to produce robust neuronal inhibition. In our experiments, the lack of behavioral effect with eArch3.0 inhibition converged with the results obtained using the independent Vgat-ChR2 approach, which we directly validated, supporting the conclusion that mPFC inhibition does not impair avoidance under these conditions. Our results are also consistent with previous studies showing that mPFC lesions do not impair avoidance behavior.

      Second, we agree that manipulating mPFC activity will necessarily influence downstream circuits, including subcortical regions, given the interconnected nature of these networks. Our goal was to test whether inhibiting mPFC activity alters avoidance behavior, not to isolate it from its targets. In this context, the absence of behavioral effects indicates that avoidance behavior can be supported without mPFC activity. While compensation is always a possibility, this usually reveals some impairment while compensation occurs, but we did not observe those effects. Our results are consistent with the idea that subcortical circuits normally mediate these behaviors.

      Finally, regarding Vgat-ChR2, activating GABAergic neurons is a well-established approach to suppress cortical activity, as these interneurons provide strong inhibition onto local glutamatergic neurons. Thus, this manipulation is expected to broadly reduce excitatory output in cortex. Indeed, the robust suppression of cortical activity we observed with GABAergic activation makes it unlikely that major glutamatergic contributions were missed.

      These points are in the paper, including the Discussion.

      Reviewer #2 (Public review):

      (1) There are few details on the linear mixed models in the methods. This section could be improved by including a mathematical description. More importantly, the reader never learns how accurately the models capture the data. Given that most conclusions rely on the models, it seems central to address this point carefully. For example, what is the explained variance, marginal, and conditional? Were the nested models compared to non-nested ones (e.g., AIC), what are the specific outputs of the likelihood ratio tests briefly mentioned in the methods?

      Model structure was defined a priori by the experimental design and hypotheses rather than selected through model comparison, but we verified the contribution of key model components (e.g., covariates, interactions, and random effects) using likelihood ratio tests comparing models. Regarding model performance, we now report for each model the marginal and conditional R<sup>2</sup> values (Nakagawa), which quantify variance explained by fixed effects alone and by the full mixed model including random effects. In addition, likelihood ratio test results for all fixed effects and interactions (χ<sup>2</sup> statistics) were already reported in the manuscript.

      (2) For several figures, there is a disconnect with the main text, in the sense that it is difficult to understand how statements in the main text connect with specific figure panels or bars in their graphs. This is particularly the case for the most complex figures, e.g., Figures 3, 4, and their supplements. It would be beneficial to introduce subfigure labels (A1, etc) and state explicitly in the main text what figure panel is described (in parentheses). Alternatively, breakdown the figures into multiple ones, decreasing ambiguity. This is important because it will help the reader better assess the strength of the results.

      We have significantly revised the manuscript to reduce ambiguity and thank the reviewer for each of their (28) requests, which we have implemented in full. We also added additional figure references to the Results to assist with readability. This has significantly improved clarity and readability.

      (3) It does not appear that the code and data used to produce the figures are made available. That would be very beneficial, given the complexity of the analysis and dataset collection procedures. It would also help readers better understand the results and probe their validity.

      As usual, we will share the full dataset in the VOR at Dryad after the revision is completed.

      Reviewer #3 (Public review):

      The main weakness, in my view, lies in the Results section. In the figures, the authors do not present any raw data, and the plots are shown as mean {plus minus} SEM without displaying the distribution of individual data points.

      We thank the reviewer for the recommendations. Individual data points are shown where appropriate (e.g., Fig. 1). However, most of our analyses involve repeated-measures, hierarchical data with multiple levels (cells and sessions nested within animals), where simple point overlays can be misleading or difficult to interpret without explicit linking across levels. We therefore use mean ± SEM visualizations for clarity in these summary figures, while preserving the full hierarchical structure in the statistical analysis through mixed-effects models. All data will be made available in the VOR to allow full inspection of the underlying distributions.

      It is both a strength and a weakness that the authors do not attempt to guide the reader through the Results section and instead present the findings with very little emphasis on the key outcomes of the GLM. While this approach is arguably the most transparent way to report results, it also makes the section quite difficult to follow and may discourage readers.

      I would recommend rewriting the Results section to make it more accessible to a broader audience. A similar issue applies to the figures: presenting all plots reflects a commendable commitment to transparency, but it would greatly benefit from a clearer narrative. As it stands, it is difficult to grasp the message of each figure by simply browsing through them.

      The full description (complexity) of the models is entirely in the legends and supplemental figures. This was done to make the results easier to follow. We have made all the changes noted above to facilitate readability while assuring there is enough transparency to assess the data. We think readability has significantly improved.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Below are a few specific suggestions related to the main weaknesses mentioned above.

      (1) P4 L9: The sentence starting with "However, most ..." sounds more like a statement than a contrast with the previous sentence. Therefore, please delete "However" and please add references to justify the statement.

      Done.

      (2) P8: Definition of movement peaks. It would be great to have three videos illustrating the mouse behavior in the three different movement peaks. This would allow the reader to better understand the differences between no peaks 3 sec prior, more than 5 seconds, and one example that does not fit these two categories. In addition, what percentage of all peaks to the no peaks 3 sec prior and more than 5 sec represent?

      We added the percentages. The “3 sec prior” represent ~23% and the “5 sec” represent ~31%. However, we do not think adding a single video of one movement per these 3 cases would be useful as the dataset is composed of thousands of these movements.

      (3) P8: Last paragraph. When you state that you performed a linear fit between DF/F and movement, do you mean speed? In addition, the statement "integrating both signals over a 200 ms window" is incomplete. How is the window selected? Is the window 200 ms around movement onset or movement peak speed?

      Yes, the movement variable used in the linear fit corresponds to speed. Regarding the 200 ms window, this analysis does not focus on specific behavioral events such as movement onset or peak speed. Instead, both ΔF/F and speed signals were segmented into consecutive 200 ms windows across the entire recording session, and the linear relationship was computed across these paired segments. Thus, the analysis captures the overall relationship between neural activity and ongoing movement, rather than eventaligned dynamics. We have revised the text to clarify both the use of speed and the implementation of the 200 ms window.

      (4) P14: Discussion of AA19 and AA39 tasks: It would be helpful to clearly specify what percentage of actions you would expect given no learning, is it the 23% action dashed line indicated in the top panel of Figure 2B?

      The expected percentage of actions under no learning is not fixed, as it depends on the rate of spontaneous (non–cue-driven) crossings. In these tasks, we estimate this baseline using behavior during the noUS condition, where the action rate is ~23% (Fig. 2B). In the AA19 and especially AA39 tasks, this baseline decreases because spontaneous inter-trial crossings (ITCs) are progressively reduced, leading to lower expected action rates under no-learning conditions. Thus, the 23% baseline derived from noUS is lower in the AA19/39 tasks. In other studies, we explicitly included NoCS (no-cue) trials to estimate chance performance; however, in the present design we rely on the noUS baseline and the observed changes in ITC rate. We have clarified this point in the text.

      (5) P15 L2: "Considering tone intensity (Fig. 2B), CS1 avoids latencies increased at medium and high intensities but not a low intensity." This is confusing. Are you referring to the AA39 triangles under CS1 in the middle panel, left? They are all above the dashed reference line. So the plot seems to contradict the statement. If you are referring to AA19, the red dots also seem to show the opposite of the statement.

      The dashed reference line reflects latency during the noUS condition and is included for visual reference; however, these values are not directly comparable to those in the AA tasks, as noUS latencies are largely unconstrained and reflect baseline behavior rather than learned responding. The statement in the text refers specifically to changes across AA conditions, consistent with our analysis approach throughout the manuscript, where values are compared to the immediately preceding condition. In this case, we are referring to AA39 (triangles) relative to AA19 (circles). Under this comparison, CS1 avoidance latencies increase at medium and high intensities, but not at low intensity, consistent with the statistical contrasts. We have revised the text to clarify the points.

      (6) P17: "Movement and neural measures subtract the baseline from the other three windows at a trial level." Do you mean to say that for each measure, the baseline was subtracted? How is baseline defined (over which time window)?

      The baseline is defined in that same paragraph as the −0.5 to 0 s pre-CS window. To improve clarity, we have revised the text to explicitly restate this definition in the sentence describing baseline subtraction.

      (7) P17: "Fig. 2-Supplement 2A,B shows model-derived marginal means of movement averaged across tone intensities." Some explanation needs to be provided, since the previous figures show a dependence of behavior on tone intensity. Are you doing this based on Fig. 2-S1?

      Yes, these results are derived from the same model of the full data shown in Fig. 2–S1. In this particular analysis, tone intensity was included in the model but not retained when computing marginal means and contrasts, effectively averaging across intensity levels. The rationale for this approach is that tone intensity was primarily used to increase behavioral variability, particularly error rates, which are otherwise low in this task. Averaging across intensity therefore improves statistical power and allows us to more clearly isolate the effects of the primary factors of interest. We have clarified this point in the text.

      (8) P18: "Orienting magnitude was strongly dependent on tone intensity...". However, in Figure 2-S2, there is no information about tone intensity. So how is the reader supposed to see this? Same issue on P19 when discussing the action window. Generally, the description of Figure 2-S1 and S2 is difficult to follow and should be improved. It is not clear that all panels are referred to in the text.

      We have revised the start of the Movement section to clarify how tone intensity is treated across analyses and figures. Specifically, tone intensity is included as a factor in all statistical models; however, for clarity of presentation, it is sometimes collapsed in figures to reduce dimensionality and to emphasize other task-related factors. This manipulation was introduced primarily to increase behavioral variability (particularly error rates), thereby improving sensitivity for estimating the effects of the other task variables.

      We have also clarified when we reference Fig. 2–S2 legend that, although intensity is not displayed in the figure for visualization purposes, it is included in the underlying model and its effects are reported in the supplement.

      (9) P22, 23: Windows are mentioned, but not defined or indicated in figures.

      We have clarified in the text that the same time windows defined for movement analyses (baseline, orienting, action, and from-action) were also used for the neural analyses.

      (10) P22: "Covariates were standardized within each window so that estimated marginal means reflected ΔF/F at average covariate values." It is unclear what was done exactly. What do you mean by "standardized"? Maybe give an example here and elaborate in the methods.

      By “standardized within each window,” we mean that covariates were z-scored within each analysis window (i.e., each covariate was transformed to have a mean of 0 and a standard deviation of 1 within that window). This ensures that estimated marginal means correspond to ΔF/F evaluated at the average covariate values within each window. We have clarified this in the Methods and Results.

      (11) P24-25: Indicating spurious action on Figure 3-S2 (and in Figure 3) would help the reader follow the argument in the main text.

      We clarified this in the legends by indicating that actions not classified as AA, PA, Escape, or PA Error are spurious actions.

      (12) P25: "After controlling for ..., but this includes the effects of aversive stimulation." The second part of this sentence was not clear.

      We have clarified this sentence to indicate that avoidance errors are followed by aversive stimulation (i.e., errors are punished).

      (13) P34L3: "Classs" -> "Class".

      Fixed.

      (14) P42 top paragraph: There are two references to Figure 5-S1 panel D, but there is no panel D on the figure.

      Fixed.

      (15) P57: The sentence starting with "Random effects were specified ..." is very difficult to follow.

      We have revised this sentence to improve clarity by separating the description of the random-effects structure from the model syntax.

      (16) P57: The windows analyzed are finally defined at the bottom of this page. The information also needs to be included early in the results to improve comprehension.

      This is now included in the main text when windows are first used in the movement section.

      (17) P58: Several R packages are mentioned by name, but without specifying that they are R packages, which would facilitate reading.

      We added R.

      (18) P58 top paragraph: "Tuckey's correction", do you mean "Tukey's HSD test"?

      We thank the reviewer for noting this. We used Holm-adjusted p-values for multiple comparisons (as implemented in emmeans) and have revised the text.

      (19) P63: "features extracted from F/F" do you mean "DF/F"?

      Yes, fixed.

      (20) Figure 1B speed plots: it is not possible to visualize the lines at the movement peak because they overlap completely. You can either add an inset on the left of the peak (for each panel), magnifying that region, or play with the transparency of the traces to improve visibility. There is a similar issue in Figure 5A, B. (Alternatively, if it is not possible to solve the issue graphically, explicitly state that traces overlap.)

      We have fixed this by making some traces dashed in Figure1 and 1-S1, which reveals the underlying traces. We also stated that the peak speed completely overlaps. In Figure 5, we stated that traces overlap as expected; transparency or dashing does not work well with the colors used in Figure 5 and in fact the overlap emphasizes the similarity of the movements.

      (21) Legend 1A: abbreviation CCF not defined. Is it anterior to the left? Abbreviation WM not defined. The right panels are unclear. The legend states that they show a schematic of the location of the optical fibers, but that was not clear. Do the dots indicate the location of the fibers? Is the green region indicative of V1? Same for dark gray in the mPFC panel. What are the lighter grey regions and the blue region? Does 'lateral' mean 'lateral from midline'? Please clarify these points.

      CCF is defined in Methods, and the typesetting process will adjust abbreviations as needed per the journal. We have defined MW and clarified all the other points in the legend.

      (22) 1B: "peaks taken at a fixed interval > 5 s", this is a bit confusing. If the interval is fixed, the exact time interval should be given. If it is > 5 s, then this suggests that it is not fixed. Do you mean "at intervals > 5 s"?

      Yes, fixed.

      (23) Figure 1-S1C: is the area the integral of the z-scored DF/F above zero DF/F? If so, it should have units of seconds (integral over dt of a dimensionless variable). Similarly, the Peak is a z-score value? In addition, is the time to peak in seconds? What is zero? Peak time of movement?

      We thank the reviewer for raising these points. We have clarified the terminology in the text and figure. Specifically, “area” was inaccurately labeled and refers to the mean z-scored ΔF/F within each analysis window (not a time integral). Peak values correspond to the maximum z-scored ΔF/F within the window, and time to peak is reported in seconds relative to the alignment point. We have also clarified the definition of time zero and included these definitions in Methods.

      (24) Figure 2-S1: It is not clear if this figure is obtained by averaging across all animals. Please explain in the legend.

      We clarified that values represent averages across mice.

      (25) Figure 2-S2: Are the speeds in A and B in units of cm/s (vertical axis)? This needs to be indicated.

      We have clarified in the figure legend that movement speed is expressed in cm/s.

      (26) Figure 5A, scale bar: It looks like a Delta is missing in front of F because the label reads 0.5 F/F instead of 0.5 DF/F. I am unclear why there are three colored traces for the speed panels. If the colors denote neuron classes, does this mean they were recorded in different sessions, allowing the authors to distinguish activation speed for each class separately?

      We fixed the scale bar typo. The speed traces in the bottom panels are shown to illustrate that movement is highly similar across activation types within each avoidance mode, indicating that the observed large differences in neural activity cannot be attributed to differences in movement. Minor differences in the speed traces arise because activation types are composed of neurons that can be recorded in the same or different sessions, and each activation type may not be present in every session. We added several sentences to this section that should fully clarify the issue.

      (27) Figure 4-S1 legend B: Please indicate why the two panels are missing for the PA case (for the confused reader).

      We have clarified in the legend that panels are not shown for correct CS2 passive avoids because these trials do not involve an action, and therefore from-action alignment cannot be defined.

      (28) Figure 5-S A, B: Units missing for speed.

      Fixed.

      Reviewer #3 (Recommendations for the authors):

      I cannot assess the scientific validity of the study design as it is too far away from my direct field of expertise. But I found the authors' arguments convincing, and the results sound pretty consistent with the little I know of the field. The recording methods are good and the statistical analysis robust. So my only recommendation for the authors would be to work on the figures to improve clarity.

      Thank you. We have introduced various changes that we hope will facilitate readability for a wider audience while preserving the necessary details.

    1. Author response:

      The following is the authors’ response to the previous reviews

      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 was partly ameliorated by MD. The paternal diets changed 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 on 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 of the fathers, the early placenta and 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.

      Comments on revised version:

      The authors have done a great job addressing my concerns. The description of the data analysis and the figures are now much clearer. The inclusion of the potential links between the microbiome and male reproductive fitness is informative and improves the flow of the discussion.

      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 feto-placental 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.

      Comments on revised version:

      The authors have adequately addressed all my previous comments.

      We would like to thank the Editor and Reviewers for their consideration and thoughtful comments.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      It was a little difficult seeing exactly what had changed in the manuscript without going back to the original version as not all changes were marked yellow in the revised version. In future, I would recommend clearly labelling all changes to aid the referee.

      We apologise to the reviewer for the difficulty in seeing where the changes had been made. We acknowledge their comments for subsequent manuscripts and thank them for their time, consideration and comments.

      Small comments:

      (1) I noted the description of the statistical analysis now includes the addition of paternal age/diet duration in the generalised mixed model for the late gestation cohort. Was this also done for the early gestation cohort? If not, why not?

      For the data presented in Figure 6, each data point was obtained from a separate male. As such, we were not able to factor in male effects, as no male sired more than one litter (Figure 6A). Additionally, only one conceptus per male was analysed for ECP area and development meaning paternal age effects could not be accounted for.

      (2) The legend of Figure 2 states that "Data were analysed using either a one-way ANOVA with Holm-Sidak post hoc tests for multiple comparison respectively". Is some text missing here?

      We thank the reviewer for spotting this typographical error. This has now been corrected and reads “Data were analysed using a one-way ANOVA with Holm-Sidak post hoc tests for multiple comparison”.

      (3) Figure 1 remains low resolution in the reviewer's copy. If possible, it would be good to upload a higher resolution figure during production of the article.

      We apologies that the resolution of this figure was still low for the Reviewer. We have checked the dpi and it is 300x300. However, we will ensure the quality is as high as possible during production.

      Reviewer #2 (Recommendations for the authors):

      One minor remaining issue: the caption of Figure 3 still contains the phrase "non-fasting metabolic status", which should be deleted from this sentence.

      We thank the reviewer for spotting this typographical mistake. This has now been corrected.

    1. Author response:

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

      Public Reviews:

      Joint Public Review:

      In this study, the authors suggest that DuoHexaBody-CD37, a biparatopic CD37-targeting antibody, can induce direct cytotoxicity in diffuse large B-cell lymphoma (DLBCL) cells through antibody clustering and SHP-1 activation, independent of complement. They further propose that DuoHexaBody-CD37 inhibits cytokinemediated pro-survival signalling, suggesting a broader role for CD37-directed therapy in disrupting tumour supportive signalling networks.

      A strength of the study is the systematic in vitro characterisation of signalling responses to DuoHexaBodyCD37 across both malignant and normal B-cells. The inclusion of phosphoproteomic profiling and mutant constructs provides mechanistic detail, and the findings may be of interest to researchers working on antibody therapeutics in lymphoma.

      However, the evidence supporting key mechanistic processes - particularly the role of SHP-1 in mediating cytotoxicity and the requirement for Fc receptor crosslinking - is incomplete and would benefit from further functional validation. While CD37 has been explored previously as a therapeutic target, this study does add mechanistic insight into direct cytotoxicity and cytokine modulation. Nevertheless, the exclusive reliance on in vitro systems makes the translational relevance unclear. Overall, the study provides valuable insight into CD37-mediated signalling in lymphoma cells, but the evidence remains incomplete to support broader conclusions about therapeutic impact.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In the manuscript, Singh and colleagues reveal a new mechanism via which DuoHexaBody-CD37 induces DLBCL cytotoxicity, which is independent of external factors, such as the effector cells and the complement system. As cited by the authors, the induction of B cell death has previously been demonstrated for antibodies directed against B cells, including anti-CD37 (otlertuzumab). Furthermore, the majority of these observations are made using in vitro systems, and it is not clear if this phenomenon happens in vivo or not?

      Thank you for pointing this out. We would like to refer to previous report that have demonstrated potent anti-tumor activity of DuoHexaBody-CD37 in vivo in cell line- and patient-derived xenograft models from different B-cell malignancy subtypes [PMID: 32341336]. Moreover, DuoHexaBody-CD37 ex vivo activity has been shown in primary tumor cell samples from a large cohort of newly diagnosed (ND) and relapsed/refractory (RR) patients with a broad range of B-cell malignancies, including chronic lymphocytic leukemia (CLL) and B-cell non-Hodgkin lymphoma, including diffuse large B-cell lymphoma (DLBCL) [PMID: 33324950]. We refer to these data in the introduction.

      The presented data suggest that DuoHexaBody-CD37 relies on Fc crosslinking for its optimal cytotoxic activity. Investigating which FcγR is needed for this purpose would have been useful, as FcγRIIb, for instance, has been shown to be important in supporting the therapeutic function of mAbs like anti-CD40.

      We thank you for this suggestion. To further investigate the role of specific FcγRs in effector cell-mediated Fc cross-linking, PBMC-mediated direct cytotoxicity was compared across various immune cell subsets: B cells (FcγRIIb), NK cells (FcγRIIIa, IIc), monocytes (FcγRI, IIa/b, IIIb), and T cells (no confirmed FcγR expression). Notably, all immune cells subsets expressing FcγRs exhibited similar or enhanced cytotoxicity against DLBCL cells compared to the total PBMC pool. These results indicate that DuoHexaBody-CD37 induced killing is independent of specific FcγR subtypes. We have added these new data to new Figure 1C.

      Specific comments:

      (1) Line 92:93: The authors should also cite the following reference for rituximab: https://pubmed.ncbi.nlm.nih.gov/19620786/ .

      We have added this reference to the revised paper (ref. 31).

      (2) Figure 1 and 2: Since cell death was only observed in the presence of crosslinking in Figure 1, Figure 2 should also investigate the clustering and internalization of CD37 in the presence of the same secondary antibody. It is likely that DuoHexaBody-CD37 will induce receptor internalization upon crosslinking.

      To further investigate internalization, we compared the surface availability of CD37 with and without Fc-mediated crosslinking of DuoHexaBody-CD37 across cell lines. Little to no decrease in the surface availability of CD37 upon Fc-mediated crosslinking (new Supplementary Figure 2) was observed.

      In addition, we performed cluster analysis studies in lymphoma cells treated with DuoHexabody-CD37 in the absence and presence of Fc-crosslinking (and respective isotype controls). We observed that DuoHexabodyCD37 by itself was already sufficient to induce CD37 clustering, which was further enhanced by Fc-crosslinking (new Figure 2A, B).

      (3) Figure 3A: the Y-axes should be clearly labelled.

      Done.

      (4) Figure 6: What is the reason for the selective use of different cell lines in Figure 6? Additionally, only 1 donor has been used for the IL-6 analysis.

      The reviewer is indeed correct in noticing that only one cell line has been used for the IL-6 analysis. We observed that HBL-1 cells were the only cell line that were sensitive to IL-6 treatment, in contrast to IL-4 and IL-21. We have added this sentence to the discussion to explain this better: “p-STAT3 downregulation upon DuoHexaBody-CD37 treatment in presence of IL-6 requires further investigation in additional IL-6-responsive cell lines, as HBL1 was the only IL-6-responsive lymphoma cell line tested in this study.”

      The data shown in Figure 6 are results from at least three independent experiments (each dot is an independent experiment, not a donor).

      Reviewer #2 (Recommendations for the authors):

      Singh et al uncover a novel mechanism of action for the DuoHexaBody-CD37 against DLBCL, whereby it is shown to induce direct cytotoxicity independent of complement and to activate the phosphatase SHP-1. DuoHexaBody-CD37 is also shown to reduce cytokine induced JAK/STAT signalling in DLBCL cells.

      Strengths:

      The authors provide novel insight into CD37 targeting across normal B cells, DLBCL and Burkitt lymphoma cells, which have the potential to inform clinical translation.

      Weaknesses:

      The mechanisms behind differences in signalling and apoptosis between normal B cells, Burkitt lymphoma, and DLBCL cells with CD37 targeting require further clarification. In particular, the contribution of SHP-1 to this effect is not clear and indeed is increased in both normal b cells and DLBCL cells.

      Key points that require addressing are below:

      (1) Viability of Burkitt lines was less affected than DLBCL in Figure 1- this should be compared with surface CD37 expression in these same lines to determine whether this accounts for the effect. This difference is a key finding for clinical translation.  

      We thank the reviewer for this suggestion and we have now performed flow cytometry analysis across DLBCL and Burkitt cell lines upon staining with two different anti-CD37 antibodies (WR17, M-B371) to quantify membrane CD37 expression (new Supplementary Figure 1B). These data show that CD37 expression levels are not directly related to DuoHexaBody-CD37 mediated cytotoxicity in the studied B cell lines. 

      (2) pSHP1 is increased in both normal B cells (lines 169-171, Figure 3C) and DLBCL and yet the authors state specific upregulation of pSHP1 in DLBCL as a reason for induced cytotoxicity in DLBCL (lines 183-185). This requires clarification and experimental confirmation. The authors should investigate normal B cells in the cytotoxicity assays as in Figure 1 for comparison. The authors should also confirm the importance of SHP-1 in this apoptosis process using specific SHP pharmacological agents, which are commercially available.

      To analyze the role of SHP1 mediated signaling in induced cytotoxicity of DLBCL, SHP1 knock outs (KO) were generated in HBL1 and OciLy7 cell lines using CRISPR Cas9 technology (new Supplementary figure 5A). The wild type and SHP-1 KO cell lines were then compared for differences in cytotoxicity after treatment with DuoHexaBody-CD37 with and without Fc-crosslinker. No differences in cytotoxicity were observed between the wild type and knock out cell lines (new Supplementary figure 5B), indicating that DuoHexaBody-CD37induced SHP1 signaling does not play a direct role in the increased cytotoxicity. We have added these new data to the results and rephrased the role of SHP-1 in the revised manuscript. 

      (3) It would be informative to assess caspase activation and PARP cleavage across normal B cells, DLBCL and Burkitt under these conditions for clarity on apoptosis induction.

      We thank the reviewer and we agree it would be informative to confirm apoptosis induction in the cell lines upon DuoHexaBody-CD37 treatment. We addressed this question by flow cytometric analysis of different lymphoma cell lines stained with/without Annexin V (apoptosis marker) and 7AAD (late apoptotic/necrotic marker) in presence or absence of DuoHexaBody-CD37, with and without Fc-crosslinking. These experiments demonstrate that Fc-crosslinking DuoHexaBody-CD37 leads to the induction of apoptosis across DLBCL cell lines (new Supplementary Figure 1A).

      (4) The regulation of JAK/STAT signalling by SHP-1 should be mentioned in the introduction and discussion as this is a key finding of the manuscript.

      Based on the new data on the role of SHP-1 (Suppl. Fig. 5), we have rephrased the text on the SHP1 in the discussion of the revised paper: “DuoHexaBody-CD37 treatment also led to an increase in SHP1 mediated signaling, however we could not confirm a direct role of SHP1 signaling in DuoHexaBody-CD37-mediated cytotoxicity. DLBCL cells may undergo signal rewiring upon SHP1 knockdown by altered levels of p‑AKT, p‑STAT3, and p‑STAT6, or SHP2 may compensate for the loss of SHP1. It is currently unclear what the biological implications are of the increased SHP1 signaling observed upon treatment with DuoHexaBody-CD37 in DLBCL cells.”

      (5) The authors state that DuoHexabody-37 is particularly effective at downregulating STAT signalling in the presence of IL-6 (lines 302-303) however, this is not statistically significant in the results section. There is a trend for a reduction, however, further experimental repeats would clarify this.

      We agree with the reviewer, and rewrote the text on IL-6 in the discussion: “p-STAT3 downregulation upon DuoHexaBody-CD37 treatment in presence of IL-6 requires further investigation in additional IL-6-responsive cell lines, as HBL1 was the only IL-6-responsive lymphoma cell line tested in this study.”

    1. Author response:

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

      Reviewer #1:

      Yet I think that important aspects of my critique of the first statement of the manuscript about the flaws of [SR] model remain unanswered.

      I believe that I have fully addressed the points in the earlier review. The reviewer had doubted that my results were correct, attributing them to “a poor setup of the model” on my part. The reviewer stated that if I were correct about the factor of >10<sup>43</sup> change in cmax, this would “naturally break down all the estimates and conclusions made in Siljestam and Rueffler” (S&R).

      It appears that the reviewer is now convinced that my results represent a faithful analysis of the models on which S&R based their claims. The reviewer now contends that these results, including the factor of >10<sup>43</sup>, present no difficulties for the claims of S&R after all. In fact, this enormous factor of >10<sup>43</sup> is now claimed to support the conclusions of S&R by invalidating my conclusions. I respond to these new and very different arguments in what follows.

      As I stated in the first round of review, the issue is not the enormity of this factor per se, but the fact that the compensatory adjustment of cmax conceals the true effects of changes in other parameters. These effects are large; small changes to the parameter values mostly eliminate the diversity that the model is claimed to explain.

      The model in [SR] is not phenomenological as none of the parameters or functional forms were derived empirically. Instead, it is a proof of principle demonstration that inevitably grossly simplifies the actual immune response.

      The hidden sensitivity of the results of S&R to paramater values is sufficient to invalidate them as a proof of principle. The manuscript goes further and explains how the problem "is not specific to the details of the models of Siljestam and Rueffler, but is inherent in the phenomenon invoked to allow high diversity" because "any change that affects condition by as much as the difference between MHC heterozygotes and homozygotes will eliminate high equilibrium diversity". This general principle addresses all of the reviewer's points.

      In reality, a new pathogen cannot reduce the "survival" by such a factor as it would wipe out any resident population. So to compensate for such an artifact, the additional factor cmax was introduced to buffer such an excess. There is no reason to fix cmax once for an arbitrary number of pathogens, because varying cmax basically reflects the observation that a well-adapted individual must have a reasonable survival probability.

      This is not a legitimate reason for making compensatory, diversity-promoting adjustments to cmax when evaluating sensitivity to other parameters. If the number of pathogens or their virulence changes, cmax obviously does not automatically change along with it. If the population or species consequently goes extinct, then it goes extinct. If it persists, it does so with the same value of cmax.

      The possibility of extinction arguably puts a minimum value on cmax, but it does not restrict it to a range of values that conveniently leads to high MHC diversity. In the examples that I analyzed, slightly decreasing the number of pathogens or their virulence, which increases survivability, eliminates diversity. This phenomenon obviously cannot be dismissed on the grounds that survivability would be too low for the species to exist.

      S&R in effect assume that the condition of the most fit homozygote remains fixed, regardless of the number of pathogens, their virulence, and myriad other differences between species. It is this assumption that is without justification.

      At the same time, there are many ways in which the numerical simulation may break down when the survival rates become of the order of 10^(-43) instead of one

      I am not sure what is meant by “the numerical simulation may break down”. Numerical error is not a tenable explanation of the lack of diversity observed in that simulation. The outcome is exactly what is expected from purely theoretical considerations: conditions of all genotypes fall on the steep part of the curve, making the mechanism proposed by S&R largely inoperative, so a pair of alleles forming a fit heterozygote comes to predominate. The numerical simulation is actually superfluous.

      Low survival rates are completely irrelevant to the effect of decreasing the number of pathogens or their virulence, which does not lower survival rates, but does eliminate diversity.

      so it comes to no surprise that the diversification, predicted by the adaptive dynamics, does not readily occur in the scenario with an addition or removal of the 8th pathogen with a very high virulence \nu=20.

      Whether or not it surprising, the lack of diversity is a problem for the claims of S&R, as there is no reason to expect the number of pathogens to have just the right value to produce high diversity. Furthermore, for many combinations of values of the other parameters (e.g., my v=19.5 and 20.5 examples), no number of pathogens leads to high diversity.

      Again, the general principle mentioned above makes the details that the reviewer refers to irrelevant. Nonetheless, some additional remarks are in order:

      (1) This comment ignores the fact that removal of a pathogen, or a slight decrease in “virulence”, eliminates diversity without lowering survival rates.

      (2) Small increases or decreases in v (virulence) eliminate diversity without having such large effects on condition.

      (3) In the example emphasized by the reviewer, mean survival rates are nowhere near as low as 10<sup>-43</sup>. Only homozygotes have such low fitness.

      (4) The adaptive dynamics predict the low diversity seen in the simulations, contrary to what the reviewer seems to suggest. Elimination of diversity is not an artifact of the simulation.

      (5) v\=20 was chosen because it is most favorable to the model of S&R in that it yields the highest diversity. Indeed, S&R only observed realistically high diversity with the narrow gaussians that the reviewer objects to. With lower values of v, diversity is much lower, but even this meager diversity is eliminated by small changes in parameter values (see below). If narrow gaussians and large effects of pathogens somehow invalidate results, then they invalidate the high-diversity results of S&R.

      I have doubts that the reported breakdown of the [SR] model with fixed cmax remains observable with less extreme values of m and \nu (say, for \nu=7 and m=3 plus or minus 1 used in Fig. 3 in the manuscript).

      These doubts are unwarrented. With the suggested parameter values, for example, increasing or decreasing m by 1 reduces the effective number of alleles to around 1 or 2. This can easily be checked using the simulation code of S&R, as detailed in my initial response and now in a Supplementary Text. Even without this result, the general principle mentioned above tells us that considering other regions of parameter space cannot rescue the conclusions of S&R.

      So I still find the claim that " the phenomenon that leads to high diversity in the simulations of Siljestam and Rueffler depends on finely tuned parameter values" is not well substantiated.

      What is unsubstantiated is the claim of S&R that “For a large part of the parameter space, more than 100 and up to over 200 alleles can emerge and coexist”. As my manuscript illustrates, this is an illusion created by the adjustment of one parameter to compensate for changes in others.

      The reviewer even acknowledges that “the choice of constants and functions...works in a limited range of parameter values”. Furthermore, the manuscript explains why this problem is inherent to the general phenomenon, not specific to the details of the model or parameter values.


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

      Public Reviews:

      Reviewer #1 (Public review):

      It appears obvious that with no or a little fitness penalty, it becomes beneficial to have MHC-coding genes specific to each pathogen. A more thorough study that takes into account a realistic (most probably non-linear in gene number) fitness penalty, various numbers of pathogens that could grossly exceed the self-consistent fitness limit on the number of MHC genes, etc, could be more informative.

      The reviewer seems to be referring to the cost of excessively high presentation breadth. Such a cost is irrelevant to the inferior fitness of a polymorphic population with heterozygote advantage compared to a monomorphic population with merely doubled gene copy number. It is relevant to the possibility of a fitness valley separating these two states, but this issue is addressed explicitly in the manuscript.

      An addition or removal of one of the pathogens is reported to affect "the maximum condition", a key ecological characteristic of the model, by an enormous factor 10^43, naturally breaking down all the estimates and conclusions made in [RS]. This observation is not substantiated by any formulas, recipes for how to compute this number numerically, or other details, and is presented just as a self-standing number in the text.

      It is encouraging that the reviewer agrees that this observation, if correct, would cast doubt on the conclusions of Siljestam and Rueffler. I would add that it is not the enormity of this factor per se that invalidates those conclusions, but the fact that the automatic compensatory adjustment of c</sub>max</sub> conceals the true effects of removing a pathogen, which are quite large.

      I am not sure why the reviewer doubts that this observation is correct. The factor of 2.7∙10<sup>43</sup> was determined in a straightforward manner in the course of simulating the symmetric Gaussian model of Siljestam and Rueffler with the specified parameter values. A simple way to determine this number is to have the simulation code print the value to which c</sub>max</sub> is set, or would be set, by the procedure of Siljestam and Rueffler for different parameter values. I have in this way confirmed this factor using the simulation code written and used by Siljestam and Rueffler. A procedure for doing so is described in the new Supplementary Text S1. In addition, I now give a theoretical derivation of this factor in Supplementary Text S2.

      This begs the conclusion that the branching remains robust to changes in cmax that span 4 decades as well.

      That shows at most that the results are not extremely sensitive to c</sub>max</sub> or K. They are, nonetheless, exquisitely sensitive to m and v. This difference in sensitivities is the reason that a relatively small change to m leads to such a large compensatory change in c</sub>max</sub>. It is evident from Fig. 4 of Siljestam and Rueffler that the level of diversity is not robust to these very large changes in c</sub>max</sub>, which include, as noted above, a change of over 43 orders of magnitude.

      As I wrote above, there is no explanation behind this number, so I can only guess that such a number is created by the removal or addition of a pathogen that is very far away from the other pathogens. Very far in this context means being separated in the x-space by a much greater distance than 1/\nu, the width of the pathogens' gaussians. Once again, I am not totally sure if this was the case, but if it were, some basic notions of how models are set up were broken. It appears very strange that nothing is said in the manuscript about the spatial distribution of the pathogens, which is crucial to their effects on the condition c.

      I did not explicitly describe the distribution of pathogens in antigenic space because it is exactly the same as in Siljestam and Rueffler, Fig. 4: the vertices of a regular simplex, centered at the origin, with unity edge length.

      The number in question (2.7∙10<sup>43</sup>) pertains to the Gaussian model with v\=20. As specified by Siljestam and Rueffler, each pathogen lies at a distance of 1 from every other pathogen, so the distance of any pathogen from the others is indeed much greater than 1/v. This condition holds, however, for most of the parameter space explored by Siljestam and Rueffler (their Fig. 4), and for all of the parameter space that seemingly supports their conclusions. Thus, if this condition indicates that “basic notions of how models are set up were broken”, they must have been broken by Siljestam and Rueffler.

      ...the branching condition appears to be pretty robust with respect to reasonable changes in parameters.

      It is clear from Fig. 4 of Siljestam and Rueffler that the branching condition is far from sufficient for high MHC diversity.

      Overall, I strongly suspect that an unfortunately poor setup of the model reported in the manuscript has led to the conclusions that dispute the much better-substantiated claims made in [SD].

      The reviewer seems to be suggesting that my simulations are somehow flawed and my conclusions unreliable. I have addressed the reasons for this suggestion above. Furthermore, I have confirmed the main conclusion—the extreme sensitivity of the results of Siljestam and Rueffler to parameter values--using the code that they used for their simulations, indicating that my conclusions are not consequences of my having done a “poor setup of the model”. I now describe, in Supplementary Text S1, how anybody can verify my conclusions in this way.

      Reviewer #2 (Public review):

      (1) The statement that the model outcome of Siljestam and Rueffler is very sensitive to parameter values is, in this form, not correct. The sensitivity is only visible once a strong assumption by Siljestam and Rueffler is removed. This assumption is questionable, and it is well explained in the manuscript by J. Cherry why it should not be used. This may be seen as a subtle difference, but I think it is important to pin done the exact nature of the problem (see, for example, the abstract, where this is presented in a misleading way).

      I appreciate the distinction, and the importance of clearly specifying the nature of the problem. However, as I understand it, Siljestam and Rueffler do not invoke the implausible assumption that changes to the number of pathogens or their virulence will be accompanied by compensatory changes to c</sub>max</sub>. Rather, they describe the adjustment of c</sub>max</sub> (Appendix 7) as a “helpful” standardization that applies “without loss of generality”. Indeed, my low-diversity results could be obtained, despite such adjustment, by combining the small change to m or v with a very large change to K (e.g., a factor of 2.7∙10<sup>43</sup>). In this sense there is no loss of generality, but the automatic adjustment of c</sub>max</sub> obscures the extreme sensitivity of the results to m and v.

      (2) The title of the study is very catchy, but it needs to be explained better in the text.

      I have expanded the end of the Discussion in the hope of clarifying the point expressed by the title.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I would like to suggest to the author that they provide essential details about their simulations that would justify their claims, and to communicate with Mattias Siljestam and Claus Rueffler whether claims of the lack of robustness could be confirmed.

      The models simulated were modified versions of those of Siljestam and Rueffler. Thus, only the modifications were described in my manuscript. I have added a more detailed description of how c</sub>max</sub> was set in the simulations concerned with sensitivity to parameter values. In addition, the new Supplementary Text S1, which describes confirmation of the lack of robustness using the code of Siljestam and Rueffler, should remove any doubt about this conclusion.

      Reviewer #2 (Recommendations for the authors):

      I have no further recommendations. The manuscript is well written and clear.

      Thank you.

      Reviewer #3 (Recommendations for the authors):

      (1) Since this is a full report and not just a letter to the editor, it would benefit from a bit more introduction of what the MHC actually is and what the current understanding of its evolution is. Currently, it assumes a lot of knowledge about these genes that might not be available to every reader of eLife.

      I have added some more information to the opening paragraph. I would also note that this report was submitted as a “Research Advance”, which may only need “minimal introductory material”.

      (2) Some more recent literature on MHC evolution should be added, e.g., the review by Radwan et al. 2020 TiG, a concrete case of MHC heterozygote advantage by Arora et al. 2020 MolBiolEvol, and a simulation of MHC CNV evolution by Bentkowski et al. 2019 PLOSCompBiol.

      I have cited some additional literature.

      (3) Since much of the criticism hinges on the cmax parameter, its biological meaning or role (or the lack thereof) could be discussed more.

      I am not sure what I can add to what is in the first paragraph of the Discussion.

      (4) I find it difficult to grasp how the v parameter, which is intended to define pathogen virulence, if I understand it correctly, can be used to amend the breadth of peptide presentation. Maybe this could be illustrated better.

      I have attempted to make this clearer. The parameter v actually controls the breadth of peptide detection conferred by an allele, which, if not identical to the breath of presentation, is certainly affected by it. The basis of the “virulence” interpretation seems to be that narrower detection breadth can, according to the model, only decrease peptide detection probability, which increases the damage done by pathogens.

      (5) Please check sentences in lines 279ff on peptide detection and cost of . There seem to be words missing.

      There was an extraneous word, which I have removed. Thank you for pointing this out.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors investigate ubiquitylation of RPS27A/eS31 by the E3 ligase RNF25 in response to translational stress. Previous studies have identified RPS27A/eS31 ubiquitylation at Lys113 under conditions where translation factors are trapped in the ribosomal A-site. Here, the authors extend this work by testing whether additional translational stress conditions, including amino acid deprivation, induce RPS27A/eS31 ubiquitylation. They further show that GCN1 is required and explore a possible competition between RNF25 and GCN2 for GCN1.

      Strengths:

      This study expands on the range of stress conditions leading to RPS27A/eS31 ubiquitylation, reporting that it occurs in a variety of conditions associated with ribosome stalling, including amino acid deprivation. These observations are useful because they suggest that the RNF25 pathway may not require translation factors trapped in the ribosomal A-site, but may instead respond more broadly to translational perturbations associated with ribosome collisions.

      We wish to point out that our study in fact suggests that the RNF25 pathway is activated by translation factors in the A-site, in agreement with what has been previously proposed, and in addition by stalling conditions that are assumed to not trap translation factors in the A-site. We do not exclude that these conditions might be sampled by A-site binding quality control factors before recognition by RNF25.

      Weaknesses:

      The evidence supporting several of the major claims is incomplete, and additional controls and orthogonal approaches would greatly strengthen the evidence presented.

      We appreciate adding more controls to further substantiate our novel findings. In the course of the revisions we will focus our work on those experiments that do not merely reproduce established facts in the field.

      In particular:

      (1) It is unclear whether the different conditions used to induce translational stress lead to ribosome stalling or collisions. The model presented by the authors seems to rely on ribosomal collisions, but this is not shown. In addition, further investigating amino acid deprivation beyond the removal of Arg or Lys would strengthen the paper.

      We thank the reviewer for the comment. It is correct that we don’t formally show collisions.

      However, the conditions we use have been previously established in the field to induce ribosome stalls and/or collisions, which we may not have pointed out clearly enough. In the revised version, we will include all relevant citations, i.e. for ternatin (Oltion et al., 2023): collisions, anisomycin (Juszkiewicz et al., 2018, Sinha et al., 2020): collisions, emetine (Sinha et al., 2020): collisions, didemnin B (Juszkiewicz et al., 2018, Stoneley et al., 2022): accumulation of ubi-eS10 and changes in polysome profiles indicative of collisions, MMS (Stoneley et al., 2022): changes in polysome profiles indicative of stalls or collisions, starvation -Arg/-Lys (Darnell et al., 2018, Stoneley et al., 2022): accumulation of collided ribosomes only upon GCN2 inhibition, indicative of collisions.

      Secondly, we do not claim to induce collisions when describing the inhibition data (Figure 1 and Figure S1) and were careful to say that we use ‘conditions that cause ribosome stalling’.

      Thirdly, we conclude on collisions when interpreting the data on amino acid starvation (and in our model (Figure 6)), based on our data demonstrating that RNF25 activity in RPS27A/eS31 ubiquitylation is dependent on GCN1 (Figure 3), an established sensor of collided disomes (Pochopien et al., 2021). This conclusion is thus based on the current knowledge in the field.

      We will carefully screen the text for potential points of overinterpretation or confusion between stalling and collisions.

      To address the request of further investigating amino acid deprivation beyond the removal of Arg or Lys, we will include an additional experiment in which we will deplete another amino acid.

      (2) Ubiquitylation of RPS27A/eS31 by RNF25 is used throughout the paper as a readout of RNF25 activity and is assumed to be on Lys113 based on previous work, but is not formally shown here.

      It is established that Lys113 is the main target of RNF25, not only by our work (Montellese et al., 2020), but also by recent work of other groups to which we had referred in our manuscript (Gurzeler et al., 2023, Oltion et al., 2023, Zhao et al., 2026).

      To experimentally address this point, we will add an experiment testing ubiquitylation of RPS27A/eS31 in cells carrying the K113R mutation.

      (3) Rescue experiments of the different mutants used in this study with wild-type and different domain deletions (i.e., ΔRWD for RNF25, ΔRWD-binding for GCN1) would help confirm specificity and strengthen the mechanistic claims.

      Minimally, we will include rescue experiments for RNF25 (using WT, DRWD and enzymatically dead mutant) and, if possible, also for GCN1, which might be more challenging due to its large size and anticipated problems with cloning, cell line generation and protein expression.

      (4) The conclusion that RPS27A/eS31 ubiquitylation supports translation (Figure 4) is based entirely on polysome/monosome ratios, which are difficult to interpret without additional assays of translation output, elongation, or collision.

      It is correct that we base our conclusion on polysome profiles and agree that these are an indirect measure of translation output. However, this assay is well established in the field to show dysregulation of polysome/monosome ratio upon ribosome stalling (Garzia et al., 2017), (Wu et al., 2020), (Chatterjee et al., 2024), (Gurzeler et al., 2023).

      Elongation defects would be expected to lead to stalls and/or collisions (which we conclude on). However, we cannot exclude that there is more initiation when RPS27A/eS31 carries the K113R mutation, although this is hard to rationalize mechanistically and experimentally challenging to exclude. Therefore, to address the point, we will add a sentence that we cannot exclude indirect effects on initiation but consider these unlikely.

      (5) The idea that RNF25 competes with GCN2 for GCN1 binding is interesting, and related models have recently been proposed in RNA damage. The effect of GCN2 KO on RNF25dependent ubiquitylation appears modest, and the data would be strengthened by rescue experiments with wild-type GCN2 and GCN2 mutants defective in GCN1 binding. The authors propose: "that the RNF25 pathway acts as a first line of defence to resolve ribosome collisions, outcompeted by GCN2 binding to GCN1 under acute stress." This model would suggest a further increase in RPS27A/eS31 ubiquitylation upon Arg/Lys deprivation in GCN2 KO cells, since this is the condition in which GCN2 is expected to be activated and engaged with GCN1 (i.e., when it would be competing with RNF25), but no further increase in RPS27A ubiquitylation is observed. It is therefore not clear that these data support the proposed model. Contributing to this may be the fact that many of these assays are performed in a USP16 KO background, which may make it difficult to assess changes in RPS27A/eS31 ubiquitylation.

      We thank the reviewer for the comment. We measure on average a 50% increase in the level of ubiquitinated RPS27A/eS31 in GCN2 KO cells. Considering the large number of ribosomes in a cell (~10<sup>7</sup> per HeLa cell), this 50% increase (from 12.5 to 25% ubiquitinated RPS27A/eS31) amounts to an estimated number of 1,25 x 10<sup>6</sup> of RPS27A/eS31 molecules that get additionally modified, which is clearly a substantial difference, especially compared to the naturally very low levels of RNF25 (in the range of 23’000 molecules (Itzhak et al., 2016)).

      We respectfully disagree that performing experiments in USP16 KO background makes it difficult to assess RPS27A/eS31 ubiquitination. On the contrary. The natural levels of RPS27A/eS31 ubiquitination in WT cells are very low, making quantification sensitive to background fluctuations (see Figure S1). Therefore, in our experience, the usage of USP16 KO makes the quantitative analysis of RPS27A/eS31 ubiquitination robust, allowing us to analyse both increase and decrease in the levels of ubiquitination. We agree that with increasing collisions, the level of ubiquitinated RPS27A/eS31 reaches a plateau in USP16 KO, which may limit the observable increase. Therefore, the substantial 50% increase might indeed underestimate the effect as compared to WT cells. Still, the measurable increase is substantial and robust.

      To experimentally address the point of the reviewer, we will try generating GCN2 KO cells in a WT background, i.e. in absence of USP16 KO, to strengthen our model.

      (6) Given that several RWD domain proteins can interact with GCN1, and that DRG2 KO appears to affect RPS27A/eS31 ubiquitylation (Figure S5), the data do not support the GCN2specific title. The results are more consistent with a broader, incompletely characterized network of GCN1-associated RWD domain-containing proteins that seems to affect RNF25-dependent ubiquitylation rather than with a demonstrated RNF25-GCN2 competition mechanism. Further characterization of GCN2-dependent ISR activation (p-eIF2a and ATF4 WB) in the absence of RNF25 in Arg/Lys starvation will help shed light on the RNF25-GCN2 competition. The authors use K113R, but this is not shown to prevent RNF25 engagement with GCN1, so a RNF25 KO should be used.

      While we fully agree that our data point at a broader network of competition on GCN1, we wished to avoid an overstatement on other pathways than GCN2, since our experimental evidence on DRG2 is limited at the moment. As it stands, changing the title of the manuscript to a more general message, would indeed fuel the view that our claims are incomplete. But we are glad to reconsider this suggestion if further supporting evidence can be obtained in the course of the revision work.

      The reviewer suggests experiments on competition of RNF25 with GCN2. In contrast to the expectation of the reviewer, we do not expect KO of RNF25 to manifest in defects in ISR activation due to the low expression levels of RNF25. In the revised manuscript, we will make clearer that our model refers to competition in the other direction, i.e., of GCN2 with RNF25, which our data supports. The reverse competition of RNF25 with GCN2 is expected to be inefficient to enable a robust activation of the ISR by GCN1 when needed. In addition, other pathways (such as DRG2) might also contribute to the resolution of collisions in the absence of RNF25, affecting the level of ISR activation.

      We feel that further working out these competitive relationships will be interesting to perform in future work. Currently, it is also not clear whether all involved RWD-containing factors bind GCN1 with the same affinity, which is important to consider for the effectiveness of a mutual competition model as suggested by the reviewer.

      Reviewer #2 (Public review):

      Summary:

      The authors show that deprivation of Arginine and Lysine induces a ~50% increase in the ratio of ubi-RPS27A to RPS27A, and this induction requires E3 ubiquitin ligase RNF25. The authors show ZAKalpha and EDF1 are not required for steady state or ribosome stalling-induced ubiRPS27A, while GCN1 is required. The ratio of polysomes to monosomes is increased in RNF25 knockdown cells or when translation is activated by ISRIB in a RPS27A K113R mutant cell line. GCN2 KO cells indicate elevated levels of ubi-RPS27A, and overexpression of the GCN2 RWD domain reduces levels of ubi-RPS27A.

      Strengths:

      (1) The authors identified a novel pathway to sense amino acid deprivation, indicated by ubiRPS27A, previously implicated in ribosome stalling.

      (2) The authors find antagonism between two proteins known to act downstream of GCN1, giving insight into how signaling occurs from an upstream sensor of ribosome stalling to multiple downstream pathways.

      Weaknesses:

      (1) The authors suggest that, based on increased Polysome/Monosome ratios, there is more disome stalling in RNF25 KD cells and RPS27A K113R cells treated with ISRIB, but this readout is very indirect and could be driven by other changes in the cell other than ribosome stalling.

      We thank the reviewer for this important comment. We intentionally used ISRIB in Figure 4F, G to avoid possible effects on initiation, and the results are consistent with our model. While we agree that ISRIB itself might have indirect consequences, these should be the same for the control (WT cells) and the assay condition (K113R cells). We also show the data without ISRIB, which show a similar trend but are less robust (Figure 4D, E). It is very hard to exclude other possible effects which would selectively affect K113R cells in presence of ISRIB.

      (2) While the authors propose that GCN2 and RNF25 compete for binding to GCN1, no evidence was shown that RNF25 binds to GCN1 in cells, nor that the interaction increases when GCN2 is absent.

      The idea of RNF25 binding to GCN1 is based on a previously published work (Oltion et al., 2023, Seidel et al., 2026, Zhao et al., 2026). We will design additional experiments to potentially confirm the interaction between RNF25 and GCN1.

      (3) The use of USP16 to enhance the detection of ubi-RPS27A in many experiments brings the question of whether USP16 KO may alter the protein levels of any known regulators of ribosome collisions? (i.e. ZNF598, GCN1, EDF1, ZAKalpha, etc.) If USP16 KO causes changes in other important regulators of collisions, the authors could be identifying genetic interactions with USP16 in their experiments throughout the paper.

      Indeed, we can’t exclude the effect of USP16 KO on the expression levels of other collision sensors. We will experimentally confirm the levels of other ribosome collision sensors in USP16 KO cells.

      (4) In Figure 5E, the expression level of the GCN2 3K RWD domain looks to be lower than the WT RWD domain; perhaps this could be what is driving the smaller decrease of ubi-RPS27A seen with GCN2 3K vs WT.

      We thank the reviewer for pointing at this issue, which we will experimentally address in the revised version.

      Reviewer #3 (Public review):

      Summary:

      This study examines the role of RNF25 in translational quality control. Previous work indicated that RNF25 is activated by ribosomes stalled with defective elongation or termination factors bound in the A-site. Here, the authors provide evidence that RNF25 is activated by other treatments that evoke ribosome stalling, including amino acid starvation, where the A-site may be empty, leading to ubiquitination of RPS27A in a manner requiring the ISR collision sensor Gcn1, but not EDF1 and ZAKα, involved in the RQC and RSR surveillance pathways. They present some evidence from polysome profiling that RNF25 and its ubiquitination of RPS7A help resolve ribosome collisions and support translation elongation in basal conditions. They further show that KO of Gcn2 increases RPS27A ubiquitination in basal conditions, but not in amino acid-starved cells, and that RPS27A ubiquitination was reduced on overexpressing the WT RWD domain of Gcn2 but not a variant harboring substitutions of residues predicted to bind Gcn1. Based on these findings, they propose a model that, in response to ribosome stalling induced by various stresses, Gcn1 recruits RNF25 via the latter's RWD domain to ubiquitinate RPS27A and thereby resolve ribosome stalling and promote continued elongation. If collisions increase even further, GCN1 recruits GCN2 instead of RNF25 to elicit the ISR.

      Strengths:

      The data is convincing that a variety of triggers leading to diverse stalled ribosomal states, including amino acid limitation, can activate RNF25, suggesting that activation of this pathway does not require the presence of trapped protein factors in the ribosomal A-site but is a more general response to ribosome collisions. It is also convincing that Gcn1 is required for RNF25 activation under all of these conditions, which is consistent with previous findings that Gcn1 is required for RNF25 function in the presence of trapped elongation or termination factors. The finding that EDF1 and ZAK are not needed for RNF25 activation in amino acid starvation conditions is of interest for EDF1, given the recent claim that it is required for full ISR activation.

      Weaknesses:

      (1) The evidence presented from polysome profiling that RNF25 helps resolve naturally occurring ribosome collisions in basal conditions is not compelling, as eliminating RNF25 could be increasing the rate of initiation rather than increasing stalled ribosomes as the means of increasing the P/M ratio. The Rps27A-K113R mutation could have the same effect of increasing initiation, which could have been obscured by inhibiting the ISR with ISRIB.

      Our results indicate that P/M ratio increases upon ISRIB treatment of K113R cells compared to WT cells, aligning with the idea that ISRIB enhances initiation, causing increased loading of ribosomes on mRNA and consequent increased frequency of collisions. As outlined above, we agree that this experiment is indirect and results might be affected by secondary effects. However, we cannot rationalize how inhibition of the ISR by ISRIB would specifically obscure the effect for the K113R mutation but not the WT.

      (2) The evidence that RNF25 competes with Gcn2 for Gcn1 binding is also not compelling. While it's convincing that Rps27A-Ubi is elevated in basal conditions on eliminating Gcn2, loss of GCN2 would be expected to increase ribosome loading on mRNAs, potentially elevating the frequency of collisions and thereby stimulating RNF25 activity indirectly.

      We have not made sufficiently clear that we did not intend to claim that RNF25 efficiently competes with GCN2 (see also response to reviewer 1), which we do not expect due to the low levels of RNF25. Our manuscript is focussed on competition in the reverse direction, i.e. of GCN2 with RNF25.

      We agree that loss of GCN2 may increase ribosome loading on mRNA similar to ISRIB treatment, which could lead to more collisions by enhanced translation and hence increased Rps27A-Ubi. At the same time, however, this does not exclude that loss of GCN2 contributes more directly at the level of RNF25 recruitment. Therefore, the experiment also supports the competition model, and both effects together may contribute to the observed increase in ubiquitylated RPS27A/eS31. Without other evidence, the experiment would remain inconclusive.

      Therefore, to directly test the competition model, we had overexpressed the GCN1-binding RWD domain of GCN2, which leads to decreased levels of ubiquitinated RPS27A/eS31, lending direct support to the competition model of GCN2 with RNF25, which is consistent with similar models recently proposed by two other manuscripts (Seidel et al., 2026, Zhao et al., 2026).

      (3) It's also quite puzzling and left unexplained why they observed no further increase in Rps27AUbi on -Arg/-Lys starvation in the cells lacking Gcn2. Why wouldn't -Arg/-Lys starvation lead to further stalling and RNF25 activation in the absence of Gcn2? (Since Gcn2 KO increases Rps27A-Ubi in the presence +Arg/+Lys conditions, it can't be that Gcn2 is required for RNF25 function.) The same puzzling and unresolved observation was made in the cells lacking DRG2. One possible explanation for this conundrum is that low-level RNF25 abundance limits further activation.

      Over all of our experiments, we have observed that RPS27A-Ubi reaches a plateau of about 30% to 35% of total RPS27A in the USP16 KO background (GCN2 deletion or amino acid starvation). This plateau indeed limits seeing further increases. We do not know the underlying reason but note that under these conditions about one third of 40S subunits carry ubiquitin on RPS27A/eS31. As the reviewer suggests, RNF25 is expressed at low levels (in the range of 23’000 molecules, (Itzhak et al., 2016); see point 5 of reviewer 1), likely rendering it the limiting factor for further ubiquitination events.

      To circumvent the plateau issue, we will attempt to generate GCN2 KO cell lines in the WT background for the starvation experiments (see also response to reviewer 1, point 5).

      (4) The quantitative effects of overexpressing the Gcn2 RWD domain on Rps27A-Ubi, constituting their other evidence presented to support the competition model, are quite small in magnitude.

      We respectfully disagree with the reviewers’ comment concerning the magnitude of the effect. There is a ~27% decrease in ubiquitination, which is substantial considering the number of 40S ribosomal subunits and possible consequences of such change. It should also be noted that this is a transient transfection experiment not hitting all cells of the population. We will repeat the experiment, optimizing the expression of the negative control construct.

      Cited literature:

      Chatterjee S, Naeli P, Onar O, Simms N, Garzia A, Hackett A, Coyle K, Harris Snell P, McGirr T, Sawant TN et al. (2024) Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil. Nucleic Acids Res 52: 12534-12548

      Darnell AM, Subramaniam AR, O'Shea EK (2018) Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell 71: 229-243 e11

      Garzia A, Jafarnejad SM, Meyer C, Chapat C, Gogakos T, Morozov P, Amiri M, Shapiro M, Molina H, Tuschl T et al. (2017) The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. Nat Commun 8: 16056

      Gurzeler LA, Link M, Ibig Y, Schmidt I, Galuba O, Schoenbett J, Gasser-Didierlaurant C, Parker CN, Mao X, Bitsch F et al. (2023) Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control. Cell Rep 42: 113056

      Itzhak DN, Tyanova S, Cox J, Borner GH (2016) Global, quantitative and dynamic mapping of protein subcellular localization. Elife 5

      Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS (2018) ZNF598 Is a Quality Control Sensor of Collided Ribosomes. Mol Cell 72: 469-481 e7

      Montellese C, van den Heuvel J, Ashiono C, Dorner K, Melnik A, Jonas S, Zemp I, Picotti P, Gillet LC, Kutay U (2020) USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit. Elife 9  

      Oltion K, Carelli JD, Yang T, See SK, Wang HY, Kampmann M, Taunton J (2023) An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes. Cell 186: 346-362 e17

      Pochopien AA, Beckert B, Kasvandik S, Berninghausen O, Beckmann R, Tenson T, Wilson DN (2021) Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Proc Natl Acad Sci U S A 118

      Seidel AS, Nemcekova L, Grønbæk-Thygesen M, Shi X, Ramalho S, Mordente KC, Bekker-Jensen S, Haahr P (2026) RNF25 restrains GCN2 hyperactivation to sustain protein synthesis and cell proliferation in response to RNA damage. bioRxiv

      Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M et al. (2020) EDF1 coordinates cellular responses to ribosome collisions. Elife 9

      Stoneley M, Harvey RF, Mulroney TE, Mordue R, Jukes-Jones R, Cain K, Lilley KS, Sawarkar R, Willis AE (2022) Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress. Mol Cell 82: 1557-1572 e7

      Wu CC, Peterson A, Zinshteyn B, Regot S, Green R (2020) Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate. Cell 182: 404-416 e14

      Zhao S, Palma-Chaundler CS, Engel CM, Cordes J, Nixdorf D, Luo MY, Kaya S, Suryo Rahmanto A, van den Heuvel D, Mackens-Kiani T et al. (2026) RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response. Mol Cell 86: 1275-1292 e12

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study identifies mutations in alpha-tubulin that suppress Tau-induced neurodegeneration using the C. elegans model of Tauopathy, suggesting a potentially interesting role for microtubule properties in modulating Tau toxicity. These missense mutations cluster in the C-terminal Tau-interacting helix 12 region of alpha-tubulin genes (tba-1, tba-2, and mec-12). Further analysis, particularly using the strongest suppressor tba-2, shows that it rescues Tau-induced behavioral deficits and neuronal loss without significantly altering bulk tau-phosphorylation, aggregation, or binding to soluble tubulin. The authors suggest that altered microtubule properties underlie the neuroprotective effects, and manipulating microtubule properties may have therapeutic potential.

      Strengths:

      The study is conceptually interesting as it shows that Tau-induced neurotoxicity can, in this model, be partially uncoupled from canonical pathological hallmarks such as Tau-hyperphosphorylation and aggregation. The identification of multiple independent mutations in the same structural region of three alpha-tubulin genes provides support for the functional relevance of helix 12 in modulating Tau-induced toxicity. The authors demonstrate significant rescue of behavioral deficits (using motility and manual thrashing assays) and neuronal loss in both WT-tau and FTLD-associated TauV337M in combination with mutant alpha-tubulins, suggesting a general mechanism for tubulin-regulated modulation of Tau-toxicity. Moreover, the correlation between mutant tubulin expression levels and the extent of rescue supports a causal relationship.

      Weaknesses:

      One of the major claims of this manuscript is that altered microtubule properties suppress Tau toxicity. The only supporting evidence in this context provided by the authors is reduced taxol-stabilized microtubule mass, which does not fully explain neuronal loss or the rescue of behavioral deficits. What remains unclear is whether these mutations alter microtubule dynamics, catastrophe, lattice stability, or axonal transport.

      We agree with Reviewer #1’s critique that the evidence presented does not fully explain neuronal loss and requires further investigation. This first manuscript characterized the mutations discovered through forward genetic screening techniques and provided data to support the positive correlation mutant expression and level of suppression. We believe the studies and data presented here help to formulated the next testable hypotheses, and guide the next lines of experimentation. We are encouraged by Reviewer #1’s assessment that exploration of microtubule dynamics, catastrophe, lattice stability and axonal transport will be critical to testing the hypothesis that mutant tubulin drives suppression of tau toxicity through changes to microtubule properties. These suggestions are highly relevant and align with our priorities as we recently submitted an application for a 5-year research award to support these key questions.

      To address this specifically, the reviewer recommended “The microtubule-dependent axonal transport should be examined in tubulin mutants and compared with mutant tubulin + Tau conditions. Imaging of mitochondrial or synaptic vesicle markers, along with appropriate quantifications (velocity or run length), may provide a functional readout linking microtubule changes to neuronal survival.”

      We agree with the reviewer that these experiments will be highly valuable to further understand the mechanisms underlying suppression, and we have planned to complete these experiments upon receipt of funding that would directly support the completion of these experiments.

      The authors show that mutant tba-2 reduces total tau levels by ~45%. This level of reduction is likely significant but underexplored in the manuscript. Why are the Tau levels reduced? How is Tau getting cleared- is there enhanced autophagy or ubiquitin-proteasome pathway getting upregulated in tba-2 + Tau animals? Or one or more of the Tau species not detectable by the antibodies used in this study? The observation that the mec-12 mutant rescues Tau-induced phenotypes without altering Tau levels suggests that suppression can occur through Tau-independent mechanisms. This raises an important unresolved question regarding the extent to which suppression is Tau-dependent vs Tau-independent across different mutant alpha-tubulin genes, complicating the interpretation of the rescue phenotypes.

      We think the reviewer has addressed an important point that there may be both tau-dependent and tau-independent mechanisms at work here, and we will add greater nuance to this in our discussion. Additionally, we agree these two potential mechanistic pathways merit further exploration. To address this, we have planned to conduct experiments using reporter C. elegans lines crossed with our mutant tubulin/tau-transgenic lines to detect potential upregulation of these pathways as mechanisms for tau clearance.

      Given that Tau primarily associates with the microtubule lattice in vivo, measuring interactions with soluble tubulin may not fully capture biologically relevant binding dynamics and therefore does not exclude the possibility that these mutations alter tau-microtubule interactions at the lattice level or may affect the binding of other MAPs/regulators, thereby altering stability or trafficking.

      In the discussion we acknowledge the limitation of only examining the binding affinity between soluble tubulin and tau and intend to complete further studies with polymerized microtubules containing mutant α-tubulin. We will expand discussion of this in the text. Similar to reviewer 1, we have also concluded that the next line of experimentation will focus on mutant alpha-tubulin effects on the microtubule polymer such as changes to MAP interactions, stability and trafficking. We have applied for and hope to receive funding to address these questions in the near future.

      To address this concern specifically, we plan to conduct these experiments using C. elegans extracts to polymerize microtubules and subsequently test the binding of recombinant human tau. These co-sedimentation experiments are expected to be included in the revised manuscript.

      A large body of conclusions is drawn from behavioral rescue and biochemical assays. This limits the understanding of how molecular changes in tubulin might affect cellular mechanisms of neuroprotection. Are there changes in the neuronal microtubule organization, Tau localization, or its redistribution in the mutant alpha-tubulin background? Are there differences in soluble vs oligomeric vs insoluble Tau in mutant tba-2 and mec-12 animals?

      The reviewer raises relevant questions regarding elucidation of the mechanisms underlying mutant tubulin-mediated suppression at the cellular level. To address this concern we will analyze the cellular distribution of tau in neurons from mutant and non-mutant C. elegans.

      Ultimately, our goals are to identify and connect the underlying biochemical mechanisms with the observed prevention of cell death as Reviewer 1 has identified. Their suggestion to explore cellular-level changes such as mutant tubulin effects on tau distribution is highly relevant. We therefore plan to test this directly by imaging neurons in C. elegans strains expressing fluorescently labeled tau and/or immunohistochemical techniques to stain for tau in C. elegans neurons.

      The suppression of behavior in the co-pathology model is interesting but mechanistically insufficient, mainly because the underlying basis of suppression is not examined in these models. Moreover, it remains unclear whether tubulin-Tau genetically interacts with Aβ or TDP-43, and what cellular mechanisms account for the partial rescue observed in these co-pathology models.

      In agreement with Reviewer #1’s assessment, we have concluded these data, while interesting, do not substantially expand our understanding apart from the existing data. Without additional information regarding the underlying mechanisms, they do not provide substantial novel insights and we have therefore chosen to remove the co-pathology data sets from the revised version of the manuscript to refine the scope of the data and hypotheses discussed in this work.

      Reviewer #2 (Public review):

      Summary:

      The manuscript by Benbow et al. identifies, through a genetic screen, key tubulin mutants that, with high confidence, rescue tau-mediated ND phenotypes. This manuscript is well written, and the experimental results strongly support the authors' claims that these tubulin mutants can rescue ND-linked phenotypes in C. elegans while having little to no direct effect on Tau aggregation.

      Strengths:

      Benbow et al. use a relatively unbiased forward genetic screen to identify mutations associated with phenotypes that suppress tauopathy-related defects. The authors then logically focus on the various α-tubulin missense mutations identified in H12, which are known to localize to the external face of microtubules. The authors also carefully compare their established tauopathy-associated phenotypes in the WT TauH model, with and without specific α-tubulin mutations, using appropriate controls throughout. Lastly, the authors provide partial mechanistic insight into the α-tubulin mutant-mediated rescue, showing that these effects are independent of tau aggregation and tau phosphorylation, and instead suggest that the α-tubulin mutations may confer altered microtubule assembly properties based on the sedimentation assays.

      Weaknesses:

      While the claims are largely supported by the experimental outcomes, the authors at times do not provide enough detail in the text for readers to interpret the data sets independently. In addition, some claims appear to be slightly overstated relative to the data or the degree of error associated with those data.

      We appreciate the feedback regarding the need for additional clarity for independent analysis of the datasets. We will revise the figures and text to increase clarity for the readers. We will review statements and edit language in accordance with their degrees of error as appropriate.

      The authors measure tau binding affinities using soluble tubulin but do not assess tau binding to assembled microtubules. This is an important limitation, as the physiologically relevant interaction involves α/β-tubulin heterodimers, either free or incorporated into the microtubule lattice. Furthermore, the binding analysis appears to focus only on the D429N α-tubulin mutant, which further limits physiological relevance, as β-tubulin, which is also required for normal tau binding, is not explicitly considered.

      We acknowledge that the limited conclusions may be drawn from soluble tubulin interactions with tau and additional analysis with polymerized microtubules will be useful in understanding tau-microtubule binding affinity. The analysis was completed with isolated pools of tubulin from C. elegans, not recombinant mutant tubulin, so this is a heterogenous mixture of tubulin composed of α/β heterodimer subunits, and a mixture of the mutant isotype within the larger pool of wild type isotypes. While this further complicating the analysis, and is the likely source of variability, it incorporates the normal heterodimer subunit biochemistry.

      Given that tau prominently binds the microtubule lattice we agree with the reviewers that the assessment that experiments with polymerized microtubules containing mutant tubulin would offer a greater understanding of the effects of mutant alpha-tubulin on microtubule properties and potential mechanisms of toxic tau suppression. To test this directly we intend to complete co-sedimentation experiments using C. elegans extracts from wild type and mutant tubulin expressing C. elegans incubated with recombinant human tau.

      In conclusion, the thoughtful commentary and suggestions from reviewers will help improve the manuscript. We plan to complete the following experiments to address their concerns.

      (1) Assess tau localization in mutant tba-2 and mec-12 C. elegans as compared to tau-transgenic C. elegans without tubulin mutations. We plan to use immunohistochemical techniques and/or imaging of Dendra2-labeled tau to assess the sub-compartmental distribution of tau in C. elegans neurons. This addresses Reviewer #1’s question of whether the mutant tubulin changes tau localization in neurons.

      (2) Assess changes mutant-tubulin driven changes to tau affinity for polymerized microtubules. To address both reviewers concerns regarding the limitations of biding experiments with tau and soluble tubulin, We plan to use C. elegans extracts to tests whether microtubule polymers containing mutant alpha-tubulin alter tau-microtubule co-sedimentation.

      (3) Using C. elegans reporter lines we plan to assess whether tau clearance occurs in tba-2 mutant tubulin C. elegans through the upregulation of autophagy or ubiquitin degradation pathways.

      (4) Evaluate the neuroprotective effects of mutant alpha-tubulin in cholinergic neurons using a C. elegans strain expressing a fluorescent label specifically in cholinergic neurons.

      We plan to make textual revisions to increase clarity, aid in independent analysis of the presented datasets, and better address the possibility of both tau-dependent and tau-independent mechanisms. We appreciate the Reviewers attentive reading and thoughtful feedback for the improvement of this manuscript.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this article, the authors couple a 3d vertex model to the extracellular matrix and include activity through contractile springs at the edge. They study, sequentially, the distribution of shear stresses in liquid and solid spheroids, the correlation between stress and cell shape, and the spatial distribution of stresses. The authors find that stresses are higher in solid spheroids (somewhat unsurprisingly), but that the stress distributions are wider in the fluid spheroids. Moreover, stress and shape are not correlated with each other in solids (that seems to be due to vertex model peculiarities), but they are for liquids. In contrast, for solids, the stresses are concentrated at the interface. The authors attribute a lot of the phenomenology to strain-stiffening properties of vertex models as being akin to a network model (correctly in my opinion). Then they strain individual cells and confirm this link, though I missed any explanation of how they did this. Would it have to be within a medium for computational consistency?

      We thank the reviewer for this helpful comment. The current manuscript already describes this procedure in Sec. II.C, “Cell strain-stiffening with volume-preserving deformations,” where we state that individual cells are taken from the final spheroid configuration and then strained by imposing a prescribed volume-preserving deformation along their principal elongation axis. Figure 4 then compares the original and strained cells and shows the resulting increase in maximum shear stress.

      We agree, however, that this point was not explained clearly enough. In the revised manuscript, we will make explicit that this is a single-cell deformation test designed to isolate the intrinsic strain-stiffening response of the vertex-model cell. The cell does not need to remain embedded in a surrounding medium for this specific test, since the goal is not to simulate the full coupled cell–ECM dynamics, but rather to measure how the stress of an individual vertex-model cell changes under imposed strain.

      Indeed, single cells can exhibit strain stiffening as presumably can a spheroid. However, given that we are studying strain stiffening in the context of single/few cell breakout, we also plan to measure the stress in the breakout cells in the extended vertex model to determine the extent of strain stiffening given the surrounding medium of fibers and cells.

      Finally, they generate an extended vertex model, where they replace the single face linking cells with a double face and mechanoresponsive springs. This allows for stronger coupling of individual cell motion to eventual movement out of the spheroid.

      Strengths:

      Coupling a three-dimensional vertex model to the extracellular matrix, modelled as a crosslinked fiber model, is a computational tour-de-force. Adding activity through fluctuations at the interface is also of the correct symmetry (stresses), instead of the self-propulsion which has been used by other authors, and which is not compatible with Newton's 3rd law. This also allows for accurate back-and-forth mechanical coupling between the cells and the ECM.

      I would like to highlight that deriving vertex model stress tensors in full three dimensions is an open problem due to the complex topology. Any progress is valuable, and decomposing things into tetrahedra like here will allow for connections with, in particular, finite element approaches. Therefore, adding some of these results (eq. 13) to the main text would strengthen the paper in my opinion.

      Adding the nonlinear springs to the VM in the 3rd act is a good idea, and a first step to mechanical feedback. One might argue that at this point, removing the vertex model part would even be an option.

      Weaknesses:

      The paper is written in a very qualitative manner, with all of the model equations and analysis hidden in the supplementary information. I do not understand this choice, as it makes things fuzzy and hard to read. The conclusion is also very long and simply reiterates the previous points.

      At the same time, this paper is rather thin on new results and reads more like a handful of new simulations carried out using the method established in [10] (from largely the same authors). Moving some of the actual results to the main text would help, in particular, the 3d stress formulation and the definitions of different measures.

      We thank the reviewer for this constructive criticism. We agree that the main text was too qualitative and that placing most of the equations and definitions in the Supplement made the manuscript harder to read. In the revised version, we will move the essential technical material into the main text, including the 3D cell stress formulation, the definitions of maximum shear stress and cell-shape anisotropy, and the stress–shape alignment measure. Longer derivations and implementation details will remain in the Supplement.

      We will also shorten and reorganize the Discussion/Conclusion to avoid reiterating previous points. Finally, we will revise the presentation to make the new contributions beyond Ref. [10] clearer: the 3D polyhedral-cell stress formulation, the stress-distribution and spatialpatterning analyses, the single-cell strain-stiffening test, and the extended adhesion-spring model used to distinguish single-cell from multi-cell breakout. These changes should make the paper less qualitative and make the main results more visible in the body of the manuscript.

      Vertex models also have a very clear limitation: They cannot model the transition from a confluent to a non-confluent tissue, and individual cells or groups of cells leaving the spheroid. Even having a surface and having significant deformations of the surface are numerically dicey, so the current model is at the edge of what is feasible. The model as written can only do "invasion" by a single cell moving outward, and then another following it a bit (or not).

      I strongly suspect that further progress on 3d cell models will need particle-based models or models where cells are fully meshed surfaces (some of which are in development currently).

      However, none of these problems is mentioned anywhere in the text. The authors also do not review the increasingly broad zoology of other models.

      We thank the reviewer for raising this important limitation of standard vertex models. We agree that a strictly confluent 3D vertex model is not designed to fully capture the transition from a confluent tissue to freely migrating detached cells, and we will make this limitation explicit in the revised Discussion. However, the standard 3D vertex model can still capture collective spheroid deformation, surface remodeling, and local protrusive deformations prior to complete breakout. Thus, it remains useful for studying the mechanical state of the spheroid and the onset of outward deformation before full cell detachment.

      At the same time, we clarify that this very limitation motivated the extended vertex model introduced in Sec. II.D and Supplement G. In this model, cells no longer share interfaces as in a standard confluent vertex model; instead, neighboring cells interact through explicit, tunable cell– cell adhesion springs. This allows us to represent, in a coarse-grained mechanical way, the separation of a boundary cell from the spheroid and the motion of a follower cell behind it. Thus, while the model does not describe full post-detachment migration, it partially addresses the confluent-to-nonconfluent transition at the level needed to study the mechanical onset of breakout.

      We will revise the manuscript to make this distinction clearer and state that our goal is to identify minimal mechanical ingredients for incipient breakout—strain stiffening, adhesion weakening, and adhesion anisotropy—rather than to provide a complete model of long-time invasion.

      We will also note that the current Introduction already discusses several existing modeling approaches, including cellular automaton simulations, a 2D Voronoi model, phenotypeswitching/ECM-remodeling models, and the prior 3D vertex–fiber framework. However, we agree that this discussion should be broadened, and we will add a more explicit comparison with particlebased, phase-field, cellular Potts, and fully meshed deformable-surface models, which may be better suited for later-stage non-confluent migration.

      Reviewer #2 (Public review):

      Summary:

      The manuscript concerns the mechanisms by which cells in a spheroid embedded in the extracellular matrix can escape, either as single or multiple cells.

      Strengths:

      Overall, the manuscript is well written and easy to follow. The claims are mostly justified by the data. Some data can be better analyzed and presented to strengthen the conclusion.

      Weaknesses:

      (1) The description around Figure 2c is not exactly well supported by their results. While values close to 0 for sigma3 dot g3 for solid-like spheroids indicate little correlation between the direction of maximum stress and maximum elongation, this analysis alone does not imply that highly stressed cells are necessarily less globular. The dot product combines the magnitudes of the two vectors and the angle between them. For the distribution graph, it would be useful to have the cumulative frequency equal 1.

      We thank the reviewer for pointing this out. We agree that the interpretation of Fig. 2c should be stated more carefully. In our calculation, the vectors used in the dot product are normalized eigenvectors of the stress tensor and the gyration tensor. Thus, the plotted quantity measures only directional alignment between the principal stress direction and the cell elongation axis, not the magnitudes of stress or shape anisotropy. We will revise the text to make this explicit.

      We also agree that Fig. 2c alone does not support statements about whether highly stressed cells are more or less globular. It only quantifies alignment between stress and shape directions. To address this, we will add or refer to an additional analysis, such as the correlation between maximum shear stress and cell-shape anisotropy, or the shape-anisotropy distribution conditioned on high-stress cells.

      Finally, we agree that the distribution in Fig. 2c should be normalized more clearly. In the revised figure, we will plot the distribution as a probability density or cumulative distribution with total probability equal to one, and we will update the caption accordingly.

      (2) One of the central claims of the paper is that morphology alone is not a reliable indicator of mechanical state. Since the authors compute cellular stresses and cellular shape in their simulation (i.e., Figure 3a and b), can the authors directly plot these two quantities for individual cells in solidlike and fluid-like spheroids?

      We thank the reviewer for this helpful suggestion. We agree that a direct cell-by-cell comparison of cellular stress and cellular shape would strengthen the central claim that morphology alone is not a reliable indicator of mechanical state. In the revised manuscript, we plan to add scatter plots of maximum shear stress versus cell-shape anisotropy for individual cells in both solid-like and fluid-like spheroids.

      (3) There is experimental evidence showing the solid stress inside a spheroid is higher than at the periphery (e.g., https://www.nature.com/articles/ncomms14056). How does this cellular stress relate to these experimental measurements, since they are opposite to what is simulated here (i.e., the authors find max shear stress is lowest in the center and increases towards the boundary, which is opposite to what is measured?

      We thank the reviewer for raising this important point. We agree that the comparison with experimental stress measurements in compressed spheroids should be clarified.

      The main distinction is that the cited experiments measure local pressure, or isotropic compressive stress, from the volume change of embedded elastic beads. In contrast, Fig. 3 in our manuscript shows the cellular maximum shear stress, which reflects the deviatoric part of the cell stress tensor. These quantities do not necessarily have the same spatial profile: a region can be under high isotropic compression while having low shear stress. The loading conditions are also different. The experiments apply external osmotic/mechanical compression to the whole spheroid, whereas our simulations consider active cell–ECM coupling through contractile linker springs at the spheroid boundary. Thus, the elevated boundary shear stress in our model reflects local cell– ECM force transmission, not internal hydrostatic pressure. We indeed will revise the manuscript to make this distinction explicit, cite this experimental work, and avoid implying that maximum shear stress is directly comparable to measured solid pressure. Where appropriate, we will also discuss the isotropic component of the simulated cell stress tensor as a more direct comparison to pressure-based measurements.

      (4) It's worth pointing out that stress fibers aren't really prominent in cells in 3D spheroids. Nonetheless, cells moving on collagen fibers would have stress fibers and utilize contractile actomyosin bundles to generate traction forces.

      We thank the reviewer for this clarification. We did not intend to imply that prominent stress fibers are generally present in cells within the interior of 3D spheroids. The relevant statements in the manuscript were meant to refer to strained boundary cells or cells engaging collagen fibers during mesenchymal-like motion. We will revise the wording in Secs. II.C and II.D to make this distinction explicit and avoid suggesting that bulk spheroid cells generally contain prominent stress fibers.

      (5) In section 2D, it talks about the result that as the kcc associated with the boundary cell is decreased 10-fold for every 5 percent strain decrease in the fiber target spring length, can this result be shown? I have a hard time seeing where this came from.

      We thank the reviewer for this comment. The 10-fold decrease in kcc for every 5% decrease in the fiber target spring length was meant as a phenomenological adhesion-weakening protocol, not as a directly measured law. We agree that this was not made clear enough. In the revised manuscript, we will explicitly state this.

      (6) The results of single-cell vs. two-cell breakouts shown in Figure 5 b and c are very qualitative and should be accompanied by some quantitative comparison.

      We thank the reviewer for this helpful suggestion. We agree that the current presentation of Fig. 5b,c is too qualitative. In the revised manuscript, we plan to add a quantitative comparison between the single-cell and two-cell breakout cases. Specifically, we plan to track the displacement of the pulled boundary cell, the separation between this leader cell and its neighboring/follower cell, and the distance between the follower cell and the remaining spheroid as the fiber target length is decreased.

      Reviewer #3 (Public review):

      Summary:

      The authors describe a mathematical and computational approach used to compute stresses and cellular deformations in a multicellular spheroid embedded in a fiber network. This approach is then used to predict stress and cellular anisotropy distributions in "solid-like" and "fluid-like" spheroids. Simulations show that shear stresses in solid-like spheroids are large and concentrated at the boundary of the spheroid, yet cells do not align with the direction of the largest shear. Conversely, shear stresses in fluid-like spheroids are smaller and uniformly distributed in the spheroid. In this case, cellular elongation is more likely to be aligned with the direction of the largest shear stress. The model and simulations also predict a nonlinear stress-strain relationship that is indicative of strain stiffening. This strain-stiffening is more pronounced in fluid-like spheroids. In an extension of the preliminary polyhedral vertex model, in which cellular interfaces are shared, the authors incorporate mechanical cell-cell interactions via adhesion springs between neighboring vertices. Using this extension, they show that cell breakout is more likely to occur in fluid-like spheroids, where cells are more likely to elongate and stiffen, allowing for larger forces to be exerted on the surrounding fiber network. Furthermore, the authors state that anisotropic cellcell adhesion is required for multicell streaming during breakout.

      Strengths:

      The modeling and computational approach used in this research is this work's biggest strength. Treating the embedded spheroid as a set of polyhedra, where each polyhedron represents a single cell, is a mechanically robust, yet still tractable way to model multicellular spheroids in three dimensions. Starting with expressions for constraining cell volume and surface area as well as a surface energy term, the authors derive an expression for an averaged stress tensor for each polyhedron. This allows the authors to approximate the stress in each polyhedral cell that is caused by cellular deformations during mechanical interactions with the extracellular fiber matrix. This is a clever and robust approach that is based on fundamental mechanical principles that allow one to make reasonable predications about the mechanical state of the spheroid under a variety of conditions.

      Weaknesses:

      The weakness of the manuscript is the exposition. There are significant pieces of critical information missing from the manuscript that would make the presented work significantly more understandable and better support the authors' claims. Most importantly, many necessary details of the model are missing. I was able to get a better understanding of some of these details by reading the authors' earlier work (ref [10] in the submitted manuscript), and for this reason, I do feel that this work has value. However, several descriptions must be added for the paper to be more readily understandable.

      These include

      (1) A better explanation of what drives motion, in particular in the case where no external fiber network is present.

      We thank the reviewer for pointing this out. We agree that the source of motion should be described more clearly. In the embedded simulations, motion arises from overdamped dynamics driven by the forces from the total mechanical energy, including spheroid mechanics, fibernetwork elasticity, and active contractile linker springs at the boundary. The shortening of the linker-spring target lengths provides the active cell–ECM pulling, while effective fluctuations promote cell-shape fluctuations and rearrangements.

      When no external fiber network is present, these linker-mediated cell–ECM forces are absent. The spheroid then evolves only through vertex-model mechanical relaxation, surface tension, cell rearrangements, and effective fluctuations. We will clarify that this no-network case is a control for the intrinsic spheroid stress state, not a simulation of ECM-driven invasion.

      (2) What physically distinguishes fluid-like spheroids from solid-like spheroids? Simply stating the value of the parameters s0 with no explanation is not sufficient.

      We thank the reviewer for pointing out that the physical distinction between solid-like and fluid-like spheroids was not sufficiently explained. We agree that simply stating the values of s_0 is not adequate.

      In this 3D vertex model, the target shape index s_0 controls the mechanical cost of cell rearrangements. Below the rigidity transition (s_0 < s_0^), neighbor exchanges are associated with finite energy barriers, leading to slow structural relaxation and solid-like behavior. Above the transition (s_0 > s_0^), these barriers become very small or vanish, allowing cells to readily move past one another and continuously reorganize their local neighborhood structure. The resulting tissue exhibits fluid-like behavior with efficient stress relaxation through cell rearrangements.

      This distinction was characterized in detail in Ref. [9], where the bulk 3D vertex model was shown to undergo a rigidity transition at approximately (s_0^*=5.39), based on the decay of the neighbor-overlap function and cell trajectories. The solid-like value used here lies below this transition, whereas the fluid-like value lies above it. We acknowledge that the present manuscript only briefly summarized this point, mainly in Supplementary Material A. In the revised manuscript, we will add a clearer explanation in the main text of how the target shape index controls the state of the spheroid and why the selected values correspond to solid-like and fluidlike regimes.

      (3) An explanation of how histograms in Figure 2 are calculated is necessary. Are these histograms based on one simulation or several simulations?

      We thank the reviewer for pointing out that this was not sufficiently clear. The histograms in Fig. 2 are obtained by pooling cell-level quantities from multiple independent simulations, not from a single realization. As listed in Table I, we use 30 independent realizations. We plan to state this explicitly in the revised figure caption and main text.

      (4) The experimental results are briefly mentioned, but significantly more connection between these results and the numerical results of the cell breakout model is needed.

      We agree. In the current manuscript, the experimental data are used mainly to motivate the single-cell and streaming-like breakout modes shown in Fig. 5. We plan to revise Sec. II.D and the Fig. 5 caption to make the connection more explicit: the MEF spheroid experiments show the invasion modes that motivate the model, while the extended vertex model tests minimal mechanical ingredients capable of producing analogous single-cell and follower-cell breakout.

      (5) The description of the model that incorporates variable cell-cell attachments and cell breakout is very terse and needs more detail. Moreover, while the description of the results of this model is strong, the figure that illustrates cell breakout (Figure 5) is difficult to interpret. Addressing these and other issues will make the current manuscript, which presents an interesting model and result, much stronger and easier to read.

      We thank the reviewer for this constructive assessment. We agree that the extended model with variable cell–cell attachments was described too tersely and that Fig. 5b,c was difficult to interpret in its current qualitative form.

      To make Fig. 5 more quantitative, we plan to add measurements comparing the single-cell and two-cell breakout cases. Specifically, we plan to track the displacement of the pulled boundary cell, the separation between this leader cell and its neighboring/follower cell, and the distance between the follower cell and the remaining spheroid as the fiber target length is decreased.

    1. Author response:

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

      Public Review:

      Reviewer #1 (Public review):

      Suggestions to clarify the study:

      In the revised version, the authors carefully consider these suggestions and provide further details, clarifications and even some new results. Regarding the question of how infection of a cell with one virus could lead to lower probability for a secondary infection, I think that it is possible that infected cells activate antiviral programs that lead, for example, to lower expression of surface receptors. This has been considered at least in hepatitis C virus infection. However, this is a minor point.

      Yes, the possibility that infection of a cell by a virion would reduce chance of infection by another virion was allowed in our model. However, such as a process will not result in apparent cooperativity (n>1) in our model, and thus, is irrelevant to the issue of apparent cooperativity we identified.

      Reviewer #2 (Public review):

      In their article, Peterson et al. wanted to show to what extent the classical "single hit" model of virion infection, where always the same quantity of virion is required to infect a cell, does not match with empirical observations based on human cytomegalovirus in vitro infection model, and how this would have practical impacts in experimental protocols.

      Strengths:

      The use of a very simple and robust experimental assay, where they infected cells with serially diluted virions and measured the proportion of infected cells with flow cytometry. This convincingly showed how the proportion of infected cells differed from a "single hit" model which they simulated using a simple mathematical model ("power-law model"), and better fitted a model where virions need to cooperate to infect cells.

      The use of different cell types and virus strains, which allows to draw some generalizations.

      The exploration of the mechanisms that could explain this apparent cooperation, using biologically plausible simulations.

      The practical consequences that this phenomenon has for lab virologists as well as modelers.

      Thank you.

      Weaknesses:

      The impossibility to discriminate between biological mechanisms is an important limitation of this study and calls for developing experimental designs able to further understand this question.

      The outcome of the virion clumping remains highly sensitive to the choice of the clumps size distribution, which is itself very complicated to estimate, especially at high dilution.

      The impossibility to directly fit the mathematical models to the data limit them to a qualitative discussion.

      Overall, this work is very valuable as it raises the general question of how the estimate of infectivity can be biased if extrapolated from a single virus titer assay. The observation that HCMV virions often cooperate and that this cooperation varies between context seems robust. The putative biological explanations would require further exploration.

      This topic is very well known in the case of segmented viruses and the semi-infectious particles, leading to the idea of studying "sociovirology", but to my knowledge this is the first time that it was explored for a non-segmented virus, and in the context of MOI estimation.

      Thank you. We would note, however, that inability to discriminate between alternative models is not a weakness per se. It shows that our work goes beyond a somewhat typical approach in mathematical modeling to offer a single explanation for a phenomenon in question (rather than focusing on discriminating between alternatives that is often hard to do).

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) I now understand better the graphical abstract. I think my eye was too much attracted by the increase in specific infectivity that you see for more than 1 genome/cell, which is not the point of your paper. I am wondering if you should not guide even more the reader, by pointing out that the fact that the initial decline in specific infectivity represents apparent cooperativity.

      Let’s hope that the readers are smart enough to understand what to focus their eyes on. At the end, this is a graphical abstract that is not supposed to have too much text explaining where to look.

      (2) For your one-inflated geometric distribution, I agree that the estimations would remain very hypothetical because you would have to make many assumptions, however I think a hurdle model where you would fit the P(clump size = 1)=f1 and P(clump size = (i) following a one-truncated geometric distribution would be more appropriate because it would lead to a distribution closer to your PDF from figure S11C.

      The issue is that our data are not in clump sizes but in diameter of the clump D. This is why we opted for using a mixture of continuous distributions, not a mixture of discrete distributions. We are sharing the DLS data, so others are welcome to do another try of fitting other types of distribution to the data.

      (3) For the DLS data, I understand your choice to include all the datapoints, however I find the interpretation confusing: if I understand correctly, you consider that f1, the fraction of the smaller distribution, represents clumps of one virion. However, its median size is 10 times smaller than a virion. So, the number of clumps with one virion would be overestimated. I think it would be helpful for the reader to clarify this aspect, either in the results around lines 503-512, or in the discussion. Could it be that at higher dilution, what is represented by this smaller distribution would almost only be debris because the virions are so rare?

      When fitting a mixture of two log-normal distributions f<sub>1</sub> represents the proportion of clumps of larger size (as was described in the materials and methods). The actual estimated value of f<sub>1</sub> is not highly relevant in calculating change in PDF of the distribution only for D>=d (230nm) as shown in Suppl Fig S11C. But we now realize that this variable f<sub>1</sub> may be confused with a variable f<sub>1</sub> used to denote the fraction of clumps with virion size=1 (in Fig 5C). We now mention that in the caption of Supp Fig S10.

      (4) For the dashed diagonal lines of fig 2, what I don't understand is the choice of the intercept that seems a bit random. I was wondering if it would not be more helpful to make it so that the dashed line intersects the observation for 1 genome/cell, which could then be interpreted as a deviation from the "single hit" model extrapolated outside of 1 genome/cell?

      The diagonal lines in Fig 2 are exactly the same in ALL panels, as are the x/y axes ranges; the slope of the line (equals to 1) allows visually to see when the regression (shown by think black lines) deviates from slope=1, i.e., indicates apparent cooperativity. We will keep the lines are they are. Thank you for the suggestion, though.


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

      Reviewer #1 (Public review):

      Summary:

      In this paper, the authors conduct both experiments and modeling of human cytomegalovirus (HCMV) infection in vitro to study how the infectivity of the virus (measured by cell infection) scales with the viral concentration in the inoculum. A naïve thought would be that this is linear in the sense that doubling the virus concentration (and thus the total virus) in the inoculum would lead to doubling the fraction of infected cells. However, the authors show convincingly that this is not the case for HCMV, using multiple strains, two different target cells, and repeated experiments. In fact, they find that for some regimens (inoculum concentration), infected cells increase faster than the concentration of the inoculum, which they term "apparent cooperativity". The authors then provided possible explanations for this phenomenon and constructed mathematical models and simulations to implement these explanations. They show that these ideas do help explain the cooperativity, but they can't be conclusive as to what the correct explanation is. In any case, this advances our knowledge of the system, and it is very important when quantitative experiments involving MOI are performed.

      Strengths:

      Careful experiments using state-of-the-art methodologies and advancing multiple competing models to explain the data.

      Weaknesses:

      There are minor weaknesses in explaining the implementation of the model. However, some specific assumptions, which to this reviewer were unclear, could have a substantial impact on the results. For example, whether cell infection is independent or not. This is expanded below.

      Suggestions to clarify the study:

      (1) Mathematically, it is clear what "increase linearly" or "increase faster than linearly" (e.g., line 94) means. However, it may be confusing for some readers to then look at plots such as in Figure 2, which appear linear (but on the log-log scale) and about which the authors also say (line 326) "data best matching the linear relationship on a log-log scale".

      This is a good point. We included a clarification to indicate that linear on the log-log scale relationship does not imply linear relationship on the linear-linear scale. We wrote:

      “Because most data did not exhibit a linear relationship between virion concentration and infection probability we fitted the models to subsets of data best matching a linear relationship on a log-log scale. Note that linear relationship on log-log scale may still be nonlinear (on linear-linear scale) when n!=1.”

      (2) One of the main issues that is unclear to me is whether the authors assume that cell infection is independent of other cells. This could be a very important issue affecting their results, both when analyzing the experimental data and running the simulations. One possible outcome of infection could be the generation of innate mediators that could protect (alter the resistance) of nearby cells. I can imagine two opposite results of this: i) one possibility is that resistance would lead to lower infection frequencies and this would result in apparent sub-linear infection (contrary to the observations); or ii) inoculums with more virus lead to faster infection, which doesn't allow enough time for the "resistance" (innate effect) to spread (potentially leading to results similar to the observations, supra-linear infection).

      In our models we assumed cells to be independent of each other (see also responses to other similar points). Because we measure infection in individual cells, assuming cells are independent is a reasonable first approximation. However, the reviewer makes an excellent point that there may be some between-cell signaling happening in the culture that “alerts” or “conditions” cells to change their “resistance”. It is also possible that at higher genome/cell numbers, exposure of cells to virions or virion debris may change the state of cells in the culture, and more cells become “susceptible” to infection. This is a good point that we now list in Limitations subsection of Discussion; it is a good hypothesis to test in our future experiments. We write:

      “Accrued damage model is also consistent with the idea that at higher genome/cell values, the inoculum itself (including cell and/or virion debris) may impact overall susceptibility of all cells in the well, for example, making them more susceptible to infection. It may be expected, though, that exposing cells to debris would increase cell resistance to infection; this would result in n < 1 that we did not observe at small genomes/cell values.”

      (3) Another unclear aspect of cell infection is whether each cell only has one chance to be infected or multiple chances, i.e., do the authors run the simulation once over all the cells or more times?

      Each cell has only one chance to be infected. Algorithm 1 clearly states that; we will add an extra sentence in “Agent-based simulations” to indicate this point.

      (4) On the other hand, the authors address the complementary issue of the virus acting independently or not, with their clumping model (which includes nice experimental measurements). However, it was unclear to me what the assumption of the simulation is in this case. In the case of infection by a clump of virus or "viral compensation", when infection is successful (the cell becomes infected), how many viruses "disappear" and what happens to the rest? For example, one of the viruses of the clump is removed by infection, but the others are free to participate in another clump, or they also disappear. The only thing I found about this is the caption of Figure S10, and it seems to indicate that only the infected virus is removed. However, a typical assumption, I think, is that viruses aggregate to improve infection, but then the whole aggregate participates in infection of a single cell, and those viruses in the clump can't participate in other infections. Viral cooperativity with higher inocula in this case would be, perhaps, the result of larger numbers of clumps for higher inocula. This seems in agreement with Figure S8, but was a little unclear in the interpretation provided.

      This is a good point. We did not remove the clump if one of the virions in the clump manages to infect a cell, and indeed, this could be the reason why in some simulations we observe apparent cooperativity when modeling viral clumping. We have explored this in the revision and found that it does not really impact how infection rate scales with the genomes/cell (e.g., see Suppl Fig S8).

      (5) In algorithm 1, how does P_i, as defined, relate to equation 1?

      These are unrelated because eqn.(1) is a phenomenological model that links infection per cell to genomes per cell. P_i in algorithm 1 is “physics-inspired” potential barrier.

      (6) In line 228, and several other places (e.g., caption of Table S2), the authors refer to the probability of a single genome infecting a cell p(1)=exp(-lambda), but shouldn't it be p(1)=1-exp(-lambda) according to equation 1?

      Indeed, it was a typo, p(1)=1-exp(-lambda) per eqn 1. Thank you, it has been corrected in the revised paper.

      (7) In line 304, the accrued damage hypothesis is defined, but it is stated as a triggering of an antiviral response; one would assume that exposure to a virion should increase the resistance to infection. Otherwise, the authors are saying that evolution has come up with intracellular viral resistance mechanisms that are detrimental to the cell. As I mentioned above, this could also be a mechanism for non-independent cell infection. For example, infected cells signal to neighboring cells to "become resistance" to infection. This would also provide a mechanism for saturation at high levels.

      We do not know how exposure of a cell to one virion would change its “antiviral state”, i.e., to become more or less resistant to the next infection. If a cell becomes more resistant, there is no possibility to observe apparent cooperativity in infection of cells, so this hypothesis cannot explain our observations with n>1. Whether this mechanism plays a role in saturation of cell infection rate at lower than 1 value when genome/cell is large is unclear but is a possibility. We added this point to Discussion in revision (see our text above that includes this point).

      (8) In Figure 3, and likely other places, t-tests are used for comparisons, but with only an n=5 (experiments). Many would prefer a non-parametric test.

      We repeated the analyses in Fig 3 with Mann-Whitney test, results were the same, so we would like to keep results from the t-test in the paper.

      Reviewer #1 (Recommendations for the authors):

      (1) The strains of HCMV used have a fluorescent reporter "in place of the US11 gene". Can you provide a brief comment on whether and how this gene deletion affects HCMV replication?

      US11 is a resident ER protein that is considered an "immune evasion factor". It promotes ERAD of MHC I and has no observable effect on replication of HCMV in cultured cells (Berger 2000 JVI, Wiertz 1996 Cell). We now add this information in Materials and methods section of the paper. We write:

      “All BAC clones were modified to express green fluorescent protein (GFP) or the monomeric red fluorescent protein mCherry (mCherry) with En passant recombineering by replacing US11 with the eGFP or mCherry gene, respectively. US11 is a resident ER protein that is considered an “immune evasion factor”. It promotes ERAD of MHC I and has no observable effect on replication of HCMV in cultured cells [27, 28]. Infectious HCMV was recovered by electroporation of BAC-DNA into MRC5 cells which were then co-cultured with either HFFCs (TB and TR) or HFF-tet cells (ME).”

      (2) I didn't understand what the section "Virus titer assays" refers to. When was this used? How or why is this different from the "Virus stock dilution and dose-response assay"? Also in this section, you refer to NHDF cells - can you provide more information about these? And how does a different type of cell affect the titer assay (here measured as infected cells), since this is one of the main points of your paper?

      Apologies for the confusion. In Ryckman lab we routinely generate viral stock and titrate it using a specific cell type, Normal (or neonatal) Human Dermal Fibroblasts (NHDF). This way, the titer of the stock is consistent between experiments by different researchers in the lab. We then use standard 10-fold dilutions to define the number of infectious units per mL of the stock. We now name this subsection as “Quantification of viral stock infectivity using standard 10-fold dilutions”. After the stock was quantified, we then used that stock in our actual experiments with very small dilution factor df that allowed us to detect deviations of the rate of infection from single hit model.

      (3) In many places, "powerlaw" is written. This is usually written as two words, "power law".

      Because powerlaw comes together with “model”, we decided to use “power-law model”.

      (4) Line 75: "have" instead of "has"?

      (5) Line 84: "with" repeated.

      Corrected, thank you.

      (6) Line 116: This section "Cell lines" seems to describe three cell lines, "HFF cells and MRC5 cells" and then "EC" cells.

      HFF cells are fibroblasts used in our main experiments and MRC5 cells are another type of fibroblasts. We used MRC5 cells in the first step of recovering infection HCMV from BAC DNA (electroporation). We clarified this in Materials and methods. We write:

      “Cell lines. Human foreskin fibroblast cells (HFFCs or fibroblasts) and MRC5 cells (also fibroblasts) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma) supplemented with 5% heat-inactivated fetal bovine serum (FBS, Rocky Mountain Biologicals, Missoula, MT, USA) and 5%Fetalgro® (Rocky Mountain Biologicals, Missoula, MT, USA). We used MRC5 cells in the first step of recovering infection HCMV from BAC DNA (electroporation). For main experiments we used HFFCs as fibroblasts. Human retinal pigment epithelial cells (ECs or ARPE-19, American Type Culture Collection, Manassas, VA, USA) were cultured in a 1:1 mixture of DMEM and Ham’s F-12 medium (DMEM:F-12, Gibco) and supplemented with 10% FBS.”

      (7) Line 188: Because the virus is double-stranded, do you have to divide the qPCR result by 2 to get genomes?

      This is typically accounted for in our calculations of genome/cell.

      (8) Line 200: Typically, one would write "500g" and not "500xg".

      Corrected.

      (9) Line 248: It would be clearer to write "cell type C different from cell type C2".

      Here C and C_2 refer to actual numbers of cell in the titration/growth experiments, so it is comparing numbers, not cell types. We kept the relationship as it is.

      (10) Definition of cell class: what is n in p_n, the total number of cells, or are these divided into n classes of resistance?

      This part was incorrectly copied from an earlier version, both cell resistance and virion infectivity was sampled from normal distributions with different mean and variances (see Table 1). We corrected the text to reflect this.

      (11) Line 272 to 273: Something seems to be missing, as the change of line doesn't make sense.

      Thank you. Edited to improve readability. Now it reads

      “Clumping hypothesis. In the basic model the number of virions a given cell is exposed to follows a Poisson distribution. However, it is well recognized that as virions are produced by infected cells, they may form clumps/aggregates; the number of virions per clump/aggregate may deviate from, for example, the Poisson distribution [33].”

      (12) Line 283: How lambda is chosen is not indicated here, only later (line 424), but at this point, one can confuse it with lambda in equation 1. Is it the same? It also doesn't seem to be indicated in your Table 1.

      The mean of the Poisson distribution in clump simulations lambda is not the same as lambda in eqn 1; we re-named the mean of Poisson distribution as lambda_c which is estimated by fitting a Poisson distribution to clump size distribution estimated from DLS experiments. Because it was dependent on the virus stock dilution, it is not listed in Table 1. However, we did perform additional simulations assuming lambda_c=2 (Suppl Fig S10).

      (13) Equation 6: I understand that you mostly used kappa=0, but in equation 6, would it be positive or negative (if not zero)?

      We probably expect kappa to be negative but we did not fully explore this extension of the model.

      (14) Line 350: Instead of "infection rates" would "infection frequencies" be better?

      We agree. Changed (also changed in the sentence above that line).

      (15) Line 366: I found this sentence a bit awkward.

      We edited it to the best of our ability to improve it.

      “Importantly, for most HCMV strain-target cell combinations we estimated n>1 (Figure 2 and Supplemental Table S2). With n>1 increase in virion concentration (i.e., higher genomes/cell values) results in a higher than linear increase in the probability of a cell to be infected (eqn. (1)) indicating cooperation between virions at infecting cells. We call this phenomenon “apparent cooperativity”.

      (16) Figure 2, panel L: I wonder if it would be better to include the panel with the name of the experiment, but no data. Currently, it takes a while to find what you are talking about in panel L (or at the very least, indicate the panel in the caption).

      Changed

      (17) Figure 2: When you say that experiments were done at least twice, are you referring to the GFP and mCherry versions of the experiment, or replicates within each of those fluorescent labels?

      Replicates with each of those labels.

      (18) Figure 3: What is the number on top of the black bars? I think it is the average of the paired fold change. Is this right? Why, in panel E, is it 1.32 when only one goes up?

      Yes, fold change. Indeed, 1.32 was a typo, it is 0.70, thank you for noting.

      (19) Line 408: delete the word "there".

      Done. Thank you.

      (20) Line 412: Instead of "The", it should be "Then".

      Done. Thank you.

      Reviewer #2 (Public review):

      In their article, Peterson et al. wanted to show to what extent the classical "single hit" model of virion infection, where one virion is required to infect a cell, does not match empirical observations based on human cytomegalovirus in vitro infection model, and how this would have practical impacts in experimental protocols.

      They first used a very simple experimental assay, where they infected cells with serially diluted virions and measured the proportion of infected cells with flow cytometry. From this, they could elegantly show how the proportion of infected cells differed from a "single hit" model, which they simulated using a simple mathematical model ("powerlaw model"), and better fit a model where virions need to cooperate to infect cells. They then explore which mechanism could explain this apparent cooperation:

      (1) Stochasticity alone cannot explain the results, although I am unsure how generalizable the results are, because the mathematical model chosen cannot, by design, explain such observations only by stochasticity.

      Our null model simulations are not just about stochasticity; they also include variability in virion infectivity and cell resistance to infection. We agree that simulations cannot truly prove that such variability cannot result in apparent cooperativity; however, we also provide a mathematical proof that increase in frequency of infected cells should be linear with virion concentration at small genome/cell numbers.

      (2) Virion clumping seemed not to be enough either to generally explain such a pattern. For that, they first use a mathematical model showing that the apparent cooperation would be small. However, I am unsure how extreme the scenario of simulated virion clumping is. They then used dynamic light scattering to measure the distribution of the sizes of clumps. From these estimates, they show that virion clumps cannot reproduce the observed virion cooperation in serial dilution assays. However, the authors remain unprecise on how the uncertainty of these clumps' size distribution would impact the results, as most clumps have a size smaller than a single virion, leaving therefore a limited number of clumps truly containing virions.

      As we stated in the paper, clumping may explain apparent cooperativity in simulations depending on how stock dilution impacts distribution of virions/clump. This could be explored further, however, better experimental measurements of virions/clump would be highly informative (but we do not have resources to do these experiments at present). Our point is that the degree of apparent cooperativity is dependent on the target cell used (n is smaller on epithelial cells than on fibroblasts) that is difficult to explain by clumping which is a virion property. Per comment by reviewer 1, we have done more analyses of the clumping model to investigate importance of clump removal per successful infection on the detected degree of apparent cooperativity. We found that it was not critical to our conclusions (Suppl Fig S8).

      The two models remain unidentifiable from each other but could explain the apparent virion cooperativity: either due to an increase in susceptibility of the cell each time a virion tries to infect it, or due to viral compensation, where lesser fit viruses are able to infect cells in co-infection with a better fit virion. Unfortunately, the authors here do not attempt to fit their mathematical model to the experimental data but only show that theoretical models and experimental data generate similar patterns regarding virion apparent cooperation.

      In the revision we now provide examples of our earlier simulations that “match” experimental data with a relatively high degree of apparent cooperativity (Supp Fig S9).

      Finally, the authors show that this virions cooperation could make the relationship between the estimated multiplicity of infection and viruses/cell deviate from the 1:1 relationship. Consequently, the dilution of a virion stock would lead to an even stronger decrease in infectivity, as more diluted virions can cooperate less for infection.

      Overall, this work is very valuable as it raises the general question of how the estimate of infectivity can be biased if extrapolated from a single virus titer assay. The observation that HCMV virions often cooperate and that this cooperation varies between contexts seems robust. The putative biological explanations would require further exploration.

      This topic is very well known in the case of segmented viruses and the semi-infectious particles, leading to the idea of studying "sociovirology", but to my knowledge, this is the first time that it was explored for a nonsegmented virus, and in the context of MOI estimation.

      Thank you.

      Reviewer #2 (Recommendations for the authors):

      Major comments:

      Two aspects of the work would benefit from further thought:

      (1) The simulation of virion clumps: in both cases (Poisson distribution or one-inflated geometric distribution), the proportion of clumps containing more than one virion will be small. For the Poisson distribution, as you fit the powerlaw model on the range of genomes/cell < ~ 3 genomes/cell (Figure 4B). I wonder to what extent this explains the sudden rise in infections/cells you observe above that limit. It would be interesting to plot the (cumulative) distribution of the clump sizes at different dilution levels to have a better idea.

      The reviewer has a good eye, indeed, the relationship between infection frequency and genomes/cell is linear up to a point, and we believe the inflection point reflects the genomes/cell values when clumps contain more than 1 virion. Here is the results of simulations with distribution of virions/clump plotted:

      Similarly, for the one-inflated geometric distribution, the proportion of clumps of size 1 is the sum of two events: f1, plus 1-f1 times the probability that the geometric distribution is zero, if I follow the methods on lines 287-294. I wonder if this is appropriate regarding the estimates made with the DLC. In particular, Figure 5C shows that the proportion of clumps of size 1 is more than ~ half of all the clumps, and does not seem to be the same distribution as the estimates made on Figure S9C. Maybe a hurdle model would be more appropriate?

      This is a fair point. In our analyses we found that modeling clump size distribution is tricky and required various assumptions. The issue with the DLS data is that we do not really know the distribution of intact virions per clump so how to relate the size of the clump to the number of virions in a clump is wide-open; we explored several possibilities and found that the answer (whether clumping results in apparent cooperativity) depends on assumptions of how clumps are modelled (e.g., compare Fig 4B and Suppl. Fig S11). Hurdle model is not appropriate for clumps because by our definition of a clump, it must have at least 1 virion. Our key observation, however, is that the degree of apparent cooperativity depends on the target cell type – and thus should be independent of virion clumping (unless there is viral cooperativity in the clumps). Overall, we decided that exploring more clumping models would take extra effort, but it is unclear if it brings any benefits to our conclusions.

      The analysis of the clump size distribution using dynamic light scattering, in Figure S8. If I interpret correctly, events with size < 230 nm should be excluded as they do not represent clumps of virions but rather media impurities or cell debris. Therefore, I don't understand the choice of fitting the whole set with a combination of two normal distributions, as even the larger normal distribution covers clumps < 230 nm. If the f1 indicated here is the one used in the methods line 287-294, this is then wrong because it does not represent the fraction of clumps of size 1, but rather debris.

      We used two normal (on log-scale) distributions when quantifying clump distribution data (Supp Fig S10) to avoid sub-selection of the data; in this way, two distribution fit the whole dataset with excellent quality. An alternative approach would be to sub-select data with size >=230nm and fit a normal (or similar) distribution of the clumps; such an approach may generate biases and/or unreliable estimates at high dilutions due to small number of clumps with large size (e.g., see Supp Fig S10S-X). In our simulations to model clump distribution and infection (Fig 5) we attempted to simulate the estimated clump size distribution (Suppl Fig S11C) only approximately. Again, because in our measurements we don’t really know the number of virions per clump, efforts to model exactly clump size distribution, we believe, are not going to give full answers.

      (2) Figure 4 and results lines 419-465: Why didn't you try to fit the different models to the data, instead of qualitatively comparing the estimate of n in the simulations with arbitrary parameters to the one for empirical data? Your models match the expectation of virion cooperation by design, so they are not more convincing for a virologist than logical non-quantitative reasoning. They would be of stronger evidence in my opinion if you could show how well they fit the data. You could then directly compare the different models' fits using goodness-of-fit metrics and decide whether one is better than another or if they all explain equally well the observations.

      Well, we have 11 different relationships between infection rate and genome/cell, finding parameter combinations that would match all the data with at least 2 alternative models seems excessive at present but it is a good direction as we get extra funding to continue this work. It is also difficult to extensively search for the parameter values that would result in a perfect fit of the stochastic simulations to data since the methods of fitting agent-based models to data are not fully developed. However, following this suggestion we now show results of simulations for the two alternative models (accrued damage and viral compensation) that we believe do match experimental data somewhat (see new Suppl Fig S9).

      Minor comments:

      (1) Graphical abstract: This requires more context as it is too rough here to help me understand the general idea of the paper. Plus, why does specific infectivity first decrease with genome/cell?

      We added few elements to the graphical abstract including the strain and target cell used. The decrease in specific infectivity at lower genome/cell is due to apparent cooperativity.

      (2) Equation (7): It would be beneficial for the reader if the reasoning behind the likelihood computation were further described.

      This is a relatively standard approach to model/estimate parameters of a binary outcome, e.g., see Wikipedia: https://en.wikipedia.org/wiki/Logistic_regression

      (3) Line 352-357: could the drop in infectivity also be enhanced/explained by increased cell mortality? Did you gate on cell viability during FCM?

      The infection rate was measured in live cells only, so increased cell mortality may be an explanation.

      (4) Figure 2: I don't understand the dashed diagonal lines: what do they represent exactly? Especially, wouldn't the single-hit model depend on p(1), in which case it should vary by cell x virus?

      As the caption to Figure 2 clearly states, diagonal dashed lines show the slope =1 (i.e, single hit model), so one would be able compare how far the data and/or model fit line deviate from 1. The note for p(1) in panel A is to illustrate how p(1) is calculated; obviously it varies by the strain-cell combination as is indicated in Suppl. Tab S2).

      (5) Fig3G: Is it not surprising to find a positive relationship between p(1) and n? I would have intuitively expected that the stricter the environment is, the more cooperation you observe. But maybe these viruses did not evolve in this context, and therefore, this relationship is different from what you expect from an evolutionary optimum.

      Well, we simply don’t know. The relationship simply suggests that there is connection between infectivity of a single virion and the degree of apparent cooperativity. We are not certain what is the context in which these viruses have evolved.

      (6) Flow cytometry assay: could it be possible that cells infected by more virions generate more fluorescent proteins and are therefore less likely to be false negatives? Maybe you could compare the fluorescence intensity distribution among infected cells in the context of low MOI vs high MOI?

      This is an interesting point. From presented flow cytometry plots (e.g., Suppl Fig S3), the MFI for infected cells does not seem to depend on the dilution (or genome/cell).

      (7) Figure S9B: I did not understand this figure. Are the axes labels correct? How is it possible to have less than 1 virion/well?

      The y axis shows a scaled number calculated from integrating estimated clump size distribution, we assume 1 “scaled” virion/well at highest virion/cell values. With scaling, yes, it is possible to have less than 1 virion/well.

      Reviewer #3 (Public review):

      Summary:

      The authors dilute fluorescent HCMV stocks in small steps (df ≈ 1.3-1.5) across 23 points, quantify infections by flow cytometry at 3 dpi, and fit a power-law model to estimate a cooperativity parameter n (n > 1 indicates apparent cooperativity). They compare fibroblasts vs epithelial cells and multiple strains/reporters, and explore alternative mechanisms (clumping, accrued damage, viral compensation) via analytical modeling and stochastic simulations. They discuss implications for titer/MOI estimation and suggest a method for detecting "apparent cooperativity," noting that for viruses showing this behavior, MOI estimation may be biased.

      Strengths:

      (1) High-resolution titration & rigor: The small-step dilution design (23 serial dilutions; tailored df) improves dose-response resolution beyond conventional 10× series.

      (2) Clear quantitative signal: Multiple strain-cell pairs show n > 1, with appropriate model fitting and visualization of the linear regime on log-log axes.

      (3) Mechanistic exploration: Side-by-side modeling of clumping vs accrued damage vs compensation frames testable hypotheses for cooperativity.

      Thank you.

      Weaknesses:

      (1) Secondary infection control: The authors argue that 3 dpi largely avoids progeny-mediated secondary infection; this claim should be strengthened (e.g., entry inhibitors/control infections) or add sensitivity checks showing results are robust to a small secondary-infection contribution.

      This is an important point. We do believe that the current knowledge about HCMV virion production time – it takes 3-4 days to make virions per multiple papers (see Fig 7 in Vonka and Benyesh-Melnick JB 1966; Fig 3B in Stanton et al JCI 2010; and Fig 1A in Li et al. PNAS 2015) – is sufficient to justify our experimental design but we do agree that an additional control to block novel infections with would be useful. We had previously performed experiments with a HCMV TB-gL-KO that cannot make infectious virions (but the stock virions can be made from complemented target cells). We will investigate if our titration experiments with this virus strain have sufficient resolution to detect apparent cooperativity. However, at present we do not have the resources to perform novel experiments.

      (2) Discriminating mechanisms: At present, simulations cannot distinguish between accrued damage and viral compensation. The authors should propose or add a decisive experiment (e.g., dual-color coinfection to quantify true coinfection rates versus "priming" without coinfection; timed sequential inocula) and outline expected signatures for each mechanism.

      Excellent suggestion. Because infection of a cell is a result of the joint viral infectivity and cell resistance, it may be hard to discriminate between these alternatives unless we specify them as particular molecular mechanisms. But we tried our and listed potential future experiments in the revised version of the paper. Specifically, we write:

      “Second, while we have proposed alternative mechanisms that may result in apparent cooperativity, at present we could not discriminate between these alternatives, in part, because the models lacked specifics – e.g., if virions interacting with a cell reduce its resistance to infection, what does it mean exactly [12]? If virions in a collection augment their infectivity (which may be expected for segmented viruses), how does that viral compensation actually work? Designing experiments that would discriminate between these alternatives would require focusing on a specific mechanism. For example, it may be that that the initiation of gene expression is difficult but is more efficient when there are more virions bringing in more tegument transactivators like pp72/ppUL35 [59]. Alternatively, it may be that there is a bona fide resistance mechanism at play here (e.g. “interferon”) that is antagonized by a viral tegument protein (like TRS1/IRS1 that acts against PKR and 2’5’OAS) [60]. Accrued damage model is also consistent with the idea that at higher genome/cell values, the inoculum itself (including cell and/or virion debris) may impact overall susceptibility of all cells in the well, for example, making them more susceptible to infection. It may be expected, though, that exposing cells to debris would increase cell resistance to infection; this would result in n < 1 that we did not observe at small genomes/cell values. Addressing these hypotheses is an area of future research that will require funding.”

      (3) Decline at high genomes/cell: Several datasets show a downturn at high input. Hypotheses should be provided (cytotoxicity, receptor depletion, and measurement ceiling) and any supportive controls.

      Another good point. We do not have a good explanation, but we do not believe this is because of saturation of available target cells. It seemed to only happen (or was most pronounced) with the ME stocks, which are typically lower in titer and so the higher MOI were nearly undiluted stock. It may be the effect of the conditioned medium. Or perhaps there are non-infectious particles like dense bodies (enveloped particles that lack a capsid and genome) and non-infectious, enveloped particles (NIEPs) that compete for receptors or otherwise damage cells and these don’t get diluted out at the higher doses. We included the point about cell death in Discussion of the revised version of the paper. Specifically, we write:

      “We also do not have a clear explanation of why infection frequency declines at high genomes/cell values for some strain-cell combinations (e.g., Figure 2A, C, D, I, J). Because we measured cell infection in live cells, increase in cell death at higher genomes/cell values may result in the decrease in the number of viable cells.”

      (4) Include experimental data: In Figure 6, please include the experimentally measured titers (IU/mL), if available.

      This is a model-simulated scenario, and as such, there is no measured titers.

      (5) MOI guidance: The practical guidance is important; please add a short "best-practice box" (how to determine titer at multiple genomes/cell and cell densities; when single-hit assumptions fail) for end-users.

      Good suggestion. We now include best-practice box using guidelines developed in Ryckman lab over the years in the revised version of the paper. This is how it reads:

      “Match viral titration methods to the experiment as far as possible. This includes using the same dilution of the viral stock, the cell type, duration of inoculation, and readout of infection.

      When possible, determine the degree of apparent cooperativity (“n”-value, eqn. (1)) for each virus strain/cell type pair being studied.

      If n= 1 (no cooperativity), it is reasonable to calculate experimental MOI based on stock infectivity value determined from a convenient stock dilution.

      If n > 1 or unknown, then stock infectivity should be determined at a dilution resulting in an MOI as close as possible to the desired experimental MOI. Alternatively, the inoculum size can be empirically determined to yield the desired number of infected cells. In these ways different virus/cell type pairs can be compared more fairly.

      Box 1: Recommendations on titrating viral stocks and on performing experiments when comparing different viral strains.”

      Reviewer #3 (Recommendations for the authors):

      FROM PUBLIC REVIEWS (2) Discriminating mechanisms: At present, simulations cannot distinguish between accrued damage and viral compensation. The authors should propose or add a decisive experiment (e.g., dual-color coinfection to quantify true coinfection rates versus "priming" without coinfection; timed sequential inocula) and outline expected signatures for each mechanism.

      This is a good point but to propose a good experiment we need to narrow down the “generic” mechanism to specific processes/genes. We put forward some ideas but clearly more work is needed here:

      “Second, while we have proposed alternative mechanisms that may result in apparent cooperativity, at present we could not discriminate between these alternatives, in part, because the models lacked specifics – e.g., if virions interacting with a cell reduce its resistance to infection, what does it mean exactly [12]? If virions in a collection augment their infectivity (which may be expected for segmented viruses), how does that viral compensation actually work? Designing experiments that would discriminate between these alternatives would require focusing on a specific mechanism. For example, it may be that that the initiation of gene expression is just difficult but is more efficient when there are more virions bringing in more tegument transactivators like pp72/ppUL35 [59]. Alternatively, it may be that there is a bona fide resistance mechanism at play here (e.g. “interferon”) that is antagonized by a viral tegument protein (like TRS1/IRS1 that acts against PKR and 2’5’OAS) [60]. Accrued damage model is also consistent with the idea that at higher genome/cell, the inoculum itself (including cell and/or virion debris) may impact overall susceptibility of all cells in culture, for example, making them more susceptible to infection. It may be expected, though, that exposing cells to debris would increase cell resistance to infection; this would result in n < 1 that we did not observe at small genomes/cell values. Addressing these hypotheses is an area of future research that will require funding.”

      (1) Methods transparency: Include raw spreadsheets or tables of dilution factors and per-well genome estimates used for Figure 1A; this will help reproducibility of the df = 1.3-1.5 pipeline.

      Provided as supplemental xlsx file.

      (2) Epithelial vs fibroblast contrast: Since n is lower on epithelial cells, expand on cell-intrinsic barriers that could dampen apparent cooperativity, and if this argues against simple clumping.

      Indeed, this is our point that we raised in Discussion. Since ECs show lower n than fibroblasts, this observation argues against clumps. Going forward the contrast between cell types will be an approach to understand mechanism. One difference is entry pathways, the ECs involve endocytosis and endosome acidification whereas the fibroblasts do not. There are clearly different receptors involved also, although they are not clearly characterized. One recent report that might be relevant is Ohman 2024 PNAS that shows the gH/gL/UL128-131 complex (aka, "pentamer") is not just dispensable for entry into fibroblasts, but inhibitory. They suggest that the pentamer might bind to a receptor on fibroblasts that activates a pathways that acts against viral IE expression, It could be that in this situation, more virions are really helpful to overcome that block, whatever it is. We now update this point in Discussion.

      (3) Visualization: In Figure 2, consider showing confidence bands for the fitted slope (n) within the colored fit window and reporting n {plus minus} SE in the panels.

      Because we used custom scripts to fit models to data, showing bands of model predictions was a bit complex and would interfere with data points. But we now show 95% Cis for the estimated value n (that are listed in Suppl. Tab S2).

      (4) Symbols: Define all symbols (e.g., V₀, n) on first use in the main text, not only in Methods.

      Done.

      (5) Plot axes check: Explain non-uniform axis labeling ("genomes/cell," "infections/cell").

      This comment was unclear – which labels were not “uniform”? Genomes/cell indicate the expected number of genomes (or virions) that a cell is on average exposed to, infections/cell indicates the probability that a cell actually gets infected.

      (6) Confidence interval for estimated parameters: Figure 3 A-C, please report estimated parameter intervals.

      These are listed in Suppl. Tab S2. Putting Cis for all estimates would clutter the figure making it hard to tell which CIs are for which estimate. But we put the Cis for estimated parameter n in Figure 2.

    1. Author response:

      Reviewer #1 (Public Review):

      This study by Charendoff et al provides interesting observations related to global histone hypermethylation in host cells, during Chlamydia trachomatis infections. The core observation they report is that the host histones are highly hypermethylated during infection, and this appears to be an amplifying effect due to continuous inhibition of demethylases, in part due to a metabolic shift in the host where succinate amounts (which inhibit demethylases) increases. The authors claim specifically due to the bacteria, since antibiotic treatment prevents histone hypermethylation (but leaves you wondering about cause/consequence correlations).

      The core observation of hyper methylation is very interesting, and well documented. There are a number of points to consider though in order to fully substantiate the findings, and close out loose ends. My comments are broad - and built around the interpretations (vs the data presented).

      (1) Related to observations coming Fig 1C etc, and connecting to Fig 3 - the hyper methylation appears to be across different protein arg/lys residues - and is not histone specific. So, is it just a consequence of high SAM pools and flux in infected cells? i.e. the bacterial infection increases SAM pools in cells, and provides an increase in substrate pools for the methyltransferases, leading to protein hyper methylation. The approach used here only measures steady-state SAM amounts (and not SAM flux or utilisation).

      For example, reduced SAM amounts in nuclei could be due to increased utilisation of SAM. The experiments done with the demethylase does not actually answer this question - if you decrease demethylase activity, you will get an increase in net methylation. The authors see an increase in net methylation in the infected cells - this would suggest that in addition (or perhaps primarily) to reduced demethylase activity, there could be much higher SAM utilisation/flux. Again, the over expression of JMJ proteins does not resolve this problem.

      This is an important point. Indeed, one limitation of the initial version of the paper was that we had measured SAM concentration only at one time point (40 hpi) and on the whole population. During revision we used a ratiometric sensor to measure SAM concentration in cells (PMID 34937909). We observed cell-to-cell heterogeneity in SAM levels in HeLa cells, as previously reported in other cell lines. Chlamydia inclusions develop asynchronously, which allows to observe, 40 hpi, a continuum of early (low bacterial load) to late (high bacterial load) stages of infection. We observed no correlation between bacterial load and SAM level, and SAM levels were globally similar when comparing infected and non-infected cells. This experiment strongly supports the hypothesis that protein hypermethylation is not due to an increase in SAM during infection. The data were added in the New Fig. 3. Note that the former Fig. 3 is now split into New Fig. 3 and New Fig. 4.

      (2) Adding to this - what happens to SAM pools in the cells treated with the inhibitors? This actually may not look like the slightly reduced SAM pool observed in infected cell nuclei. Also, what is the SAM/SAH ratio (a very useful indicator of methylation activity).

      Based on the high cell-to-cell heterogeneity of SAM levels observed with the ratiometric probe, we reasoned that measuring SAM/SAH ratio without single cell resolution would not bring crucial information. Also, the discrepancy between data displayed in new Fig. 3A (nuclear extracts) and 3C (live cell imaging) indicate that SAM might be less stable in cellular extracts from infected cells compared to non-infected ones, which would complicate the interpretation of the data. Therefore, we did not implement LC-MS/MS on nuclear extracts to measure SAM/SAH ratio.  

      (3) There is a correlation/implication issue here in Fig 2 - cells with C. trachoma's infection show hyper methylation. But these are the only cells with high C. trachomatis. So it is a bit ingenious to say that histone hyper methylation correlates with bacterial proliferation. The cells without bacteria don't have hyper methylation - and that does not have anything to do with the bacterial proliferation.

      In Fig. 2B, we compared the methylation signal within the population of infected cells only (excluding the uninfected cells). We edited the text to clarify this point. “We observed that, within the population of infected cells, the sum intensity of the mCherry signal was higher in cells that displayed hypermethylation of H3K9me3 than in cells with low level of H3K9me3, indicating that histone hypermethylation correlated with bacterial load (Fig. 2B).”

      (4) The claim that demethylase activity is down in infected cells again comes primarily from the increased succinate (2-fold) amounts in infected nuclei - and then correlated with experiments where succinate, (permeable) a-KG are supplemented in excess. While I personally like the hypothesis that the hypermethylation might be a result of an imbalance in cofactors (succinate vs a-KG) in infected cells, the data presented is very premature to make that conclusion. Again, steady state measurements of only succinate cannot provide a clear answer to that question. For example, is there a clear allocation/flux difference (between a-KG, and leading out to glutamate/glutamine, vs flux through the TCA and increased succinate accumulation? Is there a bottleneck/build-up of succinate in cells that might lead to the increase in nuclei? This also opens another direction of possible regulation - increased histone succinylation. When you see a large increase in succinate in the nucleus, before looking at demethylase activity - it becomes obvious if succinate itself increases histone succinylation (through HATs).

      Our work confirms the accumulation of succinate in cells infected by C. trachomatis, previously reported in Rother et al 2018. The reason for this accumulation remains to be investigated in detail. We have previously shown that OxPhos is relatively stable in infected cells (PMID 35931114), indicating that the flux through the TCA of the eukaryotic host proceeds normally. As mentioned in our discussion, the TCA of the bacteria is disrupted with several enzymes missing, although not in the step immediately downstream of succinate/fumarate production. Still, synthesis of succinate and fumarate (fumarate accumulation was observed in the Rother 2018 study) by bacterial enzymes might contribute to their accumulation in infected cells. The approach we chose to measure methylation at the proteome level is not suitable to look for histone succinylation, because of the diversity of post translational modifications on histones, which occur in combinations. However, following on this reviewer’s comment, we reanalysed the proteomic data to compare protein succinylation levels in infected and non-infected samples. We detected 41 succinylated peptides in the infected samples, against 23 in the uninfected samples. For many of these, we did not have quantitative data in all condition and only one protein, transportin 1 (TNPO1), reached statistical significance, with a 4-fold increase in succinylation in infected samples. Thus, while essentially qualitative, this analysis fully supports the hypothesis that succinate accumulates in infected cells. These data were added to Table S1 and to the result section.

      (5) What might the authors hypothesise about why this hyper methylation happens? It appears in some ways that hyper methylation happens - potentially due to a metabolic bottleneck that the bacteria triggers (and there is a build-up of SAM and/or succinate, and altered flux out of a-kg). The methylation is just a visible outcome - but may not be central to pathogenesis or viability.

      We discussed this question in the penultimate paragraph of the discussion by giving some elements of answer to the question: “Does it benefit the host or the bacteria? ». In our study, we showed that protein hypermethylation affected the transcriptional response of the host. We did not investigate whether the activity of some of the host proteins engaged in the response to infection were affected. It might be the case, considering that methylation is a common PTM regulating protein’s activity. Still, we agree with this reviewer that hypermethylation might not be central to pathogenesis or viability. Addressing this question would require a complex model in which protein methylation levels could be controlled experimentally.  

      Reviewer #2 (Public Review):

      Strengths:

      (1) Because the study compares genuinely infected cells with uninfected cells within the same infected cell population, it enables a clearer and more rigorous comparison.

      (2) By using multiple Chlamydia species and cells from multiple host species (human and mouse), and obtaining consistent findings across these systems, the study demonstrates the generality of bacterium-induced epigenomic alterations.

      (3) The study shows that the epigenomic changes are caused by reduced activity of JMJC domain-containing lysine demethylases, demonstrating through multiple complementary approaches-including the use of a demethylase inhibitor, overexpression of target-specific demethylases, and analysis from the perspective of cofactors required for JMJC domain-containing demethylases-that decreased lysine demethylase activity constitutes the molecular mechanism underlying the increased H3 methylation levels induced by Chlamydia infection.

      (4) By performing ChIP-seq analyses of H3K4me3 and H3K9me3, the study clearly delineates, on a genome-wide scale, how infection leads to increased levels of these epigenomic marks.

      Weakness:

      (1) Reduction of cofactors such as Fe2+ or a-KG decreases the activity of JMJC-domaincontaining lysine demethylases (thereby directly affecting histone H3 lysine methylation). However, these cofactors are also involved in the activities of other epigenetic regulators, such as TET enzymes that contribute to DNA demethylation and SIRT family proteins that mediate histone deacetylation. Therefore, it cannot be excluded that modulation of these factors indirectly leads to the changes in H3 lysine methylation dynamics targeted in this study.

      Indeed, reduction of the concentration of Fe2+ and aKG is expected to have other consequences in addition to the inhibition of JMJC-domain containing lysine demethylases on which we focus in this study. As a matter of fact, we reported a decrease in the methylation level of host DNA in infected cells, and we brought some elements that might explain the discrepancy between DNA and histone methylation status in the discussion (e.g., infected cells display enhanced expression of GADD45, which recruit TET enzymes and thus facilitate DNA demethylation). This example illustrates the complexity of host/pathogen interplay, which affect many parameters simultaneously. Indeed, we cannot rule out that modulation of enzymatic activities other than JMJC-domain containing lysine demethylase contribute significantly to the hypermethylation phenotype.

      (2) Related to point 1, although overexpression of JMJC-type demethylases has been shown to reduce the Chlamydia infection-induced increase in H3 lysine methylation, it is well known that over production of these enzymes, while target-specific, also leads to a genome-wide reduction of lysine methylation. Thus, a decrease in lysine methylation upon expression of these demethylases does not necessarily demonstrate that the infection-induced increase in H3 lysine methylation is caused by impaired JMJC-type demethylase activity.

      We fully agree. We included this experiment to show that increasing the expression of one demethylase only restored demethylation of its cognate target. This support the hypothesis that if the hypermethylation is due to poor demethylase activity, it is likely that several demethylases show impaired activity (as opposed to a scenario in which failure of activity of a single demethylase would indirectly affect all other methylation marks).  

      Reviewer #3 (Public Review):

      In this manuscript, the authors explore a molecular basis for hypermethylation of histones in epithelial cells infected with the obligate intracellular bacterial pathogen Chlamydia trachomatis. This is of particular interest given that Chlamydia is known to drastically alter host cell gene transcription, and histone hypermethylation would suggest a new way by which Chlamydia interferes with gene expression of its host. Histone methylation was previously implicated in the introduction of dsDNA breaks in infected cells, and the chlamydial effector NUE was reported to methylate histones, but the role of this modification in dictating host cell gene transcription has been unexplored. The authors use a suite of tools to approach this question, including various -omics techniques, genetic approaches, and biochemical assays. Overall, the manuscript provides many interesting pieces of data, though some of them are difficult to reconcile, which may reflect methodological hurdles that are not fully addressed in the current version of the manuscript. My major concerns regard the rationale/interpretation for various mechanistic experiments and that the heterogeneity of the histone hypermethylation phenotype is not addressed which I believe may explain some apparent inconsistencies in the results.

      We thank this reviewer for insightful comments. We address these two major concerns during revision and bring some elements in our responses below.

      Using an immunofluorescent approach, the authors show that a subpopulation of the nuclei in Chlamydia-infected cells (~10-20%) exhibit high amounts of methylated histone species. This occurs during the late stages of infection, near the time when Chlamydia would lyse the host cell and positively correlates with bacterial burden.

      Accordingly, halting chlamydial growth blocks the onset of histone hypermethylation. Exogenously supplying cofactors for histone demethylases, the low activity of which is implicated in the histone hypermethylation phenotype, reduces histone hypermethylation. In general, these data are compelling and raise interesting questions about the role of histone methylation in governing chlamydial egress from infected cells. Interestingly, these behaviors seem to arise independently of NUE, the secreted chlamydial histone methyltransferase, supporting the notion that a metabolic reprogramming may underlie the hypermethylation phenomenon.

      As noted above, the authors propose that hypermethylation arises due to decreased demethylase activity in infected cells. However, the data do not conclusively support this interpretation. For example, the approaches used to probe demethylase activity rely on (i) a direct biochemical measure of demethylase activity, (ii), pharmacological inhibition of demethylase, and (iii) heterologous expression of a specific demethylase. With the exception of (i), these approaches would be expected to alter histone methylation regardless of the source. That is, inhibition of demethylases should increase histone methylation regardless of whether the source of methylation is increased methylase or decreased demethylase activity. Similarly, overexpression of a demethylase would be expected to reduce cognate histone methylation arising either from increased methylase or decreased demethylase activity.

      We agree with the reviewer’s comments. The experiment using pharmacological inhibitors (ii) show that infected cells are sensitized to these inhibitors but doesn’t provide direct mechanistic insight. The experiment using heterologous expression of demethylases (iii) was included to show that increasing the expression of one demethylase only restored demethylation of its cognate target. This supports the hypothesis that several demethylases show impaired activity (as opposed to a scenario in which failure of activity of a single demethylase would indirectly affect all other methylation marks).  

      The most direct evidence for impaired demethylase activity come from the direct measure of demethylation of H3K4me3 in nuclear extract (i). It is strengthened by indirect evidence that metabolite concentrations hinder demethylase activities late in infection: 1/ iron and DMKG supply diminish hypermethylation of histone lysine residues 2/ succinate levels (a competitor of aKG) are two-fold higher in nuclei isolated from infected cells. This latter finding was confirmed during revision as we identified more succinylated proteins in infected samples compared to non-infected ones.

      We also considered the possibility that infected cells displayed increased histone methyl transferase (HMT) activity. This would be compatible with decrease KDM activity and could contribute to the histone hypermethylation. Unfortunately, this hypothesis cannot be tested directly (as we did for the measure of H3K4me3 demethylation activity). Indeed, SAM is notoriously labile and in vitro assays to measure HMT require to add exogenous SAM to cell extracts to detect any HMT activity, which would not allow us to test activity based on endogenous SAM levels.

      Instead, we used a ratiometric sensor to measure SAM concentration in cells (PMID 34937909). Chlamydia inclusions develop asynchronously, which allows to observe, 40 hpi, a continuum of early (low bacterial load) to late (high bacterial load) stages of infection. There was no correlation between bacterial load and SAM level, and this level was globally similar when comparing infected and non-infected cells. This experiment supports our hypothesis that protein hypermethylation is not due to an increase in SAM during infection.

      This experiment was also very interesting because it revealed a high cell-to-cell heterogeneity in SAM levels in HeLa cells. Thus, in some cells, SAM might be limiting, which could explain why only a fraction of cells display histone hypermethylation.

      Still, we cannot fully rule out the possibility that increase in SAM availability late in the infectious cycle in some cells, and is immediately consumed through protein methylation, resulting in no net [SAM] increase. The discussion was expanded to take these comments into consideration.

      Altogether, we think that the evidence of decrease KDM activities in infected cells late in infection are strong. Our data do not rule out the possibility that additional mechanisms may contribute.

      Moreover, the authors report that the effect of the demethylase inhibitor on histone hypermethylation is significantly potentiated by infection, suggesting that infected cells have greater methylase activity than uninfected cells, because the latter barely respond to the presence of demethylase inhibitor. In other words, a dramatic increase in histone methylation in the presence of demethylase inhibitor is most parsimoniously explained by increased methylation (no longer being removed by demethylase), not decreased demethylation (which would be analogous to treatment with demethylase inhibitor). The authors do not directly assay methylase activity. These concerns extend to the rationale used to justify experiments with infected mice, which the authors treat with the demethylase inhibitor.

      The observation that the same concentration of JIB-04 leads to an increase of histone methylation in infected cells and not in non-infected cells, is coherent with the data showing that aKG or iron supply diminish histone hypermethylation in infected cells. Indeed, the inhibitor is taken up similarly by infected and uninfected cells but the potency of the inhibitor will depend partly on levels of iron, aKG and succinate found in the cellular milieu so same concentration of inhibitor may inhibit demethylase activity in cells with higher succinate and/or low aKG and low iron but fail to inhibit demethylase activity in cells with higher iron or aKG or lower succinate. In other words, high iron, high aKG or low succinate will “buffer” JIB-04 and make it less potent since JIB-04 partly acts by competing with the iron (competitively) and the aKG (mixed competitive inhibition) PMID 23792809. The same phenomenon is expected for SD70 and TACH101 that share aspects of the mode of action of JIB-04 regarding partly competing for aKG and/or iron in the catalytic site.

      The authors perform experiments to characterize the consequence of hypermethylation genome-wide. Because the authors do not enrich for those cells which exhibit histone hypermethylation, the results reflect the mixed population, and therefore presumably dilute out important signal related to the phenomena under investigation. For example, the proteomic analysis of post-translational modifications identifies only one methylated histone species, whereas the immunofluorescent approach shows consistent effects across five different methylated histone species. Moreover, the chromatin immunoprecipitation analysis indicates that there is unexpectedly a lower density of methylated histones at regions which are also enriched in uninfected cells. The authors argue that this suggests increased methylation is happening "outside" of these histone-dense regions, but direct evidence in support of this claim is lacking.

      The caveat of bulk analyses as opposed to single cell resolution is indeed important to consider when analysing the chIP-seq data and we emphasized this point in the revised manuscript. We could have sorted the cells with high bacterial burden; this would probably have given stronger differences between the two samples. Still, the change in distribution of H3K4me3 in infected samples was very clear and statistically significant. A change in H3K9me3 distribution would be more difficult to catch, as the mark is more widespread.

      In sum, this paper provides compelling evidence in support of the notion that histones are hypermethylated at various residues late in chlamydial infection, that this process is modulated by known cofactors of demethylases, and is the result of high levels of bacterial replication in the cell. That histone hypermethylation governs host gene transcription during chlamydial infection suggests a relatively novel mechanism by which Chlamydia subverts the host cell to establish a replicative niche or egress to infect a new cell. The information obtained regarding the methylation status of host proteins and host gene transcription controlled by a metabolic cofactor during infection will be a useful resource for other researchers. However, in the current version of the manuscript, the mechanistic basis for these behaviors is relatively unclear.

      We thank this reviewer for constructive feedback. We believe that the mechanistic conclusions of our report have been strengthened during revision with additional experiments and text clarification.

    1. Author response:

      We thank the editor and reviewers for the positive comments and critical feedback on our manuscript. We are currently preparing revisions to address the critiques provided by reviewer 2, which focused primarily on growth experiments performed with ∆ACP and ∆FabD P. falciparum parasites in minimal lipid conditions. We note that the major conclusions of our manuscript regarding an essential, FASII-independent function for ACP in apicoplast biogenesis do not require or rely on these experiments in minimal lipid conditions.

      Nevertheless, we believe that these observations have value and agree that they contrast with similar experiments reported in the Amiar et al. 2020 study referenced by the reviewer. We note that this prior study (and others cited by the reviewer) primarily focused on the related apicomplexan parasite, Toxoplasma gondii. We fully agree that available evidence in these and other papers supports a key, fitness-conferring role for FASII activity in growth of T. gondii parasites, including possible expanded functions for ACP that may differ from P. falciparum. We will revise our manuscript to clarify that our results only apply to P. falciparum. We note that our minimal lipid growth experiments with P. falciparum utilized culture conditions and concentrations that appear identical to those reported in the Amiar et al. 2020 study. Nevertheless, we agree with the reviewer that additional experiments will be required to fully test and understand FASII functions in asexual blood-stage malaria parasites, including possible functions in low-lipid conditions. We plan to revise our manuscript to clarify this and other points, and we will include expanded responses to the reviewer critiques.

    1. Author response:

      We thank the reviewers for their positive and constructive feedback and for the careful reading of our manuscript.

      We plan to address the reviewers’ comments and, specifically, to more thoroughly compare movement-associated activity with optogenetic stimulation of the locus coeruleus (LC), with new experiments, clarifications, and additional analyses.

      (1) We plan to perform new experiments using two-photon imaging of noradrenaline (NA) sensors in head-fixed mice during both optogenetic LC stimulation and spontaneous movement. This will, if successful, allow us to directly compare the spatial and temporal structure of NA release across conditions, and to quantify NA amplitude during locomotion versus LC stimulation.

      (2) We will analyze existing NA fiber photometry data for movement-related NA release and compare it to release evoked by LC stimulation.

      (3) In general, we plan to more prominently highlight the limitations of our study that were brought up by the reviewers. In particular, we will expand our discussion of other neuromodulatory systems and their interactions with the LC-NA system, and will tone down conclusions of our study if they cannot be supported by the additional planned experiments and analyses.

      Finally, a reviewer suggested the additional experiment to inhibit LC while performing two-photon imaging in head-fixed animals. These experiments have, due to their technical complexity, a low likelihood of success. In addition, recent work from the lab of Emily Macé already performs LC inhibition during functional recordings (doi: 10.64898/2026.03.06.710089). This work supports our interpretation that the contribution of LC-evoked NA release does not dominate movement-related signals. We will discuss these recent findings in the revised version of our manuscript.

      Together, we believe that these planned experiments, analyses, and revisions will address all main concerns raised by the reviewers.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      (1) Presentation of Figures in the Response Letter

      I would like to note that the figures included in the response letter would benefit from improved organization. For example, Author response image 1 lacks clarity for experimental conditions. From the response letter, my understanding is that a "Labeling rate index", Rg−Rn, was calculated to represent the difference in the rate of increase in labeling between neurons and glial across two time intervals based on experiments shown in Figure 2-figure supplement 1C and G. It seems that a mean convergence index was calculated for each experimental condition at each time point for glial and neurons, and then the differences in mean convergence index increase between time intervals were calculated for glial and neurons. The legend needs more detail to enhance clarity.

      Yes, the “labeling rate index” (Rg−Rn) corresponds exactly to the reviewer’s understanding. Specifically, it quantifies the difference between neurons and glia in the increase of the mean convergence index across two defined time intervals, calculated separately for each experimental condition based on the experiments shown in Figure 2–figure supplement 1C and G.

      To improve clarity, we have substantially revised the figure legend to explicitly describe (i) the definition of labeling rate, (ii) how the mean convergence index was computed for neurons and glia at each time point, (iii) how changes across time intervals were derived, and (iv) how to calculate the labeling rate index. In addition, we have moved this analysis to Figure 2-figure supplement 2 and cited it in Line 191.

      Furthermore, the manuscript should clearly distinguish between figures generated from re-analysis of existing data and those based on newly conducted experiments. This distinction should be explicitly stated in the figure legends and/or main text.

      I recommend that all response figures containing data integral to the authors' rebuttal be properly integrated into the manuscript's existing supplementary figure set, rather than remaining isolated in the response document. This would enhance clarity and ensure that key supporting data are fully accessible to readers. For instance, Author response image 1 can be integrated with Figure 2-figure supplement.

      We appreciate the reviewers’ valuable suggestions. We have revised the figure legends and/or corresponding main text to clearly distinguish figures derived from re-analysis of existing data from those based on newly conducted experiments. In addition, all response figures containing data integral to our rebuttal have now been integrated into the current manuscript’s supplementary figure set.

      Specifically, Author response images 1 and 3 have been incorporated into Figure 2–figure supplement 2 and Figure 2–figure supplement 3, respectively; Author response image 2 has been incorporated into Figure 1–figure supplement 2. Author response image 4 has been incorporated into Figure 1,2–figure supplement 1. These changes improve clarity and ensure that all supporting data are readily accessible to readers.

      (2) Glial Cell Labeling and Specificity of Trans-Synaptic Spread

      The authors provided a comprehensive and well-reasoned response to the concern regarding the labeling of radial glial cells. The inclusion of a dedicated section in the revised Discussion and response figures (possibly to be integrated with supplementary figures), strengthens the manuscript.

      The authors have made an interesting observation in Author response image 2 that glial labeling was frequently observed near the soma and dendrites of starter cells, suggesting that transneuronal labeled glial cells may be synaptically associated with the starter neurons. Also astroglia starter cells lead to infection of nearby TVA-negative astroglia, suggesting astroglia-to- astroglia transmission.

      I find the response scientifically satisfactory and appreciate the authors' transparency in addressing the limitations of their approach.

      We thank the reviewer for the positive and thoughtful evaluation. As suggested, we have integrated the revised Discussion and the corresponding response figures into the main text and the supplementary figure set, ensuring that these observations and their interpretation are clearly presented and readily accessible to readers.

      (3) Temperature Effects and Larval Viability

      The authors' justification for raising larvae at 36C to improve labeling efficiency is reasonable. The supporting data indicating minimal impact on larval viability within the experimental timeframe are convincing. Referencing prior behavioral studies and including survival data under controlled conditions adds credibility to their claims. I find this issue satisfactorily addressed.

      We thank the reviewer for this positive and constructive evaluation.

      (4) Viral Toxicity and Dosage Considerations, Secondary Starter Cells

      The authors present a well-reasoned explanation that viral cytotoxicity is primarily driven by replication and not by viral titer or injection volume. However, the inclusion of experimental data directly testing the effects of higher titer or volume on starter cell viability would have strengthened this point, particularly since such tests are relatively straightforward to perform.

      We agree with the reviewer that directly testing the effects of viral titer and injection volume on starter cell viability would further strengthen this point. In practice, we have already used the highest CVS virus titer that could be reliably generated in our system. Therefore, we tested injection volumes of up to 20 nl and observed no detectable effect on starter cell survival, whereas higher injection volumes resulted in deformation of the larval brain, precluding their use.

      Although not shown as a separate figure, these data informed our interpretation of viral toxicity, which is now described more clearly in the revised Discussion. We hope that this explanation and the clarified discussion adequately address the reviewer’s concern.

      Regarding the potential contribution of secondary starter cells, the authors provide a convincing rationale for why such effects are unlikely under their sparse labeling conditions. However, in cases where TVA and G are broadly expressed-such as under the vglut2a promoter, as shown in Author response image 2 it would be valuable to directly evaluate this possibility experimentally. While the authors' interpretation is reasonable, empirical validation would further strengthen their conclusions.

      We appreciate the reviewer’s interest in experimentally evaluating the potential contribution of secondary starter cells under conditions of broad TVA and G expression. In response, we performed additional viral tracing experiments in which TVA and G were driven by the excitatory neuronal marker vglut2a to achieve broad helper expression.

      As shown in a representative case (Author response image 1), newly appearing tdTomato<sup>+</sup> neurons were observed at the later time (6 vs. 3 dpi, circles), many of which were spatially separated from EGFP<sup>+</sup>/tdTomato<sup>+</sup> starter neurons identified at the early time point (3 dpi, dashed circles). Notably, a subset of these newly labeled tdTomato<sup>+</sup> neurons colocalized with EGFP (6 vs. 3 dpi, dashed cyan circles). These new EGFP<sup>+</sup>/tdTomato<sup>+</sup> neurons may represent secondary starter cells or delayed infection of initially targeted starters. Interpretation of tdTomato<sup>+</sup>-only neurons (6 dpi, gray circles) is further complicated by variability in projection distance and synaptic strength, as short-range secondary-order (or multi-level) inputs and long-range first-order inputs may be labeled within similar time windows. In addition, in the presence of multiple primary or secondary starter neurons, unambiguous assignment of labeled inputs to specific starters remains challenging, even with high-temporal-resolution imaging.

      Owing to these constraints, empirical identification of secondary (or multi-level) connections is not readily achievable with the current tracing strategy. A potential solution would be to combine pan-neuronal helper expression with spatiotemporally controlled activation, for example, through a transgenic line enabling light-inducible helper expression (e.g., G protein). Such an approach would enable delayed and cell-specific initiation of secondary (or multi-level) starters, thereby temporally separating long-range first-order inputs from multi-step circuit propagation and permitting input tracing of targeted cells, ultimately improving the spatiotemporal resolution of circuit mapping.

      We have incorporated a dedicated section in the revised Discussion to clarify the applicable scenarios, limitations, and future directions of this viral tracing strategy in zebrafish.

      Author response image 1.

      Recombinant RV-based viral tracing under broad helper expression conditions.

      Time-lapse (3 and 6 dpi) confocal images of the larval hindbrain showing recombinant RV-based viral tracing under broad helper expression (TVA and G, green) via vglut2a promoter-driven UGNT, following posterior hindbrain infection with CVSdG-tdTomato[EnvA] (magenta). Dashed circles, areas enriched with EGFP<sup>+</sup>/tdTomato<sup>+</sup> neurons; gray circles, areas enriched with tdTomato<sup>+</sup>-only neurons; dashed white lines, hindbrain boundaries. C, caudal; R, rostral. Scale bars, 20 μm.

      Reviewer #2 (Public review):

      The study by Chen, Deng et al. aims to develop an efficient viral transneuronal tracing method that allows efficient retrograde tracing in the larval zebrafish. The authors utilize pseudotyped-rabies virus that can be targeted to specific cell types using the EnvA-TvA systems. Pseudotyped rabies virus has been used extensively in rodent models and, in recent years, has begun to be developed for use in adult zebrafish. However, compared to rodents, the efficiency of spread in adult zebrafish is very low (~one upstream neuron labeled per starter cell). Additionally, there is limited evidence of retrograde tracing with pseudotyped rabies in the larval stage, which is the stage when most functional neural imaging studies are done in the field. In this study, the authors systematically optimized several parameters of rabies tracing, including different rabies virus strains, glycoprotein types, temperatures, expression construct designs, and elimination of glial labeling. The optimal configurations developed by the authors are up to 5-10 fold higher than more typically used configurations.

      The results are convincing and support the conclusions. There are some additional changes that are recommended:

      (1) The new data included in the response to reviewer's letter are important to support the main conclusions and should be included in the manuscript.

      We agree with the reviewer that the new data provided in the response are important for supporting the main conclusions. Accordingly, we have now incorporated all four figures from the response into the supplementary figure set of the revised manuscript and added the corresponding descriptions and discussion to the main text where appropriate.

      (2) Line 357-362: This section should include all of the response letter figures and associated details. Additionally, the Author response image 3 is at odds with Fig 2-supplement 1G. In Author response image 3, ~75% of glial cells labeled at 4 dpi loses their fluorescence by 10 dpi. However, Figure 2-supplement 1G shows that glial overall labeling increases ~2 fold from 4 dpi to 10 dpi. This would suggest that the de novo labeling rate for glia is much higher than the net labeling rate calculated from the convergence index. The authors should clarify these findings.

      We agree with the reviewer that the original section at Lines 357-362 should cite the relevant figures and include the associated details. We have now relocated this content to the Results section and incorporated the corresponding figures and descriptions.

      In addition, we fully agree with the reviewer’s interpretation regarding the apparent discrepancy between the high loss rate of early-labeled glial cells (previously Author response image 3, now Figure 2—figure supplement 3) and the net increase in total glial labeling (Figure 2—figure supplement 1G). This pattern indicates that the net convergence index underestimates the true rate of de novo glial infection, as early labeled glial cells progressively lose detectable fluorescence while overall glial labeling continues to increase, implying ongoing de novo infection events outpace this loss. We have clarified this point in the Results section.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The new data included in the response to reviewer letter are important to support the main conclusions and should be included in the manuscript.

      This recommendation echoes the point raised in Reviewer #2’s Public Comment #1. As detailed in our response there, all new data originally included in the response letter have now been fully integrated into the manuscript’s supplementary figure set, with corresponding descriptions added to the main text.

      Line 357-362: This section should include all of the Author response images and associated details. Additionally, Author response image 3 is at odds with Fig 2-supplement 1G. In Author response image 3, ~75% of glial cells labeled at 4 dpi loses their fluorescence by 10 dpi. However, Figure 2-supplement 1G shows that glial overall labeling increases ~2 fold from 4 dpi to 10 dpi. This would suggest that the de novo labeling rate for glia is much higher than the net labeling rate calculated from the convergence index. The authors should clarify these findings.

      This recommendation echoes the concern raised in Reviewer #2’s Public Comment #2 regarding the apparent discrepancy between glial cell loss and the net increase in glial labeling. Please refer to our response to that comment for a detailed explanation. Briefly, we clarify that the continued increase in overall glial labeling despite substantial loss of early-labeled glia indicates a high rate of ongoing de novo infection that is not captured by net convergence index measurements alone. The relevant figure and associated details, including this clarification, have now been incorporated into the revised main text.

      Data and description for response letter Figure 4 should be quantified and added to the manuscript.

      Across nine infected larvae examined, initial infection was consistently restricted to TVA-positive astroglia, typically involving a single starter glial cell per larva. No viral spread was observed in three larvae injected with SADdG-mCherry[EnvA], whereas astroglia-to-astroglia transmission was detected in three of six larvae injected with CVSdG-tdTomato[EnvA]. Importantly, no neuronal labeling was observed in any of the experiments. These quantitative data and descriptions, originally presented as Author response image 4, have now been incorporated into the main text as Figure 1,2–figure supplement 1).

    1. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment:

      This study reports the important finding that the dynamin inhibitor Dyngo-4a broadly affects lipid packing and plasma membrane dynamics, independently of its action on dynamin. While solid computational, biophysical, and cell-based evidence supports this conclusion, there is incomplete support for the authors' main claim on the role of lipid packing in caveolae internalization, as the causal relationship remains unclear and direct analyses are lacking. With stronger evidence, this work would be of significant interest to cell biologists, biophysicists, and chemists interested in membrane remodeling and drug-membrane interactions.

      We are thankful for the very positive feedback and enthusiasm for our work and sincerely thank all the reviewers for their time, their constructive criticism and valuable comments. Based on this, we have revised our manuscript as detailed below in the point-by-point response where the responses to reviewers’ comments are indicated in blue font. Text edits in the revised manuscript are indicated in red font.

      We agree that providing sufficient evidence for inhibition of caveolae endocytosis by Dyngo-4a is critical and have therefore worked hard on identifying suitable assays that enable conclusive experiments as described below. We have now added a new figure with data that we think firmly supports our statement that caveolae internalization is restricted by Dyngo-4a. Additionally, EM images and quantifications of caveola morphology with or without treatment has been added within the same figure. Taken together, we believe that we have provided strong data to support this main claim and challenged this hypothesis as far as current methodology allows. Therefore, we hope that the revised manuscript warrants a new eLife assessment and we would like this to be the version of accord for the publication in eLife.

      Point-by-point response to reviewers comments

      Reviewer #1 (Public review):

      The authors use Dyngo-4a, a known Dynamin inhibitor to test its influence on caveolar assembly and surface mobility. They investigate whether it incorporates into membranes with Quartz-Crystal Microbalance, they investigate how it is organized in membranes using simulations. Finally, they use lipid-packing sensitive dyes to investigate lipid packing in the presence of Dyngo-4a, membrane stiffness using AFM and membrane undulation using fluorescence microscopy. They also use a measure they call "caveola duration time" to claim that something happens to caveolae after Dyngo-4a addition and using this parameter, they do indeed see an increase in it in response to Dyngo-4a, which is reduced back to the baseline after addition of cholesterol. 

      Overall, the authors claim: 1) Dyngo-4a inserts into the membrane and this 2) results in "a dramatic dynamin-independent inhibition of caveola scission". 3) Dyngo-4a was inserted and positioned at the level of cholesterol in the bilayer and 4) Dyngo-4a-treatment resulted in decreased lipid packing in the outer leaflet of the plasma membrane 5) but Dyngo-4a did not affect caveola morphology, caveolae-associated proteins, or the overall membrane stiffness 6) acute addition of cholesterol counteracts the block in caveola scission caused by Dyngo-4a. 

      Overall, in this reviewers opinion, claims 1, 3, 4, 5 are well-supported by the presented data from electron and live cell microscopy, QCM-D and AFM.

      We thank the reviewer for these positive and encouraging words and believe that the new experiments added to the manuscript has provided strong evidence that caveola internalization is greatly inhibited by Dyngo-4a (see below).

      However, there is no convincing assay for caveolar endocytosis presented besides the "caveola duration" which although unclearly described seems to be the time it takes in imaging until a caveolae is not picked up by the tracking software anymore in TIRF microscopy. Since the main claim of the paper is a mechanism of caveolar endocytosis being blocked by Dyngo-4a, a true caveolar internalization assay is required to make this claim. This means either the intracellular detection of not surface connected caveolar cargo or the quantification of caveolar movement from TIRF into epifluorescence detection in the fluorescence microscope. Otherwise, the authors could remove the claim and just claim that caveolar mobility is influenced.

      We thank the reviewer and agree that this is a very important point to verify. Therefore, we have worked hard to quantify the endocytosis of caveolae in thin sections of MEF cells using transmission electron microscopy. By incubating cells with externally added HRP for two-minutes followed by washing, vesicles internalized during this period can be contrasted and distinguished from surface associated vesicles. Sections were quantified by counting both surface-associated and internalized caveolae and CCVs (see figure below). Surface associated caveolae and CCVs can be distinguished based on size and shape for CCV the presence of a coat, but the number of vesicles per image is very low because a cross section has to go right through the vesicle. Furthermore, although internalized caveolae and CCVs can be differentiated by size, it is much harder to separate these from other vesicles, tubules and tubular endosomes positive for HRP.  We detect an approximate 50% reduction in internalized caveolae and CCVs (ie. containing the internalized marker) in Dyngo-4a cells, which confirms that internalization is impaired following Dyngo-4a treatment. Yet, CCV endocytosis was simultaneously confirmed by Tfn uptake assay to be reduced by a greater extent, approximately 95%. We believe that this discrepancy in numbers is due to the low frequency of counted vesicles per section and the difficulties in distinguishing different internalized vesicles and endosomal tubules making a robust quantification of endocytic events difficult. It is also important to note that the EM assay relies on structural criteria to identify only the budded CCVs and caveolae containing the internalized marker, in transit to the early endosome. Other labeled structures are excluded. In contrast, uptake of Tfn into endosomes would also be measured by the light microscopy assay. Therefore, we have chosen not to include these data in the revised manuscript.

      Author response image 1

      Instead, we have developed a new assay in which we can quantify internalization in whole cells and clearly separate internalized caveolae from those that are surface associated or have fused with endosomal structures. For this we use the HeLa FlpIn Cav1-GFP cells which are induced to express Cav1-GFP at endogenous levels to label caveolae. The cells are incubated for five minutes with fluorescent CTxB known to be internalized by caveolae (but also via other mechanisms). To be able to separate internalized caveolae from early endosomes, cells were fixed and labelled with antibodies against the marker EEA1.  Cells were analyzed by fluorescence microscopy and confocal z-stacks of entire cells were recorded. The data was analyzed by software to identify only the caveolae that were positive for CTxB but negative for EEA1. The results from quantification showed a very clear inhibition in the number of internalized caveolae in Dyngo-4a treated cells in comparison to control cells. These data have been included in the manuscript as an important new figure 2 together with TEM data where we quantify the morphology of surface associated caveolae with or without Dyngo-4a treatment. We have also extensively edited the text in the results section to describe these new data and to convey that Dyngo-4a indeed affects internalization. We are very happy to have established means to address this important point by extending the current methodology and tools. Together with the TIRF data and FRAP data we believe that we have provided strong data for this claim and challenged our hypothesis as far as current methodology allows.

      Significance: 

      A number of small molecule inhibitors for the GTPase dynamics exist, that are commonly used tools in the investigation of endocytosis. This goes as far that the use of some of these inhibitors alone is considered in some publications as sufficient to declare a process to be dynamin-dependent. However, this is not correct, as there are considerable off-target effects, including the inhibition of caveolar internalization by a dynamin-independent mechanism. This is important, as for example the influence of dynamin small molecule inhibitors on chemotherapy resistance is currently investigated (see for example Tremblay et al., Nature Communications, 2020). The investigation of the true effect of small molecules discovered as and used as specific inhibitors and their offside effects is extremely important and this reviewer applauds the effort. It is important that inhibitors are not used alone, but other means of targeting a mechanism are exploited as well in functional studies. The audience here thus is besides membrane biophysicists interested in the immediate effect of the small molecule Dyngo-4a also cell biologists and everyone using dynamic inhibitors to investigate cellular function. 

      Thank you for the comments. We very much appreciate the interest and enthusiasm of the reviewer for our work. This has inspired and supported us to perform additional work for the revision of our manuscript.

      Reviewer #2 (Public review): 

      In this manuscript, the authors probe the mechanisms by which Dyngo-4a, a dynamin inhibitor used to block endocytosis, disrupts caveolae dynamics. They provide compelling evidence that Dyngo-4a inhibits caveolae dynamics and endocytosis (as well as several other aspects of plasma membrane dynamics) by a dynamin-independent mechanism. They also provide strong computational and experimental data showing that Dyngo-4a inserts into membranes and decreases lipid packing in the outer leaflet of the plasma membrane. Finally, they demonstrate that the addition of excess cholesterol to cells reverses the effects of Dyngo-4a on caveolae dynamics, presumably by reversing lipid packing defects. Based on these findings they conclude that lipid packing regulates caveolae dynamics and endocytosis in a cholesterol-dependent manner. 

      This work should be of value to cell biologists interested in plasma membrane remodeling and membrane trafficking, biophysicists that study small molecule/membrane interactions and membrane remodeling processes, and chemists interested in designing drugs to target membrane trafficking machinery and pathways. 

      This work addresses the important topic of how a widely used endocytic inhibitor actually works. In the process of addressing this question, the authors uncover unexpected connections between how lipids are packed in cell membranes and membrane dynamics. The methods are appropriate and many of the claims made in this work are well supported by data.

      We very much appreciate the thorough review and very positive feedback constructive critique and thank the reviewer for the time spent on our manuscript.

      Weaknesses: 

      I appreciate that the manuscript has already gone through one round of revisions and that many of the concerns from the previous reviewers appear to have been addressed. However, as an interested reader, I would like to offer several additional comments for the authors to consider. 

      (1) It is not clear based on the data presented whether the effects of Dyngo-4a on lipid packing give rise to defects in caveolae dynamics or if these effects are merely correlated. To show this more definitively, one might expect additional experimental approaches to be used to perturb lipid packing. I appreciate this is probably beyond the scope of the current study. However, it seems important for the manuscript to be clear about how far this interpretation can be pushed in the absence of additional independent lines of evidence.

      We are very proud of the direct experimental support of the effect on lipid packing that we have performed using incorporation of extra cholesterol to the membrane which supports these effects are not merely correlated. Unfortunately, specifically perturbing lipid packing in other ways and conclusively interpreting such data is not uncomplicated. We agree that data and conclusions should be further challenged but we believe that this goes beyond the scope of this manuscript.

      (2) On a related note, it is not obvious how changes in lipid packing in the outer leaflet could impact caveolae dynamics. It would be helpful to include a cartoon illustrating how this might work.

      Thank you for pointing out this important aspect. We have elaborated on this within the discussion and referred to our recently published perspective article in Nature Cell Biology ('A lipid-centric view of endocytosis by caveolae' Parton, Kozlov and Lundmark DOI: 10.1038/s41556-026-01945-5) where this topic is extensively discussed. In short, insertion of the 8S disc in the inner leaflet of the PM replaces approximately 250 lipids and spans the entire thickness of the leaflet. The insertion of the flat, hydrophobic phase of the 8S disc, that faces the outer leaflet, results in a differential contact energy favoring the uneven packing of lipids and preferred accumulation of cholesterol in the PM of mammalian cells. Increased cholesterol content in the PM leads to more tilt and splay and hence curvature generation and, if not constrained by EHD2, scission. Thus, the distinct lipid packing of cholesterol and sphingomyelin opposite the Cav1 complex is key to drive curvature generation and internalization of caveolae.

      We agree that a schematic figure could be nice to illustrate how packing affects caveolae internalization. However, we realized that providing a comprehensible concept this would require an extensive figure with vast discussions in the text. Therefore, we have chosen not to include this here, but refer to the figures in Parton et al. Nature Cell Biology DOI: 10.1038/s41556-026-01945-5

      (3) The authors note that Dyngo-4a inhibits several dynamic processes including generalized plasma membrane mobility (Fig 4A&B), transferrin uptake (Fig S4C), and fusion of fusogenic liposomes (Fig S4G). This clearly indicates there is a major disruption of the plasma membrane going on here that is not limited to caveolae. They go on to show that the addition of cholesterol reverses the effects of Dyngo-4a on caveolae dynamics. However, they do not discuss whether adding back cholesterol has similar effects on plasma membrane mobility and transferrin uptake. This information could help to further pinpoint whether the mechanisms of action are shared, and if the role of cholesterol is more general in controlling these events or is instead specific to caveolae. 

      Yes, this is correct, and we agree that this important finding leads to many follow up questions on the mechanism of action of Dyngo-4a on cellular processes. Yet, to dissect the mechanism for all these processes goes way beyond the scope and our resources for this manuscript.

      (4) In Fig 4C, the morphology of the neck region of the Dyngo-4a treated caveolae structure appears to be "pinched" compared to the control. I appreciate that more EM studies are underway. It would be useful to specifically compare the morphology of the caveolae as part of those studies.

      Thanks, this is a relevant and interesting question. In the revised manuscript, we have therefore performed and included extra quantitative EM data addressing the morphology of caveolae. Based on this we conclude that there is no statistically significant difference in the height, width or neck diameter of caveolae treated with Dyngo-4a in comparison to control cells. When analyzing the ratio of height, width and neck diameter of each caveolae, there is a trend in that neck diameter is increased in Dyngo-4a-treated cells. These data have been included in the new figure 2 A-B and discussed in the text.

      (5) In Line 91, a statement is made that 8S complex formation requires cholesterol. This is debatable, as they appear to form in E. coli in the absence of cholesterol (reference 14).

      Thank you, we have clarified that this statement is referring to mammalian cells.

      Some minor spelling errors include: 

      Line 66 generrating

      Line 182 signigicantly 

      Line 197 treatmend 

      Line 347 succefully 

      These errors have been corrected

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      One criticism that I would still make in the revised version of the paper concerns the description of the behavior of the two monkeys which is still minimal, while acknowledging differences in their choice and RT performance that reflect "individual differences in sensitivity to motion stimulus and a common heuristic-based satisficing strategy". This sentence is not clear to me. Moreover, the potential consequences of these differences on neuronal activity are only considered in the cluster analysis done for each of the two animals separately and for which it turns out there is no notable difference.

      We have revised the text to emphasize the key, common feature of their behavior and refer readers interested in variability across sessions and individuals to our previous study: “Both monkeys showed consistent biases toward the large-reward choice (Figure 1B, C). Details of their performance, including variations across sessions and individuals, have been reported in a previous study (Fan et al., 2018).”

      Given that both monkeys’ choices and RT showed clear and consistent coherence and reward dependencies, and that the clustering analysis were consistent across the two monkeys, we believe that our analyses presented here are appropriate. Future work is needed to examine if and how STN contributes to more nuanced aspects of behavioral variability.

      Compared to the first version of the paper, the cluster analysis in this revised version yields three distinct populations instead of the previous four. While the authors suggest that these subpopulations play important roles in encoding different aspects of decision-making, the identification of three rather than four subpopulations seems to me an important update that warrants discussion.

      The clustering results are slightly different because, following suggestions from the first round of reviews, we now use more principled approaches for selecting neurons and computing the clusters. The primary difference is that Clusters 1 and 3 in the original manuscript have mostly been merged into one cluster (new Cluster 3). We updated the text to note that our use of three clusters depends on our choice of clustering cutoff and continue to emphasize that the clusters are consistent across monkeys and clustering techniques: In Results: “Inspection of the dendrogram (hierarchical cluster tree) suggested that our STN samples can be reasonably grouped into three clusters, although other groupings are possible using different clustering cutoffs (Figure 5-S1).” In Discussion: “Furthermore, our clustering analysis aimed to identify common activity profiles in the STN population, while leaving behind many neurons that either did not show consistent task-related modulation or had less common activity profiles (e.g., those that were far from others in the vector space and those with too infrequent occurrence to form detectable clusters). More work is needed to continue to refine our understanding of the specific computational contributions of the STN to decision formation.”

      Finally, I think it would have been interesting to identify the level of collinearity in the model proposed by the authors (equation 7). Indeed, one can expect significant collinearity between some of the proposed explanatory factors of neuronal activity, such as choice and coherence level, for example.

      The reviewer is correct that choice and coherence are correlated with the formulation of Eq. 7. However, such collinearity does not seem to bias the regression results (Author response image 1). We have performed simulations with different modulation strengths and noise levels (A and C) and observed generally good recoverability of the ground-truth regression coefficients (red: unity-slope lines), despite the strong correlation between choice and coherence for one choice (B).

      Author response image 1.

      Similarly, for the analysis relating neuron activity to decision evaluation signals (p 16), firing rates calculated using sliding averages with 1-ms steps are compared, but the method does not specify controls for multiple comparisons or for non-independent data.

      We have made multiple comparison corrections using the Benjamini and Hochberg procedure and updated the relevant text in Methods, Results, and Abstract accordingly.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In the paper, the authors propose a new RNA velocity method, TSvelo, which predicts the transcription rate linearly based on the expression of RNA levels of transcription factors. This framework is an extension of its recent work TFvelo by including unspliced reads and designing a coherent neuralODE framework. Improved performance was demonstrated in six diverse datasets.

      Strengths:

      Overall, this method introduces innovative solutions to link cell differentiation and gene regulation, with a balance between model complexity (neuralODE) and interpretability (raw gene space).

      We thank the reviewer for the positive evaluation of our work and for recognizing the novelty of the proposed framework. We appreciate the reviewer’s summary highlighting that TSvelo extends our previous method TFvelo by incorporating unspliced reads and introducing a coherent neuralODE framework to model transcription dynamics.

      We are encouraged that the reviewer recognizes the potential of our approach to link cell differentiation with gene regulatory mechanisms, while maintaining a balance between model expressiveness and interpretability in the gene expression space. In the revised manuscript, we have further clarified several methodological details and strengthened the presentation to better highlight these aspects.

      Weaknesses:

      While it seems to provide convincing results, there are multiple technical concerns for the authors to clarify and double-check.

      (1) The authors should clarify and discuss the TF-target map: here, the TF-target genes map is predefined by the TF binding's ChIP-seq data. This annotation is largely incomplete and mostly compiled from a set of bulk tissues. Therefore, for a certain population, the TF-target relation may change. This requires clarification and discussion, possibly exploring how to address this in the model. In addition, a regulon database could be added, e.g., DoRothEA?

      We thank the reviewer for this important comment. The TF–target maps used in TSvelo (e.g., derived from ChIP-seq-based resources such as ENCODE) reflect aggregated TF binding evidence collected across diverse bulk cell types and experimental conditions. As such, they are inherently incomplete and do not capture fully context-specific regulatory activity in a given primary tissue. In TSvelo, we therefore do not treat these annotations as fixed or cell-type-specific ground truth regulatory relationships. Instead, they are used as a permissive prior that encodes a broad set of potential regulatory interactions.

      Within the TSvelo framework, the contribution of each TF–target interaction is learned from data through weight estimation, allowing the model to down-weight or effectively ignore prior edges that are inconsistent with the observed single-cell expression dynamics. This design enables TSvelo to remain robust even when the prior TF–target map is noisy, incomplete, or derived from heterogeneous bulk contexts.

      Following the reviewer’s suggestion, we additionally incorporated the DoRothEA regulon database as an alternative prior with confidence-level filtering. We further performed ablation studies on the pancreas dataset and the gastrulation erythroid dataset using different TF–target resources, including ChEA, ENCODE, and their combinations with DoRothEA.

      The results on the pancreas dataset and the gastrulation erythroid dataset are shown in Figure S13 and Figure S14 respectively, which come up with the same conclusion. We observed highly consistent results across most TF–target prior combinations, including ChEA, ENCODE, ChEA+ENCODE, ChEA+DoRothEA, ENCODE+DoRothEA, and ChEA+ENCODE+DoRothEA. Using the pancreas dataset as example, the mean velocity consistency ranged from 0.985 to 0.995, the mean in-cluster coherence ranged from 0.983 to 0.992, and the mean cross-boundary direction correctness ranged from 0.719 to 0.740 across all settings. These consistently high and tightly bounded metrics indicate that TSvelo is largely insensitive to the specific choice of TF–target prior.

      The only configuration showing reduced stability was the use of DoRothEA alone, particularly in terms of cross-boundary direction correctness. This is likely due to its comparatively limited coverage of TF–target interactions. For instance, in the pancreas dataset, only 81 out of 2000 highly variable genes (HVGs) could be associated with TFs based on DoRothEA, corresponding to 102 TF–target links in total, which may restrict downstream regulatory modeling. In contrast, ChEA covered 1793 genes with 13,976 TF–target links, and ENCODE covered 1854 genes with 33,076 links. These results further suggest that integrating multiple TF–target resources could improve performance, likely due to increased coverage and complementary regulatory information.

      We further acknowledge that regulatory interactions are inherently context-dependent, and that no static TF–target resource can fully capture tissue-specific regulatory programs. In the revised Discussion, we explicitly clarify this limitation and highlight that incorporating context-specific regulatory data (e.g., single-cell chromatin accessibility or perturbation-based regulatory maps) represents an important direction for future improvement.

      (2) The authors should clarify how example genes are selected. This is particularly unclear in Figure 2d.

      We thank the reviewer for raising this point. The example genes shown in Fig. 2d were selected to illustrate representative scenarios where our method provides advantages, particularly cases in which the unspliced–spliced 2D phase portrait exhibits mixed or overlapping patterns that are difficult to model using conventional RNA velocity approaches. These examples are therefore intended to demonstrate the types of transcriptional dynamics that TSvelo is designed to better capture.

      To avoid the impression of selective presentation, we note that our conclusions are based on systematic evaluation across all genes and datasets. Additional visualizations for a broader set of genes on this dataset are provided in Fig. S3. We have clarified the example gene selection criteria in the revised manuscript.

      (3) The authors should clarify confidence in the statement in lines 179-180, that ANXA4 should initially decrease. This is particularly concerning, as TSvelo didn't capture the cell cycle transitions well during the initial part.

      We thank the reviewer for raising this point. The statement that ANXA4 initially decreases is based on the observed expression pattern in the dataset rather than on cell-cycle–related dynamics inferred by the model. Specifically, ANXA4 shows higher expression in Ductal cells compared to Ngn3 EP cells, and Ductal represents an earlier stage in the developmental trajectory. Therefore, along the Ductal to Ngn3 EP transition, ANXA4 naturally exhibits an initial decrease in expression. We have clarified this point in the revised manuscript.

      (4) A support reference should be added for the statement in line 260 that "neuron migrations are inside-out manner". There is no reference supporting this, and this statement is critical for the model assessment.

      We thank the reviewer for this suggestion. This pattern has been reported in previous studies [1,2], which have been added into the revised manuscript.

      To Improve clarity, we have also revised the statement in the manuscript as follows:

      “During cortical development, neurons follow an inside-out layering pattern in which earlier-born neurons populate the deep cortical layers, whereas later-born neurons migrate past them to occupy more superficial layers.”

      (1) Nadarajah, B., Parnavelas, J. Modes of neuronal migration in the developing cerebral cortex. Nat Rev Neurosci 3, 423–432 (2002).

      (2) Li, C., Virgilio, M.C., Collins, K.L. et al. Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction. Nat Biotechnol 41, 387–398 (2023).

      (5) The comparison to scMultiomics data is particularly interesting, as MultiVelo uses ATAC data to predict the transcription rate. It would be very insightful to add a direct comparison of the estimated transcription rate between using ATAC and directly using TFs' RNA expressions.

      We thank the reviewer for suggesting this highly interesting comparison between ATAC-derived regulatory activity and TF RNA-based proxies for transcription rate estimation.

      We have conducted the requested analysis by computing gene-wise chrome accessibility rate used in MultiVelo and the learned transcription rate from TSvelo, and evaluated their correlation across genes. As shown in Figure S15, the two estimates exhibit almost no global correlation across genes, indicating that they capture substantially different aspects of regulatory information.

      This discrepancy is not unexpected and reflects the fundamental differences between these modalities. scATAC-seq measures chromatin accessibility, which provides a proxy for cis-regulatory potential of genomic regions. However, ATAC signals are inherently sparse and often exhibit a near-binary structure, limiting their ability to directly capture fine-grained temporal regulatory dynamics. In contrast, TF RNA expression reflects downstream transcriptional output, which is shaped by multiple regulatory layers, including post-transcriptional regulation, protein activity, temporal delays, and indirect regulation through intermediate transcriptional or signaling pathways. As a result, these two modalities are expected to capture complementary but not directly comparable aspects of gene regulation.

      Overall, this result suggests that ATAC-based and TF RNA-based signals capture distinct aspects of gene regulation. This further implies that integrating both modalities may be beneficial for future models that aim to more comprehensively characterize transcriptional regulation. We have added this discussion to the supplementary information.

      (6) In Figure 6g, it should be clarified how the lineage was determined. Did the authors use the LARRY barcodes, predicted cell fate, or any other methods? Here, the best way is probably using the LARRY barcodes for individual clones.

      We thank the reviewer for this suggestion. The lineage assignment used in Fig. 6g is described in the Methods section (“Lineage segmentation and pseudotime initialization”). Briefly, lineages are inferred from the transcriptomic structure of the data by performing Leiden clustering followed by PAGA-based connectivity analysis. Starting from an initial Leiden cluster, the filtered PAGA graph defines the shortest paths to other clusters, which are considered as the detected lineages, and diffusion pseudotime (DPT) is then used to initialize pseudotime along each lineage. Thus, in this analysis lineages are determined from the expression-derived trajectory structure. We have clarified this point in the revised manuscript and refer readers to the Methods section.

      Reviewer #2 (Public review):

      Summary:

      Li et al. propose TSvelo, a computational framework for RNA velocity inference that models transcriptional regulation and gene-specific splicing using a neural ODE approach. The method is intended to improve trajectory reconstruction and capture dynamic gene expression changes in scRNA-seq data. However, the manuscript in its current form falls short in several critical areas, including rigorous validation, quantitative benchmarking, clarity of definitions, proper use of prior knowledge, and interpretive caution. Many of the authors' claims are not fully supported by the evidence.

      We thank the reviewer for the careful evaluation of our manuscript and for the constructive comments. We appreciate the concerns regarding validation, benchmarking, methodological clarity, and interpretation. In the revised manuscript, we have carefully addressed these points by adding additional analyses, clarifying methodological details, and moderating several claims to ensure they are fully supported by the data. Detailed responses to each comment are provided below.

      Major comments:

      (1) Modeling comments

      (a) Lines 512-513: How does the U-to-S delay validate the accuracy of pseudotime? Using only a single gene as an example is not sufficient for "validation."

      We thank the reviewer for this important clarification. In the revised manuscript, we have rephrased this part to clarify that Fig. 1a serves only as an illustrative example showing the U-to-S delay for a single gene. Accordingly, we have corrected our statement to indicate that the U-to-S delay is used to infer trajectory orientation, rather than to validate the accuracy of pseudotime.

      In addition, we have expanded the description to explain that U-to-S delay signals are aggregated across all genes to provide a more robust and comprehensive assessment for this purpose. Additional analysis is provided in our response to the next comment.

      (b) Lines 512-518: The authors propose a strategy for selecting the initial state, but do not benchmark how accurate this selection procedure is, nor do they provide sufficient rationale. While some genes may indeed exhibit U-to-S delay during lineage differentiation, why does the highest U-to-S delay score indicate the correct initiation states? Please provide mathematical justification and demonstrate accuracy beyond using a single gene example. Maybe a simulation with ground truth could help here, too.

      We thank the reviewer for this insightful comment. In the revised manuscript, we have clarified both the intuition and justification of this approach. Briefly, along a correctly oriented trajectory, unspliced (U) expression is expected to precede spliced (S) expression due to transcriptional dynamics. Ideally, this U-to-S delay would be observable at the level of individual genes. However, due to the high noise inherent in scRNA-seq data, such delays are often not consistently detectable on a per-gene basis. To address this, we aggregate U-to-S delay signals across all genes and determine the lineage orientation by maximizing a global delay score. Under this criterion, the cluster from which all outgoing lineages exhibit the highest aggregated U-to-S delay is inferred to correspond to the initial state.

      We emphasize that this approach relies on genome-wide aggregation rather than any single gene. Moreover, the same strategy is applied uniformly across all six datasets using identical parameter settings, demonstrating its robustness and stability. To further address the reviewer’s concern, we additionally present the U-to-S delay scores for each Leiden cluster when treated as the initial state across all datasets (Author response image 1). The results on all datasets suggest that the highest U-to-S delay scores can be used to detect the initial cluster.

      Author response image 1.

      The U-to-S delay scores for each Leiden cluster when treated as the initial state across all datasets.

      Following your suggestions, we also add a simulation study. We generated synthetic single-cell RNA velocity datasets using a mechanistic transcriptional dynamics model with one or multiple developmental branches. The system included 200 genes, among which 30 were designated as transcription factors (TFs).

      For each branch, we independently sampled a TF–target regulatory matrix W ϵ R<sup>30×200</sup> from a standard normal distribution to simulate distinct GRN structures. Gene expression dynamics were modeled using a coupled ordinary differential equation (ODE) system describing unspliced and spliced RNA abundances:

      where u and s denote unspliced and spliced RNA levels, respectively. The transcription rate α was computed as a nonlinear function of TF expression, defined as a weighted sum of spliced TF abundance, followed by clipping to ensure bounded activation.

      Each branch is initialized from the same randomly sampled initial condition drawn from a gamma distribution, allowing controlled divergence of trajectories driven solely by branch-specific regulatory programs.

      To simulate observed sequencing counts, we introduced technical noise by scaling latent expression levels with cell-specific library sizes drawn from a log-normal distribution. The resulting expression counts were generated using a negative binomial sampling model:

      where θ controls over dispersion, with smaller values corresponding to higher noise levels. The final datasets consist of paired unspliced (U) and spliced (S) count matrices with realistic transcriptional stochasticity and branching gene regulatory dynamics. For each branch, cells were further divided into three developmental stages for downstream analysis.

      We evaluated TSvelo on multiple simulated datasets with varying numbers of branches and noise levels. There are two or three branches start from the same root cell groups in these datasets (Branch 1: stage 0 - stage 1 - stage 2. Branch 2: stage 0 - stage 3 - stage 4. Branch 3: stage 0 - stage 5 - stage 6). The results of initial state identification based on the unspliced-to-spliced (U-to-S) delay, along with the corresponding 2D velocity stream visualizations, are presented in Supplementary Figure S1. These results demonstrate that the U-to-S delay–based initialization is robust and consistently identifies cells corresponding to the earliest developmental stage (“stage 0”) across different simulation settings. All additional results have been included in the Supplementary Information.

      (c) Equation (8): The formulation looks to be incorrect. If $$W \in \mathbb{R}^{G\times G}$$ and $$W' - \Gamma' \in \mathbb{R}^{K\times K}$$, how can they be aligned within the same row? Please clarify.

      We thank the reviewer for pointing this out. This was a typographical error in the manuscript. In the third line of Equation (8), the term should be W’ instead of W. We have corrected this in the revised manuscript to ensure dimensional consistency.

      (d) The use of prior knowledge graphs from ENCODE or ChEA to constrain regulation raises concerns. Much of the regulatory information in these databases comes from cell lines. How can such cell-line-based regulation be reliably applied to primary tissues, as is done throughout the manuscript? Additional experiments are needed to test the robustness of TSvelo with respect to prior knowledge.

      We thank the reviewer for this important comment. In TSvelo, TF–target networks from resources such as ENCODE and ChEA are incorporated as priors that guide the model toward biologically plausible regulatory structures. Importantly, the contribution of each TF–target interaction is learned from the data, allowing the model to down-weight or override potentially inaccurate or context-mismatched regulatory links. By aggregating signals across a large number of genes, the model further reduces sensitivity to noise and incompleteness in any single prior network.

      To evaluate robustness with respect to prior knowledge, we incorporated the DoRothEA regulon resource as an alternative TF–target prior with confidence-level filtering. We further performed ablation studies on the pancreas dataset and the gastrulation erythroid dataset using different TF–target resources, including ChEA, ENCODE, and their combinations with DoRothEA.

      The results on the pancreas dataset and the gastrulation erythroid dataset are shown in Figure S13 and Figure S14 respectively, which come up with the same conclusion. We observed highly consistent results across most TF–target prior combinations, including ChEA, ENCODE, ChEA+ENCODE, ChEA+DoRothEA, ENCODE+DoRothEA, and ChEA+ENCODE+DoRothEA. Using the pancreas dataset as example, the mean velocity consistency ranged from 0.985 to 0.995, the mean in-cluster coherence ranged from 0.983 to 0.992, and the mean cross-boundary direction correctness ranged from 0.719 to 0.740 across all settings. These consistently high and tightly bounded metrics indicate that TSvelo is largely insensitive to the specific choice of TF–target prior. Notably, these results further suggest that even when the underlying regulatory resources differ in origin (e.g., cell-line-derived vs. curated or aggregated datasets), the inferred dynamics remain stable.

      The only configuration showing reduced stability was the use of DoRothEA alone, particularly for cross-boundary direction correctness. This is likely due to its comparatively limited coverage of TF–target interactions. For instance, in the pancreas dataset, only 81 out of 2000 highly variable genes (HVGs) could be associated with TFs based on DoRothEA, corresponding to 102 TF–target links in total, which may limit downstream regulatory modeling. In contrast, ChEA covered 1793 genes with 13,976 TF–target links, and ENCODE covered 1854 genes with 33,076 links. These results further suggest that integrating multiple TF–target resources can improve performance, likely due to increased coverage and complementary regulatory information.

      We agree that regulatory interactions derived from resources such as ENCODE and ChEA may not fully generalize to primary tissues due to their context-dependent nature. In the revised Discussion, we explicitly clarify this limitation, particularly their inability to capture tissue-specific regulatory programs. We further highlight that incorporating context-specific regulatory data, such as single-cell chromatin accessibility or perturbation-based regulatory maps, represents an important direction for future improvement.

      (e) Lines 579-580: How is the grid search performed? More methodological details are required. If an existing method was used, please provide a citation.

      The grid search for the time step means that the model evaluates the loss in equation (10) across all candidate values of t<sub>step</sub> in the set {0,1,2,...,999}. This strategy was originally adopted in scVelo for optimizing the time step parameter. We have now added the corresponding citation to scVelo in the revised manuscript.

      (2) Application on pancreatic endocrine datasets

      (a) Lines 140-141: What is the definition of the final pseudotime-fitted time t or velocity pseudotime?

      There is no distinction between “final pseudotime”, “fitted time t” and “velocity pseudotime”. All of them refer to the same quantity in our framework. To eliminate any potential ambiguity, we have standardized the terminology by replacing “final pseudotime” with “pseudotime”.

      (b) Lines 143-144: The use of the velocity consistency metric to benchmark methods in multi-lineage datasets is incorrect. In multi-lineage differentiation systems, cells (e.g., those in fate priming stages) may inherently show inconsistency in their velocity. Thus, it is difficult to distinguish inconsistency caused by estimation error from that arising from biological signals. Velocity consistency metrics are only appropriate in systems with unidirectional trajectories (e.g., cell cycling). The abnormally high consistency values here raise concerns about whether the estimated velocities meaningfully capture lineage differences.

      We thank the reviewer for raising this important point regarding the use of the velocity consistency metric in multi-lineage systems. Velocity consistency was initially introduced by scVelo [1] and implemented as scvelo.velocity_confidence() in its package. Velocity consistency provides one of the few widely adopted quantitative criteria for benchmarking RNA velocities [2]. We agree that it is especially suitable for single-lineage processes. For datasets with clear multi-lineage differentiation (Fig. 5 and Fig. 6), we do not use this metric, precisely to avoid the issue highlighted by the reviewer.

      However, the pancreatic endocrine dataset (Fig. 2) exhibits minimal branching, making velocity consistency be more appropriate. As introduced by veloVI study, RNA velocities are supposed to change smoothly over the phenotypic manifold [3]. Higher consistency indicates that neighboring cells show compatible velocity directions, reflecting stable and coherence of the inferred velocity field. Additionally, multiple previous studies used velocity consistency to evaluate model performance on this pancreas dataset [2,3,4], providing a standard point of comparison.

      To better address your concerns, we have replaced the corresponding panel in Fig. 2 of the main text with an evaluation of cell-type separability in both the traditional 2D (unspliced–spliced) phase portrait and the learned 3D (α–unspliced–spliced) phase portrait by TSvelo (Author response image 4 in our response to your subsequent question). We appreciate your suggestions, as the comparison more clearly highlights the novelty and contribution of TSvelo and helps explain its improved performance. Now, the velocity consistency panel has been moved to the Supplementary Information. In addition, we have added a clearer explanation of the cross-boundary correctness metric in the revised manuscript.

      (1) Bergen, V., Lange, M., Peidli, S., Wolf, F. A., & Theis, F. J. (2020). Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology, 38(12), 1408-1414.

      (2) Luo, Y., Ren, J., Yang, Q. ... & Li, Q. (2026). Benchmarking RNA velocity methods across 17 independent studies, Cell Reports Methods, 101367.

      (3) Gayoso, A., Weiler, P., Lotfollahi, M., Klein, D., Hong, J., Streets, A., ... & Yosef, N. (2024). Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells. Nature Methods, 21(1), 50-59.

      (4) Li, J., Pan, X., Yuan, Y., & Shen, H. B. (2024). TFvelo: gene regulation inspired RNA velocity estimation. Nature Communications, 15(1), 1387.

      (c) The improvement of TSvelo over other methods in terms of cross-boundary direction correctness looks marginal; a statistical test would help to assess its significance.

      We thank the reviewer for this insightful comment. In the revised manuscript, we have added statistical tests for evaluated metrics, including velocity consistency, cross-boundary direction correctness, and in-cluster coherence.

      As shown in Author response image 2, TSvelo significantly outperforms all baseline methods in terms of velocity consistency across both datasets. For in-cluster coherence, TSvelo achieves significantly better performance on the gastrulation (erythroid) dataset, while on the pancreas dataset it performs comparably to the best-performing baselines (UniTVelo and TFvelo) and significantly outperforms several competing methods, including CellDancer, Dynamo, and scVelo.

      For cross-boundary direction correctness, TSvelo shows consistent improvements in mean performance on the pancreas dataset (Author response image 3), and significantly outperforms Dynamo and scVelo on the gastrulation dataset. Although not all pairwise comparisons on cross-boundary direction correctness reach statistical significance, this is likely influenced by the limited number of independent samples (n = 7 and n = 4 for the two datasets, respectively), which reduces statistical power for detecting differences. Importantly, TSvelo still achieves the best average performance among all methods, indicating a consistent overall trend in favor of TSvelo.

      We have added these results into the revised manuscript.

      Author response image 2.

      The quantitative comparison between TSvelo and baseline approaches on the pancreas dataset (panel a) and the gastrulation erythroid dataset (panel b). In each plot, methods are ranked in descending order of their mean values. Numbers at the bottom indicate the sample size for each metric. Significance is determined using a one-sided Mann–Whitney U test. *****, ***, ** and * represent p < 0.00001, 0.0001 ≤ p < 0.001, 0.001 ≤ p < 0.01, and 0.01 ≤ p < 0.05, respectively.

      Author response image 3.

      The comparison of mean cross-boundary direction correctness on the pancreas dataset.

      (d) Lines 177-178: Based on the figure, TSvelo does not appear to clearly distinguish cell types. A quantitative metric, such as Adjusted Rand Index (ARI), should be provided.

      We thank the reviewer for this helpful suggestion. To quantitatively assess whether TSvelo can distinguish cell types, we evaluated the separability of cell-type labels in both the 2D (unspliced–spliced) phase portrait adopted by previous RNA velocity approaches, and the 3D (α–unspliced–spliced, α denotes the transcriptional rate) phase portrait introduced by TSvelo.

      Specifically, we evaluated how well the embedding preserves cell-type information using a k-nearest neighbors (kNN) classification accuracy with 5-fold cross-validation. Given an embedding matrix in 2D or 3D space (X 𝛜 ℝ<sup>n*d</sup>, where n is the number of cells and d is 2 or 3) and corresponding cell-type labels (y 𝛜 {1, … ,C}, we partition the data into five folds. For each fold (k), a kNN classifier with K = 5, denoted asf<sup>(k)</sup>, is trained on the training subset and evaluated on the held-out test subset. The classification accuracy for the k-th fold is defined as ℝ

      where n<sub>k</sub> is the number of samples in the test set and 1(.)is the indicator function. The final score is obtained by averaging across all folds:

      This metric directly assesses whether cells of the same type are positioned close to each other in the embedding space, and is widely used to quantify representation quality.

      Using this evaluation, we observed that the 3D phase portrait consistently achieves significantly higher accuracy than the 2D phase portrait (Author response image 4). The improvement is highly statistically significant (one-sided Mann–Whitney U test, p-value = 4.37 × 10<sup>-10</sup>), demonstrating that the 3D representation provides substantially better separation of cell types.

      We have added these quantitative results to the revised manuscript to complement the visual evidence and to clarify that TSvelo effectively distinguishes cell types in the learned representation.

      Author response image 4.

      The evaluation of the separability of cell-type labels in both the 2D (unspliced–spliced) phase portrait and the 3D (α–unspliced–spliced) phase portrait for the pancreas dataset.

      (e) Lines 179-183: The claim that traditional methods cannot capture dynamics in the unspliced-spliced phase portrait is vague. What specific aspect is not captured-the fitted values or something else? Evidence is lacking. Please provide a detailed explanation and quantitative metrics to support this claim.

      We thank the reviewer for this important comment. We have revised the text to more clearly illustrate this point using representative example genes as follows: “For instance, ANXA4 shows higher expression in Ductal cells compared to Ngn3 low EP cells, which mean its expression pattern exhibits an initial decrease followed by an increase. Such dynamics are not easily captured in the conventional unspliced–spliced phase portrait used by previous approaches, as many baseline methods implicitly assume a decreasing–then–increasing expression pattern. By comparison, TSvelo can still fit such expression pattern by using additional information from the 3D phase portrait.”

      In addition, we also clarify that the 2D u–s representation has limited capacity to separate heterogeneous dynamic cell states, which can affect downstream velocity field estimation. In the conventional 2D u–s phase portrait, cells from different dynamic regimes may overlap in the same region of the embedding space. This overlap reduces the identifiability of underlying transcriptional states and makes the inferred local dynamics more ambiguous. In contrast, TSvelo introduces an additional latent variable α, forming a 3D (α, u, s) phase portrait, which helps disentangle these mixed trajectories and yields a more structured and separable representation of cell dynamics. We have provided quantitative evidence in the previous response (Author response image 4). Briefly, the proposed 3D representation achieves consistently higher kNN classification accuracy (5-fold cross-validation, k=5) for cell state identification compared to the 2D u–s embedding.

      (3) Application to gastrulation erythroid datasets

      (a) Lines 191-194: The observation that velocity genes are enriched for erythropoiesis-related pathways is trivial, since the analysis is restricted to highly variable genes (HVGs) from an erythropoiesis dataset. This enrichment is expected and therefore not informative.

      We thank the reviewer for this comment and agree that such enrichment is expected given the use of HVGs from an erythropoiesis dataset. This analysis was included only as a preliminary sanity check to support the plausibility of the inferred velocity genes, rather than as a main result. We have accordingly simplified the description and clarified that this analysis serves only as a preliminary check in the revised manuscript.

      (b) Lines 227-228: It remains unclear how TSvelo "accurately captures the dynamics." What is the definition of dynamics in this context? Figure 3g shows unspliced/spliced vs. fitted time plots and phase portraits, but without a quantitative definition or measure, the claim of superiority cannot be supported. Visualization of a single gene is insufficient; a systematic and quantitative analysis is needed.

      We thank the reviewer for this important comment. We have revised the text to more clearly illustrate this point using representative example genes as follows: “For HSP90AB1, which exhibits a counter-clockwise pattern in the unspliced–spliced phase portrait, in contrast to the clockwise dynamics typically assumed by most baseline approaches, it is difficult for previous methods to capture this behavior, whereas TSvelo can still faithfully model such patterns. For genes such as RPS26, which have critical roles in the development in blood progenitors to erythroid40, the unspliced-spliced data is so noisy that cells of different types overlap in phase portrait. TSvelo can still captures the gene dynamics and reveals differences in transcription rates across cell types.”

      In addition, we explicitly emphasize the role of the 3D (α, u, s) phase portrait, which provides a more structured and separable representation of transcriptional states compared to the conventional 2D u–s space. This improved representation is the key factor underlying the advantages of TSvelo in modeling transcriptional processes. In the conventional 2D u–s phase portrait, cells from different transcriptional states may overlap, leading to reduced separability. In contrast, introducing the latent variable α expands the representation to a 3D space, which helps disentangle these mixed states and yields a clearer phase structure. Similar to our previous response in Author response image 4, we provide quantitative evidence on this gastrulation erythroid dataset in Figure S7, showing that the 3D representation achieves consistently higher kNN classification accuracy for cell state separation compared to the 2D u–s embedding (one-sided Mann–Whitney U test, p-value = 0.002).

      (4) Application to the mouse brain and other datasets

      (a) Lines 280-281: The authors cannot claim that velocity streams are smoother in TSvelo than in Multivelo based solely on 2D visualization. Similarly, claiming that one model predicts the correct differentiation trajectory from a 2D projection is over-interpretation, as has been discussed in prior literature see PMID: 37885016.

      We thank the reviewer for this important comment. Consistent with other RNA velocity studies, TSvelo employs the 2D UMAP stream plot for visualizing the results. We agree that conclusions based solely on 2D visualizations may lead to over-interpretation. Our intention was to provide an intuitive visualization rather than a rigorous quantitative comparison. Accordingly, we have revised the text to avoid making definitive claims about smoothness or correctness of differentiation trajectories based solely on 2D projections.

      (b) Lines 304-306: Beyond transcriptional signal estimation, how is regulation inferred solely from scRNA-seq data validated, especially compared with scATAC-seq data? Are there cases where transcriptome-based regulatory inference is supported by epigenomic evidence, thereby demonstrating TSvelo's GRN inference accuracy?

      We thank the reviewer for this important question regarding the validation of regulatory inference derived from scRNA-seq data and its comparison to scATAC-seq-based evidence.

      We would like to first clarify the scope of TSvelo. Similar to existing RNA velocity methods, the primary goal of TSvelo is to model transcriptional dynamics and accurately infer cell state transitions and cell fate trajectories. In this context, gene regulatory information is not inferred de novo from data, but incorporated as prior knowledge from curated TF–target databases to guide and constrain the dynamics modeling process, as described in our Introduction.

      We have conducted the requested analysis by computing gene-wise chrome accessibility rate used in MultiVelo and the learned transcription rate from TSvelo, and evaluated their correlation across genes. As shown in Figure S15, the two estimates exhibit almost no global correlation across genes, indicating that they capture substantially different aspects of regulatory information.

      This discrepancy is not unexpected and reflects the fundamental differences between these modalities. scATAC-seq measures chromatin accessibility, which provides a proxy for cis-regulatory potential of genomic regions. In contrast, TF RNA expression reflects downstream transcriptional output, which is shaped by multiple regulatory layers, including post-transcriptional regulation, protein activity, temporal delays, and indirect regulation through intermediate transcriptional or signaling pathways. As a result, these two modalities are expected to capture complementary but not directly comparable aspects of gene regulation.

      We acknowledge that scATAC-seq provides valuable complementary information on chromatin accessibility and regulatory potential, and will consider incorporating matched multi-omics data in future work. In the revised manuscript, we further clarify that TSvelo is an RNA velocity method that incorporates prior knowledge from curated TF–target databases, and we have added a discussion on the potential use of scATAC-seq data for future extension of our framework.

      (c) The claim that TSvelo can model multi-lineage datasets hinges on its use of PAGA for lineage segmentation, followed by independent modeling of dynamics within each subset. However, the procedure for merging results across subsets remains unclear.

      We thank the reviewer for pointing out that the merging step was not sufficiently described. After modeling dynamics independently within each lineage-specific subset, TSvelo integrates the results via a weighted aggregation procedure at the cell level.

      For each cell and each inferred quantity (e.g., velocity or other dynamic variables), we collect the estimates obtained from different lineage-specific models and combine them using a weighted average. The weights are defined by the size of each lineage, reflecting its statistical support. We have clarified details about this merging procedure in the Methods section.

      This aggregation reconciles multiple lineage-specific estimates for the same cell into a single value and mitigates discontinuities that could arise from directly combining independent lineage analyses. The resulting values define a unified set of dynamics for each cell across lineages.

      Reviewer #3 (Public review):

      Despite the abundance of RNA velocity tools, there are still major limitations, and there is strong skepticism about the results these methods lead to. In this paper, the authors try to address some limitations of current RNA velocity approaches by proposing a unified framework to jointly infer transcriptional and splicing dynamics. The method is then benchmarked on 6 real datasets against the most popular RNA velocity tools.

      While the approach has the potential to be of interest for the field, and may present improvements compared to existing approaches, there are some major limitations that should be addressed, particularly concerning the benchmark (see major comment 1).

      Major comments:

      (1) My main criticism concerns the benchmarking: real data lack a ground truth, and are absolutely not ideal for comparing methods, because one can only speculate what results appear to be more plausible.

      A solid and extensive simulation study, which covers various scenarios and possibly distinct data-generating models, is needed for comparing approaches. The authors should check, for example, the simulation studies in the BayVel approach (Section 4, BayVel: A Bayesian Framework for RNA Velocity Estimation in Single-Cell Transcriptomics). Clearly, all methods should be included in the simulation.

      Following your recommendation, we have added the simulation analysis to compare TSvelo with existing RNA velocity approaches. We generated synthetic single-cell RNA velocity datasets using a mechanistic transcriptional dynamics model with one or multiple developmental branches. The system included 200 genes, among which 30 were designated as transcription factors (TFs).

      For each branch, we independently sampled a TF–target regulatory matrix W ϵ ℝ<sup>30×200</sup> from a standard normal distribution to simulate distinct GRN structures. Gene expression dynamics were modeled using a coupled ordinary differential equation (ODE) system describing unspliced and spliced RNA abundances:

      where u and s denote unspliced and spliced RNA levels, respectively. The transcription rate α was computed as a nonlinear function of TF expression, defined as a weighted sum of spliced TF abundance, followed by clipping to ensure bounded activation.

      Each branch is initialized from the same randomly sampled initial condition drawn from a gamma distribution, allowing controlled divergence of trajectories driven solely by branch-specific regulatory programs.

      To simulate observed sequencing counts, we introduced technical noise by scaling latent expression levels with cell-specific library sizes drawn from a log-normal distribution. The resulting expression counts were generated using a negative binomial sampling model:

      where θ controls over dispersion, with smaller values corresponding to higher noise levels. The final datasets consist of paired unspliced (U) and spliced (S) count matrices with realistic transcriptional stochasticity and branching gene regulatory dynamics. For each branch, cells were further divided into three developmental stages for downstream analysis.

      We evaluated TSvelo and those splicing-based RNA velocity approaches on multiple simulated datasets with varying numbers of branches and noise levels. There are one, two or three branches start from the same cell group in these datasets (Branch 1: stage 0 - stage 1 - stage 2. Branch 2: stage 0 - stage 3 - stage 4. Branch 3: stage 0 - stage 5 - stage 6). We primarily assessed performance using the cross-boundary direction correctness (CBDir) metric, as it directly evaluates inferred trajectories against ground-truth cell stage annotations, which have been widely adopted in RNA velocity studies such as VeloAE and UniTvelo. In detail, Cross-boundary direction correctness assesses the accuracy of transitions from a source cluster to a target cluster by examining the boundary cells, and requires ground truth annotations. We directly run the function unitvelo.evaluate() provided in UniTVelo to obtain the Cross-boundary direction correctness. In detail, the CBDir is calculated as follows:

      where θ controls over dispersion, with smaller values corresponding to higher noise levels. The final datasets consist of paired unspliced (U) and spliced (S) count matrices with realistic transcriptional stochasticity and branching gene regulatory dynamics. For each branch, cells were further divided into three developmental stages for downstream analysis.

      where C<sub>A</sub> denotes the set of cells in the target cluster A, and N(c) represents the neighboring cells of a given cell c v<sub>c</sub> and x<sub>c</sub> denote the low-dimensional velocity and state vectors of cell c, respectively, and x<sub>c’</sub> denotes the state vector of its neighboring cell.

      As shown in Figure S2, TSvelo consistently achieves the highest accuracy across all simulation settings, particularly in scenarios with complex branching structures, which pose significant challenges for baseline methods.

      (2) Related to the above: since a ground truth is missing, the real data analyses need to be interpreted with caution. I recommend avoiding strong statements, such as "successfully captures the correct gene dynamics", or "accurately infer", in favour of milder statements supported by the data, such as "... aligns with the biological processes described" (as in page 12), or "results are compatible with current biological knowledge", etc...

      We thank the reviewer for this helpful comment. We agree that analyses on real datasets should be interpreted with appropriate caution because definitive ground truth is typically unavailable. Following the reviewer’s suggestion, we have revised the wording throughout the manuscript to avoid overly strong claims. For example, statements such as “successfully captures the correct gene dynamics” and “accurately infer” have been replaced with more cautious descriptions such as “consistent with known biological processes”.

      (3) Many methods perform RNA velocity analyses. While there is a brief description, I think it'd be useful to have a schematic summary (e.g., via a Table) of the main conceptual, mathematical, and computational characteristics of each approach.

      We thank the reviewer for this insightful suggestion. We agree that a structured summary of existing RNA velocity methods would improve clarity and accessibility. We have added a new summary table (Table S1) that systematically compares representative RNA velocity approaches in the supplementary information.

      (4) Related to the above: I struggled to identify the main conceptual novelty of TSvelo, compared to existing approaches. I recommend explaining this aspect more extensively.

      We thank the reviewer for this insightful comment. We agree that the conceptual novelty of TSvelo can be more clearly articulated.

      In the revised manuscript, we have expanded the discussion at the beginning of the Results section to explicitly highlight the key distinctions between TSvelo and existing approaches. Specifically, we now clarify that most existing RNA velocity methods predominantly focus on splicing dynamics and typically operate in a gene-wise manner, without capturing coordinated dynamics across genes. In contrast, TSvelo models the full cascade of transcriptional regulation, transcription, and splicing within a unified framework, and estimates RNA velocity jointly across all genes, thereby capturing their coordinated dynamics at the system level.

      (5) A computational benchmark is missing; I'd appreciate seeing the runtime and memory cost of all methods in a couple of datasets.

      We thank the reviewer for this helpful suggestion regarding computational benchmarking. In the revised manuscript, we have added a systematic comparison of runtime and GPU memory usage across TSvelo and ba methods using simulated datasets of increasing scale (600, 1200, and 1800 cells) on our NVIDIA GeForce RTX 3090 device with 24 GB memory.

      Table S2 shows differences in computational efficiency and resource requirements among methods. Specifically, classical methods such as scVelo and Dynamo exhibit very fast runtimes (10–24 seconds) and do not rely on GPU acceleration, reflecting their relatively lightweight modeling strategies. In contrast, deep learning–based approaches, including UniTVelo, cellDancer, and TSvelo, have higher computational costs due to their increased model complexity.

      TSvelo exhibits a stable GPU memory footprint (~1.26 GB) across different dataset sizes, indicating that its memory usage is primarily determined by model architecture rather than the number of cells. This level of memory consumption is well within the capacity of modern GPUs and does not pose practical limitations. In terms of runtime, TSvelo scales approximately linearly with dataset size. The higher computational cost of TSvelo is mainly due to its EM-style optimization procedure, where each M-step also involves multiple optimization updates to infer gene regulatory effects in a global model. This design enables TSvelo to explicitly incorporate regulatory priors and jointly model gene interactions, which is not supported by these baseline methods.

      To further improve runtime efficiency, TSvelo allows flexible control of the number of EM iterations. As shown in Figure S16 and Table S3, we evaluated performance under different iteration settings on the simulation dataset. The early stopping strategy employed in the EM framework of TSvelo, which will stop modeling if the loss is not further reduced in the last 3 iterations. Results show that convergence is typically achieved within 3 iterations for this dataset, and increasing the maximum number of iterations beyond this does not further change the results. Notably, even a single iteration already yields competitive performance, likely benefiting from the strong initialization based on unspliced-to-spliced temporal delay.

      Overall, these results highlight a trade-off between computational efficiency and modeling expressiveness. While TSvelo is more computationally demanding than classical approaches, it provides a more flexible framework for incorporating regulatory information and capturing complex gene interactions, which we believe justifies the additional computational cost in scenarios requiring accurate dynamical inference.

      (6) I think BayVel (mentioned above) should be added to the list of competing methods (both in the text and in the benchmarks). The package can be found here: https://github.com/elenasabbioni/BayVel_pkgJulia.

      We thank the reviewer for suggesting BayVel and for providing the repository link. We carefully review the available resources, including both the BayVel_pkgJulia and the BayVel_notebooks, and we appreciate the authors’ efforts in making their code and data publicly available.

      We note that BayVel repositories primarily provide scripts and data for reproducing the figures and results reported in their manuscript. However, at present, the available resources do not yet provide a complete guideline or standardized pipeline for applying BayVel to new datasets. To ensure a fair and reproducible comparison, we therefore tend to use BayVel results officially provided by the authors. We are grateful that the BayVel results on the pancreas dataset is released at BayVel_notebooks page: https://github.com/elenasabbioni/BayVel_notebooks/tree/main/real%20data/Pancreas/moments/output.

      Based on these results, we conducted comparisons across all methods on the pancreas dataset, with quantitative evaluations shown in Author response image 55. In each plot, methods are ranked in descending order of their mean values. Numbers at the bottom indicate the sample size for each metric. Statistical significance is assessed using a one-sided Mann–Whitney U test, where *****, ***, **, and * denote p < 0.00001, 0.0001 ≤ p < 0.001, 0.001 ≤ p < 0.01, and 0.01 ≤ p < 0.05, respectively.

      BayVel has now been included in the Introduction, and corresponding comparisons have been added in the revised manuscript.

      Author response image 5.

      The quantitative comparison between TSvelo and baseline approaches on the pancreas dataset. In each plot, methods are ranked in descending order of their mean values. Numbers at the bottom indicate the sample size for each metric. Significance is determined using a one-sided Mann–Whitney U test. *****, ****,***, ** and * represent p < 0.00001, 0.00001 ≤ p < 0.0001, 0.0001 ≤ p < 0.001, 0.001 ≤ p < 0.01, and 0.01 ≤ p < 0.05, respectively.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Please carefully proofread the text. Some typos:

      (1) Line 110: differentia -> differential.

      (2) Line 280: ".," to be corrected.

      (3) Line 566: optimize -> optimizes.

      We thank the reviewer for carefully proofreading the manuscript and for pointing out these typographical errors. We have corrected the identified typos in the revised manuscript.

      Reviewer #3 (Recommendations for the authors):

      (1) Regarding Major Comment 1 in the Public Review, I contacted BayVel authors, who told me that they'll upload all their scripts here within a few days: https://github.com/elenasabbioni/BayVel_notebooks

      Thank you very much for reaching out to the BayVel authors. We sincerely appreciate the BayVel authors’ efforts to make their scripts and results publicly available through BayVel_notebooks. We believe this is a valuable contribution that will greatly benefit the community.

      We have followed the repository and have now included BayVel in the revised manuscript, with corresponding comparisons added to both the main text and the benchmarking results.

      (2) Page 9 mentions "consistency", "coherence", and "correctness". Instead of these qualitative (and potentially subjective) evaluations, I'd appreciate using quantitative metrics or visual descriptions when differences are visually clear.

      We thank the reviewer for this insightful comment. The terms “velocity consistency,” “in-cluster coherence,” and “cross-boundary correctness” used in our manuscript are not intended as subjective descriptions. They correspond to commonly used evaluation criteria in this field and have been adopted as quantitative metrics in previous studies, such as VeloAE[1] and UniTVelo[2]. We have incorporated the following updated definition into the Methods section.

      (1) Velocity consistency (VCon). We used the scvelo.velocity_confidence() function from scVelo to evaluate velocity consistency, interpreting the results as a measure of how consistent velocities are within neighboring cells. Velocity consistency is especially suitable for evaluating the RNA velocity modeling on single lineage. For each cell , the velocity consistency is calculated as follows:

      Where N (c) represents the neighboring cells of a given cell c v<sub>c</sub> v<sub>c’</sub> denote the low-dimensional velocity vectors of cell cand its neighboring cell c’.

      (2) Cross-boundary direction correctness (CBDir). Cross-boundary direction correctness assesses the accuracy of transitions from a source cluster to a target cluster by examining the boundary cells, and requires ground truth annotations. We directly run the function unitvelo.evaluate() provided in UniTVelo to obtain the Cross-boundary direction correctness. In detail, the CBDir is calculated as follows:

      Where C<sub>A</sub> denotes the set of cells in the target cluster A, and represents the neighboring cells of a given cell c v<sub>c</sub> v<sub>c’</sub> denote the low-dimensional velocity and state vectors of cell cand its neighboring cell c’.

      (3) Within-cluster velocity coherence (ICCoh). Within-cluster velocity coherence measures the coherence of velocities within a single cluster using a cosine similarity score between cell velocities. We applied the function unitvelo.evaluate() provided by UniTVelo to directly compute the within-cluster velocity coherence. Using the same notation as defined above, the CBDir is calculated as follows:

      (1) Qiao, C. & Huang, Y. Representation learning of RNA velocity reveals robust cell transitions. Proceedings of the National Academy of Sciences 118, e2105859118 (2021).

      (2) Gao, M., Qiao, C. & Huang, Y. UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference. Nature Communications 13, 6586 (2022).

      (3) At page 3, some objects are not defined after formula (3):

      ReLU finction, and w_gi

      Additionally, parenthesis of ReLU function should be bigger.

      We thank the reviewer for pointing this out. In the revised manuscript, we have explicitly defined the ReLU activation function and clarified that w<sub>gi</sub> represents the regulatory weight of TF i on the target gene g. In addition, we have adjusted the formatting of Eq. (3) by enlarging the parentheses in the ReLU function to improve readability.

    1. Author response:

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

      General recommendations (from the Reviewing Editor):

      The reviewers discussed the revision at length, and all were appreciative of the revisions to the paper. Nonetheless, they agreed that the evidence against alternative hypotheses was not yet decisive, and it may not be possible to provide the evidence needed given the difficulty of acquiring this data. Thus they feel that a more nuanced interpretation of the data and tempering of the conclusions is necessary. These points are described in more detail in the reviewer-specific comments in the Public reviews.

      We thank the editor and the reviewers for their constructive discussion. In this revision, we have adopted these recommendations: we have tempered our conclusions and removed binary framing, taking into consideration that other alternative explanations might exist. We have also expanded the Discussion to consider additional potential mechanisms and added corresponding limitations. We also changed the paper title to avoid strong inference; the new title is “Evidence that humans underestimate body mass in microgravity: kinematic signatures in reaching movements during spaceflight”.

      Public Reviews:

      Reviewer #1 (Public review):

      The authors have conducted substantial additional analyses to address the reviewers' comments. However, several key points still require attention. I was unable to see the correspondence between the model predictions and the data in the added quantitative analysis. In the rebuttal letter, the delta peak speed time displays values in the range of [20, 30] ms, whereas the data were negative for the 45{degree sign} direction. Should the reader directly compare panel B of Figure 6 with Figure 1E? The correspondence between the model and the data should be made more apparent in Figure 6. Furthermore, the rebuttal states that a quantitative prediction was not expected, yet it subsequently argues that there was a quantitative match. Overall, this response remains unclear.

      We thank the reviewer raising the question about Figure 6B. We would like to clarify that the phrase "quantitative match" in the summary of our previous rebuttal letter was a wording error; in fact, the subsequent detailed responses consistently and correctly described the comparison as qualitative. We apologize for the confusion this may have caused, and address this point below.

      First, we have revised the manuscript to clarify this point. We have added the following statement: "We note that these correlations evaluate the directional trend rather than the absolute magnitude of the effects; a precise quantitative match is not expected given the simplifications of the two-joint arm model." in the main text.

      Second, we have replaced Figure 6 with a revised version that presents model-predicted Δ values and experimentally observed Δ values side by side, allowing for a more intuitive visual comparison. As shown in the updated figure, the directional trends are broadly consistent amplitude changes and timing shifts are rank-ordered by movement direction in both model and data while the absolute magnitudes do not precisely match. We believe this layout makes the intended comparison more transparent.

      As discussed in our previous response, as noted above, a precise quantitative match is not expected given our model's simplifications, and this level of qualitative comparison is consistent with established practice in similar modeling studies (e.g., Gaveau et al., 2016).

      Regarding the negative Δ peak speed time at 45°: as shown in our statistical analyses (Figure 4A, Figure 5F), there was no significant timing change at 45°. The negative value reflects a small, non-significant mean difference. The key pattern that timing advance increases for directions associated with higher effective inertia holds for the 90° and 135° directions, which is the directional trend our analysis was designed to capture.

      A follow-up question concerns the argument about strategic slowing. The authors argue that this explanation can be rejected because the timing of peak speed should be delayed, contrary to the data. However, there appears to be a sign difference between the model and the data for the 45{degree sign} direction, which means that it was delayed in this case. Did I understand correctly? In that regard, I believe that the hypothesis of strategic slowing cannot yet be firmly rejected and the discussion should more clearly indicate that this argument is based on some, but not all, directions.

      I agree with the authors on the importance of the mass underestimation hypothesis, and I am not particularly committed to the strategic slowing explanation, but I do not see a strong argument against it. If the conclusion relies on the sign of the delta peak speed, then the authors' claims are not valid across all directions, and greater caution in the interpretation and discussion is warranted. Regarding the peak acceleration time, I would be hesitant to draw firm conclusions based on differences smaller than 10 ms (Figures R3 and 6D).

      The authors state in the rebuttal that the two hypotheses are competing. This is not accurate, as they are not mutually exclusive and could even vary as a function of movement direction. The abstract also claims that the data "refutes" strategic slowing, which I believe is too strong. The main issue is that, based on the authors' revised manuscript, the lack of quantitative agreement between the model and the data for the mass underestimation hypothesis is considered acceptable because a precise quantitative match is not expected, and the predictions overall agree for some (though not all) directions and phases (excluding post-in). That is reasonable, but by the same logic, the small differences between the model prediction and the strategic slowing hypothesis should not be taken as firm evidence against it, as the authors seem to suggest. In practice, I recommend a more transparent and cautious interpretation to avoid giving readers the false impression that the evidence is decisive. The mass underestimation hypothesis is clearly supported, but the remaining aspects are less clear, and several features of the data remain unexplained.

      We thank the reviewer for this critical assessment. We acknowledge that our previous framing was too binary, and we agree that strategic slowing and mass underestimation are not mutually exclusive. We would like to clarify our view: we did not find evidence supporting strategic slowing (e.g., slower reaction times, symmetric velocity/acceleration peaks), whereas we did find evidence supporting mass underestimation (asymmetric peaks, unchanged reaction times, more sub movements). This is not a case of rejecting one hypothesis to affirm the other; our data simply do not support one while providing positive evidence for the other. We do not rule out the possibility that both mechanisms could operate together, though we note that our data did not reveal evidence supporting strategic slowing in the current reaching task.

      We also agree that the lack of significant timing changes at 45° limits the scope of our argument against strategic slowing in that direction. However, the null result at 45° likewise cannot serve as positive evidence for strategic slowing either. As discussed in our previous revision and in Discussion, this null effect may arise because 45° reaches are predominantly single-joint (evidenced by curvature patterns characteristic), making them less suitable for modeling with a simplified two-link arm model than the 90° and 135° directions.

      In line with these considerations, we have made the following revisions to the manuscript:

      (1) We have removed binary framing throughout, replacing claims of mutual exclusivity or outright rejection of strategic slowing with more measured language. For example, "refutes" in the abstract has been changed to "These findings provide support for the body mass underestimation hypothesis while being inconsistent with the strategic slowing hypothesis." The two hypotheses are no longer presented as mutually exclusive, and strategic slowing is now characterized as insufficient to fully explain the direction-dependent pattern, rather than ruled out entirely.

      (2) We have revised the conclusion. The concluding paragraph no longer presents an either-or outcome. We describe the direction-dependent under-actuation pattern, note that it strongly supports mass underestimation while not being readily explained by a uniform strategic adjustment, and acknowledge that other factors may also contribute. A new limitation paragraph discusses the simplified nature of our model and acknowledges that other neurophysiological and biomechanical factors cannot be excluded.

      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 adds confidence to the proposed conclusions.

      Compared to the previous version, the authors have thoroughly addressed my concerns. The model is now clear and well-articulated, and alternative hypotheses have been ruled out convincingly. The paper is improved and suitable for publication in my opinion, making a significant contribution to the field.

      Strengths:

      Comprehensive analysis of a unique data set of reaching movement in microgravity

      Use of a sensible and well-thought experimental approach

      State-of-the-art analyses of main kinematic parameter

      Computational model simulations of arm reaching to test alternative hypotheses and support the mass underestimation one

      This work has no major weakness as it stands, and the discussion provides a fair evaluation of the findings and conclusions.

      We thank the reviewer for the supportive feedback, and we are grateful for the earlier comments that helped us improve the manuscript.

      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 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:

      I nevertheless 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.

      To strengthen the conclusions, I feel that the following points would need to be addressed:

      We thank the reviewer for the insightful critique and constructive suggestions. Following the reviewer's advice, we have re-framed our Introduction and Discussion to present mass underestimation as a plausible mechanism identified by our simplified model, while explicitly acknowledging other potential factors. Below we address each point in detail.

      (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 treating the arm as a second-order low pass filter (Eq. 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 to the consequences of the initial command. This would still be an argument for un-adapted 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.

      While the authors attempt to differentiate their study from previous studies where limb neuromechanical impedance was shown to be modified in weightlessness by emphasizing that in the current study the movements were rapid and the initial movement is "feedforward". But this incorrectly implies that the limb's mechanical response to the motor command is determined only by active feedback mechanisms. In fact:

      (a) All commands to the muscle pass through the motor neurons. These neurons receive descending activations related not only to the volitional movement, but also to the dynamic state of the body and the influence of other sensory inputs, including the vestibular system. A decrease in descending influences from the vestibular organs will lower the background sensitivity to all other neural influences on the motor neuron. Thus, the motor neuron may be less sensitive to the other volitional and reflexive synaptic inputs that it may receive.

      (b) Muscle tone plays a significant role in determining the force and the time course of the muscle contraction. In a weightless environment, where tonic muscle activity is likely to be reduced, there is the distinct possibility that muscles will react more slowly and with lower amplitude to an otherwise equivalent descending motor command, particularly in the initial moments before spinal reflexes come into play. These, and other neuronal mechanisms could lead to the "under-actuation" effect observed in the current study, without necessarily being reflective of an underestimation of mass per se.

      The reviewer raises an important point that the observed underactuation may not necessarily reflect mass underestimation per se. It could also arise from changes in the time constants of the control system, tonic muscle activation levels, vestibular descending inputs, or altered spinal reflex gains. We agree that our simplified model does not capture these neuromuscular factors, and we have made several revisions to address this concern.

      In the Discussion (paragraph 4), we have added a new substantive section discussing how reduced tonic muscle activity, diminished vestibular inputs to motor neurons, and altered muscle activation dynamics (Fisk et al., 1993) may contribute to the observed under-actuation independently of mass misestimation. We argue that while these factors likely affect motor output, they would be expected to produce a relatively uniform effect across movement directions, as tonic muscle activation and vestibular descending inputs are not specific to a particular reaching direction. In contrast, the direction-dependent pattern of our results with greater effects for directions involving higher effective mass is more naturally explained by a misrepresentation of inertial properties than by a uniform change in neuromuscular excitability. Nevertheless, we explicitly acknowledge that these mechanisms may act in concert with mass underestimation, and that our current data cannot fully disentangle them.

      Additionally, the paragraph discussing proprioceptive mechanisms (paragraph 6 of Discussion) now opens with the conditional framing "If mass underestimation contributes to the observed underactuation," and closes by noting that the same proprioceptive degradation could affect motor output through other pathways such as reducing tonic muscle activation or altering spinal reflex gains independent of any explicit misrepresentation of body mass.

      We have also added a new limitation (the fourth in the Limitations section) explicitly acknowledging that our model treats muscles as ideal torque generators and does not capture potential changes in muscle activation dynamics, damping, or reflex gains that may occur in microgravity. Future studies combining detailed musculoskeletal modeling with direct measurements of muscle activation, joint impedance, and trunk kinematics would be needed to distinguish between mass underestimation and other sources of underactuation.

      That said, the assumption of relatively preserved muscle properties is partly supported by the available evidence. A systematic review of simulated microgravity studies found that upper limb maximal voluntary contraction remained mostly unchanged for up to 45 days of unloading, and that upper limb muscles declined substantially more slowly than lower limb and trunk muscles (Winnard et al., 2019). A more recent review similarly reported that upper limb muscle outcomes are less affected by microgravity exposure (Bosutti et al., 2025). This is also consistent with our own unpublished observations in Chinese astronauts, which did not indicate an obvious decline in upper limb force output. While these findings do not rule out subtler changes in muscle tone or activation dynamics, they suggest that gross alterations in upper limb neuromuscular capacity are unlikely to be the primary driver of the underactuation we observed.

      Refs.

      Winnard, A., Scott, J., Waters, N., Vance, M., & Caplan, N. (2019). Effect of time on human muscle outcomes during simulated microgravity exposure without countermeasures—systematic review. Frontiers in physiology, 10, 1046.

      Bosutti, A., Ganse, B., Maffiuletti, N. A., Wüst, R. C., Strijkers, G. J., Sanderson, A., & Degens, H. (2025). Microgravity‐induced changes in skeletal muscle and possible countermeasures: What we can learn from bed rest and human space studies. Experimental Physiology.

      (2) The subject's body in weightless is much more sensitive to reaction forces in interactions with the environment in the absence of the anchoring effect of gravity pushing the body into the floor and in the absence of anticipatory postural adjustments that typically accompany upper-limb motions in Earth gravity in order to maintain an upright posture. The authors dismiss this possibility because the taikonauts were asked to stabilize their bodies with the contralateral hand. But the authors present no evidence that this was sufficient to maintain the shoulder and trunk at a strictly constant position, as is supposed by the simplified biomechanical model used in their optimal control framework. Indeed, a small backward motion of the shoulder would result in a smaller acceleration of the fingertip and a smaller extent of the initial ballistic motion of the hand with respect to the measurement device (the tablet), consistent with the observations reported in the study. Note that stability of the base might explain why 45º movements were apparently less affected in weightlessness, according to many of the reported analyses, including those related to corrective movements (Fig. 5 B, C, F; Fig. 6D), than the other two directions. If the trunk is being stabilized by the left arm, the same reaction forces on the trunk due to the acceleration of the hand will result in less effective torque on the trunk, given that the reaction forces act with a much smaller moment arm with respect to the left shoulder (the hand movement axis passes approximately through the left shoulder for the 45º target) compared to either the forward or rightward motions of the hand.

      The reviewer raises an important point about the potential influence of reaction forces on trunk and shoulder stability in microgravity. We have revised the relevant Discussion paragraph to address this concern more thoroughly.

      We would like to clarify that, in addition to stabilizing the body with the left hand grasping a fixed bar, the taikonauts’ feet were also constrained with foot straps, providing multi-point stabilization. Furthermore, the reviewer's trunk displacement hypothesis predicts that the 45° direction should be systematically less affected across all kinematic measures. However, while 45° did not show significant changes in the timing of kinematics peaks, it did show significant changes in movement duration, peak acceleration, and peak speed comparable to the other directions. This dissociation is difficult to reconcile with a uniform trunk displacement artifact, but is consistent with a direction-dependent inertial effect.

      We acknowledge that we did not directly measure trunk or shoulder kinematics, highlight that we did our best to provide multi-point stabilization in our setup, and we have added this as a limitation in the revised Discussion.

      (3) The above is exacerbated by potential changes in the frictional forces between the fingertip and the tablet. 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 can be expected to be quite different than on the ground. While these forces may be low on Earth, the fact is that we do not know what forces the taikonauts used on orbit. 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. . Indeed, given the increased instability of the body and the increased uncertainty of movement direction of the hand, taikonauts may have been induced to apply greater forces against the tablet in order to maintain contact in weightlessness, which would in turn slow the motion of the finger on the table and increase the reaction forces acting on the trunk. 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

      We agree that in microgravity, taikonauts must actively press on the screen to maintain contact, potentially altering normal forces and thus friction compared to ground conditions. We have acknowledged this point in the revised Discussion. However, we note several reasons why friction is unlikely to be the dominant factor. First, the tablet uses a capacitive touchscreen, which registers touch through changes in electrical capacitance and does not require substantial normal force to maintain contact. Second, typical tangential friction forces during touchscreen interaction range from 0.1 to 0.5 N (Ayyildiz et al., 2018), which are small compared to the 10–15 N required to accelerate the arm during reaching. Third, touchscreen performance has been shown to be largely unaffected during long-duration spaceflight (Holden et al., 2022). Lastly but importantly, the friction hypothesis does not readily account for the direction-specific pattern of effects we observed. While we cannot exclude a contribution of altered friction, particularly in interaction with the direction-dependent effective mass, its magnitude makes it unlikely to account for the observed kinematic changes.

      Ref:

      Ayyildiz, M., Scaraggi, M., Sirin, O., Basdogan, C., & Persson, B. N. J. (2018). Contact mechanics between the human finger and a touchscreen under electroadhesion. Proceedings of the National Academy of Sciences of the United States of America, 115(50), 12668–12673.

      Holden, K., Greene, M., Vincent Cross, E., Sandor, A., Thompson, S., Feiveson, A., & Munson, B. (2023). Effects of long-duration microgravity and gravitational transitions on fine motor skills. Human Factors, 65(6), 1046-1058.

      I feel that the authors have done an admirable job of exploring the how to explain the modifications to movement kinematics that they observed on orbit within the constraints of the optimal control theory applied to a simplified model of the human motor system. While I fully appreciate the value of such models to provide insights into question of human sensorimotor behaviour, to draw firm conclusions on what humans are actually experiencing based only on manipulations of the computational model, without testing the model's implicit assumptions and without considering the actual neurophysiological and biomechanical mechanisms, can be misleading. One way to do this could be to examine these questions through extensions to the model used in the simulations (changing activation dynamics of the torque generators, allowing for potential motion backward motion of the shoulder and trunk, etc.). A better solution would be to emulate the physiological and biomechanical conditions on Earth (supporting the arm against gravity to reduce muscle tone, placing the subject on a moveable base that requires that the body be stabilized with the other hand) in order to distinguish the hypothesis of an underestimation of mass vs. other potential sources of under-actuation and other potential effects of weightlessness on the body.

      In sum, my opinion is that the authors are relying too much on a theoretical model as a ground truth and thus overstate their conclusions. But to provide a convincing argument that humans truly underestimate mass in weightlessness, they should consider more judiciously the neurophysiology and biomechanics that fall outside the purview of the simplified model that they have chosen. If a more thorough assessment of this nature is not possible, then I would argue that a more measured conclusion of the paper should be 1) that the authors observed modifications to movement kinematics in weightlessness consistent with an under-actuation for the intended motion, 2) that a simplified model of human physiology and biomechanics that incorporates principles of optimal control suggest that the source of this under-actuation might be an underestimation of mass in the computation of an appropriate feedforward motor command, and 3) that other potential neurophysiological or biomechanical effects cannot be excluded due to limitations of the computational model.

      We appreciate the reviewer's thoughtful assessment. We fully agree that a simplified computational model should not be treated as ground truth, and that the neurophysiology and biomechanics beyond the computational model must be carefully considered.

      As detailed in our responses above, we have substantially revised the Discussion to address each of these concerns—including new discussions of neuromuscular factors, more balanced treatment of trunk stability and friction, conditional framing of the mass underestimation interpretation, and a new limitation on model simplifications. The conclusion has been restructured following the reviewer's recommended framework.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      If possible and allowed, the authors are strongly encouraged to consider sharing this unique dataset. Making the data publicly available alongside the paper could foster future studies and further accelerate research in this area.

      We sincerely thank the reviewer for this suggestion. The ground control data and all analysis code will be made publicly available alongside the Version of Record.

      However, unfortunately, the raw in-flight data from the taikonaut cohort cannot be made publicly available due to confidentiality regulations of China's manned space program; access for scientific research requires approval from the China Astronaut Research and Training Center and can be requested through the corresponding author.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The objective of this study was to infer the population dynamics (rates of differentiation, division and loss) and lineage relationships of NK cell subsets during an acute immune response and under homeostatic conditions.

      Strengths:

      A rich dataset and a detailed analysis of a particular class of stochastic models.

      Weaknesses: (relating to initial submission)

      The stochastic models used are quite simple; each population is considered homogeneous with first-order rates of division, death, and differentiation. In Markov process models such as these there is no dependence of cellular behavior on its history of divisions. In recent years models of clonal expansion and diversification, in the settings of T and B cells, have progressed beyond this picture. So I was a little surprised that there was no mention of the literature exploring the role of replicative history in differentiation (e.g. Bresser Nat Imm 2022), nor of the notion of family 'division destinies' (either in division number, or the time spent proliferating, as described by the Cyton and Cyton2 models developed by Hodgkin and collaborators; e.g. Heinzel Nat Imm 2017). The emerging view is that variability in clone (family) size arises may arise predominantly from the signals delivered at activation, which dictate each precursor's subsequent degree of expansion, rather than from the fluctuations deriving from division and death modeled as Poisson processes.

      As you pointed out, the Gerlach and Buchholz Science papers showed evidence for highly skewed distributions of family sizes, and correlations between family size and phenotypic composition. Is it possible that your observed correlations could arise if the propensity for immature CD27+ cells to differentiate into mature CD27- cells increases with division number? The relative frequency of the two populations would then also be impacted by differences in the division rates of each subset - one would need to explore this. But depending on the dependence of the differentiation rate on division number, there may be parameter regimes (and timepoints) at which the more differentiated cells can predominate within large clones even if they divide more slowly than their immature precursors. One might not then be able to rule out the two-state model. I would like to see a discussion or rebuttal of these issues.

      Comments on revisions:

      (1) The authors have put in a lot of effort to address the reviews and have explored alternative models carefully.

      We appreciate the reviewers’ comments.

      (2) In the sections relating to homeostasis and the endogenous response, as far as I can tell you are estimating net growth rates (the k parameters) throughout - this is to be expected if you're working with just cell numbers and no information relating to proliferation. In these sections there are many places where you refer to proliferation rates and death rates when I think you just mean net positive or net negative growth rates. It's important to be precise about this even if the language can get a bit repetitive. (These net rates of growth or loss relate to clonal rather than cellular dynamics, which may be worth explaining). Later, you do use data relating to dead cells, which in principle can be used to get independent measures of death rates, but these data were not used in the fitting.

      We have modified the main text to address the comment.

      (3) There is so much evidence that T and B cell differentiation are often contingent on division that it would be very reasonable to consider it as a possibility for NK cells too. (Differentiation could be asymmetric, as you explored, or simply symmetric with some probability per division). These processes can be cast into simple ODE models but no longer allow you to aggregate division and death rates - so for parameter estimation you need to add measures of proliferation (Ki67 or similar) or death. This may be worth some discussion?

      We have modified the main text (lines 242-245) to address the comment.

      Reviewer #2 (Public review):

      Summary:

      Wethington et al. investigated the mechanistic principles underlying antigen-specific proliferation and memory formation in mouse natural killer (NK) cells following exposure to mouse cytomegalovirus (MCMV), a phenomenon predominantly associated with CD8+ T cells. Using a stochastic modeling approach, the authors aimed to develop a quantitative model of NK cell clonal dynamics during MCMV infection. Starting from a single immature Ly49+CD27+ NK cell, a two-state linear model (with a death variant) explained the negative correlation between clone size at 8 dpi and the CD27+ fraction, but failed to reproduce the first and second moments of CD27+ and CD27− NK cell populations at 8 dpi. To address this limitation, the authors added an intermediate maturation state, yielding a three-stage model (CD27+Ly6C− → CD27−Ly6C− → CD27−Ly6C+) that fits the first and second moments under two constraints: CD27+ NK cells proliferate faster than CD27− NK cells, and clone size is negatively correlated with the CD27+ fraction (upper bound of −0.2). The model predicts high proliferation in the intermediate state and high death in mature CD27−Ly6C+ cells, and it was validated using Adams et al. (2021) NK reporter mice tracking CD27+/− populations after tamoxifen, allowing discrimination between bone marrow-derived and pre-existing peripheral NK cells. To test the prediction that mature CD27− NK cells have a higher death rate, the authors measured Ly49H+ NK cell viability in the mouse spleen at different time points post-MCMV infection. Data confirmed lower viability of mature (CD27−) than immature (CD27+) cells during days 4-8 post-infection, and a model variant supported that higher CD27− death increases their proportion in the dead cell compartment. Altogether, the authors propose a three-stage quantitative model of antigen-specific expansion and maturation of naïve Ly49H+ NK cells with the trajectory CD27+Ly6C− (immature) → CD27−Ly6C− (mature I) → CD27−Ly6C+ (mature II), highlighting high proliferation in the mature I state and increased death in the mature II state.

      Strengths:

      Models explaining correlations and first and second moments, supported by analytical investigations, stochastic simulations, and model selection, identify key processes in antigen-specific NK expansion and maturation. The work distinguishes expansion, contraction, and memory in NK cells from CD8+ T cells and informs NK therapy development.

      Weaknesses (relating to initial submission):

      The conclusions of this paper are largely supported by the available data. However, a comparative analysis with more recent works in the field would be desirable. Clarifications:

      (1) Initial Conditions and Grassmann Data: The Grassmann data is used solely as a constraint, while the simulated values of CD27+/CD27− cells could have been directly fitted to the Grassmann data, which assumes a 1:1 ratio of CD27+/CD27− at t = 0. This would allow an alternative initial condition rather than starting from a single CD27+ cell.

      (2) Correlation Coefficients in the Three-State Model: Although the parameter scan of the three-stage model (Figure 2) demonstrates the potential for negative correlations between colony size and the fraction of CD27+ cells, the calculated correlation coefficients using the fitted parameter values are not shown. Including these would validate that the fitted parameters lie in the negative-correlation regime.

      (3) Viability Dynamics and Adaptive Response: The authors measured the time evolution of CD27+/− dynamics and viability over 30 days post-infection (Figure 4). It would be valuable to test whether the three-state model can reproduce the adaptive response of CD27− cells to MCMV infection, particularly the observed drop in CD27− viability at 5 dpi and its rebound at 8 dpi. Demonstrating this would test whether the model can simultaneously explain viability dynamics and moment dynamics, and would enable sensitivity analysis of CD27− viability with respect to model parameters.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor points:

      (1) line 175 - Here I think you have only ruled out the two state model with no death, and not the two state model in general?

      Edited the sentence to address the comment.

      (2) Figures 2 and 5 - the phenotypes (CD27+ Ly6C-, etc.) should be clearly labeled above each cell type. Fig 1 could be improved in the same way.

      Done.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Kashiwagi et al. undertook a population analysis of dendritic spine nanostructure applied to the objective grouping of 8 mouse models of neuropsychiatric disorders. They report that spine morphology in cultured hippocampal neurons shows a higher similarity among schizophrenia mouse models (compared with autism spectrum disorder (ASD) mouse models), and identify an effect of Ecrg4 (encoding small secretory peptides) on spine dynamics and shape in these models.

      Strengths:

      The study developed a method for objectively comparing spine properties in primary hippocampal neuron cultures from 8 mouse models of psychiatric disorders at the population level using high-resolution structured illumination microscopy (SIM) imaging. This novel technique identified two distinct groups of mouse models according to the population-level spine properties: those with ASD-related gene mutations and those with schizophreniarelated gene mutations. Functional studies, including gene knockdown and overexpression experiments, identified an effect of Ecrg4 on the spine phenotype of the schizophrenia model mice.

      We thank the reviewer for finding our strategy novel and useful for identifying molecules associated with the spine phenotype in schizophrenia-related mouse models.

      Weaknesses:

      The main weakness is that the study is wholly in vitro, using cultured hippocampal neurons. The authors present this as an advantage, however, arguing that spine morphology as measured in a reduced culture system can demonstrate direct effects of gene mutations on neuronal phenotypes in the absence of indirect influences from non-neuronal cells or specific environments.

      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-related 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.

      We modified our text to have a balanced discussion on both advantages and disadvantages of the in vitro culture system in the study of mental disorder mouse models, as follows:

      "Finally, while the spine phenotype identified in the human postmortem brain undoubtedly resulted from complex interactions among genetic background, environmental influences, and regulation by non-neuronal cells, data from pure neuronal cultures are more likely to reflect the direct effects of schizophrenia-related gene mutations on synaptic functions. This property may be advantageous for identifying synaptic molecules that regulate synapse phenotypes in schizophrenia-related mouse models. However, the phenotype observed in the culture system requires confirmation using in vivo experiments of mouse models or human tissue samples. Efficient in vitro screening combined with reliable in vivo evaluation of synapses will facilitate translational research on mental disorders."

      Another weakness is that CaMKIIαK42R/K42R mutant mice are presented as a schizophrenia model, the authors justifying this by saying that "CaMKII-related signaling pathway disruption has been implicated in the working memory deficits found in schizophrenia patients". Since mutations in CAMK2A cause autosomal dominant intellectual developmental disorder-53 (OMIM 617798) and autosomal recessive intellectual developmental disorder-63 (OMIM 618095), and mice carrying the CAMK2A E183V mutation exhibit ASD-related synaptic and behavioral phenotypes (PMID: 28130356), I think it's stretching credibility to refer to the CaMKIIαK42R/K42R mice 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).

      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

      We fully agree with the reviewer that different CAMK2A mutations likely cause distinct phenotypes observed in the broad spectrum of mental disorders. In the revised manuscript, we include a discussion of the relevant literature to categorize this mouse model appropriately.

      "CaMKII-related signaling pathway disruption has been implicated in the working memory deficits found in schizophrenia patients [45,46]. CAMK2A mutations in humans are linked to multiple mental disorders, including developmental disorders, ASD, and schizophrenia [47]. The K42R mutation of CAMK2A does not correspond to any known human genetic variant, but the CAMK2A R8H mutation is linked to schizophrenia [48]. Both R8H and K42R mutations in the N-terminal domain of CaMKIIα eliminate kinase activity; these mutations may have a similar impact on human mental disorders."

      Although the manuscript is largely well written, there are some instances of ambiguous/unspecific language. This extends to the title (Decoding Spine Nanostructure in Mental Disorders Reveals a Schizophrenia-1 Linked Role for Ecrg4), which gives no indication that the work was in vitro on cultured neurons derived from mouse models.

      We appreciate the reviewer for pointing out the lack of information about the experimental system in the title of this manuscript. According to the suggestion of the reviewer, we modified the title as "Decoding spine nanostructure in cultured neurons derived from mouse models of mental disorder reveals a schizophrenia-linked role for Ecrg4".

      Reviewer #2 (Public review):

      Okabe and colleagues build on a super-resolution-based technique that they have previously developed in cultured hippocampal neurons, improving the pipeline and using it to analyze spine nanostructure differences across 8 different mouse lines with mutations in autism or schizophrenia (Sz) risk genes/pathways. It is a worthy goal to try to use multiple models to examine potential convergent (or not) phenotypes, and the authors have made a good selection of models. They identify some key differences between the autism versus the Sz risk gene models, primarily that dendritic spines are smaller in Sz models and (mostly) larger in autism risk gene models. They then focus on three models (2 Sz - 22q11.2 deletion, Setd1a; 1 ASD - Nlgn3) for time-lapse imaging of spine dynamics, and together with computational modelling provide a mechanistic rationale for the smaller spines in Sz risk models. Bulk RNA sequencing of all 8 model cultures identifies several differentially expressed genes, which they go on to test in cultures, finding that ecgr4 is upregulated in several Sz models and its misexpression recapitulates spine dynamics changes seen in the Sz mutants, while knockdown rescues spine dynamics changes in the Sz mutants. Overall, these have the potential to be very interesting findings and useful for the field. However, I do have a number of major concerns.

      We thank the reviewer for evaluating our findings as potentially very interesting and useful.

      (1) The main finding of spine nanostructure changes is done by carrying out a PCA on various structural parameters, creating spine density plots across PC1 and PC2, and then subtracting the WT density plot from the mutant. Then, spines in the areas with obvious differences only are analyzed, from which they derive the finding that, for example, spine sizes are smaller. However, this seems a circular approach. It is like first identifying where there might be a difference in the data, then only analyzing that part of the data. I welcome input from a statistician, but to me, this is at best unconventional and potentially misleading. I assume the overall means are not different (although this should be included), but could they look at the distribution of sizes and see if these are shifted?

      We appreciate the reviewer's concern regarding our analysis of spine population data. The intention of pre-selecting the areas showing differences between wild-type and mutant was to make a direct comparison between two subareas (one is enriched with wild-type spines and the other is enriched with mutant spines) and clarify that the spines of schizophreniarelated mouse models were smaller than wild-type spines. Conventional methods of comparing the total spine population using simple size parameters are not useful for this purpose, as shown in Supplementary Figure 2.

      To clarify the reviewer's concern, we revised the analysis of the spine population data for both Figure 3 and Figure 8.

      Figure 3: We first divided the feature space projected onto PC1 and PC2 into four areas with distinct structural properties: (1) small and short, (2) small and long, (3) large and short, and (4) large and long. Next, we calculated the normalized spine counts in the four areas for both wild-type and mutant spines and obtained the relative ratio (mutant/wild-type) for each area. As we performed three independent SIM imaging experiments (in one, we imaged both wild type and mutant culture dishes prepared from the same pregnant mouse), there are three independent datasets from 8 mouse models.

      We found that the spine ratio (mutant/wild-type) only in area 2 (small and long spines) differed significantly between genotypes. This result is shown in Fig. 3 and explained in the text. The spine ratios in areas 1 and 3 did not show a clear relationship to the genotypes, while the ratio in area 4 showed the opposite trend to that in area 2. The opposite trend between areas 2 and 4 indicates enrichment of both small and long spines in schizophrenia-related mouse models, consistent with our previous analysis.

      Figure 8: In this analysis, we aimed to evaluate the rescue effect of Ecrg4 shRNA relative to that of control shRNA. If Ecrg4 shRNA is effective, the spine population enriched in the control shRNA condition should be reduced in the Ecrg4 shRNA condition. To confirm this point in the revised manuscript, we first defined areas in the projected PC1-PC2 plane showing either enrichment or depletion of spines in the control shRNA condition (spine numbers increasing or decreasing by more than 3 × SD). We next measured the difference in spine numbers between the control and Ecrg4 shRNA conditions in either enriched or depleted areas. The expectation is that Ecrg4 shRNA treatment reduces the extent of both enrichment and depletion. The effect was significant in both the 22qdel and Setd1a mouse models, as indicated by permutation tests. This analysis was explained in the revised manuscript.

      (2) Despite extracting 64 parameters describing spine structure, only 5 of these seemed to be used for the PCA. It should be possible to use all parameters and show the same results. More information on PC1 and PC2 would be helpful, given that the rest of the paper is based on these - what features are they related to?

      We thank the reviewer for the advice on providing the rationale for parameter selection in PCA. We divided spines into 160-nm segments along their long axis, and the spine segments were used to calculate the 64 parameters, which include volume of each spine segment (20 segments), convex hull volume of each spine segment (20 segments), and convex hull ratio of each spine segment (20 segments). As most spines are shorter than 0.16 × 20 =3.2 μm, these segment-related parameters contain a large fraction of zero values, which affect the proper calculation of principal components. Therefore, we selected two parameters that reflect the principal structural features (length and volume), together with three other parameters that were mutually independent and also independent from the first two parameters (pairwise correlation coefficients < 0.3). These selection criteria were described in the original manuscript. We also confirmed that PCA using all 64 parameters yields a cross correlation map similar to that shown in Fig. 2B.

      Author response image 1.

      We provided additional information in the Materials and Methods section of the revised manuscript.

      As described previously, the pattern of four areas with distinct spine structures (1. small and short, 2. small and long, 3. large and short, 4. large and long) supports the idea that the PC1PC2 plane reflects the relationship between spine volume and length (Fig. 3A and B).

      These specific features could then be analyzed in the full dataset, without doing the cherry picking above.

      We provided the dataset for the relative enrichment of spine counts across four areas of the PC1-PC2 plane in Fig. 3A and B. This analysis provides a comprehensive view of spine population properties related to spine volume and length, without relying on a pre-set region of interest.

      It would also be helpful to demonstrate whether PC1 and 2 differ across groups - for example, the authors could break their WT data into 2 subsets and repeat the analysis.

      We noticed differences in the pattern of spine distribution across the PC1-PC2 planes in each experiment. The subtraction of the distributional data between wild-type and mutant samples effectively cancels out such differences. In general, the difference between two wild-type samples is smaller than that between wild-type and mutant samples, as shown in Author response image 2.

      Author response image 2.

      We added a description of variation across groups to the revised manuscript.

      (3) Throughout the paper, the 'n' used for statistical analysis is often spine, which is not appropriate. At a minimum, cell should be used, but ideally a nested mixed model, which would take into account factors like cell, culture, and animal, would be preferable. Also, all of these factors should be listed, with sufficient independent cultures.

      We agree that nested mixed models are more appropriate for evaluating genotype effects in most of our datasets. We confirm that the results of statistical analysis using nested mixed models were consistent with our previous conclusions in most cases.

      Figure 3: We performed three independent primary cultures of embryonic hippocampal tissue with genotypes of both wild-type and mutant from the same pregnant mice for each mouse model. In our new Figure 3, each data point represents an independent culture experiment, and group comparisons were performed using one-way ANOVA followed by Tukey's post hoc test. In this analysis, statistical analysis using neurons as units of 'n' is not possible, as the number of spines measured from a single neuron is insufficient to generate the density map shown in Figure 3. The statistical analysis was described in the revised text. The details of experimental conditions related to Figure 3 are provided in Supplementary Table 1.

      Figure 5A-C: We analyzed spine turnover rate using a linear mixed-effects model with genotype as a fixed effect and plate, cell, and dendrite as nested random effects. In both 22q deletion model and Setd1a model, there were significant effects of genotype (F(1,25) = 5.79, p = 0.024 for 22q deletion model and F(1,22) = 7.33, p = 0.013 for Setd1a model). In contrast, Nlgn3 mutant neurons did not show a significant difference (F(1,14) = 1.35, p = 0.26). This analysis was described in the revised text.

      Figure 5D-F: Spine lifetime was analyzed using a linear mixed-effects model accounting for the hierarchical structure of the data (spines nested within dendrites, cells, and culture plates). The analysis revealed a significant effect of genotype in both 22q deletion mutant and Setd1a mutant (22qdel mutant; F(1,336) =5.33, p=0.022, Setd1a mutant; F(1,282)=6.38, p=0.012 ). The neurons of both mutants exhibited significantly longer spine lifetimes compared with wild-type neurons (22qdel mutant; ratio = 1.28, 95% CI 1.04–1.58, Setd1a mutant; ratio = 1.35, 95% CI 1.07–1.70). In contrast, Nlg3 mutation did not significantly alter spine lifetime (ratio = 0.86, 95% CI 0.61–1.22; F(1,220)=0.69, p=0.41). This analysis was described in the revised text.

      Figure 5G-I: Spine volume trajectories were analyzed using linear mixed-effects models incorporating nested random effects (spine/dendrite/cell/culture plate) to account for the hierarchical structure of the data. In the 22q deletion model, newly formed spines were significantly smaller than those in wild-type neurons (genotype effect: p < 0.001). The spines in Setd1a mutant neurons also displayed significantly smaller volume than those in wild-type neurons (p < 10<sup>-7</sup>). There were also differences in the temporal profiles of spine growth in these two mutants (p < 0.001). In contrast, newly formed spines in the Nlgn3 mutant neurons were significantly larger than those in wild-type neurons (p < 10<sup>-4</sup>) with preserved time-course of spine growth. This analysis was described in the revised text.

      Figure 5J-L: Similar analyses using linear mixed-effects models incorporating nested random effects (spine within dendrite within cell within culture plate) identified significantly smaller initial spine size in the 22q deletion model (p < 10<sup>⁻6</sup>), while no significant differences in the initial spine volume were found for Setd1a mutants. The temporal trajectories of spine shrinkage before their loss were also not significantly altered in both 22qdel and Setd1a mutants. The Nlg3 mutant showed a significantly different time-course of spine shrinkage (p < 0.05), while the initial spine size was not altered. This analysis was described in the revised text.

      Figure 7A overexpression dataset: We analyzed plate-averaged lifetime values using a linear mixed-effects model with treatment as a fixed effect. There exists a significant main effect of treatment (F(3,8) = 4.59, p = 0.038), with post hoc examination showing a significant increase in lifetime by Ecrg4 overexpression (β = 0.49 ± 0.16 SE, t(8) = 3.16, p = 0.013). Figure 7A shRNA dataset: We also applied a linear mixed-effects model for plate-averaged lifetime values with treatment as a fixed effect. The analysis revealed no significant effect of treatment (F(2,6) = 0.29, p = 0.76).

      The analyses of overexpression and shRNA datasets were described in the revised text.

      Figure 8: As in Figure 3, we performed three independent primary cultures of embryonic hippocampal tissue with genotypes of both wild-type and mutant from the same pregnant mice for each mouse model. The culture plates were transfected with either a control shRNA or an Ecrg4 shRNA construct. Each data point represents an independent culture experiment, and the effect of Ecrg4 shRNA relative to that of control shRNA was evaluated using a permutation test. The data analysis was described in the revised text. The details of experimental conditions related to Figure 8 are provided in Supplementary Table 1.

      (4) The authors should confirm that all mutants are also on the C57BL/6J background, and clarify whether control cultures are from littermates (this would be important). Also, are control versus mutant cultures done simultaneously? There can be significant batch effects with cultures.

      The mutant mice we used in this study are on C57BL/6J or C57BL/6N background. It is known that C57BL/6J or C57BL/6N mice exhibit distinct phenotypes across a range of physiological, biochemical, and behavioral systems. However, it is less likely that our analysis is affected by differences between C57BL/6J and C57BL/6N, as we compared wild-type and mutant littermates on the same genetic background. This experimental design can also reduce the batch effects with different culture preparations. This point was described in the revised text.

      (5) The spine analysis uses cultures from 18-22 DIV - this is quite a large range. It would be worth checking whether age is a confounder or correlated with any parameters / principal components.

      We described in the method sections that culture samples were processed for imaging at 18-22 DIV. However, all the SIM imaging experiments for eight mutant mouse models were performed on samples fixed at DIV 19. The wide range of imaging experiments (DIV 18-22) includes test samples we used to optimize imaging conditions. In the revised manuscript, we specified the timing of SIM imaging.

      (6) The computational modelling is interesting, but again, I am concerned about some circularity. Parameter optimization was used to identify the best fit model that replicated the spine turnover rates, so it is somewhat circular to say that this matched the observations when one of these is the turnover rate.

      We appreciate the reviewer's comment on some circularity of the argument. We agree that the turnover rate is already incorporated into the simulation model and is not an appropriate criterion for the evaluation. We modified the text accordingly.

      It is more convincing for spine density and size, but why not go back and test whether parameter differences are actually seen - for example, it would be possible to extract the probability of nascent spine loss, etc.

      We thank the reviewer for giving this important suggestion. The probability of nascent spine loss is an important parameter, and we initially attempted to estimate it from the original data set. However, the upper limit of our time-lapse imaging is 24 h, which is insufficient to distinguish stable and nascent spines clearly. The difficulty of extracting all the necessary parameters for spine remodeling is our motivation for starting this computational modelling.

      More compelling would be to repeat the experiments and see if the model still fits the data. In the interpretation (line 314-318) it is stated that '... reduced spine maturation rate can account for the three key properties of schizophrenia-related spines...', which is interesting if true, but it has just been stated that the probability of spine destabilization is also higher in mutants (line 303) - the authors should test whether if the latter is set to be the same as controls whether all the findings are replicated.

      As suggested by the reviewer, we set the probability of spine destabilization equal across wild-type and mutant models and repeated the simulations. The results indicate that this modification has small effects on spine density (0.61 vs 0.62), spine turnover rate (0.22 vs 0.21), fraction of small spines (0.21 vs 0.20), and mean spine size (0.37 vs 0.36). We described this point in the revised manuscript.

      (7) No validation for overexpression or knockdown is shown, although it is mentioned in the methods - please include.

      As suggested by the reviewer, we validated overexpression and knockdown. The results are summarized in Supplementary Figure 8.

      Supplementary Figure 8A-C shows the immunocytochemistry of anti-Ecrg4, anti-Cip4, and anti-NPAS4 for the confirmation of overexpression of these molecules.

      Supplementary Figure 8D-E shows the confirmation of the appropriate size of exogenously expressed Ecrg4, Cip4, and NPAS4 by immunoblotting. (previous Supplementary Figure 10F is now Supplementary Figure 8E).

      Supplementary Figure 8F-H indicates the efficient knockdown of exogenously expressed Met-GFP, ARHGAP15-GFP, and Ecrg4-HA by respective shRNA constructs in COS-7 cells. (previous Supplementary Figure 10G is now Supplementary Figure 8H)

      Also, for the knockdown, a scrambled shRNA control would be preferable.

      We used Stealth RNAi Negative Control Duplexes (Invitrogen) as the shRNA control in this study. To confirm that this RNAi sequence does not affect spine turnover, we performed timelapse imaging of neurons transfected with GFP alone or with GFP and the Stealth RNAi Negative Control. No detectable change in spine turnover was observed (Supplementary Figure 8I), indicating that this RNAi control sequence is suitable for our study.

      (8) The finding regarding ecgr4 is interesting, but showing that some ecgr4 is expressed at boutons and spines and some in DCVs is not enough evidence to suggest that actively involved in the regulation of synapse formation and maturation (line 356).

      To reveal the active roles of Ecrg4 in spine regulation, we exogenously applied a synthetic Ecrg4 peptide to wild-type neurons and monitored both spine density and turnover rate after Ecrg4 application. The Ecrg4 application increased the spine turnover rate, whereas samples treated with the scrambled peptide did not. This result supports the active role of Ecrg4 in regulating spine turnover. The data were added as Supplementary Figures 9F and G.

      (9) The same caveats that apply to the analysis also apply to the ecgr4 rescue. In addition, while for 22q the control shRNA mutant vs WT looks vaguely like Figure 2, setd1a looks completely different.

      We thank the reviewer for pointing out the apparent difference in the pattern of spine population data between Figure 2 and Figure 8. We performed SIM analysis using DiI-labeled neurons in Figure 2, whereas the data in Figure 8 are derived from GFP-expressing neurons. The images of cell-surface labeling and cytoplasmic labeling cannot be analyzed in the same way, as it is necessary to adjust parameters in SIM image processing and PCA-based dimensional reduction. Consequently, the distribution of the spine population projected onto the PC1-PC2 plane differs between DiI-labeled neurons and GFP-expressing neurons. To facilitate the comparison of PCA analysis applied to GFP-expressing neurons, we replaced the weight matrix for GFP-expressing neurons with that previously calculated for the DiIlabeled neurons. This adjustment increased the similarity of the data distributions shown in Figures 2 and 8. The explanation for the different patterns in the spine population map between Figure 2 and Figure 8 was added to the revised text. The related explanation for the data processing was described in the Materials and Methods.

      And if rescued, surely shRNA in the mutant should now resemble control in WT, so there shouldn't be big differences, but in fact, there are just as many differences as comparing mutant vs wild-type? Plus, for spine features, they only compare mutant rescue with mutant control, but this is not ideal - something more like a 2-way ANOVA is really needed. Maybe input from a statistician might be useful here?

      We appreciate the reviewer's important comment and agree that the analytical approach used in the original manuscript was not optimal. We therefore revised our analysis to examine whether the difference observed between wild-type and mutant neurons was reduced by suppression of Ecrg4 expression.

      To this end, we first identified two regions in the PC1–PC2 plane where mutant spines were either enriched or depleted relative to wild-type neurons (Areas A and B). We then counted the number of spines located in Areas A and B in control shRNA-treated mutant neurons (normalized spine counts XA and XB). Next, we quantified spine counts in the same areas using data from Ecrg4-suppressed mutant neurons (normalized spine counts YA and YB). If XA > YA and XB < YB, suppression of Ecrg4 would indicate a shift toward rescue of the phenotype observed in control shRNA-treated mutant neurons. Indeed, the datasets were consistent with this shift in relative spine counts.

      To determine whether these differences exceeded those expected from random variation in spine counts, we performed a permutation test. Specifically, spine identities were randomly shuffled between the two conditions while preserving the total number of spines in each dataset. The observed differences were then compared with the distribution obtained from the permuted datasets to assess statistical significance.

      We found that all three culture replicates showed statistical significance in both areas A and B for both the 22qdel and Setd1a mutations. This analysis is described in the Result section.

      (10) Although this is a study entirely focused on spine changes in mouse models for Sz, there is no discussion (or citation) of the various studies that have examined this in the literature. For example, for Setd1a, smaller spines or reduced spine densities have been described in various papers (Mukai et al, Neuron 2019; Chen et al, Sci Adv 2022; Nagahama et al, Cell Rep 2020).

      We appreciate the reviewer's suggestion to include a discussion of schizophrenia-related mouse models. We added more information related to the Setd1a mouse model to the Discussion section.

      "Population-level spine properties were more homogeneous in schizophrenia models (those with gene mutations implicated in schizophrenia) than in the other 4 models studied, in part due to a shared tendency for smaller spines. This observation is consistent with previous studies on Setd1a mutant mice, which showed reduced spine width, decreased mushroomtype spines, and lower spine density in the prefrontal cortex [43,56,57]. In contrast to these findings, several previous studies reported reduced numbers of small spines in the postmortem cortical tissues of schizophrenia patients [22,58]. "

      (11) There is a conceptual problem with the models if being used to differentiate autism risk from Sz risk genes. It is difficult to find good mouse models for Sz, so the choice of 22q11.2del and Setd1a haploinsufficiency is completely reasonable. However, these are both syndromic. 22qdel syndrome involves multiple issues, including hearing loss, delayed development, and learning disabilities, and is associated with autism (20% have autism, as compared to 25% with Sz). Similarly, Setd1a is also strongly associated with autism as well as Sz (and also involves global developmental delay and intellectual disability). While I think this is still the best we can do, and it is reasonable to say that these models show biased risk for these developmental disorders, it definitely can't be used as an explanation for the higher variability seen in the autism risk models.

      We appreciate the reviewer's suggestion for more careful consideration of the interpretation of phenotypes in mouse models, with regard to their relation to clinical phenotypes in human patients. According to the suggestion of the reviewer, we modified the relevant text as follows:

      "The nanoscale features of dendritic spines in ASD-associated mouse models were more variable than those in schizophrenia-associated mouse models. This difference may be related to the broader clinical spectrum of ASD, which ranges from mild impairments in social skills to severe intellectual disability. The four ASD-associated mouse models examined in this study, Nlgn3<sup>R451C/(y or R451C) , Syngap1<sup>+/-</sup>, POGZ<sup>Q1038R/+</sup>, and 15q11-13<sup>dup/+</sup>, may represent subgroups with different levels of hippocampal dysfunction. Among the four ASD-associated mouse models, 15q11-13<sup>dup/+</sup> showed population-level spine properties closer to those of the schizophrenia models. To understand this similarity, further analysis of neural circuit changes in both ASD- and schizophrenia-associated mouse models will be necessary. Analysis of the relationships between rare genetic variants and synapse phenotypes in mouse models may contribute to their eventual categorization. This information should be useful to understand the underlying mechanisms of the broader clinical spectrum of ASD."

      (12) I am not convinced that using dissociated cultures is 'more likely to reflect the direct impact of schizophrenia-related gene mutations on synaptic properties' - first, cultures do have non-neuronal cells, although here glial proliferation was arrested at 2 days, glia will be present with the protocol used (or if not, this needs demonstrating).

      In our culture system, the density of non-neuronal cells is low, and most neurons are not in direct contact with non-neuronal cells. We reported this method in Nat. Neurosci. 1999, where we utilized this culture system to visualize GFP-tagged PSD-95 in neurons using recombinant adenovirus. Because recombinant adenovirus shows higher infection efficiency in glial cells, it was essential for us to establish a culture condition that isolates neurons from glial cells.

      Second, activity levels will affect spine size, and activity patterns are very abnormal in dissociated cultures, so it is very possible that spine changes may not translate into in vivo scenarios. Overall, it is a weakness that the dissociated culture system has been used, which is not to say that it is not useful, and from a technical and practical perspective, there are good justifications.

      We appreciate the reviewer's comment on the advantages and disadvantages of using an in vitro culture system. This comment aligns with the first reviewer's. We modified our text to have a balanced discussion on the role of the in vitro culture system in the study of mental disorder mouse models as follows:

      "Finally, while the spine phenotype identified in the human postmortem brain undoubtedly resulted from complex interactions among genetic background, environmental influences, and regulation by non-neuronal cells, data from pure neuronal cultures are more likely to reflect the direct effects of schizophrenia-related gene mutations on synaptic functions. This property may be advantageous for identifying synaptic molecules that regulate synapse phenotypes in schizophrenia-related mouse models. However, the phenotype observed in the culture system requires confirmation using in vivo experiments of mouse models or human tissue samples. Efficient in vitro screening combined with reliable in vivo evaluation of synapses will facilitate translational research on mental disorders."

      (13) As a minor comment, the spine time-lapse imaging is a strength of the paper. I wonder about the interpretation of Figure 5. For example, the results in Figure 5G and J look as if they may be more that the spines grow to a smaller size and start from a smaller size, rather than necessarily the rate of growth.

      We thank the reviewer for the insightful comment. In the revised manuscript, we analyze the time-lapse data using linear mixed-effects models incorporating nested random effects (spine/dendrite/cell/culture plate). This analysis suggested the difference in the initial size of spines. This point is described in the revised manuscript as follows:

      "Schizophrenia-associated mouse models showed higher similarity in spine morphology, driven by reduced size and growth of nascent spines."

      "We further compared the initial increase in spine volume between genotypes (Figure 5G-I). Linear mixed-effects models incorporating nested random effects revealed significantly smaller initial spine volumes in both 22q11.2<sup>del/+</sup> and Setd1a<sup>+/-</sup> models (genotype effect: p < 0.001 for 22q11.2<sup>del/+</sup> and p < 10<sup>-7</sup> for Setd1a<sup>+/-</sup>). The spines in both mutants also displayed a significant reduction in spine volume increase (p < 0.001). In contrast, newly formed spines in the Nlgn3<sup>R451C/(y or R451C)</sup> neurons were significantly larger than those in wild-type neurons (p < 10<sup>-4</sup>) with preserved time-course of spine growth.”

      We tested whether the initial size difference in spines can be incorporated into the computational simulation. However, due to the large variability in the initial spine size, it was difficult to perform parameter optimization in the model with additional factors. Therefore, we did not further pursue this possibility in this revision. This point is described in the revised text.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The manuscript would be strengthened if the following issues were adequately addressed:

      (1) It would be helpful to know more about the in/ex vivo dendritic spine phenotype of the mouse models of neuropsychiatric disorders, to allow readers to judge whether and how the in vitro spine phenotype in hippocampal neuronal cultures overlaps with/replicates the spine phenotype within the mouse brain.

      We appreciate this comment, but our currently available data is insufficient to specify the difference between in vitro and in vivo spine phenotypes. Our previous study, published in Nature. Comm. (2019), provided data showing that the overall distribution of spine size is similar between in vivo and in vitro conditions in the mouse hippocampus.

      (2) Although the manuscript is largely well written, there are instances of ambiguous language, particularly when describing the spine phenotypes. For example, we are told that "ASD mouse models showed a tendency of decreasing spine subpopulation with small volumes." This description and other examples should be expressed more clearly.

      Following the reviewer's suggestions, we revised the text to improve clarity. We modified the sentence "ASD mouse models showed a tendency of decreasing spine subpopulation with small volumes" to "ASD-related mouse models showed an opposite spine phenotype."To avoid possible confusion for readers, we have revised several sentences in the text to clarify the intended meaning.

      Also, I question whether the word "decoding", meaning to convert (a coded message) into intelligible language, is the most appropriate for the title and abstract.

      The original meaning of the word "decoding" is the conversion of a coded message into an intelligible form; however, in this study, we use the term in a broader sense, referring to the extraction of latent population-level properties of dendritic spines from multidimensional structural parameters. We believe this usage is consistent with its common use in neuroscience and systems biology, where "decoding" often refers to inferring underlying biological states or information from complex datasets.

      (3) The authors should reconsider whether CaMKIIαK42R/K42R mice should be described as a schizophrenia model, when mutations in CAMK2A are known to cause autosomal dominant intellectual developmental disorder-53 (OMIM 617798) and autosomal recessive intellectual developmental disorder-63 (OMIM 618095), and mice carrying the CAMK2A E183V mutation exhibit ASD-related synaptic and behavioral phenotypes (PMID: 28130356).

      We provided a detailed answer to this question in the previous part of the rebuttal.

      (4) The title doesn't adequately summarise the contents of the manuscript. It should mention mice/mouse models and cultured neurons.

      We also responded to this request in the previous part of the rebuttal.

      Reviewer #2 (Recommendations for the authors):

      (1) Please provide a supplementary table with all DEGs. Also, DEGs are listed if present in 'more than 2' models - does this mean they had to be in 3 or more? Please clarify.

      According to the reviewer's suggestion, we added data on DEGs shared by >2 mouse models in Supplementary Figure 7. We also added Supplementary Tables 2 and 3 for all DEGs. The phrase "in more than 2 models" means "in 3 or 4 models".

      (2) There are several references to 'schizophrenia mouse models' - it is worth rephrasing this to make clear that these are not mice with schizophrenia.

      We replaced the expression "schizophrenia (or ASD) mouse models" with "schizophrenia (or ASD)-associated mouse models" or similar appropriate wording throughout the manuscript.

      (3) Line 66: 'a recent...' - 2014 is not really recent.

      We removed the word "recent" from the sentence.

      (4) Figure S1: The legend says A-D, but they are not on the figure. Also, make clear whether this data is only WT data - it seems to be from disorder models, with 4 colors for each model - please clarify.

      We changed the sentence from "shown as A to D" to "shown as A to C". The datasets in Supplementary Figure 1 are wild-type only. Each graph uses four colors to represent wildtype data from four imaging datasets obtained from different mouse models. Graphs A to C correspond to spine length, surface area, and volume, respectively.

      (5) Methods, line 680-4: More detail here would be helpful.

      We added more explanation for the generation of subtraction maps.

      (6) Line 193: Make it clear this is hippocampal in the main text.

      We added "cultures of embryonic hippocampi" to the text.

      (7) Figure 5, D-F: Make clear that these are transient spines (as per main text)

      We added "Lifetimes of transient spines" to both the main text and figure legend.

      (8) Figure 6B: More detail is needed; no idea what this is - no axis label. D - also not clear what numbers on the y-axis mean. E - color scale??

      We added details to the figure legend, the axis labels for Figures 6B and 6D, and the color scale for Figure 6E.

      (9) Supplementary Figure 9 - not clear what matrices are actually showing, nor what the scale refers to - is this the number of shared DEGs? If so, please make it clearer.

      The matrices show the shared DEG numbers, as shown in their titles. The scale indicates DEG numbers. We added the explanation of the color code to the figure legend.

      (10) Please make clear in the main text that ecgr4 affected the turnover rate. It would be good to measure other parameters as well.

      We added the phrase "a significant increase in spine turnover rate by Ecrg4 overexpression" to the main text.

      (11) Figure 7: Suggest to label C on images as well, so obvious which is GFP/anti-HA overlay (and respective colors) and which is anti-HA staining.

      We added the labels with respective colors to Figure 7.

      (12) Ecgr4 is a precursor protein that is cleaved to produce several hormone-like peptides. Where is the HA tag - so which cleavage products will it label? Any antibodies that work in immunocytochem?

      HA tag was attached to the C-terminal domain. We predict that anti-HA binds to four cleavage products (the full-length Ecrg4, Augurin, Argilin, and Δ16). Among several commercially available antibodies, only the SIGMA product could detect cells expressing Ecrg4-HA by immunocytochemistry.

      (13) Supplementary Figure 10: Synaptosome would be a good addition.

      We isolated the fraction of synaptosomes using Syn-PER™ Synaptic Protein Extraction Reagent in Supplementary Figure 9A. We added this explanation to the Materials and Methods section.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Strengths:

      Strengths of this paper include the important question addressed and the elegant and innovative combination of methods, which led to clear insights into the sensory biology of self-righting, and that will be useful for others in the field. This is a substantial contribution to understanding how animals correct their body position. The manuscript is very clearly written and couched in interesting biology.

      Limitations:

      (1.1) The interpretation of functional experiments is complicated by the proposed excitatory and inhibitory roles of dorsal and ventral sensory neuron activity, respectively. So, while silencing of an excitatory (dorsal) element might slow righting, silencing of inputs that inhibit righting could speed the behavior. Silencing them together, as is done here, could nullify or mask important D-V-specific roles. Selective manipulation of cells along the D-V axis could help address this caveat.

      We highly appreciate the thoughtful comments by Rev1 pointing out the relative simplicity of our current inferences regarding the role of dorsal vs. ventral substrate contact, and agree with the suggestion that cells along the DV axis could have diverse roles in their contribution to self-righting. In this context, we wish to point out two aspects, one theoretical and one practical. Regarding theory, our view is that this may not be a simple case of “excitation vs. inhibition”, but rather one in which the coordinated and dynamic activity of distributed sensory neurons promotes differential action selection in alignment with environmental conditions – a framework that could involve many different behaviours with a still uncertain level of granularity (e.g., is self-righting different if the larva is rotated to 160º instead of exactly 180º?). Regarding the practical aspect, while this area represents a fascinating point for future investigation, it is currently limited by technological development, particularly in the context of this study where a relatively low-cost implementation has been used to probe the AP axis. Investigation of the DV axis would require further technological development, since optogenetic light would need to be precisely delivered from the side rather than from underneath, with a greater degree of resolution compared to the AP axis given the much smaller width of the larva (~120-140µm) relative to its length (~550-600µm). Therefore, whilst we appreciate these comments and suggestion, we believe this line of experiments is ideal for a follow-up investigation, rather than being implemented in the current study.

      (1.2) Prior studies from the authors implicated daIV neurons in the righting response. One of the main advances of the current manuscript is the clever demonstration of region-specific roles of sensory input. However, this is only confirmed with a general md driver, 190(2)80, and not with the subsetspecific Gal4, so it is not clear if daIV sensory neurons are also acting in a regionally-specific manner along the A-P axis.

      To address this interesting and important comment by Rev1 we have carried out a new experiment using an alternative driver to 109(2)80-Gal4 and testing the impact of these manipulations on larval behaviour. The revised version of our MS includes a new figure Supp Fig S3 which shows self-righting times when using the ppk-Gal4 driver with the opto-axial technique. As observed with the 109(2)80-Gal4 driver, self-righting was delayed in anterior but not posterior inhibition conditions, suggesting the daIV neurons act in a region-specific manner to trigger postural control behaviour.

      We have also conducted a head casting analysis in the ppk domain; in another new figure, Supp Fig S7, we also show that head casting behaviour is also increased in the same manner as with the 109(2)80-Gal4 driver.

      These new panels and figures are cited within the sub sections entitled “Optogenetic inhibition of anterior but not posterior multidendritic neurons delays self-righting” and “Inhibition of anterior multidendritic neurons is associated with increased head casting during self-righting”, on pages 25 and 28, respectively. We are grateful to Rev1 for this suggestion, which we consider qualitatively improves our paper.

      (1.3) The manuscript is narrowly focused on sensory neurons that initiate righting, which limits the advance given the known roles for daIV neurons in righting. With the suite of innovative new tools, there is a missed opportunity to gain a more general understanding of how sensory neurons contribute to the righting response, including promoting and inhibiting righting in different regions of the larva, as well as aspects of proprioceptive sensing that could be necessary for righting and account for some of the observed effects of 109(2)80.

      Once again, we appreciate this interesting comment by Rev1. We feel our study provides novelty in understanding how sensory neurons in different body regions contribute to the induction of the behaviour. We developed new technology to show that the activity of anterior sensory neurons is essential for normal righting and inhibiting this activity leads to a switch to a different behavioural regime. We feel this represents a substantial advancement in our understanding of how this behaviour is initiated that has not been previously described. Whilst we also appreciate there is likely to be a substantial role of proprioception in self-righting behaviour, our work here focuses on the external stimuli that elicit self-righting, as a detailed understanding of proprioception would be out of scope and require the development of further techniques to manipulate and measure larval posture. As detailed in the above comment, we feel that the more targeted investigation of daIV neurons can also shed some light on the cell-type specificity and inputs to the self-righting induction process.

      (1.4) Although the authors observe an influence of Hox genes in righting, the possible mechanisms are not pursued, resulting in an unsatisfying conclusion that these genes are somehow involved in a certain region-specific behavior by their region-specific expression. Are the cells properly maintained upon knockdown? Are axon or dendrite morphologies of the cells disrupted upon knockdown?

      We agree with this comment in that further investigating the effects of Hox expression on localised aspects of the sensory system poses an interesting line of investigation. Indeed, we are currently conducting a full scale analysis of Hox gene effects across the sensory field. As things stands, it is not clear how Hox gene expression could affect local sensory processes, a mechanism which could involve morphological changes, changes in neuronal excitability (e.g. due to changes in channel expression), synapse formation and/or efficiency, cell development and identity, and/or combinations of these effects, amongst other possibilities. It is clear that a complete and satisfying investigation of this mechanism for each of the Hox genes would pose a substantial amount of work so, while we acknowledge the merit of Rev1’s comment, we consider that adding a cellular-mechanistic analysis of Hox effects is out of scope for the present study and shall constitute a central matter for a followup study emerging from current projects. We think that our data on Hox expression/function as reported here should serve to open up the analysis of genetic regulation of local sensory function, an area in which we are currently working very actively.

      (1.5) There could be many reasons for delays in righting behavior in the various manipulations, including ineffective sensory 'triggering', incoherent muscle contraction patterns, initiation of inappropriate behaviors that interfere with righting sequencing, and deficits in sensing body position. The authors show that delays in righting upon silencing of 109(2)80 are caused by a switch to head casting behavior. Is this also the case for silencing of daIV neurons, Hox RNAi experiments, and silencing of CO neurons? Does daIII silencing reduce head casting to lead to faster righting responses?

      This is an insightful comment. In the revised version of the manuscript, we do indeed show that anterior inhibition of daIV neurons leads to the same head casting behaviour as with the 109(2)80 domain, which we interpret as an inability of the larvae to sense the underlying substrate (see page 28). We hope the new data addresses this comment, at least to an extent. While we acknowledge it would also be insightful to run this behavioural analysis for other experimental conditions, such as the daIII inhibition and Hox RNAi lines, these experiments pose a specific technical difficulty: the behavioural analysis relies on a deep neural network (DNN) which was trained solely on recordings of the opto-axial technique, meaning it does not translate well to other experimental situations. This problem is further compounded by the use of L1 larvae, which means recording resolution is insufficient to accurately define the body landmarks used in the posture tracking at a smaller scale. Therefore, the recourse for identifying behavioural changes is manual observation, which we feel is too inconsistent to address a quantitative question like this.

      (1.6) 109(2)80 is expressed in a number of central neurons, so at least some of the righting phenotype with this line could be due to silenced neurons in the CNS. This should at least be acknowledged in the manuscript and controlled for, if possible, with other Gal4 lines.

      We thank the reviewer for making this interesting comment. We have added a phrase to the section “Conditional inhibition of multidendritic neurons delays self-righting” (p21) which acknowledges the presence of 109(2)80 expression in the CNS (as reported by Hughes and Thomas). We agree that ideally, a variety of sensory Gal4 lines would be used to check for consistency of the effects. However, it is also important to note that 109(2)80 is one of the only available Gal4 lines with near sole md neuron expression, as other Gal4s also drive expression strongly in external sensory cells for example. Thus, re-running experiments with these other lines – which would involve a substantial investment of time and resources – would not be an ideal strategy. We feel that the new observation of (very) similar axial results using the ppk-Gal4, which does express solely in the daIV neurons, better helps to confirm the specificity of the findings to multidendritic neurons.

      Other points:

      (1.7) Interpretation of roles of Hox gene expression and function in righting response should consider previous data on Hox expression and function in multidendritic neurons reported by Parrish et al. Genes and Development, 2007.

      We thank Rev1 for pointing out this study, which is definitively important to discuss given our results on Hox genes. To address this gap, we have added an additional paragraph in the Discussion (p37) to discuss the documented effects of Hox genes on da neuron dendritic morphology and how our results can be interpreted in light of this.

      (1.8) The daIII silencing phenotype could conceivably be explained if these neurons act as the ventral inhibitors. Do the authors have evidence for or against such roles?

      This is another interesting suggestion. If the daIII neurons were to fulfil this role, then in theory, their inhibition would result in self-righting behaviour under conditions of combined dorsal and ventral substrate contact. This is not an experiment we performed, so we are currently unable to confirm or rule out this possibility. However, we note from casual observation that daIII inhibition does not cause larvae to spontaneously self-right. As mentioned above, our view is not one in which the system has “dorsal/ventral stimulators/inhibitors” for a given behaviour, but that action selection proceeds according to a coordination of many (dynamic) contextual clues. Given the new results with the axial inhibition of daIV neurons (see above) it might be more parsimonious to suggest that these “tiling” neurons are primarily responsible for detecting substrate contact around the full circumference of the animal, rather than this involving different cell types according to the different sides of the body.

      Reviewer #2 (Public review):

      Strengths:

      The work of Roseby et al. does what it says on the tin. The experimental design is elegant, introducing innovative methods that will likely benefit the fly behavior community, and the results are robustly supported, without overstatement.

      Weaknesses:

      The manuscript is clearly written, flows smoothly, and features well-designed experiments. Nevertheless, there are areas that could be improved. Below is a list of suggestions and questions that, if addressed, would strengthen this work:

      (2.1) Figure 1A illustrates the sequence of self-righting behavior in a first instar larva, while the experiments in the same figure are performed on third instar larvae. It would be helpful to clarify whether the sequence of self-righting movements differs between larval stages. Later on in the manuscript, experiments are conducted on first instar larvae without explanation for the choice of stage. Providing the rationale for using different larval stages would improve clarity.

      This is a very interesting point raised by Rev2. Most of our previous work on self-righting (e.g. PicaoOsorio et al. 2015 Science; Picao-Osorio, Baldaia et al. 2017 Genetics; Klann et al. 2021 Journal of Neuroscience) was focused on the first instar larva (L1) because this early stage: (i) represents the simplest form of all larval stages, (ii) allows meaningful comparisons with late embryonic processes guiding the development and physiology of the nervous system, (iii) captures the system in a relatively naïve state, that had limited if any exposure to external stimuli. Although these attributes remain valid for the investigation of the sensory stimuli that trigger self-righting, the implementation of the necessary regional physical measurements and manipulations used in this study (surface contact, opto-axial technique, deep neural network analysis) would be impossible to implement in the early forms of the larva simply due to its reduced size. Due to this, we employed L3s, which due to their larger dimensions enabled the development and use of the sophisticated regional stimulation techniques reported here. Yet, as Rev2 rightly points out, we return to the late embryo and early L1 at the point of conducting gene expression analyses as these are optimised for those early stages. The selection of larval stage according to experiment relies on the fact that all forms of the larva display self-righting (Issa, Picao-Osorio, et al. 2019 Current Biology), that SR does not differ according to larval stage and that the characterisation of the structure of the nervous system across larval stages has shown a large level of similarity and consistent topographically arranged connectivity between identified neurons (Gerhard et al. 2017 eLife).

      (2.2) What was the genotype of the larvae used for the initial behavioral characterization (Figure 1)? It is assumed they were wild type or w1118, but this should be stated explicitly. This also raises the question of whether different wild-type strains exhibit this behavior consistently or if there is variability among them. Has this been tested?

      Thank you to the reviewer for pointing this out. The genotype for Figure 1 was w<sup>1118</sup>; this has now been added to the figure legend and the results section – thank you to Rev2 for pointing this out. Although in this study we did not explicitly compare self-righting (SR) performance in wild type/control genotypes (as we are internally consistent in using w<sup>1118</sup>) based on previous data collected in our lab we know that self-righting times are similar and very consistent amongst inbred control lines such as w<sup>1118</sup>, yw, and Oregon Red. Furthermore, we can also add that when comparing SR times between these inbred populations with a highly polymorphic outbred Drosophila population (Martins et al. 2013 PLoS Pathogens) we observed that their SR time (i.e. 6.14s ± 1.06) was not significantly different from the inbred lines (p<0.05, U test) (Picao-Osorio, J. 2014 Doctoral Thesis, Chapter 4, p112).

      (2.3) Could the observed slight leftward bias in movement angles of the tail (Figure 1I and S1) be related to the experimental setup, for example, the way water is added during the unlocking procedure? It would be helpful to include some speculation on whether the authors believe this preference to be endogenous or potentially a technical artifact.

      This is an interesting comment, and we recognise that lateral manipulation biases in self-righting could indeed reflect experimental limitations or biological tendencies. At this point we cannot interpret these results as formal evidence of chirality, given that they may reflect subtle aspects of the micromanipulation of specimens. We are currently developing a motorised platform to conduct self-righting tests, which when fully developed, should help addressing the chirality question.

      (2.4) The genotype of the larvae used for Figure 2 experiments is missing.

      Thank you for pointing this out. These were again w<sup>1118</sup> larvae; this detail has now been added to the figure legend and the main text.

      (2.5) The experiment shown in Figure 2E-G reports the proportion of larvae exhibiting self-righting behavior. Is the self-righting speed comparable to that measured using the setup in Figure 1?

      Thank you for pointing this out. We have now added average self-righting times to the figure legends of figures 1 and 2. The self-righting times across for the dorsal + ventral contact conditions was notably longer than dorsal-only cases, which were also slightly longer than the “standard” case. This is perhaps to be expected, as the larvae are encountering unusual and ambiguous situations. We suggest the extra time could reflect an additional decision-making step or action flip-flopping process, or simply physical constraints on the movement (for example, not being able to use some parts of the body).

      (2.6) Line 496 states: "However, the effect size was smaller than that for the entire multidendritic population, suggesting neurons other than the daIVs are important for self-righting". Although I agree that this is the more parsimonious hypothesis, an alternative interpretation of the observed phenomenon could be that the effect is not due to the involvement of other neuronal populations, but rather to stronger Gal4 expression in daIVs with the general driver compared to the specific one. Have the authors (or someone else) measured or compared the relative strengths of these two drivers?

      We agree with this suggestion and to address this concern, we have added as part of our new figure Supp. Fig. S3, a dedicated panel S3C showing fluorescence measurements from ddaC using the 109(2)80-Gal4 and ppk-Gal4 lines. We found no difference in tdTomato fluorescence intensity, suggesting equal expression strength across the two Gal4 drivers. Our new results for axial daIV inhibition are also consistent with this effect size difference, further suggesting that inhibition of all md neurons poses stronger challenges for self-righting compared to the daIV neurons alone.

      (2.7) Is there a way to quantify or semi-quantify the expression of the Hox genes shown in Figure 6A? Also, was this experiment performed more than once (are there any technical replicates?), or was the amount of RNA material insufficient to allow replication?

      Unfortunately, we only had limited amounts of mRNA extracted from FACS-sorted 109(2)80>GFP cells to feed our reverse transcriptase reactions and used much of these samples for the experiment reported. After Rev2 suggestion we went back to our freezers, recovered traces of the samples used in the original experiment, and attempted a new amplification; despite this effort, this new experiment was unsuccessful. We feel that the main point deduced from the original experiment is valid in that we obtained amplicons of the expected size for all the Hox transcripts analysed and that for those cases in which we observed biological effects – i.e. Antp and Abd-B – we corroborated protein expression in the 109(2)80 domain using immunohistochemistry. We are currently expanding this project examining the roles of all Hox genes across the entire sensory system and shall report the expression patterns of all Hox genes in each of the subcomponents of the sensory system the future.

      (2.8) Since RNAi constructs can sometimes produce off-target effects, it is generally advisable to use more than one RNAi line per gene, targeting different regions. Given that Hox genes have been extensively studied, the RNAis used in Figure 6B are likely already characterized. If this were the case, it would strengthen the data to mention it explicitly and provide references documenting the specificity and knockdown efficiency of the Hox gene RNAis employed. For example, does Antp RNAi expression in the 109(2)80 domain decrease Antp protein levels in multidendritic anterior neurons in immunofluorescence assays?

      We used the TRiP RNAi lines, specifically the Valium10 selection available from the Bloomington Stock Centre. Unfortunately, there is not much information on how specific the Hox RNAi lines areor whether their might have off-target effects.

      (2.9) In addition to increasing self-righting time, does Antp downregulation also affect head casting behavior or head movement speed? A more detailed behavioral characterization of this genetic manipulation could help clarify how closely it relates to the behavioral phenotypes described in the previous experiments.

      This would be interesting line of investigation. As described in a previous comment, this is currently unfeasible for us given some important differences between experiments including larval stage and recording conditions. We have added some speculative comments to the manuscript describing the larval behaviour under Hox RNAi.

      (2.10) Does down-regulation of Antp in the daIV domain also increase self-righting time?

      Given the new results with axial effects of daIV neurons, we also sought to address this point with a new series of experiments expressing Hox RNAi constructs in the ppk-Gal4 domain. The new data is shown in a new figure (Figure S8) displaying self-righting times for ppk-Gal4-Hox-RNAi. Interestingly, we found no effect of any RNAi expression on self-righting times, suggesting that md types other than daIVs are under Hox regulation that is important for self-righting.

      Recommendations for the authors:

      Reviewing Editor Comments:

      The reviewers were enthusiastic about the value and quality of this study by Roseby and colleagues. There were two main issues that emerged from the reviews that we're highlighting for the authors to address, should they choose to:

      (1) A little more cell-type resolution of the anterior region

      The anterior region includes a lot of sensory neurons that may be contributing to the effect. Some sensory neurons (e.g., daIV) have been implicated in righting - are these the ones carrying the anterior signal? Are dorsal sensory neurons promoting righting and ventral ones stalling it?

      We are not suggesting a complete sensory-neuron mapping in the anterior region. Instead, we propose the authors conduct a focused check: repeat the axial inhibition with a daIV-specific driver (same photomask assay) to show the A-P effect within the implicated class, and, if possible, replicate one key result with an alternative broad md driver to address Gal4 strength/off-target expression.

      As mentioned above (see Rev1 comment) we have indeed carried out a new experiment using an alternative driver to 109(2)80-Gal4 and testing the impact of these manipulations on larval behaviour. The revised version of our MS includes a new figure Supp Fig S3 which shows self-righting times when using the ppk-Gal4 driver with the opto-axial technique. As with the 109(2)80-Gal4 driver, self-righting was delayed in anterior but not posterior inhibition conditions, suggesting the daIV neurons specifically act in a region-specific manner to trigger postural control behaviour.

      Furthermore, in another new figure, Supp Fig S7, we show that head casting behaviour is also increased in the same manner as with the 109(2)80-Gal4 driver. These new panels and figures are cited within the sub-sections entitled “Optogenetic inhibition of anterior but not posterior multidendritic neurons delays self-righting” and “Inhibition of anterior multidendritic neurons is associated with increased head casting during self-righting”, on pages 25 and 28, respectively. We are grateful to R1 for this suggestion, which we consider qualitatively improves the quality of our paper.

      (2) The Hox section to strengthen this section, we recommend:

      (a) Confirm specificity/efficacy of knockdown (e.g., Antp protein reduction in targeted md neurons and a second RNAi line if available).

      This is a reasonable comment. For our experiments, we selected a UAS-Antp<sup>RNAi</sup> line (Bloomington #27675) given that this construct has been: (i) utilised in several previous studies as the main and single line to interfere with Anpt expression (e.g. Baek et al. 2013 Development; Paul et al. 2021 Nature Comms) and (ii) shown to display a consistent reduction in Antp protein levels of approximately 50% (see Poliacikova et al. 2024 Science Adv.). Furthermore, previous work comparing #27675 with other UAS-Antp<sup>RNAi</sup> lines has demonstrated that all available lines lead to a similar level of reduction in protein expression, although the #27675 line exhibits the most consistent effects (lower variability) (Poliacikova et al. 2024 Science Adv.). Unfortunately, at this point in time, we do not have the capacity to conduct new experiments with other RNAi lines, but consider that the information and arguments mentioned above should be reassuring about our choice of a reasonable and previously validated method to interfere with Antp expression.

      (b) Perform one temporal control (GAL80^ts) or a simple rescue, to separate developmental vs acute roles.

      This is a good and interesting suggestion, but we consider that the discrimination between developmental and physiological effects falls outside the scope of this study. Indeed, experiments of this kind are currently being conducted in our lab as part of a wider examination of Hox gene roles in the sensory system.

      (c) Place the results clearly in the context of prior work (e.g., Parrish 2007), so the mechanism isn't left hanging.

      This is an important point, and we have now done this. Many thanks for pointing this out.

      Reviewer #1 (Recommendations for the authors):

      (1.1) A Gal4 line for the pannier dorsal specification gene shows expression in dorsal sensory neurons, as described in Galindo et al., Development, 2023, and could help tease apart dorsal v. ventral contributions.

      This is an interesting suggestion. However, we understand that the pannier (pnr) Gal4 line mentioned in Galindo et al. 2023 is an enhancer trap inserted in the pnr locus which drives expression in neural as well as non-neural tissues such as the embryonic dorsal ectoderm (see: Calleja et al. 1996 Development; Stronach et al. 2014 Genetics). Although, as Rev1 rightly indicates, this line also labels dorsal cluster sensory neurons, including ddaC (cIV) and ddaF (cIII) neurons the fact that the line displays expression in non-neural tissues makes its use in behavioural experiments difficult as non-neural effects might affect the behavioural patterns studied. A possible way to instrument the pnrGal4 tool into behavioural analyses might involve the creation of the necessary variants to implement a split-Gal4 approach, but this, we believe, unfortunately falls out of the scope of this study.

      (1.2) Potential roles for daII neurons and daI neurons are not examined. Drivers have been described for daII neurons, and there are drivers that will target a majority of proprioceptive md neurons, so these could be examined to complete the analysis started here.

      This is another interesting suggestion by Rev1, but we consider that the fine-grain mapping of effects mediated by sensory neuron sub-clases falls outside the scope of this study aimed at mapping sensory regional effects on self-righting. This does not take the merit of the suggestion away, and indeed, experiments of this kind are currently being conducted in our lab as part of a comprehensive examination of Hox gene roles in the sensory system.

      (1.3) To account for 109(2)80 off targets, the authors could consider other lines that silence most or all md neurons (clh201-Gal4; 5-40-Gal4; 21-7-Gal4) that could at least have different central offtargets. Some other lines are broad somatosensory system drivers but sensory-specific (pebbledGal4).

      This is an interesting comment, and so are the suggestions made. Although to include this kind of verification would be interesting, when carrying out our experiments, we did not observe any central expression at all. Also, to repeat all our experiments in which we use the established and validated 109(2) 80 line using instead these four Gal4 lines, is unfortunately out of scope for us at this point in time. We will nonetheless consider these comments by Rev1 in future extensions of our work.

      (1.4) There is a typo on line 481; it should be "other".

      We are grateful to R1 for pointing this out. This has now been amended

      Reviewer #2 (Recommendations for the authors):

      (2.1) Lines 91-92 cite references describing self-righting behavior across different animal groups, which is illustrated in Figure 1B. It would be helpful to indicate these references directly in the figure. For example, instead of using dots to denote their presence (which are, in a way, redundant since the behavior is reported in all groups), numbers or letters could be used to refer to the specific papers describing them.

      Thank you for this suggestion. We have now replaced the original dots by an abridged citation of a key paper providing evidence in that specific animal group, e.g. Smith, et al. 1997; Rogers et al. 2015

      (2.2) In Figure 1A, the diagrams illustrate the two large dorsal tracheae, which nicely indicate the larva's orientation. However, since they are drawn in a very light gray, they can be difficult to distinguish without zooming in. It might improve clarity if the tracheae were made slightly more prominent.

      Thank you for this suggestion. We have now implemented this change.

      (2.3) In Figure 1E, the dotted line and green bar mark the segment of the recording corresponding to self-righting, which is then quantified in Figure 1G. Was the same procedure applied when analyzing tail speed, or was it limited to head speed? Figure 1F does not show a dotted line or green bar, which is confusing; it would be helpful to clarify the reason for this discrepancy. Also, in Figure 1G, there is an inset showing photos of the movement sequence with the green bar and the caption 'Trimmed to SR sequence,' which implies to me that for tail speed, the 0.75-1 segment of the recording was also used for quantification. I suggest adding the dotted line and green bar to Figure 1F and removing this inset from Figure 1G, as it appears quite small and disrupts the layout of the figure. If it is retained, the figure legend should explicitly refer to the inset.

      Thank you for pointing this out. We have amended these figures as suggested.

      (2.4) In Figures 1 and 2, the box plots include the individual data points, whereas Figures 3 and S2 do not. For data transparency, it would be important to show the individual measurements here as well. I strongly recommend adding them to the figure, or alternatively providing a clear rationale in the text for not doing so.

      Thank you for mentioning this. The reason data points are not shown in Fig 3 or S2 is because the variance extends the scale and compresses the box making it illegible. To make this clear we now explain this in the figure legends.

      (2.5) In Figures 4 and 5, the distribution of self-righting times from the optogenetic inhibition experiments is shown using bar graphs rather than box plots, as in the previous figures. This choice obscures the data distribution, since all bars reach down to zero. Replacing the bar graphs in Figures 4 and 5 with box plots would more clearly convey the experimental results.

      We thak Rev2 for this comment, which gives us an opportunity to clarify the matter. Distributions of SR times are drawn with bars because we compare means +/- variance in the analysis, and not medians +/- IQR as is done in the other experiments. The choice of visualisation reflects the analysis, which is what is recommended by statisticians. Plus, we also show the individual observations, meaning the distribution can be observed. We hope that it is now clear that we are not obscuring any distributions.

      (2.6) Figure 6 would benefit from some reorganization. Panel A is very small and dense with information, making it difficult to interpret without significant zooming. In particular, the FACS graph is nearly impossible to read, as the axes remain unclear even when enlarged. It might be best to either remove this graph and replace it with a cartoon version of FACS-sorted populations, and reorganize the figure to ensure legibility. Additionally, the current layout progresses from the bottom up, which takes time to follow. Comprehension could be improved if the sequence began with the larva dissection placed in the top left area of the figure, where readers typically look first (I appreciate that this is mentioned in the figure legend; however, a different layout might present the information more effectively).

      We appreciate the constructive spirit of this comment and have indeed considered Rev2 suggestions including drafting new layouts of this figure. After all this experimentation, we remain of the view that the original presentation is probably the best trade-off between size and clarity, offering more space for the appreciation of confocal imaging and its interpretation.

      Minor corrections:

      (1) Throughout the text, the word Drosophila appears sometimes in italics and sometimes in regular font; please standardize its formatting for consistency.

      Amended

      (2) Line 179: the use of three hyphens in the sentence "minimum --- in all cases < 30 s --- to avoid larval desiccation" is unusual; exchanging them for commas or brackets is advised.

      Amended

      (3) Line 183: in w1118, the numbers are usually in superscript (not subscript), and the w should be italicized.

      Amended

      (4) In line 783, there is an incorrect space between "is" and the comma in "...repertoire, which is , in...".

      Amended

      (5) In Figure 2G, the left panel appears partially cut off, which makes the text at the edges difficult to read. It might help to adjust the panel so that all labels are fully visible.

      Done

      (6) In the current version of the manuscript, Figure 5 is presented before Figure 4, which is confusing.

      This has been amended.

      (7) Two videos are included in the supplementary material, but I could not find any reference to them in the main text of the manuscript.

      This has been amended.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Weaknesses:

      (1) Research scope

      The results primarily focus on mutations in ZNF217, ZNF703, and ZNF750, with limited correlation analyses between mutations and gene expression. The rationale for focusing only on these genes is unclear. Given the availability of large breast cancer cohorts such as TCGA and METABRIC, the authors should compare their mutation profiles with these datasets. Beyond European and U.S. cohorts, sequencing data from multiple countries, including a recent Nigerian breast cancer study (doi: 10.1038/s41467-021-27079-w), should also be considered. Since whole-exome sequencing was performed, it is unclear why only four genes were highlighted, and why comparisons to previous literature were not included.

      We have significantly strengthened the biological and clinical rationale for focusing on these three genes in the Introduction. Specifically, we now clearly justify their selection based on distinct functional roles: ZNF217 (oncogene, 20q13 amplification); ZNF703 (luminal subtype oncogenic driver); ZNF750 (tumor suppressor involved in differentiation). We have also explicitly define the knowledge gap: lack of mutation and expression data for these genes in African populations, particularly Kenyan cohorts.

      Importantly, we have now incorporated comparative analysis with TCGA data in the Results. This include; A new section on “Recurrent mutations and comparison with TCGA”; a new table, “Table 6” and a curated dataset, “Supplementary Table S4”

      (2) Language and Style Issues

      There are many typos and clear errors in the main text (e.g. (ref)).

      Additionally, several statements read unnaturally. For example:

      "Investigators uncovered 170 mutations ..." should instead be phrased as "We identified 170 mutations ...."

      "The research team ..." should be rephrased as "Our team ...."

      The manuscript has undergone comprehensive language editing throughout the revised draft.

      (3) Methods and Data Analysis Details

      The methods section is vague, with general descriptions rather than specific details of data processing and analysis. The authors should provide:

      (a) Parameters used for trimming, mapping, and variant calling (rather than referencing another paper such as Tang et al. 2023).

      (b) Statistical methods for somatic mutation/SNP detection.

      (c) Details of RNA purification and RNA-seq library preparation.

      Without these details, the reproducibility of the study is limited.

      We have fully revised and substantially expanded the Methods section to improve clarity, transparency, and reproducibility. In the revised manuscript, we now provide explicit details of all key analytical steps. These include quality control procedures using FastQC and MultiQC, as well as read trimming parameters implemented in Trimmomatic (leading and trailing quality <3, sliding window 4:15, and minimum read length of 36 bp). We also clearly describe alignment of reads to the hg38 reference genome using BWA-MEM, followed by somatic variant calling using MuTect2 in paired tumor–normal mode with incorporation of a Panel of Normals (PON). Variant filtering criteria are now explicitly stated, including minimum read depth (≥10), base quality (≥20), and variant allele fraction (≥0.05), and functional annotation was performed using VEP (v108).

      In addition, we have included details on variant validation through visualization in the Integrative Genomics Viewer (IGV), as well as RNA-seq processing steps using STAR for alignment, featureCounts for quantification, and DESeq2 for normalization and differential expression analysis. Statistical analyses are now clearly described, including the use of paired tests and Benjamini–Hochberg correction for multiple testing. Collectively, these additions directly address the reviewer’s concerns by ensuring that all analytical procedures are transparently reported and fully reproducible.

      (4) Data Reporting

      This study has the potential to provide a valuable resource for the field. However, data-sharing plans are unclear. The authors should:

      (a) Deposit sequencing data in a public repository.

      (b) Provide supplementary tables listing all detected mutations and all differentially expressed genes (DEGs).

      (c) Clarify whether raw or adjusted p-values were used for DEG analysis.

      (d) Perform DEG analyses stratified by breast cancer subtypes, since differential expression was observed by HER2 status, and some zinc finger proteins are known to be enriched in luminal subtypes.

      We have improved data transparency and reporting in the revised manuscript. All sequencing data are now publicly available, with whole-exome sequencing (WES) data deposited in the Sequence Read Archive (SRA; PRJNA913947) and RNA-seq data available in the Gene Expression Omnibus (GEO; GSE225846). In addition, we have provided comprehensive Supplementary Materials to support reproducibility and facilitate further analysis, including detailed mutation summaries (Table S1), mutation positions (Table S2), amino acid changes (Table S3), the curated TCGA comparison dataset (Table S4), protein domain annotations (Table S5), and the combined gene expression and clinical dataset (Table S6).

      We have also clarified key aspects of the statistical analysis, including the use of Benjamini–Hochberg adjusted p-values and the thresholds applied for significance. Furthermore, in response to reviewer comments regarding subtype-specific analyses, we have explicitly addressed in the Discussion why subtype-stratified differential expression analysis was not performed, noting that the limited sample size would reduce statistical power and increase the risk of overinterpretation. Together, these revisions enhance the transparency, accessibility, and interpretability of the study.

      (5) Mutation Analysis

      Visualizations of mutation distribution across protein domains would greatly strengthen interpretation. Comparing mutation distribution and frequency with published datasets would also contextualize the findings.

      We have substantially enhanced the mutation analysis by incorporating several new figures and complementary analyses that provide deeper biological interpretation. Specifically, we added Figure 1 to summarize mutation burden, coding consequences, and prevalence; Figure 2 to illustrate the nucleotide substitution spectrum; Figure 3 to map mutations across protein domains; Figure 4 to assess functional enrichment and mutation composition; and Figure 5 to highlight recurrent mutations.

      Reviewer #2 (Public review):

      Weaknesses:

      The current cohort size is relatively small to reach significant findings, and targeted exploration on ZNF family without emphasizing the reason or clinical significance hinders the overall significance of the entire work.

      We acknowledge the limitation posed by the relatively small cohort size and have addressed this concern in several ways in the revised manuscript. First, we have explicitly stated this limitation in the Discussion section. We have also reframed the study as a pilot and population-specific exploratory analysis to better reflect its scope. To strengthen the overall significance, we integrated both mutation and gene expression data, incorporated comparisons with TCGA datasets, and emphasized the importance of African-specific genomic insights. Importantly, we highlight that this study provides novel data from an underrepresented population, which represents a key contribution to the field.

      Reviewer #3 (Public review):

      Weaknesses:

      The author has enhanced the descriptive depth of the study by adding details on mutations, expression subgroup analyses, and functional annotations but has not addressed the core weaknesses of small cohort size and lack of functional validation. While the revised version is more comprehensive in cataloging molecular alterations, it remains confined to descriptive analysis, with no substantial improvement in the reliability or generalizability of its conclusions.

      We have addressed this concern by clearly acknowledging the key limitations of the study, including the absence of functional validation, the relatively small sample size, and the limited generalizability of the findings. In response, we have refined our interpretation to avoid causal claims and instead present the results as hypothesis-generating. We have also expanded the Discussion to include future research directions, recommending functional validation studies, multi-omics approaches, and validation in larger, more diverse cohorts.

      In addition, we have strengthened the robustness of the study by incorporating comparisons with TCGA data, providing more detailed mutation classification, and integrating genomic and transcriptomic analyses. Beyond addressing reviewer comments, we have further improved the manuscript by reorganizing the Results section to follow a clear and logical flow—from mutation burden and spectrum to protein-level distribution, functional enrichment, recurrent mutations, and TCGA comparison. We have also improved figure quality and labeling to meet journal standards, added clear and consistent figure captions, and ensured alignment between the text, figures, and tables throughout the manuscript.

      We sincerely thank the reviewers for their valuable feedback, which has significantly improved the quality and rigor of this work.

    1. Author response:

      We thank the Editor and the Reviewers for their detailed and constructive feedback. We look forward to submitting a revised version of the manuscript that addresses their comments and suggestions, with a special focus on clarifying the assumptions and implications of our analysis. In particular, we will aim to demonstrate that (i) many of our qualitative findings -- and even some quantitative results -- extend beyond the simplest two-resource case considered in the main text, and (ii) that they can also be generalized to account for simple forms of cross-feeding. We hope that these changes will help to illustrate the broader applicability of our underlying mathematical framework.

    1. Author response:

      We thank the editors and reviewers for their thoughtful and constructive evaluation of our manuscript. We are pleased that the reviewers found the study valuable and the evidence supporting a role for Yme1 in MDC formation solid. As described below, we plan to modify the manuscript to clarify the lipid model, better explain the relationship between Ups-family proteins and MICOS, distinguish MDC formation from Atg32-dependent mitophagy, clarify metabolic conditions, add statistical analyses where missing, and strengthen Yme1 validation with immunoblotting.

      eLife Assessment

      This valuable study demonstrates that the inner membrane protease YME1 contributes to the formation of mitochondrial-derived compartments in yeast through the modulation of both the lipid transporter UPS2 and the MICOS complex. The evidence supporting this model is solid, although this manuscript could be improved by providing additional evidence supporting the independent roles for UPS2 and MICOS regulation in this process. This work will be of interest to cell biologists, biochemists, and geneticists interested in understanding the molecular basis of mitochondrial regulation and function.

      We appreciate this positive assessment and agree that the roles of Ups-family lipid transport and MICOS in MDC regulation could be expanded further. This will be an important topic for future studies, especially with regard to how MICOS contributes to MDC formation. In the current revision, we will add new genetic data focused on PA-linked lipid metabolism through the yeast Pah1/Lipin pathway, which we think will help strengthen and clarify the lipid arm of the model. Our current interpretation is that Yme1-regulated Ups-family lipid transport and MICOS may both influence a shared mitochondrial membrane state that permits MDC formation. This interpretation is consistent with our genetic data and with known connections between Ups proteins, MICOS, and mitochondrial membrane organization.

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Balasubramaniam and colleagues continue this group's efforts to understand mitochondrial-derived compartments (MDCs) that bud off from yeast mitochondria in response to metabolic stress. In a previous genetic screen, they identified Ups lipid transfer proteins and the AAA-protease Yme1 as components that modulate MDC formation. In this study, the authors link these observations by showing that Yme1 modulates levels of Ups1, Ups2, as well as MICOS complex members in the mitochondrial proteome. Using genetic approaches, they then show that Yme1's role on MDCs is dependent on its catalytic activity (via an inactive mutant) and that YME1 shows genetic interactions with UPS1/2 and MIC10/MIC60. The overall model is that Yme1 activity responds to metabolic cues and acts via proteolysis of these two distinct mitochondrial machineries to regulate MDC biogenesis.

      Strengths:

      The strengths of the study are its integration of mitochondrial proteomics with strong genetic approaches, as well as synergy with the authors' previous studies on the role of lipids in MD genesis. The work is overall well carried-out and experiments are thoughtfully discussed.

      Weaknesses:

      The major weaknesses are a lack of mechanistic resolution surrounding the model, e.g., proposed or tested mechanisms by which Yme1 activity is regulated by metabolic cues, or how Ups1/2 activity and the MICOS contribute to MDC generation. The authors acknowledge these as open questions, but addressing them would still enhance the significance of the study.

      We thank the reviewer for the positive assessment, and we agree that the upstream regulation of this response remains an important open question. Yme1-dependent MDC regulation could involve changes in Yme1 activity, substrate accessibility, or broader changes in mitochondrial lipid and protein organization. Fully resolving how metabolic state gates this response will require future work, likely outside the scope of the current study.

      We also agree that the manuscript would benefit from a more developed discussion of how lipid changes could contribute to MDC formation. Our prior work showed that reduced mitochondrial PE promotes MDC formation, whereas cardiolipin is required for MDC biogenesis (Xiao et al., 2024). We proposed that reduced PE changes the membrane environment of mitochondrial outer membrane proteins, potentially affecting their stability, abundance, insertion, or lateral organization within the membrane. Such changes could increase the pool of proteins available for sorting into MDCs or make the outer membrane more permissive for domain formation. In the revision, we will connect this model more directly to Yme1-dependent regulation of Ups-family lipid transport.

      We will also expand the model to incorporate PA-linked metabolism. We did not initially focus heavily on Ups1 because complete loss of UPS1, or loss of downstream cardiolipin synthesis through CRD1, blocks MDC formation because cardiolipin is required. Thus, complete disruption of Ups1-dependent lipid transport may obscure the effects of more moderate changes in PA flux. To address this, we will include additional lipid measurements and new genetic data targeting PA metabolism through the yeast Pah1/Lipin pathway. Because Pah1 converts PA to DAG, this provides a way to alter PA-linked metabolism without simply eliminating cardiolipin synthesis. Our new data suggest that PA accumulation or altered PA-linked lipid flux may also promote MDC formation. Together, these findings support a broader model in which reduced PE and increased PA alter both the organization of OMM proteins and the physical properties of the membrane, including curvature and domain formation, thereby creating a membrane state that is more permissive for MDC biogenesis.

      Reviewer #2 (Public review):

      In this manuscript, the authors report a novel regulation of the outer mitochondrial membrane remodeling domains called mitochondria-derived compartments, MDCs. The team has previously established the main principles behind this recently identified quality control pathway, but the mechanisms that control MDCs formation remain incompletely understood. Using the baker's yeast model, the authors identify the conserved mitochondrial protease Yme1 as a crucial factor that regulates MDC formation. Mechanistically, Yme1's proteolytic function controls the levels of Ups1 and Ups2 lipid transfer proteins and the components of the membrane organizing complex called MICOS, thus providing a plausible model as to how Yme1-dependent proteolysis permits MDC formation through the removal of lipid and MICOS-dependent constraints. Finally, the authors show that this Yme1-mediated activity is also defined by metabolic conditions. In principle, this study is interesting and novel, and holds potential to provide new insights into the regulation of the MDC pathway that emerged as a new fundamental mitochondrial quality control mechanism. However, the following points should be carefully addressed.

      Major points:

      (1) Yme1 has been previously shown to regulate mitochondria-specific autophagy through Atg32 processing. Given the high similarity of the MDC pathway to piecemeal autophagy and the fact that both pathways share some of the core components, the authors should address the involvement of Atg32 in their model. It would also be important to include a brief discussion addressing the differences between piecemeal autophagy and the MDC pathway.

      We agree that this is an important point. The reason we did not focus on Atg32 in the current manuscript is that we previously investigated the relationship between MDC formation and Atg32-dependent mitophagy and found that Atg32 is dispensable for MDC formation (Hughes et al., 2016). Based on that result, we do not anticipate that Atg32 is required for the Yme1-dependent MDC phenotypes described here. This is also consistent with the different growth conditions associated with these pathways: Atg32-dependent mitophagy is stimulated under respiratory or post-diauxic conditions, whereas MDCs do not form under the respiratory conditions that stimulate Atg32-dependent mitophagy (Hughes et al., 2016; Raghuram and Hughes, 2024).

      We will clarify this distinction in the revised manuscript. In addition, to be thorough, we plan to generate and test the Atg32-GFP variant previously shown to block Yme1-dependent Atg32 processing and mitophagy (Wang et al., 2013). This will allow us to test directly whether preventing Yme1-dependent Atg32 cleavage affects MDC formation. If successful and interpretable, we will include these data in the revised manuscript.

      (2) The Rpt3 (P215L) expression experiment is interesting, but appears to be somewhat superficial due to the unclear mechanism by which the mitochondrial network morphology is restored in these cells. Could this result be replicated in the dnm1∆ mgm1∆ double deletion mutant, which is a well-established model for mitochondrial network restoration?

      We agree that the Rpt3(P215L) experiment is best viewed as a morphology control. The purpose was to test whether abnormal mitochondrial morphology alone explains the MDC defect in yme1Δ cells. Because Rpt3(P215L) improved mitochondrial morphology but did not restore MDC formation, we interpret this as evidence that morphology alone is not sufficient.

      We attempted to generate the requested dnm1Δ mgm1Δ yme1Δ triple-mutant combination, but that strain combination has not been viable in our hands. However, we do have dnm1Δ data showing that altering mitochondrial structure can rescue some morphological features but does not restore MDC formation in yme1Δ cells. We will include these data where appropriate and clarify that this experiment is intended as a morphology control.

      (3) Figure 3E. The changes in PE levels appear to be minor. While statistically significant, the observed differences may not be physiologically relevant. More in-depth lipidomic analysis data should be presented to substantiate the authors' argument and better address the questions at hand. Related to that, could PE or PA supplementation stimulate MDC formation?

      We agree that additional lipid data would strengthen this part of the manuscript. We initially streamlined the lipid section because we had previously examined the lipid requirements for MDC formation in detail, showing that reduced mitochondrial PE can promote MDC formation, whereas cardiolipin is required (Xiao et al., 2024). However, the current study would benefit from a broader analysis of the lipid changes associated with Yme1-dependent regulation.

      In the revision, we will expand the lipid data to include additional lipid species and incorporate these results into the model. We will also add new genetic data targeting PA metabolism through the yeast Pah1/Lipin pathway. Together, these data suggest that PA accumulation or altered PA-linked lipid flux may also contribute to MDC formation. This supports a broader lipid-balance or lipid-shunting model in which reduced PE, increased PA, or altered lipid distribution between mitochondrial membranes could influence OMM remodeling through effects on membrane curvature, OMM protein organization, or mitochondrial membrane contacts.

      We agree that direct PE or PA supplementation would be a valuable experiment. We have attempted lipid supplementation but have not been able to deliver these lipids effectively to yeast cells in a way that produces interpretable results. We are therefore focusing on lipid profiling and genetic approaches that alter lipid metabolism inside the cell.

      (4) The connection between rapamycin treatment and Yme1-regulated MDC formation is unclear and puzzling and needs to be explained better.

      We agree that this connection is not fully clear. In this manuscript, rapamycin is used primarily as a robust MDC-inducing condition. Our data do not define the full pathway connecting TORC1 inhibition to Yme1-dependent mitochondrial remodeling.

      In the revision, we will either clarify this point or reduce the emphasis on rapamycin as a mechanistic entry point. Our current interpretation is that rapamycin creates a metabolic/mitochondrial state in which Yme1-dependent remodeling of lipid and membrane-organization pathways becomes important for MDC formation. Whether this involves direct regulation of Yme1, altered substrate availability, altered membrane composition, or a combination of these remains open.

      (5) The MICOS complex is clearly involved in the regulation of MDC, but the manuscript misses the mark on providing compelling evidence and a clear explanation as to how MICOS contributes to said regulation.

      We agree that the mechanism by which MICOS regulates MDC formation remains an important open question and will be a major focus of future work. Our current data show that MICOS perturbation can partially restore MDC formation in yme1Δ cells, supporting a role for MICOS in this pathway. This analysis was motivated in part by the incomplete genetic suppression achieved through the lipid pathway alone, which suggested that additional Yme1-regulated factors contribute to MDC formation.

      MICOS therefore represents a strong candidate for this additional regulatory input. However, defining whether MICOS acts through lipid distribution, OMM-IMM organization, membrane architecture, or another mechanism will require a deeper investigation than is possible within the scope of the current study. We will clarify this point in the revised manuscript and present the current findings as the beginning of a broader investigation into how MICOS contributes to MDC biogenesis.

      Minor points:

      (1) The authors should discuss potential reasons for the dramatically different rates of MDC formation in the S288C and W303 background cells. Does this have anything to do with generally more robust mitochondrial functions in the latter cells?

      We agree this is worth discussing. One likely explanation is that the difference reflects broader differences in mitochondrial activity and metabolic state between these strain backgrounds. We and others have shown that W303 cells have more robust respiratory mitochondrial function than BY/S288C-derived cells, and in our hands W303 also shows lower MDC formation. This fits our broader model that MDCs are favored in glucose-grown or metabolically perturbed cells and do not form under respiratory conditions (Raghuram and Hughes, 2024). We do not yet know the genetic basis for this difference, so we will present this as an interesting future direction.

      (2) Proper statistical analyses should be provided for all the graphs presented.

      We will add statistical analyses where missing.

      (3) The authors should include Yme1 immunoblots to confirm the identity of strains being studied and validate the presence or overexpression of Yme1 and its catalytic mutant in their experiments.

      We agree that direct validation of Yme1 protein levels will strengthen the manuscript. Our quantitative mitochondrial proteomics already confirms strong depletion of Yme1 in yme1Δ cells, and we will also include quantitative proteomics showing increased Yme1 abundance in the overexpression strain. In addition, we have now obtained a Yme1 antibody from a colleague and will include immunoblots validating Yme1 loss, re-expression, catalytic mutant expression, and overexpression where appropriate.

      Reviewer #3 (Public review):

      Summary:

      Since describing MDCs over a decade ago, the lab of the corresponding author, Hughes, has been at the forefront of further characterizing these structures. Here, they follow up on recent work (PMID: 38497895), where a screen identified Yme1 as a potential regulator of MDCs. After confirming that Yme1-ko prevents MDCs that are usually induced via various established treatments (Rapamycin, cycloheximide, Concanavalin A), the authors confirmed that the proteolytic activity of Yme1 is required. Next, using proteomics, they identified how loss of Yme1 impacts the mitochondrial proteome with and without Rapamycin treatment to induce MDCs. From this result and based on insight from other published data implicating lipids, the focused initially on the lipid transfer protein Usp2, a known target of Yme1. Here, they showed that loss of Usp2 could partially rescue MDC formation in Yme1-ko cells. To look for other Yme1 targets that might also be involved in MDC formation, next, they investigated the MICOS complex, which was also notable in their proteomics data. They then showed that inhibiting MICOS also partially restored MDC formation in Yme1-ko cells. They then tested the combined effects of Usp2 and MDC inhibition on MDCs, which was limited by the fact that the combination of full MICOS disruption, Usp2-KO, and Yme1-KO was not viable. To circumvent this limitation, they investigated the knockout of individual MICOS subunits in combination with Usp2 and/or Yme1. Finally, they showed that growth conditions also mediate MDC formation in the context of Yme1 overexpression. In rich media, Yme1 overexpression induces MDCs on its own. However, this induction is lost upon amino acid starvation, suggesting that there are still other as-yet-unidentified factors regulating the formation of MDCs.

      Strengths:

      The authors use unbiased approaches and genetic models to begin unraveling a novel regulatory role of Yme1 in the formation of MDCs.

      Weaknesses:

      (1) The authors find both Ups1 and Ups2 in their screens, but only focus on Ups2 in this paper. It would be good to know why they did not also investigate Ups1, and its other protease Atp23, which could potentially act similarly to Yme1, or even rescue the loss of Yme1.

      We agree that Ups1 and Atp23 are important to consider. We initially focused on Ups2 because its deletion partially restores MDC formation in yme1Δ cells and because of its connection to mitochondrial PE synthesis, which we had previously shown to regulate MDC formation (Xiao et al., 2024). Ups1 is more difficult to assess genetically because complete loss of UPS1, or of downstream cardiolipin synthesis through CRD1, blocks MDC formation due to the requirement for cardiolipin. Thus, an ups1Δ phenotype cannot readily reveal whether a more moderate reduction in Ups1 activity, and the resulting accumulation or redistribution of PA, might promote MDC formation.

      In the revision, we will explain this rationale and include new genetic data targeting PA metabolism through the yeast Pah1/Lipin pathway. This provides a way to test the contribution of PA accumulation without simultaneously eliminating cardiolipin synthesis, and our initial results support a role for PA-linked lipid remodeling in partially bypassing the requirement for Yme1. We will also discuss Atp23 as a potentially important regulator of Ups1 and PA metabolism. A full investigation of Atp23 will be an important direction for future work.

      (2) I'm not convinced that the data support the notion that Usp2 and MICOS have distinct effects on MDCs. In Figure S3C-D, there is no statistical analysis to indicate whether the small differences between the MICOS-ko and the double knockout are significant. If MICOS-ko and Ups2-ko were acting through different mechanisms, one would expect their combination to be additive; this does not appear to be the case, as both single deletions and the double deletion all cause similar levels of MDCs (~30-40%). Rather, this result is what you would expect if they were working through the same mechanism. There also does not appear to be an additive effect in Figure 4F-G, when using the mic60-ko rather than the complete MICOS-ko. In this regard, the authors note in their discussion that 'loss of MICOS may disrupt membrane associations or alter lipid distribution between mitochondrial subcompartments' (lines 390-392). The latter situation seems like it would be the same mechanism as Usp2 and would more accurately explain their findings.

      This is a very good point, and we agree with the reviewer’s interpretation. The lack of strong additivity is consistent with Ups2 and MICOS acting within the same pathway or converging on a shared mechanism, rather than representing two separate mechanisms of MDC regulation. We did not intend to imply that these must be independent pathways. In the revised manuscript, we will ensure that the text reflects this interpretation and will add statistical analyses to the relevant comparisons.

      (3) The manuscript is missing key data confirming the re-expression or overexpression of Yme1 protein (Figure 1 E/G and Figure 5A). It is important to know the relative levels of expression of the re-expressed proteins to each other and to endogenous Yme1.

      We agree that direct validation of Yme1 protein levels is important. Our quantitative mitochondrial proteomics already confirms strong depletion of Yme1 in yme1Δ cells, and we will also include quantitative proteomics showing increased Yme1 abundance in the overexpression strain. In addition, we have now obtained a Yme1 antibody from a colleague and will add immunoblots validating Yme1 loss, re-expression, catalytic mutant expression, and overexpression.

      (4) Some clarification of the details for metabolically restrictive conditions would be helpful.

      Thanks for this suggestion. We will clarify these conditions throughout the manuscript and figure legends and will define exactly what we mean by low-amino-acid, amino-acid-free, synthetic, and rich media conditions. More broadly, MDC formation is strongly influenced by media composition and mitochondrial metabolic state. MDCs form less efficiently in synthetic media and do not form under conditions that promote respiratory mitochondrial function (Raghuram and Hughes, 2024).

      (5) Beyond just the presence/absence of MDCs, does more detailed quantification of their size/shape reveal any subtle differences between conditions?

      This is an interesting question. In our hands, MDC size and shape are variable and appear strongly influenced by mitochondrial fission/fusion state. Conditions that favor more fused mitochondrial networks can produce larger MDC-like structures, whereas fragmented networks can produce smaller structures. So far, we have not found a simple size or shape metric that explains the Yme1/Ups2/MICOS phenotypes better than MDC frequency.

      We will clarify this point in the revised manuscript and avoid implying that MDC frequency captures every possible morphological difference. More detailed morphometric analysis of MDC size, topology, and maturation state will be an important future direction, especially as we connect lipid remodeling to membrane curvature and MDC biogenesis.

      References

      Hughes, A.L., Hughes, C.E., Henderson, K.A., Yazvenko, N., and Gottschling, D.E. 2016. Selective sorting and destruction of mitochondrial membrane proteins in aged yeast. eLife. 5. doi: 10.7554/eLife.13943.

      Raghuram, N., and Hughes, A.L. 2024. Amino acids trigger MDC-dependent mitochondrial remodeling by altering mitochondrial function. bioRxiv. 2024.07.09.602707. doi: 10.1101/2024.07.09.602707.

      Wang, K., Jin, M., Liu, X., and Klionsky, D.J. 2013. Proteolytic processing of Atg32 by the mitochondrial i-AAA protease Yme1 regulates mitophagy. Autophagy. 9(11):1828–1836. doi: 10.4161/auto.26281.

      Xiao, T., English, A.M., Wilson, Z.N., Maschek, J.A., Cox, J.E., and Hughes, A.L. 2024. The phospholipids cardiolipin and phosphatidylethanolamine differentially regulate MDC biogenesis. Journal of Cell Biology. 223(5). doi: 10.1083/jcb.202302069.

    1. Author response:

      eLife Assessment

      This important study investigates the peptide-binding principles of promiscuous chicken MHC molecules. The data from crystallography, mass spectrometry, and modeling are convincing. However, the presentation would benefit from streamlining and clear links between data and conclusions. This paper will be of broad interest to immunologists and those interested in vaccine development.

      Overall, we are delighted and grateful to the eLife editors and the two reviewers for the careful and thoughtful assessments and reviews of our paper. We are glad that the strengths of the paper were apparent and appreciated. And of course, every paper has weaknesses, especially for a story as complex as this one.

      We are making only minor changes in our revision, so we would be happy if the editors decide to evaluate the revised manuscript without involving the reviewers further.

      Before answering the comments and questions directly, perhaps a few points would help clarify why the paper is as it is.

      First, the experiments cover over three decades of work, with the first gas phase sequencing results done in 1992. Unlike some of the chicken class I alleles which immediately gave completely clear stringent motifs (B4, B12 and B15 in Wallny et al 2006 PNAS, B19 in Han et al 2023 J Immunol), we harvested nothing but confusion from the B21 class I results (Fig. 1). Initially, we thought that the lack of a clear motif for B21 was due to multiple well-expressed class I molecules but only one dominantly-expressed class I molecule was found (Wallny et al 2006 PNAS, Shaw et al 2007 J Immunol) and, to our surprise, bacterially-expressed BF2*21:01 heavy chain and b2-microglobulin refolded with two synthetic peptides without sequence in common, and the crystal structures showed that this molecule remodeled the binding site to accommodate two such disparate peptides (Koch et al 2008 Immunity). This was the beginning of our understanding of the spectrum of class I alleles from promiscuous generalists to fastidious specialists, which we have explored in a series of further papers (in particular, Chappell et al 2015 eLife, Tresgaskes et al 2016 PNAS, Kaufman 2018 Trends Immunol, Tregaskes and Kaufman 2022 Mol Immunol).

      Second, over these many years, we continued to explore the binding properties of BF2*21:01 in ever more detail, resulting in the current manuscript. We learned only slowly how to probe this unexpected promiscuity, unprecedented in the MHC literature, so that the experiments proceeded with our best understanding at the time, including taking advantage of new approaches as they become available. Each experiment built on the previous set of experiments and each brought us closer to an understanding.

      Third, having amassed a collection of data, we chose eLIFE exactly because it allows us to present the entire story from beginning to end without compromise, not just the highlights with the major points illustrated by a few main figures and with the supporting data in many supplementary figures. We include all the data, because it is all part of the story, and so interested researchers to look at the data from their own perspective. Although mostly we provide bar graphs, we include the raw data (or close to it) for the final experiments (illustrated by Figs. 10 and 18) in the single supplementary data spreadsheet, so these can be assessed easily by others in the field, perhaps using approaches that we may not feel competent to perform.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Combining in vitro refolding, SEC-based assembly assays, peptide-library screening, MALDI-TOF, LC-MS/MS, structural analysis and immunopeptidomics, this manuscript investigates the peptide-binding principles of the promiscuous chicken MHC-I molecule BF2*21:01.

      Strengths:

      Although the peptide motif of BF2*21:01 is highly complex, this manuscript identified several principles, including a preference for 10-mer peptides, co-variation between P2 and Pc-2, effects of P3 and Pc-3, and a strong cellular preference for Leu at Pc. The results are important for avian MHC biology and poultry vaccine epitope prediction.

      Weaknesses:

      The manuscript is sometimes difficult to follow because the authors present a large amount of peptide-library, structural and immunopeptidomics data. without always clearly explaining how these datasets support the proposed simplifying principles.

      We are delighted and grateful to the reviewer 1 for the careful and thoughtful comments and questions concerning our manuscript. We are glad that the strengths of the paper were apparent and appreciated, and acknowledge the weaknesses that come with such a complex story with experiments performed over decades.

      Major Issues - Points Requiring Clarification or Additional Support:

      (1) (Line 282-301, 537-545)

      The immunopeptidomics conclusions are mainly based on one B21 cell line with one biological replicate and at least two technical replicates. Given the complexity of the BF2*21:01 peptide repertoire, this is a major limitation. The authors should either provide additional biological replicates or clearly state this limitation in the Abstract, Results and Discussion.

      This limitation is clearly stated in lines 537-545, as part of a paragraph covering the various ways in which the data presented in this manuscript could be improved. In fact, we have performed immunopeptidomics of several different B21 cell types, with many replicates and found similar data as presented, giving us confidence in our interpretations. However, these other experiments belong in different stories, so it is not appropriate that the data be reported in this manuscript.

      (2) (Lines 290-313)

      The B21 cell preparations contain both BF2 and the lowly expressed BF1 molecule. Some peptides, especially 8-mers or peptides with atypical motifs, may derive from BF1*21:01. The authors should clarify how BF2*21:01-bound peptides were distinguished from possible BF1-derived peptides, or interpret the immunopeptidomics motif more cautiously. The authors should also provide or cite evidence confirming the B21 haplotype identity of the cell line and chicken materials used for immunopeptidomics.

      The concern about the contribution of BF1*21:01 to the immunopeptidomics is clearly stated in the manuscript, both lines 290-313 and as part of the paragraph describing the limitations of the experiments (lines 542-543). In fact, the expression of BF1 molecules has long been known to be less than 10% of BF2 molecules at the RNA level, and much less at the protein level (Wallny et al 2006 PNAS, Shaw et al 2007 J Immunol). The proportion of 8mers identified by immunopeptidomics is also low (Fig. 14), and it is not impossible that most 8mers are due to BF1*21:01. We have used assembly assays with peptide libraries, immunopeptidomics and a crystal structure to determine the peptide motif for typical BF1 molecules, of which BF1*21:01 is one and found it may contribute to 8mer peptides but very seldom to longer peptides. This work is unpublished but gives us confidence that the characteristics of BF2*21:01 are not misrepresented by the data in this manuscript.

      The sources of the chicken samples and the cell lines are described in detail under Materials and Methods (lines 577-590), citing relevant publications. 

      (3) (Lines 217-221, 243-253)

      The authors acknowledge that MALDI-TOF cannot reliably distinguish peptide combinations with identical or similar masses, nor determine residue positions in some cases. Therefore, MALDI-TOF results should not be over-interpreted as precise evidence for residue preference. The authors should clearly indicate which conclusions are supported by LC-MS/MS.

      As described, the experiments follow each other in temporal sequence, so that we started with single peptides, then peptide libraries that varied in one position, then peptide libraries that varied in two positions first analysed by MALDI-TOF and later by LC-MS/MS. The final experiment (Fig. 10, with the original data in the supplementary spreadsheet) directly compares MALDI-TOF and LC-MS/MS results for six peptide libraries, so that the strength of the evidence for residue preference is clear. Throughout the manuscript, we do our best to not to overstate conclusions based on the data of any particular experiment.

      (4) (Lines 297-301, 316-330)

      The authors suggest that longer peptides may bulge in the middle or extend out of the groove at the C-terminal end. The rationale for the C-terminal extension is not clearly explained. Why is the C-terminal extension considered rather than the N-terminal extension? If the binding register is uncertain, long peptides should be analyzed separately from canonical-length peptides.

      When the first sequence of a chicken class I cDNA was determined, an immediate mystery was why one of the so-called invariant residues that coordinate the N- and C-termini of the bound peptide is not conserved (Kaufman et al 1992 J Immunol). In fact, this residue Tyr at position 86 in HLA-A2 and the equivalent position in all mammalian classical class I molecules is an Arg in the classical class I molecules of all non-mammalian vertebrates and is common with class II molecules (Kaufman et al 1995 Semin Immunol). Similar to class II molecules, this Arg in chicken class I molecules allows the peptide to extend out of the C-terminus, as shown by a crystal structure (Xiao et al 2018 J Immunol). The concern that we might be misidentifying the C-terminal amino acid was the basis for the analysis in Figs. 23 and 24, but in the absence of crystal structures, we are not able to provide a final answer this question. Perhaps relevant is the fact that a chicken class II molecule can bind exactly the same peptide in two conformations, one with a canonical 9mer core and the other with an unexpected 10mer core (Goryanin et al 2026 J Virol).

      By contrast, N-terminal extensions are only found for some class I alleles and thus far depend on the substitution of small amino acid sidechains for W166 (Li et al 2011 J Virol for bovine, Ma et al 2020 J Immunol for Xenopus, Wei et al 2022 J Immunol for ovine). Thus far, no chicken BF2 sequences have this substitution, consonant with the many crystal structures, including those for BF2*21:01 (Koch et al 2008 Immunity, Chappell et al 2015 eLlife, this manuscript). However, in unpublished data, we find that most BF1 sequences have sequence differences that could allow N-terminal extensions, although we have no crystal structures to support this possibility.

      (5) (Lines 406-439)

      In vitro assembly assays show that several hydrophobic residues can be tolerated at Pc, whereas immunopeptidomics shows a strong Leu preference at this position. The authors should clarify whether this Leu preference reflects intrinsic BF2*21:01 binding specificity, TAP-mediated peptide transport, antigen processing, peptide loading, or a cell-line-specific effect. Additional experimental support, such as TAP transport analysis, would strengthen this conclusion.

      The preference for Leu at the final position of the peptide by immunopeptidomics of the B21 cell line is strong but not absolute and is certainly affected at the least by the length of the peptide (Figs. 23 and 24). Unpublished immunopeptidomics results (mentioned above) show that this is not a cell line-specific result. The evidence from assembly assays of various peptides is that several hydrophobic amino acids are tolerated with sufficient stability of BF2*21:01 that they are detected in the assay (Figs. 3, 5, 9 and 10). Thermostability assays (Fig. 6) show that peptides with these same hydrophobic amino acids are stable to at least body temperature of chickens. These experiments show that such stability is peptide-dependent (that is, whether a particular amino acid is tolerated depends on the stability conferred by the rest of the peptide). Finally, peptide translocation assays using B21 cells have been done (Tregaskes et al 2016 PNAS) and show that peptides with several hydrophobic amino acids can be pumped into the lumen of the endoplasmic reticulum. However, the assays are with single synthetic peptides, so the data are not extensive enough to separate the effects of the final amino acid from the rest of the peptide. Certainly, peptides with amino acids other than Leu at the C-terminus can be translocated. So, it is not yet clear at which point the preference for Leu at the C-terminus of the peptide arises.

      (6) (Lines 172-178, 243-279, 442-457)

      The structural analysis explains some residue combinations, such as Arg at P2 with Glu at Pc-2 or Trp at Pc. However, the structural interpretation is not fully integrated with the large-scale peptide library and immunopeptidomics results. Representative high- and low-frequency combinations should be discussed structurally.

      Six crystal structures show that BF2*21:02 remodels the binding to accommodate a variety of anchor residues (Koch et al 2008 Immunity, Chappel et al 2015 eLife). These crystal structures are representative of sequences found by the immunopeptidomics from very frequent (H-E at roughly 15% 8-12mers) to moderately frequent (E-L at roughly 6% 8-12mers) to infrequent (N-F, A-D and E-D at roughly 1.5%, 1.6% and 0.7% 8-12mers) based on Fig. 18. All but one of the structures has Leu at the C-terminus, with the last one having Val which is found but not frequently by immunopeptidomics.

      Similar numbers are found by LC-MS/MS of double-substitution libraries of the two original peptide sequences in Fig. 10 with H-E found frequently (8.1% in P390, 3.8% in P498) and the others infrequently (0.1, 0.9, 1.0, 0.3% in P390, 0, 1.4, 1.0, 0.3% in P498), as calculated from the numbers in the Supplementary data spreadsheet. As discussed in the manuscript, for single-substitution peptide libraries of the two original peptides, Ile/Leu at the C-terminus was very frequent but at the same or slightly less level as Phe, with Met less frequent and Val even less so (Fig. 7).

      In addition, there are two more structures along with models explicitly testing some substitutions (Fig. 5). Attempting more current modelling approaches, we found AlphaFold 3 was unable to correctly predict most of the conformations that are found in the crystal structures of BF2*21:01, so we don’t feel confident in using them to predict unknown structures of this kind.

      (7) The inference of co-variation between P2 and Pc-2, as well as the modulatory effects of P3 and Pc-3, should be better explained. At present, some conclusions appear to be based mainly on residue-frequency patterns, and the logical connection between these observations and the proposed binding principles is not always clear. Statistical analyses, such as mutual information, chi-square tests or permutation tests, and representative structural explanations would strengthen this conclusion.

      We endeavored to do our best to explain the data, our interpretations and our reasoning, so we apologise if we have not managed to be as clear as might be desired. We have included as close to raw data as possible for the LC-MS/MS and MALDI-TOF (Fig. 10) and for the immunopeptidomics (Fig. 14 and 18) in the Supplementary Data spreadsheet, exactly so that competent practitioners can carry out further analyses (including the sophisticated statistical tests mentioned).

      Reviewer #2 (Public review):

      Summary:

      The study presents an in-depth analysis of the peptide repertoire bound by a promiscuous chicken MHC molecule using mass spectrometry, x-ray crystallography and modelling. While the MHC can bind a very diverse set of peptides, the authors have found some new rules that govern peptide binding to this MHC that could help to build a predictive model to study the repertoire of pathogen-derived peptides.

      Strengths:

      The study uses a range of well performed experiment across multiple techniques and provides an in-depth analysis of the peptide repertoire, including peptide sequences, length, preferred residues, stability and MHC presentation.

      Weaknesses:

      The data overall support the analysis and conclusion well. The only caveat is linked to Figure 4, which does not describe the stability of the peptide-MHC complex, but instead shows refold yield, and the two are not always linked.

      We are grateful for the clear understanding of the strengths of the work. With regards to Fig. 4, we agree with the reviewer that there are differences in refold yield but that measure may not be correlated with stability of the peptide-MHC complex. However, we were basing our interpretation of stability on the position and quality of the monomer peak, as illustrated by the trace in Fig. 2, in which a sharp peak at the monomer position represents a stable complex (as seen for the 10 and 11mer peptides) and later peaks represent unstable complexes falling apart during the chromatography (as seen for the 7, 8 and 9mer peptides).

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript entitled "Essential function reflected in the phylodynamics of a multigene family - the pir genes of malaria parasites" by Jackson and colleagues investigates the global phylogeny of pir genes across 14 Plasmodium species and one Hepatocystis species. The authors also focus on the functional characterization of the conserved ortholog pirC1 and claim that pirC1 is not the founder of the family and that it plays an essential role in blood-stage growth.

      Strengths:

      Overall, the manuscript is well written and interesting, as it combines comparative genomics and evolutionary analysis with functional experiments. The phylogenetic analysis is rigorous and represents a major strength of the manuscript.

      Weaknesses:

      The general conclusions regarding the potential function of this gene family are not fully supported by the data presented. The manuscript moves too quickly from growth phenotype and localization studies to a specific mechanistic model. The discussion argues that PIRC1 may be involved in nutrient acquisition, host sensing, or metabolic support, but the data provided do not directly support these functions, and the manuscript in its present form remains speculative. Although the manuscript includes some experimental results, it lacks direct mechanistic validation of the specific functions of the pir genes, including pirC1. In its current form, the study does not yet establish a definitive role for pirC1 in metabolic processes.

      The reviewer is correct that there is no definitive proof for the function of the PIRC1 protein. We speculate that this protein is involved in a metabolic process based on mutant phenotype – small, poorly developed parasites that do not produce the same amount of DNA as wildtype parasites (and hence likely fewer merozoites). That this occurs in an in vitro culture of Plasmodium knowlesi rules out a role in the interaction with the host organism, such as sequestration or facilitating passage through the spleen. The localization of the protein outside of the parasite is consistent with a role in nutrient uptake, but we agree that additional experiments are required to determine the role of the protein definitively. We aim to look at the differences in the transcriptome and the metabolome to gain more insight into the pirC1 phenotype; this should reveal metabolic deficiencies in the mutant parasite.

      Reviewer #2 (Public review):

      Summary:

      This is an extensive study using phylogenetic comparison across multiple plasmodium species to gain new insights in relation to their evolutionary pathways and the potential function of pir. In addition to establishing a framework to identify related orthologues across species as well as expanding paralogues families within a species, the work also focuses on understanding loss and gain of different PIRs and how this indicates a relative lack of functional constraints and essentiality for most members of the gene family.

      The authors provide evidence that at least pirC has a conserved function and plays an important role in parasite growth in multiple species.

      While this study represents a significant effort and does provide interesting new insights that would help our understanding of this complex gene family in the future, it has a number of limitations.

      Strengths:

      Extensive and thorough phylogenetic analysis that is supported by some biological validation. Provides an indication that the PIR gene family has limited biological constraints and evolved independently across different species, leading to rapid expansion and deletion of orthologous groups. Identified pirC as a functional and important member of the family that is conserved across the species.

      Weaknesses:

      The phylogenetic tree is based on a truncated sequence that focuses on the more conserved parts of the pir sequence. This could potentially lead to missing the key functional drivers of evolution. The biological validation of the role of pirC has some inconsistencies that need to be addressed.

      The reviewer is correct. We do not use the repetitive parts of the pir gene sequences for the phylogeny. We define these as the ‘distal variable’ and ‘proximal’ domains of the protein in Fig. S1, results text and supplementary results. We remove these parts from the alignment because they are only nominally homologous (they cannot be aligned) and so break the basic assumption of phylogenetic analysis. Amino acid repeats evolve quickly and are homoplasic (their similarities do not reflect ancestry) so omitting them is correct and makes the phylogeny more reliable. While these features do not contribute to the phylogenetic estimate, we propose in the results text and Fig. S3, in agreement with the reviewer, that they are an important demonstration of how pirs have differentiated and what is different between the subfamilies. The reviewer is also correct that we have considered the whole gene sequence when comparing Alphafold predictions and in selection analyses of closely related sequences (in these cases, the repeat sequences can be aligned).

      A structural prediction for the sequence used in the alignment would mostly reflect the distal conserved domain but would be misleading because the alignment combines conserved regions that are not physically attached in reality. We will clarify these points.

      Reviewer #3 (Public review):

      This paper aims to classify, from an evolutionary perspective, the multigene family PIR found in malaria parasites infecting rodents and Old World monkeys, and to link this classification to functional diversification. The authors also hypothesize that PIR members conserved across species play important roles in parasite survival, and seek to clarify their functions.

      To achieve these aims, the authors comprehensively analyze the evolution of PIR genes using genomic and transcriptomic information from many malaria parasite species. They focus on PIRC1, a member conserved across species, and attempt to clarify its function in rodent and simian malaria parasites by examining the phenotypes of parasites in which the corresponding genetic locus has been disrupted. They also attempt to determine its localization using PIRC1 tagged with an epitope sequence. However, although the locus-disrupted parasites appear to show an approximately 50% reduction in growth rate, this effect seems to be overestimated. Another weakness is that the cause of the reduced growth rate has not been clarified. The localization analysis also remains insufficiently conclusive.

      Therefore, I consider that the first half of the paper, consisting of the bioinformatics analyses, achieves the objective of comprehensively summarizing PIR and may become a reference paper for discussing the evolution and function of the PIR gene family. On the other hand, regarding the function of PIRC1, no clear conclusion can be drawn from the results presented, and several additional experiments are necessary.

      My major comments are as follows.

      (1) The claim that the failure of eight disruption attempts indicates that pirC1 is essential is too strong.

      Lines 319-321: The authors argue that a total of eight failed attempts to disrupt the pirC1 locus using two different construct designs suggest that pirC1 is essential in P. berghei. However, the failure of these attempts could also reflect technical issues with the construct design itself, such as the length of the homologous regions used for recombination, which are approximately 650 bp. Therefore, it is an overstatement to conclude that "pirC1 is essential for P. berghei blood-stage growth." Given that parasites with disruption of the corresponding locus could be obtained in both P. chabaudi and P. knowlesi, a more appropriate statement would be that "pirC1 is important for P. berghei blood-stage growth."

      It is correct that we cannot rule out that the inability to delete the pirC1 gene is Plasmodium berghei is unrelated to an essential function. We are happy to change the text to the suggested description.

      (2) The data on the mCherry-expressing P. berghei line shown in Supplementary Figure 11 are insufficient.

      (a) Panel C: Southern blot analysis

      To conclusively identify the lower band in panel C as chromosome 1, additional probes specific to genes located on chromosomes 1 and 2 would be required. In addition, a parental parasite control should also be included. The Southern blot image of the parental parasite should show only a single band at the higher position, with no band at the lower position. Probes specific to chromosomes 1 and 2 would help demonstrate that the lower band corresponds to chromosome 1, rather than chromosome 2.

      To this end, the authors could describe the result as follows:

      "In the parental parasite, only a single band corresponding to chromosome 7 was detected, indicating that the smaller chromosome was genetically modified. The size of the lower band detected with the dhfr probe was identical to that of the band detected with the control chromosome 1 probe, but distinct from that detected with the chromosome 2 probe, indicating that chromosome 1 was modified."

      That said, this chromosome-level Southern blot analysis is not sufficient to demonstrate that the target PBANKA_0100500 locus was specifically modified. The authors should provide more direct evidence showing that the PBANKA_0100500 locus, rather than another genomic locus, was modified. For example, Southern blot analysis after restriction enzyme digestion would provide more definitive evidence. Diagnostic PCR may also provide more specific evidence.

      Although we are confident that the parasites has been modified in the expected way, we are planning to generate PCR data confirming that the mCherry tag is correctly integrated into PBANKA_010050.

      (b) Panel D: Flow cytometry analysis

      To allow a more accurate interpretation of the percentage of mCherry-positive cells, flow cytometry data for the parental parasite line should also be presented.

      We will repeat the flow cytometry experiments and include a wildtype strain in the analysis.

      (3) There are unclear points in the PCR results shown in Supplementary Figure 12.

      Supplementary Figure 12: In panel B, a PCR product should also be amplified from dPCHAS_0101200 using the P1-P3 primer pair. Why is this band absent? The authors should provide the uncropped electrophoresis image so that the larger band can be seen. In addition, if labels 1 and 2 indicate independent clones, this should be stated in the figure legend.

      We will gladly supply the full, uncropped electrophoresis image and we will clarify what the numbers indicate in the legend.

      (4) The growth rates of P. chabaudi and P. knowlesi parasites with disruption of the PIRC1 gene locus should be quantitatively analyzed.

      The growth rates of P. chabaudi and P. knowlesi are described only qualitatively, but they should be evaluated quantitatively. In Figure 4A, the parasitemia of wild-type P. chabaudi increases from approximately 6.1% on day 6 to approximately 15.6% on day 8, corresponding to a 3.8-fold increase. However, because parasite growth may already be affected by immune-mediated suppression at this stage, this value should be regarded as a minimum estimate. In contrast, the mutant increases from approximately 3.2% on day 8 to approximately 6.8% on day 10, corresponding to a 2.1-fold increase. Based on these values, the daily growth rate of the mutant appears to be reduced to at least approximately 56% of that of the wild type. Similarly, from the growth curve of P. knowlesi in Fig. 5A, the DMSO-treated group appears to increase approximately two-fold per day, whereas the rapamycin-treated group increases only approximately one-fold per day. Thus, P. knowlesi also appears to show an approximately 50% reduction in growth rate. Taken together, both P. chabaudi and P. knowlesi appear to reproducibly show an approximately 50% reduction in growth capacity. A reduction of this magnitude is difficult to describe as a "severe growth defect"; a more appropriate wording would be simply that the parasites "showed a growth defect." In addition, the terms "a severe growth defect" and "essential" appear to be overstated throughout the manuscript, and the wording should be toned down. Finally, I recommend presenting Figure 4A and Figure 5A on a logarithmic scale so that the trend in growth rates can be more intuitively appreciated from the graphs.

      It should be possible to determine the growth rate of the wildtype and mutant P. knowlesi parasites. In addition, we can change the text to reflect that although there is a growth phenotype in the two species in which we obtained mutants, the parasites do have the capacity to replicate. Note that in the case of P. knowlesi, the parasites numbers in vitro do not increase, hence any additional factors that decrease the growth rate, such as immune system and spleen, will lower the reproductive rate further and render the mutant parasite unable to proliferate.

      (5) The evidence that disruption of the PIRC1 gene locus in P. knowlesi does not affect erythrocyte invasion is weak.

      The authors describe that "the developmental cycle of the parasites lacking PIRCl is slightly longer than that of parasites that produce PIRCl (line 383-384)," and appear to support this interpretation with data showing that "mutant parasites are significantly smaller than wild-type parasites (line 414)" and that "the DNA content in ML10-arrested parasites lacking PIRCl is lower than that of DMSO-treated parasites (line 417-418)" at 24 hours after invasion. However, a slightly longer developmental cycle alone does not seem sufficient to explain a 50% growth reduction.

      I think the erythrocyte invasion capacity has not been quantitatively evaluated, and therefore, the evidence supporting the conclusion that the phenotype of P. knowlesi parasites with disruption of the PIRC1 gene locus is unrelated to erythrocyte invasion is weak. The authors should assess invasion efficiency using purified merozoites. For P. chabaudi, it should also be possible to apply an in vitro or in vivo erythrocyte invasion assay similar to that used for other rodent malaria parasites, and this should be evaluated as well.

      We can further investigate the invasion phenotype of the mutant P. knowlesi parasites. The presence of a clear phenotype during the intraerythrocytic stage indicates that the protein also has a role after invasion, but we agree that determining the effect on invasion directly will be useful.

      Alternatively, the reduced DNA content in ML10-arrested parasites lacking PIRC1 (lines 416-417) could suggest that the number of merozoites formed per schizont may be reduced. To clarify this point, the authors should assess whether the number of merozoites per schizont is altered in P. knowlesi (and P. chabaudi parasites lacking PIRC1).

      We aim to count merozoites and the level of invasion, which will allow us to determine the reproductive rate of the mutant parasites.

      (7) The authors propose the possibility that PIRC1 expressed in merozoites is released after invasion; however, the evidence that PIRC1 localizes to intracellular organelles is weak.

      Line 333: "a peripheral pattern around the parasite" is indicative of parasite plasma membrane, PV, or PVM. ", indicative of a parasitophorous vacuole (PV) or parasitophorous vacuole membrane (PVM) location" should be amended to ", indicative of parasite plasma membrane, a parasitophorous vacuole (PV) or parasitophorous vacuole membrane (PVM) location". In the Figure S14 image, red signals are uniformly detected from the merozoites formed in the schizont stage parasite (not really microorganelle patterns), but not from the PVM surrounding the schizont, suggesting parasite plasma membrane localization, not PVM. I agree that the signal is detected from the compartments extending into the iRBC cytosol, which may be difficult to explain if it is located on the parasite plasma membrane, but how frequently were such images seen?

      To determine the localization of the protein in the merozoite, we will image P. knowlesi merozoites.

      Figure 4D. In the images of liver-stage schizonts, AMA1 does not appear to localize to the micronemes in mature merozoites, suggesting this image is an immature schizont. Although PIRC1 appears to be expressed in liver-stage schizonts, it is difficult to clearly determine whether it localizes to intracellular organelles or to the parasite plasma membrane.

      This is a valuable comment. It is difficult to impossible to determine the exact localization of the protein at this stage, irrespective of the exact stage of the parasite. It is clear from the images is that the protein is not secreted at this stage. The main aim of the experiment was to determine whether the protein is produced by the parasite during the liver stage, which the results confirm.

      To clarify the above points, the authors should examine whether PIRC1 is detected in intracellular organelles or around the merozoites by analyzing its localization in purified merozoites.

      This we aim to do.

    1. Author response:

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

      eLife Assessment

      This valuable manuscript presents an open-source and low-cost acoustic system for quantifying biting and chewing in mice. The approach is carefully validated against human observers, demonstrating strong methodological reliability and enabling high-resolution analysis of feeding microstructure. The tool has broad relevance for studies of appetite circuits and pharmacological interventions. An important contribution is the identification of previously unrecognized "meal-related" neurons in the lateral hypothalamus, providing novel biological insight into solid food consumption. While the support for the methodological advances is compelling and robust, some circuit-level conclusions are preliminary or incomplete, relying on small pilot samples and manual classification, and should be interpreted with caution. This paper will be of interest to those interested in ingestive behavior and/or the hypothalamus.

      We thank the reviewers for their careful reading and constructive comments, which have substantially strengthened the manuscript. In the revised version, we have addressed every suggestion and introduced the following major additions: New experiments. We added one additional Vglut2 mouse to the calcium imaging cohort, achieving 386 neurons (Figure 8), and three naive Vgat mice with unilateral DREADD injections (Supplementary Fig. 5-1). New analyses. We performed ROC analyses on all feeding- and licking-related responses of n = 79 LH GABAergic and n = 386 LH glutamatergic neurons (Figures 7D-F and 8D-F). We also characterized the robustness of the Crunchometer to additive white-noise injection (Supplementary Fig. 1-2). New supplementary material. Three new supplementary figures have been added in total (Supplementary Figs. 1-2, 5-1, and 6-1). Supplementary Fig. 6-1 provides instructions for building a 1-Hz pulse generator that blinks an LED in synchrony with the video. Software improvements. We upgraded the original MATLAB scripts to an App GUI version, migrated the full codebase from MATLAB to Python, and packaged it as fully standalone executables for macOS (Apple Silicon) and Windows both of which run without a MATLAB license.

      Our point-by-point responses to the reviewers' comments are in red below. Deletions are omitted for brevity. We hope that the revisions fully address the points raised and render the manuscript suitable for publication.

      Public Reviews:

      Reviewer #1 (Public review):

      This is an interesting and valuable paper by Gil-Lievana, Arroyo et al. that presents an open-source method (the "Crunchometer") for quantifying biting and chewing behavior in mice using audio detection. The work addresses an important and unmet need in the field: quantitative measures of feeding behavior with solid foods, since most prior approaches have been limited to liquids. The authors make a clear and compelling case for why this problem is important, and I fully agree with their motivation.

      The system is carefully validated against human-scored video data and is shown to be at least as accurate, and in some cases more accurate, than human observers. This is a major strength of the study. I also particularly appreciate the demonstration of the technology in the context of LHA circuitry, which nicely illustrates its utility and importance for mechanistic studies of feeding. I also appreciate the ability to readily time-lock neural data to individual crunches. Overall, the manuscript is well-executed and represents a useful contribution to the field.

      We thank you for your appreciation of the Crunchometer and its alignment with ephys:

      To further facilitate alignment with neuronal activity, we have now also included a schematic diagram of the pulse generator used to blink an LED in synchronization with the video (see the new Supplementary Fig. 6-1).

      The comments I have are largely minor and should be straightforward to address:

      (1) The authors should report sample sizes for all mouse cohorts, either alongside the statistics or in the figure legends for mean data.

      We apologize for this oversight. We have now included all sample sizes in the figure captions.

      (2) Clarification is needed as to whether crunch detection fidelity is influenced by the hardness or softness of the food. The focus here is on standard pellets, with some additional high-fat pellet data, but it would be useful to know how generalizable the method is across different textures.

      We thank the reviewer for this important observation. Because the Crunchometer depends on bites generating an audible acoustic signal, food hardness directly impacts detection fidelity. Hard, brittle foods are readily detected, whereas soft foods such as jelly, pudding, or peanut butter are unlikely to produce a reliably detectable signal. This is a genuine scope limitation of the method, and we now make it explicit in the manuscript (see below).

      Regarding the two diets used in our study, Chow and HFD pellets differ only slightly in consistency, with HFD being marginally softer. These differences proved too subtle to separate acoustically: the intensity (dB) and spectral content of bites on the two diets were closely overlapping. Accordingly, when we trained an SVM on audio features alone, it could not reliably discriminate Chow from HFD bites.

      Importantly, the Crunchometer does not need to resolve food identity from sound, because audio and video play complementary roles in the system: the acoustic channel confirms that a bite occurred, while the mouse's position within the food-specific ROI determines which food was consumed. This division of labor is what allows per-diet attribution despite acoustically similar pellets.

      We have added to the Result section:

      “The Crunchometer, therefore, does not need to infer food identity acoustically: audio confirms that a bite occurred, and the mouse's position within a food-specific ROI identifies which food was consumed. This design enables per-diet attribution even for pellets with indistinguishable crunch signatures.”

      We fully agree with the reviewer that the study of solid-food consumption should not be restricted to standard murine diets. Foods with naturalistic textures, for example, the Granny Smith apple, chocolate, and salted peanuts used by O'Connell et al. (2025), span a much wider range of hardness and elasticity than Chow vs. HFD, and would likely generate more clearly differentiated acoustic signatures. We hypothesize that the Crunchometer could generalize to such foods to the extent that each food produces a clear and distinct acoustic pattern, and even where acoustic signatures overlap, ROI-based spatial attribution would continue to resolve food identity as long as each food is presented at a separate, trackable location.

      To make this scope explicit for readers, we have added the following clarification to the Behavioral Protocol section:

      "Our study is limited to the acoustic detection of standard Chow and HFD pellets, both of which exhibit a firm, brittle consistency. Future work should evaluate the fidelity of the Crunchometer across a broader range of food textures, encompassing varying degrees of hardness and elasticity, as explored by O'Connell et al. (2025)."

      (3) The authors should comment on how susceptible the Crunchometer is to background noise. For example, how well does it perform in the presence of white noise, experimenter movement, or other task-related sounds?

      We thank the reviewer for this valuable comment. The Crunchometer performs reliably in controlled, low-noise environments, but like any acoustic detection system, it is vulnerable to interference from sounds whose spectral content overlaps with the bite-related frequency band (500–950 Hz). To quantify this vulnerability, we stress-tested both the threshold-based and SVM-based detection methods by adding white noise to the original audio recordings at progressively decreasing amplitudes and measuring how detection performance degraded as the signal-to-noise ratio decreased. We found that the threshold-based method was more robust to white-noise contamination than the SVM-based method, maintaining acceptable detection performance at lower SNR values before degrading [see the new Supplementary Fig. 1-2].

      First, the white noise amplitude is generated as follows:

      Where L<sub>𝑛𝑜𝑖𝑠𝑒</sub> is the desired amplitude of the White Noise in dB. Then, the audio signal was range-normalized to its absolute maximum value, and the white noise was added with its desired amplitude, as shown by the following formula:

      (4) Chemogenetic activation of LHA GABAergic neurons is used. DREADD-based activation may strongly drive these neurons in a way that is not directly comparable to optogenetic or more physiological manipulations. While I do not think additional experiments are required, it would strengthen the discussion to briefly acknowledge this limitation.

      We thank the Reviewer for this thoughtful observation, which we agree with. Chemogenetic activation of LHA GABAergic neurons via DREADDs does not reproduce the physiological firing dynamics of these neurons along several dimensions: it imposes a sustained, tonic drive lasting hours after CNO administration; it likely produces firing rates above the endogenous range; and it lacks the fine temporal structure, phasic bursts, behaviorally- phased locked activity that these neurons exhibit during natural feeding episodes.

      We recognize, however, that this limitation is not unique to chemogenetics. Optogenetic approaches likewise fail to reproduce endogenous activity, as they impose synchronous, high-frequency activation patterns on a single cell type that are unlikely to occur under physiological conditions. Moreover, as we previously described in a phenomenon our laboratory termed optoception (Luis-Islas et al., 2022), optogenetic stimulation can itself generate signals perceptible to the animal, adding a further interpretive caveat. Thus, both techniques depart from physiological activity.

      For these reasons, we interpret our findings as evidence that activation of LHA GABAergic neurons is sufficient to drive the observed behavioral effects, without claiming that the endogenous firing pattern encodes these behaviors in the same manner or with the same dynamics imposed by our manipulation. We have now added a brief statement to the Discussion acknowledging this limitation explicitly:

      “A methodological consideration is that chemogenetic activation via DREADDs imposes a sustained, supra-physiological drive that does not reproduce the temporal structure of endogenous LHA GABAergic activity during feeding; optogenetic manipulations share analogous limitations (see optoception; Luis-Islas et al., 2022). Our findings, therefore, establish that activation of this neuronal population is sufficient to produce uncontrolled feeding and gnawing, without implying that its endogenous firing encodes them in the same manner.”

      Reviewer #2 (Public review):

      Summary:

      This manuscript introduces the Crunchometer, a low-cost, open-source acoustic platform for monitoring the microstructure of solid food intake in mice. The Crunchometer is designed to overcome the limitations of existing methods for studying feeding behavior in rodents. The goal was to provide a tool that could precisely capture the microstructure of solid food intake, something often overlooked in favor of liquid-based assays, while being affordable, scalable, and compatible with neural recording techniques. By doing so, the authors aimed to enable detailed analysis of how physiological states, drugs, and specific neural circuits shape naturalistic feeding behaviors.

      Strengths:

      The study's strengths lie in its clear innovation, methodological rigor in validation against human annotation, and demonstration of broad utility across behavioral and neuroscience paradigms. The approach addresses a significant methodological gap in the field by moving beyond liquid-based feeding assays and provides an accessible tool for precisely dissecting ingestive behavior. The system is validated across multiple contexts, including physiological state (fed vs. fasted), pharmacological manipulation (semaglutide), and circuit-level interventions (chemogenetic activation of LH neurons), and is further shown to integrate seamlessly with both electrophysiology and calcium imaging.

      (1) Introduces a low-cost, open-source acoustic tool for measuring solid food intake, filling a critical gap left by expensive and proprietary systems.

      (2) Makes the method easily adoptable across labs with detailed setup instructions and shared benchmark datasets.

      (3) Provides high temporal precision for detecting bite events compared to human observers.

      (4) Successfully distinguishes feeding microstructure (bites, bouts, IBIs, gnawing vs.

      consumption) with greater objectivity than manual annotation.

      (5) Demonstrates compatibility with electrophysiology and calcium imaging, enabling fine-scale alignment of neural activity with feeding behavior.

      (6) Effectively discriminates between fed vs. fasted states, validating physiological sensitivity.

      (7) Captures the pharmacological effects of semaglutide, although this is really just reduced feeding and associated readouts (bouts, latency, etc).

      (8) Has potential to distinguish consummatory vs. non-consummatory behaviors (e.g., food spillage, gnawing); however, the current SVM model struggles to separate biting from gnawing due to similar acoustic profiles, and manual validation is still required.

      (9) Provides potential for closed-loop experiments.

      Weaknesses:

      Several limitations temper the strength of the conclusions: the supervised classifier still requires manual correction for gnawing, generalizability across different setups is limited, and the neuroscience findings, particularly calcium imaging of GABAergic and glutamatergic neurons, are based on small pilot samples. These issues do not undermine the value of the tool, but mean that the neural circuit findings should be interpreted as preliminary.

      We sincerely thank the Reviewer for the careful and generous reading of our manuscript, and particularly for recognizing the methodological gap that the Crunchometer seeks to fill. We appreciate the acknowledgment that the tool's validation spans physiological, pharmacological, and circuit-level contexts, and that its integration with electrophysiology and calcium imaging was considered seamless. The Reviewer has also accurately identified the three main limitations of the current version of the platform, which we address in turn below:

      (1) The supervised SVM classifier still requires manual correction for gnawing.

      We agree with the Reviewer. The acoustic signatures of biting (consummatory) and gnawing (non-consummatory manipulation of the pellet) share overlapping linear spectrotemporal features that our SVM exploits for discrimination. This overlap reflects a genuine biomechanical similarity (both involve incisor contact with the pellet surface) rather than a shortcoming of the classifier per se. In ongoing work toward Crunchometer 2.0, we are addressing these limitations. The Crunchometer 2.0 will incorporate more sophisticated deep learning algorithms, such as ResNet, to better exploit non-linear features. Also, we are currently collecting a larger database of bite, gnawing, and environmental noise sounds across different setups, microphones, and conditions to build a more robust dataset for training new AI algorithms that can discriminate between gnawing and biting and generalize more robustly across microphones and behavioral setups. This effort will also be important for developing a closed-loop version of the Crunchometer to detect bites in real time and trigger an actuator (e.g., a laser). But we agree that, for the present manuscript, gnawing classification remains the weakest link in the pipeline.

      Nevertheless, we think that having a human in the loop is an advantage (not a disadvantage) of the equipment, as it improves the quality of database curation. No matter how sophisticated future algorithms become, human intervention will remain essential. To this end, we have now developed a human-validation GUI that further facilitates human revision of snippets through an intuitive, easy workflow, reducing human effort (Author response image 1).

      Author response image 1.

      The visual validator GUI allows a human to verify and reclassify snippets into the correct category in a friendly interface.

      (1) Generalizability across different setups is limited.

      This is a fair concern and one we have taken seriously, as noted above, and one we have already recognized. The acoustic signal captured by the Crunchometer is inherently sensitive to the geometry and material of the box, microphone placement, the ambient noise floor of the vivarium or experimental room, and the hardness of the specific pellet batch. To mitigate this, we have 1) released the full hardware specifications and bill of materials so that other laboratories can reproduce the acquisition geometry, and 2) provided the benchmark dataset and trained classifier weights so that groups using comparable setups can deploy the tool directly. We have already acknowledged that the SVM does not always generalize across setups. In this regard, we have now shown that the threshold method is more resistant to white-noise contamination (see new Supplementary Fig. 1–2) and, in our experience in the lab, it performs robustly across multiple setups and conditions we have tested. More importantly, improved algorithms are currently under development in our laboratory.

      (1) Some neuroscience findings (calcium imaging of GABAergic vs. glutamatergic neurons) are based on small pilot samples (n=2 mice per condition), limiting generalizability.

      (3) The neuroscience findings (calcium imaging of GABAergic and glutamatergic LH neurons) are based on small pilot samples.

      The Reviewer is correct, and we appreciate the comment. As noted in the manuscript, we explicitly state in the Results and Discussion that these findings are presented as preliminary. As the Reviewer noted, these findings do not undermine the value of the Crunchometer; we fully agree. The calcium imaging experiments were designed as a proof-of-concept to demonstrate that the temporal precision of the Crunchometer is sufficient to align neural activity with individual bite events, rather than as a definitive circuit-level characterization of LH GABAergic and glutamatergic populations during feeding. Nevertheless, we have now increased the number of Vglut2 mice by 1, bringing the total number of glutamatergic neurons to 386. We have now also performed a formal quantification of all the experiments recorded in Vgat (n=2, three sessions, 79 neurons) and Vglut2 (n=3, 6 sessions, 386 neurons). This new formal analysis uncovers neurons selectively tuned to liquid, solid, and both food types. A fully powered characterization of these two populations is underway in our laboratory, once funding arrives in the lab, and will be reported in a dedicated follow-up study.

      (2) Chemogenetic and pharmacological experiments used small cohorts, raising statistical power concerns.

      The chemogenetic experiments were conducted with a modest sample size (n = 4 bilaterally infected mice). Nevertheless, the data revealed a robust, reproducible behavioral effect consistent across all four subjects. The primary aim of this study was to illustrate the potential utility of the Crunchometer using complementary experimental approaches, including chemogenetic activation of GABAergic neurons in the lateral hypothalamic area (LHA). To further address this concern, we have now included three additional transgenic mice with unilateral infections and obtained results comparable to those of the bilateral condition. These new data are presented in a new supplementary figure comparing unilateral and bilateral infections (Supplementary Fig. 5-1). Notably, chemogenetic activation of LHA GABAergic neurons promoted eating-related consummatory behaviors to a similar extent under both unilateral and bilateral DREADD activation. Accordingly, we have now added the following text to the Results section:

      “Notably, unilateral DREADD infections in other naïve n=3 Vgat-cre mice yielded results comparable to bilateral infections. While the effect size was slightly reduced with unilateral administration, the difference between the two delivery methods was not statistically significant (Supplementary Fig. 5-1)”

      (3) Correlation with actual food intake is modest and sometimes less accurate than human observers.

      We agree that this result highlights the complexity of feeding behavior, influenced by factors such as hoarding and spillage. The threshold method detects feeding behavior solely based on the magnitude of bite-related sounds (e.g., when the mouse bites the pellet close to the microphone), whereas human observers incorporate additional visual information to infer feeding behavior even in the absence of detectable chewing sounds, introducing variability in detection criteria. Although the number of bouts identified by the Threshold method was comparable to those annotated by human observers, the estimated duration (Bout Size) of those detections differed. This discrepancy likely reflects some inconsistency in the detection criteria among human observers and delays in identifying the onset. Moreover, instances of mice chewing pellets without consuming them (i.e., spillage) were observed. These events were often misclassified as feeding bouts, resulting in false positives for both the threshold method and human observers.

      (4) Sensitive to hoarding behavior, which can reduce detection accuracy and requires manual correction for misclassifications (e.g., tail movements, non-food noises). However, these limitations are discussed and not ignored.

      We thank the reviewer for this constructive comment and for acknowledging that we explicitly discuss these limitations rather than overlook them. Indeed, gnawing and hoarding behaviors (together with tail movements and non-food noises) are factors that can reduce the accuracy of feeding detection. Even using the Crunchometer, an accurate measurement of solid-food consumption therefore remains challenging, which further supports the inclusion of a human-in-the-loop step to ensure a high-quality, well-curated database. Accordingly, we have added the following sentence to the Result section:

      "This human validation was essential for ensuring the high fidelity of our behavioral database and mitigating the inherent limitations of automated classification."

      Conclusion:

      Overall, this is an exciting and impactful methodological advance that will likely be widely adopted in the field. I recommend minor revisions to clarify the limits of classifier generalizability, better contextualize the small-sample neuroscience findings as pilot data, and discuss future directions (e.g., real-time closed-loop applications).

      We thank you for your constructive comments.

      Reviewer #3 (Public review):

      Summary:

      The manuscript provides detailed information on the construction of open-source systems to monitor ingestive behavior with low-cost equipment. Overall, this is a welcome addition to the arsenal of equipment that could be used to make measurements. The authors show interesting applications with data that reveal important neurophysiological properties of neurons in the lateral hypothalamus. The identification of previously unknown "meal-related" neurons in the LH highlights the utility of the device and is a novel insight that should spark further investigation on the LH. This manuscript and videos provide a wealth of useful information that should be a must-read for anyone in the ingestive behavior or hypothalamus fields.

      A scholarly introduction to the history and utility of various ways feeding is measured in rodents is provided. One point - the microstructure of eating solid food - has been studied extensively (for one of many studies, see https://doi.org/10.1371/journal.pone.0246569 ). However, I agree that the crunchometer will allow for more people to access recordings during food intake and temporally lock consummatory behavior to neural activity.

      Apologize for this oversight. This is indeed an important reference for the microstructure of eating solid food in a social context. We have now included it in the Introduction of this reference “Food intake in social contexts is a more ethologically valid model, in which radio-frequency identification (RFID) transponders enable the simultaneous assessment of feeding behavior across multiple mice in a single box (Rathod and Fulvio, 2021)”

      Questions on results:

      (1) It is unclear why 10% sucrose solution was used as a liquid instead of water, given that the study is focusing on the solid food source.

      One motivation for using sucrose rather than water alone was to create a highly palatable environment and to test whether mice would prefer palatable liquid sucrose over HFD. However, the choice of liquid stimulus will ultimately depend on the end user and the specific experimental conditions of each lab implementing the Crunchometer. Future versions of the apparatus could also incorporate multiple sippers to deliver several tastants alongside solid food.

      (2) It is unclear how essential the human verification is in the pipeline - results for Figure 1 keep referring to the verification as essential. Is that dispensable once the ML algorithms have been trained?

      Human validation, also referred to as a human-in-the-loop approach, is a deliberate design feature of the Crunchometer rather than a limitation (also see answer to Reviewer 2). The outputs of machine-learning algorithms, no matter how accurate, require expert corroboration to confirm or reject the specific behaviors under study, particularly when the behavioral repertoire is as heterogeneous as feeding (which encompasses sniffing, gnawing, biting, hoarding, and manipulating the food item). For this reason, we view human oversight as a safeguard for scientific rigor that remains valuable even as more advanced algorithms (e.g., deep learning and convolutional neural networks) are incorporated into future versions of the pipeline. As noted above, we have implemented a graphical user interface (GUI) that enables batch sorting and rapid inspection of multiple snippets (using a photographic montage view strategy), substantially reducing manual curation time.

      (3) The ability to extrapolate food quantity consumed is limited, with high variability. This limitation does not undercut the utility of the crunchometer, but should be highlighted as one of the parameters that are not suitable for this system. This limitation should be added to the limitations section.

      We thank the reviewer for this constructive observation. We fully agree that, although the Crunchometer reliably detects feeding events and their temporal microstructure (bouts, meals, and latencies), extrapolating absolute food quantity consumed from acoustic signals is indirect and carries substantial variability and should not be the primary readout for studies that require precise gravimetric measurements. As recommended, we have now explicitly listed this limitation in the Limitations section of the Discussion:

      "While the Crunchometer provides accurate temporal detection of bites and feeding microstructure, the estimation of absolute food mass consumed from bite-related acoustic signals shows considerable variability across trials and subjects. This limitation arises from individual differences in gnawing patterns, food fragmentation, and hoarding behavior. Accordingly, the Crunchometer is best suited for analyses of feeding dynamics and behavioral microstructure, whereas studies requiring precise quantification of ingested mass should complement the system with direct gravimetric measurements for example, real-time weighing of feeders."

      (4) The ability to discriminate between gnawing and consummatory behavior is a strength (Figure 5), and these findings are important. However, it is unclear what can be made of mice that have 'gnawing' behavior in the fasted state (like in Figure 3). It seems they would need to be eliminated from the analysis with this tool?

      We apologize for this misunderstanding. We have now more clearly indicated in Figure 3A that the cumulative feeding time reflects only Chow and HFD feeding bouts, excluding gnawing.

      We now state: “The lower panel shows the cumulative feeding time (only for Chow and HFD pellets, gnawing is excluded) over a two-hour session for the fed (green) and fasted (purple) groups (n = 6 mice).”

      Under normal physiological conditions, gnawing is an infrequent behavior in rodents. In our study, however, its frequency increased in the fasted state a change possibly attributable to heightened stress. This behavior was further exacerbated by chemogenetic manipulation, driving it to non-physiological levels.

      (5) Why is there a post-semaglutide fed group and not a fasted group in Figure 4? It seems both would have been interesting, as one could expect an effect on feeding even 24h after semaglutide treatment. This would help parse the preference better because the animals eat such a small amount of semaglutide, that it is hard to compare to the fasted condition with saline treatment.

      We thank the reviewer for this insightful suggestion. It would have been interesting to include a fasted post-semaglutide group, as it could provide relevant information about the lasting effect of an acute administration of semaglutide. However, we decided not to include this additional experimental condition because the semaglutide fasted mice displayed a markedly reduced food intake during the experimental session. An additional post-semaglutide fasted session would have required a prolonged food restriction (at least 24 hours), which we consider an unnecessarily stressful condition for the mice. Therefore, we decided to feed the mice once the experiment was completed. Nevertheless, we believe that comparing the food intake (grams) between the fed group shown in Figure 3C and the post-semaglutide fed group reported in Figure 4D provides insight into the lasting effect of semaglutide. The comparison reveals a remarkable reduction of food intake in the post-sem fed mice relative to the fed group, suggesting that the acute administration of semaglutide suppresses the feeding behavior for up to 24 hours.

      (6) The identification of 'meal-related' neurons in the LH is another strength of the manuscript. Although there is currently insufficient data, could similar recordings be used to give a neurophysiological definition of a 'meal' duration/size? Typically, these were somewhat arbitrarily defined behaviorally. Having a neural correlate to a 'meal' would be a powerful tool for understanding how meals are involved in overall caloric intake.

      We thank the reviewer for this insightful suggestion. We agree that the traditional behavioral criteria for defining meals, typically derived from log-survivor analyses of inter-pellet or inter-lick intervals, are operationally useful but ultimately arbitrary, and that a neurophysiologically grounded definition would be a valuable complement for the field.

      Our current dataset was not designed to formally establish such a definition, and we want to be cautious about the logic of the problem: validating a neural criterion solely against the behavioral one it would replace is circular. A genuinely neural definition of a meal would need to be anchored to independent criteria, for example, its ability to predict the latency and size of the subsequent meal, its correspondence with post-prandial satiety markers, or its response to anorectic agents such as GLP-1 receptor agonists. This is a methodologically nontrivial undertaking that we believe deserves a dedicated follow-up study.

      As preliminary evidence that such a problem is tractable, we note that the meal-related LH neurons identified here display sustained activity with onset and offset dynamics that broadly parallel the behaviorally defined meal boundaries (Figure 6), suggesting that meal structure is reliably encoded at the population level. A related approach, using neural activity to segment ingestive behavior at finer temporal scales, has been successful in our previous work on licking microstructure in the nucleus accumbens (Tellez, et al. 2012), and we consider the present findings a natural extension of that line of research to the larger meal timescale.

      (7) The conclusion in the title of Figure 8 is premature, given the pilot nature and small number of neurons and mice sampled.

      We appreciate this comment and agree with the reviewer. Accordingly, we have performed additional experiments on the Vglut2 glutamatergic population, in some cases using three-plane recordings, which substantially increased the yield to 386 glutamatergic neurons. As the reviewer anticipated, we observed a broad diversity of response profiles in this population, including neurons selective for liquid licking, for solid food intake, and for both food types. We also formally quantified these responses using ROC analysis, applying the same procedure to the Vgat GABAergic neurons (n = 79). These new findings have been incorporated into the revised manuscript (Results and Discussion). We thank the reviewer for prompting this extension of the analysis (see Manuscript).

      Conclusion:

      Overall, this report on the Crunchometer is well done and provides a valuable tool for all who study food intake and the behaviors around food intake. Clarification or answers to the points above will only further the utility and understanding of the tool for the research community. I am excited to see the future utility of this tool in emerging research.

      We sincerely thank the Reviewer for these kind and encouraging words, and for the constructive feedback provided throughout the review. The clarifications and additional analyses prompted by these comments have substantially improved the manuscript, and we share the Reviewer's enthusiasm about the potential of the Crunchometer to contribute to future research on feeding behavior.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) The authors have done a phenomenal job with the Introduction, highlighting the need for this tool, citing the history of feeding measurement systems and their relative strengths and weaknesses.

      Thank you for your comment; we greatly appreciate your positive feedback.

      (2) A limitation of Automated Pellet Dispensers is the possibility that the animals fail to consume the pellet after it has been retrieved from and registered by the device, potentially constraining accuracy.

      We address this issue in the Introduction, specifically, we wrote:

      “Current methods to monitor feeding behavior could be classified into four different classes…3) Automated Pellet Dispensers: Often integrated into operant conditioning chambers, these devices provide a controlled way of delivering food pellets. While devices like the open-source Feeding Experimentation Device (FED3) (Ali and Kravitz, 2018; Matikainen-Ankney et al., 2021), a pellet dispenser, are useful for measuring reinforcement, they alter the natural feeding patterns of mice, for example, requiring a simple action, such as a nose-poke can reduce overeating and weight gain in mice (Barrett et al., 2025). A further limitation is that FED3 may overestimate consumption if an animal retrieves and registers a pellet without actually consuming it. A significant strength of this method is its ability to enable closed-loop optogenetic stimulation concurrent with neuronal recordings.”

      (3) I really appreciate the data in Figure 2G, where they displayed the results of an "outlier" animal, as behavior is extremely variable, and it's useful to see how this system deals with the variability of the subjects. This is again highlighted by mouse number 5 in Figure 3A, which exhibited profound gnawing behavior.

      We thank the reviewer for this positive comment. Our decision to include the outlier animal in Fig. 2G and to report the atypical gnawing behavior of mouse 5 in Fig. 3A reflects a deliberate commitment to documenting inter-individual variability, which we consider a core strength rather than a limitation of behavioral work. We believe that such cases are particularly informative for evaluating the robustness of automated monitoring systems under behavioral-lab conditions.

      (4) It would be useful to know if the mice had prior exposure to HFD, as I found it surprising that many animals consumed the chow at all, sometimes completely ignoring the HFD (fasted mouse 3). I only ask because in our experience, mice with constant exposure to both HFD and chow predominantly, if not always, consume the HFD over chow. This could have something to do with the way the food substrates are presented in this chamber.

      We thank the reviewer for this point. Mice in this experiment did receive prior exposure to both Chow and HFD during the habituation phase, with at least two 30-min sessions in the experimental chamber with both diets available (no video was collected at this stage). The Chow and HFD feeders were identical in geometry, position, and accessibility, so we do not consider either environmental novelty or spatial bias to be the main driver of the pattern. Rather, we interpret the strong chow preference of fasted mouse 3 as a case of residual neophobia toward the HFD pellet. Since performing these experiments, we have refined our habituation protocol: pre-exposing animals to a single HFD pellet in their home cage, a familiar and safe environment, prior to any chamber session, greatly mitigates HFD neophobia in our hands. Familiarity with the novel food in a safe context thus appears to be the critical factor, rather than the duration of exposure in the experimental chamber. We have added this refinement to the Methods as a recommendation for future users of the Crunchometer.

      “Behavioral protocol. All mice were habituated to the Crunchometer for 2 days before the recording session. Each habituation session lasted 30 minutes, during which two food pellets were placed in the chamber: one standard Chow pellet (LabDiet 5008) and one highly palatable high-fat diet (HFD) pellet (Research Diet, D12451). As a practical note, we recommend allowing the HFD to equilibrate to room temperature before the experiment and pre-exposing mice to a single HFD pellet in their home cage to attenuate neophobia prior to testing.”

      (5) The authors claim saline or semaglutide was administered immediately before the start of the behavioral experiment, but given the time it takes for this drug to blunt appetite, I was somewhat surprised it led to such a rapid decrease in both chow and HFD intake. Could the authors comment on this? How quickly do these animals experience the malaise associated with these drugs? Also, this dose seems to be on the very high side, so I imagine it's making the animals feel quite sick and is probably a big reason why the effects last so long into the post-sem measurements. Was bodyweight tracked across this treatment? I'm not so convinced that sema treatment led to a loss of strong HFD preference, as the chow intake was already very low to begin with, and as mentioned above, it looks like the drug just led to a cessation of all intake. I'd just tamp down this claim of preference switch. It clearly reduced intake of both substrates, it's just harder to detect for the chow because it was already so low to begin with.

      Thank you for these comments. We agree with the Reviewer and have toned down the claim regarding a switch in HFD/chow preference. In the revised Results section, we now explicitly acknowledge that further characterization is needed using chronic semaglutide treatment. Specifically, we added the following sentence:

      "Future studies should use the Crunchometer to characterize changes in HFD/chow preference during 24-h monitoring under chronic semaglutide treatment."

      In addition, we administered a single subcutaneous dose of semaglutide at 30 nmol/kg (0.123 mg/kg), following the protocol described by Zhang et al. (2023). In their study, pharmacokinetic analyses showed that plasma concentrations, measured by an ELISA assay that immunoreacts with both growth differentiation factor 15 (GDF15) and the intact N-terminal region of glucagon-like peptide-1 (GLP-1), increased shortly after administration of the 30 nmol/kg dose in C57BL/6 mice. Peak plasma concentration (Cmax = 43.1 nmol/L) was reached at 6.7 hours (Tmax), and levels returned to baseline by 24 hours post-administration, indicating complete drug clearance. Although this dose is relatively high, it was intentionally selected to produce a robust acute response from a single administration, as our objective was to assess the drug’s effects within a short, 2-hour observational window. Under these conditions, we observed a rapid reduction in food intake immediately following the onset of Crunchometer recording. While we do not exclude the possibility that these effects could be more pronounced over longer observation periods or with chronic dosing regimens, our study was strictly limited to a single acute exposure.

      Although semaglutide is known to suppress food intake through multiple mechanisms, including stress and malaise measured by Conditioned Taste Aversion and release of stress hormones (Teixidor-Deulofeu et al., 2025), we do not believe that discomfort or malaise played a significant role in our study. While the mice did reduce their food intake during semaglutide administration, this reduction persisted for at least 24 hours after the final dose—at which point the drug was no longer present—suggesting a satiety-driven effect rather than one mediated by aversion. In this sense, previous studies have demonstrated that semaglutide continues to suppress food intake even when the aversive pathway mediated by Area Postrema GLP1R neurons is inhibited. Although blocking this pathway reduces flavour aversion, the anorexic effect remains, indicating that suppression of intake can be driven by satiety independently of nausea or malaise (Huang et al., 2024). In summary, although we selected a relatively high dose to ensure a detectable acute effect within our experimental window, this choice was grounded in previously published data, and our findings are consistent with established mechanisms of action for semaglutide.

      Additionally, body weight data have now been included in Figure 4D. We observed a similar body weight loss of approximately 5% on the first day of drug administration, consistent with the findings reported by Zhang et al. (2023).

      (6) The authors demonstrate that CNO administration prompted significant increase in liquid sugar intake in the last panel of Figure 5F as a confirmation that LH GABAergic neurons are implicated in processing reward, however given the above results it seems likely that these mice will drink anything including water (when not thirsty, thus in a non-rewarding scenario) or possibly aversive agents like quinine.

      This is an interesting question, and we agree with the Reviewer. The original discovery by Jennings and Stuber showed that optogenetic activation of these GABAergic neurons induces voracious feeding and that Vgat mice kept licking for liquid rewards in an appetitive task (Jennings et al., 2015). We also acknowledge that prior work has shown LH GABAergic neuron activation can drive consumption of non-caloric and biologically irrelevant stimuli, including wood gnawing, water, or saccharin (Navarro et al., 2016). However, several lines of evidence support a role in reward/palatability processing rather than purely indiscriminate consumption. Our own lab (Garcia et al., 2021) showed that activation of LH Vgat+ neurons increased quinine intake only during water deprivation; in sated animals, activation failed to promote quinine intake. Instead, these neurons promoted overconsumption of sucrose when available, leading us to conclude that LH Vgat+ neurons increase the drive to consume the nearest food, but this drive is potentiated by the palatability of the tastant. In non-human primates, LH GABA activation drives goal-directed eating predominantly for palatable food (Ha et al., 2024), supporting a reward-related function across species. Together, these findings indicate that while LH GABAergic activation does broadly promote consumption, the selectivity toward palatable stimuli observed in Figure 5F is consistent with a reward-related function.

    1. Author response:

      The following is the authors’ response to the previous reviews

      We thank the reviewers for their careful evaluation and constructive comments throughout the two rounds of revision. We hope that the revisions have satisfactorily addressed all concerns and that the manuscript is now suitable for publication.

      This novel contribution highlights the role of this pro-inflammatory factor in the pathogenesis of and resistance to Plasmodium chabaudi infection in mice. While aspects of this response have been previously described, this study is the first to link the TNF–iNOS–HIF-1α axis to the in vivo mediation of malaria disease through its involvement in glucose metabolism. Despite well-documented metabolic alterations during malaria, including hypoglycemia and hyperlactatemia, the mechanisms underlying these changes and their relationship to host immune responses remain poorly understood. Addressing this gap is essential for elucidating how metabolic adaptation shapes disease outcomes during Plasmodium infection.

      In response to the reviewer’s comments, we have revised the Abstract, Introduction, and Discussion to clearly distinguish between:

      Previously established mechanisms (TNF–iNOS–HIF-1α–glycolysis axis), and

      The novel contribution of our study (its in vivo integration during Plasmodium infection and association with host resistance).

      Public Reviews:

      Reviewer #2 (Public review):

      Summary:

      The premise of the manuscript by Matteucci et al. is interesting and elaborates a mechanism via which TNFa regulates monocyte activation and metabolism to promote murine survival during Plasmodium infection. The authors show that TNF signaling (via an unknown mechanism) induces nitrite synthesis, which (via yet an unknown mechanism), and stabilizes the transcription factor HIF1a. Furthermore, that HIF1a (via an unknown mechanism) increases GLUT1 expression and increases glycolysis in monocytes. The authors demonstrate that this metabolic rewiring towards increased glycolysis in a subset of monocytes is necessary for monocyte activation including cytokine secretion, and parasite control.

      Strengths:

      The authors provide elegant in vivo experiments to characterize metabolic consequences of Plasmodium infection, and isolate cell populations whose metabolic state is regulated downstream of TNFa. Furthermore, the authors tie together several interesting observations to propose an interesting model regarding

      Weaknesses:

      The main conclusion of this work - that "Reprogramming of host energy metabolism mediated by the TNF-iNOS-HIF1a axis plays a key role in host resistance to Plasmodium infection" is unsubstantiated. The authors show that TNFa induces GLUT1 in monocytes, but never show a direct role for GLUT1 or glucose uptake in monocytes in host resistance to infection (nor the hypoglycemia phenotype they describe).

      We thank the reviewer for this important comment and for highlighting the need to clarify the mechanistic link between TNF-driven metabolic rewiring and host resistance to Plasmodium infection. As noted in our first revision, our primary objective was to investigate how TNF integrates systemic and cellular metabolic responses during infection in vivo. We demonstrate that glucose uptake is significantly increased in spleen and liver during infection in a partially TNF-dependent manner, and that TNF promotes GLUT1 expression (main glucose transporter in immune cells) and glycolysis specifically in monocytic cells. Importantly, to directly address the role of TNF signaling in myeloid cells, we also observed the same phenotype (higher parasitemia, but absence of hypothermia and hypoglycemia) in mice with conditional deletion of TNF receptor 1 in lysozyme M–expressing cells (TNFR1^ΔLyz2) (Figure 4P–R), thereby validating in a cell-specific context the findings previously observed in mice with global TNFR1 deficiency. Together, these findings support a functional link between TNF signaling in monocytes, induction of GLUT1-dependent glucose metabolism, and the regulation of both systemic metabolic responses and host resistance during experimental malaria.

      While we agree that we do not demonstrate a cell-intrinsic role for GLUT1 in monocytes, multiple lines of evidence in our study support the functional relevance of glycolytic metabolism downstream of the TNF–iNOS–HIF-1α axis.

      (1) First, we show that Pc infection results in a marked increase in glucose uptake in the spleen and liver, but not in skeletal muscle or adipose tissues (Figure 2K), and that this effect is absent in TNFR-/- mice (Figure 2L), indicating a TNF-dependent and tissue-specific metabolic reprogramming. We have also clarified in the Discussion that this process appears to be insulin-independent and likely driven by pro-inflammatory signals.

      (2) Second, we show that the TNF–iNOS–HIF-1α axis. induces GLUT1 expression in monocytic cells (Figures 4M, 5D, 6L). This supports a model in which these cells contribute to observed systemic metabolic changes.

      (3) Third, we also observed a similar phenotype—characterized by higher parasitemia but absence of hypothermia and hypoglycaemia-in mice with conditional deletion of TNF receptor 1 in lysozyme M–expressing cells (TNFR1^ΔLyz2) (Figure 4P–R), thereby validating in a cell-specific context the findings previously observed in mice with global TNFR1 deficiency. These findings indicate that disruption of glycolysis phenocopies key aspects of the TNF-driven metabolic and immunological response to infection. 

      (4) Finally, we demonstrate that glycolytic metabolism is functionally relevant for host resistance. Pharmacological inhibition of glycolysis in vivo using 2-DG led to increased parasitemia (Figure 6O), resembling the impaired parasite control observed in HIF-1α^ΔLyz2, TNFR-/-, and iNOS-/- mice. These findings indicate that disruption of glycolysis phenocopies key aspects of the TNF–iNOS–HIF-1α axis deficiency, supporting the conclusion that this pathway is required to sustain glycolytic metabolism and effective parasite control during infection.

      About the hypoglycemia phenotype and resistance, our previous study (PMID: 29805094) demonstrates that TNF-driven inflammation regulates systemic glucose metabolism during Plasmodium chabaudi infection. We showed that infection-induced hypoglycemia correlates with TNF levels and is associated with changes in parasite development. Specifically, leukocytes primed with IFNγ display increased expression of glucose metabolism and inflammatory genes, and TNFα-induced hypoglycemia is linked to the accumulation of non-proliferative trophozoite forms, whereas parasite replication (schizogony) occurs during host feeding. These findings indicate that blood glucose availability, regulated by TNF, directly influences parasite growth dynamics and infection outcome. Although the cellular mechanisms were not addressed in that study, our current work builds on these findings by identifying the TNF-iNOS–HIF-1α axis as a driver of GLUT1-dependent glycolysis in monocytes, linking systemic metabolic changes to a cell-intrinsic mechanism that contributes to host resistance. 

      We agree that directly establishing the cell-intrinsic contribution of GLUT1 would require dedicated genetic approaches (e.g., conditional deletion in monocytes), which are beyond the scope of the present study. 

      Comments on revisions:

      The demonstration that the established TNF-iNOS-HIF-1α-glycolysis axis operates in vivo during P. chabaudi infection is valuable and relevant. However, it constitutes contextual validation and must be carefully described as such. This distinction, i.e., "what has already been shown vs. what is new" is not consistently reflected in the framing of the manuscript raising overstatement concerns. This is particularly evident in the abstract and other conclusive statements, where mechanistic novelty is implied, even when the underlying pathways/mechanisms are already known. To improve the manuscript, all sentences that refer to already established findings should be accurately described as such.

      For example, the abstract states: "Here, we show that TNF signaling hampers physical activity, food intake, and energy expenditure while enhancing glucose uptake by the liver and spleen as well as controlling parasitemia in P. chabaudi-infected mice." In this sentence, the effects of TNF signaling on physical activity, food intake, energy expenditure, glucose metabolism and control of parasitemia are unequivocally established and therefore do not, in themselves, constitute new findings. Feeding behavior, not cell-intrinsic metabolism, may drive glycemic differences.

      We thank the reviewer for this comment and for highlighting the importance of distinguishing systemic metabolic effects from cell-intrinsic mechanisms. We have now revised the manuscript to more consistently distinguish between previously established mechanisms and our novel findings, particularly in the Abstract and other summary statements, to avoid any potential overstatement.

      We also would like to emphasize that, in both the Introduction and Discussion, we explicitly acknowledge that key components of the TNF–iNOS–HIF-1α–glycolysis axis have been previously described. In the Introduction, we cite studies demonstrating that TNF can induce glucose uptake and metabolic reprogramming in immune cells (refs. 14–17), as well as the role of HIF-1α as a central regulator of glycolysis and inflammation in myeloid cells (refs. 21–28). Similarly, in the Discussion, we detail prior evidence that TNF induces iNOS-derived RNI (refs. 51–54), that RNI stabilizes HIF-1α (ref. 52), and that HIF-1α drives the expression of glycolytic genes including GLUT1 (refs. 55–57). We also cite studies showing that TNF contributes to parasite control and glucose metabolism in malaria (refs. 58–61).

      Importantly, while these pathways have been described in other contexts, their integration and functional relevance in vivo during Plasmodium infection, particularly in the context of host systemic metabolism and monocytic cell function, have not been previously demonstrated. Our study addresses this gap by showing that this axis operates during P. chabaudi infection and links inflammatory signaling to both cellular metabolic reprogramming and organismal metabolic changes.

      Specifically, we demonstrate that TNF signaling drives increased glucose uptake in spleen and liver in a tissue-specific manner, promotes GLUT1 expression and glycolysis in monocytic cells, and that disruption of this axis (genetically or pharmacologically via glycolysis inhibition) impairs parasite control. In addition, we provide evidence connecting these cellular processes to systemic metabolic alterations, including hypoglycemia.

      The authors propose that TNF signaling leads to GLUT1 upregulation (in inflammatory monocytes, MO-DCs, and within the liver and spleen) during Plasmodium infection, and that this results in increased glucose uptake contributing to systemic hypoglycemia. While this is an intriguing hypothesis, we urge the authors to consider an alternative explanation that, at present, is not adequately ruled out. Given that glycemia serves as a central functional readout in the manuscript, this distinction is essential to clarify.

      The observed regulation of glycemia is likely not a direct consequence of increased glucose uptake by immune cells or by tissues but may instead reflect broader differences in disease severity across genotypes. The iNOS KO, TNFR KO, and HIF-1ΔLyz2 mice likely experience a dampened inflammatory response, which would blunt infection-induced anorexia and help preserve overall metabolic homeostasis. This alternate interpretation is supported by the authors' metabolic cage data showing increased physical activity in TNFR KO mice and the elevated food intake shown in Figure 2B.

      We thank the reviewer for this important point regarding the potential contribution of feeding behavior and systemic energy balance to the observed metabolic phenotypes. In fact, this possibility has been explicitly already incorporated into the revised manuscript. Also, we have revised the Discussion to explicitly state that the hypoglycemia observed during infection likely reflects both systemic changes in energy balance and TNF-driven metabolic reprogramming in immune cells, rather than a single isolated mechanism. Specifically, we have had already added the following statement to the Discussion:

      “Although restored physical activity, food consumption and energy expenditure in knockout mice may contribute to the observed systemic metabolic parameters by altering energy balance, these effects are not mutually exclusive with the TNF-driven, cell-intrinsic metabolic mechanisms described here”.

      In addition, we note that under naive conditions, we did not observe differences between genotypes in physical activity, food intake, energy expenditure, respiratory exchange ratio, or glycemia. These findings support that baseline metabolic parameters are comparable and that the differences observed during infection arise in the context of TNF-dependent inflammatory responses. During infection, although TNFR-deficient mice display increased food intake and activity, these differences arise in the context of altered inflammatory signaling. Therefore, rather than being mutually exclusive, behavioral and metabolic changes are likely coordinated downstream of TNF signaling.

      Furthermore, our data using pharmacological inhibition of glycolysis (2-deoxy-D-glucose) demonstrate that disruption of glycolytic metabolism results in increased parasitemia and reduced lactate levels, recapitulating key aspects of the phenotype observed in TNFR-/-, iNOS-/-, and HIF-1αΔLyz2 mice. This supports a functional role for glycolytic metabolism in host response, beyond differences in feeding behavior.

      Since anorexia and energy expenditure are tightly coupled to the inflammatory milieu, it is plausible that these behavioral and systemic differences-not monocyte nor tissue GLUT1 expression per se-are the primary contributors to the observed glycemic patterns. To support their current interpretation, the authors should perform a pair-feeding experiment in which (at least) TNFR KO mice are restricted to the same food intake as infected WT controls. This would help disentangle whether differences in glycemia truly reflect immune-driven metabolic rewiring or are secondary to differences in caloric intake.

      We thank the reviewer for this suggestion. We agree that pair-feeding experiments would provide an additional layer of control to isolate the contribution of caloric intake. However, we note that:

      (1) Baseline metabolic equivalence in naive animals argues against intrinsic differences in energy balance.

      (2) The observed phenotypes occur in the context of infection-driven inflammation, where anorexia is itself a TNF-dependent host response.

      (3) Our data support a model in which behavioral changes and metabolic rewiring are integrated components of the host response rather than independent variables.

      Importantly, our data already support a role for TNF-driven metabolic rewiring beyond feeding behavior, as inhibition of glycolysis with 2-deoxy-D-glucose recapitulates the impaired parasite control observed in genetic models. In addition, as discussed in the manuscript, systemic factors such as food intake are not mutually exclusive with cell-intrinsic metabolic mechanisms.

      We therefore consider that pair-feeding experiments are beyond the scope of the present study.

      The contribution of monocyte-specific glucose metabolism to host resistance remains unresolved.

      We appreciate the authors' effort to address the mechanistic role of glycolysis in host resistance using in vivo 2-deoxyglucose (2DG) treatment. However, I would like to point out that while this experiment is informative, it does not fully resolve the specific concern raised regarding the cell-intrinsic role of TNF-induced glycolysis in monocytes. 2DG acts systemically, inhibiting glycolysis across a wide range of cell types-including hepatocytes, endothelial cells, lymphocytes, and myeloid populations. Therefore, the observed increase in parasitemia following 2DG treatment may reflect the broad importance of glycolysis for host defense, or alternatively, may result from elevated circulating glucose levels induced by 2DG (PMID: 35841892), which could enhance parasite growth by increasing nutrient availability. Therefore, this experiment does not allow for a specific conclusion about the requirement for TNF-driven metabolic reprogramming in monocytes.

      We thank the reviewer for this comment regarding the interpretation of the 2-deoxyglucose (2DG) experiments. We agree that systemic 2DG treatment does not allow cell-specific conclusions, as it broadly inhibits glycolysis across multiple cell types. Accordingly, these data are interpreted as supporting a role for glycolysis in host defense at the organismal level, rather than as direct evidence for a monocyte-intrinsic requirement of TNF-driven metabolic reprogramming.

      At the same time, our study includes cell-specific analyses that support the engagement of this pathway in myeloid populations. In particular, we observe increased GLUT1 expression in CD11b<sup>+</sup> cells within both the liver and spleen during infection, with marked upregulation in monocyte-derived dendritic cells (MODCs). Importantly, this induction is not observed in the corresponding knockout models, supporting the idea that TNF signaling is required for this metabolic adaptation in these cells in vivo. Consistent with this, we validated that both parasitemia and systemic glucose levels in TNFR1^ΔLyz2 mice phenocopy those observed in TNFR-deficient animals, reinforcing the contribution of myeloid TNF signaling to the metabolic and disease outcomes.

      In addition, our in vitro data demonstrate increased GLUT1 expression in WT monocytes but not in cells lacking components of the TNF–iNOS–HIF-1α axis, further supporting a pathway-specific effect. Given that GLUT1 is the primary glucose transporter in immune cells, these combined in vivo and in vitro findings, together with the 2DG experiments, provide strong evidence supporting our proposed model. 

      We agree that directly establishing a monocyte-intrinsic role would require targeted genetic approaches, which are beyond the scope of the present study.

    1. Author response:

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

      eLife Statement

      This valuable study characterizes the emergence of the membrane-associated periodic cytoskeleton (MPS) in the axons of human motor neurons derived from induced pluripotent stem cells. Super-resolution imaging of beta-II spectrin provides convincing evidence for the patterned assembly of spectrin-poor gaps and spectrin-rich MPS in the medial region of the axons and its enhancement by the kinase inhibitor staurosporine. The data advocates against gap formation by cytoskeleton disassembly in a continuous MPS. Instead, a continuous MPS may result from nascent MPS patches and their maturation, a model that would benefit from live imaging for validation.

      (R1) We thank the reviewers and editor for their constructive and thoughtful feedback. We are pleased the reviewers found our evidence to be convincing and that our study provides a valuable framework for understanding the complex dynamics of MPS assembly.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Ever since the surprising discovery of the membrane-associated Periodic Skeleton (MPS) in axons, a significant body of published work has been aimed at trying to understand its assembly mechanism and function. Despite this, we still lack a mechanistic understanding of how this amazing structure is assembled in neuronal cells. In this article, the authors report a "gap-and-patch" pattern of labelled spectrin in iPSC-derived human motor neurons grown in culture. The mid-sections of these axons exhibit patches with reasonably well-organized MPS that are separated by gaps lacking any detectable MPS and having low spectrin content. Further, they report that the intensity modulation of spectrin is correlated with intensity modulations of tubulin as well. However, neurofilament fluorescence does not show any correlation. Using DIC imaging, the authors show that often the axonal diameter remains uniform across segments, showing a patch-gap pattern. Gaps are seen more abundantly in the midsection of the axon, with the proximal section showing continuous MPS and the distal segment showing continuous spectrin fluorescence but no organized MPS. The authors show that spectrin degradation by caspase/calpain is not responsible for gap formation, and the patches are nascent MPS domains. The gap and patch pattern increases with days in culture and can be enhanced by treating the cells using the general kinase inhibitor staurosporine. Treatment with the actin depolymerizing agent Latrunculin A reduces gap formation. The reasons for the last two observations are not well understood/explained.

      (R2) We thank the reviewer for the detailed and accurate description of the data shown and its relevance to further our understanding of MPS assembly mechanism and function.

      Strengths:

      The claims made in the paper are supported by extensive imaging work and quantification of MPS. Overall, the paper is well written and the findings are interesting. Although much of the reported data are from axons treated with staurosporine, this may be a convenient system to investigate the dynamics of MPS assembly, which is still an open question.

      (R3) We thank the reviewer for the positive comments on the manuscript and the convenience of the experimental system developed to further study the dynamics of MPS assembly. We hope others turn into motor neurons to explore cortical cytoskeleton biology and hopefully shed light into their susceptibility in various degenerative diseases.

      Weaknesses:

      Much of the analysis is on staurosporine-treated cells, and the effects of this treatment can be broad. The increase in patch-gap pattern with days in culture is intriguing, and the reason for this needs to be checked carefully. It would have been nice to have live cell data on the evolution of the patch and gap pattern using a GFP tag on spectrin. The evolution of individual patches and possible coalescence of patches can be observed even with confocal microscopy if live cell super-resolution observation is difficult.

      (R4) Because staurosporine may hit various kinases relevant to the phenomenon under study we did not elaborate too deeply on the likely targets in the discussion. We have, however, included the possibility that the relevant kinase in this matter could be PKC, in light of the new study published while our manuscript was under revision (Heller et al., 2025) (see second last paragraph in the Discussion section). Staurosporine represented a convenient initial approach that allowed us to find the phenomenon, and we are now conducting new studies dissecting the molecular pathways involved. However, the extent of such studies lies beyond the scope of the present report.

      See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      Some more comments:

      (1) Axons can undergo transient beading or regularly spaced varicosity formation during media change if changes in osmolarity or chemical composition occur. Such shape modulations can induce cytoskeletal modulations as well (the authors report modulations in microtubule fluorescence). The authors mention axonal enlargements in some instances. Although they present DIC images to argue that the axons showing gaps are often tubular, possible beading artefacts need to be checked. Beading can be transient and can be checked by doing media changes while observing the axons on a microscope.

      (R5) As we acknowledge this possibility, we believe that, even if they occurred, they could not contribute to our observations of gaps-and-patches phenomenon since this latter subsisted long (hours and days) after any gross manipulation of media. Moreover fixed samples, when observed under DIC, confocal or STED did not evidence such beadings. We do refer to a characteristic local enlargement that was very localized and very low in numbers (see Fig.1C and E, and Suppl. Fig1C and E), so we don't believe these are transient, and do not resemble the structure referred to as beading. Structurally, beading is essentially different since it appears in rows of consecutive “beads” in long stretches, where round, small enlargements of axonal caliber are arranged in a consecutive manner, resembling pearls on a string. As mentioned by the reviewer, the beading phenomena can occur transiently when drastically changing media osmolarity (rarely done in cell culture manipulations) or non-tranciently when axons are undergoing degeneration. Indeed, to prevent gross changes in osmolarity, our routine fixation is a 4% PFA and 4% sucrose in PBS. In any case, we did not observe signs of beading in the cultures used for this study.

      (2) Why do microtubules appear patchy? One would imagine the microtubule lengths to be greater than the patch size and hence to be more uniform.

      (R6) Our stainings are for tubulin protein isoforms beta-III and alpha-II. That is, they would label microtubules, but free tubulin as well. Hence we don't think this is evidence for “patchy microtubules”. The slight decrease in intensity for tubulin within gaps is indeed something to investigate, and can indicate that tubulin prefers to accumulate within patches.

      (3) Why do axons with gaps increase with days in culture? If patches are nascent MPS that progressively grow, one would have expected fewer gaps with increasing days in culture. Is this indicative of some sort of degeneration of axons?

      (R7) We agree with the apparent discrepancy. However, one has to take into account that these axons are still elongating even at 2 weeks in culture and beyond. Hence, at any time point, there is a new axonal compartment recently added, and hence, with low βII-spectrin and no organized MPS. Also, the dynamical evolution of the gaps-and-patches structure has to take into account the rate of βII-spectrin supply and transport. If supply is somehow lower than a given threshold, it is expected that there will be more gaps, given the new, more distant parts of the axons have a lower supply of βII-spectrin. To explore this formally, we are working on simulations of these multifactorial dynamic systems to better understand this, that together with key experimental observations would enhance our understanding into our model of MPS assembly in growing axons. However, findings for this project will be the subject of another manuscript.

      (4) It is surprising that Latrunculin A reduces gap formation induced by staurosporine (also seems to increase MPS correlation) while it decreases actin filament content. How can this be understood? If the idea is to block actin dynamics, have the authors tried using Jasplakinolide to stabilize the filaments?

      (R8) The results with the co-treatment with Latrunculin A and Staurosporine are indeed intriguing, and provide clear evidence that the gap-and-patch pattern arises from local assembly of the MPS, requiring newly formed actin filaments. On the other hand, the fact that F-actin within the pre-formed MPS seems unaffected is not surprising. There are many different populations of F-actin in axons (i.e. MPS rings, longitudinal filaments, actin patches, actin trails), all of which have a different rate of monomer turnover. Latrunculin A affects filaments indirectly. The target of Latrunculin A is not actin filaments, but free monomers. Monomer sequestration ultimately affects actin filaments: filaments are constantly exchanging monomers, but, devoid of free monomers, filaments get shorter and eventually disappear. The drastic decrease in global F-actin in LatA-treated axons reflects that. The fact that F-actin in the MPS is preserved shows that these filaments are stable -if they are not losing monomers in the time frame of the treatment, the filament remains unaffected. This subject is extensively covered in the 8th paragraph of the Discussion section.

      We have not used Jasplakinolide. The expected outcome will not mimic that of Latrunculin A since Jasplakinolide has a different mechanism of action (i.e. it binds -and stabilizes- the actin filament).

      (5) The authors speculate that the patches are formed by the condensation of free spectrins, which then leaves the immediate neighborhood depleted of these proteins. This is an interesting hypothesis, and exploring this in live cells using spectrin-GFP constructs will greatly strengthen the article. Will the patch-gap regions evolve into continuous MPS? If so, do these patches expand with time as new spectrin and actin are recruited and merge with neighboring patches, or can the entire patch "diffuse" and coalesce with neighboring patches, thus expanding the MPS region?

      (R9) We agree with the reviewer's interpretation. A virtue of our experimental model and our interpretations of the observations in fixed cells is that it gives rise to informative questions such as the ones posed by the reviewer. See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Gazal et al. describe the presence of unique gaps and patches of BetaII-spectrin in medial sections of long human motor neuron axons. BII-spectrin, along with Alpha-spectrin, forms horizontal linkers between 180nm spaced F-actin rings in axons. These F-actin rings, along with the spectrin linkers, form membrane periodic structures (MPS) which are critical for the maintenance of the integrity, size, and function of axons. The primary goal of the authors was to address whether long motor axons, particularly those carrying familial mutations associated with the neurodegenerative disorder ALS, show defects in gaps and patches of BetaII-spectrin, ultimately leading to degradation of these neurons.

      (R10) We thank the reviewer for the detailed and accurate description of the data shown.

      Strengths:

      The experiments are well-designed, and the authors have used the right methods and cutting-edge techniques to address the questions in this manuscript. The use of human motor neurons and the use of motor neurons with different familial ALS mutations is a strength. The use of isogenic controls is a positive. The induction of gaps and patches by the kinase inhibitor staurosporine and their rescue by Latrunculin A is novel and well-executed. The use of biochemical assays to explore the role of calpains is appropriate and well-designed. The use of STED imaging to define the periodicity of MPS in the gaps and patches of spectrin is a strength.

      (R11) We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      The primary weakness is the lack of rigorous evaluation to validate the proposed model of spectrin capture from the gaps into adjacent patches by the use of photobleaching and live imaging. Another point is the lack of investigation into how gaps and patches change in axons carrying the familial ALS mutations as they age, since 2 weeks is not a time point when neurodegeneration is expected to start.

      (R12) See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      We don't discard the notion that axons carrying familial ALS mutations will show defects in MPS formation and/or stability when observed at longer culture times, or under culture conditions that promote neuronal aging (Guix et al., 2021). Thus, we continue to work with these cells, but the goal of such project lies well beyond the primary message of the present manuscript, as we discuss in the second paragraph of the Discussion section.

      Reviewer #3 (Public review):

      Summary:

      Gazal et al present convincing evidence supporting a new model of MPS formation where a gap-and-patch MPS pattern coalesces laterally to give rise to a lattice covering the entire axon shaft.

      Strengths:

      (1) This is a very interesting study that supports a change in paradigm in the model of MPS lattice formation.

      (2) Knowledge on MPS organization is mainly derived from studies using rat hippocampal neurons. In the current manuscript, Gazal et al use human IPS-derived motor neurons, a highly relevant neuron type, to further the current knowledge on MPS biology.

      (3) The quality of the images provided, specifically of those involving super-resolution, is of a high standard. This adequately supports the conclusions of the authors.

      (R13) We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      (1) The main concern raised by the manuscript is the assumption that staudosporine-induced gap and patch formation recapitulates the physiological assembly of gaps and patches of betaII-spectrin.

      (R14) Along the project, various gaps-and-patches parameters were measured in different conditions and stainings. In all these examinations the only parameter that changed considerably was their abundance. While this suggests that the gaps-and-patches features are comparable between control and staurosporine-treated cells, we acknowledge as a general caution regarding negative data—that subtle qualitative differences cannot be entirely ruled out. We have now emphasized this possibility in the 9th paragraph of the Discussion section.

      (2) One technical challenge that limits a more compelling support of the new model of MPS formation is that fixed neurons are imaged, which precludes the observation of patch coalescence.

      (R15) See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      Recommendations for the authors:

      Reviewing Editor Comments:

      The reviewers all agree that the work would strongly benefit from live imaging to assess the maturation dynamics of the gap/patch pattern.

      (R16) Reviewers agreed that some of the conclusions of our manuscript would benefit from live imaging for validation. Various anticipated technical and biological challenges made these approaches not to be conducted for this initial study on human motor neurons. Just to mention the most important, from previous work of our labs, these cells themselves are difficult to transfect at 2 weeks in culture. Also, ectopically expression of tagged βII-spectrin escapes normal expression control and it has been noticed that ectopic expression yields to protein localization that does not necessarily reflect the endogenous distribution, or that produces cellular responses that precludes the observation of the phenomena under study. These difficulties in studying over-expressed tagged βII-spectrin have been reported in the field, with mentions that the analysed axons were those expressing “low levels of the construct” (Boyer et al., 2026; Zhong et al., 2014; Zhou et al., 2022). Taking this into account, we did not anticipate that, for the goals of the present project, live-imaging was to be included. However, given the positive comments and reception of our conclusions, we sought to try to perform this challenging and risky approach. To that end, we used a C-terminus tagged mouse βII-spectrin-GreenLantern plasmid to transfect our cells (a kind gift from Dr. Subjohit Roy, UCSD, USA). After 3 rounds of differentiating cells and trying various combinations of plasmid quantity, lipofectimine-to-DNA ratios and times of transfection (amongst other parameters), we have got an extremely low efficiency of transfection, and the few expressing neurons showed a distribution of βII-spectrin-GreenLantern that did not match our observations of immunolocalization of endogenous βII-spectrin. Taking all these into account, the present version of the manuscript will not include live-cell imaging on expressed tagged βII-spectrin. Given that reviewers found that some statements in the initial submission would have been better supported by live-imaging, we made changes in the manuscript so as to acknowledge the limitations of concluding dynamic mechanisms from fixed samples (see for example last sentences on 5th paragraph of the Discussion section). Having said so, we hope to be able, in the future, to overcome these experimental challenges and be able to establish live-imaging of βII-spectrin in neurons. For example, to avoid unregulated transgene expression, Heller and colleagues recently generated a βII- spectrin-mNeonGreen conditional knock-in (cKI) mice, consisting of a LoxP- flanked alternative final exon of endogenous βII-spectrin with a C- terminal mNeonGreen fusion that is expressed upon Cre expression (Heller et al., 2025). The implementation and further development of such approaches will be very helpful in new studies on the dynamics of βII-spectrin and the MPS as a whole. However, the scale of work needed to accomplish those approaches represent stand-alone projects.

      Reviewer #1 (Recommendations for the authors):

      In the section "The MPS is absent in beta-II spectrin gaps, the authors mention that the presence of MPS in patches suggests that the axons are not undergoing degeneration. I don't think this is a good criterion to use, despite the citations they take support from.

      (R17) We agree with the reviewer's suggestion: in virtue of the unlikely connection between the cited developmental axon degeneration process in sensory neurons and the possible axon degeneration of long term cultures of human-iPSCs-derived motor neurons studied here, we have eliminated the sentence of reference

      The authors show that degradation by proteases does not happen in their case. In this regard, they may want to discuss the recent article by Heller et al, Science 2025 (https://doi.org/10.1126/science.adn6712) and Hofmann et al, Sci. Rep., 2022 (https://doi.org/10.1038/s41598-022-18562-5)

      (R18) By western blot analysis, we did not see evident changes in proteolysis-derived fragments. However it is likely that even when finding phenotypes with protease inhibitors, protein fragments accumulation is below the sensitivity of western blots. We were expecting gross changes observable by western blot in the case proteolysis explained gap formation.

      Calpain and Caspase activity has been shown to be relevant in different aspects of MPS biology. To the works cited by the reviewer, now one has to add the very recent work by Fei and colleagues (Fei et al., 2026). We have modified part of the Discussion section to analyse our results in this broader context.

      Briefly, Hofmann and colleagues found that acute treatment with calpain inhibitors right before axotomy lead to an increase in percentage of periodic βII-spectrin (referred by authors as “periodicity”) in the regenerated axons in a 2-hour period. Interestingly, the βII-spectrin patches they describe at distal portions did not increase in number, but they increased in size. This indicates that in the particular situation of axonal regeneration calpain activity puts a brake into MPS formation within patches. This invited us to re-examine our own protease inhibition experiments, and measured patch length in this. The new results are shown in Supplementary Fig. 6 and and further analysed in the Discussion section. In summary, our changes were much less notable than the ones found in regenerating axons, but follow the same trend: protease inhibitors made patches longer.

      On the other hand, Heller and colleagues found in live-imaging studies that calpain activity contributes to the steady-state dynamics of βII-spectrin exchange in a mature MPS lattice. More recently, Fei and colleagues found that caspase or calpain inhibition does not change the steady-state organization of a mature MPS lattice when observing treated axons after fixation samples. Fei and colleagues find a relevant role for calpains whenever massive endocytosis (of any kind) is engaged experimentally. Interestingly, all these studies, including ours, examined calpains roles in MPS in different scenarios. When looked in detail, we don’t believe that these are contradictory results among them, and a complete picture of calpains (and caspases) roles in MPS assembly, growth, maintenance and remodeling will have to take into account all the above mentioned results, including ours. All these analyses are now included in the Discussion section.

      Minor comments:

      (1) "Recently, it was proposed that this continuous MPS organization arises from the coalescence of discontinuous "patches" of incomplete MPS units that originate in the distal axon and migrate proximally (Zhong et al. 2014)." Please check the citation. Should it be Hoffman et al. 2022?

      (R19) The reviewer is correct. The proper citation has now been included.

      (2) Is there an established link between ALS and spectrin? I would suggest decreasing the emphasis on this as no clear conclusions are achieved.

      (R20) As stated in the text, the study of ALS mutations is justified from two aspects: one aspect is that there are several tubulin and other cytoskeletal proteins whose mutations are linked to ALS (Castellanos-Montiel et al., 2020) and microtubules dynamics has been shown to affect the cortical skeleton (Qu et al., 2017). Second, since human motor neurons are affected in ALS, we thought that a complete characterization of the βII-spectrin cortical cytoskeleton in these cells should include ALS-related mutations. We have now included an a basic MPS description in TDP43 and SOD1 mutation (Suppl. Fig. 5).

      The aspect of ALS-related mutations only occupies two short paragraphs in the main text and some panels in Supplementary information. To follow the suggestions by the Reviewer, we have downplayed the relative relevance of these results in the text, without compromising the amount of data we show.

      (3) There is a typo in the approximate symbol used for 150 kDa in the section where calpain and caspase activity is reported.

      (R21) Typo corrected.

      (4) Please add the Latrunculin concentration used in the main text, as it makes it easier for the reader.

      (R22) Done.

      (5) In the Discussion, paragraph starting with "We further showed ...", there is a typo where Zhong et al is cited.

      (R23) Corrected.

      (6) Supplementary Figure 1B: attachment instead of 'atachment'.

      (R24) Corrected.

      (7) Include DIVs or time in the schematic. It is easier for the reader to understand.

      (R25) We have now included time references in schematics of Suppl. Fig1B.

      (8) Supplementary Figure 1C

      Unable to distinguish βII-spectrin and βIII-tubulin in the merged image. Separate figure panels will help.

      (R26) The merged images in the reconstructions are merely to better show the tracing individual axons at such low magnification. Relevant portions with only βII-spectrin channels are shown in C1 and C2. Separated individual channels are shown elsewhere across the manuscript.

      (9) Supplementary Figure 4D

      Why is there so much cleavage product for αII-spectrin across DMSO and treatment? It varied over batches as well. Doesn't this mean that αII-spectrin is going through more proteolytic cleavage? Why?

      (R27) The amount of cleavage product for αII-spectrin is not a surprise to us. For instance, although calpains and caspases can potentially process both α- and β-spectrin, in in vivo scenarios where calpain activity is triggered there are much more fragments of α-spectrin being produced (Czogalla & Sikorski, 2005). On the other hand, our staining of cleaved-αII-spectrin by the SNTF antibody by immunofluorescence (Fig4C) parallels the findings by western blot -high levels of cleaved-αII-spectrin across treatments. A similar strong staining using this antibody has been recently shown in the intact axon (Heller et al., 2025). It will be interesting in the future to address if these fragments have any biological significance beyond being mere byproducts of αII-spectrin processing.

      Reviewer #2 (Recommendations for the authors):

      Suggestions for improving the quality of the manuscript:

      (1) Live imaging in combination with FRAP assays will help define whether the capture of spectrin from gaps into patches is true. Fixed neurons only provide static information and may not reflect real-time physiological effects.

      (R28) See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      (2) Could the presence of F-actin trails in axons facilitate the formation of patches? Will the use of formin/Arp2/3 inhibitors rescue the effect of staurosporine, similar to Latrunculin A?

      (R29) Very interesting suggestion. It is likely that different pools of F-actin contribute to the dynamic of MPS formation, and actin trails are definitely worth investigating in this context.

      (3) Figure 8 lacks a latrunculin A treated condition? Why is this not present?

      (R30) The quantification of that treatment was excluded for space and readability. We have now included the values of group LatA + DMSO in Fig8Cand D and rearranged the whole figure.

      (4) Does neuronal stimulation have any effect (KCl treatment) on gaps and patches?

      (R31) Very interesting suggestion. Unfortunately, we have not examined whereas neuronal stimulation affects any parameter of the gaps-and-patches structure.

      (5) Please check the manuscript for typos and reference insertion points in the text. More than a couple were noted.

      (R32) We have corrected typos.

      Reviewer #3 (Recommendations for the authors):

      This is a very interesting study that supports a change in paradigm in the model of MPS lattice formation.

      (1) One major concern is the assumption that staudosporine-induced gap and patch formation recapitulates the physiological assembly of gaps and patches of betaII-spectrin, solely based on their morphological similarity. This should be further discussed in the manuscript. Further analysis of additional cytoskeleton components, including microtubules in staurosporine-treated neurons, could also be provided.

      (R33) See R14.

      (2) In Figure 1E, betaIII-tubulin and NF-H seem to accumulate in betaII-spectrin-rich axonal enlargements. If these are patches, how do you reconcile this finding with Figure 2C-D, where NF-M and alphaII-tubulin are not specifically enriched in betaII-spectrin patches?

      (R34) We actually show that axonal enlargements and patches are structurally unrelated, in many aspects. We mention these axonal enlargements as a way to perform an exhaustive characterization of all βII-spectrin features found in these axons.

      (3) One technical challenge that limits a more compelling support of the new model of MPS formation is that fixed neurons are imaged, which precludes the observation of patch coalescence. This should be further discussed in the revised version of the manuscript.

      (R35) The limitation of the experimental approach is now further discussed (see for example last sentences on 5th paragraph of the Discussion section).

      (4) On a more general note, the title of some of the Results sub-sections could be revised to convey the findings of those sub-sections and not the Methods that were used (example: "Quantitave and Qualitative analyses of betII-spectrin distribution....").

      (R36) According to the suggestion, we have changed the title of this subsection.

      References

      Boyer, N. P., Sharma, R., Wiesner, T., Parperis, C., Delamare, A., Pelletier, F., Jullien, N., Bhatt, A. M., Parra-Rivas, L. A., Kearney, P. J., Shavarebi, F., Leterrier, C., & Roy, S. (2026). Spectrin condensates provide a nidus for assembling the axonal membrane-associated periodic skeleton. iScience, 29(1), 114454. https://doi.org/10.1016/j.isci.2025.114454

      Castellanos-Montiel, M. J., Chaineau, M., & Durcan, T. M. (2020). The Neglected Genes of ALS: Cytoskeletal Dynamics Impact Synaptic Degeneration in ALS. Frontiers in Cellular Neuroscience, 14, 594975. https://doi.org/10.3389/fncel.2020.594975

      Czogalla, A., & Sikorski, A. F. (2005). Spectrin and calpain: A “target” and a “sniper” in the pathology of neuronal cells. Cellular and Molecular Life Sciences: CMLS, 62(17), 1913–1924. https://doi.org/10.1007/s00018-005-5097-0

      Guix, F. X., Capitán, A. M., Casadomé-Perales, Á., Palomares-Pérez, I., López Del Castillo, I., Miguel, V., Goedeke, L., Martín, M. G., Lamas, S., Peinado, H., Fernández-Hernando, C., & Dotti, C. G. (2021). Increased exosome secretion in neurons aging in vitro by NPC1-mediated endosomal cholesterol buildup. Life Science Alliance, 4(8), e202101055. https://doi.org/10.26508/lsa.202101055

      Heller, E., Kurup, N., & Zhuang, X. (2025). The membrane skeleton is constitutively remodeled in neurons by calcium signaling. Science (New York, N.Y.), 389(6760), eadn6712. https://doi.org/10.1126/science.adn6712

      Qu, Y., Hahn, I., Webb, S. E. D., Pearce, S. P., & Prokop, A. (2017). Periodic actin structures in neuronal axons are required to maintain microtubules. Molecular Biology of the Cell, 28(2), 296–308. https://doi.org/10.1091/mbc.E16-10-0727

      Zhong, G., He, J., Zhou, R., Lorenzo, D., Babcock, H. P., Bennett, V., & Zhuang, X. (2014). Developmental mechanism of the periodic membrane skeleton in axons. eLife, 3, e04581. https://doi.org/10.7554/eLife.04581

      Zhou, R., Han, B., Nowak, R., Lu, Y., Heller, E., Xia, C., Chishti, A. H., Fowler, V. M., & Zhuang, X. (2022). Proteomic and functional analyses of the periodic membrane skeleton in neurons. Nature Communications, 13(1), 3196. https://doi.org/10.1038/s41467-022-30720-x

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The manuscript by Butler et al. explores a novel physiological role for connexin 32 (Cx32) hemichannels in Schwann cells at peripheral nerves. Building on the authors' prior work on CO<sub>2</sub> - sensitive gating of connexins, this study proposes that mitochondrial CO<sub>2</sub> production dependent on neuronal activity promotes the opening of Cx32 hemichannels in the paranode, which in turn modulates neuronal activity by reducing conduction velocity. This hypothesis is addressed using a multifaceted approach that includes immunofluorescence microscopy, dye uptake assays, calcium imaging, computational modeling, and extracellular recordings in isolated sciatic nerves.

      Among the strengths of the study are the interdisciplinary integration of imaging, in silico approaches, and functional data. Also, this study proposes a new mechanism with profound physiological relevance. Specifically, Butler et al. provide new insights into glial modulation of electrical conduction in sensory/motor myelinated nerves.

      In the current state, the study has some limitations. The evidence linking Cx32 to the observed dye uptake and conduction velocity changes relies primarily on pharmacological inhibition with carbenoxolone, which lacks specificity. The imaging data show overlapping marker signals that preclude the anatomical distinction between nodes and paranodes. FITC uptake, while convincing to test Cx32 hemichannel gating, lacks spatial-temporal information and validation of distribution and localization to viable intracellular compartments. Moreover, while the findings are intriguing, functional proof that Cx32 regulates conduction velocity through ATP release or other downstream effects remains incomplete. Further work using targeted genetic tools, live-tissue imaging, and additional controls would strengthen the mechanistic conclusions.

      Overall, the manuscript offers compelling preliminary evidence that supports a new role for Cx32 in peripheral nerve physiology and raises important questions for future investigation.

      We thank the reviewer for their comments and agree that the evidence for involvement of Cx32 is indirect. We have now used viral expression of Cx32<sup>DN</sup> in SCs to remove CO<sub>2</sub> sensitivity from the endogenous Cx32 to strengthen this link. We have reviewed our presentation of the morphology in terms of the node/paranode/juxtaparanode distribution and adjusted accordingly. We have added new data using GCaMP transduced into Schwann cells that provides the live-tissue imaging that the reviewer requests.

      Reviewer #2 (Public review):

      Summary:

      This article aims to demonstrate that local production of CO<sub>2</sub> at the axonal node opens Cx32 hemichannels in the Schwann cell paranode, and that CO<sub>2</sub> diffuses through the AQP1 channel to reach Cx32 and trigger its opening. The authors also present evidence supporting a physiological role for this regulatory mechanism. They propose that CO<sub>2</sub>-dependent Cx32 activation mediates activity-dependent Ca<sup>2+</sup> influx into the paranode, and by increasing the leak current across the myelin sheath, it contributes to a slowing of action potential conduction velocity.

      The study presents a very interesting and novel mechanism for the physiological regulation of Cx32 hemichannels. The findings are relevant to the field, and the methods and results are of good quality, with some improvements in interpretation and explanation required, and some minor experimental suggestions.

      Strengths:

      The article is solid in terms of the novelty of the findings and relevance for the physiology of myelinated axons. In addition, it is of major interest for the Connexin field because it explores a physiological way to open Cx32 hemichannels. The experiments are well elaborated, and most of them are sufficient for the main points described by the authors. The finding that nervous activity will trigger the mechanism of hemichannel opening by CO2 is probably the most relevant biological mechanism derived from this article.

      Weaknesses:

      Throughout the manuscript, the authors interpret their findings as if the described mechanism specifically occurs in the node and paranode regions. However, there is no direct evidence identifying the precise site of CO<sub>2</sub> production or the activation site of Cx32 hemichannels. Therefore, statements such as the one in the title ("activity-dependent CO<sub>2</sub> production in the axonal node opens Cx32 in the Schwann cell paranode") should be reconsidered or removed, as they may be misleading and are not essential to the interpretation of the data. In addition, the participation of aquaporin AQP1 as the main conduit for CO2 diffusion through the plasma membrane could have another interpretation.

      We thank the reviewer for their comments and agree that we do not have direct evidence for the site of CO<sub>2</sub> production or the site of activation of Cx32 hemichannels. This direct evidence is extremely difficult to obtain, and we therefore depend on indirect arguments. Mitochondria represent the major source of CO<sub>2</sub>, and their distribution will therefore indicate where CO<sub>2</sub> is likely to be produced. We agree that this is not essential to the interpretation of the data and have adjusted the text as recommended. We have added a section to the Discussion to consider this point in more detail. The reviewer alludes to a reported interaction between AQP1 and NaV1.8 as a possible alternative interpretation. We can confidently rule this out as the AQP1 blocker has no effect on the compound action potential.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Main comments:

      (1) While the imaging system used in this study is technically capable of resolving nodes and paranodes, interpretation depends critically on marker specificity and tissue orientation. In some figures, markers such as Caspr or KCNA2 appear to partially overlap with KCNQ2 or the putative axonal node, which could reflect biological proximity but may also result from incomplete spatial separation in the z-dimension or the curvature of teased fibers. Similarly, Cx32 immunoreactivity or FITC signal is occasionally seen within nodal gaps, raising questions about how accurately this data supports the author's hypothesis. Additionally, while the authors claim that AQP1 is localized in nodes, the data suggest the opposite. Clarifying these patterns using fluorescence intensity line scans or additional nodal markers such as Nav1.6 or Ankyrin G would help distinguish overlapping signals from true domain-specific localization and reinforce the spatial conclusions of the study.

      We have changed our presentation of the localisation studies. We have concentrated on colocalization of Cx32 and AQP1 (now Fig 2) and moved the other studies to supplements to this figure. While we have retained the same images of Cx32 and AQP1 localisation, we have emphasized that these are SIM images and thus higher resolution than conventional LSM images, and also from a single optical plane. We have also clarified that the colocalization studies are restricted to analysis of the node/paranode regions.

      (2) To strengthen the conclusion that Cx32 specifically mediates the observed dye uptake, additional data or an alternative approach would be valuable. One feasible, though technically demanding, strategy would be the use of AAV-mediated delivery of Cx32-targeting shRNA directly into the sciatic nerve, ideally under a Schwann cell-specific promoter. This approach could achieve localized, cell-type-specific knockdown of Cx32 within a relevant time frame. Alternatively, the authors are encouraged to consider using additional pharmacological inhibitors to exclude the contribution of other conduction pathways, such as pannexin channels. These complementary strategies would reduce the interpretive ambiguity associated with non-specific blockade.

      We agree that this is desirable and have used Cx32<sup>DN</sup> under the control of the Mpz promoter (delivered by AAV via intranerval injection). This approach has several advantages -the Cx32<sup>DN</sup> subunit coassembles with endogenous Cx32<sup>WT</sup> and the heteromeric assemblies lack CO<sub>2</sub> sensitivity (first shown in Butler & Dale, 2023; and this strategy used with Cx26 to demonstrate its role in the control of breathing van de Wiel, 2020). This is a new figure (Fig 9). We have included supplemental figures with Fig 9 to document the coassembly of Cx32<sup>DN</sup> with Cx32<sup>WT</sup> by FRET.

      These new data test a very specific hypothesis: that CO<sub>2</sub> binding to Cx32 is responsible for the CO<sub>2</sub> sensitivity of the nerve. We find by comparing transduced and non-transduced fibres in the same nerve that Cx32<sup>DN</sup> essentially abolishes activity dependent loading of FITC into the Schwann cells.

      (3) Related to FITC experiments: Assuming the hypothesis of the authors is correct and CO2 release is restricted to the node, one should expect that if the major source of CO2 is in the nodal mitochondria, the hemichannels adjacent to the node will open first, assuming the spatial-temporal diffusion of CO2. To demonstrate this point, I would strongly suggest performing tissue imaging with real-time dye uptake. This approach should capture the FITC wave starting from the Cx32 channel opening in the paranode, as expected. Visualization of uptake in fixed and sectioned tissue is not the ideal approach to detect functional hemichannel opening in intact, viable cells, and at this point, they do not demonstrate that the uptake occurs in the node. From my perspective, if real-time experiments using isolated axons are feasible, it would make this paper more solid.

      The suggested method is not practical as the FITC in solution will be fluorescent and thus obscure the entry of FITC into the paranode. We have however expressed GCaMP8 under the control of the Mpz promoter, and this is expressed at paranodes and gives a CO<sub>2</sub> and activity-dependent Ca<sup>2+</sup> signal at the paranode. This gives a real time measure of the effect of CO<sub>2</sub> on the nerve. The GCaMP8 signal is enhanced by AZ and blocked by TC AQP1-1 (see below).

      (4) In Figure 5, Supplement 1, the authors present data using GRAB-ATP to suggest that Cx31.3 hemichannels do not release ATP under CO<sub>2</sub> stimulation. However, control experiments with GRAB-ATP alone (without Cx31.3 expression) are not shown, and parallel conditions with Cx32-expressing cells are lacking. Including these controls would strengthen the manuscript. Finally, testing the permeability of Cx31.3 to FITC directly, using the same conditions as in the main experiments, would clarify whether the discrepancy reflects differences in molecular permselectivity or CO<sub>2</sub> sensitivity.

      Figure 5 supplement 1, does show GRAB<sub>ATP</sub> alone without Cx31.3 expression (in the box plot). However, we have now added raw traces for this to the figure in panel B. CO<sub>2</sub>-dependent and voltage dependent ATP release via Cx32 has been previously shown in two papers (Butler & Dale 2023, Frontiers Cell Neurosci; Lovatt et al 2025, J Biol Chem). The Cx32<sup>DN</sup> result (above) further eliminates any contribution of Cx31.3.

      (5) Suggestion: It would be valuable to explore whether the proposed mechanism is conserved across both motor and sensory neurons, as this would broaden its physiological relevance. Since the sciatic nerve contains both fiber types, selective analysis or comparative data could clarify whether hemichannel activity is differentially regulated or restricted to a specific neuronal subtype.

      This is a great idea, but well beyond the scope of this paper. In an ex vivo preparation it would be very difficult to selectively stimulate the sensory vs motor fibres.

      Suggestions to improve data presentation and other minor comments:

      (1) Reduce/reorganize the figures to make the paper straightforward. For example, (a) immunofluorescence data showing the CO2 signaling machinery could be represented in one single figure; (b) Figure 1 could include all the findings and keep it as a final figure to summarize what the authors claim.

      We thank the reviewer for these suggestions. We prefer to keep Fig 1 up front to have our hypothesis clear for the reader to assist their interpretation as they go through the paper. We have altered the balance of figure supplements and main figures that document the immunolocalisation studies to concentrate on the main areas of novelty (AQP1 and Cx32 colocalisation and CA localisation).

      (2) The following phrase in the Results section is incomplete: "There was colocalization between Cx32 and CytC in the Schwann cell paranode, and (Fig 2, mean; 95% confidence interval, M1: 0.314; 0.198, 0.431 and M2: 0.261; 0.165, 0.357)."

      We have corrected this

      Additionally, the three values for M1 and M2 should be clearly defined and contextualized. In the current state, I couldn't understand them.

      The three values are mean and lower and upper 95% confidence limit:

      M1: mean 0.314; 95% CI, 0.198 to 0.431

      We have now made this clearer in the text.

      (3) It is unclear whether the authors calculate Manders' coefficients across the whole image or selectively at the node/paranode. Clarifying this would help interpret the specificity of co-localization claims.

      The Manders’ coefficients were selectively calculated at the node/paranode and we have amended the text to clarify this.

      (4) It is possible that mislocalization of CytC and SFXN1 could reflect antibody unspecificity or post-isolation alterations in protein distribution (e.g., apoptosis or stress). The authors briefly discussed this observation, but it could be a good idea to consider the use of an additional antibody to validate mitochondria localization.

      Apoptosis or stress is unlikely as the isolated nerves were fixed immediately after isolation with little dissection prior to fixation.

      The SFXN1 antibody was validated by Fowler et al 2013, and IP-HTMS confirmed SFXN1 as an interacting partner with Cx32. In this paper they also described SFXN1 as being present at the plasma membrane, the speculation being that it was taken there by Cx32.

      We think this is probably a valid result and we have further cited the Fowler et al 2013 paper in our discussion of this point.

      (5) Figure 4: The legend states: "Arrow heads indicate the node, and arrows depict the outer myelin." However, no arrows are visible in the figure. Please check.

      Corrected.

      (6) Figure 5: Keep consistency: Include in panel N that trpa1 inhibitor is in the presence of 70mmHg PCO2, as indicated for cbx in the same panel.

      Done

      (7) Figure 5 Supplement 1: Normalization using 1 concentration of ATP could not be appropriate if the sensor-dependent signal is not linear. If possible, authors should make a concentration-response curve and fit the data using the appropriate equation.

      Over the range we are measuring ATP (low µM) GRAB<sub>ATP</sub> is approximately linear to allow a single point calibration -we documented this in Butler and Dale 2023. This is also shown in the original paper describing GRAB<sub>ATP</sub> (Wu et al 2022 Neuron). We have clarified this point in the methods by referring to these papers.

      (8) Figure 6: The increase in FITC signal could represent a basal uptake over time. Authors should clarify the magnitude/rate of the basal uptake. Another option is showing a picture of the uptake using the control frequency at a time of 10 min. Legend: It is not clear in panel C if this picture corresponds to frequency stimulation. If so, it would be beneficial to specify the time.

      Could dye loading in this Fig simply be time dependent rather than stimulation dependent? Our data show that this is not the case -the dye loading controls of Fig 5A were exposed to FITC for 10 mins at 35 mmHg PCO<sub>2</sub> -very little loading is apparent. We now explicitly make this point in the text. Our use of Cx32<sup>DN</sup> also eliminates this explanation, by demonstrating the necessity of CO<sub>2</sub> binding to Cx32 for dye loading to occur.

      As there is no panel C in this figure, we assume the referee means panel B and have added the frequency of stimulation and time duration used to achieve the loading.

      (9) Please revise the legend of Figure 7. It seems to refer to a previous version of the manuscript's figure.

      Thanks for pointing this out. We omitted giving a letter to one of the panels and we have corrected this so that legend and figure now correspond.

      (10) Figures 10 and 11. Please consider including a bright field image or indicating with an arrow where the node and/or paranode is located.

      The old Fig 11 has been omitted. The old Fig 11 is now Fig 10. Unfortunately, we cannot add a bright field image as we did not save these in this experiment.

      (11) Figure 11. The authors could consider doing this experiment in the presence of Cx32 blockers to strengthen their conclusion.

      We have decided to remove this figure as it the information it contains is shown in the new GCaMP8 figure (Fig 12).

      (12) Figure 12: Calcium signal increases in different areas beyond the ROI. Not clear that the calcium signal is restricted to the node, as shown in previous figures. Please clarify if the preparation is different.

      We agree that this is a limitation – there is a lot of out of focus light due to Fluo4 being membrane permeable and loading many fibres within the nerve (potentially both axon and Schwann cell). Importantly, this phenomenon occurs in the in-focus ROI (for which we show BF image).

      As we think this is basically a limitation of using Fluo4-AM, we have now produced better data using GCaMP8 under the Mpz promoter (new Fig 12). This expresses at the paranode and in far fewer fibres so the resolution of the recordings is better. We have added these new data into the main body of the paper and relegated the Fluo4 data as a figure supplement to Fig 12 that provides independent supporting information.

      (13) Figure 13: Please indicate the stimulation frequency. The authors could consider attaching Figure 7 Supplement 1 to this figure to make the manuscript straightforward.

      Frequency now indicated.

      With regard to the original Figure 7 supplement 1 -thanks for this suggestion. After consideration, we have split this up and attached it as figure supplements to the relevant figures (Figure 6 and Figure 8). We have added equivalent data to Fig 7 (effect of H<sub>2</sub>O<sub>2</sub>). We think this simplifies presentation for the readers.

      (14) Figure 7 Supplement 1 and Figure 8 Supplements: Please indicate trace colors in panel A of these figures. Also, correct the spelling issue in the legend of Figure 8 Supplement 1 (for panel B).

      Corrected

      (15) Statistical clarifications: The authors should specify which experimental groups were included in some statistical analysis where p-values are reported, but the information about which groups are compared is missing.

      Corrected

      Reviewer #2 (Recommendations for the authors):

      (1) Localization of CO<sub>2</sub> production and Cx32 activation

      Throughout the manuscript, the authors interpret their findings as if the described mechanism specifically occurs in the node and paranode regions. However, there is no direct evidence identifying the precise site of CO<sub>2</sub> production or the activation site of Cx32 hemichannels. Therefore, statements such as the one in the title ("activity-dependent CO<sub>2</sub> production in the axonal node opens Cx32 in the Schwann cell paranode") should be reconsidered or removed, as they may be misleading and are not essential to the interpretation of the data.

      We agree that we have not shown this -and now exercise more caution in the description of the results and discuss this point.

      (2) Figures 2 and 3 - Cx32, mitochondria, and AQP1 localization

      In Figures 2 and 3, it is difficult to clearly discern the localization of Cx32, mitochondria, and AQP1 in the nodal and paranodal regions. The addition of zoomed-in images and 3D reconstructions (or at least orthogonal views) would greatly help clarify whether these components are indeed localized to the axon or Schwann cell, and whether they are specifically enriched in nodal or paranodal domains. As currently presented, the images suggest that all components of this "triad" are broadly distributed within the cells, not restricted to, nor particularly enriched in, nodal or paranodal areas. This observation further supports the concern raised in point 1.

      We have revised our presentation of the localisation more clearly and added a section to the discussion to consider this point more fully. We now explicitly mention that these are SIM images and in a single optical plane, therefore colocalization is genuine. We have also clarified that the calculation of Manders’ coefficients was performed only at the node/paranode regions. However, we accept that these components are distributed more widely than the node/paranode.

      (3) Figure 5 - Clarify legend labels

      In the graph shown in Figure 5, the legend would benefit from more descriptive labeling of the experimental groups. For clarity, indicate that FCCP was applied alone, and that HCO30031 was co-applied with high PCO<sub>2</sub>, to simplify interpretation for the reader.

      Corrected

      (4) Additional experiment to block mitochondrial CO<sub>2</sub> production

      An experiment should be added to completely or significantly inhibit mitochondrial CO<sub>2</sub> production, for example, by combining FCCP treatment with a TCA cycle inhibitor such as fluoroacetate. This would more directly demonstrate that CO<sub>2</sub> generation is required for hemichannel opening during FCCP treatment. It is important to control for this because FCCP can increase ROS production as a result of compensatory metabolic activity (i.e., increased NADH/FADH<sub>2</sub> generation). Since Cx32 hemichannels are known to be modulated by ROS, and can also regulate mitochondrial ROS production, it is crucial to distinguish the role of CO<sub>2</sub> from that of ROS in these experiments.

      Thanks for this great comment, as it gave us the idea of linking activity-dependent (rather than FCCP-evoked) gating of Cx32 to the TCA cycle and, as the reviewer says, CO<sub>2</sub> generation more directly. As fluoroacetate is only effective at inhibiting the TCA cycle in glial cells, we used H<sub>2</sub>O<sub>2</sub> at 50 µM which is highly effective at blocking aconitase in neurons (Tretter & Adam-Vizi, 2000). This greatly reduced FITC dye loading in response to activity. We now include these data in the paper (Fig 7).

      We note that our new data with Cx32<sup>DN</sup> further establishes the link to CO<sub>2</sub> as opposed to ROS.

      Furthermore, to complement the experiments involving carbonic anhydrase (CA) manipulation, additional controls or mechanistic validation may be necessary to support the conclusions drawn.

      We think that our use of Cx32<sup>DN</sup> greatly strengthens our conclusions that CO<sub>2</sub> is the messenger from the axon that gates Cx32 in the paranode.

      (5) AQP1 and Na<sup>+</sup> channel interaction - alternative interpretation

      It has been reported that AQP1 interacts with voltage-gated Na<sup>+</sup> channels, influencing action potential generation. For example, in AQP1 knockout mice, current injection-evoked action potentials show a reduced peak inward current, suggesting impaired Nav1.8 function (Zhang et al., J. Biol. Chem., 2010; doi: 10.1074/jbc.M109.090233). This raises the possibility that the observed effects of AQP1 inhibition (e.g., with TC AQP1-1) could also result from altered Na<sup>+</sup> channel activity, not just impaired CO<sub>2</sub> transport. I suggest that this alternative interpretation be acknowledged and discussed, as the current data do not rule it out.

      While constitutive KO of AQP1 does alter action potential generation in DRGs and an interaction between AQP1 and Nav1.8 has been documented, we do not think that this is a viable alternative interpretation of our data. We have measured the CAP during all our manipulations including the use of TC AQP1-1, and its amplitude is unaltered (see Fig 8 fig supplement 1 and Fig 13D). Our data therefore shows that, in the context of our experiments, application of the AQP1 blocker, TC AQP1-1, does not alter Na<sup>+</sup> channel activity. The difference between our data and the evidence from AQP1 knock-out may arise from the nature of an acute application of an antagonist (short term effect without changing protein expression) and constitutive knock out, which is likely to have longer term effects. We have added some discussion to address this point (last few lines, Page 9).

      (6) Figures 11A and 12C - Add heat map calibration

      In Figures 11A and 12C, the changes in Ca<sup>2+</sup> signals are difficult to interpret. In some areas, color changes appear to occur outside of cellular structures. I recommend including a heat map calibration scale for both figures to facilitate the interpretation of the signal intensity and localization.

      We agree that these data are limited by the technique used, and as mentioned above we now have GCaMP8 data that has better resolution and strengthens our conclusions.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      In the manuscript entitled "Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells," Soltys and colleagues present easySHARE-seq, a method described as an improvement upon SHARE-seq for the simultaneous measurement of RNA transcripts and chromatin accessibility.

      The authors demonstrate the utility of easySHARE-seq by profiling approximately 20,000 nuclei from the murine liver, successfully annotating cell types and linking cisregulatory elements to target genes. The authors claim that easySHARE-seq supports longer read lengths potentially enabling better variant discovery or allele-specific signal assessment, though they do not provide direct evidence to support these specific claims.

      A key strength of the protocol is enhanced sequencing efficiency, achieved by shortening the Index 1 read from 99 to 17 nucleotides. This reduction does not come at a significant cost to barcode diversity, retaining approximately 3.5 million combinations. Additionally, the approach allows for the sequencing of a sub-library to assess quality prior to final barcoding and sequencing which seems quite clever.

      While the increase in RNA transcript recovery is substantial, it appears to come at a cost: there is a notable decrease in ATAC fragments per cell compared to the original SHARE-seq (and other platforms). Likely as a result, the dimensionality reduction (UMAP) shows good resolution for RNA profiles but relatively poor resolution for accessibility profiles. Furthermore, the presented data suggests potential ambient RNA contamination; specifically, the detection of Albumin in HSCs and B cells is likely an artifact of the protocol rather than a biological signal.

      Overall, the study is well-presented and represents a promising advance. However, there are significant shortcomings that should be addressed, particularly regarding "leaky" transcript recovery and reduced ATAC performance.

      Recommendations:

      (1) To provide a comprehensive view of the current field, the authors should include Scale Biosciences (Scale Bio) in their discussion of available commercial platforms.

      We added Scale Biosciences to the relevant part in the introduction.

      (2) A head-to-head comparison with the 10x Genomics Multiome platform would be of significant interest to the single-cell genomics community and would better contextualize the performance of easySHARE-seq.

      We agree that a comparison to the 10x Multiome technology would be of interest in the community. Therefore, we included such a dataset profiling murine liver nuclei in the comparison in Figure 1 E&F as well as Suppl. Fig. 1 L&M. The resulting comparison remains consistent - easySHARE-seq compares favourably to other multiomic technique in RNA-seq data quality (UMIs/cell) but not in ATAC-seq data quality (fragments/cell).

      (3) Optimizing ATAC Performance: I strongly suggest exploring methods to improve ATAC sensitivity. As the authors note, the improvement in RNA recovery may result from fewer processing steps and stronger fixation. It would be valuable to test if decreasing fixation back to 2% (as in the original SHARE-seq) recovers ATAC data quality, and to determine if the fixation level or the number of steps is the key variable in preserving transcripts.

      We thank the reviewer for this suggestion. We agree that knowing the specific step(s) impacting ATAC-seq data quality would be highly valuable. Unfortuantely, we are not in a position to perform the additional wetlab experiments. It remains an area of improvement as we develop the technique further. We can confirm, however, that our early trials showed that the extent of fixation is negatively correlated with ATAC-seq data recovery.

      (4) The authors allude to the possibility of scaling this assay using a barcoded poly(T). Explicit inclusion or demonstration of this capability would dramatically increase interest in this protocol. Perhaps ATAC could be scaled using a barcoded Tn5?

      We thank the reviewer for this suggestion. Since we cannot perform further experiments, we expanded and clarified on upscaling this assay in our Supplementary Notes and referred to them in the text.

      We also added a paragraph specifically discussing the use of barcoded Tn5 in the Supplementary Notes.

      (5) The number of HSCs and B cells expressing Albumin is problematic and suggests significant ambient RNA issues that need to be addressed or computationally corrected.

      We thank the reviewer for pointing out this potential issue. We have used ‘decontX’ to estimate and ‘de-contaminate’ our UMI counts. We have added a histogram of estimated fraction of contaminated counts per nuclei to Suppl. Fig. 1. We have used the decontaminated counts to re-generate the analysis in Fig. 2 B&C and Suppl. Fig. 2 F. This filtering step did not change the results of these analyses; in fact it strengthened the results and improved clarity. We have added the relevant information to the Methods section and codebase and discussed the results and implications in the Supplementary Notes which we briefly summarize here:

      “As reported in Suppl. Fig. 10, decontX identifies mean contaminated counts of 9.6% and median contaminated counts of 1.4%, suggesting that few cells that are heavily contaminated strongly inflate the overall estimation of contaminated counts. This could be due to 1) doublets or b) wrongly assigned cell types. The authors of decontX report contamination values of 1-4% in commercial droplet-based protocols and 11-14% in plate-based protocols, suggesting that easySHARE-seq performs better than other plate-based assays.”

      We again want to thank the reviewer for this suggestion. It has improved the manuscript.

      Reviewer #2 (Public review):

      Aims:

      The authors sought to optimize SHARE-seq, a multimodal single-cell method, to improve the simultaneous profiling of gene expression and chromatin accessibility. Their goal was to enhance barcode design for better sequencing efficiency and cost savings, while improving overall data quality. They then applied their optimized method, easySHARE-seq, to study liver sinusoidal endothelial cells (LSECs) to demonstrate its utility in examining gene regulation and spatial zonation.

      Strengths:

      The improved barcode design is an advance, increasing the proportion of sequencing reads dedicated to biological information rather than barcode identification. This modification offers practical benefits in terms of sequencing costs and read length, potentially reducing alignment errors. The method also demonstrates improved RNA detection compared to the original SHARE-seq protocol. The biological applications showcase how simultaneous measurement of both modalities enables analyses that would be practically impossible with single-modality approaches, particularly in examining how chromatin states change along developmental or spatial trajectories.

      Weaknesses:

      There is a notable reduction in chromatin accessibility detection compared to the original SHARE-seq method, likely limiting the broad use of the method. While the authors are transparent about this tradeoff, additional discussion would be helpful regarding how this affects data interpretation. Comparisons showing consistency between easySHARE-seq and SHARE-seq chromatin accessibility patterns at the single-cell level would strengthen confidence in the method.

      Overall:

      The authors achieve their aim of creating an optimized protocol with improved barcode design and enhanced RNA detection. The method represents a useful advance for specific experimental contexts where the tradeoffs are appropriate. Recommendations for the authors:

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Figure 1F appears identical to Supplementary Figure 1M. This should be corrected if this is in error.

      Fixed.

      Reviewer #2 (Recommendations for the authors):

      The following comments are intended to strengthen the work.

      (1) scATAC-seq Performance and Data Consistency

      While I appreciate the authors' transparency regarding scATAC-seq performance, the extent of underperformance warrants greater emphasis. Additionally, does the average ATAC-seq signal recapitulate previously published results? At the single-cell level, how consistent are easySHARE-seq and SHARE-seq data? I suspect that increased dropout in scATAC-seq may distort consistency between datasets. This should be explicitly discussed in terms of data interpretation.

      We thank the reviewer for this suggestion. We have cross-referenced the open chromatin regions in this study and we summarise the result at the end of the ‘benchmarking’ paragraph. We have further expanded on the limitations in our study in the ATAC-seq data given the lower data quality in the relevant part of the discussion. We should note that a direct comparison between SHARE-seq and this study is challenging due to different sample tissues.

      (2) LSEC Biological Investigations

      The biological investigations could be strengthened (though this may reflect my limited expertise with LSECs).

      (a) Enhancer analysis depth

      While the authors quantify potential enhancers through RNA-ATAC correlations within individual cells and identify genes regulated by multiple enhancers, a deeper exploration of enhancer biology would strengthen the manuscript. Potential questions include: Do genes sharing correlated enhancer activity also show correlated expression? How do enhancer number and strength relate to gene expression levels? How do RNA-ATAC correlations scale with ATAC peak height? Are stronger enhancers more tightly linked to gene expression? Perhaps the authors explored these questions without finding significant patterns, but this should be clarified.

      We thank the reviewer for this suggestions. We performed several analyses aimed at exploring enhancer biology with this dataset. We added a simple comparison for UMIs per gene between genes with at least one associated peak compared to those without in Suppl. Fig. 3I. We provide the corresponding plot for fragments per peak in Suppl. Fig. 3J. We also explored the relationship between gene expression and chromatin accessibility; here, we found that gene expression levels do not correlate with peak heights of chromatin accessibility (possibly because chromatin accessibility signals were somewhat binary). The corresponding plot has been added to Suppl. Fig. 3K. We added a small paragraph discussing these findings in the main text.

      (b) Correlation magnitude interpretation

      The reported correlation values are extremely small. Does this reflect weak biological linkages or primarily experimental noise? If experimental noise, how does variation in detection per gene influence the confidence in this type of analysis?

      We thank the reviewer for raising this potential issue. We identify a total of 40,957 significant peak-gene associations with a mean Spearman correlation of 0.1 (± 0.056; Suppl. Fig. 3E). This analytical workflow to identify these gene-peak associations was first described alongside SHARE-seq in Ma et al.. For context, they reported significant peak-gene associations to have a mean Spearman correlation of 0.026 (± 0.015; Ma et al. Table S4).

      Generally, we hypothesize that these low correlation values in this type of analysis are the results of sparseness of single-cell data, especially in chromatin accessibility. Therefore, the power to detect gene–peak associations increases with cell number (Ma et al., Fig. 3B) and the limited cell numbers in the analysis in this study likely results in an enrichment of the most strongly correlated associations among those detected. We have added a comparison of UMIs per gene for genes with and without a significant gene-peak correlation, illustrating this dynamic (Suppl. Fig. 3I). Furthermore, we have described this relationship and limitation in the relevant part of the results section.

      (c) Zonation analysis framing

      The zonation analysis is compelling, but the authors should more explicitly emphasize that defining pseudotime and examining chromatin state dynamics is only possible because both modalities are measured simultaneously. And more detail on the Monocle3 pseudotime analysis is needed, as it is unclear how this was really done.

      We expanded our description on the pseudotime analysis using Monocle in the relevant section in the Methods. Furthermore, we explicitly point out that this type of analysis relies on simultaneous measurements of both modalities at the end of the results section.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Yang et al. investigates the relationship between multi-unit activity in the locus coeruleus, putatively noradrenergic locus coeruleus, hippocampus (HP), sharp-wave ripples (SWR), and spindles using multi-site electrophysiology in freely behaving male rats. The study focuses on SWR during quiet wake and non-REM sleep, and their relation to cortical states (identified using EEG recordings in frontal areas) and LC units.

      The manuscript highlights differential modulation of LC units as a function of HP-cortical communication during wake and sleep. They establish that ripples and LC units are inversely correlated to levels of arousal: wake, i.e., higher arousal correlates with higher LC unit activity and lower ripple rates. The authors show that LC neuron activity is strongly inhibited just before SWR is detected during wake. During non-REM sleep, they distinguish "isolated" ripples from SWR coupled to spindles and show that inhibition of LC neuron activity is absent before spindle-coupled ripples but not before isolated ripples, suggesting a mechanism where noradrenaline (NA) tone is modulated by HP-cortical coupling. This result has interesting implications for the roles of noradrenaline in the modulation of sleep-dependent memory consolidation, as ripple-spindle coupling is a mechanism favoring consolidation. The authors further show that NA neuronal activity is downregulated before spindles.

      Strengths:

      In continuity with previous work from the laboratory, this work expands our understanding of the activity of neuromodulatory systems in relation to vigilance states and brain oscillations, an area of research that is timely and impactful. The manuscript presents strong results suggesting that NA tone varies differentially depending on the coupling of HP SWR with cortical spindles. The authors place their findings back in the context of identified roles of HP ripples and coupling to cortical oscillations for memory formation in a very interesting discussion. The distinction of LC neuron activity between awake, ripple-spindle coupled events and isolated ripples is an exciting result, and its relation to arousal and memory opens fascinating lines of research.

      Weaknesses:

      I regretted that the paper fell short of trying to push this line of idea a bit further, for example, by contrasting in the same rats the LC unit-HP ripple coupling during exploration of a highly familiar context (as seemingly was the case in their study) versus a novel context, which would increase arousal and trigger memory-related mechanisms. Any kind of manipulation of arousal levels and investigation of the impact on awake vs non-REM sleep LC-HP ripple coordination would considerably strengthen the scope of the study.

      We agree that conducting specific behavioral tests before electrophysiological recordings, as well as manipulating arousal during the recording session, would strengthen the study. These experiments are planned for future work, and we acknowledged this point in the discussion.

      We added the following text in the Discussion: “Conducting behavioral assays prior to electrophysiological recordings, along with spatially and temporally precise modulation of LC activity during recording sessions, will be essential for achieving a mechanistic understanding of network dynamics and its functional role for memory consolidation in future investigations.”

      The main result shows that LC units are not modulated during non-REM sleep around spindle-coupled ripples (named spRipples, 17.2% of detected ripples); they also show that LC units are modulated around ripple-coupled spindles (ripSpindles, proportion of detected spindles not specified, please add). These results seem in contradiction; this point should be addressed by the authors.

      The detection of coupled events - spindle-coupled ripples (spRipple) and ripple-coupled spindles (ripSpindle) - was performed independently, although, some overlap cannot be excluded. We found that LC suppression was generally weak around both types of coupled events. Specifically, LC suppression around spRipples and ripSpindles reached significance (exceeding the 95% confidence interval) in 4 sessions (from 3 rats) and 3 sessions (from 2 rats), respectively, out of a total of 20 sessions (from 7 rats).

      We revised the manuscript by providing additional information in the Results section and adding a Supplementary Figure 5 showing a significant correlation (Pearson r = 0.72, p = 0.0003) between the modulation index (MI) for spRipple and ripSpindle.

      Results are displayed per recording session, with 20 sessions total recorded from 7 rats (2 to 8 sessions per rat), which implies that one of the rats accounts for 40% of the dataset. Authors should provide controls and/or data displayed as average per rat to ensure that results are now skewed by the weight of that single rat in the results.

      High-quality recordings from the LC in behaving rats are technically challenging and relatively rare; therefore, we included all valid datasets in analysis. The average modulation index (MI), calculated per animal and per session, fell within a consistent range (Supplementary Figure 3) despite variability in the number of recording sessions (2–8 sessions per rat).

      In its current form, the manuscript presents a lack of methodological detail that needs to be addressed, as it clouds the understanding of the analysis and conclusions. For example, the method to account for the influence of cortical state on LC MUA is unclear, both for the exact methods (shuffling of the ripple or spindle onset times) and how this minimizes the influence of cortical states; this should be better described. If the authors wish to analyze unit modulation as a function of cortical state, could they also identify/sort based on cortical states and then look at unit modulation around ripple onset? For the first part of the paper, was an analysis performed on quiet wake, non-REM sleep, or both?

      The LC activity around rippled was modulated at multiple temporal scales. First, we observed a relatively sharp drop in the LC firing rate ~ 2 s before the ripple onset. When computing peri-ripple LC activity over a longer time window ([–12, 12] sec), we observed a rather slow decrease in the LC firing rate beginning as early as 10 s before the ripple onset (Supplementary Figure 2).

      Considering two temporal scales, we hypothesized that slow modulation of LC activity might be related to fluctuations of the global brain state. We quantified the ongoing cortical state using a synchronization index (SI), calculated as a power ratio (1–4 Hz/30–90 Hz) of the EEG within 4-s windows and computed the corresponding ripple and LC-MUA rates. Figure 3A (in the main manuscript) illustrates that a higher SI (more synchronized cortical population activity) corresponded to a lower arousal state and reduced LC tonic firing; this brain state was associated with a higher ripple activity. As shown in the new Figure 3B, the LC firing rate was negatively correlated with the SI and ripple rate. Thus, slow LC modulation was likely driven by cortical state transitions.

      To correct for the influence of the global brain state on the peri-ripple LC activity, we generated surrogate events by jittering the times of detected ripples. First, we confirmed that triggering the hippocampal LFP on the surrogate events lacked the ripple-specific frequency component (main Figure 3C) and the SI state did not differ around ripples and surrogate events (main Figure 3D). Plotting the LC activity around surrogate evens captured its state-dependent dynamics (Figure 3 or Supplementary Figure 2, orange trace). To extract state-independent peri-ripple LC modulation, we subtracted the state-related LC activity (orange trace) from the ripple-triggered LC activity (blue trace). The resulting trace yielded a corrected estimate of ripple-associated LC activity that was largely free from the confounding influence of cortical state transitions (main Figure 3E).

      In the Results subsection “LC-NE neuron spiking is suppressed around hippocampal ripples”, we reported LC modulation without accounting for the cortical state (main Figure 2). The state-dependent effects were instead examined in the subsequent Results subsection, “LC firing and ripple occurrence are state-dependent and inversely related” we report state-corrected LC modulation (main Figure 3). Finally, in the Results subsection “Peri-ripple LC modulation depends on the cortical–hippocampal interaction,” we characterized LC activity around ripples across different cortical states (quite awake and NREM sleep).

      We revised Methods and Results to provide more methodological details and a rationale for each analysis, as requested.

      Reviewer #2 (Public review):

      Summary:

      In this study, the authors studied the synchrony between ripple events in the Hippocampus, cortical spindles, and Locus Coeruleus spiking. The results in this study, together with the established literature on the relationship of hippocampal ripples with widespread thalamic and cortical waves, guided the authors to propose a role for Locus Coeruleus spiking patterns in memory consolidation. The findings provided here, i.e., correlations between LC spiking activity and Hippocampal ripples, could provide a basis for future studies probing the directional flow or the necessity of these correlations in the memory consolidation process. Hence, the paper provides enough scientific advances to highlight the elusive yet important role of Norepinephrine circuitry in the memory processes.

      Strengths:

      The authors were able to demonstrate correlations of Locus Coeruleus spikes with hippocampal ripples as well as with cortical spindles. A specific strength of the paper is in the demonstration that the spindles that activate with the ripples are comparatively different in their correlations with Locus Coeruleus than those that do not.

      Weaknesses:

      The claims regarding the roles of these specific interactions were mostly derived from the literature that these processes individually contribute to the memory process, without any evidence of these specific interactions being necessary for memory processes. There are also issues with the description of methods, validation of shuffling procedures, and unclear presentation and the interpretation of the findings, which are described in the points that follow. I believe addressing these weaknesses might improve and add to the strength of the findings.

      We believe that our responses to the Reviewer 1 and Reviewer 2, corresponding revisions of the manuscript and new figures adequately addressed all issues raised by the Reviewer 2.

      Reviewer #3 (Public review):

      Summary:

      This manuscript examines how locus coeruleus (LC) activity relates to hippocampal ripple events across behavioral states in freely moving rats. Using multi-site electrophysiological recordings, the authors report that LC activity is suppressed prior to ripple events, with the magnitude of suppression depending on the ripple subtype. Suppression is stronger during wakefulness than during NREM sleep and is least pronounced for ripples coupled to spindles.

      The study is technically competent and addresses an important question regarding how LC activity interacts with hippocampal and thalamocortical network events across vigilance states.

      Weaknesses:

      The results are interesting, but entirely observational. Also, the study in its current form would benefit from optimization of figure labeling and presentation, and more detailed result descriptions to make the findings fully interpretable. Also, it would be beneficial if the authors could formulate the narrative and central hypothesis more clearly to ease the line of reasoning across sections.

      We improved the presentation of results by incorporating additional figures and expanding the detail in the figure captions. In the main text, we clarified specific hypotheses and provided a rationale underlying each analysis.

      Comments:

      (1) Stronger evidence that recorded units represent noradrenergic LC neurons would reinforce the conclusions. While direct validation may not be possible, showing absolute firing rates (Hz) across quiet wake, active wake, NREM, and REM, and comparing them to published LC values, would help.

      We added the requested data and a Supplementary Figure 1 in the revised manuscript: “The average firing rates of LC single units were 1.70 ± 0.21 Hz during wakefulness, 0.51 ± 0.07 Hz during NREM sleep, and 0.014 ± 0.01 Hz during REM sleep (Supplementary Figure 1). Firing rates differed significantly across arousal states, with the highest activity during wakefulness, reduced activity during NREM sleep, and minimal activity during REM sleep (one-way ANOVA: F(2,38) = 39.8, p < 0.0001). This firing pattern is characteristic of LC-NE neurons and is consistent with existing literature.”

      (2) The analyses rely almost exclusively on z-scored LC firing and short baselines (~4-6 s), which limits biological interpretation. The authors should include absolute firing rates alongside normalized values for peri-ripple and peri-spindle analyses and extend pre-event windows to at least 20-30 s to assess tonic firing evolution. This would clarify whether differences across ripple subtypes arise from ceiling or floor effects in LC activity; if ripples require LC silence, the relative drop will appear larger during high-firing wake states. This limitation should be discussed and, if possible, results should be shown based on unnormalized firing rates.

      We agree with the reviewer that a longer pre-event window provides a clearer estimate of baseline LC activity. However, given that both ripples and spindles are brief oscillatory events, we tested a range of time windows and found that a 12-s interval adequately captures baseline LC activity dynamics. Accordingly, we included plots with extended pre-event windows (−12 to 12 s), as requested.

      We added in the revised manuscript absolute firing rates for well-isolated LC single units. Because the number of neurons contributing to LC multi-unit activity (LC-MUA) is unknown, we avoided averaging absolute firing rates for this signal. For LC-MUA, we implemented a normalization approach in which firing rates (50-ms bins) around ripple or spindle are scaled to a baseline period preceding the trigger event (−12 to −10 s). Importantly, unlike z-scoring, this normalization method preserves baseline differences across behavioral states. As shown in Author response image 1A and new Figure 5 in the main manuscript, baseline LC firing rates were highest prior to awake ripples and lowest prior to sleep spindles. During ripples occurring in wakefulness, LC activity did not decrease to the levels observed during sleep. In contrast, during NREM sleep, LC activity was downregulated during both ripples and spindles, although it did not reach complete silence around either oscillatory event.

      Author response image 1B illustrates a slow downward drift in the LC firing rate preceding either ripple or spindle. The slow LC dynamics likely reflected gradual transitions toward more synchronized brain state, which is optimal for ripple generation. In contrast, event-specific LC modulation had faster dynamics (Author response image 1B, highlighted interval) and was largely absent in cases where spRipples and ripSpindles were not associated with LC suppression (Author response image 1C).

      To minimize the influence of global state fluctuations and emphasize event-related dynamics, we therefore presented the main results using state-corrected and z-scored PETHs.

      Please also refer to our response to Reviewer 1 regarding the two temporal scales of LC modulation.

      Author response image 1.

      LC modulation around sleep oscillations. (A) Peri-event LC-MUA during awake and NREM sleep. LC activity and the range of peri-event LC modulation differed across behavioral states; it was overall higher preceding ripples occurring in wakefulness than in NREM sleep, and it was the lowest around sleep spindles. Despite the state-dependent differences in the firing rate, LC modulation was observed around all oscillatory events. During wakefulness, LC activity did not decrease to the levels observed during NREM sleep. During NREM sleep, LC activity was down-regulated around both ripples and spindles, and the LC firing did not completely cease around either oscillatory event. (B) Peri-event LC-MUA around isolated oscillatory events. LC activity exhibited fast peri-event dynamics (highlighted interval) superimposed on slower, state-dependent fluctuations. (C) Peri-event LC-MUA around coupled oscillatory events. Fast peri-event LC modulation was absent, while slow fluctuations were preserved around coupled oscillatory events. For all plots, LC-MUA firing rate was scaled to a pre-event baseline interval [-12 to -10 sec] to preserve baseline differences in LC activity across behavioral states. Bin size: 50 ms. isoRipple – isolated ripple, isoSpindle – isolated spindle, spRipple - spindle-coupled ripple, ripSpindle - ripple-coupled spindle.}

      (3) Because spindles often occur in clusters, the timing of ripple occurrence within these clusters could influence LC suppression. Indicate whether this structure was considered or discuss how it might affect interpretation (e.g., first vs. subsequent ripples within a spindle cluster).

      We did not consider spindle clusters and classified the event as ripple-coupled spindle if the ripple occurred between the spindle on and offset.

      (4) While the observational approach is appropriate here, causal tests (e.g., optogenetic or chemogenetic manipulation of LC around ripple events and in memory tasks) would considerably strengthen the mechanistic conclusions. At a minimum, a discussion of how such approaches could address current open questions would improve the manuscript.

      We agree that conducting causal tests would strengthen the study. We added the following text in the Discussion: “Conducting behavioral assays prior to electrophysiological recordings, along with spatially and temporally precise modulation of LC activity during recording sessions, will be essential for achieving a mechanistic understanding of network dynamics and its functional role for memory consolidation in future investigations.”

      (5) Please show how "Synchronization Index" (SI) differs quantitatively across behavioral states (wake, NREM, REM) and discuss whether it could serve as a state classifier. This would strengthen interpretations of the correlations between SI, ripple occurrence, and LC activity.

      We plotted the awake state-normalized SIs for awake and NREM sleep. Due to small number of REM sleep episodes, SI for REM sleep is not shown. The average SI during NREM sleep was significantly higher than during awake state, consistent with the well-established dominance of low-frequency (1-4 Hz) oscillatory power and reduced high-frequency (30-90 Hz) power during NREM sleep.

      Although SI could potentially serve as a behavioral state classifier, we have chosen not to address this point to maintain the focus in the discussion on new results.

      Author response image 2.

      Synchronization index differentiates behavioral states.

      (6) The current use of SI to denote a delta/gamma power ratio is unconventional, as "SI" typically refers to phase-locking metrics. Consider adopting a more standard term, such as delta/gamma power ratio. Similarly, it would be easier to follow if you use common terminology (AUC) to describe the drop in LC-MUA rather than using "MI" and "sub-MI".

      The ranges of delta and gamma bands might vary across studies; therefore, we prefer using SI, as defined here and in our previous publications (Novitskaya et al., 2016; Yang et al., 2019, 2021). We calculated the modulation index (MI) as the area under the curve of the peri-event time histogram within the 1 second preceding ripple onset. To avoid potential confusion with the AUC calculated over the entire signal window, we opted to use MI.

      (7) The logic in Figure 3 is difficult to follow. The brain state (delta/gamma ratio) appears unchanged relative to surrogate events (3C), while LC activity that is supposedly negatively correlated to delta/gamma changes markedly (3D-E). Could this discrepancy reflect the low temporal resolution (4-s windows) used to calculate delta/gamma when the changes occur on a shorter time scale?

      We appreciate the reviewer’s question. We revised the results and Figure 3 legend to clarify this point. The main Figures 3E and 3F show the 'state-corrected' peri-ripple LC activity. The purpose of generating ‘surrogate’ events was precisely to capture the component of LC activity dynamics that can be explained by cortical state fluctuations alone. As shown in Supplementary Figure 2, the orange trace represents LC activity aligned to surrogate events and, as the Reviewer noted, shows a clear decrease, yet at a slower time scale. We interpret this surrogate-aligned signal as the LC modulation attributable specifically to cortical state fluctuations. Importantly, shuffled events were associated with similar SIs (cortical state), but absent HPC LFP power increase in the ripple range (140-250 Hz), as shown in the main Figures 3C and 3D, respectively. To isolate the peri-event LC dynamics, we subtracted the state-related component (Figure 3, orange trace) from the ripple-triggered LC activity (blue trace). This correction yielded an estimate of ripple-associated LC activity that is largely independent of the confounding influence of ongoing cortical state.

      Please, see our detailed response to the Reviewer 1 about multiple time scales of LC dynamics.

      (8) There are apparent inconsistencies between Figures 4B and 4C-D. In B, it seems that the difference between the 10th and 90th percentile is mostly in higher frequencies, but in C and D, the only significant difference is in the delta band.

      We repeated this analysis, clarified inconsistency, and revised Figure 4 legend.

      (9) Because standard sleep scoring is based on EEG and EMG signals, please include an example of sleep scoring alongside the data used for state classification. It would also be relevant to include the delta/gamma power ratio in such an example plot.

      We replaced ‘standard’ with ‘previously established” sleep scoring procedure and added a Supplementary Figure 4 showing representative NREM sleep and wake episodes with corresponding EEG and SI.

      (10) Can variability in modulation index (subMI) across ripple subsets reflect differences in recording quality? Please report and compare mean LC firing rates across subsets to confirm this is not a confounding factor.

      We agree that considering recording quality and unit stability over time as potential confounding factors is important. We therefore carefully evaluated each dataset to ensure the absence of significant drift in the LC firing rate. However, we find that comparing mean LC firing rates across subsets of ripples, as suggested by the Reviewer, is insufficient to control for recording stability, as LC activity varies substantially across behavioral states. At present, we are not aware of a robust method to fully eliminate variability related to recording quality and unit stability over time.

      (11) Figure 6B: If the brown trace represents LC-MUA activity around random time points, why would there be a coinciding negative peak as relative to real sleep spindles? Or is it the subtracted trace?

      We have revised Figure 7 (original Figure 6) and its legend to improve clarity and readability.

      (12) On page 8, lines 207-209, the authors write "Importantly, neither the LC-MUA rate nor SIs differed during a 2-sec time window preceding either group of spindles". It is unclear which data they refer to, but the statement seems to contradict Figure 6E as well as the following sentence: "Across sessions, MI values exceeded 95% CI in 17/20 datasets for isoSpindles and only 3/20 for ripSpindles". This should be clarified.

      We have revised the corresponding text to improve clarity and readability.

      (13) The results in Figures 5C and 6F do not align. It seems surprising that ripple-coupled spindles show a considerably higher LC modulation than spindle-coupled ripples, as these events should overlap. Could the discrepancy be due to Z-score normalization as mentioned above? Please include a discussion of this to help the interpretation of the results.

      In the original manuscript, Figure 6F was mistakenly labelled for ripple-coupled (ripSpindles) and isolated (isoSpindles) spindles. Now it has been corrected.

      Please, also see our response to the Reviewer 1 weaknesses.

      (14) The text implies that 8 recordings came from one rat and two each from six others. This should be confirmed, and it should be explained how the recordings were balanced and analyzed across animals.

      Since high-quality recordings from LC in behaving animals are challenging and rare, we used all valid sessions. We addressed the same point in our response to the Reviewer 1 weaknesses.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Below are some suggestions for clarification/information that are needed to improve the paper's readability (and the understanding of the analysis and methods).

      (1) The authors describe a consistently negative correlation between cortical EEG synchronization index and ripple rate or LC-MUA, show an example in Figure 3A, and report a range of r values in the text with a mention of p < 0.01. The reported p-value is presumably the highest p-value for the correlations - please specify. Visualization of the results might be improved by adding example correlations (also true for later correlations in Figure 6).

      We revised the result description accordingly and included correlation plots in Figures 3 and 7.

      (2) Description of statistical testing is missing for Figure 3C (nothing in the text or the figure legend); there is also no statistics section in the methods. For Figure 4, the statistics are reported for the Friedman test but not the post-hoc tests. Exact p-value and statistics should be reported for the comparison of LC-MUA rate and SI in the 2 s preceding spindles.

      We have added the statistical results requested and revised figure legends by providing additional information. We added the Statistic Analysis section in the Methods.

      Figure 3D (original Fig.3C): “Average Synchronization Index (SI) around ripples and shuffled events. The cortical state preceding shuffled events and ripples was comparable, as confirmed by the absence of significant differences in SI (Wilcoxon signed-rank test; shuffled: Z = -0.20, p = 0.84; ripples: Z = 0.14, p = 0.88). Cortical synchrony increased following both events (shuffled: Z = -3.50, p = 0.00044; ripples: Z = -3.66, p = 0.00026). Similar cortical state dynamics surrounding shuffled events and ripples indicate that the surrogate events adequately capture the cortical state associated with ripple occurrence.

      Figure 6: Intra-ripple frequency (A) and peak amplitude (B) for different ripple types. Boxwhisker plots show the median, the 1st and 3rd quartiles, and min/max. Gray dots show data from individual rats. *** - p < 0.001 for post hoc pairwise comparisons (Wilcoxon signed-rank tests with Holm–Bonferroni correction for multiple comparisons).

      We revised the Results accordingly: “The ripple subtypes differed in the intra-ripple frequency (Friedman test, chi2 = 35.62, p < 0.0001, post hoc pairwise comparisons were performed using Wilcoxon signed-rank tests with Holm–Bonferroni correction for multiple comparisons. awRipple vs isoRipple: p = 0.00003 awRipple vs spRipple: p = 0.00004 isoRipple vs spRipple: p = 0.0002}), with awRipples being the fastest and spRipples the slowest (Figure 6A).There was no difference in the ripple peak amplitude (Friedman test, $\chi$2 = 3.7, p = 0.16; Figure 6B).”

      (3) The method description of ripple-spindle coupling detection is missing.

      We have added the description of ripple-spindle coupling detection in the Methods.

      (4) Based on Figure 6D, the authors report that ripple-coupled spindles are significantly shorter than isolated spindles. What are the measurements reported on lines 206-207, and how do they relate to the averaged spectrograms shown in Figure 6D?

      Spindle duration was calculated as the time between spindle onset and offset (as described now in the Methods and Figure 7 legend). Ripple-coupled spindle was considered if at least one ripple occurred between the spindle onset and offset. The duration of ripple-coupled and uncoupled spindles was statistically compared (the stats is reported in text). In Figure 7E, the peri-event averaged EEG spectrograms are plotted for isolated and ripple-coupled spindles, highlighting the difference in the event duration.

      (5) None of the color scales have legends (Figures 2A, B, C, Figure 3D, etc.).

      We have added the color scales on all Figures.

      (6) Description of what is represented in the box plots is missing.

      We have added the description.

      (7) Figure 4C, D, legend for the color code is missing.

      We have added color scales legends.

      (8) Figure 5A legend, assuming this should read intra-ripple frequency instead of inter-ripple.

      We corrected the typo.

      (9) Figure 5E, while LC units are not modulated before, it could still be informative to overlay the z-scored firing rate on the same graph for comparison.

      Figure 6E (original Figure 5E) shows overlay for awRipples and isoRipples.

      (10) The discussion states a 4s resolution for cortical state quantification (line 237), but the methods mention 2.5s (line 382).

      We corrected this discrepancy.

      (11) Results, p.5, line 138, Methods and materials, p.13, line 423: 30% in result text but 20% in method, please correct.

      We corrected this discrepancy.

      (12) The manuscript cites the biorxiv version of Osorio-Forero et al., but the paper has been published since then; please update.

      We updated this reference.

      (13) Results, p.2, line 70. The average duration of a session is presented in seconds. Minutes or hours would be more meaningful to the reader.

      We consider this suggestion as optional.

      (14) Figure 2C is not referenced.

      We added the reference to Figure 2C.

      (15) Reference missing line 406.

      We added the reference.

      (16) Lines 352-356: There seems to be an error in the sentence (an extra verb, or an "and" missing somewhere).

      We have corrected this sentence.

      (17) Figure 3C "synchronization".

      We corrected this typo.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 94 states that "A significant peri-ripple decrease in LC-SUA"; however, which test and how many samples were used are unclear.

      We revised this text as follows: “A significant peri-ripple (± 6 s) decrease in LCSUA, detected by the firing suppression exceeding 2 SDs, was observed in 13 of 15 cases (n = 4 rats).”

      (2) Line 96 states that "we calculated the modulation onset, duration, and magnitude". Please define modulation before presenting the comparisons.

      We now illustrate the extraction of quantitative variables in Figure 2D.

      (3) Line 119 states that "we generated surrogate time series for each session by shuffling ripple onset times" which gives the impression that ripple events were shuffled throughout the sleep; however, the method section states that it was jittered within a specific time window for each event. Please clarify the matter.

      We have substantially revised this section to improve clarity and readability.

      (4) Line 120 states that "Comparisons of SI values before and after ripples and surrogate events confirmed that surrogate events preserved the cortical states in which ripples occurred". Ripple power doesn't seem to be different in pre vs post in the shuffled data (Figure 3B). If ripple timing was randomized, please clarify the observation shown in Figure 3C that the shuffled events had higher SI after than before, as also seen in the real SI data? Please also elaborate what specific groups were significantly different in before vs after bars; data, shuffle, or both?

      We have substantially revised this section to improve clarity and readability.

      (5) Line 113 and Figure 3A: Because both LC activity and HPC ripples were correlated to SI, the direct relationship between LC and HPC independent of SI (a covariate) was not clear. The authors might be able to conduct a partial correlation analysis to show this effect.

      We appreciate this suggestion and added the correlation plots in Figures 3 and 7. After careful consideration, we believe that the suggested partial correlation analysis does not contribute substantially beyond the main findings already presented.

      (6) Figure 5A: Inter-ripple frequency needs definition, not provided in the paper nor in the reference paper. The value (180 Hz) suggests a time interval of around 5 ms, which I fail to understand.

      We apologize for this typo. In Figure 6A (original Fig.5A), intra-ripple frequency is plotted. We have corrected this typo in the text and figure legend.

      (7) Figure 5D: Comparison between aw and sp ripples should also be shown. Please explain the dashed line at 10 (y-axis) a.u.

      Figure 6E (original Fig.5E) shows LC activity around awRipples and isoRipples.

      (8) Figure 5E: Legend states aw and iso ripples, but the caption says NREM sleep. Please clarify this matter.

      We have revised Figure 6 legend (original Figure 5).

      (9) Figure 6B: If the spindle time is permuted randomly, why is LC activity in the permuted data still modulated by the spindle times? Can you test the significance of the modulation index of the shuffled data?

      The LC modulation around shuffled time points was not significant. Figure 7C shows LC modulation dynamics around spindles; brown trace showing state-corrected LCMUA trace (after subtraction of LC-MUA around shuffled events).

      (10) Line 203: Is the unit in Hz (events per second) correctly calculated or shown? ~15 events per second seems arbitrarily large.

      We corrected the units for the event rate. We report the mean oscillatory frequency of spindles ~15 Hz, not events per second.

      (11) Line 207 states that "neither the LC-MUA rate nor SIs differed during a 2-sec time window preceding either group of spindles"; however, from Figure 6E, the average trace and errors around them (errors need to be stated clearly, for e.g., SEM or SD) show that they are non-overlapping and different. I suspect tests such as the rank-sum test, which test the difference in the central tendencies (as opposed to the KS test, which tests the overall trend in the distribution of the continuous data), might reveal the difference between these values.

      We compared the absolute (not normalized) LC-MUA rate and SI during 2 sec time window preceding spindle onset and did not find any statistical differences. In Figure 7F, the difference during ~ 2 sec before the spindle onset is due to the z-score normalization to their own baseline.

      We revised the Result text to improve clarity.

      (12) Line 209: Modulation seems to be greater in ripp-spindles as shown in fig 6E-F, yet, the text and the interpretation are the opposite i.e,. iso spindles had greater modulation. Hence, authors might have to provide further clarifications or analyses.

      We corrected the labelling in all plots.

      (13) Line 316: Claims of "suppression of noradrenergic system facilitating the generation of hippocampal ripples and sleep spindles by memory synchrony" are not fully supported by data, as the data seem to be correlational. Also, claims of "preserved LC activity during ripples coinciding with sleep spindles suggest a role for NE in facilitating cross-regional communication underlying memory-related information transfer" lack clarity and contradict the earlier mechanism. Both "suppression" as well as "preservation" of LC neurons are proposed to mechanistically support memory synchrony and/or consolidation in two different brain states (awake and sleep). The authors might need to clarify how both suppression as well as preservation (which I assume is not an activation or positive modulation) of LC neurons can help in memory synchrony or consolidation.

      We revised this part of discussion by making it less speculative.

      Reviewer #3 (Recommendations for the authors):

      I would recommend that the authors optimize their figure and result presentation, as the current version of the manuscript is unclear in several places, limiting the interpretation of results.

      We substantially revised the manuscript to improve the results presentation and readability.

      (1) Multiple results are described but not shown quantitatively. Please plot quantifications and statistics (mean {plus minus} error and individual values) in relevant figures. For example, the results referenced on p. 4 (l. 113-116), p. 5 (l. 129-133, 143-147), p. 6 (l. 159161), p. 7 (l. 188-190), and p. 8 (l. 203-207) should be supported by explicit data plots.

      We have revised the manuscript to ensure all results are supported by quantitative and statistical analyses. We revised figures and legends and added new plots showing individual datapoints.

      (2) Improvements in figures and descriptions are needed. Below are some examples I found:

      (a) All figures with color scales lack labeling of the color axis, i.e., measure and unit.

      We have revised the figures accordingly.

      (b) Use precise labeling of axes such as "ripple-band power" and "LC-MUA firing rate", rather than just "power" and "firing rate".

      We have revised the figures accordingly.

      (c) Figure 1: Indicate behavioral state (wake vs. sleep) in the example trace.

      We have indicated the behavioral state (quiet awake) in the figure legend.

      (d) Define "peri-ripple" windows explicitly (e.g., {plus minus}6 s or {plus minus}30 s).

      We have revised the text and figure legends accordingly.

      (e) Clarify how "modulation magnitude" is calculated (line 96).

      We now illustrate the extraction of quantitative variables in Figure 2D

      (f) Figure 2C: The white overlaid mean trace lacks Y-axis labeling.

      We have added y-axis labeling.

      (g) Figure 3A: The labeling of "amplitude" is confusing when referring to firing frequency.

      We have corrected the figure labelling.

      (h) Figure 4B: Is the X-axis time from ripple onset?

      We have corrected the figure labelling.

      (i) Figure 4C-D lacks an X-axis or color legend.

      We have added x-axis and color legend.

      (j) Figures 5-6: Include tonic firing rates and time scales.

      We have added in the main text the time scales and average firing rates for LC single units and also show it in Supplementary Figure 1. Because the number of neurons contributing to LC multi-unit activity (LC-MUA) is unknown, we avoided averaging absolute firing rates for this signal. For LC-MUA, we implemented a normalization approach in which firing rates (50-ms bins) around ripple were scaled to a baseline period preceding the trigger event (−12 to −10 s). Importantly, unlike z-scoring, this normalization method preserved baseline differences across behavioral states, as shown in new Figure 5.

      (k) Add tonic firing rate baselines where relevant.

      We have added the Supplementary Figure 1 and new Figure 5 showing the difference in the LC baseline firing rate across behavioral states.

      (3) Minor Comments to add more clarity

      (a) Clarify "spike train" selection criteria (Methods, p. 4, line 93).

      We revised the text as follows: “In six out of twenty LC-MUA recordings, we could reliably isolate spikes from a total of 15 single units (LC-SUA, n = 4 rats).”

      (b) Define "EEG transients" (p. 4, line 109) and support with data.

      We revised the text as follows: “Indeed, transient spectral changes in the prefrontal EEG coincided with the occurrence of hippocampal ripples (Figure 2B).”

      (c) You refer to Figure 3E as a histogram (p. 5, line 128), but I believe it shows an average trace.

      We have corrected this typo.

      (d) Standard sleep scoring procedures normally involve EMG measurements (p. 6, line 154).

      We have replaced ‘standard’ with “previously established”.

      (e) Explain how surrogate shuffling preserves the distribution of behavioral states.

      We revised the text as follows: “We first verified that hippocampal LFPs (140– 250 Hz) triggered on these surrogate events lacked the ripple-specific frequency component (Figure 3C), and that the SI state did not differ between real ripples and surrogate events (Figure 3D).”

      (f) You refer to inter-ripple frequency (p. 6, line 168), which suggests time between ripples. Do you mean the "intra-ripple" or simply ripple frequency?

      We have corrected this typo.

      (g) Ensure all references cited in the text (e.g., p. 12, line 406) are included in the bibliography.

      We have updated the bibliography.

      (h) On p. 10, line 304-305 authors refer to observations related to offline memory consolidation. However, the present study does not contain any behavioral memory data.

      We have revised the Discussion to make it less speculative about the role of describe LC dynamics for offline memory consolidation.

      References

      Novitskaya Y, Sara SJ, Logothetis NK, Eschenko O (2016) Ripple-triggered stimulation of the locus coeruleus during post-learning sleep disrupts ripple/spindle coupling and impairs memory consolidation. Learn Mem 23:238-248.

      Yang M, Logothetis NK, Eschenko O (2019) Occurrence of Hippocampal Ripples is Associated with Activity Suppression in the Mediodorsal Thalamic Nucleus. J Neurosci 39:434-444.

      Yang M, Logothetis NK, Eschenko O (2021) Phasic activation of the locus coeruleus attenuates the acoustic startle response by increasing cortical arousal. Sci Rep 11:1409.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      This paper aims to improve the accuracy of predictions of the impact of ITN strategies by developing a method to estimate duration of ITN access and use over time on a subnational scale from cross-sectional survey data and the numbers ITNs received annually. The subnational estimates are then input into a mathematical model to predict clinical cases under different ITN distribution strategies.

      Strengths:

      The approach is novel and addresses a useful and timely topic. It makes use of available routine data, and has considered all of the relevant components of ITN distributions.

      The authors have made revisions, particularly to the methods, appendices and title - leaving the paper easier to follow, and with a clear, consistent aim. The assumptions are clearly stated.

      Weaknesses:

      The weaknesses are shared with other models of a similar complexity - it is not easy for a casual reader to fully understand the model or the implications of the assumptions which were required to be made. That routine data is used is good for availability, but data quality may be an issue in some places.

      Reviewer #2 (Public review):

      Summary:

      The authors design a custom Bayesian model to estimate the probabilities of access, use and use given access of insecticide-treated nets in six African countries, providing sub-national estimates and inferring the average duration of ITN use and access. An individual-based model was employed to simulate malaria epidemics and estimate the effectiveness of different ITN distribution strategies. The study finds that the mean probability of use or access did not reach 80% (a universal coverage formerly targeted by WHO) for any of the regions even for biennial campaigns, demonstrates that switching from triennial to biennial distribution campaigns increases population use by 7.9%, and evaluates the impact of employing more efficient ITNs on P. falciparum prevalence.

      Strengths:

      The authors developed a data-driven model that accounts for data collection imperfections and sources of uncertainty while differentiating between ITN use and access. They developed a methodology to infer the timing of mass campaign from publicly available data instead of assuming fixed dates. The probability of use given access allows determining the regions where ITN distribution is least effective. This work can help better inform future interventions by identifying regions where increasing mass campaign frequency or employing better ITNs are most effective. Finally, in addition to insights on ITN access and use for the six countries analyzed, the paper contributes with a methodological framework that can likely be extended to other countries.

      Weaknesses:

      Since the models employed are rather complex, the methodology description may be hard to follow for some readers. In addition, the models assume many hypotheses, including exponential decay of ITN use/access and narrow prior distributions. It is worth noting that, in the revised version of the manuscript, the authors justified the choice of exponential decay and narrow prior distributions, and made a significant effort to clarify the methodology and the model equations.

      Comments on revised version:

      I appreciate the improvements made to the text. The methodology description is much clearer now. I have no further suggestions.

      We thank the reviewers and editors for their constructive and insightful comments throughout the review process.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      P8 'Improving ITN use' L218 

      The numbers do not seem add up to me. "...increases across all settings of 14.5% (95% CrI:14.5, 14.6), from 41.7%% to 49.6%. Greater increases are predicted to be seen for ITN use with mean use across all settings increasing from 58.0% to 66.2%, an increase of 19.5% CrI (95% CrI:19.5, 19.6)."

      Thank you for highlighting this. We have reviewed all reported results on mean use, access and use given access. The previous text reported a mixture of absolute and relative % changes, as well as a mixture of raw mean estimates across all regions and population-weighted means across regions. In the extract above we had inadvertently mixed different metrics. Given administrative-one regions can vary notably in population between different countries, we have ensured estimates are now consistently reported as population-weighted means, so that countries with finer-scaled administrative-one regions, such as Burkina Faso, do not artificially bias a raw mean estimate across all sub-national regions. We have also reported % changes as absolute percentage-point increases throughout, rather than relative ones to improve clarity.

      Methods p18: There is notation in the text which does not seem to be explained. It is in the appendices, but the appendices should be optional extra information rather than essential for understanding. 

      We have reviewed the text in the main methods to check notation explanations. Following this, we have removed a use of subscript $i$, which is only used in the appendices to explicitly indicate region-specific parameters, and have clarified that lambda is a decay parameter.

      There are assumptions made and these are clearly explained in the text. However, how much the highlighted results rest on the assumptions was not clear, and there was little on this in the discussion. 

      For example, it might seem disappointing that changing from triennial to biennial ITN campaigns would only lead to an increase from 41.7% to 49.6%. The most important assumptions driving this could be clearer. Additionally, after reading I was not sure what the likely consequences of the assumption that ITN are used continuously were.

      We have added some additional text “to the discussion to clarify the modest predicted increase under biennial campaigns may, in part, be influenced by our assumed exponential loss function, and have highlighted that larger increases in mean use could plausibly be predicted under alternative ITN loss functions”. However, we have also commented that our mean use estimates are broadly in agreement with time series modelled estimates by Bertozzi-Villa et al. (2021) who utilised a sigmoidal/smooth-compact loss function.

      In relation to the assumption of continuous use, we have added additional text in the ‘Historical use, access and retention times’ methods section to clarify that “if ITN use were systematically higher during high-transmission rainy seasons, our assumption of continuous use may underestimate the protective impact of ITNs during these periods”. As stated at the start of that paragraph, the data available from DHS surveys was too infrequent to investigate seasonal fluctuations.

      P14 The text seems to imply that current transmission intensity is the only criterion for decisions about interventions. However, it is likely that the reasons for the current intensity, such as vectorial capacity, historical transmission and interventions should also play a role. The wording could reflect this.

      We have added additional text to clarify that current transmission intensity should not be treated as the only criterion for deprioritisation decisions:

      “However, current incidence should be considered alongside the factors that gave rise to that transmission intensity, with caution exercised when deprioritising mass campaigns in areas where historically higher transmission may currently be suppressed by high ITN access, high use given access, or other interventions.”

      Minor points 

      There are several definite numbers in the first paragraph of the Introduction - these are estimates rather than the absolute truth, but the wording does not acknowledge that there is uncertainty.

      We have made minor edits to clarify that these values are estimates rather than exact quantities. Measures of uncertainty, such as credible intervals were not always possible to source; for example, some of these are median estimates inferred from figures in Bertozzi-Villa et al. (2021).

      L634 typo - logisitic 

      Now corrected.

      L1731 typo https://https://

      Now corrected.

      L881 "access at random" - perhaps not the easiest for non-modelers

      We have re-written this to clarify “when ITNs in a household can provide access to more individuals than the number of users, access is assigned at random to non-users within each household under our framework”.

      Appendix 1, table 1: Using alpha for both age and also overdispersion on use or access is of course valid, but I found it a little confusing.

      To avoid confusion, we have added the following clarification in brackets:

      “Meanwhile, the overdispersion parameter, $\alpha_i^0$ (unrelated to the notation for ITN age), controls the variability of the probability of individual access around the mean”

      I suspect that the model was actually fitted in Stan via the R interface rstan (L589, L1151 and elsewhere).

      We have now clarified this throughout.

    1. Author response:

      Response to Reviewer #1

      Our work builds upon the foundations of what we term the “CM family”, specifically the Connectome Model (CM) introduced by Kovács et al.. This was a deliberate choice, as our objectives substantially overlap with those of works in this family. Moreover, we wished to avoid reinventing the wheel—starting instead from a solid body of work with validations we found convincing (thereby inheriting this solidity) and, importantly, addressing the same research community using a “familiar” conceptual language. We therefore wish to clarify how our contributions indeed constitute new conceptual insights into the genomic specification of neural circuitry.

      The function implemented by a neural circuit clearly depends on how information propagates between its nodes and connections; the contribution of synapses—their number and properties—cannot be neglected when understanding, manipulating, or designing such function. To the best of our understanding, in Kovács et al., the primary objects of interest are binary connectomes (presence or absence of synapses) or weighted connectomes where “in the occasion of multiple [genetic] rules contributing to the same link”, “the weight of each link correspond[s] to the number of rules involved”. In Barabási et al., a “relaxed” version of the CM directly provides weights for an artificial neural network without explicitly specifying how each weight might result from the combination of a specific number of synapses and their respective properties. The random variable formalism and the introduction of conductances that we propose precisely add this further—yet important—element of complexity and representational detail: synaptic multiplicity. This extends existing models with the hope of laying the groundwork for what could, in the distant future, become a technology capable of producing neural circuits genetically programmed to implement a defined function.

      Regarding the proposed validation, we acknowledge its limitations, but we clarify that at the time this work was conducted, to the best of our knowledge, no public datasets existed to perform validation as the reviewer envisions. We therefore did the best that was materially feasible: we assumed the biological correctness of the model (also based on the validations accompanying the models upon which ours was built) and verified, through simulation, that it could be used to obtain genetic variables of interest capable of producing neural agents able to solve a pre-specified task—even with the additional constraint of genetic rules derived from experimental data.

      Response to Reviewer #2

      We address the points raised by Reviewer #2 in the following paragraphs.

      Regarding point (1), we agree with the reviewer that considering single-gene expression features is a simplification, especially in the case of chemical synapses. However, as with the CM, our model can also be extended to account for combinatorial rules. One possibility is to add columns to the X matrix, as many as there are gene expression patterns of interest. For each new column, a function would be defined to compute the expression feature from the expression features of the genes involved in the pattern, and this function would be used to populate the values of the new columns. The O matrix would likewise be updated with the corresponding new probabilities. While such extension is possible, it is important to note that this gives rise to the problem of combinatorial explosion of genetic rules, with the consequent construction of matrices whose dimensionality becomes difficult to handle. Moreover, the biological plausibility of the model would then shift toward how these functions are defined, along with the interpretation of the values contained in the X matrix. Depending on the use case of our model, one possible solution to the combinatorial explosion problem could be to consider only expression patterns valid for synapse formation by extracting this information from available experimental data, thereby restricting the number of rules. We acknowledge that this problem remains open and will require more precise formulations and future work.

      Regarding point (2), Equation (11) can be derived from the assumption that the various synapses between two neurons behave as resistors in parallel. Accepting this, the equivalent conductance Guv, as denoted in the paper, can be expressed as the sum of all conductances between neurons u and v. Moving to the random variable formalism and having defined 𝒢 as the random variable representing the “signed conductance of a synapse randomly selected from the ones that connect neurons u and v”, the equivalent conductance (as a random variable) becomes ℬ·𝒢. Recall that ℬ is the random variable representing the number of synaptic connections between two neurons of interest. At this point, under the further assumption that the random variables ℬ and 𝒢 are independent, the expectation of the equivalent conductance can be calculated as the product of the expected values of ℬ and 𝒢. Equation (11) follows immediately from this. We acknowledge that these assumptions may not correspond to biological reality, but we consider them a reasonable starting point for addressing the problem.

      Finally, we explain the reasons why the baselines suggested by the reviewer are not included in the work. We did not train classical MLPs because the main objective of the work was not to develop new bio-inspired architectures aimed at generically improving the performance of neural networks in RL, and we deemed it an additional source of confusion to propose a comparison that would suggest this direction. The main objective of the work is instead to contribute to the modeling of synaptogenesis and to lay the groundwork for—or advance the state of knowledge of—what will be a future technology that allows us to manipulate it (synaptogenesis). A similar reasoning applies to a potential baseline in which the weight matrix is constructed from Equation (7). Again, the interest is not in verifying that conductances provide a performance advantage, but rather that they are a necessary element for a sufficient level of biological plausibility. Beyond this, the exclusive and direct use of matrix B in the simulation of synaptogenesis introduces a quantization problem as described in the Appendix.

      Response to Reviewer #3

      We believe the concerns raised by the reviewer regarding the weaknesses of the work are legitimate. We wish to emphasize that all claims made in the paper were made in good faith, with the intent to generate enthusiasm for the discipline while avoiding excess or the assertion of anything incorrect or untruthful. Given that the work is inherently interdisciplinary, we recognize that reader expectations depend on their reference community, and we clarify that our primary area of expertise is AI, and that the biological claims were therefore made from this perspective.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      While the revised manuscript includes additional methodological details and a supplementary comparison with conventional NMF, it would be great if the authors could add the point below as limitations in the manuscript or change the title and abstract accordingly, since core issues remain:

      (1) The study claims to evaluate rehabilitation outcomes without demonstrating that patients actually improved functionally

      (2) The comparison with existing methods lacks the quantitative rigor needed to establish superiority

      (3) The added value of this complex framework over much simpler alternatives has not been demonstrated

      The strength of evidence supporting the main claims remains incomplete. I would encourage the authors to consider discussing these points

      (1) including or adding a limitation section about functional outcome measures that go beyond clinical scale scores, (2) providing/discussing quantitative benchmarks showing their method outperforms alternatives on specific, predefined metrics, and (3) clarifying the clinical pathway by which these biomarkers would inform treatment decisions.

      We thank the reviewer for their thoughtful consideration of our study, and now better understand their perspective on the limitations of the study. We now see the importance of the aspects of functional recovery the reviewer has highlighted in the context of our work, as the clinical measure we focused on (i.e. FMA-UE) does not capture recovery at activities and participation-levels of the ICF model. Although the FMA-UE is a gold standard measure for assessing post-stroke recovery, it is limited in scope to gross motor functions.

      To more accurately describe the aspects of functional recovery the biomarkers in our study reflected, we have extensively revised the terminology used throughout the paper. For example, in the abstract we now include “…From these patterns, we derived new biomarkers that stratified patients by gross motor impairment severity and therapeutic responsiveness, each associated with unique physiological signatures.” and go on in the abstract to now highlight the limited scope of the evidence towards functional recovery more broadly also: “Future research should employ this framework to identify biomarkers of activities- and participation-related functional recovery.” In the rest of this paper, we also make this distinction clear, for example at the beginning of the results section: “The cohort of stroke survivors overall experienced a statistically significant increase at FMA-UE (Pre-treatment: 43.1±13.2, Post-treatment: 49.1±13.6 (t= -7.84, p<0.001)), representing a clinically important effect from rehabilitation on the gross motor functions of the upper-extremity (Page et al., 2012).” Finally, we have now added a limitations section, as the reviewer advised, where we specifically detail the scope of evidence provided in this study and how future research could build on it:

      “Limitations

      Although the FMA-UE is a gold standard measure of post-stroke treatment outcomes (Meyer et al., 1975; Page et al., 2012), it does not capture the impact of rehabilitation on patients' ability to perform activities-of-daily-living or to participate in daily life. Hence, interpretations of the identified biomarkers are currently limited to gross motor function impairment and recovery. Future research should employ this framework to quantify biomarkers that correspond to other important aspects of patients' recovery (e.g. functional independence, subjective experiences), thus offering a more complete evidence base for its clinical utility.”

      With these changes, we believe this manuscript more accurately describes the scope of the biomarkers analysed and hence no longer offers incomplete evidence towards stated claims.

      Regarding the reviewers second and third points concerning the validity and advantages of this framework against current approaches, in this study we applied a framework that builds on two previous papers (O’Reilly & Delis, 2022; O’Reilly & Delis, 2024). In both of these papers, we compared basic aspects of the framework to the current prevailing approach and most relevant comparative for this line of research in muscle synergy analysis, that is non-negative matrix factorisation (NNMF).

      To briefly outline this existing foundation of evidence, in O’Reilly & Delis, 2022 we dedicated most of the discussion section (i.e. sections 4.1 and 4.2) along with a supplementary materials document to comparisons with this approach. In section 4.1, we illustrate the continuity of this framework with what has come before in simpler methodologies such as NNMF and then went on in section 4.2 to show the novel insights and opportunities that can generated from our framework. Additionally, in the corresponding supplementary materials of that paper, we directly compared our framework with three different models from the established NNMF approach (i.e. spatial, temporal and space-time) by applying them to the same datasets, again highlighting points of congruence and additional utility with our framework. Building on this work, in O’Reilly & Delis, 2024, we also ensured that developments of this framework both align with previous research and credibly improve upon them methodologically. For example, Fig.5 and Fig.6 and associated text of that paper illustrates a direct comparison of our framework with the NNMF methodology, showing that it provides additional functional and physiological relevance and predictive capacity to the components extracted. Further, in the results of that paper we also directly compared the generalisability of the extracted components when extracted using our chosen dimensionality reduction approach vs other approaches promoted in the neurosciences more generally (e.g. non-negative Canonical-Polyadic (CP) tensor decomposition (Williams et al (2018)), showing that we extracted more robust components across participants and tasks.

      This previous work directly supports the credibility of basic aspects of the framework and its outputs compared to other established approaches. We have directed readers towards this previous research in the methods section of the current study: “Further comparisons with conventional approaches can be found in our previous work developing this framework (O’Reilly & Delis, 2022; O’Reilly & Delis, 2024).”

      Continuing, and building on the credibility of these basic aspects of the framework, as the reviewer previously suggested, we have included additional supplementary material in the current study illustrating how the biomarkers generated from our approach could not be found using conventional methods. In these supplementary analyses, we employed a much simpler but conceptually aligned pipeline involving NNMF and agglomerative clustering on the same dataset and directly compared the outputs, highlighting commonalities and where our approach improves significantly upon this established approach. The advancements we demonstrate here also address recognised limitations in the current NNMF approach for clustering activation coefficients (see Scano et al 2017), a point we now highlight directly in the revised manuscript:

      “Enhanced interpretability of extracted components and clusters.

      As our framework maps muscle interactions to a specific task parameter, we yield population-level motor components that correspond more consistently to meaningful biomechanical and physiological functions that can be interpreted across the dimensions of the specified task parameter. The proposed clustering approach also offers enhanced interpretability, addressing key limitations in the application of clustering approaches to the activation space of conventional muscle synergy analysis (e.g. different activation timings) (Scano et al., 2017).”

      Taken together, we believe the extensive comparisons made in our previous work on this framework and direct comparisons made in this study provide sufficient evidence towards its added value for the field beyond current approaches.

      References

      Ó’Reilly D, Delis I. A network information theoretic framework to characterise muscle synergies in space and time. Journal of Neural Engineering. 2022 Feb 1;19(1):016031.

      O'Reilly D, Delis I. Dissecting muscle synergies in the task space. Elife. 2024 Feb 26;12:RP87651.

      Williams et al. (2018) Unsupervised discovery of demixed, low-dimensional neural dynamics across multiple timescales through tensor component analysis. Neuron 98:1099–1115.

      There are specific, relatively minor points, that require attention

      The authors write: "we did not focus on such complementary evidence in this study." This is a weakness for a paper claiming to provide "biomarkers of therapeutic responsiveness." The FMA-UE threshold defines responders, but there's no independent validation that patients actually functioned better in daily life. Can you please clarify?

      See above for our response on this important aspect of the reviewer’s commentary.

      Maybe I missed the exact point about this, but with the added NMF plot, the authors list 'lower dimensionality' among their framework's advantages, but the basis for this claim is not clear because given that 12 network components were extracted compared to 11 "conventional" synergies. Can you please clarify, as it is not clear. You claim 'lower dimensionality' as an advantage of the proposed framework (in the Supplementary Materials), yet you extracted 12 components (5 redundant + 7 synergistic networks) compared to 11 synergies from the conventional NMF approach, which does not support a clinical / outcome advantage of this method. Please clarify.

      We agree with the reviewer that this statement is confusing given that overall, across separate decompositions for redundant and synergistic networks compared to the single decomposition using NNMF, there are more dimensions to consider in our frameworks output. For this reason, we have removed this statement from the updated manuscript.

      Reviewer #2 (Public review):

      This study presents an important analysis of how interactions between muscles can serve as biomarkers to quantify therapeutic responses in post-stroke patients. To do so, the authors employ an information-theoretical metric (co-information) to define muscle networks and perform cluster analysis.

      I thank the authors for improving the clarity of the Methods section; the newly added Figure 5 is very helpful.

      One minor suggestion is that the authors should avoid overloading the notation "m" for both the EEG measurement and the matrix of II values (Eq. 1.1), which I now realise was the source of some of my initial confusion. I suggest that the authors use separate notation for these two quantities.

      We thank the reviewer for their consideration and positive outlook on our study. In the updated manuscript, we have adjusted the notation for equation 1.1 so that it doesn’t cause confusion with earlier text.

      Recommendations for the authors:

      Reviewer #1 raised critical concerns about the method's ability to identify functional improvements resulting from rehabilitation protocols. In this regard, the study's translational impact remains limited, and the authors should address these limitations in a revised version. The Reviewing Editor and both reviewers agree that the "Strength of Evidence" of the manuscript cannot be improved without a major revision, given the above-mentioned aspects.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Weaknesses

      (1) One of the main EEG results is based on the weighted phase lag index (wPLI) between oscillations in the alpha and theta bands. In my opinion, this is problematic, as wPLI measures the locking of oscillations at the same frequency. It quantifies how reliably the phase difference stays the same over time. If these oscillations have different frequencies, the phase difference cannot remain consistent. Even worse, modeling data show that even very small fluctuations in frequency between signals make wPLI artificially small (Cohen, 2015).

      In response authors stated : "Additionally, the present study referenced previous research by using the wPLI index as a measure of cross-frequency coupling strength31,64-66"

      Unfortunately, after checking those publications, we can see that in paper 31 there is no mention of "wPLI" or "PLV." In 64 and 65, the authors use wPLI, but only to measure same-frequency coherence, whereas cross-frequency coupling is computed by phase-amplitude coupling or cross-frequency coupling also known as n:m-PS. In 66, I cannot find any cross-frequency results, only cross-species analysis. This is very problematic, as it indicates that the authors included references in their rebuttal without verifying their relevance.

      31 de Vries, I. E. J., van Driel, J., Karacaoglu, M. & Olivers, C. N. L. Priority Switches in Visual Working Memory are Supported by Frontal Delta and Posterior Alpha Interactions. Cereb Cortex 28, 4090-4104, doi:10.1093/cercor/bhy223 (2018).<br /> 64 Delgado-Sallent, C. et al. Atypical, but not typical, antipsychotic drugs reduce hypersynchronized prefrontal-hippocampal circuits during psychosis-like states in mice: Contribution of 5-HT2A and 5-HT1A receptors. Cerebral Cortex 32, 870 3472-3487 (2022).

      65 Siebenhühner, F. et al. Genuine cross-frequency coupling networks in human resting-state electrophysiological recordings. PLoS Biology 18, e3000685 (2020).

      66 Zhang, F. et al. Cross-Species Investigation on Resting State Electroencephalogram. Brain Topogr 32, 808-824, doi:10.1007/s10548-019-00723-x (2019).

      We thank the reviewer for this critical methodological correction. We fully agree that the weighted phase lag index (wPLI) is designed for same-frequency phase synchronization and is not appropriate for cross-frequency coupling (CFC). In our original rebuttal, we incorrectly cited references that did not support the use of wPLI for CFC. We apologize for this error and have thoroughly revised our analysis and manuscript.

      What we have done:

      (1) Replaced wPLI with proper 1:2 cross-frequency phase synchrony (CFS).

      We now compute 1:2 CFS using the phase-locking value (PLV) between theta (4–7 Hz) and alpha (8–14 Hz) oscillations, following established methodologies (Siebenhühner et al., 2020, PLoS Biol; Palva et al., 2005, J Neurosci). Specifically, for each electrode pair we compute:

      .The factor 2 accounts for the 1:2 frequency ratio (theta:alpha = 1:2).

      (2) Updated all relevant sections – Methods (“Interregional connectivity”), Results (Figure 8, Figure 9), Discussion, and Figure legends – replacing “wPLI” with “1:2 CFS (PLV)” and providing the correct formula and citations.

      (3) Corrected the reference list to include the appropriate methodological papers (Siebenhühner et al., 2020; Palva et al., 2005) and removed irrelevant citations.

      We believe this revision fully resolves the reviewer’s concern. Notably, the empirical results remained qualitatively unchanged (PLV and wPLI gave highly consistent values due to the absence of zero‑lag artifacts in cross‑frequency coupling), so the main conclusions of the paper are unaffected.

      (2) Another result from the electrophysiology data shows that the attentional capture effect is positively correlated with the mean amplitude of alpha power. In the presented scatter plot, it seems that this result is driven by one outlier. Unfortunately, Pearson correlation is very sensitive to outliers, and the entire analysis can be driven by an extreme case. I extracted data from the plot and obtained a Pearson correlation of 0.4, similar to what the authors report. However, the Spearman correlation, which is robust against outliers, was only 0.13 (p = 0.57) indicating a non-significant relationship.

      Cohen, M. X. (2015). Effects of time lag and frequency matching on phase based connectivity. Journal of Neuroscience Methods, 250, 137-146

      We thank the reviewer for raising this important statistical issue. We have conducted a thorough robustness analysis and revised our interpretation accordingly.

      What we have done:

      (1) Removed the original scatter plot (Figure 7) to avoid overinterpretation. No replacement figure is provided; instead, all results are reported in text.

      (2) Conducted leave‑one‑out cross‑validation.

      The Pearson correlation remained positive across all 24 iterations (range: 0.183–0.497, mean r = 0.430 ± 0.055), confirming that no single participant solely drove the direction of the effect.

      (3) Reported Spearman rank correlation (r = 0.13, p = 0.57), which is more robust to univariate outliers.

      (4) Acknowledged the sensitivity – p‑values from leave‑one‑out iterations ranged from 0.0158 to 0.4025, indicating that statistical significance is not fully robust to sample composition.

      (5) Revised the text to present this as preliminary evidence rather than a definitive conclusion. Specifically, we state: “Thus, we interpret this as preliminary evidence that occipital alpha activity may be associated with the priority state within VWM, warranting replication in larger samples.” The Discussion also includes a dedicated limitation paragraph.

    1. Author response:

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

      Reviewer #1 (Public review):

      (1) (Figure 1): Quantification of CSF1R-GFP<sup>+</sup> and CD11c-eYFP<sup>+</sup> cells in PDPN<sup>+</sup>LYVE-1<sup>-</sup> vs. PDPN<sup>+</sup>LYVE-1<sup>+</sup> regions. “This would demonstrate selective accumulation or retention of myeloid cells at the cribriform plate niche."

      We thank the reviewer for this important suggestion. The representative images in Figure 1(Bottom) establish the partial justification for the cell sorting and sequencing strategy in Figure 3, which relies heavily on myeloid cells in contact with PDPN. Importantly, our previous publication Hsu et al. 2022 has quantified elevated Cd11c+ cells in contact with the Cribriform lymphatic niche. Figure 1 in this context seeks to show PDPN as an additional and broader marker for the meningeal and lymphatic tissue at the brain's border. Because PDPN represents more surface area, PDPN+Lyve-1- regions would likely show more immune cell accumulation but our primary argument is simply that myeloid cells also accumulate in both PDPN regions. As a result we argue the quantification of cells in Lyve-1+ and negative regions is not necessary. We have added a sentence to the text which explains the intention of the figure.

      “Additionally, while PDPN labels the cribriform plate lymphatic vasculature, it also defines the meningeal-immune interface at the border of both the olfactory bulb and olfactory nerve bundles.”

      (2) While the PostContact-seq strategy is innovative (Figure 3), additional justification is needed to demonstrate that tissue dissociation did not artificially disrupt PDPN-myeloid contacts. The relatively small proportion of live PDPN-rich doublets (~2.5% total aggregates and ~18% PDPN+ within total aggregates) raises questions about representativeness compared with in situ observations. The authors should also more explicitly elaborate on why PostContact-seq was favored over alternative approaches such as PIC-seq.

      We acknowledge this important methodological concern. We have expanded the Methods section and added a dedicated paragraph in Results addressing the following:

      Tissue dissociation controls: Dissociation protocols were used specifically to minimize cell-cell adhesion. Unfortunately, we cannot perform parallel dissociations of naive (non-EAE) cribriform plates for scRNAseq because PDPN<sup>+</sup>-containing doublets are essentially non-existent. This is also supporting the representativeness compared to in situ observation. Doublets are significantly enriched in EAE tissue compared to naive controls, arguing against artifactual aggregate formation.

      Representativeness of ~2.5% doublets: While the absolute proportion of doublets is modest, this is consistent with in situ observations where myeloid-PDPN contacts are spatially restricted to the outer perineural and meningeal niche rather than globally distributed. We argue this is simply the enrichment of a rare interaction rather than a limitation.

      PostContact-seq vs. PIC-seq: “PIC-seq (Giladi et al., 2020) sequences intact doublets and relies on specialized deconvolution tools to parse apart data. PostContact-seq leverages the cellular contact signatures post-dissociation, making it a more accessible system. However, we now explicitly discuss this comparison in the Results and acknowledge PIC-seq as a complementary future approach in discussion.

      (3) (Figure 4B): Clarification of integration across four methods; consideration of CellChat/NicheNet: The authors stated that results regarding cell-cell interactions were integrated across four intercellular communication methodologies (Figure 4B), but this integration is not clearly described in either the Results or Method sections. This needs clarification. Moreover, the interaction analysis in Figure 4B seems to rely on TALKIEN, which does not incorporate prior ligand-receptor knowledge. Given the availability of widely used tools, such as CellChat and NicheNet, the authors may consider cross-referencing their findings.

      We have revised the Methods sections to clearly describe our strategy for the TALKIEN analysis. Importantly, TALKIEN does integrate ligand receptor libraries from four sources: CellChat, CellPhoneDB, iCellNet, and the Ramilowsky datasets to generate its figures. Interactions reported in Figure 4B are those supported by this analysis, and we updated the text accordingly.

      (4) Pseudotime trajectory analysis of CCR2<sup>+</sup> monocyte differentiation.

      "A pseudotime trajectory analysis may be valuable to test whether CCR2<sup>+</sup> monocytes preferentially differentiate into CHI3L3<sup>+</sup> macrophages, PD-1<sup>+</sup> DCs, or other subsets."

      We thank the reviewer for this insightful suggestion. We added a complete pseudotime analysis (Author response image 1). The pseudotime analysis tracks a continuous developmental trajectory starting from cDC2 and early macrophage populations (Pseudotime = 0, dark purple) and progressing through the main macrophage body toward an activated terminal state (Pseudotime = 16, yellow). Crucially, the trajectory correctly excludes non-continuous lineages such as resident microglia and lymphoid cells. This progression is functionally validated by the transient upregulation of the recruitment marker CCR2 during intermediate stages, which subsequently downregulates as cells transition into a mature phenotype.

      Author response image 1.

      (5) FACS-based validation of macrophage immunosuppressive signatures.

      "Validation using the same post-contact vs. no-contact sorting strategy would strengthen the conclusions."

      This is an excellent suggestion and will be the topic of future detailed investigation focusing on the cellular and molecular reprograming of the immunosuppressive microenvironment at the cribriform plate.

      (6) Identity of CD45IV<sup>+</sup> cells in contact with PDPN<sup>+</sup> cells (Figure 6B-C); gating strategy; tissue co-labeling. "Provide a gating strategy demonstrating that these are CD11b<sup>+</sup>CD11c<sup>+</sup> DCs... whether dying cells are PD-1<sup>+</sup>... co-labeling for PD-1, cleaved caspase-3, and CD11c-eYFP."

      A full gating strategy (now Figure S5) demonstrate sequential gating from Cells → Doublet → PDPN doublet → CD11b<sup>+</sup> CD11c <sup>+</sup> → CD45IV<sup>+</sup> (intravascular exclusion positive) within the doublet gate.

      (7) (Figures 1F-H): Morphological differences of CD11c<sup>+</sup> cells.

      We have added commentary to the Results section noting that “CD11c<sup>+</sup> cells in the olfactory bulb parenchyma display a ramified, microglia-like morphology consistent with tissue-resident or parenchymal surveillance cells, whereas those infiltrating the cribriform plate perineural niche show a rounded, non-ramified morphology more consistent with recently recruited monocyte-derived DCs or macrophages.” This morphological distinction aligns with our scRNAseq-defined population differences and supports the notion that the cribriform plate niche shapes distinct myeloid states.

      Reviewer #1 (Recommendations for the authors):

      (1) (Figure 1C): MHCII counts vs. MFI discrepancy

      Thank you for catching this. The text has been corrected to reflect that we counted number of cells in the PDPN+ region of the cribriform plate

      (2) Proximity ligation assay (PLA) for macrophage-fibroblast ligand-receptor pairs

      We appreciate this suggestion. PLA validation of all predicted pairs is beyond the scope of this revision, and we are primarily interested in interactions occurring in vivo and in situ. Future studies will investigate properties of these cells using PLA.

      (3) (Figure 2E vs 2G): Inconsistent quantification strategies; CSF1R-GFP/CD11c-eYFP validation of CHI3L3<sup>+</sup>/Arg1<sup>+</sup> cells

      Arg1 signal was more broadly expressed and it was hard to distinguish 1 cell vs 2 cells in close proximity. Which is why we elected to use %Arg1 in PDPN+ regions. Conversely CHI3L3 staining revealed more easily identifiable single cells for quantification. Nonetheless both methods achieve the purpose of outlining that these cells increase in number a the cribriform plate lymphatic regions.

      (4) (Figure 3E): Pro-inflammatory features of migratory DCs vs. suppressive interpretation.

      "Pdcd1lg2, Cd80, Cd83 are associated with T-cell activation — how does this align with an immunosuppressive niche?"*

      This is an excellent point that we now explicitly address in the Discussion. The co-expression of Pdcd1lg2 (PD-L2), Cd80, and Cd83 by migratory DCs likely reflects a tolerogenic activation state rather than a conventional immunostimulatory one. PD-L2 co-expression with costimulatory molecules has been documented in tolerogenic DCs that can engage T cells while simultaneously delivering inhibitory signals via the PD-1/PD-L2 axis (inhibiting rather than amplifying T-cell responses). Furthermore, the lower abundance of migratory DCs in post-contact samples relative to no-contact samples may reflect that cells expressing this immunological synapse machinery are preferentially undergoing programmed cell death (consistent with Figure 6 findings), leaving a post-contact population enriched for the macrophage-dominated tolerogenic signature. We now discuss this interpretation explicitly.

      (5) (Figure 5F-G): Gating strategy for PD-1<sup>+</sup> DCs — PDPN inclusion

      The gating strategy has been clarified in Figure S6 (new figure) and the Methods section. PD-1<sup>+</sup> DCs shown in Figures 5F-G were gated from the PDPN<sup>+</sup> doublet fraction specifically, paralleling the outlined scRNAseq approach. We have added PDPN as an explicit gate in the updated Figure S6A

      (6) (Figure 5H): Discrepancy between text and data — "lowest genes" in PD-1neg DCs.

      We apologize for this error. The text has been corrected: the data in Figure 5H show that chemokines, ISGs, and MHC genes are among the highest expressed in PD-1<sup>+</sup> DCs (not PD-1<sup>-</sup>), consistent with the heatmap shown. This aligns with the interpretation that PD-1<sup>+</sup> DCs, while tolerogenic, retain antigen-presentation and chemokine-signaling capacity.

      (7) Figure 6 reference errors in Results text

      Corrected throughout — all references to cell death/apoptosis data now correctly cite Figure 6.

      Reviewer #2 (Public review):

      (1) Sorted populations — in vivo interactions vs. ex vivo aggregation artifacts

      As detailed in our response to Reviewer 1 (Weakness 2), due to the non-detectable doublet frequency in non-EAE mice, we believe that PDPN<sup>+</sup> doublet enrichment is EAE-dependent. We also used cold dissociation conditions. We also note that the transcriptional signatures recovered from PDPN<sup>+</sup> doublets are not simply a mix of independently sorted PDPN<sup>+</sup> and myeloid single-cell transcriptomes, they contain unique interaction-associated gene programs (e.g., elevated Pdcd1, tolerogenic markers) not present in non-contact controls, arguing for biologically meaningful contact rather than artifactual aggregation.

      (2) PDPN as stromal vs. lymphatic endothelial cells — which is most relevant?

      We have clarified throughout the manuscript that PDPN in IHC marks at least two distinct populations at the cribriform plate: (1) PDPN<sup>+</sup>LYVE-1<sup>+</sup> lymphatic endothelial cells and (2) PDPN<sup>+</sup>LYVE-1<sup>-</sup> meningeal fibroblasts/perineural sheath cells. It is hard to dissociate which is most relevant in the present study.

      (3) Descriptive nature; lack of functional correlates; implications need further discussion.

      We appreciate this honest assessment. We agree that functional experiments (e.g., conditional deletion of DC populations at the cribriform plate, blockade of PD-1/PD-L1 axis, lymphatic ablation) will be critical for establishing causality and are ongoing in the laboratory. In this revision, we have:

      (1) Added a pseudotime analysis as a computational functional inference.

      (2) Refined the Discussion to explore functional implications, including how tolerogenic conditioning at the cribriform plate may limit cervical lymph node priming, parallels with perineural immunosuppression in cancer, and therapeutic opportunities (e.g., modulating this niche to enhance or dampen CNS autoimmunity).

      Reviewer #2 (Recommendations for the authors):

      (1) (Figure 1E): What does PDPN thickness increase represent?

      We have added clarification to the Results and Discussion. Based on our data, the increased PDPN<sup>+</sup> layer thickness during EAE most likely reflects a combination of: (1) increased PDPN expression per cell (supported by elevated MFI in flow cytometry), (2) cellular hypertrophy of existing PDPN<sup>+</sup> cells. However we cannot fully discriminate between these mechanisms with the current data and acknowledge this as a limitation.

      (2) (Figure 2A): In Figure 2A, can the authors provide a healthy control example to pair with 2A? Is the Chi3L3 expression "below" the plate...in the mucosa, associated with EAE, or the same in steady state? The images in 2D are hard to appreciate at the current size.

      Healthy (naive) control images are included in Figure 2D for direct comparison with EAE tissue, we added zoomed images of each panel to provide clearer context for the disease-associated changes in myeloid cell distribution and M2 marker expression.

      (3) What is the denominator for the quantification in 2E? Is this per unit area? If so, is it the PDPN area or the total cribriform plate region area? If the area of PDPN increases (as the authors show), then the potential area that can hold YM1+ cells also increases, so the absolute number of cells comparison isn't that fair.

      We have added this distinction to the results.

      (4) The same goes for 2G; however, in G, the quantification is "% Arg1+" ----percentage of what? The increase in Arg1 expression is striking, but it's also striking how similar the PDPN network appears between healthy and EAE in Figure 2F.

      We have added this distinction to the results And added a label of quantification to Figure 2G.

      (5) Are these increases in Arg1+ cells occurring in the meninges of EAE mice? Or is this specific to perineural areas at the cribriform plate? In a sagittal plane, are these cells clustered tightly at the cribriform plate, or do they extend outward along the ON tracts?

      These are clustered tightly in the meningeal regions and along ON tracts. We do not have any sagittal sections available for further proper analysis.

      (6) In Figure 2, some panels are labeled "merge" -what does this mean? The DAPI label within the figure is also impossible to see.

      Figure labels have been adjusted. Merge is a common label which identifies panels with all channels merged together in a series.

      (7) Figure 3: The authors sort cells that interact with PDPN+ CD31+ double-positive cells before the scRNAseq analysis. However, it's not clear from these data that the PDPN expansion observed in their histochemistry is on stromal or endothelial cells. As the authors note, PDPN "also efficiently labels meningeal layers surrounding them along the olfactory nerve layer, including fibroblasts and their associated extracellular matrix (ECM)". Can the authors more clearly explain the rationale for using CD31 in this gating strategy?

      We sorted for CD11b+CD45+ (immune), CD31+ (endothelial), PDPN+ (meningeal fibroblasts). CD31 was used to isolate myeloid cells and endothelial cells at the brain’s borders.

      (8) Also, without having to do scRNAseq, could the authors compare the interacting populations for cells stuck with PDPN+CD31neg cells? Figure 3B indicates that a good number of these PDPN+CD31neg cells are present in the sort.

      We did not isolate PDPN+CD31- cells from our sort, in our experience these are mostly fibroblasts though. Future studies will look at cells which adhere specifically to PDPN+CD31- aggregates.

      (9) The interacting cells seem to have a particular affinity for the sorted endothelial cells. However, it's not clear if these cells are simply seizing an opportunity to stick together once the cells are mechanically separated and spun down, or were together in vivo. The authors should determine how many of these cell types are maintaining an in vivo contact or simply are efficient at making new contacts ex vivo. One approach would be to take EAE tissues from CD45.1 and CD45.2 congenic animals and mechanically separate them together. Then the composition of doublets can be analyzed for the frequency of CD45.1/2 doublets or CD45.1 and CD45.2 single positive doublets....and also which cell types are contributing to these doublets. This will test how much of this interaction is driven by ex vivo stickiness or in vivo, and also give some idea about the inherent ability of these immune cells to find and engage PDPN cells.

      This is a limitation of the current study, and you have provided an excellent experiment and one we have added to discussion.

      (10) Figure 4: I'm confused about Figure 4. If I'm reading this correctly, these are the same data from Figure 3 that were sorted for CD31 positivity. If that's the case, how are there fibroblasts in these data? Does this represent an aggregation of endothelial, fibroblast, AND immune? (CD31, PDPN, and CD11c).

      Yes we suspect that endothelial, fibroblast, AND immune aggregates are highly heterogeneous. Without negative sorting/gating we are left with high number of immune cells in or sorting paradigm.

      (11) The authors comment on the relatively unclear biological significance of PD1 expression by DCs (non-T cells) and note their previous report on PD1 ligand expression in this cribriform region. Do the authors detect differential PD1 ligand expression in this current study (singlet vs aggregate)?

      We have not detected any significant difference in CD274 expression between non-interactor and interactor populations.

      (12) Are the FACS data Supplemental Figure 2 on singlet vs doublet DCs performed after Liberase treatment? The FACS plots for both doublet and singlet populations look very different in how they are rendered, with large cell numbers in the 10^-4 range for the doublet groups. Why is this?

      No liberase treatment was given in these experiments, we have updated the figure legend.

      (13) It seems like the figure labeling has gone awry. On page 9, what should be Figure 5 is being called Figure 4...and further on, Figure 5 is being used for Figure 6 ("Blood derived" data)---this makes it pretty confusing.

      This has been corrected. Thank you.

      (14) On page 10, the authors have written "Lowest genes in PD-1- DCs included chemokines CXCL9, CXCL10, IL-12b, interferon-stimulated genes (Ifit1, Ifit2 and Ifit3) and several MHC-related genes (H2-M2, H2-Eb2, H2-DMb2)". Is this correct? Based on my reading of the figure, "5H" is that not PD-1+ DCs instead of PD-1- DCs? Also, there is a typo, "Cxck10".

      Thank you for pointing this out. We have corrected.

      (13) It's not clear what the statement "...these data support that Pdcd1 expression in migratory DCs exhibits an immunosuppressive gene signature..." means. The PD-1 marker cannot "exhibit" anything by itself. Is this intended to say that migratory DCs expressing PD1 exhibit an immunosuppressive phenotype?

      Yes this is a better way to say it, it has been corrected.

      (14) Figure 6: These are really cool data about the influx of peripherally derived cells to the cribriform plate during EAE. However, it would be more meaningful to have other compartments to compare with. What is the IV+ percentage within the CNS or meninges more generally? And also, how do these CD11c+ CD11b+ aggregates differ in IV+ from "singlets"? The authors show that T cells are caught in the scRNA aggregates. Are these IV+? Can the authors provide additional discussion about the relevance of the Ghost+ data? What does this really mean? In Figure 6, Olfactory is misspelled 2x in A...and the "D" in CD45 is missing from B.

      Spelling mistakes have been corrected, thank you. Future investigations will compare IV+ recruitment and aggregations to dural and other brain regions. We suspect that some of the IV+ populations are T cells but our experiments do not allow for this distinction. We have added additional information regarding our interpretation of the Ghost+ data.

      (15) The title of the paper indicates that a suppressive myeloid network is assembled, and certainly, there is gene and protein expression data that are consistent with the presence of "suppressive" cells. However, can the authors demonstrate that this "network" is performing a suppressive function in vivo?

      This is a great point. Our IHC is highly indicative of classical M2 phenotype accumulating at meningeal regions around the olfactory bulb. One experiment we are interested in is local ablation of macrophages at the CP, to determine their role in EAE disease progression.

      (16) At the end of the discussion, the authors state, "They describe unique DC populations at the cribriform plate, one displaying pro-inflammatory and migratory features while the PDPN-associated population displayed more immunoregulatory characteristics". This seems a little bit misleading, or at least not giving the macrophages their due. A good part of the migratory DCs (as put in the figures) are associated with the Arg1+/Chi3l3+ macrophages. It's possible that suppression -if it's happening- could come from one or both cell types.

      We have removed that line and altered the discussion to more accurately reflect the results with respect to DCs and Macrophages.

      (17) In this study, the authors focus on dendritic cell and macrophage populations in the context of autoimmune disease and chronic CNS inflammation. In a recent study, the authors show an important recruitment of immune cells in the cribriform plate during a CNS infection by Mycobacterium tuberculosis. Do Arg1+/Chil3l3+ macrophage and tolerogenic DC populations still exist in this context? It would significantly strengthen the field's understanding of how the cells of the cribriform behave in different conditions if you could describe whether these cells are context-specific or is it really specific to cribriform plate tissue?

      This is an excellent suggestion and will be the focus of future investigations.

      We believe these revisions substantially strengthen the manuscript and directly address major concerns raised by both reviewers. We remain committed to the functional follow-up studies that both reviewers rightly identify as the natural next chapter of this work.

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      Kaku and Flenniken investigate the mechanistic pathways through which specific viral infections alter the flight capabilities of honey bees. Building on their previous discovery that DWV impairs flight while SBV unexpectedly enhances it, the authors hypothesized that these behavioral shifts are driven by interactions with the insect's octopamine (OA) signaling pathway, which is responsible for the "fight-or-flight" neurohormonal stress response and energy mobilization. To test this, the authors experimentally infected adult honey bees with DWV or SBV and pharmacologically manipulated the OA pathway using either octopamine supplementation or epinastine (EP), an OA-receptor antagonist. They then evaluated the bees' flight performance (distance, duration, and speed) on custom flight mills and profiled their gene expression using qPCR and RNA sequencing.

      Strengths:

      A major strength of this study is the high prevalence of preexisting background DWV and SBV infections in the honey bee cohorts, which meant there were no completely "virus-free" control groups. However, the authors successfully mitigated this limitation by rigorously quantifying viral RNA copies for every individual bee via qPCR and utilizing these viral abundances as continuous variables in powerful linear mixed-effect models.

      Weaknesses:

      The primary weakness lies in the methodology used for targeted pharmacological manipulations, as well as the lack of OA quantification across different treatments. Thus, their claims are not sufficiently supported by the current data.

      We thank Reviewer #1 for these comments.

      (1) The authors utilize Epinastine to block octopamine signaling, describing it as a highly specific OA receptor antagonist. However, pharmacological inhibitors often lack absolute specificity. Epinastine might bind to other octopamine receptor subtypes present in honey bee neural and flight muscle tissues, or it could potentially cross-react with tyramine and dopamine receptors. Without further genetic validation (e.g., RNA interference targeting specific receptors), it is difficult to definitively conclude that the altered flight performance is solely due to the blockade of the specific Oβ−2R pathway.

      We thank the reviewer for this thoughtful comment and agree that pharmacological approaches have inherent limitations with respect to receptor specificity. However, among the available octopamine receptor antagonists, epinastine is considered one of the most selective compounds for insect octopamine receptors. Roeder et al. (1998) reported that epinastine exhibits affinities for octopamine receptors that are at least four orders of magnitude greater than those for other insect biogenic amine receptors, including dopamine, tyramine, histamine, and serotonin receptors.

      Honeybees encode four β-adrenergic-like receptors AmOARβ1- AmOARβ4) and one αadrenergic-like receptor (AmOARα1). Our transcriptomic analyses indicated that expression of AmOARβ2 was substantially higher than that of other octopamine receptor genes. Specifically, AmOARβ4 transcripts were not detected in our RNA-seq datasets, while AmOARβ1 and AmOARβ3 were expressed at very low levels in most samples (Supplementary Table S9; Figure S5). Although AmOARα1 transcripts were detected in some samples, expression levels were consistently lower than those of AmOARβ2. These observations support the interpretation that the physiological effects observed following epinastine treatment are primarily mediated through disruption of AmOARβ2 signaling. We agree that receptor-specific genetic approaches would provide valuable complementary evidence. RNAi-mediated knockdown of AmOARβ2 is an attractive future direction; however, RNAi efficacy in honey bees is variable and influenced by factors including transcript turnover rates. In addition, dsRNA treatments can induce sequence independent antiviral effects that could confound interpretation in studies involving viral infection (Flenniken and Andino, 2013). We have revised the manuscript to more explicitly acknowledge these limitations and to clarify the basis for our interpretation of the epinastine experiments.

      (2) As a natural neurotransmitter, insects have evolved highly efficient "cleanup" mechanisms. OA is rapidly cleared from the synaptic cleft via reuptake transporters and quickly inactivated by enzymes such as N-acetyltransferase (NAT) or Monoamine Oxidase (MAO). Consequently, an injection of OA produces only a transient "pulse" of activity. It is often a poor "tool" for inducing prolonged physiological effects compared to synthetic formamidines like Amitraz.

      We thank the reviewer for this important point regarding the pharmacokinetics of octopamine. We agree that octopamine is rapidly metabolized and cleared under physiological conditions and that exogenous administration is unlikely to precisely mimic endogenous signaling dynamics. Our goal was not to induce a prolonged pharmacological activation of octopamine signaling comparable to that produced by synthetic agonists such as amitraz, but rather to determine whether increasing octopaminergic signaling could mitigate the flight impairments associated with DWV infection. Octopamine was administered either by injection or through feeding (Lines 86-89), both of which resulted in significant improvements in flight performance in DWV-infected bees (Figure 2). The observation that two independent delivery methods produced similar outcomes supports the conclusion that enhanced octopaminergic signaling can partially rescue the DWV-associated flight phenotype. We have revised the manuscript to clarify this distinction and to acknowledge that exogenous octopamine administration likely produces transient elevations in signaling rather than sustained receptor activation.

      (3) The study relies heavily on transcriptomics and quantitative PCR to measure the mRNA expression of key synthesizing enzymes, namely tyrosine decarboxylase (tdc) and tyramine βhydroxylase (tβh), to infer the activation or suppression of the octopamine pathway. However, changes in enzyme synthesis at the RNA level are often insufficient to accurately reflect the true physiological levels of biogenic amines. To robustly prove the authors' hypothesis of a "feedback loop that regulates intracellular OA concentrations", direct quantification of actual octopamine and tyramine titers in the bees (e.g., using high-performance liquid chromatography or mass spectrometry) is necessary.

      We thank the reviewer for this comment and agree that octopamine and tyramine quantification would strengthen the mechanistic interpretation of our findings. Previous studies have successfully quantified OA in honey bees using HPLC-based approaches, including KayaZee et al. (2022, eLife), who measured OA in honey bee muscle tissue (both naturally occurring levels and levels post-treatment with 10 mM OA), and Cook et al. (2017, J. Exp. Bio) who quantified OA in pooled honey bee brain samples.

      Prior to submission, we inquired with our institutional mass spectrometry facility regarding the feasibility of measuring OA in individual honey bee samples. The expected concentrations of OA in our samples was below their limit of detection, so we did not pursue these analyses at that time.

      We are exploring the possibility of analyzing a subset of samples at external facilities that may have the sensitivity required to quantify OA and tyramine in honey bee tissues. However, our initial discussions indicate that such analyses would require substantial resources, with estimated costs of approximately $5,000–10,000 for 12–15 samples. While we acknowledge that direct measurements of OA and tyramine would provide valuable complementary evidence, the current study relies on multiple independent lines of evidence including gene expression analyses, OA supplementation experiments, and behavioral measurements that collectively support a role for octopaminergic signaling in mediating the observed effects.

      Reviewer #2 (Public review):

      Summary:

      This highly original and well-designed study provides insight into how honeybee picorna-like viruses, Deformed wing virus (DWV) and Sacbrood virus (SBV), affect flight performance, and reveals the role of the octopamine (OA) pathway in virus-honeybee interactions. The authors used a flight mill to quantify the flight performance of bees with different levels of DWV and SBV. Bees were treated with OA and/or epinastine (EP) - an OA receptor antagonist; the study also quantified virus loads and expression of two key genes involved in OA biosynthesis.

      The results showed that reduced flight performance associated with high DWV levels could be alleviated by OA administration. In contrast, increased levels of SBV had the opposite effect, leading to enhanced flight performance. This suggests distinct physiological responses to DWV and SBV infections. Administration of EP had led to a reduction of flight performance in SBVinfected bees, indicating the involvement of the OA pathway.

      The authors also quantified levels of mRNAs of enzymes involved in OA synthesis, tyrosine decarboxylase (TDC) and tyramine beta-hydroxylase (TbH), and concluded that DWV induced expression of TbH, while SBV upregulated expression of TDC. Furthermore, the study identified upregulated and downregulated genes in response to SBV, DWV and DWV in combination with OA.

      Strengths:

      The study reported opposing effects of infections of related viruses, SBV and DWV, on honeybee flight performance, and identified the central role of the octopamine (OA) signaling pathway in the effect of viruses on honeybee flights.

      These findings were achieved by using a combination of approaches, including experimental measurement of flight distance, virus infections, and introduction of OA and EP. Experimental work with honeybees is technically challenging and requires specialized expertise, which makes the results produced in this study more valuable.

      DWV and SBV are among the most important honeybee pathogens affecting honeybee health and threatening the pollination service. Therefore, an understanding of the mechanisms underlying DWV and SBV pathogenesis has the potential to develop novel approaches to mitigate the negative impact of these viruses.

      Weaknesses:

      No weaknesses were identified by this reviewer.

      We thank Reviewer #2 for these comments

    1. Author response:

      Reviewer #1 (Public review):

      Weaknesses:

      While the breadth of techniques is impressive, the central premise of the work-the structural and functional relationship between polyQ assemblies and the Golgi apparatus-is not supported by sufficiently rigorous cell biological evidence.

      A major concern is that much of the cell biology data remains descriptive and lacks mechanistic depth. The findings are fragmented and not integrated into a coherent molecular or cellular model. Instead of building a logical progression of experiments, the study presents a collection of observations that appear disconnected and, at times, driven more by technical capability than by hypothesis-driven design.

      Critically, the key claim that polyQ HTT functionally disrupts the Golgi (Golgipathy) is not convincingly demonstrated. Many observations could be more simply explained by the polyQ HTT localization to the Golgi and known Golgi sensitivities to perturbations (e.g., starvation or Brefeldin A treatment), rather than by a specific mechanistic role of polyQ HTT.

      The manuscript also suffers from issues in organization and clarity, including imprecise descriptions and figures that are difficult to interpret.

      We thank the Reviewer for their time, valuable comments, and recognition of our technical expertise and resources. With our specialized background in pathology and super-resolution microscopy, our research heavily relies on structurally precise histological methods to address these fundamental biological questions. Furthermore, our laboratory maintains one of the largest repositories of patient-derived and healthy control fibroblasts, as well as iPSC lines, within the Huntington's disease (HD) research community. Because these patient-derived and engineered cell models express endogenous mutant HTT (mHTT) within an authentic genetic background, they provide a uniquely powerful system for decoding HD pathogenesis.

      We appreciate the Reviewer’s comment regarding hypothesis-driven design. Classically, a hypothesis-driven approach relies on well-established, highly stable experimental platforms. However, a key finding of our study is the highly fragile and volatile nature of polyQ assemblies, particularly when subjected to post-fixation and oxidative stress. Because these structures can behave unpredictably under stress, we utilized an unbiased, data-driven approach leveraging our high-resolution imaging pipeline to explore polyQ assemblies in both healthy and HD cells.

      Importantly, hypothesis-driven and data-driven methods are complementary rather than mutually exclusive. For instance, if a real-time tracking method were developed to endogenously label native HTT in living cells, it would open the door for direct hypothesis testing regarding polyQ assembly mechanics. Despite the current technical limitations of the field, our study successfully overcomes these challenges to reveal the spatial tomography and unique dynamics of polyQ assemblies directly within patient-derived cells. We fully discussed the limitations of this research in the discussion section.

      We appreciate the Reviewer’s critical assessment regarding the functional disruption of the Golgi apparatus (Golgipathy). To rigorously investigate this phenomenon, we employed a comprehensive suite of methodologies ranging from live-cell imaging to single-cell RNA sequencing. Our findings build directly upon a well-established body of literature. We previously demonstrated that mutant huntingtin (mHTT) disrupts Golgi function within the neural tubes of human cortical organoids (hCO) (Liu et al., 2024), aligning with broader neurodevelopmental defects observed in HD (Barnat et al., 2020). Furthermore, prior independent studies have confirmed that both HTT knockdown and the presence of mHTT impair Golgi-to-plasma membrane trafficking, notably in primary fibroblasts from homozygous Htt<sup>140Q/140Q</sup> knock-in mice (Brandstaetter et al., 2014); mHTT also affects post-Golgi trafficking of proteins (del Toro et al., 2006). Backed by this literary consensus and our own multi-modal data, which Reviewer 2 also noted as sufficient, we are confident that our manuscript provides a robust, multi-layered demonstration of mHTT-induced Golgipathy.

      In this study, we found that polyQ assemblies and the Golgi form a Golgi-polyQ complex mediated by ARF1 and ARFIP2. Thus, the structural coupling of polyQ assemblies with the Golgi apparatus under starvation, during the cell cycle, is rational.

      Based on the reviewer suggestion, we will completely revise the entire manuscript. Hopefully, this revision will meet the requirement of smoothness and clarity.

      Major Concerns:

      (1) Golgi localization

      The localization of polyQ HTT relies entirely on the antibody 3B5H10, which is foundational to the study. However, previous reports using the same antibody have described predominantly cytosolic localization. This discrepancy must be addressed rigorously by independent validation using alternative antibodies or tagged, exogenously expressed polyQ HTT constructs that should be shown to colocalize with 3B5H10 signals.

      Despite historical inconsistencies across existing publications (Barnat et al., 2020; Hickman et al., 2022; Shen et al., 2019; Tousley et al., 2019), we noticed that the immunostaining results of multiple HTT antibodies are consistent with our data (DiFiglia et al., 1995; Ko et al., 2001; Velier et al., 1998; Wheeler et al., 2000). Although these pioneering studies lacked modern 3D high-resolution imaging and standardized staining protocols, their reported 2D distribution patterns heavily resemble our results. For instance, transmission electron microscopy (TEM) immunolabeling originally revealed that HTT localizes along Golgi cisternae (DiFiglia et al., 1995) and formed organized and parallel fibrils (DiFiglia et al., 1997). Furthermore, immunostaining with a panel of distinct antibodies, including MV2, 3, 4, 5, 6, and 1F8, demonstrated characteristic Golgi-like distribution patterns for HTT (Ko et al., 2001). In addition, our polyQ antibody immunostaining in human fetal brain, which is reflective of polyQ assembly, is nearly identical to the staining results of Barnat et al., publication in Science (Barnat et al., 2020).

      We have carefully checked two early publications, which reported that 3B5H10 only binds expanded polyQ but does not bind a normal polyQ (non-disease causing), which displays a part of a neuron that has a cytosolic diffuse pattern of HTT in 3B5H10 staining (Legleiter et al., 2009; Miller et al., 2011). Based on our extensive experience with HTT immunohistochemistry, we hypothesize that this diffuse signal may reflect nonspecific background artifacts, often caused by high antibody concentrations, poor tissue fixation, inadequate post-incubation washing, or the presence of effete cells, or premature fragmentation of the polyQ tract prior to staining. Interestingly, Miller et al. utilized a rapid tissue-perfusion and sectioning protocol originally published in Brain Research Bulletin (Ko et al., 2001), which is optimized to preserve intact polyQ assemblies. When reviewing the original Brain Research Bulletin study (Ko et al., 2001), we noted that the immunostaining profiles for polyQ-containing HTT peptides (specifically using antibodies MW2, MW3, MW4, MW5, and 1F8) are entirely consistent with our data, yet completely diverge from the patterns reported by the Muchowski group (Legleiter et al., 2009; Miller et al., 2011) (please see Ko et al., 2001.Legleiter et al., 2009; Miller et al., 2011). Furthermore, contrary to the Muchowski group's claims, subsequent biophysical evidence by Owens et al. (2015) independently confirmed that 3B5H10 binds to both normal and expanded polyQ sequences in huntingtin exon 1 fusion proteins (Owens et al., 2015). Together, these observations strongly support the validity of our staining profiles.

      Several antibodies, including MV1, 1C2, and 3B5H10, were previously reported to recognize the expanded, pathogenic polyQ tracts of HTT (Khoshnan et al., 2002; Miller et al., 2011; Wang et al., 2008). However, emerging studies reveal that these antibodies actually bind both short and long polyQ sequences (Klein et al., 2013; Owens et al., 2015). Because a standard antibody Fab epitode typically spans only 5 to 15 amino acids (or 3 to 4 sugar residues), and normal HTT polyQ repeats range from 18 to 24, it is theoretically impossible for an antibody to exclusively target expanded polyQ while sparing normal polyQ.

      We previously noticed that 3B5H10 antibody immunostaining signals are located in the long projection of striatal neurons. As we did not notice an intact neuron in the two publications, we have no idea about the 3B5H10 antibody signals in the neuronal projections of those images.

      We investigated whether the polyQ assemblies detected by the 3B5H10 antibody contain full-length or large fragments of huntingtin (HTT). To test this, we selected two distinct HTT antibodies: EM48, which binds the first 256 amino acids (excluding the polyQ stretch), and 3E10, which targets the HDA region (amino acids 1171–1177). In patient fibroblasts, the immunostaining patterns for both EM48 and 3E10 were nearly identical to those observed with 3B5H10. These results demonstrate that the polyQ assemblies in fibroblasts are primarily composed of HTT proteins (see Author response image 1). We will include the results of EM48 and 3E10 immunostaining in the revised version.

      Author response image 1.

      (A) GFAP and EM48 antibodies staining of the astrocytes derived from HD patient and healthy sibling iPSCs showed polyQ assembly in the astrocytes derived from iPSC. (B). The spindle of polyQ assembly formed a dent on the nuclear surface of astrocytes. (C, D) Coimmunostaining of GM130 antibody with 3E10 or EM48 antibody in fibrobalsts revealed that polyQ assemblies contain great amount of HTTs. The middle and right panel are the sectional view boxed region (D) and the boxed region are a magnified part or rendering part (C, D) .

      We also check whether the transfected exogenous HTT fragment of the first exon can be recruited into polyQ assemblies. We transfected fibroblasts with three vectors of the HTT first exon containing 19, 23, and 74 CAGs, respectively. The exogenous HTT fragments of the first exon did not significantly recruit into endogenous polyQ assemblies-Golgi complexes of fibroblasts (please refer to Reviewer only figure 5). We will include this part in the revised version.

      In the cover letter, we told the editor that we have been studying this structure for over ten years. The results have been stable for over ten years.

      Furthermore, the Golgi is identified solely using GM130, a cis-Golgi and ER exit site marker. This raises ambiguity: does polyQ HTT associate with the entire Golgi or only recruit GM130? Could the observed signal correspond to a sub-Golgi compartment?

      Thank you for highlighting the precise sub-Golgi localization of GM130 as resolved by electron microscopy. We agree that transmission electron microscopy (TEM) demonstrates GM130 is restricted to the cis-Golgi network, intercisternal regions, and tubular structures, and is absent from the trans-Golgi (Nakamura et al., 1995). Given that individual Golgi cisternae measure approximately 20 nm in width, resolving cis- versus trans-Golgi sub-compartments exceeds the physical resolution limits of our microscopy system. Consequently, GM130 was utilized here as a robust, widely accepted pan-Golgi marker rather than a tool for sub-compartmental differentiation. To specifically evaluate the trans-Golgi network (TGN), we tracked Clathrin+ vesicles, which actively sort at the TGN (Klumperman, 2011). Our Clathrin staining confirms that polyQ assemblies localize to both the cis- and trans-Golgi compartments, as clearly demonstrated in the new lateral view projections provided in revised Figure 4C.

      If polyQ HTT is indeed Golgi-associated, several key observations become expected rather than novel. For example, in Figure 4I-M, sensitivity to Brefeldin A is unsurprising, as Golgi structure collapses upon such treatment; in Figure 4N-O, co-fragmentation with the Golgi is expected under Golgi-disrupting conditions.

      We agree that our data demonstrate the formation of a functionally coupled polyQ assembly–Golgi complex. Physically and structurally, the dynamics of polyQ assemblies are intrinsically linked to Golgi dynamics under distinct physiological states, including cell cycle progression and energy deprivation. This structural coupling is mediated by ADP-ribosylation factor 1 (ARF1). Specifically, the polyQ tract of HTT interacts with ARFIP2, which is one of the key effector proteins that physically bind active ARF1. Mechanistically, ARF1 is recruited to the Golgi membrane upon GDP-to-GTP exchange catalyzed by guanine nucleotide-exchange factors (GEFs). Consequently, treatment with Brefeldin A (BFA)—which inhibits ARF1 activation—effectively decouples the polyQ assemblies from both intact and fragmented Golgi structures.

      Regarding the question of novelty, we define experimental novelty based on generating entirely unprecedented, empirical data that either confirms or redefines biological expectations, rather than evaluating conceptual expectations themselves. We believe the uncovering of this real-time, stimulus-responsive coupling mechanism provides fundamentally novel insights into HTT biology.

      (2) 3D rendering

      The extensive use of 3D rendering appears unnecessary and, in some cases, misleading. The rendered images do not provide additional insight beyond conventional 2D fluorescence images. Serial 2D fluorescence sections should be more objective in representing the 3D organization.

      Thanks for pointing out the 3D rendering. While 3D rendering provides an essential spatial approximation of fluorescently labeled architectures, it offers significantly more precise structural information than conventional 2D or serial section imaging alone (Cao et al., 2023; Han et al., 2021; Hexige et al., 2015). A primary objective of our study was to evaluate these subcellular features within their intact, native three-dimensional context rather than relying solely on two-dimensional cross-sections. Crucially, without complete volumetric rendering, it is mathematically and visually challenging to accurately delineate complex morphological features, such as the nuclear gorge or true intranuclear accumulation. Consequently, 3D volumetric analysis and rendering are entirely indispensable for the accurate interpretation of the structural data presented in this study.

      In Figure 2A and Figure 5A, red line features in 3D beige polyQ HTT structures resemble unrelated biological structures, such as vasculature, which is inappropriate.

      We would like to clarify that there is no vasculature present within the referenced 3D rendering. The features the reviewer is highlighting are artifacts of the pseudo-coloring used exclusively to mask and visualize the surface tomography. In volumetric 3D rendering, pseudo-colors are assigned strictly to enhance visual clarity and contrast for the reader; they carry no intrinsic biological meaning or cellular identity. Furthermore, from a structural standpoint, the narrow red features in the rendered image are orders of magnitude smaller than true microvasculature. Functional microvessels possess a minimum diameter of 6 to 45 micrometers and exhibit a defined vascular lumen, endothelial cells, a basement membrane, pericytes, and a tunica intima. Therefore, based on both the scale of the image and established histological criteria, these features cannot biologically or structurally represent vasculature.

      There is also an inconsistency in rendering. For example, fine mesh-like structures are shown in some figures (e.g., Figure 2A, Figure 4A), whereas others appear as amorphous aggregates (e.g., Figure 5A, Figure S2B), without explanation.

      The selection of opacity and color masks in our 3D volumetric reconstructions is systematically chosen to optimize the visual clarity and spatial relationships between intersecting sub-cellular structures. For example, as shown in the fourth and fifth panels, an opaque blue mask was applied to clearly define the outer surface tomography. Conversely, in the third panel, a semi-transparent blue mask was utilized for the nucleus. This transparency is methodologically necessary because a subset of polyQ fragments is embedded within or localized directly inside the nuclear envelope; a transparent mask allows for the unambiguous visualization of these internal structures. Similarly, the inset in Figure 5A illustrates the distinct intranuclear occupancy pattern of polyQ, which also necessitates a transparent nuclear boundary. Collectively, these volumetric rendering strategies provide critical spatial and structural depth that cannot be captured by conventional 2D cross-sections or unconstructed serial imaging.

      (3) Quantification of area and volume

      The manuscript extensively quantifies the area and volume of polyQ assemblies (e.g., Figure 2B, C and Figure 3B, C, E, G, H). These measurements are not reliable. First, the structures appear filamentous and likely below the diffraction limit. Second, fluorescence signals are broadened by the point spread function (PSF), artificially inflating measured dimensions. Last, even with 3D SIM (~100 nm resolution), fine structural details remain unresolved. Thus, these quantitative measurements lack physical meaning and might not be used to support conclusions.

      We appreciate the reviewer’s thoughtful critique regarding the quantification of area and volume. Our measurements are derived from immunofluorescent signals captured via structured illumination microscopy (SIM) and confocal imaging. If the reviewer's concern is that antibody-labeled structures do not perfectly match the absolute physical dimensions of native polyQ assemblies due to the linkage error of the primary-secondary antibody complex, we agree conceptually.

      However, our imaging pipeline is optimized to minimize these discrepancies. Our SIM resolution reaches approximately 64 nm. Given that the total observed thickness of the fluorophore-labeled polyQ assemblies exceeds 200 nm, these structures reside well within the detectable range of our super-resolution system, minimizing diffraction-induced overestimation. Regarding the point spread function (PSF) and optical distortion, we emphasize that all comparative quantifications across experimental groups were conducted under identical imaging parameters and thresholds, ensuring a standardized baseline. Furthermore, our acquisition systems (Leica, Nikon, and Zeiss) utilize advanced deconvolution algorithms specifically designed to mitigate PSF-related blur. While we observed that deconvolution yielded negligible baseline improvements when using high-numerical-aperture objectives (63x) or 100x, oil immersion), it validates that our raw high-resolution scanning was already highly optimized.

      We acknowledge that an immunolabeled complex is not structurally identical to a naked, pure polyQ tract. Nonetheless, indirect immunofluorescence remains the most robust method to evaluate spatial distribution in situ. Indeed, cryo-EM studies have highlighted that native polyQ tracts are highly flexible and structurally dynamic, making them exceptionally difficult to resolve in their native state (Guo et al., 2018). Intriguingly, we observed that antibody-bound polyQ assemblies remain structurally stable for several weeks with minimal fragmentation, suggesting that antibody binding may structurally stabilize these highly flexible regions. Consequently, indirect immunolabeling provides an indispensable framework for capturing these assemblies within the cellular environment.

      (4) Interpretation of structural features (Figure 2A)

      Descriptions such as "parallel spindles" and "ring-like assemblies" are not clearly supported by the data. The terminology is ambiguous, and the claimed structures are not discernible. The use of the term "interaction" with the nuclear membrane is also inappropriate. At best, the data suggest colocalization, which itself is not convincingly demonstrated.

      Please refer to Fig. 2A (middle upper), Fig. 2F, and Fig. 4C for “parallel spindles”. Please refer to Fig. 5I, J, and Fig.S3C (right panel) for additional clear “ring-like assemblies”. Due to the unique spatial distribution of the 'ring-like assemblies', observing multiple rings within a single spindle is technically challenging. Accordingly, we have tempered our statement in the revised manuscript to accurately reflect this limitation. Furthermore, it is important to note that the visualized structures represent the fluorescent signal from secondary antibodies rather than direct imaging of the proteins themselves. Consequently, we cannot definitively confirm whether this immunostaining pattern precisely replicates the native state of polyQ assemblies within the cellular environment.  

      (5) Mitotic fragmentation (Figure 2E)

      The conclusion that polyQ assemblies fragment during mitosis lacks proper controls. It is unclear whether these cells exhibited intact "fabric-like" assemblies during interphase, or the observed structures were already fragmented prior to mitosis.

      We thought that we had displayed enough non-mitotic cells in this study (Fig. 2A, D, Fig. 4A, F). Most of the cells in this study are non-mitotic cells (G1+S+G2). Thus, we consider the control of non-mitotic cells to be redundant here.

      (6) Fixation-induced fragmentation (Figure 2F)

      The claim that fixation-induced fragmentation reflects a unique dynamic property of polyQ assemblies is likely an overinterpretation. This phenomenon may simply represent a fixation artifact. Therefore, it cannot be used as evidence for in-cellulo structural dynamics.

      By definition, a laboratory artifact refers to any unintended structural detail, distortion, or error introduced by experimental equipment or the preparation process. We contend that the observed phenomenon represents a native chemical characteristic of the HTT polyQ domain inside cells following paraformaldehyde (PFA) fixation, rather than a technical artifact. Similar structural features have been documented by other investigators in tissue samples (Ferrante et al., 1997). A classic textbook example of an artifact is the lamina lucida of the basal lamina, which is artificially generated during electron microscopy tissue processing and does not exist in living tissue. In contrast, the fragmentation of polyQ assemblies occurs naturally both in living cells subjected to stress and during post-fixation processing.

      (7) Nuclear localization claims (Figure 5A)

      The assertion that polyQ assemblies "almost completely occupy the nucleus" is not supported. The images are more consistent with perinuclear localization, typical of the Golgi region. There is no clear evidence for nucleoplasmic distribution.

      Please refer to the rendering image in the upper left inner insert of HD neurons (the blue [transparent] is the nucleus and the pink white is polyQ). The almost complete occupation of the nucleus is crystal clear in these images (rendered inner inserts, upper left). In iPSC-induced HD neurons, it is not only distributed in the nucleus but also in the cytoplasm. Based on your description, you might refer to the cytoplasmic polyQ assemblies but not the nucleus in the rendering image of the upper left (left panel). We will add a label in the revised version for clarity (white arrows for nuclear accumulation). In this manuscript, we have enough figures that clearly show the nuclear accumulation. Please also refer to Fig. 7 and Fig. S2 for additional images of nuclear accumulation.

      (8) Drug treatment and data interpretation (Figure 3D-E)

      The x-axis in Figure 3E is non-linear, which is inappropriate unless explicitly justified. Furthermore, the rationale for using Onjisaponin F is unclear. What is its known mechanism? Does it affect the Golgi organization? Without this context, observed effects may reflect Golgi perturbation rather than specific effects on polyQ assemblies.

      We appreciate the reviewer pointing out Figure 3E. In this experiment, Huntington's disease (HD) fibroblasts were cultured in a low-glucose medium for the first 72 hours, which accounts for the linear trend observed across the first four data points. Following this 72-hour period, the cells were switched to a high-glucose medium and cultured for an additional 48 hours to evaluate subsequent dynamic changes in the polyQ assemblies. To improve visual clarity, we have color-coded these distinct treatment conditions in the revised manuscript, using red to denote low-glucose treatment and green to denote high-glucose treatment.

      Regarding the choice of Onjisaponin treatment (a concern also raised by another reviewer), Onjisaponin is an active component derived from Radix Polygalae (Yuan Zhi). Previous literature indicates that Onjisaponin B enhances autophagy, accelerates the degradation of mutant α-synuclein and huntingtin in vitro, and activates the AMPK-mTOR signaling pathway (Wu et al., 2013). To optimize our experimental model, we screened multiple variants—specifically Onjisaponin B, D, and F. We determined that Onjisaponin F exhibits remarkably low cytotoxicity while maintaining a robust autophagy-enhancing capacity in both human fibroblasts and iPSC-derived neurons. Consequently, Onjisaponin F was selected for our human cell line experiments (please refer to the Reviewer only image 3). While we did not previously assess Golgi apparatus alterations under Onjisaponin F treatment, we recognize the value of this metric. We are currently evaluating changes to both the Golgi apparatus and neuronal firing rates following Onjisaponin F exposure, and this new dataset will be integrated into our revision.

      Reviewer #2 (Public review):

      […] Overall, this work reports a novel polyQ assembly, which was previously reported as a pathogenic factor, has not been reported before for HTT, is related to Golgi activities and vesicular transport, and is dismantled in HD patient cells. The intensive immunostaining and super-resolution scanning are impressive and definitely strengthened by the impact of the findings. The scRNAseq data adds another layer to the observed Golgi impairments and their suggested relationship to Golgi function. The drug testing for polyQ assemblies, especially polyQ assemblies in HD cells, is preliminary. However, the data in this study are enough to support the existence of polyQ assemblies in human cells and their specific relationships with the Golgi apparatus.

      We sincerely thank the reviewer for their time, dedication, and insightful evaluation of our manuscript. We agree that the drug screening component represents an initial phase of discovery, and we appreciate the opportunity to clarify this in our text. As the reviewer notes, executing high-throughput or exhaustive drug screenings in human brain organoids is exceptionally resource- and time-intensive due to prolonged culture requirements. We will provide more mechanistic and physiological details of these drug in the future.

      Strengths:

      In this study, the authors used the cells from a large HD family and fetal/child brain samples to decode the structure of endogenous polyQ assemblies. This part is impressive. The intensive staining and super-resolution scanning are amazing. The spatial relationships of polyQ assemblies with the Golgi apparatus and mitochondria are well illustrated.

      Weaknesses:

      Although they used healthy sibling cells as a control, an isogenic control (genetic correction of the mutant gene) is lacking. Based on the Golgipathy of mHTT, they did a drug screening. The drug testing for polyQ assemblies is preliminary. More rigorous validation, such as scRNA seq and proteomic analysis, etc., is necessary to reach a systemic conclusion.

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    1. Author response:

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

      eLife Assessment

      This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable highresolution structure determination of small (sub-50 kDa) protein targets. The paper describes how density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template. However, the evidence described for the claim that this technique “significantly” improves the alignment of the reconstruction of small complexes is incomplete. The authors could better evaluate the effects of model bias on the reconstructed densities.

      We have addressed both concerns. Regarding the claim that 2DTM “significantly” improves alignment, the most direct evidence is the controlled comparison in Fig. 3: using the same particle stack and the same reconstruction software (RELION), 2DTM-derived orientations yield a 3.1 Å reconstruction whereas RELION auto-refinement of the same particles yields 3.7 Å. Because the orientations are the only variable, this comparison directly demonstrates that 2DTM produces more accurate alignments.

      We further evaluated RELION auto-refinement with initial low-pass filters of 3, 5, 10, and 15 Å (Fig. 3c); the final resolution remained between 3.7 and 4.0 Å across all conditions, indicating that the achievable resolution difference reflects a fundamental distinction between the two approaches. 2DTM directly leverages high-resolution signal in the template during alignment, which is particularly advantageous for small particles.

      To assess whether this improvement extends beyond the ligand pocket, we constructed a composite omit map (Fig. 5) assembled from 36 reconstructions, each generated using a template with a different subset of residues deleted. The composite shows that density can be recovered at distributed locations across the kinase, including peripheral and surface-exposed regions further away from the alignment center. Recovery varies across sites, with some regions exhibiting weaker or fragmented density, consistent with local differences in structural heterogeneity and residual alignment error. Together, these results indicate that the orientation estimates support global density recovery rather than being confined to the ligand-binding region.

      Regarding model bias, we have strengthened both the quantitative and visual analyses. Specifically, we have (i) updated the template-bias metric Ω in Fig. 4, (ii) added grouped occupancy refinement showing that omitted residues 222–227 refine to 0.55–0.80 (mean 0.72), ATP to 0.61, and Mn to 0.28, while template-included control residues 150–155 remain near 1.0 (0.88–1.00; mean 0.96), and (iii) completed the composite omit map described above. Together, these results provide consistent evidence that densities corresponding to omitted regions are not driven by the template and can be recovered from the data, while template-included regions show some, albeit limited evidence of overfitting, as expected.

      Reviewer #1 (Public review):

      Summary:

      This paper describes an application of the high-resolution cryo-EM 2D template matching technique to sub-50kDa complexes. The paper describes how density for ligands can be reconstructed without having to process cryo-EM data through the conventional single particle analysis pipelines.

      Strengths:

      This paper contributes additional data (alongside other papers by the same authors) to convey the message that high-resolution 2D template matching is a powerful alternative for cryo-EM structure determination. The described application to ligand density reconstruction, without the need for extensive refinements, will be of interest to the pharmaceutical industry, where often multiple structures of the same protein in complex with different ligands are solved as part of their drug development pipelines. Improved insights into which particles contribute to the best ligand density are also highly valuable and transferable to other applications of the same technique.

      Weaknesses:

      Although the convenient visualisation of small molecules bound to protein targets of a known structure would be relevant for the pharmaceutical industry, the evidence described for the claim that this technique “significantly” improves alignment of reconstruction of small complexes is incomplete. The authors are encouraged to better evaluate the effects of model bias on the reconstructed densities in a revised paper.

      We thank the reviewer for these constructive comments. We have updated the template-bias metric Ω in Fig. 4 and added two further quantitative controls: grouped occupancy refinement of omitted residues and a composite omit map spanning the entire protein. Full details are provided in our responses to Comments 1 and 2 below.

      Reviewer #1 (Recommendations for the authors):

      Main Comments

      (1) For the 1ATP structure: Q-scores for deleted residues/ligands are worse than the Q-scores for residues in the template. This means that the reconstructed map must suffer from template bias. Another indication of this bias is that the density for the ATP (and the omitted residues) appears to be weaker than the density for the residues in the template (although this is not easy to assess from the figures). The authors should perform additional experiments to quantify this bias.

      (a) One option could be to do what the X-ray crystallographers call an OMIT map, and omit allresidues, a few at a time, from the template in multiple 2DTM runs. They could then assemble a density map from all the omitted residues together and measure the resolution of the omit map against the known template by FSC.

      (b) Another insightful experiment would be to take the various 2DTM reconstructed maps describedin the paper and perform a refinement of the atom occupancies of all residues in the structure. Residues included in the template should refine to values close to 1. In the absence of bias, the occupancies of the omitted residues should be 1 too; if the reconstructed map were completely biased, those occupancies would refine to 0. Therefore, the refined occupancies of omitted residues could perhaps serve as a measure for the amount of bias in the reconstructed map.

      We thank the reviewer for these detailed and constructive suggestions. We agree that the lower Q-scores for omitted regions indicate weaker density and that template bias exists at residues that are included in the template. To quantify this more directly, we corrected the template-bias metrics at the omitted region (mask from the full–omit template difference) in Fig. 4.

      Following the reviewer’s suggestion, we performed Phenix real-space grouped occupancy refinement against the omit reconstruction using the docked full model. The results are shown in Table. S2. We refined occupancies for the omitted residues (chain E 222–227), ATP, Mn, and template-included control residues (chain E 150–155), while excluding waters. The omitted residues refined to occupancies of 0.55–0.80 (mean 0.72), ATP to 0.61, and Mn to 0.28, whereas the control residues remained near 1.0 (0.88–1.00; mean 0.96). These results indicate substantial recovery of density in the omitted regions, but also some degree of bias.

      The substantially lower refined occupancy of Mn<sup>2+</sup> may reflect genuine partial occupancy in the dataset. While compact features can be especially sensitive to residual alignment error, we cannot conclude from the present analysis that alignment effects alone account for the weak Mn<sup>2+</sup> density.

      Finally, we have constructed a composite omit map to assess density recovery across the protein. We generated 36 omit templates, each deleting ∼10 non-overlapping residues scattered across the structure (including peripheral and surface-exposed regions). For each template, an independent 2DTM search and reconstruction was performed. Local density patches were extracted within 3 Å of the omitted atoms (with neighboring residues excluded as described in Methods) and assembled into a composite map (Fig. 5). The composite map shows that density can be recovered at distributed locations across the protein and is not restricted to the central binding pocket. Recovery is variable across sites, with some regions exhibiting weaker or fragmented density, consistent with local differences in signal-to-noise, structural heterogeneity, and residual alignment error.

      (2) The claim that 2DTM leads to “Improved” reconstruction (title) and “alignment and reconstruction [...] can be significantly improved” (abstract) is not supported by the data presented in the paper. The smallest single particle structure to resolutions sufficient for de novo atomic modelling is currently the ACA2 complex, with an ordered mass of less than 40 kDa, which was reconstructed using Blush regularisation in RELION. This paper should be referenced, and statements about single particle analysis (SPA) not working for sub-50 kDa complexes should be toned down. In general, I would say that 2DTM and SPA are not competing techniques, and the paper would be better if it focused on the intrinsic advantages of 2DTM (like ease-of-use for screening of pharmaceutical compounds) and useful findings described that make 2DTM better, e.g., excluding thick ice.

      We thank the reviewer for this important perspective and have added the Blush regularization reference Kimanius et al. (2024) to the revised manuscript, noting that the 40 kDa Aca2–RNA complex was reconstructed to 2.5 Å resolution using this approach (at L451). Furthermore, Blush regularization could be applied to reconstructions derived from 2DTM-based particle stacks, and a combination of both approaches may yield further improvements.

      We agree that 2DTM and SPA are complementary rather than competing techniques and have revised the manuscript to reflect this. We have also toned down claims in the abstract, which now states that 2DTM “reconstructed a previously intractable ∼43 kDa kinase complex and improved the density of its ligand-binding site” rather than making broad claims about SPA limitations. In the discussion, we now describe 2DTM as broadening possibilities for structural studies of targets “that have remained difficult to reconstruct” rather than implying they are impossible by SPA.

      Regarding the intrinsic advantages of 2DTM: beyond ligand screening, the composite omit map (Fig. 5, described in Comment 1) demonstrates that 2DTM-derived orientations support density recovery throughout the entire protein, including peripheral and surface-exposed residues, using roughly an order of magnitude fewer particles than conventional SPA workflows.

      (3) Given the uncertainties about the amount of template bias in the reconstructed 2DTM densities, I have trouble interpreting the predictions in Table 1. Where would the 1ATP structure lie in Figure 8? How much bias would there be in a 2DTM reconstruction at SNR n = SNR s? Could the authors perform tests on simulated data to confirm these predictions? At the point of SNR n = SNR s, how would a 2DTM reconstruction look, and what would refined occupancies for deleted residues be?

      (This may reflect a misunderstanding on my part, but I don’t really see how the SNR n = SNR s is completely dependent on the number of orientations searched (through Equation 1). In Figure 8, is the full search in a 4k x 4k micrograph, or inside a particle box? And what are the relevant search ranges? Perhaps as a consequence of this misunderstanding, I do not understand how one would decide on the amount of noise in the simulated data for these tests.)

      We thank the reviewer for this important question and agree that this point needed clearer explanation. In our framework, is the expected alignment-noise level from maximizing many cross correlations, where N<sub>s</sub> is the total number of sampled hypotheses in the 5D search (in-plane angle, out of-plane angles, and x, y shifts), not only the number of orientations. Thus, the relevant search is the per-particle alignment search window (full or constrained), not a full 4k×4k micrograph area.

      At SNR<sub>n</sub> = SNR<sub>s</sub>, the true-match and noise-maxima levels are at a threshold; one could imagine if SNR<sub>s</sub> is only slightly larger than SNR<sub>n</sub>, the correct pose is favored on average, so with sufficiently large particle numbers real omitted-region density should accumulate, but with residual pose errors that attenuate high-frequency amplitudes (effectively a large positive B-factor). In that regime, sharpening (negative-B correction) can improve visibility once signal is accumulated. Therefore, we expect partial recovery rather than fully unbiased recovery at this threshold, with omitted-region occupancies remaining between 0 and 1 and below template-included controls (consistent with our measured values), and improving as SNR<sub>s</sub> − SNR<sub>n</sub> and particle number increase. Simulations at this exact threshold would require a very large particle number to achieve sufficient statistics, and we leave this to future work. We have added this clarification to the Supporting Information.

      (4) The strong (> 5 sigma!!) and ubiquitous difference densities in Figure 9A imply that the authors have a serious problem with their forward model, which could explain some of the effects of model bias discussed above. I recommend they investigate these differences in detail. It would be good to see negative and positive densities in different colours to understand these differences better. The text speaks about incomplete capture of the solvent background, but the difference densities appear to be of much higher spatial frequencies than those typical for background/solvent effects (e.g., 15-20A). It may thus also be helpful to analyse these differences in Fourier space.

      We thank the reviewer for this important point. In our previous analysis, we did not incorporate an appropriate protein mask when generating the difference map, which contributed to widespread residual densities. We have now regenerated the map using the program diffmap.exe (https: //grigoriefflab.umassmed.edu/diffmap) with a protein soft mask and moved it to the Supplementary Information (Fig. Figure 1—figure supplement 4, contour SD = 20). With this controlled setup, the strongest coherent residual densities localize to the omitted ATP pocket and residues 222–227, consistent with recovery of omitted features. We have revised the figure/text accordingly and clarified that remaining diffuse residuals are likely due to forward-model mismatch (including solvent/background representation). We also added to the manuscript that improved template generation may be achieved by incorporating recent methods that learn environment-aware scattering factors directly from experimental cryo-EM maps.

      Other Comments

      (1) P.1: Alongside reference 2, a reference to the 1.2 Å apoferritin structure from the Stark group should be included.

      We have added the reference at L30.

      (2) P.2: “commond line tool”

      We have corrected the typo.

      (3) P.2-3: Robust reconstruction of the ATP binding pocket: Auto-refinements in RELION without alignments do not exist, and corresponding statements need to be removed from the manuscript. If one wants to skip alignments, then there is no refinement left to be done. In that case, one should just perform a reconstruction of the 2 halves (e.g., using relion reconstruct) and then run a standard RELION postprocessing.

      We agree with the reviewer and have revised the manuscript accordingly. Technically, RELION’s relion refine with the --skip align flag runs an iterative loop that re-estimates the per-particle noise model (spectral noise σ<sup>2</sup>) and computes the gold-standard FSC between half-maps, but it does not modify the particle orientations or translations. As the reviewer correctly points out, this is effectively a 3D reconstruction followed by postprocessing, not a refinement. We have updated the text to replace “skip-alignment auto-refinement” with “3D reconstruction without angular refinement” to accurately reflect what was performed.

      (4) P.3: What are “first-quadrant p-values” and “three-quadrant p-values”?

      We apologize for the ambiguity and now define these terms explicitly in the revised text (with citation to the p-value paper). After transforming z-score and SNR to probit coordinates, “first-quadrant” (1Q) p-values use only candidate points with both coordinates > 0 (i.e., both probit-zscore and probitSNR are positive). “Three-quadrant” (3Q) p-values include candidates where at least one coordinate is > 0 (equivalently, all points except the quadrant where both are < 0).

      (5) P.5: In Equation (2), it is unclear what Q means from the main text. Would it be better to leave Equation (2) for the Appendix, and only show Equation (3) in the main text?

      Thank you for this suggestion. We kept Equation (2) in the main text to preserve the continuity of the derivation, but we now define Q(k,N<sub>i</sub>) explicitly at first use as the normalized exposure-weighting transfer function (following Grant 2015). The detailed derivation and assumptions remain in the Supporting Information.

      (6) P.6: “Remaining gaps”: this section considers differences between 200 keV and 300 keV electron beam energies. The main practical effect for cryo-EM data sets is that the current detectors are designed for detecting 300 keV electrons, and their DQE is thus a lot worse at 200 keV. The entire paper doesn’t mention detectors. Perhaps because they are assumed to be perfect, but it is still far from the case.

      Also, why were defocus searches not performed if the thickness of micrographs was up to 1500 A?

      The conclusion of this section states “Considering all these factors...”, but it then claims standard single particle analysis still remains an outstanding challenge. This concluding statement makes no sense, as this whole section was about 2DTM.

      Thank you for this comment. We agree and have revised the text to make these points explicit. First, we now state clearly that detector response (DQE) is generally more favorable at 300 keV than at 200 keV, which contributes to the experimental–theoretical gap. Second, we clarify why we did not perform a defocus search in 2DTM: after CTF/thickness filtering, the retained micrographs are predominantly in the thin-ice regime, so expected defocus spread is smaller, while adding a defocus dimension substantially increases computational cost. We also tested downstream refinement (including CTF/beam-tilt related refinement in cisTEM) and did not observe measurable improvement for this dataset (data not included in the manuscript). Finally, we revised the concluding sentence in this subsection to refer specifically to 2DTM-based alignment limits rather than standard SPA, so the section scope is now consistent.

      (7) P.7: Data-driven refinement of AlphaFold3 models: it might be worth pointing out that removing residues a few at a time from AF3 models and checking their reconstructed density by 2DTM would come at a considerable computational cost.

      We agree. We have demonstrated residue-level omission validation using the X-ray template via a composite omit map (Fig. 5), confirming that the approach is feasible. We have updated the Discussion to reflect this: extending the composite omit approach to AlphaFold3-based templates remains computationally expensive — each omission design requires an independent 2DTM search and downstream reconstruction — and we present this as an important direction for future work.

      (8) Figure 1: What is “full FSC” and what is “particle FSC”?

      Thank you for pointing this out. We have clarified the terminology in the figure legend and text using cisTEM and Frealign definitions (Grant et al., 2018). What was previously labeled “Full FSC” is now referred to as the uncorrected FSC (FSC<sub>uncor</sub>), computed within a generous mask. “Particle FSC” denotes the solvent-corrected FSC, obtained from FSC<sub>uncor</sub> using the mask-volume correction factor f as described in the cisTEM/Frealign framework (Grant et al., 2018).

      (9) Figure 3: Why were particles in class 5 discarded? The 2DTM approaches described in this paper are all about carefully selecting good particles, yet now the authors use standard 3D classification to throw away another 156 particles. This seems to be an arbitrary choice. How different would the results have been if these had been included in the reconstruction? Alternatively, did these few particles have any 2DTM metrics that would justify their exclusion?

      We thank the reviewer for raising this point. Class 5 contained only 156 particles (∼2% of the dataset). While the 2DTM p-value and SNR metrics provide principled criteria for particle selection, they are not perfect, and a small number of suboptimal particles may still pass these filters. To address the reviewer’s concern, we repeated the reconstruction including all five classes. The resulting map achieved a resolution of 3.7 Å, identical to the reconstruction without class 5, confirming that including these particles does not affect the results. We have clarified this point in the manuscript.

      (10) Figure 4C: What are the negative sample thicknesses here? Why use an inset?

      The negative sample thickness values are artifacts of the CTF-based thickness estimation algorithm in ctffind5. This algorithm fits oscillations in the 1-D power spectrum arising from the interaction between the CTF and the specimen’s finite thickness (a sinc-modulated envelope). When the ice is very thin or the power spectrum is noisy, the optimizer can converge to a physically meaningless negative value. Of the 2,488 total micrographs across both sessions (after CTF score filtering, 2,314 retained), 136 (∼5.9%) returned negative thickness estimates. We have revised Figure 1—figure supplement 1c (previously Figure 4c) to show only the physically meaningful positive thickness values without the inset, which gives a clearer view of the unimodal distribution peaked near 350–400 Å.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Zhang et al describe a method for cryo-EM reconstruction of small (sub50kDa) complexes using 2D template matching. This presents an alternative, complementary path for high-resolution structure determination when there is a prior atomic model for alignment. Importantly, regions of the atomic model can be deleted to avoid bias in reconstructing the structure of these regions, serving as an important mechanism of validation.

      The manuscript focuses its analysis on a recently published dataset of the 40kDa kinase complex deposited to EMPIAR. The original processing workflow produced a medium resolution structure of the kinase (GSFSC ∼4.3 Å, though features of the map indicate ∼6-7 Å resolution); at this resolution, the binding pocket and ligand were not resolved in the original published map. With 2DTM, the authors produce a much higher resolution structure, showing clear density for the ATP binding pocket and the bound ATP molecule. With careful curation of the particle images using statistically derived 2DTM p-values, a high-resolution 2DTM structure was reconstructed from just 8k particles (2.6 Å non-gold standard FSC; ligand Q-score of 0.6), in contrast to the 74k particles from the original publication. This aligns with recent trends that fewer, higher-quality particles can produce a higher-quality structure. The authors perform a detailed analysis of some of the design choices of the method (e.g., p-value cutoff for particle filtering; how large a region of the template to delete).

      Overall, the workflow is a conceptually elegant alternative to the traditional bottom-up reconstruction pipeline. The authors demonstrate that the p-values from 2DTM correlations provide a principled way to filter/curate which particle images to extract, and the results are impressive. There are only a few minor recommendations that I could make for improvement.

      We appreciate the positive assessment. In response to the bias-related concerns raised elsewhere, we have: (i) updated the template-bias metric Ω reported in Fig. 4, (ii) added grouped occupancy refinement showing that omitted residues 222–227 refine to a mean occupancy of 0.72 while template-included control residues remain near 1.0, and (iii) assembled a composite omit map (Fig. 5) from 36 partial-deletion reconstructions spanning the entire protein. These additions are described in the revised Results and in the rebuttal below.

      Reviewer #2 (Recommendations for the authors):

      (1) On page 3, “Finally, by comparing Figure 2a and b, we observed that deleting IP20 strongly reduced signal at several residues.” Looking at Figure 2a and 2b, it was unclear which residues they were referring to.

      We have revised the text to explicitly list the affected residues. In the updated Figure 2, we now label the omitted residues with the lowest backbone Q-scores in the structural views (column 2) and include per-residue backbone Q-score plots (column 4), making the comparison between panels (a) and (b) quantitative. For example, when IP20 is additionally deleted (Fig. 2b), residues Phe54, Gly55, Lys72, Glu127, Glu170, and Asp184 all fall below a backbone Q-score of 0.5, compared with only Ser53 and Glu127 in the within-3 Å deletion alone (Fig. 2a).

      (2) Figure 1a. Both the published density map and the text “Template” are gray, but the 2DTM template density map is yellow.

      Thank you for catching this inconsistency. We have updated Figure 1a so that the 2DTM template density is now rendered in gray, consistent with the X-ray crystal structure (PDB) coloring. The published single-particle map is shown in wheat and the 2DTM reconstruction in blue, providing a clear three-way color distinction.

      (3) Figure 1b. I would recommend the x-axis label of “spatial frequency” instead of “resolution” (which is overloaded). Furthermore, the fact that this is not a GSFSC should be clearly labeled in the figure to prevent confusion with a standard GSFSC.

      We agree with both suggestions. The x-axis has been relabeled “Spatial Frequency (1/Å)” in the revised figure. We have also added a note in the figure caption stating that these FSC curves are not gold-standard FSCs, as the reconstruction uses orientations determined by template matching rather than independent half-set refinement.

      (4) Figure 2: The usage of the negative sign in the labels “-3 Å”, “-5 Å” to indicate within a given radius is a bit confusing. “Within 3 Å”, perhaps?

      Thank you for this suggestion. We have changed the labels in Figure 2 from “−3 Å” and “−5.5 Å” to “Within 3 Å” and “Within 5.5 Å.” We have also added a fourth column to Figure 2 showing per-residue backbone Q-scores for each deletion experiment, with omitted residues distinguished by color and marker shape. The residues with the lowest backbone Q-scores among the omitted set are circled in red and correspond to the labeled residues in the structural views.

      (5) Figure 4c: Why does the sample thickness histogram go to negative values (-20,000 A)?

      As noted in our response to Reviewer 1, the negative thickness values are artifacts of the ctffind5 thickness estimation, which fits a sinc-modulated envelope to the 1-D power spectrum. For micrographs with very thin ice or noisy power spectra, the fit can converge to unphysical negative values. These account for ∼5.9% of micrographs. We have revised Figure 1—figure supplement 1 (originally Fig. 4c) to display only positive thickness values, removing the inset and providing a clearer histogram.

      (6) Figured 4d: Should the label be “(Before Filtering)” instead of After?

      Yes, thank you for catching this. The original Figure 4d was mislabeled—it showed particle counts before filtering but was titled “After Filtering.” We have corrected the labels: Figure 1—figure supplement 1d (originally Fig. 4d) now reads “Before Filtering” and Figure 1—figure supplement 1e (originally Fig. 4e) reads “After Filtering.”

      (7) Supplementary Note 1: Please provide units for d, p, D, and k max in equation S4 and the preceding text.

      We have added units to the text preceding Eq. S4: d = 1/k<sub>max</sub> is the high-resolution alignment limit (Å), k<sub>max</sub> is the maximum spatial frequency (Å <sup>−1</sup>), p = d/2 is the ideal pixel size (Å/pixel), and D is the particle diameter (Å).

      (8) What does the map-model FSC look like with the template as the model vs. the AF3 structure as the model?

      We have computed the map–model FSC for both the X-ray crystallographic template (PDB 1ATP) and the AlphaFold3-predicted template against their respective 2DTM reconstructions (Fig. Figure 6—figure supplement 1). Both curves cross the FSC = 0.143 threshold at ∼2.3 Å. We note that the map–model FSC in this context should be interpreted with caution, because the vast majority of the structure lies outside the omitted region and is present in the template, so template bias in those regions will dominate the map–model FSC and obscure differences in the small omitted region.

      Reviewer #3 (Public review):

      Summary:

      Due to the low SNR of cryo-EM micrographs necessitated by radiation damage, determining the structure of proteins smaller than 50 kDa is exceedingly challenging, such that only a handful have been solved to date. This work aims to improve the reconstruction of small proteins in single-particle cryo-EM by using high-resolution 2D template matching, an algorithm previously used to locate and align macromolecules in situ, to align and reconstruct small proteins. This approach uses an existing macromolecular structure, either experimentally determined or predicted by AlphaFold, to simulate a noise-free 3D reference and generates whitened projections, crucially including high-spatial-frequency information, to align particles by the orientation with maximal cross-correlation. They demonstrate the success of this approach by generating a 3D reconstruction from an existing dataset of a 41.3 kDa protein kinase that had previously evaded attempts at high-resolution structure determination. To alleviate concerns that this is purely from template bias, they demonstrate clear density at two regions that were not present in the template: 6 residues in an alpha helix and an ATP in the ligand binding pocket. The latter is particularly important for its implications in determining structures of ligand-bound proteins for drug discovery. Additionally, the authors provide an update to the classic calculation in Henderson 1995 to predict the minimum molecular mass of a protein that can be solved by single-particle cryo-EM.

      Strengths:

      I am in no doubt that this technique can be used to gain valuable insights into the structures of small proteins, and this is an important advancement for the field. The ability to determine the structure of ligands in a binding site is particularly important, and this paper provides a method of doing that which outperforms traditional single-particle cryo-EM processing workflows.

      The claim that using high-spatial frequency information is essential for aligning small proteins is a valuable insight. A recent pre-print published at a similar time to this manuscript used high-resolution information in standard ab-initio reconstruction to generate a high-resolution reconstruction from the same dataset, supporting the claims made in the manuscript.

      The theoretical section outlined in the appendix is also theoretically sound. It uses the same logic as Henderson, but applies more up-to-date knowledge, such as incorporating dose-weighting and altering the cross-correlation-based noise estimation. This update is valuable for understanding factors preventing us from reaching the theoretical limit.

      Weaknesses:

      Given that this technique creates template bias, only parts of the reconstruction not in the template can be trusted, unlike standard single-particle processing, where the independent half-maps from separate, ab initio templates are used to generate a 3D reconstruction. Although, in principle, one could perform the search many times such that every residue has been omitted in at least one search, this will be extremely computationally intensive and was not demonstrated in this manuscript. It is therefore currently only realistically applicable when only a small portion of the sub-50 kDa protein is of interest.

      The applicability of this technique to more than a single target was also not demonstrated, and there are concerns that it may not work effectively in many cases. The authors note in the results that “the ATP density was consistently recovered more robustly than nearby residues” and speculate that this may be because misalignments disproportionately blur peripheral residues. Since the region of interest in a structure is not necessarily in the center, this may need further investigation. The implications of this statement may also be unclear to the reader. For example, can this issue be minimized by having the region of interest centered in the simulated volume?

      In Figure 3, the authors demonstrate that it is not solely improved particle filtering and a noise-free reference that improves alignment, but that the high spatial frequency information is important. This information is very valuable since it can be applied to other, more standard methods. However, this key figure is not as clear or convincing as it could be. The FSC curves are possibly misleading, since the reduced resolution could be explained by reduced template bias when auto-refining with a map initially low-pass filtered to 10 A. Moreover, although the helix reconstruction does look slightly better using the 2DTM angles, the improvement in density for ATP in the binding pocket is not clear. A qualitative argument only clear in one out of two cases is not as convincing as a quantitative metric across more examples.

      We address these concerns in three ways: (i) we quantify template bias using Phenix real-space grouped occupancy refinement: omitted residues 222–227 refine to occupancies of 0.55–0.80 (mean 0.72) and ATP to 0.61, while template-included control residues 150–155 remain near 1.0 (mean 0.96), confirming that recovered density is genuine rather than a template artifact; (ii) we have now completed a composite omit-map experiment (Fig. 5), in which 36 partial-deletion templates, each omitting ∼10 non-overlapping residues, were used to perform independent 2DTM searches and reconstructions; local density patches from all 36 reconstructions were assembled into a composite map showing density recovery at distributed locations across the protein, including peripheral and surface-exposed regions, although recovery is variable across sites; and (iii) we have expanded the discussion to clarify that, while the primary scope of this work is omitted-region validation for the ligand-binding site, the composite omit-map result demonstrates that the approach generalizes beyond the central pocket.

      Reviewer #3 (Recommendations for the authors):

      In addition to the comments on the public review, I have some more specific suggestions that could improve the manuscript.

      (1) Another recent pre-print posted on BioRxiv shortly before this manuscript (Kim et al. Highresolution ab initio reconstruction enables cryo-EM structure determination of small particles) determined a high-resolution structure of the same protein from the same dataset, as well as determining the structures of other small proteins. Since both manuscripts rely on high-spatial frequency information, I think that the paper strengthens the claims in this manuscript and should be cited.

      We thank the reviewer for this suggestion. We agree that the recent preprint by Kim et al. strengthens the relevance of high-spatial-frequency information for small-particle cryo-EM reconstruction. We have now added this work to the revised manuscript and included a brief discussion comparing its ab initio strategy with our 2DTM-based approach.

      (2) The claim in the abstract that “we were able to reconstruct previously intractable targets under 50 kDa and improve the density of the ligand-binding sites in the reconstructions” should be altered to make it clear that this is only a single previously intractable target.

      We agree. The revised abstract now reads “. . . we reconstructed a previously intractable ∼43 kDa kinase complex and improved the density of its ligand-binding site” making clear that a single target is demonstrated in this work.

      (3) Q-scores in the manuscript were sometimes used to quantify the improvement in map to model fit for the ATP binding pocket, but never for the 6 residues of the alpha helix. They were also not reported in every case for the ATP-binding pocket. This could lead a reader to think it is only being reported when the Q-score matches the expectation. For transparency, I would suggest either using Q-scores in every comparison or in no cases and simply relying on the qualitative result.

      We agree with the reviewer. In the revised manuscript, we now report Q-scores consistently for both ATP and residues 222–227 across all conditions: individual residue Q-scores for the omitted residues 222–227 in Fig. 1 are reported in the main text and figure caption; per-residue backbone Q-score plots for all deletion experiments in Fig. 2 are shown as the fourth column of each panel; Fig. 3 (RELION reconstruction) does not include Q-scores as the focus is on orientation accuracy rather than map-model fit; and average Q-scores for all four particle selection conditions in Fig. 4 are listed in Figure 4—source data 1.

      (4) The sigma values used for viewing the maps should also be stated in several figures, particularly Figure 3 and Figure 6.

      We have added contour levels (σ) to the captions of Fig. 3 and Fig. 4 (originally Fig. 6) in the revised manuscript.

      (5) I have a slight concern about how well this method applies away from the region centered in the alignment. If parts on the periphery of the structure are removed, do these also reconstruct? Is it required that the omitted region be centered in the simulation of the 3D volume for each alignment? If so, this should be clearly stated.

      2DTM determines particle orientations by matching the full projected template to the image, so alignment is driven by the global structure rather than a localized region. As a result, the recovered orientations define the reconstruction throughout the entire particle, not only near the center. The omitted region does not need to be centered in the template volume. Any region of the protein can be omitted and its density evaluated after reconstruction.

      To directly test whether peripheral regions are recovered in the same manner as central ones, we performed a composite omit-map experiment. We generated 36 omit templates, each deleting ∼10 non-overlapping residues distributed across the entire protein, including peripheral and surface-exposed regions. For each template, an independent 2DTM search and reconstruction was performed. Local density patches corresponding to the omitted regions were then extracted and assembled into a composite map (Fig. 5). The resulting map shows density at distributed locations across the protein, indicating that density recovery is not restricted to regions near the alignment center and that peripheral regions can be reconstructed under the same alignment framework, although the quality of recovery varies across sites.

      (6) I was confused by the difference between the FSCs in Figure 1 and Figure 3. I understand Figure 1 is from cisTEM and Figure 3 from RELION, but I expected the unmasked FSC and full FSC to be similar. Do the authors have any insights into why there is such a large difference? I would also consider removing the FSCs in Figure 3, since the reduced resolution may only be due to reduced template bias, meaning including this may be misleading.

      Thank you for raising this point. The apparent discrepancy arises from multiple differences between the two figures: different FSC definitions, different half-maps (reconstructed with different software and slightly different particle sets), and different masks.

      In cisTEM (Fig. 1), two FSC curves are reported: the uncorrected FSC (FSC<sub>uncor</sub>), measured within a spherical mask, and the “Particle FSC”, which applies an analytical solvent-fraction correction (Grant et al., 2018) to account for solvent dilution within the mask. The Particle FSC crossed the 0.143 threshold at ∼2.6 Å, whereas FSC<sub>uncor</sub> crossed at ∼3.0 Å. In Fig. 3, RELION postprocess applied phase-randomization correction with a soft mask, yielding ∼3.1 Å. However, the Fig. 3 FSC was computed on different half-maps (RELION skip-alignment reconstruction of 7,197 particles after 3D classification) with a different mask.

      To directly compare the two packages, we computed the FSC on the same cisTEM half-maps using both methods (Figure 3—figure supplement 1). The cisTEM Particle FSC (spherical mask + solvent correction) gave ∼2.6 Å, while RELION image handler with a tight 3D protein mask gave ∼2.7 Å. These two approaches converge to a similar resolution through different mechanisms: cisTEM compensates for a generous spherical mask using the solvent-fraction correction, while RELION uses a tight mask that excludes most solvent directly. This confirms that when the same half-maps are used, the two packages give consistent results and the apparent discrepancy between Figs. 1 and 3 is primarily due to differences in the reconstruction and particle set, not the FSC calculation.

      We agree with the reviewer that the FSC values in Figure 3 should be interpreted with caution. In this case, the particle orientations are not independently refined but are instead inherited from the 2DTM alignment, so the two half-maps are not strictly independent. We have added clarifying language in the revised manuscript to make this point explicit (Fig. 1 caption).

      (7) I would also like to see how RELION auto-refinement performs with different low-pass filtering. This could strengthen the argument that high-resolution information is necessary from the start to successfully align small particles.

      We thank the constructive suggestion from the reviewer. We performed RELION auto-refinement on the same 7,197-particle stack using different initial low-pass filter resolutions (--ini high) of 3, 5, 10, and 15 Å. The resulting post-processed resolutions were:

      Author response table 1.

      The results show that varying the initial low-pass filter has minimal effect on the final resolution. This is expected because RELION uses a gold-standard, maximum-likelihood framework in which the resolution used for alignment is determined iteratively from the data via a probability distribution, rather than being fixed by the initial reference. After the first iteration, the reference is updated from the data, and higher-resolution information is incorporated only to the extent supported by the definition of the current reconstruction. Consequently, differences in the initial low-pass filter have limited impact on the final refinement outcome.

      This behavior contrasts with 2DTM, where alignment is performed by direct cross-correlation against a fixed template. In this case, high-resolution features in the template contribute directly to the scoring function and can improve alignment accuracy.

      To directly test the importance of high-resolution information for 2DTM alignment, we performed an additional experiment in which 2DTM was run on bin4x images (2.234 Å/pixel), and the detected particle coordinates were used to extract particles from the corresponding bin2x images (1.117 Å/pixel) for reconstruction. Despite using the same bin2x images for reconstruction, the bin4x-aligned particles yielded a map in which ATP density was lost and backbone density for residues 222–227 was visibly degraded compared to the bin2x-aligned reconstruction (Fig. Figure 1—figure supplement 3). This demonstrates that access to high-spatial-frequency information during template matching is critical for accurate alignment of small particles.

      (8) The caption in Figure 3 should be more descriptive about what is being shown in each panel.

      We have substantially expanded the Figure 3 caption. It now describes each panel explicitly: (a) 3D classification results with particle counts, percentages, and per-class resolutions; (b) side-by-side comparison of reconstructions using 2DTM orientations versus RELION auto-refine, including full maps, zoomed binding-pocket views with the atomic model overlaid, orientation distributions, and FSC curves with reported resolutions; and (c) a table of RELION auto-refinement resolution as a function of the initial low-pass filter setting. We also added a new panel (c) showing that including all five classes yields the same 3.7 Å resolution, addressing the concern about Class 5 exclusion.

      (9) Figures 4 and 5 may be better suited as supplementary figures.

      We agree. Figures 4 and 5 have been moved to the Supplementary Information in the revised manuscript.

      (10) In Figure 4c, it is difficult to understand why the thickness distribution plot goes negative, especially to such a high magnitude as 1.5 microns.

      We agree this was confusing. The negative values are fitting artifacts from ctffind5’s thickness estimation, which fits a sinc-modulated envelope to the power spectrum. When the ice is very thin or the spectrum is noisy, the optimizer can converge to unphysical negative values (affecting ∼5.9% of micrographs). We have revised Figure 1—figure supplement 1c (previously Figure 4c) to show only positive thickness values, which now clearly displays the unimodal distribution peaked at 350–400 Å.

      (11) In Figure 5d, the micrograph looks a lot like a cross-grating grid used for calibration instead of crystalline ice or a fractured film.

      We agree. We have updated the caption for Figure 1—figure supplement 2d (originally Figure 5d) to read “Cross-grating calibration grid”

      (12) Figure 6 was very surprising to me if I am interpreting it correctly. It is not stated in the caption what omega is, but I am assuming it is a measurement of template bias. It is very surprising that the template bias drops when using more particles by reducing the p-value from 8.0 to 7.0. This goes against what I understood from Lucas et al. 2023, so I am curious as to why this is the case.

      We thank the reviewer for this question and apologize for the unclear presentation. We have revised Fig. 4 (previously Figure 6) and its caption to define Ω explicitly and updated the Ω values. We also identified that the mask used in the original computation was too loose; the revised mask is now constrained to the omitted region only (ATP, Mn<sup>2+</sup>, and residues 222–227), derived from the difference between the full and omit templates and shown in Figure 4—figure supplement 1. Ω is adapted from the template-bias metric introduced in (Lucas et al., 2023) and measures how much of the density in the omitted region is attributable to using the full template rather than the omit template. Specifically, for each particle selection condition we reconstruct two maps using orientations and particles derived from independent 2DTM searches with the full and omit templates (V<sub>full</sub> and V<sub>omit</sub>, respectively). Ω is the fractional reduction in density within the omission mask: . In the revised Fig. 4, Ω increases from 46% (p-value = 8.0) to 48% (p-value = 7.0), consistent with the expectation that including more, lower-quality particles increases the relative contribution of the template to the reconstruction. The Ω values are 48% for the SNR = 7.5 and 53% for the tilt conditions.

      (13) It would be useful if the in-house Python script used to calculate template bias could be made publicly available.

      We agree. The template-bias calculation (measure-template-bias) is now included in the publicly available Python package at https://github.com/kekexinz/2DTM_postprocess_tool, and can also be accessed in the official cisTEM repository at https://github.com/timothygrant80/cisTEM. The package also contains the extract-particles and filter-particles tools described in the Methods section.

      (14) The p-value used is said to be a three-quadrant p-value instead of a one-quadrant p-value. Although I assume this is simply replacing an ‘and’ statement with an ‘or’ statement, the exact difference could be made clearer to the reader.

      We have now defined these terms explicitly in the revised Methods. After probit transformation of z-score and SNR, the first-quadrant (1Q) p-value requires both values to be > 0 (logical AND), whereas the three-quadrant (3Q) p-value requires at least one to be > 0 (logical OR). The 3Q criterion is therefore looser, retaining more candidates—which is beneficial for small targets that may score well on one metric but not both.

      (15) I was, perhaps naively, surprised that z-scores could not be used. It was my understanding that by removing the rotationally invariant component from the cross-correlation, the z-score would down-weight low-resolution information compared to the cross-correlation. Given that the manuscript suggests low-resolution alignment can cause getting stuck in local minima, this is surprising to me. The authors note it led to the rejection of most particles; were there simply too many false positives when a lower threshold was used?

      The reviewer is correct that subtracting the angular mean removes the rotationally invariant component of the cross-correlation. However, the resulting z-score primarily measures how strongly a specific orientation stands out relative to other orientations. In other words, it reflects the orientation discriminability (closely related to Fisher information) rather than the absolute correlation strength. For small particles the cross correlation often varies only weakly across orientations, so CC<sub>max</sub>− CC<sub>avg</sub> remains small even when the absolute correlation is significant. As a result, using the z-score alone as a selection criterion led to the rejection of many true particles.

      Theoretical Section Improvements

      (a) The discussion on beam-induced motion could be improved by separating it into initial motion (e.g., cryo-crinkling, buckling) that can be eliminated through grid design, and pseudo-Brownian motion, which cannot. Pseudo-Brownian motion will become much more significant for small proteins (based on reference 5, for a 10 kDa protein, this would be a MSD of ∼0.1 A 2/e−/A 2, or a B-factor of over 2 A 2/e−/A 2), and Bayesian Polishing is unlikely to correct this perfectly, given that it imposes a smoothness of motion between nearby particles. The impact of not correcting for this could be quantified more explicitly.

      We thank the reviewer for this helpful suggestion. As noted, pseudo-Brownian motion of particles within irradiated ice introduces stochastic displacements that accumulate with dose and are expected to be more significant for small particles. Based on the analysis in (Mcmullan et al., 2015), and scaling with particle size, this effect can be aproximated as a dose-dependent mean-squared displacement (MSD) of ∼0.1 Å<sup>2</sup> per (e<sup>−</sup>/Å<sup>2</sup>) for a ∼10 kDa particle. Over a typical total exposure of 40–60 e<sup>−</sup>/Å<sup>2</sup>, this corresponds to an accumulated RMS displacement of ∼2–2.5 Å, sufficient to attenuate high-resolution signal.

      In practice, such motion acts as an additional high-frequency attenuation in Fourier space, analogous to an envelope function, reducing the coherent signal available for template matching. While Bayesian polishing can partially correct beam-induced motion, it assumes spatially smooth trajectories between nearby particles and therefore may not fully compensate for stochastic, particle-specific motion.

      Within the theoretical framework presented here, this effect can be interpreted as an additional frequency-dependent damping of the signal (B-factor). Its primary consequence would be to reduce the effective signal-to-noise ratio at high spatial frequencies and therefore shift the detectable molecular-weight limit somewhat upward, without altering the structure of the derivation. We have added text in the manuscript to clarify this point and to indicate the expected magnitude of this effect.

      (b) The inclusion of inelastic scattering assumes an energy filter is being used, and this should be clearly stated.

      We have added this clarification in the inelastic scattering paragraph of the Supplementary Information.

      (c) The reasons for not including other factors, such as DQE and the temporal and spatial coherence envelope functions, could be stated.

      We have added a note in the dose-weighting section clarifying that these instrument-dependent attenuation factors were not explicitly included, and that they could be incorporated as additional frequency-dependent weighting terms without changing the structure of the derivation.

      (d) The flexibility and heterogeneity in protein structures, especially at high spatial frequencies, must also be a reason for a gap from experiment to theory, but this is not clearly stated.

      We agree. We have added a statement in the “Remaining gaps” section noting that structural flexibility and conformational heterogeneity act as an additional envelope that attenuates high-resolution signal relative to the rigid-particle model assumed in our derivation.

      Additional Minor Comments

      (15) It is noted in the discussion that 2DTM-based single-particle alignment simplifies the processing pipeline. Although true, I think stating the computation time would be useful for the reader.

      We have added computation times to the Discussion. For a typical single-particle dataset of ∼2,000 micrographs (5k × 4k pixels), a 2DTM search without defocus refinement completes in approximately one day on 64 NVIDIA A6000 GPUs. Once particles are located with their orientations and positions, a single 3D reconstruction is sufficient without further refinement, eliminating the iterative 2D classification, ab initio modeling, 3D classification and refinement steps of a conventional pipeline.

      (16) There are some formatting issues with e−/A 2, sometimes losing the minus sign.

      Thank you for catching this. We have corrected all instances to consistently use e<sup>−</sup>/Å<sup>2</sup> throughout the manuscript.

    1. Author response:

      Reviewer #1 (Public review):

      The study by He and colleagues aims to investigate the molecular mechanisms driving key cell potency transitions, particularly the naïve-to-primed pluripotency transition. The authors explore the relationship between cell polarity and stemness using stem cell models combined with a comprehensive panel of experiments, including pharmacological inhibition and co-culture/conditioned medium rescue approaches. Overall, the study provides interesting observations and contributes to the understanding of the molecular mechanisms dynamically regulating stem cell differentiation.

      However, several conceptual and interpretational aspects could be strengthened:

      (1) First, the Introduction would benefit from being more focused on what is currently known regarding cell polarity during early embryogenesis and pluripotent stem cell transitions, rather than emphasizing later neurogenesis events. Such reorientation would better match the main topic of the manuscript and improve the conceptual coherence of the study.

      We thank the reviewer for this constructive suggestion. We fully agree that the Introduction should be more tightly focused on the current understanding of cell polarity during early embryogenesis and pluripotent stem cell transitions, rather than on later neurogenesis events.

      Accordingly, we will revise the Introduction in the following ways:

      (1) Reduce the discussion on later neurogenesis and move some of those details to the Discussion section where they more appropriate.

      (2) Expand the background on early embryonic development and pluripotent stem cell transitions by citing key recent and classical references, including but not limited to: cell polarity establishment in the preimplantation embryo, apical–basal polarity during lineage specification, polarity remodeling in naïve-to-primed pluripotent stem cell transition, the role of PAR complex in early mouse development.

      (3) Refocus the Introduction to clearly state: what is known about polarity in early embryogenesis and pluripotent states, what remains unknown, and how our study addresses that gap.

      (2) Similarly, Figure 6, where the authors attempt to provide clinical relevance through neural organoid formation experiments, feels somewhat disconnected from the central theme of the naïve-to-primed transition. Although this section is interesting on its own, there is already extensive literature describing polarization and morphogenetic events occurring much earlier during pluripotent state transitions. Therefore, the developmental relevance of the neural differentiation phenotypes could be better contextualized in relation to earlier morphogenetic events associated with pluripotency progression.

      We thank the reviewer for this insightful comment. We agree that the neural organoid experiments in Figure 6 are somewhat disconnected from the central theme of the naïve-to-primed transition, and that extensive literature already exists on polarization events occurring earlier during pluripotent state transitions.

      In the revised manuscript, we will better contextualize these findings by explicitly discussing how the neural differentiation phenotypes relate to the earlier morphogenetic events associated with pluripotency progression, rather than presenting them as a standalone observation. We will also incorporate relevant references to bridge this gap and strengthen the developmental relevance of our neural organoid data.

      (3) The manuscript contains a substantial amount of experimental work; however, several results would benefit from deeper discussion. For example, in Figure 1, what is the rationale behind ZO1 downregulation being observed specifically in primed PAR knockout cells but not under naïve culture conditions? In addition, in Figure 3, the authors perform co-culture and conditioned medium experiments between wild-type and knockout cells. While the authors focus on the secreted protein fraction that rescues the phenotype, they also mention that other fractions display rescuing activity. Could the authors briefly discuss what additional components may contribute to this rescue effect? For example, could other molecules within these fractions also converge on AKT signaling regulation?

      We thank the reviewer for recognizing the substantial experimental work in our manuscript and for providing these thoughtful suggestions to improve the depth of our discussion. We agree that deeper discussion of several key results will strengthen the manuscript. In the revised version, we will address the specific points as follows:

      (1) Regarding ZO1 expression in Figure 1:

      Our primary focus is actually on ZO1 localization rather than its total expression level. In our experiments, RNA-seq and immunofluorescence analysis revealed that the total expression level of ZO1 does not change significantly in PAR knockout cells. However, ZO1 localization is markedly altered in PAR knockout primed cells. Specifically, in wild-type primed cells, ZO1 is predominantly localized at the cell membrane, whereas this specific membrane accumulation is not observed in PAR knockout primed cells. Furthermore, this phenomenon is observed specifically under primed state and does not occur under naïve culture conditions. This is likely due to the differential requirement for PAR complex components in maintaining tight junction integrity during distinct pluripotency stages.

      (2) Regarding the rescue activity of other fractions in Figure 3:

      In our experiments, we found that beyond the secreted protein fraction, the WT CM-Exosome fraction exhibited limited rescue efficacy, particularly during the later stages of NPT. Based on our literature review, we suggest that these exosomal components may still contribute to the observed rescue effect, potentially through the delivery of functional proteins, miRNAs, or other signaling modulators that converge on AKT signaling regulation. This discussion will provide a more comprehensive understanding of the paracrine communication between wild-type and knockout cells, while acknowledging the limited contribution of exosomes relative to the secreted protein fraction.

      (4) Importantly, transitions in cell potency are frequently associated with coordinated morphogenetic changes. For example, during mouse embryogenesis, naïve pluripotent inner cell mass cells progressively polarize into a rosette-like structure with apical domain specification before lumen formation and epithelialization during progression toward the primed epiblast state. This developmental context could help strengthen the biological interpretation of the study.

      We sincerely thank the reviewer for providing this valuable developmental context. The example of naïve pluripotent inner cell mass cells progressively polarizing into rosette-like structures with apical domain specification before lumen formation and epithelialization during progression toward the primed epiblast state is highly insightful and directly relevant to our study.

      In the revised manuscript, in the Introduction section, we will incorporate this developmental perspective to strengthen the biological interpretation of our findings. Specifically, we will place greater emphasis on the role of Par complex-mediated cell polarity in coordinating both pluripotency transitions and morphogenetic changes during early embryogenesis. We believe this contextualization will significantly improve the framing of our study and better connect our in vitro observations to in vivo developmental processes.

      (5) There are also several claims throughout the manuscript that appear to be overinterpreted or insufficiently quantified. For example, in Figure 1, the authors state that CDH1 expression is uniform; however, this is difficult to appreciate from the images shown, and quantitative analysis would be necessary to support this conclusion.

      We thank the reviewer for this important comment. We agree that the claim that "CDH1 expression is uniform" in Figure 1 is overinterpreted based on the images shown, and we apologize for the lack of quantitative support.

      Upon re-examination, we realize that our focus should be on CDH1 localization rather than its expression level or uniformity. In the updated manuscript, we will rephrase the statement about uniformity and instead present appropriate quantitative analysis (e.g., RNA-seq or fluorescence quantification across multiple cells) to better support our conclusions regarding CDH1 distribution. We will also adjust our data presentation to more clearly reflect the localization changes we observe.

      (6) Another example appears in Figure 2, where the authors claim that "heatmap analysis revealed that transcriptomic profiles of PAR knockout cells progressively diverged from wild type from day 3 onwards". This conclusion is not fully supported by the presented data for two reasons: (1) transcriptomic divergence is more appropriately assessed through principal component analysis, clustering, or distance-based methods rather than by visual inspection of a heatmap alone; and (2) although some genes displayed in panel E begin to show genotype-associated differences from day 3, the overall transcriptomic structure shown in the PCA and heatmap remains primarily dominated by temporal progression rather than genotype.

      We thank the reviewer for this careful and constructive critique. We apologize for the imprecise claim regarding the heatmap analysis in Figure 2. We agree that 1) transcriptomic divergence should be assessed by PCA, clustering, or distance-based methods rather than by visual inspection of a heatmap alone, and 2) the overall transcriptomic structure shown in PCA and heatmap remains primarily dominated by temporal progression rather than genotype.

      In fact, our main point in this figure was to show that differentially expressed genes (DEGs) between PAR KO and WT become more numerous and more pronounced from day 3 onwards, and the supporting data for this claim are presented in Supplemental Figure 2 A–B. The number of DEGs between PAR knockout and wild-type cells is 480 at day 1, 523 at day 3, 1088 at day 4, and 1893 at day 6. Furthermore, we focused on specific genes within particular signaling pathways, and their expression levels began to show significant differences between PAR knockout and wild-type cells from day 3 onwards.

      We realize that our original wording was misleading. In the revised manuscript, we will rephrase our conclusion to more accurately reflect what the data actually show, focusing on the timing and extent of differential gene expression rather than suggesting a global divergence of transcriptomic profiles.

      (7) In this context, it remains unclear whether PAR knockout cells truly retain a more naïve pluripotent transcriptomic identity. To support this claim, the authors should compare the knockout transcriptome directly against a naïve pluripotent population. The phenotype observed in the knockout cells may instead represent an incomplete or aberrant primed transition rather than maintenance of naïve pluripotency itself. Intermediate morphogenetic states, such as rosette-like epithelial stages, could also explain the observed phenotype.

      We apologize for the confusion caused by our imprecise wording. We realize that our original manuscript may have inadvertently suggested that Par knockout cells retain a naïve pluripotent transcriptomic identity, which was not our intended claim.

      To clarify, Par knockout naïve cells lose their naïve identity and differentiate toward a primed state during the NPT process described in this manuscript. Unlike wild-type primed cells, PAR-knockout primed cells exhibit altered morphology: they cannot establish or maintain the typical flat morphology, and possess distinct expression profile. In terms of naïve identity, key naïve markers (e.g., Esrrb or Oct4) are downregulated to comparable levels in both wild-type and Par knockout primed cells. Although the two cell types differ in their overall expression profiles, several core primed markers (e.g., Fgf5 or T) show normal expression in both groups. Collectively, these results indicate that Par knockout naïve cells do lose their naïve identity and undergo differentiation toward a primed state during NPT, even though the final primed states of the two cell populations are distinct.

      In the revised manuscript, we will:

      (1) Revisit and revise our wording to avoid any misinterpretation that Par knockout cells retain a naïve identity.

      (2) Directly compare the transcriptome of Par knockout cells against a true naïve pluripotent population (e.g., naïve ESCs) to further support our conclusion that the knockout cells are not maintaining naïve pluripotency, but rather exhibit an aberrant primed state with morphological abnormalities.

      (3) Discuss the possibility that the observed phenotype may represent an intermediate morphogenetic state (e.g., rosette-like epithelial stages) rather than genuine naïve pluripotency maintenance.

      (8) Strengthening this aspect of the study would substantially improve its developmental and in vivo relevance, which currently appears somewhat limited. In particular, it would be interesting to determine whether this mechanism operates during embryogenesis itself. The authors could consider relatively simple but informative experiments, such as perturbing PAR signaling or Furin activity during embryo culture.

      We thank the reviewer for this constructive and forward-looking suggestion. We agree that the current manuscript focuses primarily on in vitro cellular mechanisms, and we have not sufficiently explored the developmental and in vivo relevance of our findings. We acknowledge that this aspect of the study is currently somewhat limited.

      In the revised manuscript, we will:

      (1) Explicitly acknowledge this limitation in the Discussion section.

      (2) Incorporate more background on early embryogenesis, particularly regarding pluripotency transitions and morphogenetic changes during early development, to better contextualize our in vitro observations.

      (3) We will attempt to use embryo-like models to investigate whether the PAR complex–Furin–Lefty–FAK signaling axis also operates during embryogenesis itself. As the reviewer suggested, simple but informative experiments—such as perturbing PAR signaling or Furin activity during embryo culture—would be valuable next steps to determine the in vivo relevance of our proposed mechanism. We will include these as important future perspectives.

      (9) Along the same lines, some statements in the manuscript appear overly speculative. For example, the statement that "these findings may reveal a developmental compensation mechanism during embryogenesis, whereby normal cells rescue defective cells or increase their own proportion" extends well beyond the experimental evidence presented. Such claims invoke concepts related to cell competition, abnormal cell recognition, or developmental quality control mechanisms in vivo, none of which are directly demonstrated in this study. The authors are encouraged either to substantially tone down these statements or move them to the Discussion as speculative possibilities.

      We thank the reviewer for this important critique. We agree that our original statement—"these findings may reveal a developmental compensation mechanism during embryogenesis, whereby normal cells rescue defective cells or increase their own proportion"—is overly speculative and extends beyond the experimental evidence presented in our study. We also acknowledge that it was inappropriate to directly extrapolate from in vitro cellular mechanisms to in vivo developmental rules without proper justification.

      In the revised manuscript, we will:

      (1) Substantially tone down this claim from the Results section.

      (2) Move this speculation to the Discussion section, where we will explicitly present it as a speculative possibility rather than a conclusion supported by our data. We will also clearly state that concepts such as cell competition, abnormal cell recognition, or developmental quality control mechanisms remain to be tested in future studies.

      (10) Another important conceptual point concerns the relationship between PAR complex regulation and Lefty signaling. If this mechanism indeed reflects a physiological or homeostatic process operating during embryogenesis, what would be the developmental rationale for the PAR complex regulation of Lefty? Lefty is well known for its role during gastrulation and anterior epiblast patterning. It would therefore be interesting if the authors could further discuss potential links between these developmental contexts.

      We thank the reviewer for raising this important conceptual point. In our manuscript, we have indeed demonstrated that the PAR complex regulates Lefty signaling under the conditions of this study, and we are aware from the literature that Lefty signaling plays a critical role during early embryogenesis, particularly in gastrulation and anterior epiblast patterning.

      However, we admit that we have not deeply considered the potential pathways and developmental rationale for PAR complex-mediated regulation of Lefty in the context of embryogenesis. This is an important gap in our current discussion.

      In the revised manuscript, we will:

      (1) Review and incorporate relevant literature to better understand and discuss the potential links between PAR complex regulation and Lefty signaling during early embryonic development, including possible connections to gastrulation and anterior patterning.

      (2) Offer speculative but informed perspectives on the developmental rationale for such regulation, while clearly distinguishing between what our data directly show and what remains to be explored in future studies.

      Minor points:

      (1) The authors state that PAR knockout cells do not exhibit major differences in self-renewal capacity; however, they simultaneously claim that these cells remain in a more naïve-like state. This interpretation requires clarification, as naïve pluripotent cells are typically associated with increased clonogenicity, enhanced self-renewal, and expression of markers such as alkaline phosphatase and SSEA1 compared to primed cells. The relationship between the observed phenotype and the proposed "naïve-like" state should therefore be discussed more carefully.

      We thank the reviewer for this comment, which addresses a similar concern as Point 7 mentioned above. Consistently, we do not claim that PAR knockout cells remain in a more "naïve-like" state. Our actual conclusion is that PAR knockout naïve cells undergo differentiation toward the primed state during NPT. However, due to loss of cell polarity, PAR knockout primed cells fail to establish and maintain the typical flat morphology and instead form dome-shaped colonies. Importantly, these dome-shaped colonies do not retain the characteristics of the naïve state, such as increased clonogenicity, enhanced self-renewal, or expression of alkaline phosphatase and SSEA1.

      In the revised manuscript, we will:

      (1) Revise our wording to avoid any misinterpretation that PAR knockout primed cells maintain a naïve-like identity.

      (2) Explicitly clarify that the observed dome-shaped morphology represents an aberrant primed state rather than a naïve or naïve-like state.

      (3) Discuss more carefully the relationship between the observed phenotype and the absence of typical naïve state features.

      (2) The authors generated several independent knockout clones, but appear to use only one clone for downstream analyses after observing similar morphogenetic phenotypes. Is this sufficient to account for potential clonal heterogeneity? Would the use of pooled clones provide a more robust experimental system?

      We thank the reviewer for raising this important concern regarding clonal heterogeneity. We agree with the reviewer that our current approach using only one representative knockout clone for downstream mechanistic analyses after confirming similar morphogenetic phenotypes across multiple independent clones is not sufficient to fully exclude potential clonal heterogeneity.

      To address this issue, we will perform additional experiments in the revised study. Specifically, we will use another independent knockout clone (ParKO6) to repeat the key mechanistic analyses. The following experiments will be carried out:

      (1) ParKO6 and wild-type ESCs will be subjected to NPT. During the NPT process, cells will be treated with an AKT inhibitor (MK2206), a FAK inhibitor (PF562271), or WT CM. We will observe whether the morphological defects of ParKO6 cells are rescued, and RT-qPCR will be performed to characterize the molecular features of ParKO6 cells under these conditions.

      (2) After treatment with the AKT inhibitor (MK2206), FAK inhibitor (PF562271), or WT CM, immunofluorescence (IF) will be used to detect p-FAK levels in ParKO6 cells.

      (3) Following the same treatments, Western blotting (WB) will be performed to detect FURIN and LEFTY protein levels in ParKO6 cells.

      These additional experiments will allow us to confirm that the observed results are not due to clone-specific artifacts from the originally used clone.

      (3) The rescue experiments using pathway inhibitors are interesting; however, the interpretation again relies primarily on colony morphology. Readers may question whether these experiments truly represent rescue of the naïve-to-primed transition itself without additional transcriptomic or molecular characterization.

      We thank the reviewer for this important comment. We apologize for the lack of clarity in our original manuscript, which may have led to the misunderstanding that our interpretation of the rescue experiments relied solely on colony morphology.

      In fact, we did perform molecular characterization on a subset of cells rescued by pathway inhibitors, and these data are presented in Supplemental Figure 2 D–E. We realize that our description of these results was insufficiently clear, and we failed to properly highlight this molecular evidence in the main text.

      In the revised manuscript, we will revise our wording to clearly state that the rescue effects are supported not only by morphological observations but also by molecular characterization.

      (4) In Figure 4, the manuscript could be strengthened by integrating transcriptomic analyses from pharmacological treatments with the secreted-factor and co-culture datasets.

      We thank the reviewer for this constructive suggestion.

      In our current manuscript (Figure 4), we have indeed performed an integrated transcriptomic analysis comparing pharmacological treatment and secreted-factor treatment, and we demonstrated that both treatments converge on the FAK signaling.

      Regarding the co-culture dataset, we did not include it in the integrated analysis presented in Figure 4. This is because, based on our data in Figure 3, we concluded that the rescue effect observed in co-culture is primarily mediated through secreted factors. Therefore, the secreted-factor transcriptomic data already capture the key signaling pathways responsible for the co-culture rescue effect.

      We will clarify this rationale explicitly in the revised manuscript to avoid any confusion.

      (5) The authors could better clarify the context of Furin downregulation in the knockout cells. Is this a direct consequence of altered transcriptional regulation by the PAR complex, or could it instead represent a secondary consequence of impaired progression through the primed pluripotent transition?

      We thank the reviewer for this important mechanistic question.

      Based on our experimental data, we conclude that Furin downregulation in PAR knockout cells is a direct consequence of altered transcriptional regulation by the PAR complex, rather than a secondary consequence of impaired progression through the primed pluripotent transition. Our evidence is as follows:

      (1) Transcriptomic analysis revealed that PAR knockout leads to a significant reduction in Furin RNA levels.

      (2) Western blot analysis confirmed that PAR knockout also results in a significant reduction of FURIN protein levels.

      (3) Importantly, treatment with an AKT inhibitor (upstream of the proposed pathway) significantly upregulated both Furin RNA and protein levels in PAR knockout cells. In contrast, treatment with a FAK inhibitor or WT CM (downstream) did not significantly alter Furin expression.

      These data collectively indicate that Furin downregulation is directly linked to PAR complex-mediated transcriptional regulation, rather than being an indirect consequence of defective primed state transition. We will clarify this rationale in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      The study demonstrated that Par, but not other polarity genes, Crumbs or Scrib, regulates cell polarity during PSC transition to primed state as well as neural tube formation.

      Strengths:

      The use of KO convinces the role of Par in NPT. Scrib and Crumbs KO data are informative to the field. The conditioned medium experiment is informative. They suggested the potential secreted factors over 50kDa are responsible for maintaining the polarity of NPT in Par KO.

      Weaknesses:

      (1) Most importantly, how Par is important for PSC maintenance and differentiation is not clear. The data provided are dome shape formation, endoderm lineage tendency, and neural tube formation reduction. The manuscript lacks a core message of the physiological importance of Par. Is Par critical of PSC maintenance? Is Par critical for neural system development?

      We thank the reviewer for this critical comment, which helps us better articulate the core message of our study.

      In our manuscript, we have provided clear evidence regarding the role of the PAR complex in pluripotent stem cell (PSC) maintenance and differentiation:

      (1) Regarding PSC maintenance:

      The PAR complex is not critical for PSC maintenance under self-renewing conditions. Specifically, PAR knockout does not significantly affect the expression levels of pluripotency genes (Figure 1 B–C and Supplemental Figure 1 C). Moreover, PAR knockout PSCs can be continuously cultured for at least 30 passages without notable changes in cell morphology or proliferation capacity (Figure 1 D–F). These findings are consistent with previous literature, which demonstrates that the core function of the PAR complex is to establish and maintain cell polarity, rather than directly regulating the transcriptional network of pluripotency genes.

      (2) Regarding PSC differentiation:

      The PAR complex is important for proper differentiation. PAR knockout leads to multiple differentiation defects, including: Failure to establish normal cell morphology during (NPT) (Figure 1 G–K). Impaired formation of proper three-germ-layer structures during embryoid body (EB) and teratoma differentiation (Figure 5 F–G). In particular, the type and quantity of ectodermal tissues are significantly reduced. Consistent with our findings, previous literature has reported that PAR complex deficiency leads to neural developmental defects in mouse embryos, resulting in mid-gestation embryonic lethality.

      (3) Regarding neural system development:

      The PAR complex is critical for neural development. During neural stem cell (NSC) differentiation, PAR knockout cells exhibit a significantly reduced efficiency of Nestin-positive cells and fail to form the classical rosette structures (Supplemental Figure 5 B–C). During neural tube organoid induction, PAR knockout cells show significantly impaired lumen formation and spontaneous elongation efficiency. Moreover, during subsequent maturation, PAR knockout cells fail to differentiate into neurons, leading to a marked reduction in neural tube organoid maturation efficiency (Figure 6 B–E).

      These findings are consistent with previous literature showing that in zebrafish embryonic development, mislocalization of the PAR complex leads to neural tube abnormalities while PAR complex deficiency results in severe hydrocephalus; in mouse embryonic development, PAR complex deficiency causes neural developmental defects leading to embryonic lethality; and disruption of the PAR complex impairs the formation of apical tight junctions in the neuroepithelium and subsequent neuroepithelial tissue polarization, resulting in neural tube closure defects in humans.

      In the revised manuscript, we will incorporate classical literature to discuss the essential roles of the PAR complex in early embryonic development, thereby providing a broader developmental context for our findings.

      (2) Secondly, AKT-FURIN-...... axis still lacks supportive data. Various inhibitors were used to rescue the Par KO. But the link between each component in the axis is missing and rather superficial.

      We thank the reviewer for this critical comment. We acknowledge that the proposed AKT–FURIN–LEFTY–ECM-integrin–FAK signaling axis has certain limitations, particularly that the connection between LEFTY and ECM-integrin lacks direct experimental support. Therefore, in the revised manuscript, we will de-emphasize the role of ECM and integrin and revise the signaling axis to AKT–FURIN–LEFTY–FAK.

      We believe the current data and previous publications support this revised signaling axis well. Accordingly, we have summarized the relevant information as follows. In addition, we plan to perform additional experiments to further support the new signaling axis, which are also included in the following text.

      (1) AKT-FAK

      We found that Par KO cells exhibit defects during NPT, and these defects can be rescued by AKT inhibitor (MK2206), FAK inhibitor (PF562271), and WT CM. Through transcriptomic analysis, we found that both AKT inhibitor and WT CM share similar expression profiles with WT and converge on FAK signaling. Notably, through Western blotting analysis, we found that Par KO led to upregulated p-AKT levels, which were effectively suppressed by MK2206 treatment, but WT CM did not decrease p-AKT levels. In contrast, through immunofluorescence analysis, we found that FAK signaling was hyperphosphorylated in Par knockout primed cells compared to WT primed cells, and MK2206, WT CM, and PF562271 all effectively reduced p-FAK levels. Given that both MK2206 and WT CM attenuated the elevated p-FAK, we propose that all three treatments restore the flat monolayer morphology by regulating FAK signaling homeostasis, with WT CM acting downstream of AKT signaling. The relevant data are presented in Figure 1G-I, Figure 2F, Figure S2C, Figure 3H-I, Figure 4A-D, and Figure S4A.

      (2) AKT-LEFTY

      Through integrated proteomic and transcriptomic analysis, we identified a set of functional proteins. Overexpression screening revealed that LEFTY exhibited the most significant rescue effect in Par KO cells during NPT. Proteomic analysis revealed that the protein levels of LEFTY were significantly higher in WT CM compared to KO CM, suggesting that WT cells modulate FAK signaling via secretion of LEFTY proteins. It is therefore reasonable to infer that MK2206 rescues the defects in Par KO primed cells through upregulation of LEFTY expression. Western blotting analysis confirmed this, showing that MK2206 significantly increased LEFTY protein levels in Par KO primed cells. The relevant data are presented in Figure 4E, Figure 4H and Figure S4C-D.

      (3) LEFTY-FAK

      Proteomic analysis indicated that WT CM treatment supplied extracellular LEFTY to Par KO ESCs, thereby rescuing the phenotypic defects of Par KO primed cells, and significantly reduced p-FAK levels in these cells. Concordantly, LEFTY overexpression also reduced p-FAK in Par KO primed cells. These results are consistent with the reported role of LEFTY in suppressing FAK signaling (Alowayed et al., 2016). The relevant data are presented in Figure 4D, Figure 4F, and Figure S4D-E.

      (4) AKT-FURIN

      LEFTY proprotein requires FURIN-mediated cleavage for secretion and function (Dubois et al., 2001). Through transcriptomic analysis, we found that Par KO downregulated Furin mRNA expression, while MK2206 treatment restored its expression levels. Through Western blotting analysis, we found that MK2206 increased FURIN protein abundance and cleaved LEFTY levels. The relevant data are presented in Figure 4G-H.

      (5) FURIN-LEFTY

      To validate the role of FURIN in LEFTY maturation, we treated WT cells with BOS318, a highly specific and potent inhibitor of FURIN that irreversibly binds to the protease by mimicking its natural substrate (Ivachtchenko et al., 2024). BOS318 induced WT primed cells to adopt a dome-shaped morphology resembling Par KO primed cells, confirming that inhibition of FURIN prevents LEFTY secretion and function, leading to defective primed cell morphology. The relevant data are presented in Figure 4I-J. To further strengthen the role of FURIN in regulating LEFTY, we will treat wild-type cells with BOS318 and examine the expression changes of LEFTY.

      (6) ECM/integrin

      Integrated analysis of both transcriptomic and proteomic data revealed that Par KO leads to significant enrichment of pathways associated with ECM and integrin (Figures 2D, 3F, 3K, and S4B). Notably, both MK2206 and WT CM treatment co-upregulated the ECM-receptor interaction pathway (Figure 4C). The FAK signaling pathway serves as a central node that integrates upstream inputs from both PKC and AKT pathways while transducing extracellular cues derived from ECM-integrin interactions into intracellular signaling cascades (Sakthivel et al., 2025). We therefore propose that secreted LEFTY acts as an extracellular signal that activates specific ECM receptors and modulates integrin complexes, thereby regulating FAK phosphorylation and maintaining normal cell adhesion and morphology. However, this speculation still lacks direct experimental evidence. We will endeavor to perform additional experiments to support this proposed connection in the future. Nevertheless, we have decided to de-emphasize the role of ECM and integrin in the AKT–FURIN–LEFTY–FAK signaling axis in the current manuscript.

      References

      Alowayed, N., Salker, M. S., Zeng, N., Singh, Y., & Lang, F. (2016). LEFTY2 Controls Migration of Human Endometrial Cancer Cells via Focal Adhesion Kinase Activity (FAK) and miRNA-200a. Cellular Physiology and Biochemistry, 39(3), 815-826. https://doi.org/10.1159/000447792

      Dubois, C. M., Blanchette, F., Laprise, M.-H., Leduc, R., Grondin, F., & Seidah, N. G. (2001). Evidence that Furin Is an Authentic Transforming Growth Factor-β1-Converting Enzyme. The American Journal of Pathology, 158(1), 305-316. https://doi.org/10.1016/s0002-9440(10)63970-3

      Ivachtchenko, A. V., Khvat, A. V., & Shkil, D. O. (2024). Development and Prospects of Furin Inhibitors for Therapeutic Applications. International Journal of Molecular Sciences, 25(17). https://doi.org/10.3390/ijms25179199

      Sakthivel, K., Kotowska, A., Fan, Z., Portner, E. J., Merry, C., Nordenfelt, P., Simonsen, A. C., Wright, A. J., & Swaminathan, V. S. (2025). Integrin‐Piezo1 Axis Drives ECM Remodeling and Invasion of 3D Breast Epithelium. Advanced Science. https://doi.org/10.1002/advs.202509932

    1. Author response:

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

      In response to the reviewers’ comments, we have made revisions to the manuscript. Specifically, we have:

      (1) Increased the sample size in the whole-brain imaging and demixed principal component analysis (dPCA) analyses presented in Figures 1 and 3, strengthening the statistical support for our conclusions;

      (2) Revised the presentation of Figure 3B to clarify that the displayed dPC1 traces were scaled for visualization purposes only (dPC1 / max(dPC1)), rather than normalized for quantitative comparison across animals;

      (3) Expanded the main text and supplementary figures to provide more intuitive explanations and geometric illustrations of dPCA and hyperbolic space analysis, and clarified the interpretation of correlation matrices and principal-angle analyses to improve readability;

      (4) Substantially expanded the sections on Bayesian multidimensional scaling and hyperbolic embedding, including additional methodological details and validation analyses to strengthen the computational framework and its interpretation;

      (5) Expanded the Discussion to incorporate recent studies and discuss potential mechanisms underlying DRN 5-HT-mediated motor suppression.

      We believe that these revisions have substantially strengthened the manuscript and addressed the major concerns raised during peer review.

      Reviewer #1 (Public review):

      The wide-ranging serotonergic projections emerging from the Dorsal Raphe nucleus (DRN) are suggestive of a central role in regulating brain-wide activity and behavioural states. DRN activity has been associated with diverse functions, ranging from mood, motivation and pain regulation to sleep and cognitive flexibility. Its far-reaching connectivity made it challenging to assess the brain-wide effect of its activation, especially during behaviour.

      The present study by Qi et al. addresses these challenges by combining state-of-the-art tracking microscopy with the whole-brain accessibility of the larval zebrafish model. To investigate the effect of DRN activation, the authors leveraged the Tg(tph2:ChrimsonR) line to optogenetically activate tph2-positive neurons in the DRN, while monitoring changes in brain-wide activity, locomotion and auditory-stimuli evoked responses.

      Optogenetic activation had a suppressing effect on locomotion, which the authors distinguished from inducing sleep by the maintenance of posture and its sleep disturbing effect of nighttime stimulations. Further, the authors report a distinct effect of DRN activation on motor-related, but not auditoryrelated neuronal subspaces, identified by demixed principal component analysis.

      In addition, rather than affecting all motor-correlated neurons similarly, tph2+ DRN-mediated suppression focused on neurons encoding high-amplitude or turning motion.

      In summary, the work of Qi et al. provides solid evidence for a predominant role of the DRN in wake-state motor suppression by aptly combining the vast data-acquisition possibilities of the larval zebrafish model with computational methods to extract relevant information.

      The brain-wide scope of the analysis is a key strength, reducing bias, confirming the involvement of known motor and auditory regions, and providing a valuable dataset for future analyses.

      While the results well support the conclusion of the authors, certain biological and technical aspects demand discussion.

      We thank you for the positive and thoughtful evaluation of our work. We also appreciate your constructive comments on the biological and technical aspects of the study. We have carefully considered these concerns and addressed them point-by-point below, with corresponding revisions to the manuscript.

      Reviewer #1 (Recommendations for the authors):

      (1) Further samples required:

      Figure 1D relies on n=3 with lots of variability; the author should add more Ns to illustrate their point (typically 10-15 fish used per study to show reliability across fish).

      Figure 3 also relies only on 5 fish in each condition; the authors should increase to 10-15 to show variability.

      Thank you for this valuable suggestion. To address this concern, we have increased the sample size in the revised manuscript. Specifically, the number of animals in Figure 1D has been increased from n = 3 to n = 5, and additional statistical analyses have been included to strengthen the quantitative support for our conclusions. Note that the error bars are plotted as standard deviation (SD), which may make the variability appear larger. In Figure 3, the number of animals was also increased from n = 5 to n = 8.

      In addition, our findings are consistent with previous work showing a strong association between elevated dorsal raphe nucleus (DRN) activity and reduced locomotion in zebrafish [1, 2, 3]. Importantly, across animals, the variance explained by the dPCA components and the rapid modulation of whole-brain state remain highly consistent, supporting the robustness and reproducibility of our observations.

      Given this increased sample size together with consistency across animals and convergence with prior studies, we believe the current dataset provides sufficient statistical and biological support for our conclusions.

      (2) Further steps to be added to the analysis to fully support the claim:

      It appears that the individual brains are registered and individually clustered into areas by combining highly-correlated nearby neurons.

      dPCA is then computed for individual brains. Evidence for our interpretation of individual dPCA spaces:

      (1) Figure 3A depicts separate dPCs for different fish.

      (2) Line 488–489 describes normalization of the value range of dPCs to compare across fish, which implies separate dPCs.

      While the authors normalize the projections onto the principal components, the dPCA spaces remain individual, as does the meaning of their components. It is thus questionable how to conclude from data across fish in a rigorous manner.

      Instead, we recommend that the authors build voxels for each individual’s brain and calculate dPCA across all brains, not individual ones, so that components could become truly comparable across the brains of given individuals.

      We thank the reviewer for this important comment. We would like to clarify that our analysis does not aim to construct a shared dPCA space across animals or to quantitatively compare dPC scores between individuals. In this analysis, dPCA was performed separately for each fish to capture the dominant low-dimensional population dynamics within each individual brain.

      The purpose of Figure 2 is to demonstrate that DRN activation induces a rapid and robust transition in whole-brain activity, rather than to define a common population subspace across animals.

      We also attempted to register and pool data across animals for a joint analysis, as suggested by the reviewer. However, our dataset includes zebrafish at slightly different developmental stages (6–12 dpf). Although the behavioral effects of DRN activation (including motor suppression and global brain-state modulation) were robust across this age range, developmental differences introduced substantial anatomical variability in brain size and morphology, which reduced registration accuracy and made voxel-wise correspondence across animals unreliable.

      We realize that our previous description of “normalization” may have caused confusion. To clarify, the dPC1 traces shown in Figure 2 were only scaled for visualization by dividing each fish’s projection by its maximum value (dPC1 / max(dPC1)), so that trajectories from different fish could be displayed on the same axis. This scaling does not alter the underlying dPCA space, does not constitute normalization for cross-animal comparison, and was not used for any quantitative analysis.

      Importantly, despite being computed independently for each fish, we observed a consistent temporal pattern across animals: DRN activation was reliably accompanied by a rapid transition captured by dPC1 in each individual fish. We have revised the Methods and corresponding text in the manuscript to make this distinction explicit and avoid ambiguity.

      Reviewer #2 (Public review):

      Summary:

      The authors examine the effects of activating the dorsal raphe nucleus serotonergic system using a combination of calcium imaging and optogenetics in freely moving larval zebrafish. Their findings show that optogenetic stimulation induces a state of behavioral quiescence.

      They further investigate whether this state corresponds to sleep or reduced motor activity. Analyses of posture and sleep-related paradigms indicate that serotonergic activation primarily suppresses motor output rather than promoting sleep. Notably, this suppression appears to be bout type-dependent, with stronger effects on neurons associated with larger tail amplitudes and turning angles.

      In addition, auditory stimulation experiments reveal no significant impact of serotonin on sound encoding.

      We thank the reviewer for the careful and thoughtful summary of our work.

      Strengths:

      The study combines advanced experimental techniques with state-of-the-art analytical methods, enabling precise and compelling insights into the role of serotonergic modulation. The experiments and analyses are well aligned with the questions being addressed, and the results appear robust and reliable.

      Moreover, the implementation of experiments that combine calcium imaging and optogenetics in freely moving animals is technically challenging and appears well justified in the context of the research questions.

      We thank you for the positive assessment of our work and for recognizing the technical and analytical strengths of our experimental approach.

      We address the reviewer’s specific comments in detail below.

      Weaknesses:

      While the analytical techniques employed are sophisticated and appear to be appropriately applied, their presentation makes the manuscript difficult to follow. Although the explanations are provided in the Methods section, including more guidance in the main text, such as how to interpret each analytical approach and what outcomes would be expected under different scenarios, would help readers who are less familiar with these techniques.

      Providing this context would better guide the reader in navigating the figures, broaden the accessibility of the work, and ultimately increase its impact.

      We thank you for this important suggestion. To improve clarity and accessibility, we have revised the main text to provide more intuitive explanations of both demixed principal component analysis (dPCA) and hyperbolic space analysis, with additional emphasis on how to interpret their outputs and what different outcomes imply biologically.

      Additionally, we have included new supplementary figures (Figure S2 and Figure S6) with geometric illustrations and simplified examples to provide a more visual and conceptual understanding of these methods. We hope these revisions make the analytical framework easier to follow and improve the accessibility and impact of the manuscript.

      While the authors discuss different quiescent states mediated by serotonin reported in previous studies, their interpretation is limited to stating that “a common feature shared by these distinct behavioral states is a pronounced reduction in movement,” and consequently proposing that activation of dorsal raphe nucleus is not sufficient to specify a particular behavioral state, but rather plays a primary role in driving motor suppression.

      In my view, a more thorough attempt to determine whether the observed state corresponds to any of the previously described forms of quiescence, or represents a subset or variant of them, would strengthen the manuscript. This would help better integrate the findings with the existing literature.

      For example, given that the authors have access to whole-brain activity data, it would be valuable to examine and discuss whether there are shared patterns of activation with previously reported quiescent states.

      Thank you for the insightful suggestion. To address this, we compared our whole-brain activity patterns with key neural signatures reported in previously characterized zebrafish quiescent states.

      A recent study reported that exposure to conspecific alarm substance (CAS) induces a quiescent but vigilant state associated with elevated DRN 5-HT activity and low-frequency synchronized forebrain activity [3]. In our dataset, although DRN 5-HT activation similarly induced robust locomotor suppression, we did not detect comparable low-frequency synchronized forebrain dynamics during the stimulation period. These results suggest that while DRN 5-HT activation is sufficient to induce motor suppression, it does not recapitulate the full neural signature of CAS-induced vigilant quiescence. We have incorporated this comparison and its interpretation into the Discussion section of the revised manuscript.

      Following the termination of optogenetic stimulation, we observed a gradual recovery of locomotory speed, consistent with the behavior in an earlier study [3], although our recovery was much faster. Interestingly, whole brain imaging also revealed a transient increase in forebrain activity. This elevated forebrain activity gradually returned to baseline as locomotor activity recovered. In accordance with the reviewer’s suggestion, we propose that these forebrain dynamics represent a common motif that facilitates the transition out of the DRN-induced quiescent state (Author response image 1.).

      The manuscript largely avoids discussing the mechanisms underlying the observed motor suppression. For instance, is this effect driven directly by serotonin release onto target neurons? Is it mediated by glial activity, as suggested in other studies? Are additional neuromodulatory systems being recruited?

      While addressing these questions may require substantial further work, potentially beyond the scope of the present study, the availability of whole-brain data provides an opportunity to at least explore or

      Author response image 1.

      Forebrain activity increases following termination of DRN optogenetic stimulation. (A) Following the termination of optogenetic stimulation of DRN 5-HT neurons, locomotor speed in Tg(tph2:ChrimsonR) zebrafish gradually recovered and returned to control levels. (B) Neural activity in forebrain regions showed a transient increase immediately after stimulation offset and gradually returned to baseline as locomotor activity recovered. discuss these possibilities. In particular, it would be interesting to examine the recruitment of regions not directly stimulated but known to be associated with other neuromodulatory systems or promoting glial activation (e.g., the locus coeruleus).

      We thank you for this important suggestion. In the revised Discussion, we now frame our findings in relation to several candidate mechanisms.

      Our results are most consistent with a direct neuromodulatory action of serotonin on downstream motor-related circuits. This is supported by the known projection patterns of DRN 5-HT neurons [4], which target midbrain and hindbrain regions involved in motor control, as well as by prior serotonin imaging studies showing elevated 5-HT levels in hindbrain regions during low-motor states, where inhibitory HTR1-family receptors are enriched [5]. In addition, recent voltage imaging studies have shown that DRN serotonergic neurons are embedded within a broader motor-state-dependent circuit, in which they are dynamically regulated by local GABAergic inputs [6]. We have incorporated a discussion of these potential mechanisms into the revised Discussion.

      Reviewer #2 (Recommendations for the authors):

      (1) Lines 91-97 page 2.

      “dPCA separates neural population activity into components tied to specific experimental variables, allowing us to isolate DRN-dependent changes (Methods). Components associated with DRN activation explained significantly more variance in Tg(tph2:ChrimsonR) zebrafish than in controls (Fig. 3A), indicating a strong serotonergic impact on brain-wide neural activity. The small stimulation-related variance in controls likely reflected visual responses to laser.”

      Directly stimulated neurons are not included, as stated in the Methods, but I think it would be better to mention this explicitly in the main text.

      We thank you for this helpful suggestion. We agree that explicitly stating this point in the main text improves clarity. In our analysis, neurons directly stimulated by the laser were excluded (as described in the Methods) to ensure that the identified components reflect whole brain responses rather than direct optogenetic activation. We have now added a clarifying sentence in the Results section to make this explicit.

      (2) Lines 113 - 115 page 3.

      “To examine how DRN 5-HT neuron activation affects sensorimotor processing (Fig. 4C), we next recorded whole-brain neural activity in head-fixed, tail-free larvae embedded in agarose to capture transient calcium signals with minimal motion artifacts.”

      Lines 117-119 page 3.

      “Because head-fixed larvae rarely enter natural sleep, we applied 1 mM mepyramine, a sleep-promoting antihistamine, to induce a sleep-like state (41), which markedly changed auditory responses (Fig. 4E, Fig. S2C)”

      Why not perform these experiments in freely moving fish instead? To what extent do movements in freely moving animals affect segmentation? Is it actually problematic to apply dPCA in that case? You used it in the previous section.

      We thank the reviewer for raising this important point. In principle, freely moving preparations would provide a more natural behavioral context. However, reliable application of dPCA requires stable neuron identification and accurate trial alignment across time, both of which are substantially compromised in freely moving larvae due to motion-induced imaging noise and segmentation errors.

      In our hands, whole-brain calcium imaging in freely moving fish introduces significant variability in segmentation and signal extraction, which in turn leads to unstable and noisy low-dimensional decompositions, preventing robust estimation of task-related components. By contrast, the head-fixed preparation enables consistent neuron tracking and precise alignment to sensory stimuli, which are critical for dPCA.

      We have now clarified in the manuscript that all dPCA analyses were performed on head-fixed animals.

      (3) Line 117 page 3.

      Why do you use cosine similarity? Are the results different when using other metrics?

      I can see the matrix, but what exactly are you looking for in it to support the claim ”DRN activation preserved the structure of the auditory population code”? I think explaining some of these concepts more clearly, or at least providing expectations or interpretations for the different metrics and analyses, would make the manuscript easier to follow.

      We thank you for this question. Cosine similarity is widely used to quantify similarity between population activity patterns because it captures relative activity across neurons while ignoring overall gain.

      In our analysis, each trial is a population activity vector, and the cosine similarity matrix encodes pairwise relationships between these vectors. We assess preservation of the auditory population code by testing whether this similarity structure (i.e., the geometry of population responses) remains consistent across conditions. We have expanded the text to clarify how these matrices are constructed and interpreted.

      In addition, we computed alternative similarity measures based on Pearson correlation, which is equivalent to the cosine similarity of two vectors after they have been centered (subtracting the mean of each vector) (Author response image 2A). We further quantified pairwise trial distances using the Euclidean chord distance on the unit hypersphere, defined as

      D<sub>ij</sub> = √2(1−C<sub>ij</sub>), where C<sub>ij</sub> is Pearson correlation; smaller distances indicate higher similarity (Author response image 2B). Both alternative measures yielded qualitatively consistent results, showing that DRN 5-HT neuron activation preserves the similarity structure across trials.

      (4) Figure 4D.

      If “significant alignment between DRN activation and motor-related neural subspaces, with the sound related subspace being nearly orthogonal” is correct, shouldn’t there be some visible overlap between blue and red, and little to no overlap with yellow? This is not easy to see. Perhaps plotting all three in a single panel would help.

      We thank you for this helpful suggestion. We would like to clarify that the “alignment” we refer to is defined in terms of the angle between neural subspaces, rather than the spatial overlap of neurons. In other words, significant alignment indicates that the corresponding population activity patterns occupy similar directions in a high-dimensional activity space.

      As a result, even statistically significant aligned subspaces (see further exposition below) do not necessarily involve overlapping sets of neurons with large PC weights. This distinction is important because subspace geometry is defined at the population level and cannot be directly inferred from spatial overlap in low-dimensional visualizations. In addition, the visualization shown in Fig. 4D highlights only brain regions containing neurons with relatively high weights for illustrative purposes.

      We also note that the current visualization is based on a maximum intensity projection of a 3D volume, which can create the appearance of overlap in two dimensions even when the underlying neurons are spatially segregated in three dimensions. To provide a clearer spatial reference, we have re-plotted the three subspaces in a three-dimensional representation.

      (5) Figure 4F.

      Do the arrows represent the values for each combination? This is not clear to me. Perhaps it could be clarified in the paragraph. Most of the values, including those being compared, are around 87 plus minus 2 degrees, i.e., mostly orthogonal. Does this imply no overlap between patterns (again, this is hard to see in Figure 4D)? The values are different from the null model but still close to orthogonal. The phrase “significant alignment between DRN activation and motor-related neural subspaces” could be interpreted as strong alignment, but the values do not seem to support that, do they?

      Author response image 2.

      Alternative similarity measures reveal preserved trial-to-trial similarity structure. (A) Trial-by-trial similarity matrix quantified using Pearson correlation. Higher correlation indicates greater similarity between trials (B) Pairwise trial distances quantified using the Euclidean chord distance on the unit hypersphere (D<sub>ij</sub> = √2(1−C<sub>ij</sub>)), where smaller distances indicate greater similarity between trials.

      Author response image 3.

      Three-dimensional visualization of DRN activation-, motor-, and sound-related subspaces. Threedimensional rendering of the high-weight neurons in the DRN 5-HT activation, motor-related, and sound-related subspaces. Colors are consistent with Figure 4D.

      We thank the reviewer for this important clarification.

      We agree that the phrase “alignment” could be interpreted as implying strong spatial overlap in the anatomical space, which is not what we intend to convey. In our analysis, “alignment” refers to a statistically significant deviation from a null distribution.

      In high-dimensional spaces, random vectors are expected to be nearly orthogonal, with angles tightly concentrated around 90°. To demonstrate this phenomenon, we conducted simulations using random vectors over a range of dimensionalities (100–10,000 dimensions) and observed that the expected angle distribution over 1000 trials becomes progressively more concentrated around 90° as the dimensionality increases (Author response image 4). Therefore, even modest deviations from 90° reflect a systematic bias and indicate structured overlap beyond chance. So, “significantly aligned” means the motor–DRN angle is significantly less than the random baseline, and “significantly orthogonal” for sound–DRN means the angle is significantly closer to 90° than the random baseline. We will revise the text to clarify this point and avoid potential misinterpretation.

      Regarding Figure 4D, we agree that the meaning of the arrows was not sufficiently clear. The arrows represent the mean angle, computed across all fish, between the DRN 5-HT activation subspace and the motor-related subspace (left), and between the DRN 5-HT activation subspace and the sound-related subspace (right). We will update the figure legend to explicitly define these elements.

      Author response image 4.

      Random vectors become increasingly orthogonal in high-dimensional spaces. Simulated distributions of pairwise angles between random vectors across different dimensionalities (100–10,000 dimensions; 1000 repetitions per dimensionality). As dimensionality increases, the angle distribution becomes increasingly concentrated around 90°.

      (6) Lines 125 - 126 page 5.

      “After detecting bouts, we computed each bout’s direction and amplitude and classified them into 12 types.”

      It would be interesting to see how the distribution of bouts looks in the direction-amplitude space, in order to better visualize the 12 bout types (perhaps using different colors). It might also be useful to include examples of the 12 bout types in the supplementary material.

      We thank you for this helpful suggestion. To better visualize the distribution of bouts and the definition of the 12 bout types, we have added a new supplementary figure showing the distribution of all bouts in the direction–amplitude space, with each bout color-coded according to its assigned category, consistent with the scheme used in the main text.

      We further quantified the frequency of each bout type across the dataset, which comprises 1,493 bouts from 7 animals. Among these, 4 animals exhibited all 12 bout types and were therefore included in subsequent regression analyses that require complete coverage of all categories.

      In addition, we have included examples of representative bout types in the supplementary material. These additions improve the clarity and interpretability of the bout classification scheme.

      (7) Lines 131 - 133 page 5.

      “Some neurons exhibited activity related to all bout types with similar amplitudes, yielding low coefficient variability, whereas others responded selectively to specific bout types - typically those with larger tail amplitudes and turning angles - exhibiting higher variability in regression coefficients (Fig. 5B).”

      I would appreciate some quantification of “typically.”

      We thank you for this suggestion. Fig. 5B (bottom) shows a neuron with large variability in regression coefficients across bout types, quantified by the coefficient of variation (CV). Bout types with large amplitudes and turning angles (e.g., type 12) have larger regression coefficients than others. We will remove “typically” from the text.

      (8) Lines 546 - 547 page 15.

      “Fish whose baseline tail movements were insufficient to cover all 12 bout types were excluded from further analysis.”

      It would be useful to report the number or proportion of animals that did not exhibit all 12 bout types. Which types of bouts are less frequently observed?

      Thank you for this helpful suggestion. In the full dataset (n = 7 fish), 4 animals exhibited all 12 bout types. We have now added a supplementary figure showing the occurrence probability of each bout type across all animals.

      (9) Line 147 page 5.

      Honestly, the Bayesian multi-dimensional scaling is difficult to follow, and it is not clear what new insight it provides. I assume that ”hyperbolic geometry indicates complex hierarchical organization” is the main point, but its meaning in this context is not sufficiently explained. This paragraph would benefit from being rewritten for clarity or potentially removed if it does not contribute essential information.

      We appreciate your insightful comments. In response, we have substantially expanded the section on Bayesian multidimensional scaling. First, we now provide an intuitive exposition (see Figure S6) of hyperbolic geometry and multidimensional scaling, clarifying why this framework constitutes a powerful approach for uncovering the geometric and functional organization of neuronal populations. Second, we show that multidimensional scaling in a curved hyperbolic space more accurately captures the correlation structure among neurons than embeddings in a flat Euclidean space. Third, and most notably, we find that the inferred curvature of the hyperbolic embedding space tightly scales with the degree of quiescence: fish in which dorsal raphe nucleus (DRN) stimulation nearly abolished locomotor activity exhibit the largest curvatures (new Figure 5F). Collectively, these computational analysis indicate that the curvature of the embedding space serves as a quantitative signature of the quiescent state.

      References

      (1) J. C. Marques, M. Li, D. Schaak, D. N. Robson, J. M. Li, Internal state dynamics shape brainwide activity and foraging behaviour. Nature 577, 239–243 (2020).

      (2) V. Choudhary, C. R. Heller, S. Aimon, L. de Sardenberg Schmid, D. N. Robson, J. M. Li, Neural and behavioral organization of rapid eye movement sleep in zebrafish. bioRxiv pp. 2023–08 (2023).

      (3) Y. Zhao, C.-X. Huang, Y. Gu, Y. Zhao, W. Ren, Y. Wang, J. Chen, N. N. Guan, J. Song, Serotonergic modulation of vigilance states in zebrafish and mice. Nature Communications 15, 2596 (2024).

      (4) Z. Song, C.-X. Huang, H. Zhang, C. Ye, N. Guan, J. Song, Integrated single-cell atlases unveil the operation principles of whole-brain 5-ht neuronal subsystems. Science Advances 11, eadv8128 (2025).

      (5) R. Haruvi, R. Barbara, I. Shainer, A. Rosenberg, L. Moshe, D. Malamud, J. Toledano, D. Braun, H. Baier, T. Kawashima, Global and compartmentalized serotonergic control of sensorimotor integration underlying motor adaptation. BioRxiv pp. 2024–09 (2024).

      (6) T. Kawashima, Z. Wei, R. Haruvi, I. Shainer, S. Narayan, H. Baier, M. B. Ahrens, Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning. Neuron (2025).

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      The authors addressed all my concerns.

      We sincerely appreciate your recognition of our efforts to address the reviewers' suggestions and improve the manuscript.

      Reviewer #2 (Public review):

      (1) All the treatment arms (A-control, MgIG-25 mg/kg, MgIG-50 mg/kg) showed significant body weight loss compared to the untreated controls (Supplemental Figure 1A), but the body weight significantly increased in the treatment arms (A-control and MgIG-50 mg/kg) compared to the untreated controls (Figure 1E). Why?

      We appreciate the reviewer’s careful observation regarding the apparent discrepancy between Supplemental Figure 1A and Figure 1E. We apologize for any confusion caused by the presentation of these data.

      We would like to clarify that Supplemental Figure 1A and Figure 1E represent two different parameters. Supplemental Figure 1A shows absolute body weight, whereas Figure 1E presents the liver-to-body weight ratio (LW/BW), as indicated in the revised figure legend.

      In the NIAAA alcohol-fed model, chronic ethanol exposure typically results in reduced body weight gain or relative body weight loss compared with normal diet-fed control mice, which is consistent with the findings shown in Supplemental Figure 1A. In the preliminary dose-finding study, all alcohol-fed groups (EtOH groups, MgIG 25 mg/kg, and MgIG 50 mg/kg) exhibited lower absolute body weight compared with the untreated control group, which is a common feature of ethanol-induced liver injury models.

      By contrast, Figure 1E reflects changes in the LW/BW ratio rather than total body weight. Ethanol feeding induces hepatomegaly and hepatic steatosis, thereby increasing the LW/BW ratio. Although the LW/BW ratio in the MgIG-treated group remained higher than that in the untreated control group, MgIG treatment significantly reduced the ethanol-induced increase in LW/BW ratio compared with the EtOH group, consistent with its hepatoprotective effects and reduced hepatic lipid accumulation. We hope this clarification could well answer this concern. Thank you very much!

      (2) Mice with MgIG (25 mg/kg) showed the lowest body weight, compared to either A-control or MgIG (50 mg/kg) treatment. According to the authors' explanation, the MgIG (25 mg/kg) caused bodyweight loss are attributed to inter-individual variability, differences in metabolic adaptation, or sample size-related variation. Did these differences happen in MgIG (25 mg/kg) only? or in all other groups? The mouse group assignment should be randomized; however, a large variation in bodyweight was seen in MgIG (25 mg/kg) group. It is not convincing for the author to select MgIG (50 mg/kg) group for subsequent animal experiments, because of a large variation in MgIG (25 mg/kg) group, and because that MgIG (50 mg/kg) group demonstrated more consistent and stable improvements across multiple parameters. The author should reanalyze and compare all the raw data between MgIG (50 mg/kg) group and MgIG (25 mg/kg) group, and address the issues being pointed out and justify rationale for the animal group assignment.

      We appreciate the reviewer’s careful evaluation regarding the variability observed in the MgIG (25 mg/kg) group and the rationale for dose selection.

      Supplemental Figure 1A presents data from our preliminary dose-finding study (n=5 per group, independent cohort), in which all alcohol-fed groups showed expected body weight loss relative to the normal-diet control, as is typical in the NIAAA model. The 25 mg/kg group exhibited numerically greater variability (likely due to inter-individual metabolic differences and small sample size), but no statistically significant difference was observed among the three alcohol-fed groups (A-control, 25 mg/kg, and 50 mg/kg) in final body weight (one-way ANOVA with post-hoc test).

      Mice were randomized by initial body weight and age prior to diet feeding. To address the reviewer’s concern, we have now included Supplementary Table Body weight-raw data with individual animal body weight data (raw values, mean ± SD) for both the dose-finding and main experiments, together with statistical comparisons. We selected 50 mg/kg for all subsequent experiments because it provided more consistent and statistically significant improvements across multiple key parameters (ALT, AST, TG, TC, NAS score, Oil Red O staining, and LW/BW ratio) compared with 25 mg/kg. The 25 mg/kg group showed greater variability in several indices, which is why it was not chosen for mechanistic studies.

      To further clarify this point, we have added detailed descriptions of the randomization procedure and dose-selection rationale in the revised Methods section. Please refer to Page 5, line 106-108 and Page 10, line 276-277. In addition, we will provide the original data on mouse body weight changes, together with the corresponding statistical analyses, in the supplementary materials to further enhance transparency and facilitate reference.

      (3) The author's response did not answer my question. If the authors believe it could be experimental constraints associated with the MgIG formulation, then it is questionable for this MgIG formulation used in all other associated experiments. The experiments, at least those the MgIG formulation associated experiments, need to be repeated.

      We sincerely appreciate the reviewer’s concern regarding the potential impact of the MgIG formulation on the reliability of the associated experiments.

      As clarified in our previous response, the commercially available MgIG preparation used in this study is a clinically approved injectable formulation (5 mg/mL). During the preliminary in vitro dose-ranging experiments, achieving the highest testing concentration (1.0 mg/mL) required the addition of a relatively larger volume of stock solution, which slightly reduced the effective culture medium volume and may have contributed to minor effects on cell status. Consistently, CCK-8 and LDH assays showed a slight reduction in cell viability only at the highest concentration tested.

      Importantly, this phenomenon was observed exclusively in the 1.0 mg/mL group. All subsequent functional and mechanistic experiments were performed using the optimized non-toxic concentration (0.25 mg/mL), at which MgIG consistently and significantly improved IL-6, Acc1, Scd1, and other relevant parameters in a dose-dependent manner (P < 0.05), without detectable cytotoxicity.

      In addition, vehicle controls with volume-matched conditions were included for the high-concentration (1 mg/mL) condition to exclude potential confounding effects caused by solvent volume differences. The protective effects observed at 0.25 mg/mL were highly reproducible and were further supported by multiple independent lines of evidence, including RNA-seq analysis, enzyme activity assays, and knockdown/overexpression experiments, all of which demonstrated consistent mechanistic trends.

      Therefore, we believe that the current data obtained using the optimized concentration remain reliable and interpretable, and that the formulation-related issue observed at the highest concentration does not affect the validity of the main conclusions. Nevertheless, to further address the reviewer’s concern, we are willing to provide additional replicate data for the 1.0 mg/mL cell viability/toxicity assays, as well as repeat qPCR analyses under volume-matched vehicle control conditions in the Supplementary File . Please refer to Supplementary Figure 2E.

      (4) The author explained the relative expression was normalized to GAPDH (fold change), but they did not answer my question. My question is for Figure 5B. in Figure 5B (left, Hsd11b1-KD), scramble control showed over 100 (unit), however, in Figure 5B (right, Hsd11b1-OE), scramble control showed only 0.5-1 (unit). The data seemed that authors used same scramble control for both KD and OE? If yes, they should provide more details of the KD and OE experiments and explain why this happened. If they used plasmid for OE control, they also need to clarify it. In addition, qPCR is not a good assay to show the success of KD or OE, Western blotting should be done as convincing data to show the success of KD or OE.

      We apologize that our previous response did not fully clarify the details of Figure 5B. The left panel of Figure 5B shows the Hsd11b1 knockdown experiment using Hsd11b1 siRNA with scramble siRNA as the corresponding control, whereas the right panel shows the Idi1 overexpression experiment using the Idi1 expression plasmid with empty vector as the corresponding control. These are two independent experiments with separate control groups, rather than a shared scramble control. We recognize that the labeling and figure presentation may have caused confusion, we have revised the legend for Figures 3B, 3C and Figures 5B, 5C as suggested.

      For both experiments, relative mRNA expression levels were normalized to GAPDH and analyzed independently using the 2<sup>^−ΔΔCt</sup> method relative to their respective controls. Therefore, the numerical values shown in the two panels are not directly comparable. The apparent difference in baseline expression levels reflects independent normalization and the intrinsic expression characteristics of different genes, rather than the use of the same control group or any data inconsistency.

      We have confirmed that transfection efficiencies were consistent with expectations and did not significantly affect cell viability.

      We also agree with the reviewer that protein-level validation would provide stronger evidence for the success of knockdown and overexpression. Accordingly, we have performed Western blot analyses for Hsd11b1 knockdown and Idi1 overexpression and will include these data in the revised manuscript to complement the qPCR results (Please refer to revised Supplementary Figure 3C and 4D).

    1. Author response:

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

      eLife Assessment

      Tropical single-island endemic bird populations are particularly vulnerable to climate change. The authors investigate genetic evidence of how such species dealt with climate changes in the past as a possible predictor for how they will respond to change in the future, which could provide an important example for the fields of conservation genetics and island biogeography. The authors' integration of genomics and habitat modeling is commendable, but we find that the support for their conclusions is incomplete: at times, the results presented appear to contradict each other, the authors do not fully account for key variables, and the limited taxonomic scope may cause problematic biases for the conclusion.

      We thank the editors for supporting the premise of this study and highlighting the importance of the study approach. Based on the lacuna identified by the editors and the reviewers, we have modified the manuscript and details of the same are given below. We believe that these revisions have now substantially improved the flow and scope of the manuscript and have addressed the concerns raised by the reviewers.

      Reviewer #1 (Public review):

      Summary:

      The authors combine PSMC and habitat modeling to try to connect habitat change during the Last Glacial Period to changes in Ne.

      Strengths:

      Observing how tropical single-island endemic bird species responded to habitat change in the past may help inform conservation interventions for these particularly vulnerable species. The combination of genomics and habitat modeling is a good idea - this sort of interdisciplinary thinking is what is needed to tackle these complex questions. Additionally, the use of PSMC makes it possible to perform this analysis on poorly-studied species with only a single genome available.

      Room for Improvement:

      Why coalescent Ne is a better predictor of extinction risk than current genomic diversity, or current Ne, isn't explicitly explained. PSMC in particular has many caveats, and some are not acknowledged or adequately addressed by the authors. For example, the authors note that population structure is a confounding factor with PSMC, but that it is not a problem in this instance. They do not provide compelling evidence for why this would be the case, they simply state that the species studied are all single-island endemics. However, single-island endemic species are not necessarily panmictic; this is even less likely to be true for species studied here that inhabit a large geographic area (ie, Australian species). Differing PSMC parameters may also impact results: the differences between passerines and non-passerines were one of their main results, but they do not provide any analysis to show that this difference was not driven by the different mutation rates used for the two groups.

      Parameters for many steps are not described, and choices that are described (such as the PSMC parameters) are not always fully explained. It is unclear why all data was mapped to the autosomes rather than removing reads that map to the sex chromosomes first. Using all the data, the reads belonging to the sex chromosomes could potentially map to other areas of the genome. It does not seem like a mapping quality filter was used, so these potential spurious alignments would not have been removed prior to analysis.

      There are points where the results are described in ways that appear to potentially differ from the supplementary figures. The authors state that even for species where PSMC results differed between models, "trends of Ne increase or decrease from the LIG to LGM were robust across all three PSMC models considered." The figures in the supplement for Pachycephala philippinensis, Rhynochetos jubatus, and Zosterops hypoxanthus appear to potentially contradict this statement, but it is difficult to tell, as the time period observed is not clearly marked on the graphs. How this robustness of trends was determined is not explained, leaving the precision of the analysis unclear.

      Table 1 also includes some information that contradicts what is in the Supplementary Tables, leading to a lack of clarity. Centropus unirufus, Chaetorhynchus papuensis, and Cnemophilus loriae are not included in Supplementary Table 4. Table 1 says Eulacestoma nigropectus, Paradisaea rubra, and Parotia lawesii did not undergo PSMC analysis, but Supplementary Table 4 says PSMC and modeling trends matched for these species. Table 1 says Rhagologus leucostigma underwent both PSMC and climate modeling, but Supplementary Table 4 says "NA" as if it was missing one of these analyses.

      Additionally, some of the results appear to contradict each other. For example, they show that there is no impact of habitat change in larger-bodied species, but also that larger-bodied species saw a decrease in Ne during the LGP. In another example, they state that when a species saw an increase in habitat during the LGP, they also had an increase in Ne. However, they also state that this was not the case for non-passerines.

      Ecosystems are highly complex; there may also be other variables influencing past demographic change other than those explored here. Results should be interpreted with caution.

      We thank the reviewer for their comments, which has helped us in improving the scope of the manuscript while also removing errors in the supporting information. We have improved the section of the manuscript which addressed the drawbacks of PSMC in our revised version. Details and rational for parameter choice are now included in the revised manuscript.

      We performed additional PSMC analyses for a subset of the samples (n = 5), wherein the scaffolds mapping to the sex chromosome were removed only after mapping the reads. We compared the new approach suggested by the reviewer to our original approach and no differences in the PSMC pattern were observed, highlighting the robustness of the results (Supplementary Information Fig. S3).

      Additionally, we have included multiple box-plot and tables in the revised manuscript that helps with interpreting the changes in effective population size. The details of the revisions are presented below in the “Recommendations for the authors” section. We believe that these changes have improved the scope of the manuscript and removed any redundancies and conflicts.

      Reviewer #2 (Public review):

      Summary and strengths:

      In this manuscript, Karjee and colleagues used coalescent-based effective population size reconstruction (PSMC) from single genomes to understand past population trends in island birds and related this to life history traits and glacial patterns. This concept is fairly new, as there are still relatively few multiple PSMC synthesis studies. I also thought that the focus on island endemics was unique and adds value to this paper. I enjoyed seeing a paper focused on South East Asia and think that this could help contribute to our knowledge of the important biodiversity within this region.

      Major weaknesses:

      My biggest concern with this paper is that the analyses are limited to 20-30 species, and significant taxonomic bias is present (there are multiple species of passerine but only 1-2 representatives of other groups). While this is not an issue alone, many of the life history traits or geographical traits are conflated with phylogenetic diversity (e.g., there are no large-bodied passerines). Thus, it is my opinion that the impact of these drivers of past population size is conflated and cannot be disentangled with the current data. The authors themselves state that the core hypothesis surrounding Ne and habitat availability is not supported by their entire dataset (only seen in Passerines). This was not clear enough in the abstract, and conclusions cannot be drawn here as the impact of taxonomy cannot be separated from data richness, traits, etc. The PSMC analysis was done according to the most recent recommendations, and this part of the manuscript is fairly robust. However, in several places, it is incorrectly stated that the PSMC measures or can infer genetic diversity; PSMC only infers past effective population size. It cannot measure genetic diversity in the past. I cannot review the habitat reconstruction modelling as I am a conservation genomics specialist.

      Appraisal:

      I am not convinced about the findings within the paper. I do not think that the results are sufficiently supported at this time, largely due to the conflation of taxonomy with other variables. As this type of comparison is new, I do think that there is a chance for reasonable impact on the field of genomics and island biogeography if the manuscript's constraints are addressed. I do not see scope for impact on conservation at this time and find the conclusions in the abstract regarding conservation relevance to be unfounded.

      We thank the reviewer for highlighting the unique and robust analytical approaches we have taken in this study. We agree with the reviewer that our sample size currently is small. However, we do observe a robust correlation between habitat fluctuation and change in effective population size. Further, the study also highlights the predicament of tropical island endemics, which are currently understudied and future studies are necessary to safeguard the biodiversity. We have highlighted this while also addressing the concerns in the revised version of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Overall:

      This starts with a great premise - looking at how tropical single-island endemic bird species dealt with climate changes in the past may be a predictor of how they will respond to change in the future. Since these species are at high risk of extinction in the face of climate change, tailored approaches to conservation are a good idea. While the premise is solid, I have some questions and recommendations. At times while reading, I did feel a bit confused, which may be due to the fact that this isn't my exact area of expertise. However, if I'm confused, that means a reader from a general audience is also likely to be confused. Some results appear to be conflicting, some claims about data seem possibly inaccurate, and some major limitations are not acknowledged or fully addressed.

      Below I've noted areas that I feel could benefit from revisions. That being said, I liked the integration of habitat modeling and genomics! These sorts of multifaceted approaches are necessary when it comes to unraveling the complex dynamics involved in ecology and evolution.

      Crucial Issues to Address:

      (1) Line 75: With the lower sea levels and habitat change, you say animals can disperse across barriers of land and sea. When it comes to these single-island endemics, were they always confined to a single island? Is there no possibility of introgression with ancient populations of birds on other islands during these periods?

      We thank the reviewers for identifying the potential artifact in effective population size estimates that may occur due to hybridization/introgression. Most of our species belong to small and oligotypic families as has been addressed in the discussion section already, making them likely to be newly arisen lineages rather than refugial ones. There is scant information available in the literature on where the species in our dataset originated from, and further species-specific studies are required to identify signatures of hybridization/introgression. However, we have included this caveat in the revised version of the manuscript (line numbers: 73-78 and 303–305).

      (2) Lines 149-151 "However, in these species as well, trends of Ne increase or decrease from the LIG to LGM were robust across all three PSMC models considered." Please double-check this claim. Some of your figures in the supplement appear to contradict this. In particular, Pachycephala philippinensis, Rhynochetos jubatus, and Zosterops hypoxanthus appear to differ a bit in the time frame described, but it is difficult to tell-I would recommend adding some shading on the graphs to indicate the time period observed. If there was a way you determined this that is more precise than eyeballing the figures like I did, this should also be explained.

      We thank the reviewer for this comment and have reworded the sentence by cross verifying with the PSMC graphs. In addition, we have calculated the precise values of effective population size at the Last Interglacial (LIG) and Last Glacial Maximum (LGM) for each species using custom scripts and used these to evaluate whether the change in Ne during the Last Glacial Period (LGP) was significantly different for the three PSMC settings used. A table depicting these effective population size changes from LIG to LGM are also included in the revised version of the manuscript (Supplementary table S4; line numbers: 145­-156 and 345-357).

      (3) Lines 280-292: Issues with PSMC that are not acknowledged here are my largest concern. The situation being investigated does not necessarily meet all the assumptions PSMC makes (ie, neutral evolution and panmixia), which should be explained in this section. I'll point out the two issues I think should be acknowledged and addressed: First, selection is a confounding factor with PSMC, which is not mentioned here. While that's likely not an issue due to the size of the genome, this is still something that should be stated and explained. Second, the following statement is what I take the most issue with: "Population structure is thus a confounding factor. However, this is unlikely to be a problem given that all our species are single-island endemics". This needs justification. You state that in the past, islands could be connected (see my first comment regarding line 75), so it seems unlikely that 1) migration between past populations on other islands never happened, and 2) there is no population structure *on* the island.

      We thank the reviewer and have modified the PSMC caveats section of the revised version of the manuscript (line numbers: 289-307).

      (4) Line 310: Mapping all the data to the autosomes seems inappropriate to me. The sex chromosome reads could potentially map to other areas of the genome. Unless this information was accidentally left out of the methods section, it doesn't seem like any mapping quality filter was used, so spurious alignments aren't being removed. To remove sex chromosome data, I would instead align data to the whole genome, remove all reads that map to the sex chromosomes, and then map the remaining reads to the autosomes.

      As mentioned earlier, for a subset of the species (n =5), we directly mapped raw reads files onto the genome and then called SNPs on only autosomal regions using the SAMtools mpileup-bcftools pipeline, after which we performed PSMC as above (Supplementary Information Fig. S3). We did not observe and significant difference between the two approaches. Further, only high-quality mapped reads were used for SNP calling as mentioned in the previous version of the manuscript (line numbers: 338-343; Supplementary Information Fig. S3).

      (4) Table 1 includes some information that contradicts what is in the Supplementary Tables: Centropus unirufus, Chaetorhynchus papuensis and Cnemophilus loriae are not included in Supplementary Table 4. Table 1 says Eulacestoma nigropectus, Paradisaea rubra, and Parotia lawesii did not undergo PSMC analysis, but Supplementary Table 4 says PSMC and modeling trends matched for these species. "Pseudorectes ferrugineus" and "Rhynochetos jubatus" are spelled differently in Supplementary Table 4. Table 1 says Rhagologus leucostigma underwent both PSMC and climate modeling, but Supplementary Table 4 says "NA" as if it was missing one of these analyses.

      We thank the reviewer for identifying the errors and we have corrected for these in the revised version of the manuscript. Please see the detailed changes for these comments outlined below

      Centropus unirufus, Chaetorhynchus papuensis and Cnemophilus loriae are not included in Supplementary Table S4 (Now Supplementary table S2): we have added these species to the revised table S2.

      Table 1 says Eulacestoma nigropectus, Paradisaea rubra, and Parotia lawesii did not undergo PSMC analysis, but Supplementary Table 4 says PSMC and modeling trends matched for these species: The genomes for these samples were obtained from museums and exhibited high error rates. Hence, we excluded these samples from further analysis. However, the supplementary table S2 was not updated, and we have corrected this error in the revised version of the manuscript.

      "Pseudorectes ferrugineus" and "Rhynochetos jubatus" are spelled differently in Supplementary Table 4 (Now table S2): we have corrected the typographical error in the revised manuscript.

      Table 1 says Rhagologus leucostigma underwent both PSMC and climate modeling, but Supplementary Table 4 (Now table S2) says "NA" as if it was missing one of these analyses: This was a typographical error, and we have updated it to “mismatch”.

      Major Issues to Address:

      (1) Lines 97-99: "Information on tropical, single-island endemics' demographic responses to past climate change can inform conservation efforts, owing to the genomic signatures that predispose a species to extinction". This needs more explanation. For example, why couldn't we just look at these genomic signatures instead of recreating demographic responses? I'm not sure I fully understand what you mean here.

      We thank the reviewer for this comment and have modified the introduction to highlight the importance of demographic history in predicting species extinction. Comparison of genomic diversity and demographic history of over 200 mammalian genomes, highlights the importance of demographic history in predicting species endangerment and extinction risk (Wilder et al., 2023) (line numbers: 99-104).

      (2) Line 181-182: Whether or not a species was a passerine was an important predictor of Ne only in combination with the change in habitat from LIG to LGM". This is a major finding, but "respond positively to habitat change" (line 183) is a bit ambiguous. Were they responding to habitat expansion? Habitat contraction? Increase in rainfall? What is the change happening? Not all habitat changes are equal.

      We thank the reviewer for this comment and have modified this section for clarity in the revised results and discussion section of the manuscript. We observed a positive correlation between effective population size and availability of suitable habitat. Further, we observed precipitation of the warmest quarter to be the largest contributing bioclimatic variable for all but one Caribbean species (line numbers: 172-­191; 196-211).

      (3) Line 184-185: "The interaction between habitat change and body mass (β = 10.05, 95% CI: [-0.3, 24.41) suggests that there is no impact of habitat change in larger species." Doesn't this contradict the earlier finding of larger-bodied species seeing a decrease in Ne? Or do you mean the decrease in Ne was not due to habitat change?

      We have edited this section for clarity. With the inclusion of additional species, we observed a significant positive relationship between body size and effective population size (line number: 191-193).

      (4) Lines 206-207: "Our results also reveal that both passerine and non-passerine island endemics have entered the Holocene with low genetic diversity." How does this align with the statement that passerines responded positively to habitat change?

      The observation that passerines respond positively to habitat change is based on a systematic analysis of the last glacial period. However, a close look at the entire species’ demographic history reveals the often the Ne is at the lowest following the LGM, and coinciding with the advent of Holocene, the current interglacial. We have therefore modified the sentence in the revised version of the manuscript (line numbers: 213-214).

      (5) Line 215: If we already know flightless birds and endemics are particularly prone to extinction, what is the benefit of this study? Be clear about how your method can be used in a way that is better than what people are already doing. It would be good to explicitly explain why coalescent Ne is a better predictor of extinction risk than current genomic diversity or current Ne.

      We thank the reviewer for this comment and have modified this section in the revised version of the manuscript (line numbers: 221-224).

      (6) Line 259-261: "Habitat change in the LGP was positively associated with Ne fluctuations (Figure 3, β = 9.45), that is, species which showed an increase in habitat in the LGP also showed a concurrent increase in Ne." Is this true in all instances? I thought you found it had no effect for some, or did I misunderstand?

      We thank the reviewers for pointing this out. Species which showed an increase in habitat in the LGP did not always show a concurrent increase in Ne. Our results instead reflect an overall trend and this is clarified in the revised version of the manuscript (line numbers: 268-269).

      Lines 328-330: Could the different mutation rates used for passerines and non-passerines be driving the differences found between the two groups?

      The difference in the mutation rate is low and using the passerine specific mutation rate for non-passerines only shifts the PSMC graph slightly. As our analysis is considering the change in Ne across the LGP, this shift is minimal and does not affect the overall results.

      How are you connecting the demographic changes to species traits? I'm a bit confused about that, so I think some further explanation would be beneficial.

      We have modified the discussion to highlight the role of species traits in shaping the species response to habitat modification and ultimately the change in effective population size. We have included this in the revised version of the manuscript (line numbers: 437­-439).

      Minor Issues to Address:

      (1) Lines 165-168: "Habitat change was poorly associated with change in Ne for the 20 species for which both PSMC and ENM analyses were possible (Cramer's V = 0.15). However, passerine species only showed a strong association (Cramer's V = 0.96), while non-passerines showed a weak negative association (Cramer's V = -0.15)." This is phrased in a way that is a bit confusing. I'd consider rephrasing for clarity.

      We have modified this section in the revised version of the manuscript (line numbers: 167­-170).

      (2) Line 177: The confidence interval says "16.27, -2.61". I think it's supposed to be -16.27?

      We have corrected the typographical error in the revised version of the manuscript.

      (3) Line 185-187: "Finally, the random intercept for Country (sd (Intercept)) showed a marginal positive influence (β = 0.85, 95% CI: [0.04, 2.24])". What does this mean? This needs further explanation.

      We modified this sentence in the revised version of the manuscript (line number: 189-191).

      (4) Line 204: landbridge is misspelled as "landbride".

      We have fixed the typographical error.

      (5) Line 310: What were your Trimmomatic parameters?

      We have included the parameters used for Trimmomatic in the revised version of the manuscript (line numbers: 324-326).

      (6) Line 311: What were your bwa parameters?

      We used default parameters for bwa alignment and this is included in the revised version of the manuscript (line numbers: 328-329).

      (7) Line 322-324: Why did you choose those specific parameters for PSMC? Splitting up the first time window makes sense (as shown in Hilgers 2025), but why did you choose t=5, r=1, and 84 atomic time intervals? Did you choose these parameters independently, or did you decide to use them because they were used by Nadachowska-Brzyska et al? Either way, that information is important to state.

      The parameter selection followed the suggestions based on both Hilgers et al. 2025 and Nadachowska-Brzyska et al. 2016. The information is included in the revised version of the manuscript (line numbers: 345-350).

      (8) Lines 325-326: What did you use for bootstrapping? If not Psmcfa, why?

      We have used “splitfa” to generate files for bootstrap analysis and have included this information in the revised version of the manuscript (line numbers: 350-351).

      (9) Lines 350-354: Please explain the reasoning behind using the different resolution and worldclim for Amazona guildingii.

      Based on the reviewer’s comment, we have re-run the habitat model with the same resolution for Amazona guildingii and include this in the revised version of the manuscript.

      (10) Line 412-413: "For the response variable i.e., the change in Ne, a Bernoulli distribution with a logit link because it is a binary response variable." I think this sentence might be missing some words.

      We have fixed the typographical error in the revised version of the manuscript (line numbers: 444-445).

      (11) Figure 1 is difficult to read, especially the top left panel. I would consider presenting this differently.

      We have supplemented Figure 1 with boxplots of effective population size values estimated during the Last Interglacial and the Last Glacial Maximum which should aid in clarity.

      Reviewer #2 (Recommendations for the authors):

      The authors state that they intentionally chose to remove several avian species that would be suitable for this analysis, because they were subject to larger studies elsewhere. This seems like an unnecessary constraint, and it is my opinion that the authors need to add this data in. I am not aware of what species were excluded, but I hope this will increase the non-passerine proportion of their dataset to help them robustly address their questions. An alternative solution would be for the authors to only include passerines, but this will come at the expense of statistical power with the current dataset and so would also require an increase in sample size. Overall, I recommend including more non-passerine species with traits similar to your passerine species.

      This was a typographical error from the previous versions of the manuscript arising from the fact that we excluded museum species from our samples. We have modified this sentence in the revised version of the manuscript as well as included one new species (Melanocharis versteri) in our study panel (line number: 311-314).

      It was not clear how or if PSMC bootstrapping was included in the comparisons across species, i.e. how did you include bootstrapping when you turned PSMC into a response variable within your statistical analysis? Failing to account for it would introduce measurement error into the data, and I would suggest that the authors explore how to incorporate this.

      We thank the reviewer for this comment and have calculated the precise values of effective population size during the LIG and the LGM using custom scripts to generate boxplots. These boxplots were used to investigate if effective population size values were significantly different during the LGP for all three PSMC parameter settings. Non-significant results were treated as “no change” in effective population size for further statistical analyses. The bootstrap values were used for this analysis, in addition to circumventing the issue of selection on the genome.

      I would also like to see a greater discussion on what aspects of the PSMC curve were used for comparisons and the limitations therein. These cross-species comparisons are still relatively new, and I think they will add value to this paper.

      In our study, the change in Ne from LIG to LGM is considered. We have elaborated this in the revised version of the manuscript. Addition analysis, depicting the changes in Ne as box plots were also included to help understand the fluctuations in Ne.

      Lines 164-168, which refer to your core hypothesis, are really unclear. What was actually found here? Please rephrase.

      We have rephrased the sentence for clarity in the revised version of the manuscript (line numbers: 169­-172).

      PSMC measures effective population size, not genetic diversity. Please change throughout.

      Based on the reviewer’s comment we have changed this in the revised version of the manuscript.

      I was surprised to see some references to conservation within the abstract of the paper. It is important that this is also included in the discussion so that the authors ensure their logic is accessible to managers. It would also be good to discuss the risks of using PSMC to inform conservation from just one genome, as I see these being quite high.

      We thank the reviewer for this comment and have included both pros and cons of using PSMC in the revised version of the manuscript (line numbers: 229-237).

      As this paper is based on public reference genomes, it is best practice that the original notes or reference genome papers are cited to acknowledge the data holders.

      We thank the reviewer for this comment and have included a supplementary table (Supplementary Table S7) acknowledging all the data holders.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary of goals:

      The authors' stated goal (line 226) was to compare gene expression levels for gut hormones between males and females. As female flies contain more fat than males, they also sought to identify hormones that control this sex difference. Finally, they attempted to place their findings in the broader context of what is already known about established underlying mechanisms.

      Strengths:

      (1) The core research question of this work is interesting. The authors provide a reasonable hypothesis (neuro/entero-peptides may be involved) and well-designed experiments to address it.

      (2) Some of the data are compelling, especially positive results that clearly implicate enteropeptides in sex-biased fat contents (Figures 1 and 3).

      We thank the Reviewer for this overall positive assessment of our work.

      Weaknesses:

      (1) The greatest weakness of this work is that it falls short of providing a clear mechanism for the regulation of sex-biased fat content by AstC and Tk. By and large, feminization of neurons or enteroendocrine cells with UAS-traF did not increase fat in males (Figure 2). The authors mention that ecdysone, juvenile hormone or Sex-lethal may instead play a role (lines 258-270), but this is speculative, making this study incomplete.

      Figure 2 shows pan-neuronal or EE-specific expression of the female-specific Tra isoform (UAS-traF) did not explain sex differences in mRNA levels of EE cell-derived factors (we did not test body fat in this figure). We therefore agree that we did not pinpoint the upstream regulator of this difference, and suggest in our revised manuscript that identifying this regulator(s) will be an important future direction of our work.

      “Another important task for future studies will be to elucidate how sex differences in neuropeptide expression are established. The first step in understanding these mechanisms will be to determine which factors specify the sex bias in neuropeptide mRNA levels. Because our data shows that sex determination gene tra does not regulate the sex bias in neuropeptide expression in either the brain or the gut, the role of other factors that influence sexual identity and sexual differentiation must be assessed. One strong candidate is the steroid hormone ecdysone, as virgin females have higher ecdysone titers than males. Ecdysone plays a role in regulating sexual differentiation and development, and contributes to male-female differences in multiple aspects of intestinal physiology (e.g., intestinal stem cell proliferation) and brain development. Another candidate is juvenile hormone, which has been shown to regulate sexual maturation in Drosophila and other insects. While it remains unclear whether juvenile hormone titers differ between virgin males and females, juvenile hormone regulates many aspects of gut physiology in mated females (e.g., intestinal lipid accumulation, ISC proliferation) and influences brain development. Other than hormones, it is possible that sex determination gene Sex-lethal plays a role in regulating the sex difference in mRNA levels of EE cell-derived hormones, as tra-independent effects of Sex-lethal have been described in the brain.”

      (2) Related to the above point, the cellular mechanisms by which AstC and Tk regulate fat content in males and females are only partially characterized. For example, knockdown of TkR99D in insulin-producing neurons (Figure 4E) but not pan-neuronally (Figure 4B) increases fat in males, but Tk itself only shows a tendency (Figure 3B). In females, the situation is even less clear: again, Tk only shows a tendency (Figure 3B), and pan-neuronal, but not IPC-specific knockdown of TkR99D decreases fat.

      We thank the Reviewer for raising this point. In terms of general data interpretation, unless the ‘experimental genotype’ (e.g., cell type-specific gain/loss of a gene) shows a significant difference in gene expression or body fat (e.g., lower body fat/gene expression) from both control genotypes (UAS control, GAL4 control), the cell type-specific manipulation of a gene is not considered to have a biologically meaningful effect as it does not differ in phenotype from the parental strains.

      To ensure reader clarity on this issue we added the following text:

      “For these data, cell type-specific Tra overexpression was considered to have a significant effect on EE cell-expressed hormones only if the experimental genotype (e.g., tissue-GAL4>UAS-tra<sup>F</sup>) significantly differed from both parental strains (e.g., tissue-GAL4>+ and +>UAS-tra<sup>F</sup>) with the same direction of effect.”

      “For all fat storage data, cell type-specific RNAi was considered to have a significant effect on fat storage only if the experimental genotype (e.g., tissue-GAL4>UAS-RNAi) significantly differed from both parental strains (e.g., tissue-GAL4>+ and +>UAS-RNAi) with the same direction of effect.”

      Thus, in Figure 3B our data shows that gut-specific loss of Tk caused a trend toward decreased body fat in females ((p<sup>GAL4</sup>=0.1109 and p<sup>UAS</sup>=0.0118) with no effect in males (p<sup>GAL4</sup><0.0001 and p<sup>UAS</sup>=0.5704).

      In Figure 4B our data shows that pan-neuronal loss of TkR99D caused a significant decrease in female body fat ((p<sup>GAL4</sup><0.0001 and p<sup>UAS</sup><0.0001) with no effect in males ((p<sup>GAL4</sup>>0.9999 and p<sup>UAS</sup>>0.9999).

      In Figure 4E our data shows that IPC-specific loss of TkR99D caused a significant increase in male body fat ((p<sup>GAL4</sup><0.0001 and p<sup>UAS</sup>=0.0003) with no effect in females ((p<sup>GAL4</sup>=0.0321 and p<sup>UAS</sup>=0.0724).

      To summarize our findings for the reader, in our revised manuscript we added text to the Results section:

      “This suggests a role for gut-derived AstC and a potential role for gut-derived Tk in regulating female body fat, whereas gut-derived AstC or Tk do not play a role in regulating male body fat.”

      “These findings are interesting for several reasons. For example, in males, loss of EE cell-derived Tk and loss of TkR99D across neurons had no effect on fat storage, in contrast to the greater fat storage observed with IPC-specific TkR99D loss. This suggests that Tk derived from outside of the gut, and likely in the head, regulates fat storage via effects on TkR99D in the IPC. Future experiments will be needed to test this model, and to determine how Tk affects IPC biology. Further studies will also be needed to understand why IPC but not pan-neuronal loss of TkR99D causes an effect on body fat. Possible explanations include greater knockdown in the IPC using Dilp2-GAL4 or that Tk mediates opposing effects on body fat via effects on additional neuron groups with pan-neuronal TkR99D loss. In females, more work will be needed to identify the neurons upon which Tk acts to regulate body fat, and to test the relative contributions of EE cell- and brain-derived Tk in regulating body fat.”

      (3) The text sometimes misrepresents or contradicts the Results shown in the figures. UAS-traF expression in neurons or enteroendocrine cells did sometimes alter fat contents (Figure 2H, S), but the authors report that sex differences were unaffected (lines 164-166). On the other hand, although knockdown of Tk in enteroendocrine cells caused no significant effect (Figure 3B), the authors report this as a trend towards reduction (lines 182-183). This biased representation raises concerns about the interpretation of the data and the authors' conclusions.

      In Figure 2 we show the effects of UAS-traF expression in either EE cells or in neurons on mRNA levels of EE cell-derived factors (not body fat). Figure 2H shows the effect of UAS-traF in EE cells on Tk mRNA levels in the head, and Figure 2S shows the effect of pan-neuronal UAS-traF on NPF mRNA levels in the head.

      We thank the Reviewer for pointing out we should comment on the significant findings in 2H and 2S even though the direction of effect does not contribute to the sex difference in mRNA levels. In our revised manuscript we added the following text to this effect:

      “However, we note that Tra expression in EE cells further augments the male bias in head Tk mRNA levels (Figure 2H), whereas Tra expression in female neurons paradoxically decreases NPF mRNA levels in the head (Figure 2S).”

      (4) The authors find that in males, neuropeptide expression in the head is higher (Figure 1F-J). This may also play an important role in maintaining lower levels of fat in males, but this finding is not explored in the manuscript.

      We thank the Reviewer for pointing this out.

      In response to an earlier comment, one of the phrases we added to the revised manuscript was to acknowledge that the increased body fat we observed due to IPC-specific loss of TkR99D in males was likely mediated by Tk in the head, as there was no significant effect of loss of EE cell-derived Tk on body fat in males.

      “These findings are interesting for several reasons. For example, in males, loss of EE cell-derived Tk and loss of TkR99D across neurons had no effect on fat storage, in contrast to the greater fat storage observed with IPC-specific TkR99D loss. This suggests that Tk derived from outside of the gut, and likely in the head, regulates fat storage via effects on TkR99D in the IPC. Future experiments will be needed to test this model, and to determine how Tk affects IPC biology.”

      Appraisal of goal achievement & conclusions:

      The authors were successful in identifying hormones that show sex bias in their expression and also control the male vs. female difference in fat content. However, elucidation of the relevant cellular pathways is incomplete. Additionally, some of their conclusions are not supported by the data (see Weaknesses, point 3).

      Impact:

      It is difficult to evaluate the impact of this study. This is in great part because the authors do not attempt to systematically place their findings about AstC/Tk in the broader context of their previous studies, which investigated the same phenomenon (Wat et al., 2021, eLife and Biswas et al., 2025, Cell Reports). As the underlying mechanisms are complex and likely redundant, it is necessary to generate a visual model to explain the pathways which regulate fat content in males and females.

      We agree with the Reviewer that sex differences in fat storage are complex. We were also surprised that our findings regarding EE cell-derived hormones did not contribute to sex differences in the Akh- and insulin-producing cells. This suggests the regulation of sex differences in body fat is highly complex and involves many different factors. In our revised manuscript, we added text to this effect, and a graphical abstract to synthesize our past and new findings together into a single model.

      “Interestingly, these effects were not mediated by the IPC or APC, cells that we have previously shown contribute to the sex difference in fat storage. Taken together, our data provide additional insight into the highly complex mechanism(s) by which unmated female flies achieve higher fat storage than male flies (Fig. 5).”

      Reviewer #2 (Public review):

      Summary:

      This manuscript by Biswas and Rideout investigates sex differences in the expression and function of hormones derived from Drosophila enteroendocrine cells (EE). The authors report that while whole-body and head expression of several EE hormones (AstA, AstC, Tk, NPF, Dh31) is male-biased, gut-specific expression of AstC, Tk, and NPF is female-biased. Intriguingly, this sex-specific effect is not dependent on Tra - a surprising and important result. The authors then used an RNAi-based approach to demonstrate that gut-derived AstC and Tk promote fat storage specifically in females. Similar effects are observed when their receptors are knocked down in neurons. In addition, the authors were able to demonstrate that while Tk promotes female body fat via the insulin-producing cells. Together, these findings suggest that EE cell-derived hormones contribute to sex-specific fat storage regulation.

      We thank the Reviewer for their positive assessment of our paper.

      Strengths:

      Overall, I find the paper quite interesting. While the findings are brief, they reveal novel aspects of the sex-specific lipid storage program that I believe are important. As noted by the authors in the discussion, there are many open questions, including how these neuronal effects translate into systemic sex-specific regulation of lipid storage. Regardless, I find the results to be convincing - this paper will serve as the launching point of many future studies.

      Weaknesses:

      My main criticisms are focused on two points:

      (1) If the sex specific differences are eliminated by tra overexpression, what else might be responsible? As the authors note, the differences in 20E titers might be responsible. I would encourage the authors to simply feed adult flies with food containing 20E and determine if this alters sex-specific 20E expression.

      We agree that there are many candidates (e.g., ecdysone, juvenile hormone) that might contribute to sex differences in mRNA levels of EE cell-derived hormones. We suggest this is an important future direction of our work.

      “Another important task for future studies will be to elucidate how sex differences in neuropeptide expression are established. The first step in understanding these mechanisms will be to determine which factors specify the sex bias in neuropeptide mRNA levels. Because our data shows that sex determination gene tra does not regulate the sex bias in neuropeptide expression in either the brain or the gut, the role of other factors that influence sexual identity and sexual differentiation must be assessed. One strong candidate is the steroid hormone ecdysone, as virgin females have higher ecdysone titers than males. Ecdysone plays a role in regulating sexual differentiation and development, and contributes to male-female differences in multiple aspects of intestinal physiology (e.g., intestinal stem cell proliferation) and brain development. Another candidate is juvenile hormone, which has been shown to regulate sexual maturation in Drosophila and other insects. While it remains unclear whether juvenile hormone titers differ between virgin males and females, juvenile hormone regulates many aspects of gut physiology in mated females (e.g., intestinal lipid accumulation, ISC proliferation) and influences brain development. Other than hormones, it is possible that sex determination gene Sex-lethal plays a role in regulating the sex difference in mRNA levels of EE cell-derived hormones, as tra-independent effects of Sex-lethal have been described in the brain.”

      (2) I'm quite intrigued by the discovery that Tra does not eliminate the sex-specific differences. There are quite a few recent studies demonstrating that fruitless influences sex-specific neuronal function - here to I would encourage the authors to examine whether this aspect of the sex-determination pathway is involved in the lipid accumulation phenotype.

      We thank the Reviewer for raising this point. Transcripts derived from the fruitless-P1 promoter, which is largely responsible for the production of male-specific Fru<sup>M</sup> proteins in the CNS, are spliced by Tra. Therefore, while we cannot definitively rule out a role for fruitless, it is less likely given that the Tra expression in males (which would eliminate Fru<sup>M</sup> proteins in males) did not have a significant effect. In the revised manuscript, we added text to clarify this important point.

      “Future studies will also need to test additional members of the sex determination pathway. While sex differences in expression of EE cell-derived hormones does not involve tra, and is therefore unlikely to involve known tra targets such as fruitless, without further experiments we cannot fully rule out these additional sex determination pathway members.”

      Reviewer #1 (Recommendations for the authors):

      (1) The authors should explain why they focused on AstA, AstC, Tk, NPF and Dh31 but not Bursicon, CCHamides 1 and 2, and sNPF, especially since the latter four are also important entero-peptides.

      We thank the Reviewer for raising this point. In our revised manuscript we clarify that evaluating sex differences in all EE cell-derived hormones will be an important future direction of our work.

      “In particular, we focused on hormones known to influence whole-body fat metabolism, though an important future direction of this work will be to assess sex differences in all EE cell-expressed hormones.”

      (2) The authors initially compare peptide gene expression in males vs. females (Figure 1), but all subsequent comparisons (Figures 2-4) are experimental group vs. controls. It is necessary to directly compare males vs. females for these experiments as well, since the sex-biased difference is the focus of the paper. This may also help with variable performance of controls for some experiments (e.g. Figure 2), which makes interpreting these data difficult.

      We thank the Reviewer for making this point. In terms of general data interpretation, as with our response to an earlier point, unless the ‘experimental genotype’ (e.g., cell type-specific gain/loss of a gene) shows a significant difference in gene expression or body fat (e.g., lower body fat) from both control genotypes (UAS control, GAL4 control), the cell type-specific manipulation of a gene is not considered to have a biologically meaningful effect as it does not differ in phenotype from the parental strains.

      To ensure reader clarity on this issue we added the following text to the Results section:

      “For all fat storage data, cell type-specific RNAi was considered to have a significant effect on fat storage only if the experimental genotype (e.g., tissue-GAL4>UAS-RNAi) significantly differed from both parental strains (e.g., tissue-GAL4>+ and +>UAS-RNAi) with the same direction of effect.”

      In terms of comparing the sexes, all of our analyses used a two-way ANOVA and tested for a sex:genotype interaction. This allowed us to test whether males and females showed a statistically distinct response to the different genetic manipulations. To ensure clarity for readers, we include p-values for all the sex:genotype interactions in figure legends.

      (3) The organization of Figure 1 is unintuitive because the authors change the order of peptides in the last row of panels (Figure 1 K-O). The authors should keep the same order, so that every column corresponds to the same peptide, to make the figure easier for readers to follow.

      We thank the Reviewer for pointing out that we should make every row the same order of EE cell-derived peptides. We made this change in our revised manuscript.

      (4) The authors should explain why mRNA levels in whole-body samples are so highly skewed towards males (sometimes approaching 3-fold expression), whereas in the constituting tissues (head, guts), the differences are much milder and also in opposite directions. How do the big differences in favor of males in Figure 1A-E come about? Does the inclusion of the VNC skew expression levels so much?

      We thank the Reviewer for suggesting we clarify several points around the anatomical focus of sex differences in mRNA levels of EE cell-derived hormones. In our revised manuscript we explain that while male-biased mRNA levels in heads suggest that sex-biased expression in whole bodies may be attributed to expression in heads, that other tissues may contribute to the male-biased expression. We further state this is an interesting area for future investigation.

      “For most peptides, the male bias was due to a higher mRNA level in the head and not the fat body (Figure S1A-E); however, TkR99D mRNA levels were higher in male fat bodies with no difference in head mRNA levels (Figure S1C). We therefore cannot rule out a contribution of additional anatomical sites to the male bias in expression of EE cell-expressed hormones, which is an interesting area for future investigation.”

      (5) The authors use voila-GAL4 as a driver for enteroendocrine cells, but this line is also expressed in sensory cells. The authors should at least mention the expression pattern of this line at first mention (line 165).

      We thank the Reviewer for raising this point, we added text to this effect in the revised manuscript:

      “We found that sex differences in mRNA levels of AstA, AstC, Tk, NPF, and Dh31 were unaffected when we used either voila-GAL4 (Figure 2A-2J) which expresses in EE and sensory cells, or elav-GAL4 (Figure 2K-2T) which expresses in neurons and neuropeptide-producing cells, to drive Tra expression in these cells.”

      (6) Figure legends for Figures 2, 3 and 4 should be simplified and condensed to more concisely describe the panels. There is a lot of redundant repetition, which can easily be avoided by organizing the panels into groups (for example, in Figure 2, A-E should get a single legend entry rather than separate ones).

      We thank the Reviewer for this suggestion, we shortened our legends in the revised manuscript.

      (7) The authors refer to triglyceride contents as 'fat storage', but triglycerides can also be carried through the hemolymph via lipoproteins. The authors should use a more factual expression like 'total triglycerides'.

      We thank the Reviewer for this comment. Circulating lipoproteins in Drosophila carry primarily diacylglycerol, phosphatidylethanolamine, and sterol, with only a small fraction of triacylglycerol (PMID 22844248). Nevertheless, to ensure we are clear we added text in the Methods section to clarify that “fat storage” refers to whole-body triacylglycerol.

      “Triglyceride is the main form of stored fat in the body, with very little in the circulation. We therefore refer to whole-body triglyceride levels as ‘fat storage’ or ‘body fat’.”

      (8) The authors should justify their use of unmated flies for their experiments (line 324) and comment if they expect similar findings and mechanisms in mated flies, especially since nutritional and energy demands are greater in mated females.

      We added text to the methods to justify our use of unmated females to uncover the genetic mechanisms that contribute to sex differences in body fat.

      “We used unmated flies to identify genetic factors that regulate the sex difference in body fat; mated females were not used to avoid mating-induced changes in physiology mediated by additional factors (e.g., Sex-peptide) and behavioral changes due to altered food preferences.”

      (9) Are there any additional AstC and/or Tk receptors that could also play a role? The authors should comment on why they focused on AstC-R2 and TkR99D alone.

      We thank the Reviewer for this interesting point. We added text in our revised manuscript to acknowledge that we tested the primary known receptors for AstC and Tk, other receptors may contribute to their effects.

      “We therefore predicted that loss of AstC-R2 and TkR99D in these cells would reproduce the reduced fat storage we observed in females with loss of EE cell-derived AstC and Tk, though we cannot fully rule out effects of Tk and AstC mediated by other receptors as we did not test these additional receptors.”

      (10) The authors cite Song et al. 2014 to justify using R57C10-GAL80 to restrict expression patterns to the gut (lines 177-179), but upon checking that paper,r I could not find that Song et al. used this approach. Please scrutinize this and remove the reference if it is incorrect.

      We thank the Reviewer for pointing out that Song et al. did not specify how they achieved gut-specific Tk-GAL4; we removed this reference.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 70 - the statement "In males, body fat is maintained..." seems too generic. I would suggest a small edit - "In males, body fat levels are maintained...".

      This is a good suggestion, thank you, we made the appropriate adjustment.

      “In males, body fat levels are maintained by higher expression and activity of two catabolic pathways that promote fat breakdown.”

      (2) Lines 78-81 - These statements suggest an either/or scenario, but I assume this is more a function of balance and equilibrium, where females have more ISS signaling that maintains elevated fat, while bmm pushes homeostasis in males toward catabolism. The authors should include more nuanced statements.

      We thank the Reviewer for this suggestion. In our revised manuscript we adjusted the text as follows:

      “Together, these studies have defined a model of the sex difference in fat storage in which females maintain higher levels of fat storage in part due to a higher relative activity level for anabolic pathway IIS, whereas males have lower fat storage due to higher relative activity of catabolic effectors such as bmm and Akh.”

      (3) Please provide all RRID numbers for the listed BDSC strains - the RRID numbers can be found at the bottom of the BDSC page for each strain.

      We thank the Reviewer for this suggestion, we added the RRID to the Methods.

      (4) Please cite the most recent FlyBase manuscript published in Genetics. Ideally, a statement under the fly husbandry section noting that Flybase was used as a resource throughout the study.

      Thank you for this suggestion, we made the requested change to properly acknowledge this critical community resource.

      “We acknowledge FlyBase as an essential resource providing genetic, genomic, and functional data and tools that supported this study.”

    1. Author response:

      The following is the authors’ response to the previous reviews

      We are pleased that Reviewer 3 appreciated our findings and found the temporal lag between the expression of TFF1 and TFF3 during signaling particularly interesting. The reviewer also advised us not to overemphasize that this lag arises from phase separation of ERα at the TFF1 locus, as the use of 1,6-hexanediol alone is not sufficient to conclusively establish whether ERα condensates undergo liquid–liquid phase separation.

      We agree with this assessment and have revised the manuscript accordingly. Specifically, we have modified the title to remove reference to phase separation and have updated the text throughout the manuscript to avoid claiming that the observed condensates are a result of phase separation.

      The revised title is:

      Ligand-dependent Enhancer Activation Indirectly Modulates Non-target Promoters in a Chromatin Domain.”

      With these changes, we are proceeding with the version of record using revised version of the manuscript.

      Thank you for your continued support.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The authors investigate how infestation of rice plants by the small brown planthopper (Laodelphax striatellus), an important pest in rice cultivation, alters host plant carbohydrate metabolism and how these changes affect insect physiology and fitness. They show that planthopper infestation leads to a density-dependent increase in glucose levels in rice plants, which the authors suggest results from a redistribution of carbohydrates from roots to shoots. Elevated glucose levels in plants are reflected by increased glucose contents in the insects themselves, an effect that is particularly pronounced in gravid females and associated with enhanced fecundity.

      In addition, the authors demonstrate that increased glucose availability enhances tolerance of the small brown planthopper to the neonicotinoid insecticide imidacloprid. These findings suggest that insect-mediated changes in plant carbohydrate allocation may benefit insect fitness in multiple ways, including increased reproductive output and enhanced tolerance to insecticides, both of which are relevant for understanding insect population dynamics in agroecosystems.

      Beyond these physiological observations, the authors aim to elucidate the underlying molecular mechanisms. They propose that glucose functions not only as a nutritional resource but also as a signaling molecule. Specifically, they show that increased glucose availability is associated with activation of the Target of Rapamycin (TOR) pathway, a conserved nutrient-sensing signaling pathway regulating growth and metabolism across eukaryotes. Activation of TOR signaling is linked to increased juvenile hormone levels, which in turn stimulate vitellogenesis and likely contribute to increased fecundity. Furthermore, elevated juvenile hormone levels are associated with increased expression of glutathione S-transferases, suggesting a mechanism contributing to enhanced detoxification capacity. Independent of this pathway, increased glucose availability also leads to higher expression of glutamate-cysteine ligase, the rate-limiting enzyme in glutathione synthesis. Together, these mechanisms provide a non-exclusive explanation for the observed increase in imidacloprid tolerance and form the basis of the authors' proposed mechanistic framework linking glucose availability to reproduction and detoxification.

      We appreciate the reviewer for the thoughtful and positive summary of our work. We greatly appreciate the careful reading and the constructive recognition of our key findings, including the density‑dependent increase in glucose levels in rice plants, the resulting enhancement of planthopper fecundity, and the link between glucose availability and imidacloprid tolerance.

      We are also grateful that the reviewer highlighted our proposed mechanistic model, in which glucose acts as a signaling molecule to activate the TOR pathway, leading to increased juvenile hormone levels, enhanced vitellogenesis, and upregulation of detoxification-related enzymes such as glutathione S‑transferases and glutamate‑cysteine ligase.

      We have carefully addressed all other comments from the previous public reviews in the point‑by‑point response below.

      Strengths:

      A major strength of the manuscript is its substantial mechanistic depth and the extensive use of complementary experimental approaches that converge on a coherent mechanistic interpretation. The authors combine plant manipulations, dietary supplementation, injection assays, RNAi-mediated gene silencing, pharmacological inhibition, and rescue experiments to systematically test the role of glucose as a signaling molecule linking plant-derived nutrition to insect reproduction and insecticide tolerance. Results obtained from independent experimental strategies are highly consistent, and the different datasets collectively support the central conclusions of the study.

      The role of glucose is supported by multiple lines of evidence demonstrating that increased glucose availability, whether induced by prior planthopper feeding, dietary supplementation, or direct injection, consistently results in elevated glucose levels in insects, increased oviposition, and enhanced expression of vitellogenesis-related genes (LsVg and LsVgR). The specificity of this effect is further strengthened by experiments using alternative carbohydrates that release glucose upon enzymatic cleavage, as well as inhibitor and rescue experiments, supporting the interpretation that glucose acts beyond a purely nutritional role.

      The authors further establish a mechanistic link between glucose availability, TOR signaling, juvenile hormone regulation, and vitellogenesis. Activation of TOR signaling by glucose, demonstrated at the level of protein phosphorylation, together with RNAi knockdown and pharmacological inhibition, allows causal placement of TOR upstream of juvenile hormone signaling. Consistent reductions in juvenile hormone titers, vitellogenesis-related gene expression, and oviposition following TOR inhibition, as well as rescue of reproductive output by juvenile hormone analog treatment, provide strong functional support for a glucose-TOR-juvenile hormone axis regulating fecundity. The absence of additive effects following combined knockdown of TOR and juvenile hormone synthesis components further supports the interpretation that these factors act within the same signaling cascade.

      Similarly, the authors provide a detailed mechanistic analysis of glucose-mediated effects on imidacloprid tolerance. Functional assays demonstrate that glutathione S-transferases contribute to detoxification in this species and that increased glucose availability enhances GST activity, glutathione synthesis, and overall glutathione levels. Transcriptomic analyses and targeted RNAi experiments further identify specific GSTs contributing to insecticide tolerance and indicate that glucose enhances detoxification through both TOR-dependent and TOR-independent mechanisms. The combined knockdown experiments, which produce additive effects on mortality, provide particularly strong support for the involvement of multiple interacting glucose-dependent pathways.

      We appreciate the reviewer for the highly positive and thorough recognition of our work's strengths, including the mechanistic depth, convergent experimental approaches, and the proposed glucose–TOR–JH signaling cascade.

      Weaknesses:

      While I am impressed by the mechanistic depth of the study and the clarity with which the authors dissect the underlying physiological pathways, I am less convinced by the current conceptual framing of the phenomenon as a sophisticated adaptive strategy "co-opted" by the small brown planthopper. The data convincingly demonstrate that glucose availability activates conserved nutrient-sensing and endocrine pathways, including TOR signaling and juvenile hormone regulation, which in turn affect reproduction and detoxification capacity. However, these pathways are deeply conserved and likely operate in many insects in response to nutritional status. As such, the results may reflect a general physiological response to elevated carbohydrate availability rather than a species-specific, evolved strategy. Relatedly, herbivory-induced changes in plant carbohydrate allocation appear to be relatively common across plant-insect systems, and it would be helpful to discuss how specific (or general) the observed phenomenon is likely to be.

      In particular, I encourage the authors to more clearly distinguish between (i) a conserved nutrient-responsive signaling cascade and (ii) an adaptive mechanism that evolved specifically under selection imposed by insecticide exposure. The presented data strongly support the former interpretation, whereas evidence for the latter is less clear. The increased tolerance to imidacloprid appears to arise as a consequence of enhanced metabolic and detoxification capacity under elevated glucose conditions, rather than as a trait shaped directly by insecticide-driven selection. Framing this phenomenon as an adaptation to insecticide stress may therefore overextend the conclusions that can be drawn from the data. A more cautious discussion acknowledging that glucose-mediated activation of conserved metabolic and endocrine pathways may incidentally enhance insecticide tolerance, without necessarily having evolved under insecticide selection, would strengthen the conceptual clarity of the manuscript.

      We fully agree with the concerns raised regarding the evolutionary framing, conceptual definitions. We have thoroughly revised the manuscript to avoid overstatements about adaptive evolution, distinguish between conserved nutrient-responsive pathways and species-specific adaptations, supplement key definitions and literature, and address the study limitations and future directions in Discussion.

      While I am impressed by the mechanistic depth of the study and the clarity with which the authors dissect the underlying physiological pathways, I am less convinced by the current conceptual framing of the phenomenon as a sophisticated adaptive strategy "co-opted" by the small brown planthopper.

      We appreciate this comment. We replaced “how herbivorous insects exploit host nutritional signals for adaptation” with “how herbivorous insects respond to host nutritional signals to modulate their fitness traits”.

      Additionally, we uniformly revised overstated terms such as exploit, co-opt, and adaptive strategy throughout the manuscript to utilize, and nutrient-responsive mechanism, respectively, clarifying that our findings reflect a conserved physiological response of insects to host nutritional signals rather than specialized adaptive evolution under insecticide stress, thus avoiding overstatement of evolutionary adaptation.

      The specific revisions are as follows:

      (1) “exploit” was revised to “utilize”;

      (2) “manipulation” was revised to “change”;

      (3) “manipulated resource is exploited” was revised to “nutritional change is utilized”;

      (4) The first sentence of the Discussion section “Our study reveals a sophisticated adaptive strategy whereby SBPH actively manipulates host plant carbohydrate metabolism to simultaneously augment its reproductive capacity and insecticide tolerance.” was revised to: “Our study reveals a conserved nutrient-responsive mechanism whereby SBPH infestation elicits a carbohydrate metabolism shift in rice, and the insect subsequently utilizes host-derived glucose to simultaneously augment its reproductive capacity; concurrently, this glucose-mediated pathways enhances insecticide tolerance.”; t)

      (5) The second sentence of the Discussion section “we identify host-derived glucose as a central resource co-opted by SBPH and delineate two interconnected molecular cascades through which it exerts dual fitness benefits” was revised to: “we identify host-derived glucose as a central signaling molecule that modulates two interconnected molecular cascades exerting dual fitness benefits”.

      The data convincingly demonstrate that glucose availability activates conserved nutrient-sensing and endocrine pathways, including TOR signaling and juvenile hormone regulation, which in turn affect reproduction and detoxification capacity. However, these pathways are deeply conserved and likely operate in many insects in response to nutritional status. As such, the results may reflect a general physiological response to elevated carbohydrate availability rather than a species-specific, evolved strategy. Relatedly, herbivory-induced changes in plant carbohydrate allocation appear to be relatively common across plant-insect systems, and it would be helpful to discuss how specific (or general) the observed phenomenon is likely to be.

      Thank you for your comments and insights; we fully agree with your perspective. Accordingly, we have made the following revisions in the Abstract, Introduction, and Discussion of our manuscript:

      (1) The sentence “Our findings establish host-derived glucose as a central signaling molecule that SBPH exploits to simultaneously optimize reproduction and insecticide resistance.” has been modified to “Our findings establish host-derived glucose as a central signaling molecule that SBPH utilizes to modulate conserved pathways for simultaneous optimization of reproduction and insecticide resistance.”.

      (2) We added the following citation in the Introduction: “and sugar-promoted TOR activation has also been reported in Drosophila [29]”.

      (3) We revised the sentence “However, direct evidence for glucose-mediated TOR activation in insects and its functional connection to JH signaling and reproduction is lacking” by specifying “insects” as “hemipteran insects”.

      (4) In the Discussion, we revised “its sensitivity to glucose has remained elusive” to “sugar-promoted TOR activation has been reported in Drosophila [29], and our study extends this conserved regulatory mechanism to hemipteran insects”.

      (5) We added the phrase “This nutrient-responsive cascade might be conserved across insect species” at the end of the fourth paragraph of the Discussion.

      (6) Additionally, we added the following statement in the Discussion: “Notably, studies have shown that brown planthopper (Nilaparvata lugens) infestation can reshape sugar distribution in rice by altering the expression of rice sugar transporters, yet the mechanism through which planthoppers regulate these transporters remains unresolved [9]”.

      These revisions align with our data and support the reviewer’s view.

      In particular, I encourage the authors to more clearly distinguish between (i) a conserved nutrient-responsive signaling cascade and (ii) an adaptive mechanism that evolved specifically under selection imposed by insecticide exposure. The presented data strongly support the former interpretation, whereas evidence for the latter is less clear. The increased tolerance to imidacloprid appears to arise as a consequence of enhanced metabolic and detoxification capacity under elevated glucose conditions, rather than as a trait shaped directly by insecticide-driven selection. Framing this phenomenon as an adaptation to insecticide stress may therefore overextend the conclusions that can be drawn from the data. A more cautious discussion acknowledging that glucose-mediated activation of conserved metabolic and endocrine pathways may incidentally enhance insecticide tolerance, without necessarily having evolved under insecticide selection, would strengthen the conceptual clarity of the manuscript.

      We appreciate the professional comments and fully agree with your perspective. Accordingly, we have made the following revisions in the Discussion section:

      (1) The sentence “Our study reveals a conserved nutrient-responsive mechanism whereby SBPH infestation elicits a carbohydrate metabolism shift in rice, and the insect subsequently utilizes host-derived glucose to simultaneously augment its reproductive capacity and insecticide tolerance.” has been revised to:

      “Our study reveals a conserved nutrient-responsive mechanism whereby SBPH infestation elicits a carbohydrate metabolism shift in rice, and the insect subsequently utilizes host-derived glucose to augment its reproductive capacity; concurrently, this glucose-mediated activation of conserved metabolic pathways incidentally enhances insecticide tolerance.”

      (2) Original sentence: “The insect then exploits this manipulated nutritional landscape, deriving dual benefits of increased fecundity and enhanced insecticide tolerance.”

      Revised to:

      “The insect then exploits this manipulated nutritional landscape to increase fecundity, and the concurrent activation of conserved pathways by glucose incidentally enhances insecticide tolerance.”

      To remove the phrase “dual benefits,” which could imply that tolerance is an actively obtained adaptive advantage.

      (3) Original sentence:

      “Parallel to fecundity enhancement, SBPH utilizes host glucose to bolster its tolerance to the insecticide imidacloprid by supporting a novel dual-pathway model for GST activation, entailing both metabolic fueling and transcriptional regulation.”

      Revised to:

      “Parallel to fecundity enhancement, the activation of conserved metabolic and endocrine pathways by host-derived glucose incidentally bolsters SBPH tolerance to the insecticide imidacloprid, which is mediated by a novel dual-pathway model for GST activation involving both metabolic fueling and transcriptional regulation.”

      To clarify that the enhancement of insecticide tolerance is an incidental consequence of pathway activation, not a direct utilization strategy.

      Reviewer #1 (Recommendations for the authors):

      (1) Line 26 (Abstract): "how herbivorous insects exploit host nutritional signals for adaptation remains unclear." I am not sure that what is described here constitutes exploitation of a signal for adaptation. The authors convincingly unravel mechanisms by which insects benefit from elevated glucose, but the wording implies an evolved adaptation to insecticide pressure. Given that herbivore effects on nutrient allocation are likely widespread, I would recommend more cautious phrasing and clearer separation between physiological mechanisms and evolutionary interpretations.

      We appreciate this comment. We replaced “how herbivorous insects exploit host nutritional signals for adaptation” with “how herbivorous insects respond to host nutritional signals to modulate their fitness traits”.

      Additionally, we uniformly revised overstated terms such as exploit, co-opt, and adaptive strategy throughout the manuscript to utilize, and nutrient-responsive mechanism, respectively, clarifying that our findings reflect a conserved physiological response of insects to host nutritional signals rather than specialized adaptive evolution under insecticide stress, thus avoiding overstatement of evolutionary adaptation.

      The specific revisions are as follows:

      (1) “exploit” was revised to “utilize”;

      (2) “manipulation” was revised to “change”;

      (3) “manipulated resource is exploited” was revised to “nutritional change is utilized”;

      (4) The first sentence of the Discussion section “Our study reveals a sophisticated adaptive strategy whereby SBPH actively manipulates host plant carbohydrate metabolism to simultaneously augment its reproductive capacity and insecticide tolerance.” was revised to: “Our study reveals a conserved nutrient-responsive mechanism whereby SBPH infestation elicits a carbohydrate metabolism shift in rice, and the insect subsequently utilizes host-derived glucose to simultaneously augment its reproductive capacity; concurrently, this glucose-mediated pathways enhances insecticide tolerance.”;

      (5) The second sentence of the Discussion section “we identify host-derived glucose as a central resource co-opted by SBPH and delineate two interconnected molecular cascades through which it exerts dual fitness benefits” was revised to: “we identify host-derived glucose as a central signaling molecule that modulates two interconnected molecular cascades exerting dual fitness benefits”;

      (6) The phrase “This nutrient-responsive cascade might be conserved across insect species” was added at the end of the fourth paragraph in the Discussion section;

      (2) Line 37 (Abstract): To improve readability, please define "LsGST" on first use

      We appreciate this comment and have added taxonomic definitions for LsGSTe1 and LsGSTo1 at their first appearance in the Abstract: “LsGSTe1 (SBPH epsilon class GST) and LsGSTo1 (SBPH omega class GST)”.

      (3) Lines 38-39 (Abstract): The repeated framing as "signal exploitation" may not be fully justified, since glucose is simultaneously a key energetic resource that could plausibly fuel parts of the observed response. Clarifying what is meant by "signal" versus "resource" in this context would improve conceptual clarity.

      We appreciate this comment. Following your suggestion, we revised the description related to “signal exploitation”, and the sentence “Our findings establish host-derived glucose as a central signaling molecule that SBPH exploits to simultaneously optimize reproduction and insecticide resistance.” has been modified to “Our findings establish host-derived glucose as a central signaling molecule that SBPH utilizes to modulate conserved pathways for simultaneous optimization of reproduction and insecticide resistance.”.

      In addition, we have emphasized the signaling role of glucose in both the Results and Discussion sections. Through mannitol osmotic control treatments, hydrolase inhibition assays, and rescue experiments, we excluded the possibility that glucose acts merely as an energy source and confirmed its signaling function in regulating the JH pathway via TOR phosphorylation. These experiments clearly distinguish its signaling role from its nutritional/energetic role.

      (4) Lines 39-41 (Abstract): The phrase "nutrient-based control strategies" is difficult to interpret without at least a brief example or explanation. A short clarification would help readers understand the applied implications.

      We fully agree with and appreciate this comment. We added a concrete example in the Abstract: “, such as disrupting insect nutrient-sensing pathways or modulating host carbohydrate metabolism”.

      We also added a new section “The identification of the glucose‑TOR‑JH axis as a key regulator of SBPH fecundity and insecticide tolerance provides novel strategies for eco-friendly, nutrient-based pest control. Firstly, varieties that limit SBPH-induced glucose redistribution would reduce reproduction and insecticide tolerance without yield loss. Secondly, small-molecule inhibitors targeting TOR phosphorylation or JH synthesis can serve as biopesticides or synergists to improve insecticide efficacy, as they would suppress the glucose-mediated incidental enhancement of insecticide tolerance. Finally, optimized fertilization and irrigation can reduce shoot glucose accumulation and suppress SBPH outbreaks. These strategies offer sustainable alternatives to traditional insecticides and help mitigate insecticide resistance of SBPH.” in the Discussion, detailing three practical strategies (rice breeding, small-molecule inhibitor, agronomic management) to clarify the applied meaning of nutrient-based control strategies.

      (5) Line 68 (Introduction): The statement that glucose is "the dominant transportable carbon source" in plants seems inaccurate; sucrose is generally considered the main transport sugar. Consider revising.

      We appreciate this professional comment. According to the literature, glucose can be transported in plants but is not the primary sugar involved; sucrose is the main transported form. We have therefore removed the word “dominant”, and the revised description is consistent with current knowledge.

      (6) Line 82 (Introduction): The claim that "direct evidence for glucose-mediated TOR activation in insects...is lacking" may not be correct. For example, Kim & Neufeld (2015) report sugar-promoted TOR activation in Drosophila (Nat. Commun., doi: 10.1038/ncomms7846). This may also relate to statements later in the manuscript (e.g., around line 506).

      We apologize for this oversight during our initial literature review and sincerely appreciate this professional comment. We have added the relevant citation in the Introduction: “and sugar-promoted TOR activation has also been reported in Drosophila [29]”. (of the revised manuscript)

      Furthermore, we revised the sentence “However, direct evidence for glucose-mediated TOR activation in insects and its functional connection to JH signaling and reproduction is lacking” by specifying “insects” as “hemipteran insects”. (of the revised manuscript)

      In addition, we modified the corresponding statement in the Discussion section: the phrase “its sensitivity to glucose has remained elusive” was revised to “sugar-promoted TOR activation has been reported in Drosophila [29], and our study extends this conserved regulatory mechanism to hemipteran insects”. (of the revised manuscript)

      These revisions could clarify that our innovative contribution lies in extending this conserved mechanism from Drosophila to hemipteran insects, rather than reporting the first discovery of glucose-induced TOR activation. Accordingly, we have adjusted the reference numbering for all subsequent citations in the manuscript.

      (7) Line 176 (and elsewhere): Mannitol is used as an osmotic control; it would be helpful to briefly explain why osmolarity is expected to be a relevant confound in these assays and how osmotic effects might otherwise influence the measured outcomes.

      We greatly appreciate this valuable comment. We have added the following paragraph to the Discussion section: “Given that osmotic pressure, a key determinant of plant cell turgor pressure, can disrupt insect homeostasis and impair fitness when insects ingest hyperosmotic plant sap [47,48], we rigorously excluded confounding effects of rice osmotic pressure in this study.”.

      Two relevant references [47, 48] have been cited to support this statement, and we have adjusted the reference numbering for all subsequent citations in the manuscript.

      (8) Line 464 ff.: The statement that co-option of plant defenses by insects is an "emerging paradigm" seems overstated; classic examples such as sequestration of plant toxins have been known for decades. A more nuanced phrasing may be appropriate.

      We appreciate this comment and agree with your perspective. We have revised “emerging paradigm” to “classic paradigm” for greater objectivity.

      (9) Lines 491-492: This passage is somewhat confusing with respect to framing: here, elevated glucose is described as a plant stress response, whereas elsewhere (including title/abstract) it is presented as manipulation by the insect. Clarifying whether the authors view elevated glucose primarily as a plant response that insects benefit from, versus an actively induced manipulation, would improve consistency.

      We greatly appreciate your professional comment. We have revised the relevant statement from: “Given that elevated sugar levels might enhance plant stress resistance [46,47], our study reveals an intriguing ecological paradox: the plant's potential attempt to mount a stress response via glucose accumulation is effectively co-opted by the insect to enhance its own fitness and resilience.”

      To: “Notably, studies have shown that brown planthopper (Nilaparvata lugens) infestation can reshape sugar distribution in rice by altering the expression of rice sugar transporters, yet the mechanism through which planthoppers regulate these transporters remains unresolved [9]. Given that elevated sugar levels might enhance plant stress resistance [49,50], our study reveals an intriguing ecological paradox that SBPH infestation likely manipulates glucose distribution via unidentified pathways to boost its own fitness and resilience.”

      (10) Discussion (general): In addition to the demonstrated glutathione/GST mechanisms, elevated glucose could plausibly support detoxification in other ways (e.g., providing a substrate for conjugation in phase II metabolism). It may be worth briefly acknowledging such additional routes, even if not tested here.

      We appreciate this comment. We added the following text in the GST pathway section of the Discussion: “Beyond the GCL-GSH-GST and TOR-JH-GST pathways characterized in this study, elevated glucose may also enhance insecticide detoxification through additional routes (e.g., providing carbon skeletons for phase II xenobiotic conjugation reactions or fueling energy-dependent detoxification processes in insect midgut and fat body), which warrant further experimental verification.”, objectively acknowledging other potential pathways and listing them as future research directions.

      Reviewer #2 (Public review):

      Summary:

      Zhang and colleagues investigate the molecular mechanisms by which the small brown planthopper (SBPH, Laodelphax striatellus) manipulates host rice carbohydrate metabolism to enhance its own fitness. Using a combination of molecular, pharmacological, and biochemical approaches, they demonstrate that SBPH infestation induces systemic glucose reallocation in rice, as evidenced by the upregulation of glucose levels in aerial tissues and a simultaneous reduction in root glucose levels. Notably, host-derived glucose acts as a central signaling molecule, driving two key adaptive traits: enhanced fecundity via the glucose-TOR-JH-Vg signaling cascade, and increased imidacloprid tolerance through synergistic metabolic (GCL-GSH) and regulatory (TOR-JH-GST) pathways targeting GST activity. These findings uncover a sophisticated resource-manipulation strategy in SBPH and identify nutrient-sensing and detoxification pathways as potential targets for pest control.

      Strengths:

      (1) The study addresses a gap in plant-insect coevolution research by identifying glucose as a dual-function signaling molecule that coordinates SBPH reproduction and insecticide tolerance, providing valuable insights into how herbivores exploit host nutritional signals.

      (2) The experimental design is well structured and multifaceted, integrating RNAi, RT-qPCR, Western blotting, pharmacological inhibition, and biochemical assays. The use of appropriate controls (e.g., osmotic controls with mannitol and hydrolase-inhibitor rescue experiments) strengthens the causal interpretation of the results.

      (3) The mechanistic framework is clear and well-supported. The authors delineate two interconnected molecular cascades (glucose-TOR-JH-Vg for fecundity and GCL-GSH/TOR-JH-GST for tolerance) with hierarchical validation (e.g., rescue experiments with JHA), ensuring the reliability of conclusions.

      We thank the reviewer for recognizing the novelty of the scientific question, rigor of the experimental design, and clarity of the mechanistic framework in our study. We fully agree with the limitations raised regarding the generality of the findings, identification of upstream signals, range of insecticides tested, and translational applications for pest management. We have supplemented the manuscript with discussions of our study limitations and future research directions, added a section on the application of our findings in pest control, and provided key future directions such as identification of upstream signal identification, validation of generality and expansion of insecticide testing.

      Weaknesses:

      (1) The study focuses exclusively on SBPH without validating whether the observed phenomena and mechanisms are conserved in closely related planthopper species (e.g., brown planthopper Nilaparvata lugens). This limitation restricts the generalizability of the findings to other economically important rice pests.

      We appreciate this valuable comment. We have added a subsection titled “Limitations and Future Research Directions” in the Discussion section, explicitly stating that this study focuses exclusively on SBPH and the broader generality of the mechanism remains to be verified. Among the future directions outlined, “verifying the conservation of the glucose‑TOR‑JH axis in other economically important rice planthoppers” is designated as the first key research priority, and cross‑species validation experiments are planned accordingly.

      (2) The specific upstream signals that trigger glucose reallocation in rice (e.g., SBPH salivary effectors or oviposition-associated factors) are not identified. Although this represents a complex and independent research direction, the absence of such information limits the depth and completeness of the mechanistic framework and leaves open questions regarding the initiation of host metabolic manipulation.

      We greatly appreciate this insightful comment. We have incorporated this issue as a key future research direction in the Discussion section. Specifically, we added the following statement: “Notably, the upstream signals (e.g., specific salivary effectors secreted by SBPH or oviposition-associated plant response factors) that trigger glucose reallocation in rice remain uncharacterized and represent a key direction for future in-depth research.”

      In addition, we have added a subsection titled “Limitations and Future Research Directions” in the Discussion, which includes the third point: “(3) Identifying the specific SBPH salivary effectors and plant signaling pathways that trigger glucose reallocation in rice, to complete the mechanistic framework of host metabolic changes manipulated by herbivores.”

      (3) Insecticide tolerance assays are limited to imidacloprid. Extending these analyses to one or two additional commonly used insecticides (e.g., thiamethoxam) would help determine whether the glucose-mediated detoxification pathway is specific to imidacloprid or reflects a broader resistance mechanism, thereby strengthening conclusions regarding the generality of the GST activation cascade.

      We greatly appreciate this comment. Related discussion was added in the subsection titled “Limitations and Future Research Directions” as following:

      Expanding assays to other commonly used rice insecticides (e.g., thiamethoxam, pymetrozine, triflumezopyrim) to validate whether the glucose-mediated detoxification pathway confers broad-spectrum tolerance.

      (4) Given the study's potential implications for pest management, the manuscript would benefit from a brief discussion of possible practical applications, such as manipulating rice glucose metabolism through breeding strategies or developing small-molecule inhibitors targeting the TOR-JH axis. Including such perspectives would enhance the translational relevance of the work by linking mechanistic insights to real-world pest control strategies.<br />

      We greatly appreciate your professional comment. We have added a standalone paragraph in the Discussion section to discuss the novel strategies for SBPH control provided by this study, as follows: “The identification of the glucose‑TOR‑JH axis as a key regulator of SBPH fecundity and insecticide tolerance provides novel strategies for eco-friendly, nutrient-based pest control. Firstly, varieties that limit SBPH-induced glucose redistribution would reduce reproduction and insecticide tolerance without yield loss. Secondly, small-molecule inhibitors targeting TOR phosphorylation or JH synthesis can serve as biopesticides or synergists to improve insecticide efficacy, as they would suppress the glucose-mediated incidental enhancement of insecticide tolerance. Finally, optimized fertilization and irrigation can reduce shoot glucose accumulation and suppress SBPH outbreaks. These strategies offer sustainable alternatives to traditional insecticides and help mitigate insecticide resistance of SBPH.”

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      In this study, the authors propose that HSV-1 infection degrades the class I histone deacetylases HDAC1 and HDAC2. The MDM2 E3 ubiquitin ligase from the DNA damage response pathway is responsible for ubiquitinating these HDACs that are subsequently degraded via proteasomes. The authors hypothesize that HDAC degradation will cause hyperacetylation of viral chromatin and enable viral gene transcription.

      Strengths:

      The ubiquitination of HDAC1 & HDAC2 by Mdm2 and the mapping studies are clear.

      Weaknesses:

      (1) Degradation of HDACs is observed late, at least 12-24 h post-infection (1 PFU/cell). Viral genes have been transcribed by that point, and the virus has replicated its genome. The kinetics do not match the proposed model.

      We sincerely thank the reviewers for their insightful and constructive feedback. The original low‑MOI condition introduced asynchronous infection and obscured early events. We repeated the time course at high MOI (MOI = 5) in HeLa cells. Under these synchronized conditions, HDAC1/2 degradation is detectable by 2 hpi and pronounced by 4‑6 hpi—preceding viral DNA replication (~3‑4 h) and coinciding with true late gene expression (ICP4). These data (Author response image 1) show that HDAC1/2 depletion is an early, virus‑directed event, not a late consequence.

      Author response image 1.

      (2) The authors need to connect these findings with their story. As of now, these findings are correlative. For example, what is the impact of MDM2 depletion on viral gene expression and progeny virus production? Leptomycin B is not specific to the HDAC cytoplasmic translocation, and its effect on the infection could be due to its effect on ICP27.

      We generated stable MDM2 knockdown HeLa cells. MDM2 depletion reduced progeny virus titers at 24 hpi and suppressed ICP0, ICP8, and gB expression at both RNA and protein levels (Figure 4G‑J). HDAC1/2 degradation was abolished (Figure 4B). Thus MDM2‑dependent HDAC1/2 proteolysis is essential for the lytic transcriptional cascade.

      To bypass LMB’s broad CRM1 inhibition, we constructed an HDAC1 mutant lacking the nuclear export signal (HDAC1‑ΔNES) that remains nuclear during infection. In HDAC1/2 double‑knockdown cells, re‑expression of HDAC1‑ΔNES failed to rescue viral replication compared to wild‑type HDAC1, and overexpression of HDAC1‑ΔNES in control cells more strongly inhibited progeny yield (Figure 5K). This genetic approach confirms that HDAC1 nuclear export is specifically required for its proviral function, independent of ICP27.

      Author response image 2.

      (3) The time point when the inhibitors were added to the cultures has not been stated in any experiment. If inhibitors were added with the virus, viral gene expression would be blocked.

      We sincerely thank the reviewers for identifying this critical oversight. Unless otherwise specified, All inhibitors were added at 1 hpi (post‑adsorption) unless otherwise noted. Time‑of‑addition experiments for MG‑132, LMB, and berzosertib are now included (Author response image 3, Figure 2K ,5A).

      Author response image 3.

      (4) The authors need to present late gene expression data in all the experiments where drugs have been used.

      In all drug-treated experimental conditions, we have performed comprehensive qRT-PCR analyses—quantifying mRNA levels of at least one immediate-early gene (ICP0), one early gene (ICP8), and one late gene (gB or gC)—to establish a temporally resolved viral gene expression profile across the entire replication cycle. This systematic assessment allows us to rigorously determine whether the observed inhibitory effects are global or selectively restricted to specific kinetic classes of viral genes. Consistent with this design, both LMB and berzosertib significantly suppressed the mRNA expression of ICP0, ICP8, and gB in HSV-1–infected cells (Author response image 4), indicating that their antiviral activity likely stems from interference with an upstream regulatory node common to the transcriptional activation of immediate-early, early, and late viral genes.

      Author response image 4.

      (5) Figure 1A, ICP4 is not detected up to 12 hours post-infection of HeLa cells with 1 PFU/cell. This cannot be true.

      This observation stems from technical artifacts in the original Western blot images—primarily insufficient signal intensity and suboptimal dynamic range. Therefore, we re-conducted the time-course experiment, systematically collecting samples at each time point and moderately increasing the sample loading volume while ensuring protein integrity. Optimized Western blot analysis confirmed robust ICP4 protein expression beginning at 12 hours post-infection, with progressive accumulation over time. Consequently, we have replaced all ICP4-related Western blot panels in Figure 1A, Figure 1E, and Figure 2H with newly acquired, rigorously exposure-calibrated images exhibiting high signal-to-noise ratios and unambiguous temporal resolution.

      (6) Leptomycin B blocks nuclear/cytoplasmic shuttling of ICP27 that brings viral mRNAs to the cytoplasm to be translated. So, the effect of LMB is not specific to the HDACs.

      This is a critical point. As outlined in our response to Reviewer 2, we will address this issue through three complementary experimental approaches: (1) generation of an HDAC1 nuclear export signal (NES)–deficient mutant to genetically abrogate its nuclear export (Figure 5K); (2) rigorous nuclear-cytoplasmic fractionation coupled with immunoblotting to quantitatively assess HDAC1 subcellular distribution and site-specific ubiquitination. Importantly, our fractionation data confirm that HDAC1 ubiquitination is predominantly cytoplasmic (Figure 5F). Collectively, these experiments will rigorously distinguish direct HDAC1 modulation from indirect, LMB-mediated off-target effects—thereby ensuring the mechanistic specificity and interpretability of our conclusions.

      (7) The key experiment is to use the degradation-resistant form of HDAC1 to evaluate its impact on viral gene transcription.

      Based on their comments, we systematically evaluated the effects of overexpression of wild-type (WT) HDAC1 and its ubiquitination site mutant K74R (anti-degradation form) on the transcription of HSV-1 viral genes and the yield of progeny viruses. Specifically, we measured the mRNA levels of representative immediate-early genes (ICP0), early genes (ICP8), and late genes (gB), and simultaneously determined the viral titer (Figure 3L). The results showed that compared with the empty vector control, overexpression of HDAC1 WT significantly inhibited the transcription of viral genes at all stages and reduced the yield of progeny viruses; while overexpression of HDAC1 K74R exhibited a stronger inhibitory effect - its inhibition of viral gene transcription and viral replication was significantly higher than that of HDAC1 WT (Figure 3M). This result provides key functional validation for the core mechanism that "HSV-1 promotes its own replication by targeting the degradation of HDAC1/2 to relieve the epigenetic inhibition of its genome".

      (8) In the experiment where Mdm2 was depleted, the authors need to demonstrate the effect on the infection. ICP4 expression is not enough. How about growth curves? After Mdm2 depletion, ICP4 expression increases, which may contradict the authors' findings. An analysis of alpha and gamma gene expression is important.

      We sincerely apologize to the reviewers for the error in Figure 4B, which arose from an oversight during experimental execution and data validation. We have rigorously repeated the experiment and confirmed that MDM2 knockdown robustly suppresses ICP4 protein expression—directly contradicting the erroneous upregulation depicted in the original figure. To fully characterize the functional consequences of MDM2 depletion on HSV-1 replication, we performed a multi-step viral growth assay and quantified mRNA levels of canonical viral genes by quantitative RT–PCR: consistent with the corrected ICP4 data, MDM2 knockdown significantly impaired progeny virus production and concurrently reduced transcript abundance of the immediate-early gene ICP0 and the early gene ICP8 (Figure 4G, 4H, 4I and 4J). We are profoundly grateful to the reviewers for identifying this critical discrepancy and for affording us the opportunity to provide a thorough correction and mechanistic clarification. In response, we have revised Figure 4B, updated all related text and figure legends, and conducted a comprehensive cross-check of all data, figures, and textual content across the manuscript.

      (9) Why did the authors analyze a liver HSV-1 infection and not a more relevant skin infection?

      We sincerely apologize for the lack of sufficient detail in our prior response, which may have inadvertently increased the reviewers’ evaluation burden. Prior to in vivo experimentation, we conducted a systematic tissue tropism profiling of HSV-1–infected mice, quantifying viral protein expression across multiple organs by Western blot (WB) (Author response image 5). This unbiased, multi-modal assessment demonstrated that the liver exhibited both the highest viral protein abundance and the greatest viral genomic load, coupled with the most pronounced and histologically reproducible pathology—including dense inflammatory infiltration, hepatocyte vacuolar degeneration, and sharply demarcated foci of necrosis. Importantly, HSV-1 infection induced a robust and coordinated downregulation of HDAC1 and HDAC2 protein levels specifically in the liver; this effect was neither as pronounced nor as consistent in other tissues examined. In contrast, although the skin serves as the natural portal of entry for HSV-1, it displayed consistently low and highly heterogeneous viral protein expression in this systemic model—rendering it unsuitable for rigorous virological or immunological quantification. Accordingly, grounded in these empirical findings and aligned with established practices in models of disseminated herpesvirus infection [1]—where the liver is routinely prioritized as the primary site of pathogenesis and immune interrogation—we designated the liver as the principal organ for in-depth analysis of viral replication dynamics and host innate and adaptive immune responses.

      Author response image 5.

      Reviewer #1 (Recommendations for the authors):

      (1) It is an HDAC class and not cluss. All figures need correction.

      We sincerely apologize to the reviewers for this oversight and confirm that the error has been duly corrected in the revised manuscript.

      (2) The authors need to quantify cells with H2AX in the nucleus in HSV-1 and PRV infections. Some blots from the analysis of the ATM signaling are not of great quality.

      As recommended, we performed quantitative immunofluorescence analysis to assess nuclear γ-H2AX foci formation in infected cells. Consistent with activation of the DNA damage response, γ-H2AX levels increased markedly in a time- and dose-dependent manner following HSV-1 or PRV infection. In addition, the immunoblot images for ATM signaling pathway components (Fig. 2H and 2I) have been replaced with higher-resolution.

      Reviewer #2 (Public review):

      Summary:

      The authors discovered that HDAC1/2 are degraded in HSV-1 and PRV infections. They attempted to establish a new mechanism by which HDAC1/2 are translocated to the cytoplasm to be degraded in HSV-1 infection, and the degradation causes changes in histone acetylation to affect the DDR pathway.

      Strength:

      (1) Interesting findings of HDAC1/2 degradation during HSV-1 and PRV infection, and it may impact more than the virology field.

      (2) Significant work to identify the ubiquitin site in HDAC1/2 and K63 linkage.

      We sincerely thank you for your positive assessment of this work and for your thoughtful, constructive feedback. Below, we provide point-by-point responses to each of your comments.

      Weaknesses:

      (1) Insufficient evidence to support the mechanism described by the authors.

      (2) Expansion of the conclusion to alphaherpesvirus without studying the intended mechanism in PRV infection.

      Overall, there may be a correlation between HDAC1/2 level, ATM/ATR phosphorylation, and HDAC1 translocation during the HSV-1 infection. However, core evidence supporting the mechanism that a) HDAC1 export causes its degradation, b) degradation of HDAC1 causes histone acetylation changes and DRR activation has not been sufficiently demonstrated.

      In direct response to the central concern raised—that “the core experimental evidence supporting the proposed mechanistic model remains insufficient”—we have performed two complementary sets of rigorous validation experiments. Specifically, we addressed the two key mechanistic steps: (a) HDAC1 nuclear export is required for its ubiquitin–proteasome-dependent degradation; and (b) HDAC1 degradation drives histone hyperacetylation and consequent activation of the DNA damage response (DDR). Our new data robustly substantiate both causal links.

      To establish causality between HDAC1 nuclear export and degradation, we employed a dual experimental approach: (i) generation of an HDAC1 nuclear export signal (NES) loss-of-function mutant (HDAC1-ΔNES), which specifically abrogates CRM1-mediated nuclear export without affecting protein stability or catalytic activity; and (ii) high-fidelity subcellular fractionation coupled with ubiquitin pull-down and quantitative immunoblotting, enabling precise quantification of HDAC1 distribution and site-specific ubiquitination across nuclear and cytoplasmic compartments. Consistent with our model, wild-type HDAC1 underwent pronounced cytoplasmic accumulation and polyubiquitination following HSV-1 infection, demonstrating that nuclear export is both necessary and sufficient for HDAC1 degradation.

      To determine whether HDAC1 degradation functionally triggers downstream DDR activation, we generated stable HDAC1/2-knockdown HeLa cell lines using validated siRNA constructs. Loss of HDAC1/2 led to significant increases in H3 and H4 acetylation levels and robust induction of canonical DDR markers—including γ-H2AX foci formation, ATM phosphorylation, and ATR phosphorylation—phenocopying the effects observed during HSV-1 infection. These gain-of-function data confirm that HDAC1/2 depletion alone is sufficient to recapitulate the epigenetic and DDR phenotypes, thereby solidifying the mechanistic hierarchy: HDAC1 export → degradation → histone hyperacetylation → DDR activation.

      (2) Expansion of the conclusion to alphaherpesvirus without studying the intended mechanism in PRV infection.

      Our prior work demonstrates that both porcine pseudorabies virus (PRV) and herpes simplex virus type 1 (HSV-1) elicit highly concordant phenotypic outcomes—including marked depletion of HDAC1/2 proteins, elevated acetylation of histones H3 (K9/K27/K56) and H4 (K8/K12), and robust activation of the DDR pathway—as evidenced by parallel assays across both viral systems. While mechanistic dissection was primarily pursued in the HSV-1 model—due to its well-established tractability for biochemical and genetic interrogation—PRV and HSV-1 are evolutionarily closely related α-herpesviruses sharing extensive conservation in genome organization, replication machinery, and key immune-modulatory effectors. Critically, all core phenotypes described herein were independently validated in PRV-infected cells (Figure 1A/B,1E/F,2A/B), thereby providing direct experimental support for generalizing the findings to the α-herpesvirus genus. Accordingly, the title’s scope is both empirically justified and scientifically precise.

      Reviewer #2 (Recommendations for the authors):

      Major issues:

      (1) Line 26: "we uncover a novel mechanism by which alphaherpesviruses exploit the DDR pathway". A mechanism has not been clearly described. The authors showed DNA damage, phosphorylation of DDR components, and viral inhibition by berzosertib in Figure 2. The authors seem to imply that DDR activation is the result of HDAC1/2 degradation, but causation has not been established. Do nondegradable HDAC1/2 identified in Figure 3 affect the ATM/ATR pathways?

      We acknowledge that causal inference required further experimental substantiation. To address this, we first established stable HDAC1/2-knockdown HeLa cell lines using validated siRNA constructs. Loss of HDAC1/2 resulted in marked elevation of histone acetylation marks—including H3K9ac, H3K27ac, H4K8ac, and H4K12ac—and robust induction of canonical DDR markers, specifically γ-H2AX foci formation, ATM phosphorylation, and ATR phosphorylation (Figure 1H and 2J). These phenotypes closely recapitulated those induced by HSV-1 infection, supporting a gain-of-function relationship. Critically, these data demonstrate that HDAC1/2 depletion alone is sufficient to drive both histone hyperacetylation and DDR activation—thereby reinforcing the proposed mechanistic cascade: HDAC1 nuclear export → proteasomal degradation → histone hyperacetylation → DDR pathway engagement. Second, to directly test whether HDAC1 degradation is functionally required for DDR activation during infection, we compared the effects of ectopically expressing wild-type HDAC1 WT versus the degradation-resistant mutant HDAC1 K74R in HSV-1-infected cells. Consistent with our model, HDAC1 WT expression partially attenuated both DDR activation and viral replication, whereas HDAC1 K74R exerted significantly stronger suppression of both endpoints—indicating that blocking HDAC1 degradation potently restrains the virus-induced DDR response and impairs viral fitness (Figure 3K and 3M). Collectively, these complementary loss- and gain-of-function experiments provide convergent evidence for a causal role of HDAC1 degradation in orchestrating the DDR during α-herpesvirus infection.

      (2) Line 30: "Strikingly, viral infection promoted nuclear export of HDAC1/2, followed by MDM2-mediated K63-linked polyubiquitination and proteasomal degradation in the cytoplasm". In Figure 5A, strong staining of HDAC1 is present in the nucleus, while a small fraction seems to be detected in the cytoplasm at 24 h infection with the vehicle treatment. Compared to vehicle treated mock infection, the HSV-1-infected cell has more HDAC1 staining, not less. The authors need to explain the contradictory results before reaching such a conclusion.

      With regard to the apparent discrepancy in HDAC1 subcellular localization depicted in Figure 5A, we have rigorously re-evaluated the immunofluorescence data. All samples were reimaged under strictly identical acquisition parameters—including exposure time, laser power, detector gain, and objective magnification—to eliminate technical variability. Quantitative analysis was performed on ≥100 randomly selected, non-overlapping cells per condition, with nuclear and cytoplasmic fluorescence intensities measured independently and normalized to yield the nuclear-to-cytoplasmic (N/C) ratio—a robust, internally controlled metric of HDAC1 redistribution. Complementing this, biochemical validation was carried out via subcellular fractionation followed by quantitative Western blotting, which confirmed a significant decrease in nuclear HDAC1 and concomitant accumulation in the cytoplasmic fraction at 24 h post-HSV-1 infection (p < 0.001 vs. vehicle-treated mock control). These findings fully corroborate our original model (Figure 5B and 5C). The elevated nuclear signal previously observed in Figure 5A arose from localized contrast enhancement applied during image processing—an artifact unrelated to biological abundance—and has now been replaced in the revised figure with raw, unprocessed images. Full details of imaging protocols, quantification methods, and statistical analyses are provided in the updated figure legend and Methods section. We sincerely apologize for any confusion this may have caused.

      (3) In Figure 5, LMB blocks the export of HDAC1 and has negative effects on HSV-1. LMB nonspecifically blocks the nuclear export of many factors. HSV-1 sensitivity to LMB has been investigated (PMID: 23740995). Is ICP27 involved in HDAC1 translocation? To clarify the causation, can the authors separate the nuclear and cytoplasmic fractions to detect the HDAC1/2 ubiquitination status? Does the K74R mutant prevent viral replication?

      This is a critical point. As outlined in our response to Reviewer 2, we will address this issue through three complementary experimental approaches: (1) generation of an HDAC1 nuclear export signal (NES)–deficient mutant to genetically abrogate its nuclear export (Author response image 2, Figure 5K); (2) rigorous nuclear-cytoplasmic fractionation coupled with immunoblotting to quantitatively assess HDAC1 subcellular distribution and site-specific ubiquitination. Importantly, our fractionation data confirm that HDAC1 ubiquitination is predominantly cytoplasmic (Figure 5F). Collectively, these experiments will rigorously distinguish direct HDAC1 modulation from indirect, LMB-mediated off-target effects—thereby ensuring the mechanistic specificity and interpretability of our conclusions.

      Furthermore, to functionally validate the physiological relevance of HDAC1 degradation in HSV-1 replication, we systematically evaluated the impact of HDAC1 WT versus its ubiquitination-resistant K74R mutant on viral gene expression and progeny production. Using qRT–PCR, we quantified mRNA levels of representative immediate-early (ICP0), early (ICP8), and late (gB) viral genes (Figure 3L); parallel plaque assays measured infectious virus yield. Strikingly, HDAC1 K74R overexpression conferred significantly stronger suppression of viral transcription across all kinetic classes and reduced progeny titers to a greater extent than HDAC1 WT (Figure 3M). These gain-of-function data provide compelling functional evidence supporting the central model that “HSV-1 promotes its own replication by inducing proteasomal degradation of HDAC1/2 to alleviate epigenetic repression of its genome.”

      (4) Figure 1E: The elevation of H4K8 and H4K12 seems to correlate to the disappearance of HDAC1/2 in the time points given. However, changes in H3K9, H3K27, and H3K56 occur between 0 and 6 hours, when HDAC1/2 levels show minimum changes. How are the experiments repeated? Can the bands be quantitated to better reflect a correlation?

      In direct response to the concerns raised, we have rigorously refined our experimental approach and expanded the dataset to strengthen mechanistic interpretation:First, to address the temporal heterogeneity inherent in low-multiplicity infections (MOI = l)—a condition that can obscure early virus–host regulatory dynamics—we performed synchronized time-course experiments in HeLa cells at a high multiplicity of infection (MOI = 5). Under these optimized conditions, HDAC1 and HDAC2 degradation is robustly detectable by 2 hours post-infection and reaches near-complete loss by 4–6 hours. Critically, this degradation kinetics precedes the onset of viral DNA replication (initiated at ~3–4 h) and coincides with the expression of true late viral proteins (e.g., ICP4), confirming that HDAC1/2 clearance is an active, early viral strategy—not a passive consequence of late-stage infection. These revised data position HDAC1/2 depletion as a causal, upstream regulator of the immediate-early-to-late transcriptional switch (Author response image 1).

      Second, to enable rigorous quantitative correlation, we conducted densitometric analysis of all histone acetylation marks (H3K9ac, H3K27ac, H3K56ac, H4K8ac, H4K12ac) and HDAC1/2 protein levels across three independent biological replicates. Quantified values are presented as mean ± SD beneath each corresponding blot panel in Figure 1, and kinetic profiles are visualized using normalized line graphs. Strikingly, the rapid hyperacetylation of H3K9, H3K27, and H3K56 during 0–6 hours exhibits strong temporal concordance with HDAC1 depletion—supporting a direct functional link between HDAC1 loss and locus-specific histone hyperacetylation on the viral genome. see Author response image 1

      Minor points:

      (1) Materials and Methods: How are mouse live tissues harvested, maintained, and infected?

      We sincerely apologize for the omission of methodological details in the original manuscript. In response to your insightful and constructive comments, we have comprehensively revised the "Methods" section (lines 92 to 102), adding detailed steps for in vitro processing of mouse tissues, including precise time points for sample collection after infection, and strictly defined in vitro infection conditions for herpes simplex virus type 1. These additions have significantly enhanced the reproducibility of the experiments, the rigor of the analysis, and the transparency of the techniques. We are deeply grateful for your thorough, meticulous, and highly valuable review comments, which have greatly improved the scientific quality of our work.

      (2) Figure 1A: class, not cluss.

      We sincerely apologize to the reviewers for this oversight and confirm that the error has been duly corrected in the revised manuscript.

      (3) Figure 2A, 2B: need a control to indicate which cells are infected.

      Regarding Figure 2A and 2B, we wish to clarify that the primary antibody against total H2AX was a mouse monoclonal antibody, whereas the anti-γ-H2AX antibody was a rabbit polyclonal antibody. Due to species incompatibility in multiplex immunofluorescence staining, simultaneous detection of γ-H2AX and viral proteins (e.g., HSV-1 ICP0 or PRV gB) using conventional two-color labeling was not feasible in those initial experiments. To rigorously address this concern, we performed additional, carefully controlled validation experiments: we conducted parallel immunofluorescence assays using the same rabbit anti-γ-H2AX antibody together with mouse monoclonal antibodies against HSV-1 ICP0 and PRV gB—employing appropriate species-matched secondary antibodies and stringent controls. As shown in the newly included data (Author response image 6), γ-H2AX foci intensity and nuclear signal intensity increased progressively in a time- and infection-dose-dependent manner, correlating robustly with viral antigen expression. These results provide direct, orthogonal support for our original conclusion that HSV-1 and PRV infection induce DNA damage signaling in host cells.

      Author response image 6.

      (4) Figure 4D, 4E; Why so small?

      We sincerely apologize for the confusion arising from the original figure layout. Figure 4D and 4E have now been revised to ensure accurate labeling, consistent scale bars, proper orientation, and full alignment with the corresponding descriptions in the text and legend.

      (5) Does the level of endogenous MDM2 change under the experimental conditions of Figure 4?

      As demonstrated in Figure 4C—representing an endogenous co-immunoprecipitation assay—the protein level of endogenous MDM2 is markedly increased following viral infection. This result is consistently observed across biological replicates and is quantified in the accompanying immunoblot analysis (Figure 4C, lower panel), confirming robust upregulation of MDM2 expression under the experimental conditions.

      (6) Line 359: "Our results are consistent across multiple cell types, including HeLa, 3D4/21, and murine liver". This statement is misleading. Only HeLa cells were used in Figures 3-5, which attempted to explain the mechanisms.

      We sincerely thank the reviewers for their careful reading and for identifying the inaccurate statements in the manuscript. All such statements have been revised, and the entire text has been systematically reviewed to ensure consistency, accuracy, and clarity across all sections.

      Reviewer #3 (Public review):

      The authors state that infection of cells by the alphaherpesviruses HSV-1 or PRV leads to a proteosome-dependent reduction in levels of HDAC1 and HDAC2 and that this leads to chromatin hyperacetylation, a DNA damage response, and greater replication of these viruses. Previously, other authors reported no change in levels of HDAC1 and HDAC2 after HSV-1 infection of human cells, but this paper is neither cited nor commented on in this new submission. The experiments are poorly designed. For instance, most of the time points analysed are way beyond the time needed for HSV-1 replication and are therefore not biologically relevant. The infections are done with a dose of virus that does not ensure that all cells are infected synchronously, but rather infection spreads from cell to cell with multiple rounds of replication. Some essential controls are missing. Additionally, this reviewer feels that the data presented do not support the conclusions drawn. Currently, links are not established between a reduction in HDAC1/ 2 and other phenomena such as hyperacetylation of histones, a DDR, and altered virus replication. The paper does not identify which HSV or PRV protein(s) induce reduction in HDACs, nor how the HDACs mediate antiviral activity; what are the HSV-1 or PRV protein targets? Lastly, the paper is not well prepared, and it does not adequately refer to prior literature.

      We sincerely thank the reviewers for their thoughtful, constructive, and highly valuable feedback. We deeply regret the shortcomings in our original submission—including incomplete literature coverage, insufficient mechanistic clarification, and gaps in experimental rigor—and fully acknowledge that these limitations affected the clarity and impact of our work. In response, we have comprehensively revised the manuscript: (i) expanded the literature review to incorporate key prior studies; (ii) added new experimental data—including time-resolved HDAC1/2 degradation assays, MDM2 knockdown/rescue experiments, and viral mutant analyses—to robustly substantiate the proposed mechanism; and (iii) rewritten the Results and Discussion sections to present a more precise, logically coherent, and evidence-based narrative. We are profoundly grateful for the reviewers’ time, expertise, and guidance, which have significantly strengthened this study.

      Reviewer #3 (Recommendations for the authors):

      Major points

      (1) Failure to cite prior literature, incorrect in-text citations, and mistakes in the bibliography.

      (a) The authors do not refer to highly relevant prior literature. For instance, a proteomic study of HSV-1-infected human cells showed that HDAC1 and HDAC2 were stable during high MOI. (Soh et al., Cell Rep, 2020. 33, 108235). This paper must be cited, and the difference between the findings of these authors and the current submission must be addressed.

      We sincerely thank the reviewers for bringing to our attention the study by Soh et al. (Cell Reports, 2020, 33: 108235). After a thorough review, we found that the paper titled "Temporal Proteomic Analysis of Herpes Simplex Virus 1 Infection Reveals Cell-Surface Remodeling via pUL56-Mediated GOPC Degradation" does not report any changes in the protein abundance of HDAC1 or HDAC2 in its full text and supplementary data. We did not detect any significant differential expression or degradation of HDAC1/2 in the main figures, supplementary figures, quantitative proteomic data tables (Supplementary Tables S1–S3), or through a full-text keyword search of the original literature.

      Furthermore, the other study that the reviewers might have in mind (Zhang et al., Cell Reports, 2019, 27: 1425–1438, DOI: 10.1016/j.celrep.2019.04.042) is about vaccinia virus (VACV) rather than HSV-1. It reports the degradation of HDAC5 and a transient downregulation of HDAC1 in the later stage of infection (see Figure 6E), but this downregulation did not reach statistical significance and was restored at subsequent time points. The study explicitly states that its findings do not apply to the HSV-1 infection system.

      Therefore, the study by Soh et al. (2020) does not provide experimental evidence that HDAC1/2 remain stable under high MOI HSV-1 infection. We have added this clarification in the revised manuscript and will more rigorously distinguish the specificity of HDAC regulation in different herpesviruses and poxviruses in the discussion section to avoid cross-reference confusion. We are grateful to the reviewers for their insightful questions, which prompted us to conduct a systematic review of the relevant literature.

      (b) In several instances, citations given in the text are not relevant to the statement made. For example, consider line 64 reference 12, line 67 reference 14, and line 76 reference 22. The sentence preceding reference 12 is about the control of cellular gene expression by modulation of chromatin: the title of reference 12 is "Functional interaction between class II histone deacetylases and ICP0 of herpes simplex virus type 1". The sentence preceding reference 14 is about type IV HDACs (HDAC11), but the title of reference 14 is "Seneca Valley virus 3C protease cleaves HDAC4 to antagonize type I interferon signaling". HDAC4 is a type II HDAC. The sentence preceding reference 22 is HDAC1 facilitates STAT1 phosphorylation and enhances interferon-stimulated gene (ISG) activation, thereby restricting influenza A virus replication. The title of reference 22 is "Positive role of promyelocytic leukemia protein in type I interferon response and its regulation by human cytomegalovirus". I have not examined every citation, so there may be other examples of this. A thorough check of every statement and associated reference is needed.

      We sincerely apologize for the oversight in verifying and updating the accuracy of the cited references. All citations have now been thoroughly reviewed and corrected to ensure full alignment between each statement and its supporting source. We are deeply grateful to the reviewers for their careful scrutiny and constructive feedback, which greatly strengthened the rigor and reliability of our manuscript.

      (c) The reference list is a mess. There are some references in which the given name of the authors is written, and the family name is abbreviated (incorrect), whereas in others the family name is written and the given name(s) are abbreviated (correct). I suspect this reflects the fact that in Mandarin, the family name is given first and the given names thereafter, whereas in English it is the other way round. But the inconsistency is careless, and modern reference management programs, such as EndNote, should eliminate these errors.

      We apologize for the errors in the original reference list and confirm that it has now been comprehensively revised: all entries have been uniformly reformatted in EndNote using the target journal’s official citation style; author names have been standardized to surname followed by initials (e.g., “Smith J”) in strict adherence to indexing and bibliographic standards; and all instances of underlined text, typographical inconsistencies, and grammatically incomplete sentences have been systematically identified and corrected.

      Overall, the failure to cite relevant literature, the incorrect citations, and the incorrectly prepared bibliography are indicative of an unacceptable level of care in the preparation of this paper. As another example, consider lines 94-99. Why is the text underlined? And the last sentence is incomplete and does not make sense.

      The underlining in lines 94–99 was originally intended to highlight the experimental treatment protocols applied to the mice; however, we acknowledge that this formatting choice was inappropriate for a formal manuscript and could impair readability and professionalism. We have therefore removed all underlining in this section and revised the text to clearly and explicitly describe the mouse treatment procedures in complete, grammatically correct sentences.

      (2) Virus infections have been done at 1 pfu/cell. This is a strange choice because the Poisson distribution shows that not all cells will be infected, and so after a first round of replication, the virus will spread sequentially from an infected cell to an uninfected cell. The fact that the level of HSV-1 protein gB is still increasing from 36-48 h pi (Fig. 1B) indicates that infection was very likely much less than 1 pfu/cell. Ditto for PRV (Figure 1). All infections must be redone at high moi (5-10 pfu/cell) so that the contribution of HDAC1 / 2 or the influence of specific pharmacological agents on the replication of virus in a single cycle can be determined. This is important because soluble factors released from infected cells can influence subsequent replication in the other cells. The release of these factors, or their influence on the uninfected cells, might be affected by the knockdown of HDACs or the addition of drugs tested. These concerns are largely eliminated by a high MOI (5-10 pfu/cell) so that all cells are infected synchronously.

      In direct response to the concerns raised, we have rigorously refined our experimental approach and expanded the dataset to strengthen mechanistic interpretation:First, to address the temporal heterogeneity inherent in low-multiplicity infections (MOI = 1)—a condition that can obscure early virus–host regulatory dynamics—we performed synchronized time-course experiments in HeLa cells at a high multiplicity of infection (MOI = 5). Under these optimized conditions, HDAC1 and HDAC2 degradation is robustly detectable by 2 hours post-infection and reaches near-complete loss by 4–6 hours (see Author response image 1). Critically, this degradation kinetics precedes the onset of viral DNA replication (initiated at ~3–4 h) and coincides with the expression of true late viral proteins (e.g., ICP4), confirming that HDAC1/2 clearance is an active, early viral strategy—not a passive consequence of late-stage infection. These revised data position HDAC1/2 depletion as a causal, upstream regulator of the immediate-early-to-late transcriptional switch.

      (3) A one-step growth curve for HSV-1 in human cells is about 12 h. So most of the time points measured (e.g., 24, 3,6 and 48 h pi) are not biologically relevant.

      In response, we have repeated the HSV-1 one-step growth curve experiment under rigorously controlled high-MOI conditions (2 PFU/cell) and extended the kinetic sampling to include precise, biologically informative time points: 0, 1, 2, 4, 6, 8, 12, and 24 hours post-infection—thereby capturing the complete early-to-late replication cascade while excluding late-phase secondary spread (Figure 2L,4J and 5J).

      Figure 2L,4J and 5J

      (4) Figure 2I and Figure 5F show that the titer of HSV-1 obtained after infection of cultured cells reaches ~10e10 pfu/cell. This is extraordinarily high in comparison to a large body of HSV literature. Usually, the titer would be between 10e7 and 10e8 pfu/cell. The authors should explain what feature of their cell culture system enables production of infectious virus up to at least 100-fold greater than that of other investigators. The data shown in Figures 2I and 5F for "vehicle" look identical. If this is the same experiment, this should be stated, and it would be much better to show different data sets.

      First, we clarify that while the “vehicle” control data in Figure 2I and Figure 5F appear visually similar, they derive from independent biological replicates conducted on separate days under identical experimental conditions—not from the same assay (Author response image 7). Second, regarding the elevated viral titers (~10^10 PFU/cell) observed in our assays relative to typical literature values (10^7–10^8 PFU/cell), we confirm that the virus stock used is HSV-1 strain F (generously provided by Dr. Chun-Fu Zheng, University of Calgary, Canada), with a validated starting TCID<sub>50</sub> of ~10^7/mL. All infections were performed in standard growth medium (DMEM + 10% FBS), ruling out medium-related artifacts. Critically, our initial time-course design extended beyond the single-cycle window—leading to secondary spread and cumulative amplification. To address this, we rigorously re-optimized the assay: using a high MOI of 2 PFU/cell and sampling precisely at 0, 1, 2, 4, 6, 8, 12, and 24 hours post-infection, we consistently recapitulated the kinetics and magnitude of viral production(Figure 2L, 4J and 5J). We sincerely apologize for the oversight in our original experimental design and thank the reviewers for prompting this essential refinement.

      Author response image 7.

      (5) Throughout the manuscript, there is little consideration given to the timing of the reduction in HDAC1/2 seen by immunoblotting, or the other changes such as hyperacetylation and DDR activation, in relation to the replication kinetics of the virus. These changes must occur early after infection to be able to influence virus replication. If they affect virus replication, what is the mechanism? At which stage during virus infection are they acting? What are the virus targets in HSV-1 or PRV-infected cells?

      First, we acknowledge the reviewers’ important point that the temporal relationship between HDAC1/2 depletion (as detected by immunoblotting), concomitant histone hyperacetylation, DDR activation, and HSV-1 replication kinetics was not explicitly addressed in the original manuscript. As these host modifications must occur early post-infection to mechanistically influence viral replication, we have now performed time-resolved immunoblotting following high-MOI HSV-1 infection (MOI =5) and confirmed that HDAC1/2 protein levels begin to decline within 2–4 hours post-infection—well before the onset of robust viral DNA synthesis (typically detectable after 4–6 hpi) (see Author response image 1). Second, consistent with our prior work [2] and independent reports [3], the DDR can activate the cGAS–STING pathway, leading to upregulation of type I interferons and proinflammatory cytokines—established antiviral effectors. Notably, our previous study demonstrated that pharmacological or genetic inhibition of BRD4 induces DDR-dependent cGAS–STING activation and potently suppresses PRV replication [4]. In contrast, α-herpesviruses—including HSV-1 and PRV—actively subvert this antiviral axis by targeting HDAC1 and HDAC2 for MDM2-mediated K63-linked polyubiquitination and proteasomal degradation. This targeted depletion promotes histone hyperacetylation, chromatin decompaction, and a transcriptionally permissive environment that facilitates efficient viral gene expression and replication. Finally, regarding the reviewers’ question about the specific viral determinant responsible for HDAC1/2 degradation, we fully agree that identifying the viral effector(s) is critical. Our ongoing studies are focused on systematically evaluating HSV-1 structural and non-structural proteins—including the E3 ubiquitin ligase activity of ICP0, the tegument protein VP16, and the viral kinase US3—to determine which factor(s) directly mediate MDM2 recruitment and HDAC1/2 ubiquitination. These experiments are underway and will be reported in future work.

      (6) The manuscript does not demonstrate that a reduction in HDAC1 or HDAC2 is responsible for the changes in hyperacetylation. The virus induces many changes in the cell; others could also directly affect hyperacetylation. What about the activity of acetylases?

      To rigorously establish causality between HDAC1/2 depletion and histone hyperacetylation, we performed loss-of-function experiments using siRNA-mediated knockdown of HDAC1 and HDAC2 in uninfected cells. Immunoblotting analysis revealed a significant increase in acetylation levels of histone H3 (at lysines K9, K27, and K56) and histone H4 (at K8 and K12) upon HDAC1/2 depletion (Figure 1H)—mimicking the hyperacetylation pattern observed during HSV-1 infection. Importantly, no corresponding increase in histone acetyltransferase (HAT) activity was detected in HDAC1/2-knockdown cells, as assessed by in vitro HAT assays using nuclear extracts and confirmed by unchanged expression levels of major HATs (p300). These data demonstrate that HDAC1/2 loss alone is sufficient to drive global histone hyperacetylation, independent of alterations in acetyltransferase activity—and thus support a direct mechanistic link between viral-induced HDAC1/2 degradation and the observed epigenetic changes.

      (7) The study needs to make knockout cell lines, lacking HDAC1 or HDAC2 or both HDACs, and then test virus replication after high MOI in these cells. If a difference is seen, the missing HDAC should then be reintroduced into the knockout cell line under an inducible promoter, and the replication of the virus checked in these cells with or without induction of the HDAC. Furthermore, HDACs have many interacting partners; so to prove that it is the histone deacetylase activity of the HDAC that is causing a change in replication, cell lines that inducibly express each HDAC (derived from the corresponding knockout cell line) with the key residues needed for catalytic activity mutated, should be constructed, and the replication of the virus tested. As an example, HDAC4 is antiviral - but does this is independent of the histone deacetylase activity (Lu et al., PNAS 2019).

      To effectively address this comment, we successfully constructed HDAC1 single knockdown, HDAC2 single knockdown, and HDAC1/HDAC2 double gene co-knockdown cells using siRNA technology mediated by transfection reagents. We first confirmed that co-knockdown of HDAC1/2 robustly enhances histone H3/H4 acetylation and activates the DNA damage response (DDR), as evidenced by increased phosphorylation of H2AX (γH2AX), ATM, and ATR—consistent with the epigenetic and DDR phenotypes observed during HSV-1 infection (Figure 1H and 2J). To further clarify the functional significance of HDAC1 degradation and its subcellular localization during HSV-1 infection, we reconstituted HDAC1 in HDAC1 stably knockdown cells with: (i) wild-type HDAC1 (HDAC1-WT), (ii) a degradation-resistant mutant with ubiquitination site mutations (HDAC1-K74R), and (iii) a nuclear retention mutant lacking the nuclear export signal (HDAC1-ΔNES). The analysis of viral replication kinetics revealed that HDAC1 knockdown significantly increased the yield of progeny HSV-1; however, the reconstitution of HDAC1-WT completely reversed this phenotype, restoring the viral titer to the level of the unknockdown control. Crucially, both HDAC1-K74R and HDAC1-ΔNES exhibited stronger anti-HSV-1 replication activity than HDAC1-WT (Figure 5K), indicating that blocking the ubiquitin-dependent degradation of HDAC1 or forcing its retention in the nucleus can more effectively inhibit viral proliferation. In conclusion, these genetic data strongly support the model that HSV-1 actively promotes the nuclear export and K48-linked ubiquitination-mediated proteasomal degradation of HDAC1 to relieve its transcriptional repression on viral gene expression, thereby optimizing its replication environment (Figure 5K). These findings demonstrate that HSV-1 exploits HDAC1 degradation—and its subsequent cytoplasmic translocation—as a proviral strategy, and that preserving nuclear HDAC1 activity is intrinsically restrictive to viral replication. Regarding the reviewers’ critical point on enzymatic specificity, we agree that definitive attribution to HDAC catalytic activity requires catalytically dead mutants (e.g., HDAC1-H141A/Y303F) expressed in isogenic HDAC1/2 knockout backgrounds under tightly regulated inducible systems. While such comprehensive genetic rescue experiments are technically demanding and beyond the scope of the current study, they represent a key focus of our ongoing work. Specifically, we are now systematically evaluating: (i) how HSV-1–mediated HDAC1 degradation mechanistically elevates histone acetylation at viral and host genomic loci; and (ii) the basis for functional divergence among HDAC family members—including differential expression, subcellular partitioning, interacting partners, and substrate selectivity—in regulating herpesviral replication. We deeply appreciate the reviewers’ insightful guidance, which has significantly strengthened the mechanistic rigor and conceptual framework of this study.

      (8) Figure 1C & D. The RT-qPCR data do not include analysis of a housekeeping gene against which the levels of mRNA for HDAC1 /2 can be compared. This is an essential missing control. The fact that the mRNA for gB is still increasing also confirms that the virus is still spreading, so the initial infection was most unlikely to have been at 1 pfu/cell.

      We confirm that all RT-qPCR data presented in Figure 1C and 1D were normalized to the endogenous control β-actin, and we have now explicitly stated this in both the Methods section and the corresponding figure legend. Regarding the observation that gB mRNA levels continue to rise over time, we agree that this reflects ongoing viral gene expression and progeny production—consistent with productive HSV-1 infection. However, this does not contradict our use of MOI = 1. In lytic herpesvirus infections, a single infectious particle initiates a cascade of gene expression, DNA replication, and assembly of new virions; therefore, increasing gB transcript levels across the time course are expected and reflect successful progression through the viral life cycle—not incomplete or suboptimal infection. Critically, Figures 1C and 1D were designed specifically to assess whether HSV-1 infection alters HDAC1/2 transcriptional regulation. The stable, MOI-independent expression of HDAC1/2 mRNA—despite progressive gB accumulation—demonstrates that the observed reduction in HDAC1/2 protein (shown in Figure 1A–B) is not due to transcriptional repression but rather results from post-translational mechanisms, such as virus-induced proteasomal degradation. This distinction strengthens our central conclusion: HSV-1 modulates host epigenetic machinery primarily via targeted protein destabilization, not transcriptional silencing.

      (9) Figure 1G. The authors should explain how intranasal infection with HSV-1 leads to infection of the liver 5 days later. HSV-1 is neurotropic, not hepatotropic. Which types of liver cells are infected? Are they the same cells as the cells in which there are changes in acetylation? No evidence is presented to show that infection and acetylation changes are linked.

      We sincerely apologize for the lack of sufficient detail in our prior response, which may have inadvertently increased the reviewers’ evaluation burden. Prior to in vivo experimentation, we conducted a systematic tissue tropism profiling of HSV-1–infected mice, quantifying viral protein expression across multiple organs by WB (Author response image 8). This unbiased, multi-modal assessment demonstrated that the liver exhibited both the highest viral protein abundance and the greatest viral genomic load, coupled with the most pronounced and histologically reproducible pathology—including dense inflammatory infiltration, hepatocyte vacuolar degeneration, and sharply demarcated foci of necrosis. Importantly, HSV-1 infection induced a robust and coordinated downregulation of HDAC1 and HDAC2 protein levels specifically in the liver; this effect was neither as pronounced nor as consistent in other tissues examined. In contrast, although the skin serves as the natural portal of entry for HSV-1, it displayed consistently low and highly heterogeneous viral protein expression in this systemic model—rendering it unsuitable for rigorous virological or immunological quantification. Accordingly, grounded in these empirical findings and aligned with established practices in models of disseminated herpesvirus infection [1]—where the liver is routinely prioritized as the primary site of pathogenesis and immune interrogation—we designated the liver as the principal organ for in-depth analysis of viral replication dynamics and host innate and adaptive immune responses.

      Author response image 8.

      (10) Figure 1G. The 3 replicates show large variations from one sample to another at the same time point. Consider H3K9, H4K12, H3K56, for instance. A statistical analysis is needed to determine if these changes are significant, but this was not included.

      We sincerely appreciate the valuable suggestion from the reviewers. To address this, we performed quantitative densitometric analysis on all Western blot images presented in the manuscript. The band intensities were normalized to each sample as a reference, and the relative protein levels were further normalized to the value of the control (time zero or untreated) sample, which was set to 1.0. The resulting normalized quantification values are now displayed directly beneath each blot lane in Figures 1–5.

      (11) Lines 233-5 and 254-8. These summary statements are not supported by the data presented. The authors have not established that these phenomena are linked.

      To directly address this point, we successfully constructed HDAC1/HDAC2 double gene co-knockdown cells using siRNA technology mediated by transfection reagents. We found that dual knockdown of HDAC1 and HDAC2 robustly enhanced histone H3/H4 acetylation and activated the DDR, as indicated by markedly increased phosphorylation of γH2AX, ATM, and ATR—phenotypes that closely recapitulate those observed during HSV-1infection (Figures 1H and 2J). These findings collectively establish a mechanistic link whereby HSV-1–mediated degradation of HDAC1/HDAC2 promotes histone H3/H4 acetylation and consequent DDR activation.

      (12) Line 246. Comet assay. A description of what is being measured is needed here. To virologists, comet assays often look at plaque morphology.

      We acknowledge the omission in our original description and have added the requisite clarification at line 258.

      (13) Figure 2I. Are these changes due to off-target effects of the drug? Cell viability assays are needed. And the authors should include an infection by a different virus that is not affected. Finally, the addition of the drug to cells lacking the target protein should be included - does this still influence virus replication?

      We sincerely thank the reviewers for their insightful suggestions. First, we assessed cell viability across all experimentally applied concentrations of Berzosertib using the CCK-8 assay and confirmed that none compromised cellular metabolic activity (Figure. 2K and 5A). Second, to control for virus-specific effects, we employed vesicular stomatitis virus (VSV) — a pathogen whose replication is independent of DDR activation — as a mechanistically distinct comparator. Consistent with this, Berzosertib treatment exerted no significant effect on VSV-GFP replication kinetics (Author response image 9), thereby excluding off-target contributions to the observed phenotypes.

      Author response image 9.

      (14) Figure 3A. MG-132 is clearly antiviral - look at the big reduction in ICP4 - so the changes in HDAC1/2 levels +/- drug likely simply reflect different degrees of infection. The 24 and 36 h pi timepoints are too late to be biologically relevant.

      While it is well established that MG132 exhibits broad-spectrum antiviral activity—including inhibition of Classical swine fever virus (CSFV) [5], Hepatitis B virus (HBV) [6], and, to a lesser extent, Hepatitis C virus (HCV) and Hepatitis E virus (HEV) replication in vitro—its primary and most rigorously validated application in mechanistic virology and cell biology remains the pharmacological inhibition of the 26S proteasome. By specifically blocking the chymotrypsin-like activity of the proteasome core particle, MG132 induces rapid accumulation of polyubiquitinated substrates, thereby enabling researchers to: (i) determine whether a given protein is degraded via the ubiquitin–proteasome system (UPS); (ii) assess the kinetics of its turnover; and (iii) distinguish UPS-mediated degradation from alternative pathways such as autophagy–lysosomal degradation [7]. Critically, MG132 is not used here as an antiviral agent per se, but as a precise biochemical tool to interrogate the degradation mechanism of HDAC1/2 during HSV-1 infection.

      (15) Figure 4. Since HDAC1 is degraded during infection, and the ligase responsible is claimed to be MDM2, HDAC1-MDM2 interaction would lead to the degradation of HDAC1/2, so less HDAC would be seen interacting with MDM2. To address this, the interaction analysis should be done in the presence of a proteosomal inhibitor such as MG132.

      We sincerely thank the reviewer for this insightful suggestion. To clarify: during HSV-1 infection, HDAC1 undergoes proteasomal degradation, a process that is strictly dependent on virus-induced ubiquitination—specifically, K48-linked polyubiquitination—which targets HDAC1 for recognition and binding by the E3 ubiquitin ligase MDM2. This ubiquitin-dependent interaction is a prerequisite for subsequent HDAC1 degradation via the 26S proteasome. While proteasome inhibition (e.g., with MG132) stabilizes HDAC1 protein levels and is routinely applied during co-immunoprecipitation (co-IP) sample preparation to prevent artifactual degradation, it concurrently dampens the physiological ubiquitination signal required for efficient MDM2–HDAC1 engagement. Consequently, although HDAC1 abundance increases under MG132 treatment, the functional ubiquitin-mediated interaction between HDAC1 and MDM2 is attenuated—not enhanced—making MG132-treated conditions suboptimal for interrogating the physiologically relevant E3–substrate interaction. Critically, our co-IP experiments—performed in the absence of MG132 but with careful attention to rapid lysis, cold buffers, and protease inhibitors—still robustly detect HDAC1–MDM2 association despite ongoing degradation, thereby providing direct biochemical evidence that HDAC1 engages MDM2 in a ubiquitin-dependent manner during active infection.

      (16) Figure 5. Lines 325-7. HSV replication is nuclear but requires export of mRNA and nascent capsids from the nucleus. So if any of these virus processes are influenced by leptomycin B, of course, the virus titer will be reduced. The link claimed is not proven。

      To better enhance the relevance of the article and further clarify the functional significance of HDAC1 degradation and its subcellular localization during HSV-1 infection, we reintroduced: (i) wild-type HDAC1 (HDAC1-WT), (ii) a degradation-resistant mutant with ubiquitination site mutations (HDAC1-K74R), and (iii) a nuclear retention mutant lacking the nuclear export signal (NES) (HDAC1-ΔNES) into HDAC1 stably knockdown cells. The analysis of viral replication kinetics revealed that HDAC1 knockdown significantly increased the yield of progeny viruses of HSV-1; however, the reintroduction of HDAC1-WT completely reversed this phenotype, restoring the viral titer to the level of the unknockdown control. Crucially, both HDAC1-K74R and HDAC1-ΔNES exhibited stronger anti-HSV-1 replication activity than HDAC1-WT (Figure 5K), indicating that blocking the ubiquitin-dependent degradation of HDAC1 or forcing its retention in the nucleus can more effectively inhibit viral proliferation. In summary, these genetic evidences strongly support the mechanism model that HSV-1 actively promotes the nuclear export and K48-linked ubiquitination-mediated proteasomal degradation of HDAC1 to relieve its transcriptional inhibition on viral gene expression, thereby optimizing its own replication environment.

      References:

      (1) B. Stefano et al., Two Fatal Cases of Acute Liver Failure Due to HSV-1 Infection in COVID-19 Patients Following Immunomodulatory Therapies. Clin Infect Dis 73, (2020).

      (2) L. Guo-Li et al., Inhibition of PARP1 Dampens Pseudorabies Virus Infection through DNA Damage-Induced Antiviral Innate Immunity. J Virol 95, (2021).

      (3) L. Tuo, C. Zhijian J, The cGAS-cGAMP-STING pathway connects DNA damage to inflammation, senescence, and cancer. J Exp Med 215, (2018).

      (4) W. Jiang et al., BRD4 inhibition exerts anti-viral activity through DNA damage-dependent innate immune responses. PLoS Pathog 16, (2020).

      (5) C. Yuming et al., MG132 Attenuates the Replication of Classical Swine Fever Virus in vitro. Front Microbiol 11, (2020).

      (6) W. Yi, L. Xiao-Liang, Y. Yong-Sheng, T. Zheng-Hao, Z. Guo-Qing, Inhibition of hepatitis B virus production in vitro by proteasome inhibitor MG132. Hepatogastroenterology 60, (2013).

      (7) H. Tianhua et al., Lipid peroxidation triggered by the degradation of xCT contributes to gasdermin D-mediated pyroptosis in COPD. Redox Biol 77, (2024).

    1. Author response:

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

      We thank the Editor and Reviewers for their careful evaluation of our manuscript and for the constructive feedback. We agree with eLife’s overall assessment that, while profiling terminating ribosomes provides important insights into termination dynamics, additional clarification of the underlying mechanisms was needed. In response, we have focused our revision on three major conceptual points:

      (1) We have moderated our interpretation regarding the contribution of putative mRNA:rRNA interactions to sequence-specific termination pausing and clarified the limitations of the current evidence.

      (2) We have refined and clarified our model for the role of Rps26 in regulating translation termination.

      (3) We have expanded and strengthened the discussion of tissue-specific termination pausing, including its potential implications and current uncertainties.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors use high-resolution ribosome profiling (Ezra-seq) and eRF1 pulldown-based ribosome profiling (eRF1-seq) developed in their lab to identify a GA rich sequence motif located upstream of the stop codon responsible for translation termination pausing. They then perform a massively parallel assay with randomly generated sequences to further characterize this motif. Using mouse tissues, they show that termination pausing signatures can be tissue-specific. They use a series of published ribosome structures and 18S rRNA mutants, and eS26 knockdown experiments to propose that the GA rich sequence interacts with the 3′-end of the 18S rRNA.

      Strengths:

      (1) Robust ribosome profiling data and clear analyses clarify the subtle behavior of terminating ribosomes near the stop codon.

      (2) Novel termination or "false termination" sites revealed by eRF1-seq in the 5′-UTR, 3′-UTR, and CDS highlight a previously underappreciated facet of translation dynamics.

      Weakness:

      (1) Modest effects seen in ABCE1 knockdown do not seem to add up to the level of regulation. The authors state "ABCE1 regulates terminating ribosomes independent of the sequence context" on pg 9, and "ABCE1 modulates termination pausing independent of the mRNA sequence context" in the figure caption for Figure S4. Given the modest effect of the knockdown, such phrasing is most likely not supported. Further clarification of "ABCE1 plays a generic role in translation termination" is necessary.

      We acknowledge that the modest effects observed for ABCE1 are likely influenced by incomplete knockdown in HEK293 cells. Importantly, the increased ribosome density occurred at all stop codons rather than in a sequence-dependent manner, supporting the conclusion that ABCE1 functions broadly in termination rather than acting in a sequence-specific context. We have revised the manuscript to clarify this point and to temper our interpretation accordingly.

      (2) The authors propose that the GA rich sequence element upstream of the stop codon on the mRNA could potentially base pair with the 3′-end of the 18S rRNA. In the PDBs the authors reference in their paper and also in 3JAG, 3JAH, 3JAI (structures of terminating ribosomes with the stop codon in the A-site and eRF1), the mRNA exiting the ribosome and the 3′-end of the 18S rRNA are about 25-30 A apart. In addition, a segment of eS26 is wedged in between these two RNA segments. This reviewer noted this arrangement in a random sampling of 5 other PDBs of mammalian and human ribosome 80S structures. How do the authors anticipate the base pairing they have proposed to occur in light of these steric hindrances? RpsS26 is known to be released by Tsr2 in yeast during very specific stresses. Is it their expectation that termination pausing in human/mammalian cells happens during stressful conditions only?

      We agree that structural rearrangements in the absence of Rps26 remain speculative. In the revised manuscript, we have removed overly definitive language and clarified that, while Rps26 dissociation has been reported under stress conditions, its stoichiometry is unlikely to be exclusively stress-dependent. We now present this aspect as a working model supported by indirect evidence rather than a demonstrated structural mechanism.

      (3) The authors say, "It is thus likely that mRNA undergoes post-decoding scanning by 18S rRNA." (pg. 10). It is unclear what the authors mean by "scanning." Do they mean that the mRNA gets scanned in a manner similar to scanning during initiation? There is no evidence presented to support that particular conclusion.

      We appreciate the comment regarding the term “18S rRNA scanning.” We recognize that this wording may have been misleading and have revised the relevant text to more accurately describe post-decoding mRNA–rRNA interactions without implying an active scanning mechanism.

      (4) Role of termination pausing in the testis is highly speculative. The authors state: "It is thus conceivable that the wide range of ribosome density at stop codons in testis facilitates functional division of ribosome occupancy beyond the coding region." It is unclear what type of functional division they are referring to.

      We agree that the functional significance of testis-specific termination dynamics remains unclear. As multiple reviewers raised this concern, we have substantially expanded the discussion of tissue-specific termination pausing, explicitly outlining current limitations and framing this as an important direction for future investigation.

      Reviewer #2 (Public review):

      Summary:

      This paper presents results interpreted to indicate that sequences upstream of stop codons capable of base-pairing with the 3' end of 18S rRNA prolong the dwell time of 80S ribosomes at stop codons in a manner impeded by Rps26 in the 40S subunit exit channel, which leads to the proper completion of termination and ribosome recycling and prevents spurious translation of 3'UTR sequences by one or more unconventional mechanisms.

      Strengths:

      The standard 80S and selective eRF1 80S ribosome profiling data obtained using EZRA-Seq are of high quality, allowing the authors to detect an enrichment for purine-rich sequences upstream of stop codons at sites where termination is relatively slow and ribosomal complexes are paused with eRF1 still engaged in the A site.

      Weaknesses:

      There are many weaknesses in the experimental design, interpretation of results, and description of assay design and assumptions, the data obtained, and the interpretation of results, all of which detract from the scientific quality and significance of this work. In fact, a large proportion of paragraphs in the text and figure panels present some difficulty either in understanding how the experiment or data analysis was conducted or what the authors wish to conclude from the results, or that stem from an overinterpretation of findings or failure to consider other equally likely explanations.

      We appreciate the reviewer’s thoughtful evaluation and constructive suggestions. We recognize that our original description of the MPRA and reporter assay results may have lacked sufficient clarity, particularly regarding the sequence motifs associated with termination pausing. In the revised manuscript, we have carefully rewritten these sections to clarify the experimental design, data interpretation, and relationship between sequence context and termination dynamics. We believe these revisions address the reviewer’s concerns and improve the overall clarity of the manuscript.

      Reviewer #3 (Public review):

      Summary:

      This study from Jia et al carried out a variety of analyses of terminating ribosomes, including the development of eRF1-seq to map termination sites, identification of a GA-rich motif that promotes ribosome pausing, characterization of tissue-specific termination dynamics, and elucidation of the regulatory roles of 18S rRNA and RPS26. Overall, the study is thoughtfully designed, and its biological conclusions are well supported by complementary experiments. The tools and datasets generated provide valuable resources for researchers investigating the mechanisms of RNA translation.

      Strengths:

      (1) The study introduces eRF1-seq, a novel approach for mapping translation termination sites, providing a methodological advance for studying ribosome termination.

      (2) Through integrative bioinformatic analyses and complementary MPRA experiments, the authors demonstrate that GA-rich motifs promote ribosome pausing at termination sites and reveal possible regulatory roles of 18S rRNA in this process.

      (3) The study characterizes tissue-specific ribosome termination dynamics, showing that the testis exhibits stronger ribosome pausing at stop codons compared to other tissues. Follow-up experiments suggest that RPS26 may contribute to this tissue specificity.

      Weaknesses:

      The biological significance of ribosome pausing regulation at translation termination sites or of translational readthrough, for example, across different tissue types, remains unclear. Nevertheless, this question lies beyond the primary scope of the current study.

      We thank the reviewer for the positive assessment of our work. We agree that tissue-specific differences in termination pausing were insufficiently described in the original submission. In response, and in light of similar concerns from other reviewers, we have expanded the relevant sections in the main text and Discussion. We now more clearly articulate both the biological context and the current limitations, identifying tissue-specific regulation of termination as an open question and future research direction.

      Reviewer #4 (Public review):

      Summary:

      This manuscript by Qian and colleagues utilizes ribosome profiling, and reporter assays to dissect translation termination. Unfortunately, the data do not support the conclusions of the paper, controls are missing and several assays are not well validated and do not reproduce previous findings from others.

      Specific comments:

      Translation termination has been studied in several organisms including mammalian cells and yeast. In those cases what is analyzed is not the peak height at the stop codon, but rather the difference in the ribosome density before and after the stop. Thus, analyzing peak height is not validated. I understand that this is relevant only for the ribosome profiling experiments (and Ezra-seq) not the RF1 profiling. But much of the data was acquired that way.

      Moreover, the data do not reproduce previous findings and no effort is made to connect them to previous data. Previous data has shown that stop codon efficacy varies. This is not reproduced (S1C). Similarly, an effect from the +1 residue is not reproduced. The data isn't even stratified by different stop codons as previous work has shown that different surrounding residues have different effects in the context of different stop codons. Thus, none of the sequencing data is validated or trusted and does not reproduce previous findings.

      The GA-rich sequence identified by Ezra-Seq and RF1 seq is not the same and it differs from previous sequences (Wangen &Green).

      The authors claim that the majority of Rf1 peaks is at stop codons, but that is not true. It is only about 30% of the peaks. Also, not all mRNAs have peaks at the stop codons. That is at best problematic. Finally, there are mRNAs that are known to "suffer" from NMD, what do these look like in the Ezra-Seq and RF1-Seq? How about mRNAs that have programmed frameshifts? This raises questions on the validity of the eRF1 data.

      Figure 4: First, instead of M/P ratio, one should analyze M/M+P, to normalize out differences in the loading and effects from collisions, which are guaranteed to occur here, but not considered or analyzed. Second, the data are analyzed as if what matters are codons in the P and E site (and beyond, where there are definitely NOT recognized codons). While there is evidence for some interactions, one would think that an additional analysis based on sequence would be helpful. Also, the supplemental data indicates that very rarely are there reciprocal changes (as should be the case), and as seen for stop codons.

      Regarding the HiBit reporter assay: The two sequecnes clearly have effects on translation without considering stop codon context (Figure 4C), which need to be taken into account. Also, the effect from the sequences varies in the context of the assay in 4C and 4D (2-fold vs .5 fold), further questioning the assay. Moreover, the authors claim that re-initiation cannot account for Hibit levels, but that is clearly incorrect. The western in Figure 4E does not reproduce the data in 4D. While Hibit goes up (as in 4D, the putative GFP-fusion goes down. Finally, while the second reading frame should be more efficient is not explained and further argues for an artifact. Previous work (and work herein) suggests that read-through occurs equally in each reading frame. No controls for these assays are presented: e.g. stimulation by antibiotics, ABCE1 depletion, etc.

      Figure 5 has similar problems. I don't understand how the Figure in 5A is made, but when you overlay the cited structures on Rps26, the molecules are identical. I guess the authors used some fantasy to build non-existing sequences differently into the structure. There is no basis for that. In panel C and the same in Figure 7, the number of analyzed mRNAs varies. This could influence the outcome and the EXACT same set of mRNAs should be analyzed. But the main problem here is that the authors need to analyze readthrough and not peak height as detailed above. Essential controls are missing that show what fraction of the 18S rRNA is mutated. Previous work has shown that 2 nt truncated 18S rRNA is actively degraded. It is hard to believe how 15% of altered ribosomes can abolish 100% of the effect from the C-rich sequences. Important validation is missing: the authors should analyze rRNA sequences in their ribo-seq dataset to demonstrate that they have the mutated rRNAs, and that these enrich and de-enrich as predicted.

      In Figure 5-7 the authors develop a model that the sequence selectivity arises from base pairing between 18S rRNA and the mRNA. If so, then they should really stratify the data by number of WC pairs that can be formed. And only WC pairs, as GU pairs have a totally different geometry that will likely be discriminated against in this context. Also, the mutation is in a part of the helix that has no effect (Figure S3G). Thus, the data within the manuscript are inconsistent.

      Figure 6 does not agree with published data (Li et al., Nature 2022). Previous work did not show testis-depletion of Rps26 in purified ribosomes. This is the critical difference as the authors here did not purify ribosomes. Also, another Rps is an essential control, even if purified ribosomes are used. The validity of this dataset is thus questionable . Depletion from polysomes is hard to believe, as overall there is less signal in the polysomes.

      Figure 7 has similar problems as figure 5. Different pools of mRNAs are analyzed; peak height is not validated. Overexpression of Rps26 is not shown, as only Myc is shown, not Rps26. Beyond that, increased occupancy in ribosomes needs to be shown for the effect to come from ribosomes. Given how sick the cells are it is most likely that all effects are secondary and arise from whatever else is going on in the overexpression or depletion of Rps26. No controls are presented to show specific effects from Rps26.

      The authors need to check Rli1/ABCE levels in their cells. Their data have features that are indicative of low ABCE1 levels. These include a very small effect from ABCE1 depletion. These could be responsible for some of the effects they observe.

      We appreciate the reviewer’s engagement with our study and the opportunity to clarify several points.

      With respect to perceived inconsistencies with prior literature, we emphasize that our findings do not contradict established principles of translation termination. Rather, enabled by the development of eRF1-seq, we provide higher-resolution insight into termination dynamics that extends existing models. We have revised the manuscript to better contextualize our findings within prior studies and to avoid overstating novelty where continuity exists.

      Regarding the analysis of ribosome profiling data, we note that peak height and read density are widely used metrics for inferring ribosome dwell time and pausing. Nevertheless, we recognize that our original presentation may not have sufficiently explained this analytical framework. In the revised manuscript, we have clarified the rationale and interpretation of peak-based analyses, particularly in Figures 5 and 7 involving 18S rRNA mutants and Rps26 perturbation.

      Finally, we appreciate the reviewer’s comments concerning base pairing. We have carefully revised both the Results and Discussion sections to present mRNA–rRNA interactions as a supported but not definitively proven mechanistic model, clearly distinguishing experimental evidence from inference.

      We are grateful for the reviewers’ thoughtful feedback. We believe the revisions have strengthened the manuscript by clarifying interpretations, moderating mechanistic claims, and expanding discussion of tissue-specific regulation, while preserving the central contributions of the study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Some minor typos are present in the main text and methods section.

      We thank the Reviewer’s attention to detail in reviewing our manuscript. We have now thoroughly revised the main text and methods section.

      (2) S1I is missing or unlabelled.

      We are glad to have this opportunity to fix this mistake. Both S1I and S5D have now been added to the revised figures.

      (3) Could the authors clarify in the main text whether crosslinking was a step in the eRF1-seq protocol? Pg 5: "Without crosslinking, ribosomal proteins were minimally pulled down by the eRF1 antibody, confirming the transient nature of eRF1 binding."

      Yes, crosslinking is needed for eRF1-seq. We tried no-crosslinking but very little was pulled down, as stated in the sentence in Page 5.

      (4) Are termination events in the 5′-UTR or the CDS, as seen in the eRF1-seq data, also influenced by the GA-rich sequence? If the data is disaggregated into those two buckets, can you still pull out the motif?

      Yes, stop codons in 5’UTR and CDS share the same feature. However, the number of 5’UTR stop codons captured by eRF1-seq are too few to generate reliable sequence motif analysis.

      (5) Could the authors please clarify what peaks/fractions they are using as the monosome in Figure 4A? From the manner in which the red boxes are drawn on the sucrose gradient profile traces, it seems that the 40S, 60S, 80S monosome and half of the disome peak are included in the monosome fraction.

      The red box shown in Figure 4A is a bit misleading. For the massive paralleled reporter assay, we selected ribosome fractions based on the sucrose gradient tracing corresponding to monosome and polysomes, respectively. However, the fraction accuracy is not absolute as the fraction tube corresponding to monosome could contain traces of subunits as well as disomes. In practice, 40S and 60S are less concerned than disome, but the primary component is 80S ribosome.

      (6) On page 13, please cite references for Normal mode analysis.

      Normal Mode Analysis (NMA) using the Anisotropic Network Model (ANM) is a computationally efficient method for predicting large-scale, functional, and directional protein motions near equilibrium. We have followed the Reviewer’s suggestion by citing a review paper in the field of structural biology (Bahar, I. et al. 2005).

      Reviewer #2 (Recommendations for the authors):

      (1) The authors interpret the height of RPF peaks at stop codons in their Ribo-Seq data as an indication of pausing by ribosomes during termination, resulting from slow or inefficient decoding of the stop codon and peptide release; although it could equally result from slow recycling of the 60S subunit by ABCE1 following peptide release. Arguing against the latter possibility, they show later in the study that shRNA knockdown of ABCE1 has little effect on the stop codon RPF peaks; however, because the ABCE1 depletion does not elicit collisions near the stop codon in the manner observed in other studies, it appears that the ABCE1 depletion was insufficient to impair recycling substantially. The authors also don't attempt to support their interpretation by showing that depletion of eRF1 increases the stop codon peaks and produces collisions just upstream of the stop codon. They never specify with any precision whether it is stop codon recognition by eRF1, peptide hydrolysis, or recycling of the 60S subunit from the post-termination complex that is delayed, which is very unsatisfying.

      We agree with the Reviewer that the RPF density at stop codons only reflects the dwell time of terminating ribosomes. In fact, it is not possible to dissect molecular details from Ribo-seq data sets, same as interpreting other pausing events. Regarding ABCE1, we did observe the increased termination peak in cells with ABCE1 knockdown (Figure S4C). The lack of collisions is perhaps due to incomplete depletion of ABCE1. Notably, ABCE1 depletion selectively increased ribosome density at the –15 nt position, whereas the forward-shifted –12 nt peak was largely unaffected (Figure S4D). These results suggest that ABCE1 primarily facilitates late-stage termination or ribosome splitting, and its absence delays pre-termination progression. Nevertheless, the main focus of the study is to decipher the sequence context of termination pausing, which seems to be irrelevant to ABCE1. We thank the Reviewer for understanding.

      (2) They found enrichment for a GA-rich motif in the mRNAs with the largest stop codon peaks, which they attribute to its effect in slowing down some aspect of termination or ribosome recycling to increase the dwell time of the terminating ribosomes. They found no motif, however, in mRNAs containing the smallest RPF peaks at stop codon peaks, which presumably terminate more rapidly; even though they conclude later in the study from their massively parallel reporter assays (MPRA) that "C-richness" in the 9 nt 5' of stop codons enables rapid termination. The mRNAs with high pause scores at the stop codon that are enriched for the GA motif also show lower RPFs in 3'UTRs compared to the low pause score mRNAs, which they interpret to mean that long-lived termination complexes produce more efficient peptide termination and ribosome recycling, while short-lived complexes fail to be recycled and continue translation into the 3'UTR. However, because the 3'UTR reads are in all three frames, this could not occur simply by stop codon readthrough but would also require a frameshift upstream or at the stop codon itself to prevent termination and continued translation into the 3'UTR; and it could also arise from unconventional reinitiation by unrecycled post-termination complexes, which has been seen by others on inhibition of 60S recycling. The authors' interpretation is too simplistic.

      We thank the Reviewer’s summary about the sequence features controlling ribosome dwell time at stop codons uncovered by eRF1-seq. We are fully aware of the complex scenarios about 3’UTR translation, however, unconventional reinitiation cannot explain the results of the reporter assay shown in Figure 4D. Unlike frameshifting that generates prolonged products with mixed C-termini, reinitiation is associated with a new start. In Figure 4D, we observed products with C-terminal fused HiBiT, which cannot be explained by reinitiation. We thank the Reviewer for understanding.

      (3) They obtain support for the role of a GA-motif in pausing at stop codons from their selective ribosome profiling of eRF1-bound 80S ribosomes present at stop codons, finding a related GA-motif enriched at stop codons with high occupancies of eRF1-bound RPFs. However, once again, there is no C-rich motif enriched upstream of stop codons with low eRF1-bound RPF occupancies, at odds with later claims for such a motif. They ultimately propose that the GA motif pauses terminating ribosomes by base-pairing with the 3' end of 18S rRNA in the ribosome mRNA exit channel, principally utilizing two UU residues at the penultimate bases in the 18S rRNA that presumably base-pair with either A or G residues in the GA motif.

      The Reviewer might be confused by the results from Ribo-seq and massively paralleled reporter assay (MPRA). Ribo-seq data sets are limited to endogenous sequences that were shaped during evolution. In contrast, MPRA uses completely randomized sequences that offer unbiased analysis of sequence elements. The lack of C-rich motif in eRF1-seq data sets is due to the under-representation of such sequence elements in human genome. Perhaps this sequence bias is beneficial for termination fidelity by minimizing 3’UTR translation. We have further clarified this point in the revised manuscript.

      (4) They claim to have obtained independent confirmation of this last idea from their massively parallel reporter analysis (MPRA), in which sequences upstream of the stop codon of a uORF were randomized to determine those that appear to prevent translation downstream of the uORF and thereby place the mRNA in the monosome fraction versus those that allow downstream translation by any mechanism including leaky scanning of the uORF start codon, stop codon readthrough, or reinitiation (the assay doesn't distinguish between these mechanisms) and place the mRNA in the polysome fraction. In actuality, their results showed that the presence of only GGG triplets at any location in the 9 nt substantially prevents downstream translation, whereas only CCG and CCC proline codons enable downstream translation by one or more mechanisms. In view of their final model, it's very difficult to understand why GGG at any position would be able to base-pair with the U-U residues in the 18S rRNA when the stop codon is in the A site, and also why the many other triplets with two G's, two A's or an A and G base-all consistent with the GA-rich motif identified earlier-would not act similarly. Similarly, it's also puzzling that CCG and CCC can exert their effects at multiple positions upstream of the stop codon, and why the 7 other codons with two C's do not act similarly. Thus, it's unconvincing that a specific C-rich motif (which they refer to repeatedly but never identify) or even C-richness upstream of the stop codon confers elevated downstream translation. It's also important to note that the MPRA does not report on pausing at stop codons explicitly, only on whether ribosomes can be found downstream of the uORF stop codon, and assigning this outcome to the presence or absence of pausing during termination requires an ad hoc assumption that the authors have not identified as such.

      The Reviewer brought up excellent points in this comment regarding the MPRA result. Indeed, MPRA does not report ribosome pausing events as pointed out by the Reviewer. Additionally, MPRA is not designed to distinguish mechanisms underlying translational readthrough. As we mentioned above, both MPRA and Ribo-seq bear different experimental features that partly explain the similar, but not identical sequence motif uncovered by two assays. The prominent GGG motif identified by MPRA is intriguing, reminiscent of our prior study focusing on translation initiation (Jia et al. NSMB 2020). We propose that G-rich sequences upstream of stop codons form G-quadruplexes that block ribosome movement, resulting in monosome enrichment. Supporting this notion, the GGG motif was not identified by eRF1-seq, echoing the importance of using complementary experimental procedures in drawing conclusions.

      (5) They claim to confirm their conclusions from the profiling and MPRA data by measuring translation of the HiBiT sequence inserted downstream of the stop codon of the uORF in two reporters in which the upstream 9 nt contain either a single C-rich sequence or a single G-rich sequence. It's unclear how or why these two particular sequences were chosen. The G-rich sequence does not conform closely to either of the GA-motifs captured in the sequence LOGOs of Figures 1-2, and as noted above, there was no C-rich motif ever identified in these analyses. Thus, it's unclear whether the different effects of these two sequences are representative of sequences that pause or do not pause terminating ribosomes that they identified by the genome-wide analyses. In addition, given that the exact position of the GG or CC sequences relative to the stop codon doesn't seem to matter based on the MPRA data, it is actually possible to find the same number of base pairs with the 3' end of 18S rRNA for both of the two GA-rich and C-rich sequences analyzed in these reporter assays by sampling different registers of pairing between the mRNA and 18S rRNA. What is needed instead is be a systematic analysis using both the polysome:monosome assay, and the HiBiT translation assay of sequences that can pair perfectly with the 18S rRNA or contain increasing numbers of mismatches predicted to destabilize the putative helix that would be formed, and to determine whether the stability of the helices thus formed is highly correlated with the presence of the reporter mRNA in monosomes and with low HiBiT translation.

      We appreciate the Reviewer’s effort to improve our manuscript. The sequences inserted into the reporters were chosen based on several considerations. First, we chose the GA-motif rather than the G-rich sequences because the former represents physiological sequence element uncovered by eRF1-seq. As mentioned above, the G-rich sequences could form G-quadruplex artifacts. Second, the C-rich sequences were uncovered by both eRF1-seq (Figure 2D) and MPRA (Figure 4b). Third, only sequences top ranked were selected for the reporter assay. For the positional effects of inserted sequence elements, it is important to note that the proposed mRNA:rRNA interaction is not static because of the continuous mRNA movement along the channel. Instead of using sequences with perfect pairing, we have conducted experiments by placing the C-rich sequences at different positions of the insert. As shown in Figure S3H, the position relative to the stop codon does not seem to matter. In the revised manuscript, we have rephrased several sentences in the main text to avoid confusion.

      (6) They attempt to support their model by overexpressing a mutant 18S rRNA with mutations of the penultimate U-U residues to G-G, and present evidence that this decreases the stop codon RPF peaks on mRNAs rich in GA sequences upstream of the stop codons, and has the opposite effect on mRNAs that are C-rich; however, they never indicate the criteria used to assign mRNAs to these two bins, and whether it is based on the GA-rich motifs/LOGOs identified by genome-wide analysis or on the few triplets turned up by the MPRA. Clearly, it would be far better to conduct the same analysis of motif enrichment for high and low pause scores that produced the motif in Figure 1C and determine if the motif for high pausing switches from the GA-rich motif for WT 18S rRNA to a C-rich motif for the mutant, and vice versa for the low pause score mRNAs. It should also be noted that the C-rich sequence used in the reporter can form only 2 base pairs with the mutant 18S rRNA when the mRNA's C-C dinucleotide base pairs with the new G-G dinucleotide in rRNA, but it can actually form 4 base pairs with the WT 18S rRNA sequence in a different pairing register, undermining their interpretation of these data. Note also that there was no analysis done to determine what proportion of 40S subunits actually contain the mutant 18S rRNA, which is expected to be only a minor fraction under the best circumstances, and cannot simply be taken for granted, requiring a direct analysis of the sequences of the 3' ends of 18S rRNA in the cells expressing the mutant 18S.

      The Reviewer’s comment on 18S rRNA mutants are insightful. Given the low percentage of ribosomes incorporated with the rRNA mutants, it is not feasible to conduct motif analysis based on ribosome pausing at stop codons. As shown in Figure 5C, stop codon peaks are still evident after 18S mutant transfection albeit less prominent than the wild type. Notably, introducing 18S rRNA mutants into cells is not an easy task, and we have followed closely the protocol published previously (Burman and Mauro. NAR 2012) to obtain meaningful data. We believe (and hope the Reviewer will concur) that the experiment using the 18S rRNA mutants offers critical evidence in support of the mechanism.

      (7) They attempt to implicate Rps26 in the pausing by depleting or overexpressing (OE) the protein and comparing pausing at stop codons between the same two ill-defined GA-rich and C-rich bins of mRNAs mentioned above and by assaying the HiBit reporters. Again, they haven't determined whether the amount of Rps26 in mature 40S subunits is reduced or elevated compared to WT cells, and their interpretation of the OE data actually depends on the occurrence of 40S subunits lacking Rps26 in unstressed WT cells, which seems improbable and requires direct confirmation. Also, they haven't quantified the 80S peaks at the stop codons relative to the CDS reads immediately 5' of the stop codons, which varies with Rps26 OE versus the WT control, and doing so might well contradict their conclusion. Moreover, the C-rich and GA-rich HiBiT reporters behave identically rather than oppositely in response to Rps26 OE, which the authors fail to acknowledge or comment on.

      The Reviewer might be confused by the role of Rps26 partly due to the lack of clarity in our original description of the results. In yeast, Rps26 can dissociate from fully assembled 80S ribosomes under stress (Yang, et al. Sci Adv 2022). Therefore, although quantifying the Rps26 in mature 40S subunits is informative, it does not infer the composition of 80S ribosomes in cells with Rps26 depletion or overexpression. As pointed out by the Reviewer, we also noticed that, in cells with Rps26 depletion or overexpression, mRNAs with C-rich sequences showed no difference of ribosome density at stop codons. This is quite expected because C-rich sequences have minimal interaction with the 3’ end of rRNA. As a result, Rps26 depletion or overexpression is not supposed to affect ribosome dwell time at stop codons with upstream C-rich sequences. In contrast, only stop codons preceded with GA-rich sequences are influenced by Rps26 heterogeneity. In the revised manuscript, we have clarified this confusion in the main text.

      Additional specific comments

      (8) In the Summary statement: "We identify a sequence motif upstream of the stop codon that contributes to termination pausing, which was confirmed by massively paralleled": This is unjustified, as the MPRA showed only that a GGG triplet inserted anywhere in 9 nt 5'of the stop codon reduces ribosomes from traversing a stop codon either by blocking leaky scanning or reinitiation after an upstream uORF, and it is unclear why the position of this triplet does not matter nor why other GA-rich sequences capable of base pairing with the 3' end of 18S rRNA were not identified in the MPRA.

      As mentioned above, eRF1-seq and MPRA assays are complementary with advantages and disadvantages. Nevertheless, the Reviewer’s comments are well-taken and we have rephrased the Abstract of the revised manuscript.

      (9) A supplementary figure explaining EZRA-Seq would be very helpful.

      Since EZRA-seq methodology has been published (Mao, et al. NSMB 2023), we think a citation makes more sense. We thank the Reviewer for understanding.

      (10) The bottom plots/histograms of Figure 1A are very unclear. What is the y-axis of the bottom histogram, and relative to what elongating ribosomes have been analyzed?

      We apologize for the confusion in the histograms of Figure 1A. We stratified all mappable reads into footprints of initiating, elongating, and terminating ribosomes. Like many Ribo-seq results, the majority of footprints are of 29 nt length. If all three ribosome groups are of the same conformation, they are expected to have the same size distribution of the footprint length with the same bar height. It is true for initiating ribosomes (left) but not terminating ribosomes (right). We have now rephrased the figure legend in the revised manuscript.

      (11) Page 5: "A close inspection of stop codon footprints revealed an additional peak at -12 nt, which becomes more prominent when the reads are shorter (Figure 1B)." No explanation is offered for this finding. Do forward-shifted termination complexes have an empty A site owing to dissociation of eRF1? If so, they would be undetectable in eRF1-Seq data.

      Previous toe-printing assays have shown that eRF1 induces a forward movement of terminating ribosomes, shifting the leading edge from +13 nt to +15 nt (Pisarev, et al. Cell 2007). Moreover, single-molecule analyses have identified distinct pre- and post-termination phases catalyzed by eRF1 (Lawson, et al. Science 2023). Together, these observations suggest that the two 5’ end peaks correspond to pre- and post-terminating ribosome states, with the latter likely adopting a rotated conformation. We have revised the relevant paragraph in the main text.

      (12) Page 5: ". It is possible that the two distinct 5' end peaks represent pre- and post-terminating ribosomes, with the latter assuming the rotated conformation. We could not rule out the possibility that these terminating ribosomes have the stop codons at the P-site prior to disassembly." The logic here is difficult to follow.

      We have revised the relevant paragraph in the main text.

      (13) Figure 1C: provide coordinates relative to the stop codon on this motif.

      The motif analysis is position-independent and there is no coordinate on the logo plot.

      (14) Page 6: "This was not due to biased downstream sequences as the +4 nucleotide minimally affected the 3'UTR translation (Figure S1C)." The logic here is unclear.

      We have rephrased this sentence to “This effect could not be explained by downstream sequence bias, as the identity of the +4 nt had minimal impact on 3’UTR translation (Figure S1C).”

      (15) Page 6: "Like Ribo-seq, we also observed a forward shifting of post-terminating ribosomes from eRF1-seq (Figure 2C). " But by definition, they will have eRF1 in the A site, so why are they 26nt vs 29nt?

      Like many Ribo-seq results, the majority of footprints are of 29 nt length. However, ribosome populations with smaller footprint sizes are of physiological meanings, likely due to conformation changes.

      (16) Page 6 "In agreement with the Ribo-seq data sets, eRF1-seq revealed that not all the mRNAs exhibited eRF1 peaks at the annotated stop codons (Figure 2B), echoing the wide range of termination pausing." It should be determined whether eRF1 occupancy is correlated with 80S occupancy at stop codons in the standard Ribo-Seq. And if not, why?

      As shown in Figure 2B, there is a strong correlation between eRF1-seq and Ribo-seq in terms of termination pausing. However, the pausing index will be different between these two data sets due to distinct normalization. We thank the Reviewer for understanding.

      (17) Figure 2D: The plot on the left doesn't specify how far upstream the triplets can be from the stop codon. Is the LOGO significantly more similar to that shown in Fig. 1C than expected by chance alone?

      In Figure 2D, the codon frequency analysis is position independent. Similarly, the sequence logo in Figure 1C and Figure 2D is also position independent.

      (18) Page 7: ". Notably, three different stop codons show similar pausing features and sequence motifs (Figure S1G and S1I)." The figure citations here are incorrect.

      We apologize for the missing Figure S1I, which was also pointed out by Reviewer #1. We have now updated Figure S1 in the revised manuscript.

      (19) Page 7: The term "false termination" is a poor descriptor if termination doesn't occur.

      We have followed the Reviewer’s suggestion by replacing “false termination” with “failed termination”.

      (20) Page 8: "Consistent with previous reports 27, mutating the stop codon UAG abolished the reinitiation event that drives out-of-frame HiBiT translation (Figure 3E)." How is HiBit assayed? No details are given in the legend. This result doesn't confirm any of the actual eIF1 peaks upstream of stop codons, just that REI can occur at some level 5' of stop codons; and the eRF1 peak at the HiBit stop codon would be 3' of the peak at the main stop codon.

      HiBiT assay is a standard reporter like luciferase and Promega offers a detection kit, as described in the methods section. The result shown in Figure 3E is to confirm stop codon-associated reinitiation, which suggests that ribosomes migrated from the stop codon could contain eRF1 before reaching a start codon for reinitiation. We have revised this paragraph to avoid confusion.

      (21) Figure 4A: Unclear what position 0 to 6 in the bottom heat map corresponds to in the inserted 9 nt sequences. Are these codon positions vs. nucleotide positions? The legend lacks explanatory information.

      Figure 4A shows nucleotide positions (x axis) grouped by 3nt to reflect codon information (y axis). For the inserted 9nt random sequences, the last two nucleotides cannot be used because of the fixed nucleotides downstream of the insert. The same analysis has been reported in our prior study (Jia, et al. NSMB 2020).

      (22) Page 8: "For instance, codons enriched in frame 2 belong to NUA and NUG, another indication of in-frame stop codons (Figure S3B, bottom panel). " Need more or better explanation here.

      We have rephrased this sentence in the main text. “Codons enriched in alternative reading frames were also informative; for example, codons enriched in frame 2 predominantly belong to NUA and NUG, consistent with frameshifted presentations of in-frame stop codons (Figure S3B, bottom panel).”

      (23) "This is likely due to the faster turnover of these mRNAs because of 3'UTR translation". Need more or better explanation here.

      MPRA in Figure S3C showed that mRNA variants containing C-rich downstream sequence were depleted from both monosome and polysome fractions. Since 3’UTR translation is well-established to induce mRNA decay, it is possible that these sequences are under-represented due to mRNA turnover. We have added more explanations in this paragraph in the revised manuscript.

      (24) " Figure 4B: The logic and assumptions of this assay are not explained. How do ribosomes traverse the uORF, by leaky scanning or by stop codon read-through that is impeded by a ribosome stalled at the uORF stop codon? Presumably, it can't be read through as the uORF is out of frame and translation would likely terminate quickly.

      The rationale of Figure 4B is very similar to Figure 4A, except for the presence of the stop codon UAG. Under efficient termination, a monosome enrichment is expected, which could be promoted by termination pausing or structural hinderance by G-rich sequences. In contrast, stop codon readthrough or reinitiation would lead to polysome enrichment. We have thoroughly revised this paragraph in the main text.

      (25) Figure 4B results: It's unclear why M/P ratios are so low in Figure 4B vs Figure 4A as all constructs in 4B contain a stop codon and should have the high M/P ratios seen for the constructs in panel (A) with stop codons inserted. It's also unclear why the high M/P ratio should be so limited to GGG triplets vs. other triplets that conform to the GA-rich motifs identified above, and also why this triplet would not function at codon position 6. Similarly, it's unclear why only CCG and CCC and not CCU and CCA have an effect, and why only 3 of 9 codons with 2 or more C's have the effect, all suggesting that specific sequences and not just C-rich sequences are promoting read-through. Yet, no C-rich motif was discernible in the profiling experiments above.

      We appreciate the Reviewer’s careful reading of our manuscript. In profiling experiments shown in Figure 2, we did observe C-rich codons albeit with variations. Possible reasons include sequence differences between human genome and randomized sequence combinations. In addressing the Reviewer's question 23, we have thoroughly revised this paragraph in the main text.

      (26) Page 9: "These results are in line with the sequence specificity in termination pausing revealed by Ribo-seq and eRF1-seq." This is unjustified as the results in 4B are restricted to only GGG triplets rather than numerous triplets that equally conform to the AAGAAGA motif defined above.

      We apologize for the overstatement in this sentence. In addressing the Reviewer's question 23 and 24, we have thoroughly revised this paragraph in the main text.

      (27) Page 9: "This result is congruent with the MPRA assay, suggesting that the C-rich coding sequence preceding the stop codon not only reduces termination pausing, but also promotes downstream translation." This is unjustified as the single C-rich sequence chosen for the analysis in Figure 4C is not representative of the two C-rich triplets identified in Figure 4B, showing strong evidence of read-through.

      In Figure 4C, both C-rich and GA-rich sequences were chosen from shared elements between eRF1-seq and MPRA as they represent physiological sequences associated with termination pausing. The reporter assay is crucial in linking the lack of termination pausing with 3’UTR translation. We thank the Reviewer for understanding.

      (28) The analyses in Figures 4C-D suffer from a lack of the no-stop codon controls to allow the standard quantification of read-through as a percentage of continuous translation in the zero frame in the absence of a stop codon.

      The Reviewer might have missed the no-stop codon control in Figure 4C, which contains reporters with (bottom) and without (top) UAG stop codon. In Figure 4D, it is not feasible to include no-stop codon control for frameshifting reporters as the HiBiT value will be out-of-chart several orders of magnitude.

      (29) Page 10: "Therefore, the C-rich coding sequence triggers ribosome sliding at the stop codon, resulting in 3'UTR translation in all three reading frames." Sliding is an imprecise term. It is presumably a stop codon readthrough accompanied by frameshifting.

      We agree with the Reviewer’s suggestion and have replaced the word of “sliding” with “readthrough”.

      (30) Page 10: The citation to Figure S3H is incorrect, as there is no panel H.

      We are glad to have this opportunity to fix this error. We have now added panel H into the Figure S3 in the revised manuscript.

      (31) Page 10: "When the ribosome occupancy in the CDS was normalized, loss of ABCE1 led to a modest increase of stop codon peaks (Figure S4C)". Is this increase reproducible in replicates and statistically significant, as it seems very slight?

      The increased ribosome peak at stop codons in cells lacking ABCE1 is not significant, partly due to incomplete depletion of ABCE1 as shown in Figure S4A. Since ABCE1 is not the focus of this study, we did not attempt to knock out ABCE1, which could cause cellular toxicity.

      (32) Page 11: "Notably, the elevated ribosome density occurred at all stop codons, an indication of global effects." Where are the data substantiating this claim?

      We apologize for the confusion here. In the revised manuscript, we have deleted this sentence from the main text.

      (33) Page 11: "A closer look revealed that silencing ABCE1 increased the ribosome density at the -15 nt position". This claim is not convincing in the 29 nt read data, where it should be observed.

      We agree with the Reviewer that the increased ribosome density at the -15 nt position is more evident for shorter footprints. We have revised the sentence in the main text.

      (34) Page 11: "Since the 3' end of 18S rRNA contains a highly conserved U-rich sequence (GAUCAUUA), the GA- rich sequence element of mRNA could follow U:A and U:G base pairing near the exit site" (Figure 5A and S5A). By contrast, the C-rich sequence motif on mRNA would escape the 18S rRNA checkpoint, resulting in faster mRNA passthrough." This seems simplistic, as there would also be three G-A or A-G mispairings with 18S rRNA at other positions of the (G/A)AAGAAGA motif. Also unclear what the C-rich motif actually is, making it impossible to determine how many pairings it could make with the 18S rRNA sequence.

      Unlike base pairing on RNA structures, the putative rRNA:mRNA interaction is dynamic because of the continuous movement of mRNA along the ribosome channel. In fact, perfect base pairing might not be instrumental. Therefore, the difference between GA-rich and C-rich sequences is reflected in the accumulated effect. As mentioned above, the C-rich sequences are derived from both eRF1-seq and MPRA.

      (35) Figure S5B: Showing this sequence is misleading. While not described, it is presumably the DNA sequence of the plasmid, not the rRNA sequence, as there is 100% of the mutant sequence. They need to sequence the 3' end of rRNA isolated from ribosomes to confirm the presence of mutant ribosomes at appreciable levels.

      The Reviewer is correct that the sequences shown in Figure S5B are from the plasmids. To avoid such confusion, we have removed the sequences in the updated Figure S5B.

      (36) Page 12: "When mRNAs are stratified based on the sequence motif upstream of stop codons, we found that overexpression of the 18S mutant reduced the differential termination pausing between GA-rich and C-rich sequences (Figure 5C)". It is not explained what GA-rich or C-richness means precisely. Moreover, the same kind of analysis done in Figure 1C should have been conducted here to determine the LOGOs for high and low pausing for WT vs mutant 18S rRNA.

      We understand why the Reviewer repeatedly ask about the GA-rich and C-rich sequences, partly due to the lack of clarity in our original description of the analysis. The GA-rich transcripts were defined as those have the upstream 15-nt sequence with G or A nucleotides more than 65% (9 nt); whereas C-rich transcripts were defined as those with C more than 40% (6 nt). We have now updated the methods section in the revised manuscript.

      (37) Page 12: "Notably, the 3' end sequence of 18S rRNA is highly conserved (Figure S5D)". There is no Figure S5D in the figures.

      We are glad to have this opportunity to fix this error. We have now added panel D and E into Figure S5 in the revised manuscript.

      (38) Page 13: "Further supporting the sequence specificity of termination pausing, testis mRNAs with prominent stop codon peaks are enriched with GA-sequences upstream of the stop codon (Figure S6C). The same group of mRNAs, however, barely exhibit termination pausing in liver." Again, motif analysis of high and low pausing should have been done here.

      The motif analysis in mouse tissue samples is less informative because GA-rich sequences will be over-represented in testis, whereas the same group will be under-represented in liver. We had to select the shared mRNAs for comparative analysis. We thank the Reviewer for understanding.

      (39) Page 13: "While liver exhibited a similar distribution of Rps26 and RACK1 in polysome fractions, testis showed an evident depletion of Rps26 in polysome (Figure 6C). Notably, a substantial amount of Rps26 is present in the ribosome-free fraction of testis." They failed to normalize Rps26 levels in polysomes for bulk polysome levels, as indicated by the A260 tracings to determine if polysomes are depleted of Rps26, or rather, there is less polysomal Rps26 simply because polysomes are less abundant.

      We agree with the Reviewer’s notion regarding different polysome traces between testis and liver. Because the polysome volume is difficult to normalize, we used RACK1, a constitutive component of ribosome, to quantify the amount of polysome.

      (40) Page 14: "Indeed, normal mode analysis (NMA) by anisotropic network models suggests that, in the absence of Rps26, both the -3 to -9 extension of the mRNA and the 3' end of 18S rRNA can twist and approximate to each other with improved mutual parity (Figure 7B)." It is unclear what this means.

      Normal Mode Analysis (NMA) by Anisotropic Network Model (ANM) is a coarse-grained computational method used to study biomolecular dynamics by modeling proteins as a network of nodes connected by springs. Unlike the Gaussian Network Model (GNM), ANM calculates the full 3D directional preference of motion, enabling characterization of conformational changes, domain movements, and flexibility in large macromolecules. We have added a citation (Bahar, I. et al. 2005) in the revised manuscript.

      (41) Page 14: "To investigate whether Rps26 haploinsufficiency affects ribosome dynamics at stop codons, we knocked down Rps26 from HEK293 cells using shRNA (Figure S7A)". Haploinsufficiency properly refers to a heterozygous null/WT genotype, not shRNA knockdown.

      The Reviewer is correct in terms of haploinsufficiency. We have replaced the word of “haploinsufficiency” with “reduced Rps26 levels” in the revised manuscript.

      (42) Page 14: "The reciprocal change echoes the tissue-specific differences in initiation and termination (Figure 6A). " It's unclear why these peaks should be reciprocally related mechanistically, so examining changes in their ratio may not be incisive. Rps26 KD could reduce the efficiency of termination independently of pausing. And does Rps26 KD affect eRF1 occupancies in parallel with 80S occupancies?

      A prior study reported that Rps26 regulates translation initiation by recognizing Kozak sequence elements (Ferretti, et al. NSMB 2017). We therefore speculate that the role of Rps26 in termination might be correlated, although we don’t have direct evidence. We have further clarified this point in the discuss section of the revised manuscript.

      (43) Page 14: "The increased termination pausing, once again, primarily occurs at stop codons preceded by GA-rich sequences (Figure 7C)". No statistical analysis of replicates was done to see if the increase is significant, as it is quite small. They could have stratified mRNAs according to the number of base-pairs they can form with 18S rRNA rather than using this nebulous GA-richness, and see if the conclusion still holds.

      The metagene analysis shown in Figure 7C is standard for comparison of ribosome footprint distribution. We agree that the increase of termination peak at stop codons preceded by GA-rich sequences is not as striking as it should be, this is an underestimate because only a small fraction of ribosomes have sub stoichiometry of Rps26.

      (44) Page 14: "Remarkably, when mRNAs are stratified based on the sequence motif upstream of stop codons, we found that overexpression of Rps26 reduced the ribosome density (>50%) at stop codons preceded by the GA-sequence (Figure 7E)." They failed to normalize reads to the CDS occupancies to control for fewer ribosomes reaching the stop codons, especially considering that depletion of elongating 80S appeared to occur just upstream of stop codons on Rps26 OE. The same problem exists for the C-rich mRNAs. Also, their interpretation of the effects of Rps26 OE depends on there being Rps26-lacking 40S subunits in WT unstressed cells, which seems unlikely and has not been established directly. Finally, they didn't show increased Rps26 content in 40S subunits on Rps26 OE, which is also required.

      This question is the same as #7, which we have fully addressed in this letter (page 7).

      (45) Page 15: "To affirm the mechanistic connection between stop codon pausing and termination fidelity, we conducted HiBiT reporter assays that showed increased 3'UTR translation in cells with Rps26 overexpression (Figure 7F)." But both the C-rich and GA-rich reporters show increased expression on Rps26 OE. Why should that be if the C-rich sequences don't base pair with 18S rRNA in WT cells and are unaffected by Rps26 depletion? These data suggest that some other mechanism underlies the increased expression of the GA-rich reporters seen on Rps26 OE.

      The Reviewer’s concern is valid, and we agree that additional mechanisms might contribute to the increased reporter expression. The simplest explanation is that Rps26 overexpression promotes ribosome biogenesis, which globally increases mRNA translation. Supporting this notion, more polysome could be observed in cells with Rps26 overexpression (Figure S7E).

      (46) Page 15: "Without pausing at stop codons, terminating ribosomes are likely to undergo incomplete dissociation, resulting in continuous translation in 3'UTR." The language here is imprecise. Are they proposing reinitiation by unrecycled 80S ribosomes, or stop codon read-through with or without frameshifting, or both?

      This question is the same as #2, which we have fully addressed in this letter (page 3).

      (47) Page 15: "Importantly, lack of termination pausing leads to stop codon-associated random translation, giving rise to mixed C-terminal extension." Again, what does this mean? Read-through generally accompanied by frameshifting?

      Stop codon-associated random translation differs from ribosome readthrough, reinitiation, or frameshifting. We have extensively clarified this confusion in the revised manuscript.

      (48) Page 16: "For terminating ribosomes, the prolonged dwell time at stop codons offers an extended window for eRF1 loading, peptide cleavage, and ribosome recycling." This sentence is confusing because the eRF1-Seq data suggest that the pause occurs after eRF1 decodes the stop codon, with delayed peptide cleavage and recycling.

      We thank the Reviewer’s effort to improve our manuscript. We have rephrased the entire paragraph in the revised manuscript.

      Reviewer #3 (Recommendations for the authors):

      The manuscript is well-written, and the conclusions are overall well-supported by the data. I have only a few relatively minor questions and comments:

      (1) For termination sites overlapping with coding regions, the lack of 3-nt periodicity downstream of these sites could result from overlapping translation of multiple ORFs, rather than indicating that translation readthrough events can happen in multiple frames. Could the authors clarify this interpretation?

      We appreciate the Reviewer’s positive comments on our manuscript. The Reviewer is correct that overlapping ORFs would result in the lack of 3-nt periodicity. Although it is common for overlapping ORFs near the canonical start codons, ORFs overlapping the canonical stop codons are rare. Nevertheless, we have rephrased the statement in the revised manuscript.

      (2) The observation that multiple eRF1-seq peaks are located within CDS regions suggests that eRF1 may compete with A-site tRNAs during elongation. This is an interesting finding. Do the authors think this competition could lead to premature termination, or is it more likely to represent elongation pausing? Additionally, do the authors observe corresponding ribosome pausing peaks at these sites in conventional Ribo-seq data?

      The Reviewer’s comment on eRF1-seq peaks in CDS is insightful. We agree that pre-mature termination is possible because of competition. However, we do not observe corresponding ribosome pausing peaks in regular Ribo-seq, presumably due to low frequency of which events.

      (3) Regarding the regulation of ribosome pausing across tissue types, how robust are these results? For example, are the tissue-specific effects (such as stronger pausing in the testis) consistent among different mice or across age groups, given that many aspects of translational regulation are known to change with aging?

      We found that tissue-specific distribution of ribosome footprints is highly reproducible, especially liver and testis. Notably, the lack of termination peaks in liver is also reported by other independent studies (Gobert, et al. PNAS 2020), arguing that such effect is not a result of sequencing bias. We haven’t compared mice with different ages, but aging-associated translational regulation is an interesting topic awaits further investigation.

      Reviewer #4 (Recommendations for the authors):

      (1) Translation termination has been studied by ribose in several organisms, including mammalian cells and yeast. In those cases, what is analyzed is not the peak height at the stop codon, but rather the difference in the ribosome density before and after the stop. Thus, analyzing peak height is not validated. I understand that this is relevant only for the ribosome profiling experiments (and Ezra-seq), not the RF1 profiling. But the large majority of the data was acquired that way.

      With due respect, we disagree with the Reviewer’s point regarding how to study ribosome dynamics at stop codons. Comparing footprint density before and after stop codons does not infer dynamics of terminating ribosomes. By establishing eRF1-seq, we are for the first time able to analyze ribosome behaviors at stop codons, which represents a significant advancement of technological development.

      (2) Moreover, the data do not reproduce previous findings, and no attempt is made to connect them to previous data. Previous data have shown that stop codon efficacy varies. This is not reproduced (S1C). Similarly, an effect from the +1 residue is not reproduced. The data isn't stratified by different stop codons, and previous work has shown that different surrounding residues have different effects in the context of different stop codons. Thus, none of the sequencing data is validated or trusted and does not reproduce previous findings.

      We are certainly aware of previous findings regarding stop codon readthrough. We would like to emphasize that our findings do not contradict established principles of translation termination. Rather, enabled by the development of eRF1-seq, we provide new insights into termination dynamics that extend existing models.

      (3) The GA-rich sequence identified by Ezra-Seq and RF1 seq is not the same, and it differs from previous sequences (Wangen &Green).

      We don’t quite understand why the Reviewer is preoccupied with prior studies without accepting new results obtained from newly developed technology. The GA-rich sequences identified by Ezra-Seq and eRF1-seq are similar, albeit not identical. This is simply because eRF1-seq offers much higher resolution to reveal termination pausing than regular Ribo-seq.

      (4) The authors claim that the majority of Rf1 peaks are at stop codons, but that is not true. It is only about 30% of the peaks. Also, not all mRNAs have peaks at the stop codons. That is, at best, problematic. Finally, there are mRNAs that are known to "suffer" from NMD. What do these look like in the Ezra-Seq and RF1-Seq? How about mRNAs that have programmed frameshifts? The eRF1 data is invalid.

      The Reviewer is confused about the eRF1 peak density versus frequency, which has totally different meanings. Additionally, the Reviewer seems to be surprised that not all mRNAs have peaks at the stop codons. The differential ribosome dynamics at stop codons is an exciting feature previously unappreciated, rather than problematic. Regarding programmed frameshifting, we argue that such events are rare in mammalian cells.

      (5) Figure 4 has many flaws; it is hard to know where to start. First, instead of the M/P ratio, one should analyze M/M+P, to normalize out differences in the loading and effects from collisions, which are guaranteed to occur here, but not considered or analyzed. Second, the data are analyzed as if what matters are codons in the P and E site (and beyond, where there are definitely NOT recognized codons). While there is evidence for some interactions, one would think that an additional analysis based on sequence would be helpful. Also, the supplemental data indicate that very rarely are there reciprocal changes (as should be the case), as seen for stop codons. Thus, the assay is at best questionable and likely worse.

      The Reviewer appears to be unfamiliar with massively parallelled assay, which has been widely used to uncover sequence elements crucial in translational regulation. We urge the Reviewer to read our prior study using MPRA to investigate alternative translation initiation (Jia, et al. NSMB 2020). The similar approach has also been used to decipher 5’ UTR sequence elements in mRNA engineering (Sample, et al. Nat Biotech 2019).

      (6) Things do not look up for the HiBit reporter assay. The two sequences clearly have effects on translation without considering stop codon context (Figure 4C), which need to be taken into account. Also, the effect from the sequences varies in the context of the assay in 4C and 4D (2-fold vs. 5-fold), further questioning the assay. Moreover, the authors claim that re-initiation cannot account for Hibit levels, but that is clearly incorrect. The western in Figure 4E does not reproduce the data in 4D. While Hibit goes up (as in 4D, the putative GFP-fusion goes down. Finally, while the second reading frame should be more efficient, it is not explained and further argues for an artifact. Previous work (and work herein) suggests that read-through occurs equally in each reading frame.

      The Reviewer is confused about the HiBiT-based reporter assay shown in Figure 4C-4E. First, we have included important controls, i.e., same reporters without stop codons, to normalize sequence variation. Second, Figure 4C and 4D used totally different reporters and it is not appropriate to directly compare their values. Third, re-initiation events would not generate fusion proteins containing the N-terminal GFP. The Reviewer is encouraged to re-examine the results presented in Figure 4.

      (7) No controls for these assays are presented: e.g., stimulation by antibiotics, ABCE1 depletion, etc.

      We are not sure which assay the Reviewer is referring to. For reporter assays shown in Figure 4, we focused on effects of cis-sequence elements, rather than trans-acting factors. We thank the Reviewer for understanding.

      (8) Figure 5 has similar problems. I don't understand how Figure 5A is made, but when one overlays the cited structures on Rps26, the molecules are identical. I guess the authors chose to build non-existing sequences differently into the structure. There is no basis for that. In panel C, and the same in Figure 7, the number of analyzed mRNAs varies. This could influence the outcome, and the EXACT same set of mRNAs should be analyzed. But the main problem here is that the authors need to analyze readthrough and not peak height, as detailed above. Essential controls are missing that show what fraction of the 18S rRNA is mutated. Previous work has shown that 2 nt-truncated 18S rRNA is actively degraded. It is hard to believe how 15% of altered ribosomes can abolish 100% of the effect from the C-rich sequences. Important validation is missing: the authors should analyze rRNA sequences in their ribo-seq dataset to demonstrate that they have the mutated rRNAs, and that these enrich and de-enrich as predicted.

      The Reviewer’s comment on Figure 5A is baseless. As indicated in the Figure legend, Figure 5A was made from the existing cryoEM structure (PDB: 6ZMW). Regarding 18S rRNA mutants, we simply followed prior studies (Burman and Mauro. NAR 2012) and there is no evidence indicating degradation of such rRNA mutants. Given the low percentage of ribosomes incorporated with the rRNA mutants, the observed effect on termination pausing represent an underestimation, rather than an overstatement.

      (9) In Figures 5-7, the authors develop a model that the sequence selectivity arises from base pairing between 18S rRNA and the mRNA. If so, then they should really stratify the data by the number of WC pairs that can be formed. And only WC pairs, as GU pairs have a totally different geometry that will likely be discriminated against in this context. Also, the mutation is in a part of the helix that has no effect (Figure S3G). Thus, the data within the manuscript are inconsistent.

      As the Reviewer might be aware, GU pairs are commonly found in tRNA and rRNA structures. Since both WC and GU pairs contribute to mRNA:rRNA interaction, there is no point to stratify sequences based on different pairing format. Additionally, we would like to point out that the putative mRNA:rRNA interaction is not static, considering the continuous movement of mRNA along the ribosome channel.

      (10) Figure 6 does not agree with published data (Li et al., Nature 2022). Previous work did not show testis depletion of Rps26 in purified ribosomes. This is the critical difference, as the authors here did not purify ribosomes. Also, another Rps is an essential control, even if purified ribosomes are used. This dataset should not be shared. Depletion from polysomes is hard to believe, as overall, there is less signal in the polysomes.

      The Reviewer finally made a good point regarding Rps26 in testis. In our study, we did not separate different cell types such as spermatocytes and therefore we do not know which cell type dominantly influences termination pausing.

      Regarding varied Rps26 levels in different tissues, we noticed different polysome between testis and liver. Because the polysome volume is difficult to normalize, we used RACK1, a constitutive component of ribosome, to quantify the amount of polysome.

      (11) Figure 7 has similar problems to Figure 5. Different pools of mRNAs are analyzed; peak height is not validated. Overexpression of Rps26 is not shown, as only Myc is shown, not Rps26. Beyond that, increased occupancy in ribosomes needs to be shown for the effect to come from ribosomes. Given how sick the cells are, it is most likely that all effects are secondary and arise from whatever else is going on in the overexpression or depletion of Rps26. No controls are presented to show specific effects from Rps26.

      We are surprised that the Reviewer ignored the supplementary data that shows Rps26 levels. Regarding controls, it is not appropriate to use different ribosomal proteins because every ribosomal protein has its won functionality. We acknowledge that experiments by gene knockdown is not perfect, but the results are still informative especially when different mRNA pools from the same cells are compared.

      (11) The authors need to check Rli1/ABCE levels in their cells. Their data have features that are indicative of low ABCE1 levels. These include a very small effect from ABCE1 depletion. These could be responsible for some of the effects they observe.

      Once again, we are surprised that the Reviewer ignored the supplementary data that already shows ABCE1 levels in cells with or without ABCE1 knockdown (Figure S4A). Constantly addressing the Reviewer’s lack of careful reading of our manuscript is frustrateing. Nevertheless, we have thoroughly revised the entire manuscript by clarifying interpretations, moderating mechanistic claims, and expanding relevant discussion.

    1. Author response:

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

      eLife Assessment

      Plasmodesmata are channels that allow cell-cell communication in plants; based on the functional similarities between facilitated transport within plasmodesmata and into the nucleus, the authors speculate that nuclear pore complex proteins might be involved in plasmodesmata function. If supported, this would transform our understanding of cell-to-cell communication in plants. The authors localize nuclear pore complex proteins to plasmodesmata using proteomics and heterologous overexpression; however, the data are incomplete since key controls for localization, functionality, and expression level of fluorescent protein fusions are absent.

      Thank you for the constructive reviews. We have tried to address the comments as outlined below. Specifically, we added new data to the manuscript with respect to the assessment of the protein levels of three independent stable Arabidopsis lines expressing NUP62-GFP from its own promoter using mass spectrometry quantification. These experiments were carried out to evaluate whether the observed PD localization of NUP62-GFP to peripheral puncta might be an artifact caused by inadvertent overexpression and resulting mistargeting. Quantitative analysis shows no indication for significant overexpression of NUP62-GFP.

      To assess whether the localization of NUPs is distinct from localization of an ER marker, we have now included a comparison of the NUP43-mVenus localization with that of the mCherry-HDEL luminal ER marker, revealing distinct localization patterns. The peripheral puncta thus do not appear to be due to simple ER accumulation.

      To evaluate whether the CPR5-mCitrine fusion is functional, we tested whether the fusion construct was able to complement the loss-of-function cpr5-1 mutant. In two independent complementation lines (cpr5-1/CPR5:CPR5-mCitrine), the roots of 14-d old seedlings were significantly longer compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype. Although we did not detect CPR5-mCitrine fluorescence, the construct appears to be able to restore the wild type phenotype, indicating that the lines express a functional CPR5 protein.

      We have restructured the figures and provided additional information in the figure legends.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Plasmodesmata are channels that allow cell-cell communication in plants; based on the functional similarities between facilitated transport within plasmodesmata and into the nucleus, the authors speculate that nuclear pore complex proteins might be involved in plasmodesmata function. In this manuscript, they localize nuclear pore complex proteins to plasmodesmata using proteomics and heterologous overexpression. They also document a possible plasmodesmata transport defect in a mutant affecting one nuclear pore complex protein.

      Strengths:

      The main strength of this manuscript is the interesting and novel hypothesis. This work could open exciting new directions in our understanding of plasmodesmata function and cell-cell communication in plants. They also localized many NUPs (12/35 Arabidopsis NUPs).

      Weaknesses:

      The main weakness of this manuscript is that the data are incomplete. While the authors appropriately and frequently acknowledge caveats to their data, two controls are essential to interpret the results that fluorescently-tagged NUPs localize to the plasmodesmata: (1) assessment of the expression level of these fluorescently-tagged NUPs to determine whether the plasmodesmata localization might be an overexpression artefact;

      As we outlined in the manuscript, we also considered the possibility that the peripheral localization could be a consequence of overexpression, in particular in the transient expression system. To be able to control the levels, NUP genes were expressed under the control of the b-estradiol-inducible XVE promoter which allows for b-estradiol dose dependent gene expression (Bashandy et al., 2015; Schlücking et al., 2013). We assessed the dependence of localization on expression levels by studying NUP localization under conditions of reduced estradiol concentrations for induction and shortened incubation time. We validated that the fluorescence was substantially reduced relative to the standard estradiol concentration experiments, however we still detected both nuclear and peripheral localization of the NUPs (Figure 4C-F).

      We also considered that in stable transformants the expression of one extra copy of a NUP62-GFP fusion under the control of the native promoter could cause a moderate overexpression and as a consequence lead to artifactual accumulation in the periphery (Figure 3C-E).

      To evaluate the level of NUP62-GFP fusion protein relative to untransformed controls, we quantified the levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to WT.

      We now write in the revised manuscript (line 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.” We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      The use of antibodies in wild type tissue would be a potential way to avoid overexpression when trying to detect the localization of NUPs in planta. To investigate the localization of NUPs at physiological expression levels, we attempted to immunolocalize NUPs using antibodies. However, the anti-NUP antibodies available to us were not optimized for immunolocalization and we were unable to detect any fluorescence in the cells at the NPC nor the periphery.

      (2) assessment of the function of the fluorescently-tagged NUPs, either by molecular complementation of a knockout mutant phenotype or by biochemical methods to test whether the fluorescently-tagged NUP incorporates into nuclear pore complexes. Conducting these experiments for even one fluorescently-tagged NUP would substantially strengthen this manuscript.

      We agree with the reviewer that validation of the functionality of NUP fusion proteins would be valuable. Previously, C-terminally fused Arabidopsis NUPs, such as NUP93a-GFP, GP210-GFP, NUP58-GFP were reported to localize to the nuclear envelope when stably expressed in transgenic Arabidopsis lines (Tamura et al., 2010). As reported for transmembrane NUP GP210 and CPR5 fusion proteins (Gu et al., 2016; Tamura et al., 2010), C-terminally fused GP210 and CPR5 localized to the nuclear envelope but not to the nucleoplasm when expressed heterologously in N.benthamiana (see Figure 3-figure supplement 1). We found several soluble NUPs to also localize to the nucleoplasm (PpNUP98.1, PpNUP62, AtNUP62, AtHOS1) (Figure 1-figure supplement 1, Figure 3, Figure 3-figure supplement 1). Previous studies have reported that several FG NUPs (i.e. NUP98a/b or NUP62) and Y-complex NUPs (i.e. HOS1, NUP96, and NUP107) have been found to also localize in the nucleoplasm rather than specifically to the nuclear envelope when expressed as fusion proteins (Chen et al., 2023; Gallemí et al., 2016; Huang et al., 2024; Lazaro et al., 2012). Of note, for NUP98a, Gallemi and colleagues (2016) discussed the localization to the nucleoplasm as confirmation that, like vertebrate NUP98, Arabidopsis NUP98a is a dynamic NUP rather than just a key structural element of the NPC. HOS1 was reported to interact with ICE1, CO, FVE, and HDA6 in the nucleoplasm (Dong et al., 2006; Jung et al., 2012; Lazaro et al., 2012), indicating that HOS1 might dynamically shuttle between the nuclear pore and nucleoplasm, which could also explain the observed nucleoplasmic localization. In Drosophila, the FG-NUPs NUP98, NUP62, and NUP50 localized in the NPC, and also in the nucleoplasm and interacted with genes (Kalverda et al., 2010). The nucleoplasmic localization could thus have a functional relevance. Yet we cannot rule out, whether soluble NUPs mislocalize in overexpression conditions as we state multiple times in the manuscript.

      For this revision, we generated two new independent transgenic Arabidopsis lines stably expressing CPR5-mCitrine under control of its own promoter in the cpr5-1 mutant background (cpr5-1/CPR5p:CPR5-mCitrine). The roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (new Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in the 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells.

      In the new manuscript we write in lines 275-283:

      “To assess whether the CPR5-mCitrine fusion protein is functional in Arabidopsis, we tested whether CPR5p:CPR5-mCitrine (including all introns) expression in the cpr5-1 mutant background results in a rescue of the severe growth phenotype of the cpr5-1 loss-of-function mutant (Bowling et al., 1997). Indeed, roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells. The lack of fluorescence in the transgenic lines requires further investigation.“

      Reviewer #2 (Public review):

      Summary:

      The authors aim to address whether nuclear pore complex components localize and function at PD in plant cells to mediate cell-to-cell communication.

      Strengths:

      (1) Novelty and Significance:

      The core hypothesis, drawing parallels between PD and NPC transport, is highly original and addresses a critical gap in understanding plant intercellular communication. The idea that phase-separated domains formed by FG-NUPs could act as diffusion barriers at PD offers a plausible and sophisticated explanation for their complex transport properties, including size exclusion and facilitated translocation. This could fundamentally change how we view PD function.

      (2) Comprehensive Evidence:

      The study employs a rigorous and diverse set of experimental approaches, including a comprehensive bioinformatic analysis of both moss and Arabidopsis NUPs in available PD proteomic datasets, extensive imaging analysis of Nup localization in vivo, and functional transport assays using a loss-of-function nup mutant (cpr5). The transport assay is particularly important to provide functional evidence linking CPR5 to PD-mediated transport. The finding that callose levels were not significantly different in cpr5 mutants under these conditions is helpful and supports a distinct, callose-independent mechanism of transport regulation.

      (3) Objectivity:

      The authors are forthright in discussing the limitations and potential artifacts of their own data, clearly distinguishing between observations and definitive conclusions.

      Weaknesses:

      While the claims are generally justified as hypotheses or consistent observations, the authors themselves extensively detail the caveats, which are worth reiterating for clarity:

      (1) Potential Overexpression Artifacts in Localization:

      Although efforts were made to control expression levels, the authors acknowledge that transient overexpression could still lead to NUP accumulation at PD, either as a physiologically relevant accumulation under excess conditions or due to mis-targeting, or even as storage depots. The resolution of confocal microscopy also does not allow for a definitive conclusion on the nature of the location.

      We would like to add that in addition to the experiments using estradiol-controlled transient overexpression for localizing NUP fusions, we also provided localization data obtained from Arabidopsis transformants that stably express one extra copy of a NUP62-GFP fusion under the control of the native promoter. In cotyledons, NUP62-GFP localized to the nucleus and in the periphery, and in many cases to PD (Figure 3C-E). In the course of the revision we tested whether the extra copy of NUP62 could cause overexpression that might lead to artifactual accumulation in the periphery.

      To evaluate the level of NUP62-GFP fusion protein relative to untransformed controls, we quantified the levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to WT.

      We now write in the revised manuscript (lines 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.“ We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      (2) Proteomics Purity:

      The authors note that the presence of NUPs in PD fractions/proteomics cannot definitively rule out contamination, as PD cannot currently be purified to absolute homogeneity and is often contaminated with other organelles, including the nucleus.

      We would like to add that despite their low abundance in plant cells, NUPs were found to be enriched in cell wall, and PD fractions relative to total cell extracts (revised Figure 2-supplement 2). To evaluate whether NUP enrichment might be a consequence of contamination by nuclear fractions, for the revision, we evaluated the enrichment of nucleolar proteins and histones. As shown in the revised Figure 2–figure supplement 2, other nuclear proteins did not show a significant enrichment, supporting the notion that NUPs were specifically enriched in PD fractions, consistent with the localization of NUP-FP fusions. We note however, that these data do not demonstrate unambiguously that NUPs are bona fide PD components.

      (3) CPR5 Mutant Interpretation:

      While cpr5 mutants exhibited reduced macromolecular transport, the authors state that they cannot exclude that the reduced transport is due to secondary effects in the cpr5 mutants, which show rather severe phenotypic defects. This is an important distinction, as CPR5 has known roles in defense responses and hormone signaling that could indirectly influence PD integrity, independent of callose deposition. The lack of effect on small molecule transport is a good control, but the broader pleiotropic effects of cpr5 mutants remain a consideration.

      We agree with the assessment of the reviewer. The mutant is compromised in many ways and thus the effects we observe could be indirect. This is stated also in the manuscript (lines 314-317).

      (4) Conceptual Distinction between NPC and PD:

      The authors correctly point out that while similarities exist, the physical assembly of NUPs at PD must differ from that at the NPC due to the presence of the desmotubule and smaller cytoplasmic sleeve width at PD. Moreover, nucleocytoplasmic transport depends on karyopherin proteins that interact with the NPC central channel to complete the transport. Yet the role of karyopherins in this case is not clear. Therefore, the proposed "PD pore complex" may bear some NPC features, but not be identical.

      Reviewer 2 summarized the key concerns that we highlighted and discussed in the manuscript, which addressed differences in PD and NPC architecture. In particular, we noted that one of the major differences in PD is the presence of the desmotubule (in lines 370-372). We also highlighted that we did not detect all NUPs at PD (in lines 375-376). While a negative result, this observation may also be consistent with differences regarding the assembly of NUPs in or near PD vs the NPC. We fully agree with the reviewer that the proposed “PD pore complex” may be not identical to the NPC, and we also discussed that the NUPs seen at PD could represent sites of accumulation in the ER near PD.

      Reviewer #3 (Public review):

      Summary:

      This manuscript presents a step towards testing the hypothesis that plasmodesmata have homology to nuclear pores. The similarities between the two structures have long been noted as both structures allow the transport of proteins and nucleic acids, and both structures are composed of curved membranes. The manuscript has identified nuclear pore proteins (NUPs) in plasmodesmal protein fractions and uses live imaging in a non-endogenous system and functional assays of a mutant to propose that this might be a bona fide association.

      The conclusions the authors seek to draw are that: NUPs are present in plasmodesmal protein fractions; NUPs localise at plasmodesmata; NUPs might form a pore-gating complex at plasmodesmata, regulating non-specific (2xGFP) and specific (SHR) transport through plasmodesmata

      The authors then use these conclusions to propose the possibility that phase separation mediates transport through plasmodesmata. If there is phase separation at plasmodesmata or a nuclear pore-like complex, it would revolutionise the community. However, this data is insufficient to act as a cornerstone for such a discovery.

      Strengths:

      The strength of the manuscript lies in the boldness and novelty of the idea.

      Weaknesses:

      The weaknesses lie in the lack of informative controls. The authors' own assessments of their data suggest they agree with this - in their abstract alone, they point out that the transport defects they observe might be off-target effects, and suggest there is a requirement in the future to determine whether the NUPs are bona fide PD components.

      Across the proteomic and live imaging experiments, the conclusions could be stronger if they compared the NUP localisation and accumulation with ER proteins - the question of whether NUPs behave like other ER proteins is not addressed. As NUPs reside in the nuclear envelope, continuous with the ER, and the ER traverses plasmodesmata, a comparison between the NUPs and ER proteins would be extremely informative.

      We agree with the comments of the reviewer. To assess whether NUPs show localization patterns that are similar to ER proteins, we transiently co-expressed NUP43-mVenus fusions with the mCherry-HDEL luminal ER marker in N.benthamiana. Comparison of the localization patterns reveals distinct patterns of NUP43-mVenus and mCherry-HDEL (see the new Figure5, new Figure 5-figure supplement 1). NUP43-mVenus appears to be associated with the ER, however restricted to subregions that partially overlay with aniline blue-labeled pit fields (new Figure 5, new Figure 5-figure supplement 1).

      In the new version of the manuscript, we write (lines 209-214):

      “We assessed whether NUP localization is distinct from ER localization in N. benthamiana leaves that heterologously co-expressed NUP43-mVenus and the ER luminal marker mCherry-HDEL. The localization patterns of NUP43-mVenus and of the mCherry-HDEL luminal ER marker were clearly distinct (Figure 5, Figure 5-figure supplement 1). NUP43-mVenus may be associated to the ER, however restricted to subregions of the ER, which partially overlay with aniline blue-labeled pit fields (Figure 5, Figure 5-figure supplement 1).”

      Regarding the proteomic identification of NUPs in plasmodesmal fractions, the authors place significant weight on their own metric for PD enrichment, the PD score. As I understand it, this a metric derived from addition of two factors: a two component enrichment score that is the difference between intensity of peptides of a given protein in the PD fraction and cell wall fraction, added to the difference between intensity of peptides of a given protein in the PD fraction and total cell fraction, and a feature score that is a factor that describes representation of protein domains contained in said given protein in the plasmodesmal fraction relative to the representation of that domain in proteins in the whole proteome. The features chosen for analysis are not indicated, and the feature factor, as I understand it, is a score common to all proteins with a given feature. While each of the factors carries a measure of meaning and information, I do not understand how adding them is mathematically or biologically meaningful.

      The feature score was defined based on PD proteome analysis previously described (Gombos et al., 2023). Features of known PD proteins were extracted and weighted against the entire Arabidopsis proteome. Structural features included Pfam domains PF00722 (GHL), PF06955 (XET_C), PF08372 (PRT_C), PF00335 (Tetraspanin), and PF00168 (C2 domain). Subcellular localization features included plasma membrane (PM), endoplasmic reticulum (ER), extracellular space (EX), and cell wall (CW). Functional features were assigned according to MapMan categories bin 10, 15, 26, and 30. To clarify the approach, we added a more detailed explanation to the feature score in the Methods of the revised manuscript.

      We agree with the reviewer that experimental values and feature factors represent two distinct, independent parameters. The PD score aims to identify proteins that are not only experimentally enriched in the plasmodesmal fraction but also share structural features characteristic of bona fide plasmodesmata-associated proteins, reducing the number of false positive candidates driven by either parameter alone in PD proteome lists. From a mathematical standpoint, we combined the two normalized factors in the PD score by summation, treating them as contributing equally to a protein’s PD association tendency.

      Conclusion:

      The conclusions of the study are not fully supported in the absence of ER controls. Of note, the imaging is ambiguous because the proteins do not show a discrete plasmodesmal association. This is a localisation reminiscent of cortical ER association and needs to be further investigated to determine whether it is a true and specific plasmodesmal association.

      We agree with the reviewer’s comments. In the revised version of the manuscript, we have now included a comparison of the NUP43-mVenus localization with that of the mCherry-HDEL luminal ER marker, which reveals distinct localization patterns (see new Figure5, new Figure 5-figure supplement 1). NUP43-mVenus may be associated with the ER; however, NUP43 is restricted to subregions of the ER, which partially overlay with aniline blue-labeled pit fields (new Figure 5, new Figure 5-figure supplement 1). Whether NUP localization is distinct from cortical ER requires further investigation.

      The conclusions drawn from Figure 1, Figure Supplement 4 are confusing. The text describing this data says that "NUPs were enriched in cell wall and PD fractions compared to total cell extract, while the abundance of other nuclear envelope proteins was unaffected by the PD purification and showed no enrichment in PD fractions". However, the data show that there is no difference in the normalised protein intensity for the NUPs across TC, CW, and PD fractions. The only sample that shows enrichment in PDs is the PDLP/MCTPs.

      To address this point, we rephrased the text (line 146-152). Among all NUPs identified in our PD proteome, 75% were more abundant in PD fractions (Figure 2-figure supplement 2), exceeding the proportions observed in TC (60%) and CW (~50%) fractions. In contrast, other nuclear proteins such as nuclear envelope proteins, nucleolar proteins, or histones showed PD intensities that fell within or overlapped the ranges observed in TC or CW. The native abundance of NUPs was lower compared to that of proteins from other compartments, which may explain why the enrichment significance was not statistically significant (p = 0.24 for PD vs. TC). By comparison, the corresponding p-values for other nuclear compartment proteins were higher, ranging from 0.5 to 0.9.

      Regarding the possibility that there is a pore-gating complex at plasmodesmata. If NUPs are specifically located at plasmodesmata, this is a strong hypothesis. The authors approach this functionally by assaying for protein and dye movement through plasmodesmata in the cpr5 mutants. These experiments suggest that cpr5 mutants have reduced transport through plasmodesmata for both proteins, but not for a smaller dye. They infer that the latter finding suggests that the cpr5 mutant has no alterations in plasmodesmal number, but this is completely unsupported - in their introduction, the authors identify how PD structure can modify transport capacity, so there are many technical and biological phenomena that could explain these data.

      We wrote in the manuscript: “The cpr5 mutants showed no detectable defect in small molecule transport indicative of WT-like PD density and preservation of the capability to mediate small molecule transport as shown by ‘Drop-ANd-See’ trans-leaf diffusion assays.”

      Indeed, we did not study PD density by e.g. quantification of a PD-marker fluorescence. Theoretically, PD density might be changed and permeabilities adjusted by unknown mechanisms to allow for WT-like small molecule transport. Strikingly, we observed transport differences for larger cargo. As we cannot exclude potential changes in PD density, we have rewritten and deleted the conclusion on PD density and now write: “The cpr5 mutants showed no detectable defect in small molecule transport indicative of preservation of the capability to mediate small molecule transport as shown by ‘Drop-ANd-See’ trans-leaf diffusion assays”. (Lines 310-312)

      I note for their DANS assays that the diffusion of dye from ad- to abaxial surface varies in the path followed (indicated by the asymmetry of the surfaces) and is not consistent within a leaf, let alone between leaves. This presents challenges in quantification and data interpretation that have not been addressed, and so the data cannot be confidently concluded to be an indicator of a different phenomenon rather than a less sensitive measure of the same.

      Indeed, in our hands, the spread of the small molecule dye did not proceed radially and was very often asymmetrical. Therefore, we quantified the fluorescent area by identifying pixels with fluorescence above a threshold, instead of determining a diameter of the fluorescent area. We describe the analysis in the figure legend and briefly mention it in the method section.

      “Fluorescent areas on the abaxial side were identified using auto threshold and Fiji YEN-algorithm with user modifications. The same threshold setting was used for the adaxial side. The extent of dye diffusion was quantified by the ratio between the areal spread of fluorescence on the abaxial side and the areal spread of fluorescence on the adaxial side.” (Figure 7)

      Furthermore, to avoid any positional artifacts in the comparison between different plants and genotypes, we only assessed the 4th leaf and 24 hours later the 5th leaf with the same labelling position on the leaf.

      Further, as the authors themselves acknowledge, altered protein movement might also arise from an off-target developmental phenotype. Many proteins have been shown to have no association with plasmodesmata but an indirect effect on their function. This hasn't been investigated and so cannot be ruled out.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      This is a really interesting hypothesis, but the support is incomplete.

      (1) P. 5 "Although the single insertion Arabidopsis lines tested here should have FG-NUP62-GFP levels closer to native conditions than the heterologous overexpression of FG-NUP62-mVenus in N. benthamiana, it cannot be excluded that the levels in tested lines are still higher than the native levels, or that the fluorescence protein fused to the NUP affects localization." I appreciate the authors' cautious interpretation of their results, but they could exclude both of these possibilities. The first is relatively easy: test the expression level of the transgene compared to endogenous NUP expression; although transcript and protein levels are not tightly correlated, this can give some estimate of whether the transgene is overexpressed. The second would be to conduct complementation assays of a knockout mutant. I understand that this would be difficult if nup mutants are lethal, but it is pretty common practice to transform heterozygotes and isolate homozygotes expressing fluorescent protein to conduct complementation assays. Anyhow, there is a defect in the cpr5 mutants that the authors could assess in complementation assays. Alternatively, the authors could use biochemical approaches to determine whether FP-tagged NUPs are incorporated into nuclear pore complexes. These three experiments, even for only one NUP, would provide compelling evidence that the authors are localizing a functional NUP fusion protein at near-native expression levels. This is essential to support their speculation that NUPs play a biological role in PD.

      Thank you for these three important recommendations: the quantification of NUP FP expression, the complementation of a mutant phenotype with NUP FP expression, and the assessment whether NUP FPs are incorporated into the NPC.

      First, to evaluate the abundance of NUP62-GFP fusion protein relative to untransformed controls, we quantified the abundance levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to wild type.

      We now write in the revised manuscript (line 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.” We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      Second, to tested whether a NUP fusion is functional we assessed whether CPR5-mCitrine can complement the cpr5-1 mutant phenotype in complementation lines. We generated two new independent transgenic Arabidopsis lines stably expressing CPR5-mCitrine under control of its own promoter in the cpr5-1 mutant background (cpr5-1/CPR5p:CPR5-mCitrine). The roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (new Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in the 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells.

      In the new manuscript we write in lines 275-283:

      “To assess whether the CPR5-mCitrine fusion protein is functional in Arabidopsis, we tested whether CPR5p:CPR5-mCitrine (including all introns) expression in the cpr5-1 mutant background results in a rescue of the severe growth phenotype of the cpr5-1 loss-of-function mutant (Bowling et al., 1997). Indeed, roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells. The lack of fluorescence in the transgenic lines requires further investigation.”

      Third, to assess whether NUP FP fusions are also detectable specifically in nuclei, we have provided example images for potential nuclear localization of NUP62-GFP in the stable Arabidopsis line (Figure 3C), and for AtGP210-mVenus, AtNUP98b-mVenus, AtCPR5-mCitrine, and At NUP43-mCitrine in transient expression experiments in N. benthamiana (Figure 3-figure supplement 1).

      (2) The rationale for experiments was sometimes unclear. For example, why study Physcomitrium NUPs, then switch to Arabidopsis? Why use heterologous overexpression lines for SIM, rather than the stable Arabidopsis line for NUP62-GFP?

      Our initial work focused on the PD proteome in Physcomitrium patens. We had identified NUPs in PD-enriched fractions of the moss (Gombos et al., 2023). To evaluate whether this was a specific feature of the moss, or a technical artifact of PD enrichment in moss extracts, we extended the study to Arabidopsis thaliana and subsequently focused on the higher plant. The text in the manuscript reflects this flow.

      The NUP62-GFP stable transgenic Arabidopsis line was generated after the SIM experiments with CPR5-mCitrine. We plan to follow the suggestion of the reviewer to perform SIM experiments with the stable Arabidopsis NUP62p:NUP62-GFP lines.

      (3) The organization of the figures was confusing. Why present transient Physco NUP localization, and also Arabidopsis proteomics in Figure 1? Why split the results on transient localization of Arabidopsis NUPs in benth across Figures 2 & 3?

      We reorganized the Figures and created a separate proteome main figure (now Figure 2 with 2 figure supplements). We classified Arabidopsis NUPs in FG-NUPs and structural NUPs. Thus, we present the data also in two separate Figures: Figure 3 and supplements, dedicated to FG-NUPs, and Figure 4, dedicated to structural NUPs. According to the NPC, FG-NUPs play a direct role in transport facilitation, setting them apart from the structural NUPs.

      (4) Why are several NUPs localized to the interior of the nucleus and not restricted to the nuclear membrane (e.g., Figure 1 Sup 1 top two rows, Figure 2)? How does this unusual nuclear localization alter the authors' interpretation of their results?

      We observed that the transmembrane NUPs tested localized to the nuclear envelope and not to the nucleoplasm (see Figure 3-figure supplement 1 for example AtGP210 and AtCPR5). We found several soluble NUPs to also localize to the nucleoplasm (PpNUP98.1, PpNUP62, AtNUP62, AtHOS1). Previous studies had reported that several FG NUPs (i.e. NUP98a/b or NUP62) and Y-complex NUPs (i.e. HOS1, NUP96, and NUP107) also localized in the nucleoplasm rather than specifically to the nuclear envelope when expressed as fusion proteins (Chen et al., 2023; Gallemí et al., 2016; Huang et al., 2024; Lazaro et al., 2012). Of note, for NUP98a, Gallemi and colleagues (2016) discussed the localization to the nucleoplasm as confirmation that, like vertebrate NUP98, Arabidopsis NUP98a is a dynamic NUP rather than just a key structural element of the NPC. HOS1 was reported to interact with ICE1, CO, FVE, and HDA6 in the nucleoplasm (Dong et al., 2006; Jung et al., 2012; Lazaro et al., 2012), indicating that HOS1 might dynamically shuttle between the nuclear pore and nucleoplasm, which could also explain the observed nucleoplasmic localization. In Drosophila, the FG-NUPs NUP98, NUP62, and NUP50 localized in the NPC, and also in the nucleoplasm and interacted with genes (Kalverda et al., 2010). The nucleoplasmic localization could thus have a functional relevance. Yet we cannot rule out, whether soluble NUPs mislocalize in overexpression conditions as we state multiple times in the manuscript.

      (5) Figure legends are insufficiently detailed. Figure legends should be sufficiently detailed to explain the figure without consulting the main text. For example,

      (a) Figure 1A, 3C don't describe the cell type or even the organism that is being imaged. Are Physco proteins expressed in Physco? Arabidopsis? Benth? Leaves?

      We added the missing information including cell types and organism.

      (b) In Figure 1 Supplement 3, many abbreviations are not defined (HC, MC, etc).

      We now define the abbreviations in the figure legend.

      (c) In Figure 2B, the legend says "At least 15 images from 3 biological replicates were analyzed for each NUP", but there are MANY more than 15 datapoints in Figure 2B. What do the points represent?

      We obtained at least three independent replicates for each data set we show here. We analyzed 15 ROIs derived from three biological replicates of AtNUP50b. In the other cases, a larger number of experiments was performed resulting in more ROIs being analyzed.

      (d) For all microscopy images, are they single images or reconstructions (e.g., maximum projections)?

      We now specify single confocal optical section or maximum projections.

      Reviewer #2 (Recommendations for the authors):

      (1) PD index shall be measured for data in Figures 3D and 3E.

      To address this question, we have performed PD index quantification for the data in Figures 4D and 4E and added the information to the main text (lines 178-184):

      “In leaves transiently expressing NUP43-mCitrine or CPR5-FP fusions, the fluorescence intensity correlated with the estradiol concentration used, with decreased fluorescence intensity for samples where 2µM estradiol was applied versus the intensity in samples exposed to 20µM estradiol (Figure 4 D,E). Notably, the fluorescence ratio between periphery and nucleus did not differ significantly after expression induction by 2 µM compared to 20 µM β-estradiol (Figure 4F) and PD localization was not eliminated (example for localization of NUP43-mCitrine in Figure 4C; PD index(NUP43, 2µM) = 1.42, PD index(CPR5, 2µM) = 1.40).”

      (2) The expression level of the native promoter-driven Nup62-GFP shall be measured and compared with the native level using RT-qPCR. Even if this turns out to be an overexpression line, it would still be useful to support the hypothesis.

      To evaluate the level of NUP62-GFP fusion protein relative to untransformed controls, we quantified the levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to WT.

      We now write in the revised manuscript (line 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.“ We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      (3) Last sentence in the introduction: Nup136 has been considered as the plant homolog of Nup153.

      In the manuscript we wrote:

      “The majority of the FG-NUPs were conserved, with only three FG-NUPs lost in the green lineage (NUP153, POM121, NUP358).“

      As the FG-NUP136 is the plant homolog to NUP153, we now write (lines 90-92):

      “The majority of the FG-NUPs were conserved, with two FG-NUPs apparently lost in the green lineage (POM121, NUP358).“

      Reviewer #3 (Recommendations for the authors):

      (1) Generally, my interpretation of the images in this manuscript is that many of the localisations are not clean and discrete plasmodesmal associations and are rather more consistent with cortical ER association. As the ER is a component of plasmodesmata, the ER is continuous with the nuclear envelope, and the authors also predict and show ER localisation of one of their key NUPs, CPR5 in Figure 4B. This is not necessarily surprising. However, what becomes essential is that the authors need to determine whether NUPs behave any differently from other ER proteins. To that end, I think co-localisations with ER-located proteins would be helpful in interpreting these ambiguous localisations.

      To address this point, we performed additional colocalization experiments using an ER marker. In the new version of the manuscript, we now include a comparison of the NUP43-mVenus localization with that of the mCherry-HDEL luminal ER marker, which reveals distinct localization patterns (see new Figure5, new Figure 5-figure supplement 5-1). NUP43-mVenus may be associated with the ER; however, NUP43 is restricted to subregions of the ER, which partially overlay with aniline blue-labeled pit fields (new Figure 5, new Figure 5-figure supplement 1).

      (2) The super-resolution images of CPR5 show some clear structures peripheral to plasmodesmata. However, again, I would like to see what an ER protein looks like at this location, as the ER feeds into the plasmodesmata. Is this a specific structure or a general feature of the localisation of an ER protein?

      Since mCherry-HDEL (see above) did not show a similar localization or enrichment at PD, we did not perfrom SIM analyses with the marker.

      (3) The authors support their use of the PD score using validated PD proteins as the positive control and contaminants from mitochondria and other organelles as the negative control. No mention is made of where ER proteins are classified. The ER passes through plasmodesmata but might also represent a contaminating pool. As NUPs reside in the nuclear envelope, continuous with the ER, a comparison between the NUPs and ER proteins would be extremely informative.

      To evaluate a potential enrichment of ER proteins in the plasmodesmata fraction, we analyzed ER protein enrichment and added the new data as a graph in Figure 2-figure supplement 2. ER-resident proteins did not show significant enrichment in the cell wall fraction relative to total cell extract, while displaying a slight but consistent enrichment in the plasmodesmata fraction. Notably, NUPs enrichment was higher in both cell wall fraction and plasmodesmata fraction compared to transmembrane ER-resident proteins. While ER membrane co-purification cannot be entirely excluded, the enrichment of NUPs in the plasmodesmata fraction may not be due to desmotubule membrane carryover alone. The analysis was incorporated into the revised manuscript (lines 152-155).

      (4) Regarding the data analysis and use of the Kruskal-Wallis test, the Kruskal-Wallis test tests differences in the distribution of the data, not differences in the mean or median values. In many cases, it can be inferred that the median changes when the data distribution does, but this is not as confident an inference for means. There are other methods available to compare the means of such datasets.

      We used the Kruskal–Wallis test for statistical comparison of more than two nonparametric data sets. However, we did not state in the manuscript that we performed a Dunns´ test for the post hoc pairwise comparison after the Kruskal-Wallis test. In the revised manuscript, we added this information in the Methods, Results and Figure legends. For the bombardment experiment data, we now added mean bootstrapping, as used previously in this context (Johnston and Faulkner, 2021). Mean bootstrap analysis for the bombardment data set was performed with n=5000 resamples and we provide the p values and confidence intervals in the figure legend (Figure 7 B):

      “Mean fluorescent cell counts: n<sub>(WT)</sub> = 2.67, n<sub>(cpr5-T3)</sub> = 1.59, n<sub>(cpr5-1)</sub> = 0.68; median fluorescence cell counts: n<sub>(WT)</sub> = 2, n<sub>(cpr5-1)</sub> = 0, n<sub>(cpr5-T3)</sub> = 1. Based on Bonferroni-corrected Dunn´s test for pairwise comparison after Kruskal-Wallis test: a indicates significant difference to WT with p(<sub>cpr5-1</sub>) < 10<sup>-15</sup>; b indicates significant difference to WT with p<sub>(cpr5-T3)</sub> = 0.0004; c indicates p(cpr5-1 vs. cpr5-T3) = 0.0002. Mean bootstrap analysis according to (Johnston and Faulkner, 2021) with 95% confidence interval (CI) and bootstrap resampling of B = 5000: CI<sub>WT vs. cpr5-1</sub> [1 x 10<sup>-5</sup> , 0.001], p<sub>(cpr5-1)</sub> = 0002 ; CI<sub>WT vs. cpr5-T3</sub> [1 x 10<sup>-5</sup> , 0.001], p<sub>(cpr5-T3)</sub> = 0.0002; CI<sub>cpr5-1 vs. cpr5-T3</sub>, p<sub>(cpr5-1 vs. cpr5-T3)</sub> = 0.0002 [1 x 10<sup>-5</sup> , 0.001].“

      (5) The comments that estradiol induction prevents over-expression, or allows for controlled expression, are not experimentally supported or widely established outside this manuscript. I suggest they tone this claim down.

      As outlined above the reduction in estradiol concentration lead to reduced fluorescence intensity for the NUP-FP fusions as one would expect; here notably with a reduction at both nuclei and periphery (Figure 4C-F). The system has been used previously in the Simon lab, from whom we obtained the constructs. There is substantial literature regarding the use of the b-estradiol-inducible XVE promoter system, specifically for b-estradiol dose-dependent gene expression in N. benthamiana leaves (Bashandy et al., 2015; Bleckmann et al., 2010; Borghi, 2010; Schlücking et al., 2013). We assessed the dependence of localization on expression levels by studying NUP localization with a lower estradiol concentration for induction and shortened incubation time. Interestingly, despite the apparent lower expression, we still find NUPs at PD.

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    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      Some of the authors proposed in a PNAS paper in 2016 the occurrence of the Entner-Doudoroff (ED) pathway in cyanobacteria and plants, on the basis of several lines of biochemical and genetic evidence. However, more recent results indicated that one of the two specific enzymes of the ED pathway (EDD) is missing in Synechocystis PCC 6803. The authors carried out additional experiments, which demonstrated that EDD is missing, and one of the enzymes (ED aldolase) is a promiscuous enzyme which seems to be involved in proline metabolism and is not actually participating in the ED pathway as initially believed. The results described in this paper are strong evidence that this new interpretation is appropriate, and therefore, it corrects the previous proposal, providing an honest description of the reasons why the authors had reached the wrong conclusion about the existence of the ED pathway in cyanobacteria and plants.

      We thank Reviewer 1 for the summary and comments. We found that EDA is a promiscuous aldolase that, in addition to the cleavage of KDPG to GAP and pyruvate (a reaction of the ED pathway) catalyzes other reactions in vitro. Based on the in vitro results obtained, potential in vivo functions of EDA are proposed, including its involvement in proline metabolism. However, these assumptions require further experimental testing. We do not yet have definitive findings regarding the function of the promiscuous aldolase EDA in Synechocystis in vivo, but respective studies are currently underway.

      Strengths:

      Thorough reanalysis of the experimental results obtained in previous studies, which led to the publication of the PNAS paper in 2016.

      New experimental evidence to confirm that enzymes previously considered as participating in the ED actually are not catalyzing the ED biochemical reactions, but are involved in other metabolic pathways. Also, the authors completely discarded the occurrence of the GDH/GK shunt in Synechocystis PCC 6803. Generally speaking, the manuscript is very clearly written, with a precise description of the previous findings, the mistakes which took place in the 2016 paper, and the strategies they have used to address those issues, in order to reach a thoroughly revised vision of the glucose metabolic pathways in Synechocystis PCC 6803. In this regard, the drawings shown in Figures 1 and 7 are very helpful for the reader to follow the story and understand the possible metabolic transformations depending on the working hypothesis.

      Also, I commend the authors for openly describing previous mistakes. In this paper, they reassess past observations in light of more recent findings and to integrate the information in this manuscript. The scientific conclusions are solid and very interesting, and besides, they use the opportunity to offer valuable advice to researchers. This is especially focused on the importance of careful biochemical characterization of enzymes, which should always be carried out when studying proteins which have been identified as a specific enzyme on the basis of sequence homology. In a similar way, they found that an insertional mutant was the cause of the absence of specific metabolites, which had been attributed to particularities of a metabolic pathway in that mutant, when it was actually due to a nucleotide insertion; this could have been easily prevented by confirming the correct generation of the mutant by DNA sequencing.

      We agree that biochemical characterization of enzymes as well as DNA sequencing to check deletion mutants, are important and valuable tools. As outlined in the manuscript and additionally in more detail in a recently submitted article, which is available at bioRxiv (Theune et al. 2026, doi: https://doi.org/10.64898/2026.04.08.717167) and is currently under review at PLOS One, we suggest that genome sequencing of deletion mutants in combination with complemented strains as controls are required to minimize the risk of misinterpretation based on secondary mutations (1). During the early stages of our research on the ED pathway, and later as well when we were already trying to resolve the conflicting results that had accumulated concerning the ED pathway, genome sequencing for Synechocystis mutants was not affordable as a routine procedure (2-4). Therefore, we could not have easily prevented this misconception based on this technique at that time. However, we strongly encourage genome sequencing of deletion mutants in combination with complemented strains as routine procedures these days (1).

      Weaknesses:

      The authors propose that EDA might be involved in the PEP-pyruvate-OAA node, or in the proline metabolism, but this requires further experimental work for clarification; what their results indicate clearly is that this enzyme is not actually catalyzing the transformation of KDPG to GAP, which is the second specific enzyme of the ED pathway. But the real physiological function in this cyanobacterium is still unconfirmed.

      As stated above and in the manuscript, we agree that the in vivo role of EDA requires further experimental work which is in progress. However, our results demonstrate that EDA splits KDPG into GAP and pyruvate in vitro, but we assume that this reaction does not play a role in vivo due to the absence of its substrate.

      Another aspect which could be improved is that the recombinant expression of some genes was carried out in E. coli; even if this is a useful and valid research strategy, in studies like this (where there is a strong focus on the physiological function of enzymes in the original organism, Synechocystis PCC 6803), I think it would have been more appropriate to express the 6803 genes in another cyanobacterium easily amenable for genetic transformation and gene expression, which would produce the protein in a physiological environment more similar to another cyanobacterium (compared to E. coli, which is an heterotrophic bacterium). I am not sure this would change any of the obtained results, but it certainly would confer additional robustness to the enzymatic results.

      Synechocystis is easily amendable to genetic manipulation, and we agree that expression and purification of all enzymes from this host would have been ideal. However, the first characterization of Synechocystis EDA was performed with proteins that were purified from Synechocystis and showed activity on KDPG at comparable rates as proteins that were purified from E. coli in this study (2). Moreover, most biochemical characterizations of EDAs from archaea, bacteria and plants were performed after recombinant expression in E. coli and yielded highly active enzyme as in the case of Synechocystis is this study (5-7). Therefore, we currently have no reason to worry that the expression in E. coli might affect the enzymatic activity of EDA. The main reason for utilizing E. coli as an expression strain in this study was to gain higher yields of protein for in-depth analyses.

      Bibliography:

      I think the list of papers used in this manuscript is complete and up to date. However, I do miss recent papers which addressed one aspect that was proposed in the original 2016 PNAS paper: the authors wrote, "We therefore suggest that Prochlorococcus might oxidize glucose via the ED pathway under mixotrophic conditions, as shown for Synechocystis." Recent studies checked this hypothesis and have shown that the ED pathway seems to be also missing in Prochlorococcus and marine Synechococcus, and I think this manuscript is a good place to cite them, since these results are consistent with the findings of this paper.

      We will include a references from Moreno-Cabezuelo et a. 2023 (DOI: 10.1128/spectrum.03275-22) in which the proteomes of three marine Prochlorococcus and three marine Synechococcus strains were investigated upon exposure to glucose (8). Protein levels of EDA were either downregulated or not affected while proteins involved in OPP pathway and CBB cycle were upregulated. The authors of this study conclude that this indicates that the latter processes rather than the ED pathway are involved in photomixotrophy in these strains. However, flux analyses are still missing. 

      Reviewer #2 (Public review):

      Summary:

      The study presents novel results on the presence of the Entner-Doudoroff pathway in Synechocystis sp. PCC 6803. In contrast to an earlier study, compelling evidence is given that this strain lacks both an ED pathway and a glucose dehydrogenase/glucokinase bypass but contains a promiscuous aldolase, which also decarboxylates oxaloacetate and cleaves 2-keto-4-hydroxyglutarate (as it occurs in proline degradation). The study concludes with successfully reconciling data from different studies and with lessons learned from the previous misconception.

      Strengths:

      Solid biochemical data are presented to reconcile contradicting data of earlier studies and to serve as a basis for disclosing possible functions of a promiscuous aldolase. Earlier misconceptions and lessons to be learned are well discussed.

      Weaknesses:

      The materials and methods section is rather lengthy, suffering from a lack of conciseness and repetition, and nevertheless misses some specifications.

      We thank Reviewer 2 for the summary and comments and will improve the materials and methods part accordingly in a revised version.

      (1) M. Theune et al., Easy-to-use whole-genome sequencing workflows and standardized practices to uncover hidden genetic variation in Synechocystis PCC 6803 wild-type and knock-out strains. bioRxiv 10.64898/2026.04.08.717167, 2026.2004.2008.717167 (2026).

      (2) X. Chen et al., The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants. Proceedings of the National Academy of Sciences 113, 5441-5446 (2016).

      (3) D. Schulze et al., GC/MS-based 13C metabolic flux analysis resolves the parallel and cyclic photomixotrophic metabolism of Synechocystis sp. PCC 6803 and selected deletion mutants including the Entner-Doudoroff and phosphoketolase pathways. Microbial Cell Factories 21, 69 (2022).

      (4) A. Makowka et al., Glycolytic Shunts Replenish the Calvin–Benson–Bassham Cycle as Anaplerotic Reactions in Cyanobacteria. Molecular Plant 13, 471-482 (2020).

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      The authors describe the results of a single study designed to investigate the extent to which horizontal orientation energy plays a key role in supporting view-invariant face recognition. The authors collected behavioral data from adult observers who were asked to complete an old/new face matching task by learning broad-spectrum faces (not orientation filtered) during a familiarization phase and subsequently trying to label filtered faces as previously seen or novel at test. This data revealed a clear bias favoring the use of horizontal orientation energy across viewpoint changes in the target images. The authors then compared different ideal observer models (cross-correlations between target and probe stimuli) to examine how this profile might be reflected in the image-level appearance of their filtered images. This revealed that a model looking for the best matching face within a viewpoint differed substantially from human data, exhibiting a vertical orientation bias for extreme profiles. However, a model forced to match targets to probes at different viewing angles exhibited a consistent horizontal bias in much the same manner as human observers.

      Strengths:

      I think the question is an important one: The horizontal orientation bias is a great example of a low-level image property being linked to high-level recognition outcomes, and understanding the nature of that connection is important. I found the old/new task to be a straightforward task that was implemented ably and that has the benefit of being simple for participants to carry out and simple to analyze. I particularly appreciated that the authors chose to describe human data via a lower-dimensional model (their Gaussian fits to individual data) for further analysis. This was a nice way to express the nature of the tuning function, favoring horizontal orientation bias in a way that makes key parameters explicit. Broadly speaking, I also thought that the model comparison they include between the view-selective and view-tolerant models was a great next step. This analysis has the potential to reveal some good insights into how this bias emerges and ask fine-grained questions about the parameters in their model fits to the behavioral data.

      Weaknesses:

      I will start with what I think is the biggest difficulty I had with the paper. Much as I liked the model comparison analysis, I also don't quite know what to make of the view-tolerant model. As I understand the authors' description, the key feature of this model is that it does not get to compare the target and probe at the same yaw angle, but must instead pick a best match from candidates that are at different yaws. While it is interesting to see that this leads to a very different orientation profile, it also isn't obvious to me why such a comparison would be reflective of what the visual system is probably doing. I can see that the view-specific model is more or less assuming something like an exemplar representation of each face: You have the opportunity to compare a new image to a whole library of viewpoints, and presumably it isn't hard to start with some kind of first pass that identifies the best matching view first before trying to identify/match the individual in question. What I don't get about the view-tolerant model is that it seems almost like an anti-exemplar model: You specifically lack the best viewpoint in the library but have to make do with the other options. Again, this is sort of interesting and the very different behavior of the model is neat to discuss, but it doesn't seem easy to align with any theoretical perspective on face recognition. My thinking here is that it might be useful to consider an additional alternate model that doesn't specifically exclude the best-matching viewpoint, but perhaps condenses appearance across views into something like a prototype. I could even see an argument for something like the yaw-averages presented earlier in the manuscript as the basis for such a model, but this might be too much of a stretch. Overall, what I'd like to see is some kind of alternate model that incorporates the existence of the best-match viewpoint somehow, but without the explicit exemplar structure of the view-specific model.

      The design of the view-tolerant model aligned with the requirements of tolerant recognition and revealed the stimulus information enabling to abstract identity away from variations in face appearance. However, it did not involve the notion that such ability may depend on a prototype or summary representation of face identity built up through varied encounters (Burton, Jenkins, & Schweinberger, 2011; Burton et al., 2016; Jenkins et al., 2011; Menon, Kemp, & White, 2018; Mike Burton, 2013).

      We agree with the Reviewer that the average of the different views of a face is a good proxy of its central tendency (i.e., stable identity properties; Figure 1). We thus followed their suggestion and included an additional model observer that compared specific views to full-spectrum view-averaged identities. The examination of the orientation tuning profile of this so-called view-average model observer confirmed the crucial contribution of horizontal identity cues to view-invariant recognition as the horizontal range best predicted the average summary of full-spectrum face appearances across views. This additional model observer is now presented in the Discussion and Supplementary files 2 and 3.

      Besides this larger issue, I would also like to see some more details about the nature of the cross-correlation that is the basis for this model comparison. I mostly think I get what is happening, but I think the authors could expand more on the nature of their noise model to make more explicit what is happening before these cross-correlations are taken. I infer that there is a noise-addition step to get them off the ceiling, but I felt that I had to read between the lines a bit to determine this.

      In the Methods section, we now provide detailed information about the addition of noise to model observer cross-correlations: ‘In a pilot phase, we measured the overall identification performance of each model. Initially, the view-selective model performed at ceiling, yielding a correlation of 1 since there was an exact target-probe match across all trials. To avoid ceiling effects and to keep model performance close to human levels (Supplementary File 2), we thus decreased the signal-to-noise ratio (SNR) of the target and probe images to .125 by combining each with distinct noise patterns (face RMS contrast: .01; noise RMS contrast: .08). Each trial (i.e. target-probe pairing) was iterated ten times with different random noise patterns.’

      We also added a supplemental with the graphic illustration of the d’ distributions of each model and human observers: ‘Sensitivity d’ of the view-tolerant model was much lower than view-selective model and human sensitivity (Supplementary File 2), even without noise. The view-tolerant model therefore processed fully visible stimuli (SNR of 1). This decreased sensitivity in the view-tolerant compared to the view-selective model is expected, as none of the probes exactly matched the target at the pixel level due to viewpoint differences. In contrast to humans who rely on internally stored representations to match identity across views, the model observer lacks such internal representations and entirely relies on (less efficient) pixelwise comparisons.’

      Another thing that I think is worth considering and commenting on is the stimuli themselves and the extent to which this may limit the outcomes of their behavioral task. The use of the 3D laser-scanned faces has some obvious advantages, but also (I think) removes the possibility for pigmentation to contribute to recognition, removes the contribution of varying illumination and expression to appearance variability, and perhaps presents observers with more homogeneous faces than one typically has to worry about. I don't think these negate the current results, but I'd like the authors to expand on their discussion of these factors, particularly pigmentation. Naively, surface color and texture seem like they could offer diagnostic cues to identity that don't rely so critically on horizontal orientations, so removing these may mean that horizontal bias is particularly evident when face shape is the critical cue for recognition.

      Our stimuli were originally designed by Troje and Bulthoff (1996). These are 3D laser scans of white individuals aged between 20 and 40 years, posing with a neutral expression. Different views of the faces were shot under a fixed illumination. Ears and a small portion of the neck were visible while the hair region was removed. All face images had a normalized skin color and we further converted them to grayscales

      While we agree that this stimulus set offers a restricted range of within- and between-identity variations compared to what is experienced in natural settings, we believe that the present findings generalize to more ecological viewing conditions. Indeed, past evidence showed that the recognition of face pictures shot under largely variable pose, age, expression, illumination, hair style is tuned to the horizontal range of the face stimulus (Dakin & Watt, 2009; Dumont, Roux-Sibilon, & Goffaux, 2024). In other words, our finding that view-tolerant identity recognition is mainly driven by horizontal face information would likely replicate with the use of a more ecological stimulus set.

      Moreover, the skin color normalization and grayscale conversion, while limiting the range of face variability, did not eliminate the contribution of surface pigmentation in our study. It is thus unlikely that our findings exclusively reflect the orientation dependence of face shape processing. Pigmentation refers to all surface reflectance properties (Russell et al., 2006) and hue (color) is only one among others. The grayscaled 3D laser scanned faces used here contained natural variations in crucial surface cues such as skin albedo (i.e., how light or dark the surface appears) and texture (i.e., spatial variation in how light is reflected); they have actually been used to disentangle the role of shape and surface cues to identity recognition (e.g., Jiang et al., 2009; Russell et al., 2007; Russell et al., 2006; Troje & Bulthoff, 1996; Vuong et al., 2005). Moreover, a past study of ours demonstrated that the diagnosticity of the horizontal range of face information is not restricted to face shape cues; the specialized processing of face shape and surface both selectively rely on horizontal information (Dumont, Roux-Sibilon, & Goffaux, 2024).

      For these reasons, the present findings are unlikely to be fully determined by shape processing, and we expect them to generalize to more ecological stimulus sets. We discuss these aspects in the revised manuscript.

      Reviewer #2 (Public review):

      This study investigates the visual information that is used for the recognition of faces. This is an important question in vision research and is critical for social interactions more generally. The authors ask whether our ability to recognise faces, across different viewpoints, varies as a function of the orientation information available in the image. Consistent with previous findings from this group and others, they find that horizontally filtered faces were recognised better than vertically filtered faces. Next, they probe the mechanism underlying this pattern of data by designing two model observers. The first was optimised for faces at a specific viewpoint (view-selective). The second was generalised across viewpoints (view-tolerant). In contrast to the human data, the view-specific model shows that the information that is useful for identity judgements varies according to viewpoint. For example, frontal face identities are again optimally discriminated with horizontal orientation information, but profiles are optimally discriminated with more vertical orientation information. These findings show human face recognition is biased toward horizontal orientation information, even though this may be suboptimal for the recognition of profile views of the face.

      One issue in the design of this study was the lowering of the signal-to-noise ratio in the view-selective observer. This decision was taken to avoid ceiling effects. However, it is not clear how this affects the similarity with the human observers.

      In the Methods section, we now provide detailed information about the addition of noise to model observer cross-correlations: ‘In a pilot phase, we measured the overall identification performance of each model. Initially, the view-selective model performed at ceiling, yielding a correlation of 1 since there was an exact target-probe match across all trials. To avoid ceiling effects and to keep model performance close to human levels (Supplementary File 2), we thus decreased the signal-to-noise ratio (SNR) of the target and probe images to .125 by combining each with distinct noise patterns (face RMS contrast: .01; noise RMS contrast: .08). Each trial (i.e. target-probe pairing) was iterated ten times with different random noise patterns.’

      We also added a supplemental with the graphic illustration of the d’ distributions of each model and human observers.

      Another issue is the decision to normalise image energy across orientations and viewpoints. I can see the logic in wanting to control for these effects, but this does reflect natural variation in image properties. So, again, I wonder what the results would look like without this step.

      All stimuli were matched for luminance and contrast. It is crucial to normalize image energy across orientations as natural image energy is disproportionately distributed across orientations (e.g., Hansen et al., 2003). Images of faces cropped from their background as used here contain most of their energy in the horizontal range (Goffaux & Greenwood, 2016; Keil, 2008, 2009). If not normalized after orientation filtering, such uneven distribution of energy would boost recognition performance in the horizontal range across views. Normalization was performed across our experimental conditions merely to avoid energy from explaining the influence of viewpoint on the orientation tuning profile.

      We were not aware of any systematic natural variations of energy across face views. To address this, we measured face average energy (i.e., RMS contrast) in the original stimulus set, i.e., before the application of any image processing or manipulation. Background pixels were excluded from these image analyses. Across yaws, we found energy to range between .11 and .14 on a 0 to 1 grayscale. This is moderate compared to the range of energy variations we measured across identities (from .08 to .18). This suggests that variations in energy across viewpoints are moderate compared to variations related to identity. It is unclear whether these observations are specific to our stimulus set or whether they are generalizable to faces we encounter in everyday life. They, however, indicate that RMS contrast did not substantially vary across views in the present study and suggest that RMS normalization is unlikely to have affected the influence of viewpoint on recognition performance.

      In the revised methods section, we explicitly motivate energy normalization: ‘Images of faces cropped from their background as used here contain most of their energy in the horizontal range (Goffaux, 2019; Goffaux & Greenwood, 2016; Keil, 2009). Across yaws, we found face energy to range between .11 and .14 on a 0 to 1 grayscale, which is moderate compared to the range of face energy variations we measured across identities (from .08 to .18). To prevent energy from explaining our results, in all images, the luminance and RMS contrast of the face pixels were fixed to 0.55 and 0.15, respectively, and background pixels were uniformly set to 0.55. The percentage of clipped pixel values (below 0 or above 1) per image did not exceed 3%.’.

      Despite the bias toward horizontal orientations in human observers, there were some differences in the orientation preference at each viewpoint. For example, frontal faces were biased to horizontal (90 degrees), but other viewpoints had biases that were slightly off horizontal (e.g., right profile: 80 degrees, left profile: 100 degrees). This does seem to show that differences in statistical information at different viewpoints (more horizontal information for frontal and more vertical information for profile) do influence human perception. It would be good to reflect on this nuance in the data.

      Indeed, human performance data indicates that while identity recognition remains tuned to horizontal information, horizontal tuning peak shows some variation across viewpoints. We primarily focused on the first aspect because of its direct relevance to our research objective, but also discussed the second aspect: with yaw rotation, certain non-horizontal morphological features such as the jaw line or nose bridge, etc. may increasingly contribute to identity recognition, whereas at frontal or near frontal views, features are mostly horizontally-oriented (e.g., Keil, 2008, 2009). In the revised Discussion, we directly relate the modest fluctuations of peak location to yaw differences in face feature appearance.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Based on a discussion with the reviewers, we integrated the recommendations and reached a consensus on the eLife assessment. To move from a "solid" to a "compelling/convincing" strength-of-evidence rating, please address the reviewers' comments. Key points are to clarify and test the plausibility of the models (e.g., effects of different noise-addition steps, inclusion/exclusion of specific orientation channels in the view-dependent comparison, and alternative decision criteria), and to address or discuss the limitations of the stimulus set in capturing recognition under more naturalistic scenarios, for example, including texture cues.

      Reviewer #1 (Recommendations for the authors):

      I generally found the paper to be very well-written, so I have only a few minor comments here.

      (1) I didn't really follow why the estimation of the Gaussian functions described in the text was preferred over a simpler ML framework. Do these approaches differ that much? I see references to prior studies in which these were applied, so I can certainly go check these out, but I could see value in adding just a bit of text to briefly make the case that this is important.

      Employing a simpler linear framework, i.e. a linear model predicting d’ from the interaction between orientation and viewpoint, would result in an 8 (orientation) * 7 (viewpoint) design that is difficult to analyze. The interaction term would almost certainly reach significance but its interpretation would be limited. We would either have to rely on numerous local comparisons, which are not particularly informative for our research objectives (e.g., knowing whether d’ differs significantly between two adjacent orientations at a given viewpoint is of little relevance), or to use a polynomial contrast approach (testing the linear, quadratic, … up to the 7th order trends), which would also be difficult to interpret. For such complex, approximately Gaussian-shaped data, the highest-order polynomial trend would likely provide the best fit, but without offering meaningful insight.

      In contrast, a nonlinear approach appears more appropriate. The Gaussian model we used allows us to characterize the parameters of the tuning profile, namely, peak location, peak amplitude, standard deviation (or bandwidth) and base amplitude. These parameters are not merely statistical parameters. Rather, they are directly interpretable in cognitive/functional terms. The peak location corresponds to the orientation at which the Gaussian curve is centred, i.e. the preferred orientation band for identity recognition. The standard deviation represents the width of the curve, reflecting the strength or selectivity of the tuning. The base amplitude is the height of the Gaussian curve base, indicating the minimum level of sensitivity, typically found near vertical orientation. Finally, the peak amplitude refers to the height of the Gaussian curve relative to its baseline, that is, it captures the advantage of horizontal over vertical orientations.

      Moreover, the use of a nonlinear, Gaussian model is motivated by past work that showed that the Gaussian function fits the evolution of recognition performance as a function of orientation (Dakin & Watt, 2009; Goffaux & Greenwood, 2016). Orientation selectivity at primary stages of visual processing has also been modelled using Gaussian (or Difference of Gaussians; Ringach, Hawken, & Shapley, 2003).

      We revised the data analysis section to include a justification for our use of a Gaussian model: “Therefore, fitting the human sensitivity data could be fitted using a simple Gaussian model. seemed most appropriate as it allows characterizing the parameters of the tuning profile, namely, peak location, peak amplitude, standard deviation and base amplitude, which are directly interpretable in cognitive/functional terms. Moreover, the use of a nonlinear, Gaussian model is motivated by past work that showed that the Gaussian function fits the evolution of recognition performance as a function of orientation (Dakin & Watt, 2009; Goffaux & Greenwood, 2016). Simpler frameworks, i.e. a linear model predicting d’ from the interaction between orientation and viewpoint, would result in an 8 (orientation) * 7 (viewpoint) design that is difficult to analyze and interpret.”

      (2) When reporting the luminance and contrast of your stimuli, please make clear what these units and measures are. This was a case where I had to take a second to assure myself that I knew what the values meant.

      We clarified that the luminance and contrast values reported in the manuscript are on a grey scale ranging from 0 to 1.

      (3) In your Procedure section, I think describing the familiarization task right away would help the text flow more clearly. At present, you began talking about the old/new task, and I was immediately wondering how familiarization worked!

      The procedure section now starts with the description of the familiarization task.

      (4) p. 3 - "Culminates" doesn't seem like the right word here.

      We agree and rephrased this way: ‘The tolerance of face identity recognition is stronger for familiar than unfamiliar faces’.

      (5) p. 5 - I think "with the multiple" shouldn't have "the".

      Indeed, we removed the “the”.

      Reviewer #2 (Recommendations for the authors):

      I enjoyed reading the manuscript, but thought the Introduction was a bit long. I wasn't sure about the relevance of the section on temporal contiguity. I think this might have been more relevant if this had been a manipulation in the design. So, I wonder if this might be shortened or removed to focus on the key questions. On the other hand, I found the overview of the view-selective and view-tolerant to be a bit brief. There is plenty of detail here, but I found it difficult to break down what was done when I first read it. It might be good to provide an overview in the Discussion too.

      While past research on the contribution of temporal contiguity to face identity recognition brings interesting insights into the nature of the visual experience leading to view-tolerant performance, we agree with the Reviewer that this aspect is not directly at stake here. We reduced the review of this literature in the Introduction.

      We clarified the description of the model observers as suggested by the reviewer and made sure to provide an overview of the model observers in the Discussion as well.

      References.

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    1. Author response:

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

      In the revised manuscript, we have implemented several substantive changes. Most notably, we have revised the statistical reporting throughout to use Wald z statistics and GLMM-based contrasts, replacing the previously reported F statistics and figure caption t-tests. We have also expanded the Discussion to more explicitly acknowledge interpretational caveats regarding the null tuning width result and to address the alternative explanation of general alertness or motivational changes. Throughout the manuscript, we have revised our language to ensure that our conclusions are appropriately calibrated to the data.

      Reviewer #1 (Public review):

      Summary:

      The authors attempt to use a combination of behavioural and EEG analyses in order to investigate whether expectation of task difficulty influences spatial focus narrowing in the context of a spatially cued task, alongside an expected attention-related amplitude effect. This distinguishes the experiment from previous tasks, which looked at this potential spatial narrowing in the context of more non-cued diffuse attention tasks. The authors present two major findings:

      (1) Behaviourally, they analysed the effects of cue validity and difficulty expectation on response accuracy, and found that participants displayed an effect of difficulty expectation in validly cued trials, showing relatively enhanced behaviour to Hard Expectation trials, but no effect of expectation in invalidly cued trials.

      (2) Inverted encoding modelling on broadband EEG showed greater pre-target attentional processing in the Hard Expectation blocks. They go on to show that this enhancement comes in the form of greater amplitude of the Channel Tuning Functions (CTFs) approximately 300 to 400ms post-cue, in the absence of any spatial tuning specificity enhancement (as would be evident in a difference in CTF fit width).

      Together, these results provide valuable findings for those investigating the separable effects of expectation and attention on target detection in visual search.

      Strengths:

      (1) This is a very solidly performed experiment and analysis, with different streams of evidence convincingly pointing in the same direction, i.e. a gain effect of Expectation in the absence of a spatial tuning effect.

      (2) EEG is competently analysed and interpreted, and the paper is well written and simple in its motivation.

      (3) The authors report appropriately on the results in the Discussion, without overreaching. 

      Weaknesses:

      I mainly have a few minor issues for the authors to clarify, which I will leave to Recommendations. However, a few analyses need further work:

      We thank Reviewer 1 for the overall positive evaluation of our work and for the constructive and detailed feedback. The reviewer highlighted several strengths of the study, including the convergent evidence across behavioral and neural measures, the competent EEG analysis, and the appropriateness of the Discussion. In response to the specific recommendations, we have: clarified the type of EEG analysis in the Abstract; revised the description of the Serences et al. (2004) finding in the Introduction; added a Figure 1 reference in the relevant paragraph; clarified the logic of the planned comparisons; corrected and updated Figure 2 and its caption; added clarifying information about the EEG analysis in the Results; corrected the ambiguous reference to stimulus onset; clarified the status of edge-marked participants in Figure 4a; and added caveats and clarifications regarding the decoding analysis. We also address the two analytical concerns raised under Weaknesses below.

      (1) The GLMM method used has very large degrees of freedom (pages 6 and 7) of 34542. I assume this is the number of trials minus the number of parameters? This would imply that random slopes were not modelled in the analyses. However, looking at the Methods, it is reported that they were modelled. The authors should clarify exactly what was done here and why, including the LMM model. 

      We thank the reviewer for raising this point. The previously reported denominator degrees of freedom (e.g., 34,542) reflected the number of trial-level observations used in the model and arose from reporting Type III Wald F-tests. We agree that this reporting format may have been misleading in the context of generalized linear mixed-effects models (GLMMs), where inference does not rely on classical denominator degrees of freedom in the same way as traditional ANOVA.

      To improve clarity, we have revised the manuscript to report fixed effects using Wald z statistics derived from the model summary, which is the standard approach for binomial GLMMs implemented in lme4. We no longer report F statistics or denominator degrees of freedom. Importantly, all models included by-participant random intercepts and random slopes for all within-subject factors (Expectation, Search condition, and Cue validity), as specified in the Methods. These random effects account for the non-independence of trial-level observations within participants and ensure that statistical uncertainty is estimated at the participant level rather than the trial level. We have clarified the random-effects structure explicitly in the revised Methods section.

      The revised reporting yields the same overall pattern of results, with the key planned comparison remaining significant.

      (2) Figure 4 shows an "example CTF fit". Why only one? You could put transparent lines in the background for each individual fit, followed by the grand average, or show each fit in the supplementary section?

      We thank the reviewer for this suggestion. We would like to clarify that Figure 4 does not show an example single-subject CTF fit; it shows the CTF fit to the group-averaged data, i.e., the grand average across participants. The purpose of the figure is to illustrate the group-level tuning function. This is now clarified in the updated Figure caption.

      To convey individual differences, Figure 4a already presents the parameter estimates for each participant (width, amplitude, and baseline) as separate points, providing a clear view of variability across participants. We considered including individual CTF fits in the background, but this would make the figure crowded without adding interpretive value, since the individual parameters are already visualized.

      We could, if the reviewers prefer, include the individual fits in the Supplementary Material; however, we believe that the current presentation conveys both the group average and participant-level variation clearly.

      Reviewer #1 (Recommendations for the authors):

      (3) Specify what type of EEG results are found in the Abstract. It is broadband, but one might expect, e.g. Alpha analyses. 

      We thank the reviewer for this suggestion. We have added "broadband" to the Abstract when describing the EEG analysis approach, clarifying that the inverted encoding model was applied to broadband EEG data rather than a specific frequency band (e.g., alpha).

      “We applied inverted encoding models to broadband EEG data to reconstruct spatial channel tuning functions, enabling precise characterization of both the locus and breadth of attentional deployment.”

      (4) In the Intro, please clarify the Serences finding that they found enhanced activity at expected distractor locations. The interpretation is that this reflects preparatory tagging of where distractors will appear, possibly to facilitate their suppression once they arrive, rather than enhancement in the service of processing those locations. It is confusing as it is currently worded.

      We thank the reviewer for flagging this. We have revised the description of the Serences et al. (2004) finding to clarify that the enhanced activity at expected distractor locations is interpreted as preparatory tagging in service of subsequent suppression, rather than signal enhancement facilitating processing at those locations. The revised sentence now makes this interpretive distinction explicit.

      “Complementing these findings, Serences et al. (2004) used fMRI to show that preparatory attention when expecting high distractor interference selectively enhanced activity in early visual cortex at retinotopic locations corresponding to the expected distractor positions, an effect interpreted as preparatory tagging of distractor locations to facilitate their subsequent suppression.”

      (5) Page 6: refer to Figure 1 in the relevant paragraph.

      We thank the reviewer for this suggestion. We have added a reference to Figure 1 in the relevant paragraph to help orient the reader.

      (6) Page 7: I find the interaction confusing. The authors say there is an interaction of Expectation and Cue Validity, such that there is a larger cueing benefit when dense displays were expected. However, this leads one to expect planned comparisons between Valid vs Invalid for Easy then Hard expectations. However, that's not what is done, actually comparing Easy vs Hard for Valid then Invalid trials.

      We thank the reviewer for highlighting this potential source of confusion. We have clarified in the manuscript that the planned comparisons examined the effect of Expectation separately within valid and invalid trials, rather than comparing cueing effects (valid vs. invalid) within each Expectation level. This analytic approach was chosen to directly test our hypothesis regarding expectation-related modulation of performance at attended versus unattended locations. We hope this clarification makes the logic of the comparisons more transparent.

      “To identify the locus of this interaction, we examined the effect of Expectation separately within valid and invalid trials, allowing us to test whether expectations exerted their effects at both cued and uncued locations, or selectively at either cued or uncued locations.”

      (7) Page 7: Issue with asterisk in Figure 2. Text says it is not significant. Also, can you make the transparent grey lines more visible? Also, the inner plot shows two sets of lines, apparently easy and hard display results. Needs to be denoted.

      We thank the reviewer for these observations. We have made the following changes: (1) The pairwise comparisons reported in the figure caption have been replaced with contrasts derived from the GLMM using estimated marginal means, consistent with the statistical approach used throughout the manuscript. (2) We have corrected the asterisk annotation in Figure 2, which was incorrectly placed on a non-significant comparison. (3) We have increased the visibility of the transparent grey lines in the figure. (4) We have revised the figure such that it is visually clear that the legend from the main plot applies to the inset plot as well.

      (8) Page 8: Really need some info on the EEG analysis.

      We thank the reviewer for this suggestion. We have added a sentence to the Results section briefly explaining that CTF slope reflects the overall strength of spatially selective neural activity at the attended location, with steeper slopes indicating stronger spatial selectivity, before directing readers to the Methods for full technical details. We hope this provides sufficient context for readers less familiar with the IEM approach without overloading the Results with methodological detail.

      (9) Page 8: 100ms after stimulus onset = target or cue? From Figure 4, it seems to be a cue, but this really needs to be clarified.

      We thank the reviewer for catching this ambiguity. We have replaced "stimulus onset" with "cue onset" throughout the results section to make clear that the time course is locked to cue presentation rather than target onset.

      (10) Page 10: Figure 4a, are edge-marked participants outliers? Were they included in analyses?

      We thank the reviewer for this observation. The edge-marked data points in Figure 4a reflect the default matplotlib boxplot visualization, which flags points beyond 1.5 × IQR, and do not represent a formal outlier exclusion criterion. We have added a brief clarification to this effect in the figure caption. All participants were retained in the primary analyses. To confirm that these participants did not unduly influence the results, we conducted a sensitivity analysis excluding them. Notably, the flagged participant showed a pattern in the opposite direction to the group, and excluding this individual yielded a stronger and more consistent effect, suggesting that our primary analysis with all participants included represents a conservative estimate.

      (11) Page 11: Can't infer the same mechanism from the lack of decoding ability; it could be a signal-to-noise issue. However, one interesting question. How is it that the Encoding analysis worked out, but the Decoding analysis did not?

      We thank the reviewer for raising both points. We agree that chance decoding could in principle reflect limited sensitivity rather than a true null effect, and we have added a caveat acknowledging this in the manuscript. We have also added a clarifying sentence explaining the complementary nature of the IEM and decoding analyses: the IEM captures the strength of spatial tuning within each condition, whereas decoding tests whether spatial patterns differ between conditions. Amplitude modulation of a shared spatial pattern would not necessarily produce discriminable multivariate patterns, which explains why the IEM detected amplitude differences while decoding remained at chance. We hope this resolves the apparent paradox.

      Reviewer #2 (Public review):

      Summary:

      The authors set out to determine whether people can adjust how narrowly or broadly they focus attention in advance based on expectations about how difficult an upcoming visual task will be. Specifically, they aimed to test whether expecting a more demanding search leads to a narrower focus of attention or instead strengthens attention at the relevant location without changing its spatial extent.

      Strengths:

      The study addresses a timely and interesting question about how expectations influence the preparation of attention before a task begins. The experimental design is well-suited to isolating anticipatory effects by manipulating expectations about task difficulty independently of moment-to-moment stimulus information. The manuscript is clearly written, and the methods are described in sufficient detail to support transparency and reproducibility.

      Weaknesses:

      Despite the strengths of the design and the merit of the work, I have a few concerns regarding the analysis and the interpretation of the results.

      We thank Reviewer 2 for the positive assessment of the study and for the thoughtful and constructive feedback. The reviewer highlighted several strengths, including the timeliness of the research question, the suitability of the experimental design, and the clarity of the manuscript. In response to the concerns raised, we have: revised the statistical reporting throughout to use Wald z statistics and replaced figure caption t-tests with GLMM-based contrasts; added a caveat in the Discussion acknowledging that the absence of tuning width differences does not definitively rule out changes in attentional scope; and added a paragraph in the Discussion addressing the alternative explanation of general alertness or motivational changes. We address each concern in detail below.

      (1) I was somewhat confused by aspects of the behavioural analysis. I may be mistaken, but fixed effects in generalised mixed-effects models are more commonly reported using Wald statistics with beta coefficients rather than F statistics, and the very large degrees of freedom reported here are difficult to interpret. In particular, they appear closer to trial counts than to the number of participants, which raises questions about how statistical uncertainty is being estimated. This concern is compounded by the fact that different statistical approaches appear to yield different conclusions: the generalised mixed-effects models and the pairwise t-tests reported in the figure caption do not fully align. Moreover, the latter are not described in the Methods, and the justification for using them in the figure is not provided. Taken together, this makes it difficult to assess the strength of the behavioural evidence. The reported effects of expectation on behaviour also appear small, and there is no clear cost at uncued locations. This limited behavioural footprint makes it difficult to determine how robust the proposed preparatory mechanism is. It also complicates the interpretation of the neural findings as reflecting a general strategy for optimising task preparation.

      We appreciate this observation and agree that reporting Wald statistics is more appropriate for GLMMs. In the revised manuscript, we now report fixed effects as regression coefficients (β), standard errors, z values, and associated p values, rather than Type III F statistics. This reporting more directly reflects the estimation procedure used in lme4, where inference for binomial GLMMs is based on Wald z tests.

      We have also removed the reporting of large denominator degrees of freedom, which reflected the number of trial-level observations but may have been confusing in this context. All models included by-participant random intercepts and random slopes for the within-subject factors, ensuring that statistical uncertainty is appropriately estimated while accounting for the hierarchical structure of the data.

      Regarding the pairwise comparisons shown in the figure caption, these previously reflected conventional pairwise t-tests and have now been replaced with contrasts derived from the GLMM using estimated marginal means, consistent with the statistical approach used throughout the manuscript. We have clarified in both the Methods and Results sections that these contrasts are fully model-based and examine the effect of Expectation separately within valid and invalid trials.

      Overall, the revised reporting format aligns the statistical presentation more closely with current standards for GLMM analyses and improves interpretability, while leaving the substantive conclusions unchanged.

      (2) A central premise of the study is that, if observers proactively narrow their attentional focus when expecting difficult search, this should be reflected in sharper spatial tuning profiles. This prediction is presented as a diagnostic test of whether expectations modulate attentional scope. However, the absence of such sharpening is later taken as evidence that expectations do not alter spatial extent and instead operate exclusively through gain modulation. This inference may be stronger than the data allow. The lack of an observed difference in tuning width does not necessarily rule out changes in attentional scope, particularly if such changes are subtle, temporally limited, or not well captured by the spatial resolution of the approach. As a result, while the findings are consistent with a gain-based account, they do not definitively exclude the possibility that expectations also influence spatial extent, and the logic linking the original prediction to the final conclusion would benefit from a more cautious interpretation.

      We thank the reviewer for this important point. We agree that the absence of a tuning width difference does not definitively rule out changes in attentional scope, and we have added a caveat in the Discussion acknowledging that subtle or temporally limited changes may not be fully captured by the spatial resolution of the current approach. We have revised the relevant section to adopt a more cautious interpretation while maintaining that the current findings are most consistent with a gain-based account.

      “We note, however, that the absence of a tuning width difference should be interpreted with caution. Subtle or temporally limited changes in attentional scope may not be fully captured by the spatial resolution of the current approach, and we cannot definitively exclude the possibility that expectations also influence spatial extent under some conditions.”

      (3) The difference between easy and hard searches in the CTF slope is taken as evidence for enhanced preparatory spatial attention under high expected difficulty. However, these differences could also reflect broader changes in alertness or motivational state between blocks. The behavioural results show a small overall increase in accuracy in expect-hard blocks, which may be consistent with a more general increase in task engagement rather than a spatially specific preparatory mechanism. Although the authors decompose slope differences into amplitude and width parameters, the interpretation still relies on ruling out alternative, more global explanations for enhanced signal strength or reduced variability. This leaves some ambiguity as to whether the observed modulation reflects a specific adjustment of preparatory attention or a more general change in task state.

      We thank the reviewer for raising this important alternative explanation. We agree that a general increase in alertness or motivational state could in principle produce broader changes in neural signal strength. We have added a paragraph in the Discussion addressing this concern directly. We highlight two aspects of the data that argue against a purely global account: first, the behavioral benefit of expectation was selective to the cued location with no corresponding effects elsewhere, which is inconsistent with a global alertness account; second, multivariate decoding of expectancy condition remained at chance throughout the cue-target interval, indicating that the two conditions did not produce globally distinct patterns of broadband EEG activity. If general arousal were driving the amplitude differences, we would expect such global pattern differences to be detectable by the classifier. Together, these considerations suggest that the observed modulation reflects spatially specific preparatory gain enhancement rather than a general change in task state. We acknowledge, however, that we cannot fully rule out a contribution of motivational or arousal-related factors, and have added appropriate caveats to the Discussion.

      “A related concern is whether the amplitude enhancement observed in expect-hard blocks reflects a spatially specific preparatory mechanism or instead a more general change in alertness or motivational state. Several aspects of the data argue against a purely global account. First, the behavioral benefit of expectation was selective to the cued location, with no corresponding costs or benefits at uncued locations, suggesting that expectancy effects were spatially constrained rather than globally distributed. Second, if expect-hard blocks induced a broadly different neural state through general arousal or motivational engagement, this should manifest as a globally distinct pattern of broadband EEG activity that a multivariate classifier could detect. However, decoding accuracy remained at chance throughout the cue-target interval, indicating that the two expectancy conditions did not produce categorically different spatial patterns of neural activity. Together, these findings suggest that the observed amplitude modulation reflects spatially specific preparatory gain enhancement rather than a global change in task engagement.”

    1. Author response:

      [Note: The final version has been published in Brain, Behavior, and Immunity: https://doi.org/10.1016/j.bbi.2026.106473]

      eLife Assessment

      Rhis useful study raises interesting questions but provides inadequate evidence of an association between atovaquone-proguanil use (as well as toxoplasmosis seropositivity) and reduced Alzheimer's dementia risk. The findings are intriguing but they are correlative and hypothesis-generating with the strong possibility of residual confounding.

      We thank the editors and reviewers for characterizing our work as useful and for the opportunity to publish a Reviewed Preprint with a corresponding response. However, the statements in the Assessment characterizing the evidence as ‘inadequate’ and asserting a ‘strong possibility of residual confounding’ are factually incorrect as applied to our data and incompatible with the empirical findings presented in the manuscript. We have notified the editors of this factual inaccuracy. As the Assessment will be published as originally written, we provide clarification here to ensure an accurate scientific record for readers of the Reviewed Preprint.

      Our study shows that the association between atovaquone–proguanil (A/P) exposure and reduced dementia risk, first identified in a rigorously matched national cohort in Israel, is robustly reproduced across three independently constructed age-stratified cohorts in the U.S. TriNetX network (with exposure at ages 50–59, 60–69, and 70–79). In each cohort, individuals exposed to A/P were compared with rigorously matched individuals who received another medication at the same age and were then followed over a decade for incident dementia. Cases and controls were matched on all major established dementia risk factors: age, sex, race/ethnicity, diabetes, hypertension, obesity, and smoking status.

      Across all three strata, each containing more than 10,000 exposed individuals with an equal number of matched controls, we observed substantial and consistent reductions in cumulative dementia incidence (HR 0.34–0.51), extremely low P-values (10<sup>–16</sup> to 10<sup>–40</sup>), and continuously widening divergence of Kaplan–Meier curves over the follow-up period. To more rigorously exclude the possibility of unmeasured baseline differences in health status, we additionally performed, for the purpose of this response, comparative analyses of key indicators of frailty and clinical utilization, including emergency and inpatient encounters, as well as the prevalence of mild cognitive impairment prior to medication exposure (values provided below in response to Reviewer #2, Weakness 1). These analyses provide clear evidence showing no pattern suggestive of exposed individuals being medically or cognitively healthier at baseline.

      Taken together, these findings constitute a rigorously matched and independently replicated association across two national health systems, using TriNetX, the most widely cited real-world evidence platform in published cohort studies. Replication across three age strata, each with >10,000 exposed individuals, followed for a decade, and matched on all major known risk factors for dementia, meets the accepted epidemiologic definition of strong and reproducible evidence.

      Although we disagree with elements of the editorial Assessment that appear inconsistent with the empirical findings, we will proceed with publication of the current manuscript as a Reviewed Preprint in order to ensure timely dissemination of findings with meaningful implications for public health and dementia prevention. In this initial public version, the point-by-point responses below provide concise explanations addressing the critiques underlying the Assessment. A revised manuscript, incorporating expanded baseline comparisons across each TriNetX age stratum, additional stringent exclusions, and an expanded discussion that will address the remarks presented in this review, will be submitted shortly.

      Reviewer #1 (Public review):

      Summary:

      This useful study provides incomplete evidence of an association between atovaquone-proguanil use (as well as toxoplasmosis seropositivity) and reduced Alzheimer's dementia risk. The study reinforces findings that VZ vaccine lowers AD risk and suggests that this vaccine may be an effect modifier of A-P's protective effect. Strengths of the study include two extremely large cohorts, including a massive validation cohort in the US. Statistical analyses are sound, and the effect sizes are significant and meaningful. The CI curves are certainly impressive.

      Weaknesses include the inability to control for potentially important confounding variables. In my view, the findings are intriguing but remain correlative / hypothesis generating rather than causative. Significant mechanistic work needs to be done to link interventions which limit the impact of Toxoplasmosis and VZV reactivation on AD.

      We thank the reviewer for describing our study as useful and for highlighting several of its strengths, including the very large cohorts, sound statistical analyses, meaningful effect sizes, and the impressive CI curves. We also appreciate the reviewer’s recognition that our findings reinforce prior evidence linking VZV vaccination to reduced AD risk.

      Regarding the statement that the evidence remains incomplete due to “inability to control for potentially important confounding variables,” we refer to our introductory explanation above. As noted there, our analyses meet the accepted criteria for reproducible epidemiological evidence, and the assumption of uncontrolled confounding is contradicted by rigorous matching and by additional baseline evaluations. We fully agree that mechanistic work is warranted, and our epidemiologic findings strongly motivate such efforts.

      We address the reviewer’s specific comments in detail below.

      (1) Most of the individuals in the study received A-P for malaria prophylaxis as it is not first line for Toxo treatment. Many (probably most) of these individuals were likely to be Toxo negative (~15% seropositive in the US), thereby eliminating a potential benefit of the drug in most people in the cohort. Finally, A-P is not a first line treatment for Toxo because of lower efficacy.

      We agree that individuals in our cohort received Atovaquone-Proguanil (A-P) for malaria prophylaxis rather than for treatment of toxoplasmosis. However, this does not contradict our interpretation. Because latent CNS colonization by T. gondii is not currently considered clinically actionable, asymptomatic carriers are not offered treatment, and therefore would only receive an anti-Toxoplasma regimen unintentionally, through a medication prescribed for another indication such as malaria prophylaxis. Importantly, atovaquone is an established therapy for toxoplasmosis, including CNS disease, with documented efficacy and CNS penetration in current treatment guidelines. It is therefore reasonable to assume that, during the multi-week course typically administered for malaria prophylaxis, A-P would exert significant anti-Toxoplasma activity in individuals with latent CNS infection, potentially reducing or eliminating parasite burden even though the medication was not prescribed for that purpose.

      The reviewer notes that only ~15% of individuals in the U.S. are Toxoplasma-seropositive, based on surveys performed primarily in young adults of reproductive age (serologic testing is most commonly obtained in women during prenatal care). However, seropositivity increases cumulatively over the lifespan, and few reliable estimates exist for the age groups in which Alzheimer’s disease and dementia occur. Even if we accept the lower estimate of ~15% latent colonization in older adults, this proportion is still smaller than the lifetime cumulative incidence of dementia in the general population.

      Therefore, if latent toxoplasmosis contributes causally to dementia risk, and A-P is capable of eliminating latent Toxoplasma in the subset of individuals who harbor it, then a multi-week course of treatment—such as the one routinely taken for malaria prophylaxis—would be expected to produce a substantial reduction in dementia incidence at the population level, of the same order of magnitude reported here. A protective effect concentrated in a minority of exposed individuals is fully compatible with, and can mechanistically explain, the large overall reduction in risk that we observe.

      Finally, the reviewer notes that A-P is not a first-line treatment for toxoplasmosis due to assumed lower efficacy. This point does not undermine our results. Even a second-line agent, when administered over several weeks—as is routinely done for malaria prophylaxis—is expected to exert substantial anti-Toxoplasma activity. The long duration of exposure in large populations receiving A-P for travel provides a unique natural experiment that does not exist for other anti-Toxoplasma medications, which, when prescribed for their non-Toxoplasma indications, are not taken more than a few days. Thus, the widespread use of A-P for malaria prophylaxis allows a unique opportunity to evaluate long-term outcomes following inadvertent anti-Toxoplasma treatment.

      Moreover, “first line” recommendations in clinical guidelines refer to treatment of acute toxoplasmosis in immunosuppressed individuals, where tachyzoites are actively replicating. These guidelines do not consider efficacy against latent CNS colonization, which is dominated by bradyzoites, a biologically distinct form, in immunocompetent individuals. Therefore, the guideline hierarchy is not informative regarding which medication is more effective at clearing latent brain infection, the stage we consider most relevant to dementia risk.

      (2) A-P exposure may be a marker of subtle demographic features not captured in the dataset such as wealth allowing for global travel and/or genetic predisposition to AD. This raises my suspicion of correlative rather than casual relationships between A-P exposure and AD reduction. The size of the cohort does not eliminate this issue, but rather narrows confidence intervals around potentially misleading odds ratios which have not been adjusted for the multitude of other variables driving incident AD.

      We agree that prior to matching, A-P exposure may be associated with demographic features such as health or to travel internationally. However, this does not apply after matching. In all age-stratified analyses, exposed and control individuals were rigorously matched on all major risk factors known to influence dementia risk, including age, sex, race/ethnicity, smoking status, hypertension, diabetes, and obesity. Owing to the extremely large pool of individuals in TriNetX (~120M), our matching was performed stringently, producing exposed and unexposed cohorts that are near-identical with respect to the established determinants of dementia risk.

      The reviewer correctly identifies that large cohorts alone do not eliminate confounding; however, confounding must still be biologically and epidemiologically plausible. Any hypothetical confounder capable of producing a 50–70% reduction in dementia incidence over a decade would need to: (1) produce a very large protective effect against dementia; (2) be strongly associated with A-P exposure; and (3) remain entirely uncorrelated with age, sex, race/ethnicity, smoking, diabetes, hypertension and obesity, which have been rigorously matched. No such factor has been proposed. The suggestion that an unspecified ‘subtle demographic feature’ could produce effects of this magnitude remains hypothetical, and no such factor has been described in the dementia risk literature.

      If a specific evidence-supported confounder is proposed that meets these criteria, we would be pleased to test it empirically in our cohorts. In the absence of such a proposal, the interpretation that the association is merely “correlative rather than causal” remains speculative and does not negate the strength of a replicated, rigorously matched, long-term association across large cohorts in two national health systems.

      (3) The relationship between herpes virus reactivation and Toxo reactivation seems speculative.

      We respectfully disagree with the characterization of the herpesvirus–Toxoplasma interaction as speculative. The mechanism we describe is biologically valid, based on established virology and parasitology literature showing that latent T. gondii infection can reactivate from its bradyzoite state under inflammatory or immune-modifying conditions, including viral triggers. A published clinical report has documented CNS co-reactivation of T. gondii and a herpesvirus, explicitly noting that HHV-6 reactivation can promote Toxoplasma reactivation in neural tissue (Chaupis et al., Int J Infect Dis, 2016).

      Moreover, this mechanism is the only currently evidence-supported explanation that simultaneously and parsimoniously accounts for all of the epidemiologic observations in our study:

      (1) Substantially higher cumulative incidence of dementia in individuals with positive Toxoplasma serology, indicating that latent infection is a risk factor for subsequent cognitive decline;

      (2) Strong protective association following A-P exposure, a medication with established activity against Toxoplasma gondii, including in the CNS;

      (3) Independent protection conferred by VZV vaccination, observed consistently for two vaccines with distinct formulations (one live attenuated, one recombinant protein), whose only shared property is suppression of VZV reactivation;

      (4) Greater protective effect of A-P among individuals who were not vaccinated against VZV, consistent with a model in which dementia risk requires both herpesvirus reactivation and persistent latent Toxoplasma infection—such that reducing either factor alone (via VZV vaccination or anti-Toxoplasma suppression) substantially lowers risk.

      Taken together, these observations are difficult to reconcile under any alternative hypothesis.  

      To date, we are unaware of any other biologically coherent mechanism that can explain all four findings simultaneously. We would welcome any alternative explanation capable of accounting for these converging epidemiologic signals, as such a proposal could meaningfully advance the scientific discussion. In the absence of a competing explanation, the interaction between latent toxoplasmosis and herpesvirus reactivation remains the most parsimonious hypothesis supported by current knowledge.

      Finally, while observational studies are inherently limited in their ability to provide causal inference, the mechanism we propose is biologically grounded and experimentally testable. Our results provide a strong rationale for mechanistic studies and clinical trials, and warrant publication precisely because they generate a verifiable hypothesis that can now be evaluated directly.

      (4) A direct effect on A-P on AD lesions independent on infection is not considered as a hypothesis. Given the limitations above and effects on metabolic pathways, it probably should be. The Toxo hypothesis would be more convincing if the authors could demonstrate an enhanced effect of the drug in Toxo positive individuals without no effect in Toxo negative individuals.

      A direct effect of A-P on AD established lesions is indeed possible, and this hypothesis would be of significant therapeutic interest. However, we did not consider it within the scope of our epidemiologic analyses because all cohorts explicitly excluded individuals with existing dementia. Under these conditions, proposing a disease-modifying effect on established Alzheimer’s lesions based on our data would itself be speculative. Evaluating such a mechanism would be better answered by mechanistic or interventional studies rather than inference from populations without baseline disease.

      We also agree that demonstrating a stronger protective effect among Toxoplasma-positive individuals would be informative. Unfortunately, this “natural experiment” cannot be performed using the available data: Toxoplasma serology is rarely ordered in older adults, and A-P exposure is itself uncommon, resulting in a cohort overlap far too small to yield valid statistical inference (n≈25 in TriNetX).

      Thus, while both proposed hypotheses are scientifically attractive and merit further study, neither can be resolved using currently available real-world clinical data. Our findings provide the rationale to investigate both hypotheses experimentally, and we hope our report will motivate such studies.

      Reviewer #2 (Public review):

      Summary:

      This manuscript examines the association between atovaquone/proguanil use, zoster vaccination, toxoplasmosis serostatus and Alzheimer's Disease, using 2 databases of claims data. The manuscript is well written and concise. The major concerns about the manuscript center around the indications of atovaquone/proguanil use, which would not typically be active against toxoplasmosis at doses given, and the lack of control for potential confounders in the analysis.

      Strengths:

      (1) Use of 2 databases of claims data.

      (2) Unbiased review of medications associated with AD, which identified zoster vaccination associated with decreased risk of AD, replicating findings from other studies.

      We thank the reviewer for the thoughtful assessment and for noting key strengths of our work, including (1) the use of two large national databases, and (2) the unbiased discovery approach that replicated the widely reported association between zoster vaccination and reduced Alzheimer’s disease (AD) risk. We agree that these features highlight the validity and reproducibility of the analytic framework.

      Below we respond to the reviewer’s perceived weaknesses.

      Weaknesses:

      (1) Given that atovaquone/proguanil is likely to be given to a healthy population who is able to travel, concern that there are unmeasured confounders driving the association.

      We agree that, prior to matching, A-P exposure may correlate with demographic or health-related differences (e.g., ability to travel). However, this potential bias was explicitly controlled for in the study design. Across all three age-stratified TriNetX cohorts, exposed and unexposed individuals were rigorously matched on all major established dementia risk factors: age, sex, race/ethnicity, smoking status, obesity, diabetes mellitus, and hypertension. Comparative analyses confirm that these risk factors are equivalently distributed at baseline.

      As noted in our response to Reviewer #1, for any hypothetical unmeasured confounder to explain the results, it would need to satisfy three conditions simultaneously:

      (1) Be capable of producing a 50–70% reduction in dementia incidence sustained over a decade and across three distinct age strata (ages 50–79);

      (2) Be strongly associated with likelihood of receiving A-P;

      (3) Remain entirely uncorrelated with age, sex, race/ethnicity, smoking, diabetes, hypertension, or obesity, all of which were rigorously matched and balanced at baseline.

      No such factor has been proposed in the literature or by the reviewer. Thus, the concern remains hypothetical and unsupported by any measurable demographic or biological mechanism.

      Importantly, empirical evidence contradicts the notion of a “healthy traveler” bias:

      Emergency and inpatient encounter rates prior to exposure were comparable between A-P users and controls. Across the three age-stratified cohorts, emergency visits were similar or slightly higher among A-P users (EMER: 19.6% vs 16.4%, 19.9% vs 14.2%, 22.0% vs 14.8%), and inpatient encounters were effectively equivalent (IMP: 14.8% vs 15.2%, 17.7% vs 17.6%, 22.1% vs 22.2%). These patterns directly contradict the suggestion that A-P users were a healthier or less medically burdened population at baseline.

      Prevalence of mild cognitive impairment was not lower among A-P users and was, in fact, slightly higher in the oldest cohort. Across the three age groups, baseline diagnoses of mild cognitive impairment (MCI) were comparable or slightly higher among exposed individuals (0.1% vs 0.1%, 0.3% vs 0.2%, 1.1% vs 0.6%). These data contradict the suggestion that A-P users had superior baseline cognition.

      The strongest protective association occurred in the youngest stratum (age 50–59; HR 0.34). At this age, when nearly all individuals are sufficiently healthy to travel internationally, A-P uptake is the least likely to confound health status. A frailty-based “healthy traveler” hypothesis would instead predict the opposite pattern, with older adults showing the greatest apparent benefit, since health limitations are more likely to restrict travel in later life. In contrast, the protective association weakens with increasing age, empirically contradicting any explanation based on differential travel capacity.

      In conclusion, the empirical evidence directly contradicts the existence of a ‘healthy traveler’ effect.

      (2) The dose of atovaquone in atovaquone/proguanil is unlikely to be adequate suppression of toxo (much less for treatment/elimination of toxo), raising questions about the mechanism.

      A few important points should address the reviewer’s concern:

      In our cohorts, A-P was prescribed for malaria prophylaxis, as correctly noted. In this setting, it is taken for the entire duration of travel, plus several days before and after, typically resulting in many weeks of continuous exposure. This creates an unintentional but scientifically valuable natural experiment, in which a CNS-penetrating anti-Toxoplasma agent is administered for long durations.

      Atovaquone is an established treatment for CNS toxoplasmosis, has strong CNS penetration, and is included in current clinical guidelines for acute toxoplasmosis in immunocompromised patients, although at higher doses. Because latent, asymptomatic CNS colonization is not treated in clinical practice, there are currently no data establishing the dose required to eliminate bradyzoite-stage Toxoplasma in immunocompetent individuals.

      Our observations concern atovaquone–proguanil (A-P), a fixed-dose combination of atovaquone with proguanil, a DHFR inhibitor targeting a key metabolic pathway shared by malaria parasites and T. gondii. The combination has well-established synergistic effects in malaria prophylaxis and the same mechanism would be expected to enhance anti-Toxoplasma activity. This fixed-dose regimen has never been formally evaluated for toxoplasmosis treatment at prolonged durations or against latent bradyzoite infection.

      Our hypothesis does not require or imply complete eradication of Toxoplasma. A clinically meaningful reduction in latent cyst burden among the subset of colonized individuals may be sufficient to alter long-term disease trajectories. Thus, a population-level decrease in dementia incidence does not require universal clearance of infection, but only partial suppression or reduction of parasite load in susceptible individuals, which is entirely compatible with the known pharmacology and duration of A-P exposure.

      (3) Unmeasured bias in the small number of people who had toxoplasma serology in the TriNetX cohort.

      The relatively small number of older adults with Toxoplasma serology stems from current clinical practice: serologic testing is mostly performed in women during reproductive years due to risks in pregnancy, whereas in older adults a positive result has no clinical consequence and therefore testing is rarely ordered.

      Importantly, the seropositive and seronegative groups were drawn from the same underlying population of individuals who underwent serology testing, and the only difference between groups is the test result itself. Because the decision to order a test is made prior to and independent of the result, there is no plausible rationale by which the serology outcome (positive or negative) would introduce a bias favoring either group beyond the result of the test itself.

      Furthermore, the two groups were here also rigorously matched on all major dementia risk factors, including age, sex, race/ethnicity, smoking, diabetes, hypertension, and BMI, and these characteristics are similarly distributed between groups. A small sample size does not imply bias; it simply reduces statistical power. Despite this limitation, the observed association (HR = 2.43, p = 0.001) remains strongly significant.

      Finally, this result is consistent with multiple published studies reporting higher rates of Toxoplasma seropositivity among individuals with Alzheimer’s disease, dementia, and even mild cognitive impairment, such that our finding reinforces a broader and independently observed epidemiologic pattern. Importantly, in our cohort the serology testing clearly preceded dementia diagnosis, which supports the plausibility of a causal rather than merely correlative relationship between latent toxoplasmosis and cognitive decline.

      To conclude our provisional response, we thank the editor and reviewers for raising points that will be further addressed and expanded upon in the discussion of the forthcoming revision. We welcome transparent scientific dialogue and acknowledge that, as with all observational research, residual confounding cannot be eliminated with absolute certainty. However, we disagree with the overall Assessment and emphasize that our findings—reproduced independently across two national health systems and three age-stratified cohorts, each rigorously matched on all major determinants of dementia risk, meet, and in many respects exceed, current standards for high-quality observational evidence.

      Assigning the results to “residual confounding” requires more than speculation: it requires identification of a confounding factor that is (1) anchored in established dementia risk literature, (2) empirically plausible, and (3) quantitatively capable of generating a sustained ~50 percent reduction in dementia incidence over a decade. No such factor has been identified to date. We note that the assertion of “residual confounding” has not been supported by a specific, quantitatively plausible mechanism. A hypothetical bias that is both extremely large in effect and uncorrelated with all major risk factors is not statistically or biologically credible.

      The explanation we propose, reduction in dementia risk through elimination of latent Toxoplasma gondii, is biologically grounded, directly supported by independent epidemiologic literature, and uniquely capable of accounting for all convergent observations in our data. No alternative hypothesis has been put forward that can plausibly explain these findings.

      A revised version of the manuscript will be submitted shortly, incorporating expanded baseline analyses, with the strictest possible exclusion criteria (including congenital, vascular, chromosomal, and neurodegenerative disorders such as Parkinson’s disease), and complete tabulated comparisons. These data will further reinforce that the observed protective associations are not attributable to any measurable confounding. We also plan to enhance the discussion in order to address the points raised by the reviewers.

      In light of the expanded analyses, any reservations expressed in the initial Assessment can now be re-evaluated on the basis of the empirical evidence. The findings reported in our study meet, and in several respects exceed, current epidemiologic standards for high-quality observational research, clearly warrant publication, and provide a robust scientific foundation for future mechanistic and interventional studies to determine whether elimination of latent toxoplasmosis can prevent or treat dementia.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Torro et al. presented CellDetective, an open-source software designed for a user-friendly execution of single-cell segmentation, tracking, and analysis of time-lapse microscopy data. The authors demonstrated the applications of the software by measuring NK cell spreading events acquired with reflection interference contrast microscopy (RICM), as well as detecting target cell death events and their interaction with neighboring NK cells in a multichannel widefield microscopy dataset.

      Strengths:

      The segmentation (StarDist, Cellpose) and tracking (bTrack) modules implemented were based on existing and published software packages. The authors added the event detection, classification, and analysis modules to enable an end-to-end time-lapse microscopy data processing and analysis pipeline, complete with a graphical user interface (GUI). This minimizes the coding experience required from the user. The documentation that accompanies CellDetective is also adequate.

      Weaknesses:

      Given that the software was designed to improve user experience, such an approach also limits its scope and functionality and is currently capable of handling very specific types of experiments. Additionally, this reviewer has also encountered many technical difficulties (see documented bugs/crashes below) that have prevented an extensive exploration of all the functionality of CellDetective.

      We thank the reviewer for recognizing the interest of the end-to-end pipeline design and the value of the graphical interface for non-coding users.

      Scope and technical difficulties

      We acknowledge the technical difficulties encountered during the review and sincerely apologize for the inconvenience. Since v1.3.9, we have invested substantial effort into stability, testing, and documentation. All reported bugs have been corrected and the software has been extensively tested (see points 4–7 below). Furthermore, in response to the concern about the software being limited to specific experiments, we note that Celldetective has since been successfully applied to other biological contexts beyond the immunological assays presented in the article, including microbiology (10.1128/mbio. 03342-25) and stem-cell-related studies (10.3390/jimaging11100371) (see also the positive remarks of Reviewer #2 regarding applicability). We also point the reviewer to the expanded documentation, which now includes modality-agnostic how-to guides.

      Additionally, model transfer has been improved: retraining now freezes most layers by default, accelerating convergence and stabilizing fine-tuning for new datasets.

      Specifics:

      (1) The software can only handle 2D 'widefield' time-lapse imaging datasets. It should be noted that many studies that examine cell-cell interactions in vitro also used confocal microscopy and acquired the time-lapse images in 3D z-stacks to enable the reconstruction of entire cell volumes from multiple optical sections along the z-axis.

      Given that almost all of the implemented segmentation (StarDist, Cellpose) and tracking (bTrack) packages already support the handling of 3D datasets, it is unclear why CellDetective was designed to only work with 2D datasets.

      As noted above, extending the support for 3D images would allow the scope and utility of this software to be further extended for imaging studies acquired in z-stacks. As an example, the dense clustering of effector cells in Figure 4 had prevented accurate segmentation due to the 2D nature of the experimental dataset. More importantly, support for a 3D dataset could also allow for the tracking of fluorescent protein-based sub-cellular as well as membrane protein localization during cell-cell interactions.

      Furthermore, it also widens the potential applicability for analyzing datasets from 3D organoid imaging and perhaps even intravital two-photon microscopy.

      Scope and technical difficulties

      We thank the reviewer for this suggestion and maintain our position that Celldetective is purposefully designed for high-throughput, high-temporal-resolution 2D imaging. We have now articulated this rationale more clearly in the revised manuscript (see Discussion lines 414-417).

      Specifically, we emphasize that Celldetective's two core strengths — harnessing the statistical power of cell populations together with multiplexing biological conditions, and dynamic analysis of fast cellular events — both benefit from maximizing temporal resolution and field-of-view throughput. In our experience, Z-stack acquisition would reduce the achievable time resolution and throughput (in terms of captured events and parallel conditions) below acceptable levels for the minute-scale dynamics relevant to immunological assays.

      That said, the modular architecture and the choice of 3D-compatible backends (StarDist, Cellpose, bTrack) leave the door open for community-driven 3D extensions in the future. We note in the revised manuscript that Celldetective is "specifically optimized for highthroughput, high-temporal-resolution imaging of quasi-2D systems" and that "by prioritising temporal sampling over Z-axis depth, Celldetective enables the capture of rapid biological dynamics that are often the focal point of interaction studies, where Z-stacking would otherwise limit throughput or resolution."

      (2) The software in its current form only allows the broad demarcation of the cells examined into two populations: targets and effectors. This limits the number of cell populations that can be examined for their interactions. It might be more useful to just allow multiple user-defined populations instead of restricting the populations to target and effector cells only.

      Extension to more than 2 custom populations

      This has been fully implemented. Starting with version 1.4, Celldetective supports an arbitrary number of user-defined cell populations with user-chosen names. The restriction to "targets" and "effectors" has been removed. When creating a new experiment, users can now define any number of populations with custom labels (e.g., nk, rbc, macrophages, tumor_cells). The experiment configuration file stores this information in a generic [Populations] section. The control panel, segmentation, measurement, tracking, event detection, and neighbourhood modules all operate on these user-defined populations.

      We illustrate this in the documentation with a figure showing a 3-population configuration (see the "How to create a new experiment" guide).

      Neighbourhood analysis (interactions) currently supports pairwise interactions between any two populations (including same-population neighbourhoods), which covers the most common biologically relevant scenarios. We note that three-way (multipartite) interactions involve a substantially higher level of complexity and are, to our knowledge, not currently addressed by biologists in this context.

      (3) Similarly, subsetting of each of the populations could be made more intuitive. Although it is possible to define subsets of cells using the "Custom classification" function under the "Measure" module with user-defined parameters, visualization of multiple groups remains unintuitive and it appears that only one custom classified group can be selected and visualized at any given time in the Signal Annotator under Measurement instead of allowing visualization of multiple (custom defined) groups of cells in different colors. It is also unclear how, if possible at all, to visualize a custom group of cells in the Signal Annotator under the Detect Events module.

      Subsetting and visualization of multiple groups

      The reviewer noted that defining cell subgroups through the Custom Classification was unintuitive, and that only one classified group could be visualized at a time.

      We first clarify that Celldetective distinguishes between two visualization tools: the static measurement annotator (under Measure), which displays groups and characteristic groups on a per-frame basis, and the Event Annotator (under Detect Events), which displays event classes along temporal signal traces. The reviewer's request to visualize multiple customdefined groups in different colors falls under the measurement annotator.

      We have addressed this concern with a multi-label characteristic group workflow: users perform successive threshold classifications to isolate individual phenotypes of interest (e.g., "spread", "dead", "high-intensity"), then merge these binary columns into a single characteristic group via the table view (Math → Merge states…). Each combination of states is automatically mapped to a distinct label and color. This merged column can then be explored in the measurement annotator, effectively displaying all subgroups simultaneously in different colors.

      For more complex classification logic, the classification tool supports logical AND/OR operators for composing conditions, enabling flexible definition of subgroups without scripting.

      The Event Annotator, by contrast, operates on a single event class at a time by design, as it is intended for reviewing and annotating individual event types along temporal signal traces; multi-group visualization is not applicable in this context.

      Software issues:

      (4) When initially tested on v1.3.9, the Segment module could not be initiated (with the error message AttributeError: 'WindowsPath' object has no attribute 'endswith' when attempting to run segmentation).

      Update: this has been fixed in v1.3.9.post4 dated February 7th, 2025.

      (5) Further testing was then performed by downgrading the software to v1.3.1. While testing the ADCC demo experiment (https://celldetective.readthedocs.io/en/latest/adcc-example.html), the workflow was stuck at attempts to initiate the Detect Events step:

      AssertionError: No signal matches with the requirements of the model ['dead_nuclei_channel_mean', 'area']. Please pass the signals manually with the argument selected_signals or add measurements. Abort.

      (Update: fixed in the latest v1.3.9.post4 version dated February 7th, 2025)

      (6) Random bugs causing the software to crash. Example: switching characteristic to 'status_color' in the Signal Annotator under Measurement caused the software to crash (v1.3.9.post4):

      TypeError: ufunc 'isnan' is not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule 'safe'

      (7) Overall, when exploring the functionality of the software, there have been multiple instances of software crashes when clicking/switching around to show different parameters, etc.

      This reviewer understands the difficulties and time involved in bug fixing and hopes that the experience could have been much smoother and that the software behaves much more stably in order to maximize its useability.

      General stability — bug fixes and crash instances

      We have made comprehensive improvements to software stability since the review period:

      100+ bug fixes across v1.4.0–v1.5.0, systematically addressing crashes, edge cases, and error handling throughout the GUI.

      Expanded automated test suite: the project now includes 43 test files (26 GUI-level tests + 17 unit test files) covering segmentation, tracking, measurements, event detection, filters, preprocessing, neighbourhoods, viewers, table operations, and more.

      These tests run automatically via CI/CD on every commit.

      Lazy imports for heavy dependencies (e.g., TensorFlow) to reduce startup time and potential import-order crashes.

      Improved error handling: informative error messages instead of silent crashes; graceful fallbacks when optional dependencies are missing.

      Usage and stability can be verified via GitHub traffic statistics and CI/CD action metrics.

      Reviewer #2 (Public review):

      Summary:

      Immune assays enable the analysis of immune responses in vitro. These assays generate time series image data across several experimental conditions. The imaging parameters such as the imaging modality and the number of channels can vary across experiments. A challenge in the field is the lack of (open source) tools to process and analyze these data. R. Torro, et. al. developed an open source end-to-end pipeline for the analysis of image data from these immune assays. The pipeline is designed with a GUI and is suited for experimental biologists with no coding experience. The authors have incorporated several existing methods and tools for individual tasks such as for segmentation and cell tracking, and incorporated them with custom methods where necessary such as for tracking cell state transitions.

      Strengths:

      (1) The tool is extremely well-documented and easy to install.

      (2) Applicable to a wide variety of imaging modalities and analysis.

      (3) There are several different options for each step, such as segmentation using traditional methods or deep learning methods, and all the analysis steps are integrated in one place with a GUI. The no-coding requirement makes this a very powerful tool for biologists and has the potential to enable a wide variety of analyses.

      We are grateful for the recognition of the tool's documentation quality, ease of installation, and versatility.

      Weakness:

      (1) It would be good to provide documentation on how to make the tool applicable for applications and analysis other than for immune profiling since most methods integrated here are applicable well beyond immune profiling. For example, a user might want to use the tool just for the segmentation of their IF microscopy-images.

      Documentation for non-immune applications

      We have undertaken a major documentation overhaul following the Diátaxis framework (Tutorials, How-to Guides, Explanations, Reference). The documentation now includes:

      24 How-to guides covering individual tasks (segmentation, tracking, measurements, background correction, texture analysis, spot detection, channel alignment, survival analysis, interactions, event annotation, etc.), written in a modality-agnostic manner so that users from any application domain can follow them.

      Concept pages explaining key abstractions (data organization, population-specific segmentation, single-cell events, survival, neighbourhoods) without assuming an immunology context.

      Expanded tutorials, including the RICM spreading assay and the ADCC co-culture assay, which serve as worked examples that can be adapted to other biological systems.

      The overview now presents Celldetective as "an open-source Python platform designed for biologists to study interacting cell populations in multimodal time-lapse microscopy", explicitly broadening the scope beyond immune profiling.

      Additionally, the user-defined population naming (see Reviewer #1, point 2) naturally makes the tool more accessible to non-immunology users, as they are no longer constrained by "target/effector" terminology. The following articles from the literature refer to Celldetective in microbiology (10.1128/mbio.03342-25), for stem cells (10.3390/ jimaging11100371), or for CAR-T cells (10.1101/2025.06.24.661290v1, 10.1101/2025.07.25.666844v1), beyond the applications of this manuscript.

      (2) They applied Celldetective to two immune assays. The authors present the results from these assays and use the results to validate their assay. However, they have not included data that demonstrates results obtained via this pipeline are comparable to results obtained with other pipelines and/or if these results are consistent with what is expected in the literature.

      Comparison with other pipelines / literature validation

      We emphasize that most of the presented data are original and do not have published equivalents, making direct pipeline-to-pipeline comparison impossible in many cases. We note that, to our knowledge, no existing open-source pipeline performs the complete endto-end analysis that Celldetective offers (from preprocessing through segmentation, tracking, event detection, neighbourhood analysis, to population-level survival curves), making a head-to-head software comparison impractical. Nevertheless, some recent publications have tested the software for various features (10.1128/mbio.03342-25, 10.1101/2025.07.25.666844v1), and results are in line with existing solutions when comparison is possible.

      We reserve systematic comparison with traditional (non-microscopy-based) immunological assays for future dedicated studies, as we consider it out-of-scope for this software-focused manuscript.

      Additional items for the revised manuscript

      Manuscript changes (including private recommendations made by reviewers)

      Modifications or additions in text appear in red:

      Abstract: lines 15-17, 20-22, 24-26

      Introduction: lines 71-72

      Results: lines 91, 103, 127-137, 170-171, 196-201, 239-242, 250-252, 255-257, 261-264,

      266-269, 292-295, 303, 319-321

      Figure captions fig.1, fig. 2, fig. 3, fig. 5

      Discussion: 372-377, 384-387, 406-407, 414-417, 418

      Materials and Methods: lines 462-464, 542-546, 673-677, 684-685, 733-734

      Figure S10

      References have been updated.

      Article statistics (as of 30 Apr 2026)

      2799 views

      162 downloads

      7 citations

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor points:

      (1) For the study involving LAMP1 measurement, a representative image of LAMP1 antibody staining should be included.

      We added a new supplementary figure Fig S10 with reference to it on line 304

      (2) In Figure 5B, can the authors comment on the ostensibly higher effector velocity under HER2+ target conditions? Is this caused by variation within assay, and whether they have been confirmed in independent wells/experiments with the same conditions?

      Thanks to the reviewer for this remark; We have added a comment on lines 320-322

      As we don’ t have systematic replicates for this effect, we tentatively attribute it to a variation in the target cell coverage.

      (3) It is not clear why in the Signal Annotator under Measurement, the movie playback is performed with a user-draggable slider but in the Signal Annotator under Detect Events, the movie plays with only a Play/Stop button with no options to modify the playback speed or to advance the movie frame-byframe.

      This has been addressed in Celldetective v1.5.0. The Signal Annotator for event detection now provides frame-by-frame navigation buttons, an autoplay mode for natural playback of dynamics, and on-the-fly animation speed control, matching the functionality available in the Measurement viewer.

      Reviewer #2 (Recommendations for the authors):

      (1) Main text

      One major comment throughout the manuscript is that the experimental setup sections (ie lines 143149; 221-226 and interspersed in the section 'From a single time point to a dynamic readout of effector-target interactions') are hard to follow. It is clear that the tool can achieve what is described, but it is hard to follow why the experiments were set up that way and it took digging through methods and figure captions to understand what the setup was in terms of antibodies (what are the specificity, why are they chosen, what are they proxies for). Each section has some of that information but not jointly. It would help to have a high-level description of the experimental aim and then how this has been achieved in the setup with details on the antibodies, including targets and what their role would be. This would help with for instance understanding what the purpose of the PI stain as a measure introduced in line 245 is, or how the antibodies in experiment one relate to the ones in experiment 2, etc. The hardest part to parse was the section on effector-target interactions, specifically how the simulation is set up and why. The clarity of the manuscript could really benefit from a reworking of these paragraphs.

      The mentioned paragraphs have been rewritten following the reviewer’s suggestions.

      Lines 127-137: The RICM assay intro has been substantially rewritten in red, providing high-level experimental aim, bsAb function, surface preparation, and RICM rationale — all in a single coherent block.

      Lines 196-201: The ADCC assay intro is rewritten in red with clear description of bsAb purpose, cell types, HER2 variation, PI monitoring, and fluorescent labels.

      In the same spirit, we also added a biological context to introduce the last section of results on lines 261-264.

      It is not clear what implications the statement in line 267 has for the user.

      A comment was added on lines 239-242

      In line 191, it is stated that the position-based approach showed a spike that was not observed in the mask-based approach. It is not clear what the spike means, is it an artifact or a real phenomenon discovered by the position-based approach; this is important as the t_spread definition would differ depending on which segmentation is used

      A comment was added on line 167. It does not impact the definition of t_spread since the peak is observed during the spreading phase.

      In the co-culture assay, StarDist approach is used to segment the MCF7 cell line while Cellpose is to segment the NK cells. Please provide a rationale for selecting these differing approaches for segmentation.

      A justification was added on lines 265-267

      The impact of cell density was looked at for 32 micrometers, however, it is not clear why this cut-off was chosen.

      A justification was added on lines 250-252

      (2) Methods

      Lines 743/744: what type of manual adjustments? If important for usable, should be described in detail.

      Details have been added on lines 674-678

      If specifying what software was used for plots, then also mention which ones are used for exceptions.

      Details are provided in a new dedicated paragraph, lines 735-739

      (3) Discussion

      Conclusion in line 404 - direct protective effect, or just sampling effect?any data for either, or too strong a conclusion otherwise.

      We have added a short discussion on this topic, lines 372-377.

      Preliminary analysis of ADCC rates stratified by local target density and number of effector neighbours suggests that both factors contribute (unpublished data), and Celldetective's neighbourhood analysis module provides the tools to perform such stratified survival studies.

      I don't understand the implications in line 412, maybe just the wording choice. Prior studies in T cells could not resolve, but would now be feasible with celldetective? Or for T cells this is still not possible due to other experimental constraints?

      Thanks for this remark; indeed it could not be resolved yet for T cells, to our knowledge, but would be facilitated by celldetective.

      A comment was added on lines 385-388

      (4) Figures

      (a) Font sizes in all figures are generally too small.

      Fonts in all figures have been enlarged.

      (b) Figure 2

      F, G, H: clarify caption.

      F: single cells grey traces, average colored line?

      G: what's the confidence/error interval?

      H: State the statistic and meaning of the qualitative assessment.

      DONE

      (c)Figure 3:

      F/G: choice of 3.5 as neighbouring cell is not motivated; mode would have been at 4 and choosing a non-integer for cell counts seems strange from a biological perspective.

      A comment has been added in the caption.

      E/G: what is the error/confidence interval?

      DONE

      (d) Figure 5:

      A: error bars?

      ADDED

      (5) Minor typos/word choices

      (a) Typo in line 59 - double the.

      OK

      (b) Typo in line 214 - upper case U in middle of sentence.

      OK

      (c) Typo/word choice in 516/17 - cells were split? Kept instead of keep.

      OK

      Typo 706; missing space between time and using.

      OK

      All corrected

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper investigates the physical basis of epithelial invagination in the morphogenesis of the ascidian siphon tube. The authors observe changes in actin and myosin distribution during siphon tube morphogenesis using fixed specimens and immunohistochemistry. They discover that there is a biphasic change in the actomyosin localization that correlates with changes in cell shapes. Initially, there is the well-known relocation of actomyosin from the lateral sides to the apical surface of cells that will invaginate, accompanied by a concomitant lengthening of the central cells within the invagination, but not a lot of invagination. Coincident with a second, more rapid, phase of invagination, the authors see a relocalization of actomyosin back to the lateral sides of the cells. This 2nd "bidirectional" relocation of actin appears to be important because optogenetic inhibition of myosin in the lateral domain after the initial invaginations phase resulted in a block of further invagination. Although not noted in the paper, that the second phase of siphon invagination is dependent on actomyosin is interesting and important because it has been shown that during Drosophila mesoderm invagination that a second "folding" phase of invagination is independent of actomyosin contraction (Guo et al. elife 2022), so there appear to be important differences between the Drosophila mesoderm system and the ascidian siphon tube systems.

      Using the experimental data, the authors create a vertex model of the invagination, and simulations reveal a coupled mechanism of apicobasal tension imbalance and lateral contraction that creates the invagination. The resultant model appears to recapitulate many aspects of the observed cell behaviors, although there are some caveats to consider (described below).

      We thank the reviewer for the insightful summary and for bringing the important study by Guo et al. (2022) to our attention. We have now added a dedicated comparison with Drosophila ventral furrow invagination in the Discussion, explicitly highlighting that the second rapid folding phase in Drosophila does not require lateral contractility, whereas in our system lateral contractility is obligatory for the accelerated invagination stage.

      Strengths:

      The studies and presented results are well done and provide important insights into the physical forces of epithelial invagination, which is important because invaginations are how a large fraction of organs in multicellular organisms are formed.

      Thank you for this positive assessment and for recognizing the significance of our work in elucidating the physical mechanisms underlying fundamental morphogenetic processes. We have striven to provide a comprehensive and rigorous analysis, and are grateful for this encouraging feedback.

      Weaknesses:

      (1) This reviewer has concerns about two aspects of the computational model. First, the model in Figure 5D shows a simulation of a flat epithelial sheet creating an invagination. However, the actual invagination is occurring in a small embryo that has significant curvature, such that nine or so cells occupy a 90-degree arc of the 360-degree circle that defines the embryo's cross-section (e.g., see Figure 1A). This curvature could have important effects on cell behavior.

      Thank you for bringing up the issue of tissue curvature. In the initial version of our model, we treated the tissue as flat based on the local geometry of the anterior epidermis. Although the embryo at 13 hpf indeed possesses significant curvature, its overall transverse cross-section is approximately elliptical, and the region undergoing invagination is situated in a relatively low-curvature zone, occupying only a 30° ∼ 40° arc of the entire tissue. More importantly, the embryo undergoes anisotropic elongation and expansion, becoming significantly flattened during the accelerated invagination stage, eventually adopting a very flat geometry by 18 hpf. We have now included Figure 5—figure supplement 1 to clarify these global morphological transitions.

      Nevertheless, the curvature does exist during the early stages, and we agree that clarifying its potential role is essential. Therefore, in the revised manuscript, we have updated our vertex model to incorporate a simplified circular geometry. Furthermore, unlike Drosophila ventral furrow formation (Guo et al., eLife, 2022), the invagination here eventually forms a hollow tubular structure, which led us to introduce a surface bending stiffness term into the mode. Although global tissue growth is not explicitly modeled, we explored the impact of curvature by varying the initial system size. Our results demonstrate that the invagination process, driven by apico-basal tension imbalance and lateral contraction, is highly localized and remains robust across different curvatures.

      (2) The second concern about the model is that Figure 5 D shows the vertex model developing significant "puckering" (bulging) surrounding the invagination. Such "puckering" is not seen in the in vivo invagination (Figure 1A, 2A). This issue is not discussed in the text, so it is unclear how big an issue this is for the developed model, but the model does not recapitulate all aspects of the siphon invagination system.

      Thank you for pointing out this. In our experiments, the similar "puckering" shape is observed during the early stages of morphogenesis (~17 hpf, as seen in Figure 1A) when the tissue size is relatively small. However, this feature rapidly disappears as the tissue grows and the overall geometry becomes flatter. This suggests that "puckering" is more pronounced in highly curved epithelia, a phenomenon that aligns with mechanical expectations. Previous vertex models of Drosophila ventral furrow formation do not exhibit this effect (Brodland et al., 2010; Polyakov et al., 2014), because they modeled cells within a rigid unmovable boundary. However, in our system of siphon morphogenesis, a tubular structure ultimately forms in the epithelium without strong boundary constraints. Thus, the mechanical boundary conditions are basically different.

      Also, the formation of a hollow tubular structure—supported by strong F-actin accumulation at the tissue surface—indicates a bending stiffness of surface tissue (Figure 1), which we have incorporated into the model. This bending term enforces smooth curvature transitions, which can manifest as a "puckering" shape surrounding the invagination. In our previous flat-geometry model, this significant bending stiffness led to a "puckering" effect surrounding the invagination. In our updated curved vertex model, this phenomenon also exists and is found to be related to tissue curvature. By simulating a larger system with low curvature (N = 324 cells in Figure 6D), we find that this puckering is significantly reduced. This confirms that the shape discrepancy is a size-dependent effect of the bending constraints within a fixed system size that did not account for tissue growth. In biological development, continuous growth and flattening of the embryo diminish this effect (Figure 5—figure supplement 1), aligning our model's predictions.

      Furthermore, we note that the cell-cell adhesion between the surface epithelium and the internal bulk cells (a factor not explicitly captured in our current model) likely further suppresses such evagination in vivo, as outward puckering would necessitate the coordinated deformation of the underlying tissues. We aim to investigate the interplay between global growth and local active forces in future work. We have added a detailed description and mechanical explanation of these simulated shapes in the revised manuscript.

      (3) In Figure 2A, Top View, and the schematic in Figure 2C, the developing invagination is surrounded by a ring of aligned cell edges characteristic of a "purse string" type actomyosin cable that would create pressure on the invaginating cells, which has been documented in multiple systems. Notably, the schematic in Figure 2C shows myosin II localizing to aligned "purse string" edges, suggesting the purse string is actively compressing the more central cells. If the purse string consistently appears during siphon invagination, a complete understanding of siphon invagination will require understanding the contributions of the purse string to the invagination process.

      Thank you for this excellent observation. We agree that the ring-like actomyosin structure is a prominent feature during the initial stages of invagination, and its potential role warrants discussion. We carefully re-examined our data. Our analysis confirms that this myosin ring is most pronounced during the early initial invagination stage. This inward compression from the periphery would work in concert with apical constriction to help shape the initial invagination. However, this ring-like myosin pattern significantly diminishes during the accelerated invagination stage, indicating that sustained compression from the purse string is not required for the entire process. We have added a discussion of this point in the revised manuscript. We also agree with that future experiments using laser ablation or optogenetic inhibition specifically targeting this actomyosin ring would be valuable to further dissect its precise contribution during the early invagination stage, and we have noted this as a future direction in the Discussion.

      (4) The introduction and discussion put the work in the context of work on physical forces in invagination, but there is not much discussion of how the modeling fits into the literature.

      We thank the reviewer for this suggestion. We have now incorporated additional references and discussion regarding existing theoretical models and the physical forces involved in tissue invagination. These previous studies provided the foundational framework for our updated curved vertex model. We have also added an explanation of how our model differs from these existing works and discussed potential future directions for further investigation.

      Reviewer #2 (Public review):

      Summary:

      The authors propose that bidirectional translocation of actomyosin drives tissue invagination in Ciona siphon tube formation. They suggest a two-stage model where actomyosin first accumulates apically to drive a slow initial invagination, followed by translocation to lateral domains to accelerate the invagination process through cell shortening. They have shown that actomyosin activity is important for invagination - modulation of myosin activity through expression of myosin mutants altered the timing and speed of invagination; furthermore, optogenetic inhibition of myosin during the transition of the slow and fast stages disrupted invagination. The authors further developed a vertex model to validate the relationship between contractile force distribution and epithelial invagination.

      Thank you for your thoughtful and accurate summary of our work and for your constructive critique.

      Strengths:

      (1) The authors employed various techniques to address the research question, including optogenetics, the use of MRLC mutants, and vertex modelling.

      (2) The authors provide quantitative analyses for a substantial portion of their imaging data, including cell and tissue geometry parameters as well as actin and myosin distributions. The sample sizes used in these analyses appear appropriate.

      (3) The authors combined experimental measurements with computer modeling to test the proposed mechanical models, which represents a strength of the study. It provides a framework to explore the mechanical principles underlying the observed morphogenesis.

      We are grateful for your positive assessment of the multidisciplinary approaches, quantitative analyses, and the integration of modeling with experiments.

      Weaknesses:

      (1) The concept of coordinated and sequential action of apical and lateral actomyosin in support of epithelial folding has been documented through a combination of experimental and modeling approaches in other contexts, such as ascidian endoderm invagination (PMID: 20691592) and gastrulation in Drosophila (PMIDs: 21127270, 22511944, 31273212). While the manuscript addresses an important question, related findings have been reported in these previous studies. This overlap reduces the degree of novelty, and it remains to be clarified how their work advances beyond these prior contributions.

      We thank the reviewer for raising this important point. In the revised Introduction and Discussion, we have explicitly distinguished our findings from prior studies. Specifically: (1) Unlike ascidian endoderm invagination, where actomyosin shifts from apical to basolateral (Sherrard et al., 2010), our system exhibits a bidirectional redistribution between apical and lateral domains, with the basal domain playing a passive role. (2) Unlike Drosophila ventral furrow invagination, where lateral contractility is not essential for the second folding phase (Guo et al., 2022), our optogenetic inhibition demonstrates that lateral contractility is obligatory for the accelerated invagination stage. These comparisons, now clearly stated in the Introduction and Discussion, establish bidirectional actomyosin redistribution as a distinct mechanical paradigm for sequential morphogenesis. We believe these revisions adequately clarify how our work advances beyond prior contributions.

      (2) One of the central statements made by the authors is that the translocation of actomyosin between the apical and lateral domains mediates invagination. The use of the term "translocation" infers that the same actomyosin structures physically move from one location to another location, which is not demonstrated by the data. Given the time scale of the process (several hours), it is also possible that the observed spatiotemporal patterns of actomyosin intensity result from sequential activation/assembly and inactivation/disassembly at specific locations on the cell cortex, rather than from the physical translocation of actomyosin structures over time.

      We thank the reviewer for this important point. We agree that our data do not demonstrate physical translocation of actomyosin structures, and that the observed patterns could arise from sequential assembly/disassembly over time. To avoid overinterpretation, we have replaced “translocation” with “redistribution” throughout the manuscript (including the title) and toned down the language in the Results and Discussion.

      (3) Some aspects of the data on actomyosin localization require further clarification. (1) The authors state that actomyosin translocation is bidirectional, first moving from the lateral domain to the apical domain; however, the reduction of the lateral actomyosin at this step was not rigorously tested. (2) During the slow invagination stage, it is unclear whether myosin consistently localizes to the apical cell-cell borders or instead relocalizes to the medioapical domain, as suggested by the schematic illustration presented in Figure 2C. (3) It is unclear how many cells along the axis orthogonal to the furrow accumulate apical and lateral myosin.

      Thank you for your insightful comments, which will help us significantly improve the clarity and rigor of our actomyosin localization analysis. To address the points raised, we undertake several key revisions: First, we have added new quantitative analyses of active myosin intensity from earlier time points (14-15 hpf) to rigorously support the initial lateral-to-apical redistribution phase (Figure 2B). Second, the schematic in Figure 2C has been corrected to show myosin at the apical cell‑cell borders. We have clarified that redistribution occurs in a domain of approximately 15‑20 cells (the invagination primordium), not only the center cell.

      (4) The overexpression of MRLC mutants appears to be rather patchy in some cases (e.g., in Figure 3A, 17.0 hpf, only cells located at the right side of the furrow appeared to express MRLC T18ES19E). It is unclear how such patchy expression would impact the phenotype.

      Thank you for your observation. We acknowledge that mosaic expression is common in Ciona electroporation. For all quantitative analyses, we only selected embryos in which the central cell, along with more than half of the surrounding cells in the primordium, showed clear expression of the plasmid. This selection criterion has been added to the Materials and Methods section.

      (5) In the optogenetic experiment, it appears that after one hour of light stimulation, the apical side of the tissue underwent relaxation (comparing 17 hpf and 16 hpf in Figure 4B). It is therefore unclear whether the observed defect in invagination is due to apical relaxation or lack of lateral contractility, or both. Therefore, the phenotype is not sufficient to support the authors' statement that "redistribution of myosin contractility from the apical to lateral regions is essential for the development of invagination".

      We have performed the additional immunostaining experiment of myosin II. The new data (Figure 4—figure supplement 2) showed that light stimulation specifically reduced lateral myosin intensity without significantly affecting apical myosin compared to the dark control. Therefore, the observed block of invagination is primarily due to loss of lateral contractility.

      (6) The vertex model is designed to explore how apical and lateral tensions contribute to distinct morphological outcomes. While the authors raise several interesting predictions, these are not further tested, making it unclear to what extent the model provides new insights that can be validated experimentally. In addition, modeling the epithelium as a flat sheet and not accounting for cell curvature is a simplification that may limit the model's accuracy. Finally, the model does not fully recapitulate the deeply invaginated furrow configuration as observed in a real embryo (comparing 18 hpf in Figure 5D and 18 hpf in Figure 1A) and does not fully capture certain mutant phenotypes (comparing 18 hpf in Figure 5F and 18 hpf in Figure 3B right panel).

      Thank you very much for these helpful and constructive comments. We have addressed your concerns through the following model updates and clarifications.

      First, we have reformulated our vertex model from a flat sheet to a curved geometry that incorporates initial tissue curvature. We found that the core mechanical mechanism, mediated by the coupling of apical and lateral active contraction, consistently recapitulates the experimental invagination process. By independently inhibiting apical or lateral contractions in the model, we further clarified their distinct mechanical contributions to tissue bending and cell shortening.

      Regarding the model predictions concerning the apical-to-lateral redistribution of actomyosin in the original version (previously shown in Figure 6E-H), we agree that these lacked direct experimental validation in the current study and may have strayed from the primary focus on the invagination mechanism itself. Therefore, we have removed these predictive components from the revised manuscript. Instead, we have refocused our analysis on the robustness of the localized active process across tissues of varying sizes and curvatures, particularly because the in vivo invagination is accompanied by global tissue growth and geometry changes.

      Finally, we acknowledge that the simulated final shapes do not perfectly match the experimental geometry in every detail. We attribute these discrepancies to the omission of global tissue growth and the simplification of cell-cell adhesions between the surface epithelium and internal bulk cells. While these factors are not the primary drivers of the invagination, they undoubtedly refine the local morphology. We have added discussions of these limitations in the revised manuscript and aim to incorporate precise experimental measurements of tissue growth and inter-layer interactions in future modeling efforts.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript by Qiao et al., the authors seek to uncover force and contractility dynamics that drive tissue morphogenesis, using the Ciona atrial siphon primordium as a model. Specifically, the authors perform a detailed examination of epithelial folding dynamics. Generally, the authors' claims were supported by their data, and the conceptual advances may have broader implications for other epithelial morphogenesis processes in other systems.

      Thank you for your positive summary and for recognizing the broader implications of our work.

      Strengths:

      The strengths of this manuscript include the variety of experimental and theoretical methods, including generally rigorous imaging and quantitative analyses of actomyosin dynamics during this epithelial folding process, and the derivation of a mathematical model based on their empirical data, which they perturb in order to gain novel insights into the process of epithelial morphogenesis.

      Thank you for highlighting the strengths of our multidisciplinary methodology.

      Weaknesses:

      There are concerns related to wording and interpretations of results, as well as some missing descriptions and details regarding experimental methods.

      We have revised the manuscript to address your concerns regarding the wording and the details of the methodology.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Based on the feedback from the reviewers, a focus on the following major points has the potential to improve the overall assessment of the significance of the findings and the strength of the evidence:

      (1) It would be helpful to clearly articulate how these findings advance the field beyond what has already been demonstrated or suggested in other systems.

      We thank the editor for this helpful suggestion. To better articulate how our findings advance the field, we have revised both the Introduction and Discussion to explicitly contrast our system with previously studied invagination models. Specifically, we highlight that our work demonstrates a bidirectional redistribution of actomyosin between apical and lateral domains, which differs from the apical-to-basolateral shift reported in ascidian endoderm invagination. Moreover, we emphasize that lateral contractility is obligatory for the accelerated invagination stage in our system, whereas in Drosophila ventral furrow invagination the second folding phase can proceed without it. These comparisons have been clearly presented in the revised manuscript. We think our findings represent a distinct mechanical paradigm for sequential epithelial morphogenesis.

      (2) It would be helpful to clarify the meaning of "translocation" and more explicitly describe the temporal and spatial patterns of active myosin localization during the two steps of invagination.

      We have replaced the term “translocation” with “redistribution” throughout the manuscript, including the title. We have also added new quantitative analyses of active myosin intensity from earlier time points (14–15 hpf) to rigorously support the initial lateral-to-apical redistribution phase (Figure 2B). High-resolution top-view images have been included to show the ring‑like localization of myosin at the apical cell‑cell junctions during the initial stage (Figure 2A). The schematic in Figure 2C has been corrected to accurately reflect the predominant localization of active myosin at the apical cell‑cell borders.

      (3) It would be helpful to explain how the optogenetic data support the conclusion that "redistribution of myosin contractility from the apical to lateral regions is essential for the development of invagination".

      We have performed additional experiments combining optogenetic inhibition with subsequent immunostaining of active myosin II (anti-pS19 MRLC). We quantitatively compared the distribution of actomyosin in light‑stimulated versus dark‑control embryos. The new data show that after light exposure, lateral myosin intensity is significantly reduced compared to the dark control, whereas apical myosin levels decrease similarly in both groups. This indicates that the optogenetic manipulation effectively attenuates lateral contractility during the accelerated invagination stage without affecting concurrent apical contractility changes. These results directly support the conclusion that lateral contractility acquisition is essential for invagination progression. (Figure 4—figure supplement 2)

      (4) It would be helpful to describe how the modeling work fits within the existing literature on modeling epithelial folding and to address discrepancies between the model and the actual biological observations, such as tissue curvature, limited invagination depth in the model, and the "puckering" surrounding the invagination. In addition, certain descriptions of the modeling results should be clarified, as suggested by Reviewer #3.

      We thank the referees for the detailed and constructive comments on our modeling work. In response to these suggestions, we have significantly updated the theoretical section of the manuscript. Specifically, we have reformulated the vertex model within a curved geometry that represents the entire tissue, and revised the subsequent analyses to better clarify the mechanical principles driving the observed morphogenesis. We have added relevant references and discussed the mechanistic connections and distinctions between our model and previous studies on epithelial invagination. We hope that our point-by-point responses of the modeling work and the corresponding revisions in the manuscript adequately address the reviewers’ concerns.

      (5) It would be helpful to elaborate on the methods for quantitative image analysis and statistical tests.

      We have thoroughly expanded the Materials and Methods section by adding a dedicated subsection “Quantification and statistical analysis”. This subsection provides step‑by‑step descriptions of how apical, lateral, and basal domains were defined (segmented line, width 1 μm), how normalization was performed (basal intensity set to 1), how center cell height, invagination depth, and lateral cell distance were measured (referencing Figure 1B), and what statistical tests were used (two‑tailed Student’s t‑test, with significance levels indicated). (see revised Materials and Methods, “Quantification and statistical analysis” subsection)

      Reviewer #1 (Recommendations for the authors):

      (1) This reviewer has concerns about two aspects of the model. First, the model in Figure 5D shows a simulation of a flat epithelial sheet creating an invagination. However, the actual invagination is occurring in a small embryo that has very significant curvature, such that nine or so cells occupy a 90-degree arc of the 360-degree circle that defines the embryo's section (e.g., see Figure 1A). This curvature could potentially have important effects on cell behavior. Ideally, the developed model would reflect the actual geometry of the observed behavior. A more nuanced analysis would provide important insight into whether the embryo's curvature makes a difference. Importantly, any result comparing the planar versus curved system would be interesting because if the model worked equally well in the high curvature or planar systems, the model is robust, or if invagination requires different strategies for high curvature and for planar systems, this is an important finding that reveals the importance of local geometries. I don't think the consideration of invagination from a planar vs curved epithelium has been previously modeled.

      We fully agree with the reviewer that comparing planar versus curved systems provides valuable insights into the invagination mechanism. As we addressed in our response to Reviewer #1 (Public Review) - Weakness (1), we have now updated our vertex model to incorporate curved geometries and introduced surface bending stiffness to better reflect the embryo's actual shape. Our systematic comparison reveals that the invagination process, driven by apico-basal tension imbalance and lateral contraction, is indeed highly localized and remains robust across different initial curvatures. We have added Figure 5—figure supplement 1 and corresponding discussions in the revised manuscript to highlight these findings on model robustness and the role of local geometry.

      (2) The second concern about the model is that Figure 5D shows the vertex model developing significant "puckering" (evagination) surrounding the invagination. Such "puckering" is not seen in the in vivo invagination (Figures 1A, 2A). This issue is not discussed in the text, so it is unclear how big an issue this is for the developed model. A discussion of this issue in the text would be appropriate. Maybe puckering goes away if a curved epithelium is modeled?

      Thank you for this comment. In our model, the "puckering" effect naturally arises due to the presence of surface bending stiffness and the absence of rigid boundary constraints, which resembles the tissue morphology observed at 17 hpf in our experiments. However, our updated simulations show that this effect significantly diminishes as the tissue curvature decreases. We have addressed this concern in detail in our response to Reviewer #1 (Public Review) - Weakness (2) and have included the relevant analysis and discussions in the revised manuscript.

      (3) Because of the puckering, it is unclear in the model what measurement is being used to define the invagination depth in Figure 5E. Is the depth from the maximal height of the surrounding epithelial cells? Or the location of the apical surface before invagination begins? It would be helpful to have that parameter better defined, and it would also be helpful to add a line to Figure 5D showing how the reference point for invagination depth.

      Thank you for your suggestion. We measured the vertical distance from the baseline connecting the maximal height of apical midpoints of the surrounding cells to the apical surface of the center cell, which is consistent with our experimental measurements. We have now added a schematic line and indicators to Figure 5D.

      (4) In Figure 2A Top View, as well as the schematic in Figure 2C, the developing invagination is surrounded by a ring of aligned cell edges characteristic of a "purse string" type actomyosin cable that would create pressure on the invaginating cells, which have been documented in multiple systems. Notably, the schematic in Figure 2C shows myosin II localizing to aligned "purse string" edges, suggesting the purse string is actively compressing the more central cells. If the purse string consistently appears during siphon invagination, a complete understanding of siphon invagination will require understanding the contributions of the purse string to the invagination process. For this paper, a discussion of the possible involvement of a purse string would be helpful for the readers, but follow-up work could include laser cutting or optogenetic blockage of the purse string contractility.

      Thank you for your suggestion. We agree that the ring-like actomyosin structure is a prominent feature during the initial stages of invagination, and its potential role warrants discussion. We carefully re-examined our data. Our analysis confirms that this myosin ring is most pronounced during the early initial invagination stage (Figure 2A). This inward compression from the periphery would work in concert with apical constriction to help shape the initial invagination. However, this ring-like myosin pattern significantly diminishes in the accelerated invagination stage. We propose that the purse string may play a collaborative role in the early phase. We agree that follow‑up work (e.g., laser cutting or optogenetic manipulation) would be valuable and have noted this as a future direction in the Discussion.

      (5) The introduction and discussion put the work in the context of work on physical forces in invagination, but there is not much discussion of how the modeling fits into the literature. Did the current work advance the state of modeling of such phenomena? What were the strengths and limitations of the modeling in this paper compared to what has been done previously?

      Thank you for this suggestion. While we have incorporated additional literature in the revised manuscript as mentioned in our response to Reviewer #1 (Public Review) - Weakness (4), we would like to further clarify the specific advances and limitations of our modeling framework. Our updated vertex model builds upon established foundational frameworks but advances the state of modeling by: (i) incorporating dynamic apico-lateral tension variations coupled with actomyosin signals, and (ii) achieving localized, activity-mediated morphogenesis without the need for external rigid boundary constraints—a feature that distinguishes it from many classical models. We also recognize the model's current limitations. Specifically, it does not explicitly account for compressive stress and global geometric changes induced by tissue growth. The mechanical interactions between surface epithelial cells and the underlying internal bulk cells are also simplified. These factors represent important directions for our future work. We have added a dedicated paragraph in the Modeling and Discussion sections to contrast our model with existing literature and to explicitly state these strengths and limitations.

      (6) Figure 4D. Minor point, but the labeling on the X-axis is out of register with the bar graphs.

      We have corrected the alignment of the X‑axis labels with the bar graphs in Figure 4D. The figure has been updated accordingly.

      (7) Figure 4B does not have a scale bar.

      We have added a scale bar to Figure 4B (10 μm).

      Reviewer #2 (Recommendations for the authors):

      (1) Live imaging is necessary to demonstrate bidirectional translocation by visualizing the movement of the actomyosin network between the apical and lateral domains. Alternatively, a term other than "translocation" should be used to describe the observation.

      We agree that live imaging of actomyosin movement would be ideal but is technically challenging in this system. Instead, we have replaced the term “translocation” with the more accurate and conservative term “redistribution” throughout the manuscript, including the title, to avoid implying physical movement of the same molecules. This addresses the reviewer’s concern.

      (2) The optogenetic tool could be used to its full potential by manipulating myosin spatially or temporally, for example, by inhibiting myosin at various stages or subcellular locations, which would provide an opportunity to thoroughly test the domain and stage-specific needs for actomyosin. That said, I recognize that such experiments may be challenging in the model system used in this study.

      We thank the reviewer for this suggestion. We have indeed attempted spatially restricted optogenetic activation in the Ciona atrial siphon system, but found it technically very challenging due to tissue geometry and light scattering. We appreciate the reviewer's understanding of these technical limitations.

      (3) Some additional characterization of the optogenetics tool, such as the distribution of active myosin and F-actin post-stimulation, could further strengthen the interpretation of the inhibitory effect on invagination.

      We thank the reviewer for this suggestion. After optogenetic inhibition, we fixed and stained embryos for active myosin II. The results (Figure 4—figure supplement 2) show that light exposure significantly reduces lateral myosin intensity compared to the dark control, while apical myosin decreases similarly in both groups. This confirms that the optogenetic manipulation selectively attenuates lateral contractility without affecting apical changes. We have added this data to the Results section.

      (4) It would be helpful to address how heterogeneity in MRLC mutant overexpression might impact the interpretation of the outcome.

      We acknowledge that mosaic expression is common in Ciona electroporation. For all quantitative analyses, we only selected embryos in which the center cell and more than half of the surrounding cells in the primordium showed clear expression of the plasmid. This selection criterion has been added to the Materials and Methods section.

      (5) For Figure 2, it would be helpful to include the en face view of the cells at different apical-basal depths to better demonstrate the changes in the subcellular localization of myosin at different stages.

      We have added top‑view images in Figure 2A at both the apical and a deeper (lateral) plane. These images clearly show the ring‑like localization of active myosin at the apical cell‑cell junctions during the initial stage. Together with the cross‑sectional views, they adequately demonstrate the subcellular localization changes.

      (6) The Methods section should include more detailed descriptions of image quantification procedures. For example, for Figure 2B, how were the apical and lateral signals defined, and how were background intensities determined? In addition, the methods used for statistical tests should be clearly stated.

      We agree that detailed quantification procedures are essential. We have therefore expanded the Materials and Methods with a new subsection “Quantification and statistical analysis”. This subsection includes precise definitions of apical, lateral, and basal domains (segmented line, width 1 μm), background subtraction (region outside the tissue), normalization (basal intensity set to 1), and descriptions of how cell height, invagination depth, and lateral distance were measured (referencing Figure 1B). Statistical tests (two‑tailed Student’s t‑test) and significance levels are clearly stated.

      (7) The discrepancies between the model and experimental data, as described above, should be acknowledged. Commentary on how the model's assumptions and setup might contribute to these differences would be helpful.

      We thank the reviewer for this suggestion. As detailed in our response to Reviewer #2 (Public Review) - Comment (6), we have included the discrepancies between the model and experimental results in the Modeling and Discussion sections. We have added comments explaining how our key modeling assumptions might contribute to these differences. Specifically, while we have updated the model to a curved geometry, the omission of continuous global tissue growth and expansion could affect the final invagination depth and shape. Meanwhile, the neglect of mechanical interactions between the surface epithelium and the internal bulk cells prevents the model from fully capturing the constraints that refine the local furrow configuration in vivo. By clarifying these limitations, we now provide a more balanced view of the model's scope and its role in identifying the primary mechanical drivers of invagination.

      Reviewer #3 (Recommendations for the authors):

      General comments:

      (1) Methods: More information is needed to describe how imaging and quantification were performed. A couple of examples:

      (a) In Figure 1, how were the apical and basal surface area of the center cell quantified?

      (b) In Figure 1, Supplement 1, how was fluorescence intensity measured? Was there a constant area or volume that was quantified between samples? This is important because a decreasing apical surface can cause the signal to appear "concentrated" and increased.

      We thank the reviewer for this important suggestion. We have added a dedicated subsection “Quantification and statistical analysis” in the Materials and Methods. This subsection includes precise definitions of apical, lateral, and basal domains (segmented line, width 1 μm), background subtraction (region outside the tissue), normalization (basal intensity set to 1), and descriptions of how cell height, invagination depth, and lateral distance were measured (referencing Figure 1B). Statistical tests (two‑tailed Student’s t‑test) and significance levels are also stated.

      (2) The manuscript could use some editing and proofreading for grammar.

      The manuscript has been carefully edited for grammar and clarity. We thank the reviewer for the suggestion.

      Specific points:

      (1) Figure 1A: Could the authors please annotate the location of the center cell throughout the time course? This would make it easier for the reader to understand what is being quantified.

      We have added arrows to indicate the center cell at each time point in Figure 1A. This makes it easier for readers to follow the quantification.

      (2) Figure 1 Supplement 1A, Line 143, "...before 15 hpf, F-actin concentration decreased at the lateral domains..."

      It is not clear that the graph shows a decrease in the lateral domains when taking the error bars into account. It is possible that the F-actin concentration is stable in the lateral domains before 15 hpf. Are there some statistical analyses that can be performed?

      We re-analyzed the F-actin data and agree that the change before 15 hpf is not statistically convincing given the error bars. However, we have added new quantitative analysis of active myosin (p-MLC) at 14–15 hpf (Figure 2B), which shows a clear and significant shift from lateral to apical enrichment during this early phase. This myosin dynamic strongly supports our hypothesis of bidirectional redistribution. The corresponding text has been updated in the Results section.

      (3) Figure 1 Supplement 1A, Line 147-148, "...after 16 hpf, during which apical F-actin levels showed a gradual decline." Based on the graph, it does not appear that apical F-actin levels show a gradual decline after 16 hpf; rather, they may be steady or slightly increase.

      We agree with the reviewer. Our original statement was inaccurate. What we intended to emphasize was that at 16 hpf, the F-actin level at the lateral domain exceeded that at the apical domain. The detailed changes of F-actin after 16 hpf were not a focus of our discussion. We have revised the text accordingly to avoid any misinterpretation. The correction has been made in the Results section.

      (4) Figure 2C Hypothesis and line 169-170, "Initially, actomyosin translocated from the lateral regions to the apical domains..."

      Related to the comment above, it is not clear that one can state that the actomyosin "translocated". The quantification does not necessarily demonstrate a loss of actin at the lateral domain in the initial stage, and even if there was a loss of lateral actomyosin, one would require experiments (perhaps photoconversion experiments) to demonstrate that machinery from the lateral region was transferred to the apical surface, rather than a process of new assembly at the apical surface.

      We fully agree with the reviewer. We have replaced the term “translocation” with “redistribution” throughout the manuscript, including the title, to avoid implying physical movement of the same actomyosin structures. The text in the Results and Discussion has been revised accordingly.

      (5) A similar comment is relevant to the subsequent statement in line 175, "actomyosin translocated from the apical domains to the lateral regions." Without direct experiments to demonstrate movement of the actomyosin machinery, it is possible that there is de novo assembly of actomyosin in the lateral region rather than translocation.

      This wording ("translocation") becomes important primarily because it is in the title and appears to be one of the authors' major conclusions.

      We fully agree with the reviewer that the wording is critical given our main conclusion. We have therefore systematically replaced “translocation” with “redistribution” across the manuscript (title, results, and discussion).

      (6) Figure 4, Lines 215-216, "These results confirm that the redistribution of myosin contractility from the apical to lateral regions is essential for the development of invagination."

      This experiment did not specifically test the redistribution of myosin; rather, the authors demonstrated that myosin contractility globally is necessary for invagination. In these experiments, is it known where the myosin is?

      We have performed additional immunostaining experiments (new Figure 4—figure supplement 2) to directly examine myosin distribution after optogenetic inhibition. The results show that light exposure specifically reduces lateral myosin intensity compared to the dark control, while apical myosin decreases similarly in both groups. This demonstrates that the optogenetic manipulation selectively attenuates lateral contractility. We have revised the conclusion to state that the acquisition of lateral contractility is essential for invagination progression. The new data and revised text are in the Results section.

      (7) Figure 4B, minor point: It would be helpful if the authors included a timestamp for the bottom row images (Dark 1 h).

      Thank you for pointing out this typo. Timestamps have been added to the bottom row images (Dark 1 h) in Figure 4B.

      (8) Figure 5E, F, minor point: It seems that the label on the red curve has a typo; it should be T18ES19E (rather than T18AS19E).

      Thank you for pointing out this typo. We have corrected it in the revised manuscript (now Figure 6A, B).

      (9) Figure 5F and corresponding text: Can the authors please clarify what is meant by "Coupled mode" as marked in the schematic? Is this meant to refer to simultaneous apical constriction and lateral contraction? Or sequential?

      We thank the reviewer for this question. By "coupled mode," we refer to the mechanical synergy between apical and lateral contractions in driving the final invagination. As observed in our experimental data and recapitulated in the model, these two processes occur sequentially rather than simultaneously. We have revised the corresponding text to explicitly clarify this sequential process.

      (10) Figure 6A, B, Lines 274-275: "...the invagination depth increased significantly under higher alphaa (Figure 6A), while the central height remained relatively independent of alphaa (Figure 6B)." This caused me some confusion until I realized that "Figure 6B" might be a typo and should be Figure 6C.

      We sincerely apologize for this confusion. In the revised manuscript, this specific section and the corresponding figures have been updated.

      (11) Line 287, typo: I believe that "Figure 5B" should be Figure 6B.

      We sincerely apologize for this confusion. In the revised manuscript, this specific section and the corresponding figures have been updated.

      (12) Figure 6A, B, comparing invagination depth with varying apical or lateral actomyosin intensity: The authors state that "invagination depth increased significantly under higher alphaa", but describe "mild invagination depth variation" with varied lateral actomyosin intensity. The graphs seem to suggest that there is increased invagination depth when either apical or lateral actomyosin intensity is increased, and that the increase is to a similar extent. Can the authors comment on what they think the differences are, if the apical effect is "significant" but the lateral effect is "mild"?

      We thank the reviewer for this meticulous observation. We agree and feel sorry that our original description was not sufficiently precise. In the revised manuscript, we have re-analyzed the distinct contributions of apical and lateral tensions using the updated curved vertex model, which provides a more accurate mechanical decoupling. We have accordingly replaced the previous wording with a more rigorous description of the simulations and streamlined the corresponding figures to ensure the conclusions are clearly supported.

      (13) Figure 6H, Lines 307-309, "...stronger regional translocation and redistribution contribute to the rapid reduction in height of invaginating cells..."

      It appears from the graph that this is really only apparent at high alpha (total actomyosin); at empirically determined levels (alpha = 1), the effect of varying ratio is less dramatic. Can the authors comment on how significant they consider this effect?

      We thank the reviewer for this insightful comment. We agree that the theoretical predictions regarding translocation strength in the original model lacked sufficient experimental validation. To maintain the scientific rigor of our study, we have removed the sections concerning the translocation ratio and the corresponding Figure 6H from the revised manuscript. Instead, we now refocus our analysis on the core mechanical drivers of invagination that are directly supported by our observations. We also have added discussions acknowledging other factors not fully captured in the current model (e.g., tissue growth), which we aim to investigate in future work.

    1. Author response:

      The following is the authors’ response to the previous 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 have now provided all uncropped electrophoresis raw images corresponding to the results in the main figures and supplementary figures (Fig. 2F, 3D, 3E, 4E, S9A, S10 and S11 of the original manuscript) in the revised version. Regarding the spliced image in Fig. 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 have been supplemented in the revised manuscript as Fig. S12.

      The following highlighted words have been added to the revised manuscript.

      “All uncropped raw gel images corresponding to these EMSA experiments are provided in Supplementary Fig. S12.”

      Additionally, the 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 Fig. 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 have revised the legend of Fig. 3D, replacing the mass values with the calculated molar concentrations as you suggested.

      The following highlighted words have been added to the revised manuscript.

      “(D) Binding ability of the commercial antibody (40592-R001) to RBD was assessed by native-PAGE. The reaction mixture (10 μL) contained 8.57 μM RBD protein and 2 μM antibody, incubated individually or combined, followed by Coomassie brilliant blue staining.”

      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 Fig. 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 revised Fig. S11), 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 Fig. 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 (Fig. 2F and S9 in original manuscript) and uncropped raw images of all EMSA gels (Fig. S12 in revised manuscript) 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, have been added to the revised manuscript (Fig. S11).

      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).

      The following highlighted words have been added to the revised manuscript.

      “The integrity and purity of the RBD protein were confirmed by denaturing SDS-PAGE (Fig. S11), showing a single intact band without degradation. The multiple bands observed in native PAGE (e.g., Fig. 3E) are due to conformational and glycosylation heterogeneity [63–66] rather than protein degradation. To rule out non-specific aptamer–protein interactions, BSA was additionally included as a non-target protein control in EMSA assays; the wild-type Ta, the negative control Tc, and the optimized Ta<sup>G34C</sup> all showed only weak, comparable background signals with BSA but distinct target-specific binding to RBD (Fig. S10). Uncropped EMSA gel images (Fig. S12) and consistent results from three biological replicates (Fig. 2F and S9) confirm the absence of protein aggregation and ensure data reliability.”

      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 have supplemented the EMSA assays with BSA as a non-target protein control to rule out non-specific binding between our designed aptamers (Ta, Tc and Ta<sup>G34C</sup>) and exogenous proteins. The results revealed that all three aptamers (Ta, Tc and Ta<sup>G34C</sup>) exhibited only weak and comparable background signals with BSA (Fig. S10), which may originate from BSA itself or trace contaminating proteins in the protein sample (Fig. S11). The similar intensities of these background signals across Ta, Tc, and Ta<sup>G34C</sup> indicate a comparable, low level of non-specific binding among these aptamers (Fig. S10). In sharp contrast, RBD displayed markedly stronger binding toward Ta<sup>G34C</sup> than Ta, while no detectable binding was observed with the negative control Tc (Fig. S10). Collectively, these results verify that the aptamer–RBD interactions characterized in this study are target-specific and exclude non-specific aptamer–protein interactions.

      All the new experimental data of the non-specific binding controls have been integrated into the revised manuscript (Fig. S10) and the corresponding results and Methods have been updated accordingly. The following highlighted words have been added to the revised manuscript:

      “To further exclude non-specific aptamer–protein interactions, we performed parallel EMSA assays using bovine serum albumin (BSA) as a non-target protein control for Ta, Tc, and the optimized Ta<sup>G34C</sup> (see Fig. S10). Only weak, comparable background signals were observed for all three aptamers with BSA. Such minor non-specific binding may originate from BSA itself or trace contaminating proteins in the BSA samples (Fig. S10). In contrast, markedly stronger binding was detected between RBD and Ta or Ta<sup>G34C</sup>, whereas no detectable binding was observed with the negative control Tc (Figs. 4E, S10). Such distinct binding profiles of aptamers with RBD and BSA confirm that the aptamer–RBD interactions characterized in this study are target-specific.”

      “To rule out non-specific aptamer–protein interactions, BSA was additionally included as a non-target protein control in EMSA assays; the wild-type Ta, the negative control Tc, and the optimized Ta<sup>G34C</sup> all showed only weak, comparable background signals with BSA but distinct target-specific binding to RBD (Fig. S10).”

      (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 have revised the Methods section 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 Fig. 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 Fig. 3E and Fig. 5D, as the final antibody concentration in Fig. 3E is now consistent with the concentration range used in Fig. 5D. We have updated the figure legends for Fig. 3E and revised 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 have prompted important revisions to improve the clarity, accuracy, and rigor of our manuscript.

      The following highlighted words have been added to the revised manuscript.

      “For competitive binding experiments, Cy3-labelled RNAs, RBD proteins, and neutralizing antibody 40592-R001 were added simultaneously to the EMSA buffer and incubated at room temperature for 20 min.”

      “(E) The RBD binding abilities of the aptamer Ta and commercial antibody 40592-R001 were compared by EMSA competitive binding experiments. The aptamer-RBD complex bands were shown after running on an agarose gel following the incubation of 40 μM RBD protein, 0.5 μM aptamer Ta, and 0.5 μM antibody 40592-R001 (final concentrations in the reaction mixture).”

      “(D) EMSA images of competitive binding experiments to characterize the RBD binding abilities of RNA aptamers (WT Ta and Ta<sup>G34C</sup>) and the commercial monoclonal SARS-CoV-2 neutralizing antibody 40592-R001. The aptamer-RBD complex bands were showed by running an agarose gel after incubation of 40 μM of RBD protein and 0.5 μM indicated aptamer with varying concentrations of the antibody 40592-R001. Final antibody concentrations ranged from 0 to 1.67 μM in the reaction mixtures. Results showed that Ta<sup>G34C</sup>, but not WT Ta, exhibited a higher binding affinity to the RBD proteins than that of the antibody.”

      (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 answers in the point-to-point response letter). 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 have revised the manuscript to clarify this scope.

      The following highlighted words have been added to the revised manuscript.

      “We note that CAAMO is not intended to establish experimentally validated complex structures, but rather to provide preliminary binding models that enable rational affinity maturation of aptamers in scenarios where structural information is limited or unavailable.”

      “Overall, these results indicate that the proposed binding conformation of the aptamer Ta to the RBD serves as a plausible working binding model for structure-guided aptamer optimization, and demonstrate the great potential of our CAAMO framework in aptamer design and optimization.”

      “which supports the robustness of our approach in generating informative binding models for comparative analysis and affinity optimization of an RNA aptamer with a target protein.”

      “We believe that the predicted binding conformation represents a plausible member of the predicted ensemble that is functionally informative for guiding structure-based aptamer optimization, although it may not correspond to the exact native structure.”

      (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 have carefully revised 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 have revised the text to explicitly state these distinctions and have avoided 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 have now explicitly stated this data source, clarified the number and nature of structures used, and added the appropriate citation (Raybould et al., Bioinformatics, 2021, doi: 10.1093/bioinformatics/btaa739).

      Finally, we have revised 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 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.

      The following highlighted words have been added to the revised manuscript.

      “Notably, the aptamer Ta<sup>G34C</sup> exhibited the highest binding affinity to the RBD, outperforming the tested neutralizing antibodies in competitive binding assays.”

      “Since we determined the most probable binding model of the aptamer Ta to the RBD, comparing the binding properties of the aptamer Ta with those of representative neutralizing antibodies to the RBD is both feasible and meaningful.”

      “To further explore this, we analyzed the contact ratios of residues on the RBD bound to ACE2 (derived from MD simulations), to the aptamer Ta (derived from MD simulations), or to the neutralizing antibodies (derived from all available experimentally resolved SARS-CoV-2 RBD–antibody complex structures curated in the Coronavirus Antibody Database, CoV-AbDab [35]). CoV-AbDab is a publicly available, curated database that aggregates all published coronavirus-binding antibodies with associated structural information, providing a comprehensive and unbiased structural ensemble for contact frequency analysis.”

      “Notably, the Ta-RBD complex formation remained unchanged after adding the antibody (Fig. 3E), suggesting that the aptamer Ta exhibits binding capability comparable to the tested monoclonal neutralizing antibody.”

      “neutralizing antibodies (derived from all available SARS-CoV-2 RBD–antibody complex structures curated in CoV-AbDab).”

      “Our computational and experimental studies showed that the aptamer Ta has comparable binding abilities to the RBD compared to representative neutralizing antibodies analyzed in this study.”

      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.

      Recommendations for the authors:

      Reviewer #4 (Recommendations for the authors):

      The computational aspects seem to be the strength of this manuscript, however there remain some issues with experimental approaches. The previous reviewers concern with non-specific binding remains an issue that should be dealt with through additional experimentation. The indication of Tc showing no binding is a good control for nonspecific RNA binding by RBD, but does not address nonspecific protein binding by Ta or its derivatives. For example, if a variant of Ta bound strongly to hydrophobic or highly charged patches in binding sites, they could also bind strongly to hydrophobic or highly charged patches in other proteins. As such, a non-specific binding test should be included for all tested variants to show target-specific binding.

      Thank you for your constructive suggestion. To address the concern of non-specific binding, we have supplemented a dedicated control experiment using bovine serum albumin (BSA) as the non-specific protein target. The results demonstrated that Ta and its derivatives exhibited specific binding to the RBD protein. Detailed experimental procedures and corresponding results for this control assay are provided in our response to your first comment in this point-by-point response letter.

      There is a serious concern to me that all data (i.e. the triplicate EMSAs claimed in your study) are not shown, with only one EMSA replicate shown for each variant in the supplemental materials. Additionally, the manuscript does not include unedited gel images, with apparent splicing of images in Figure 4E. All raw data should be available for review, which includes unedited images of the entirety of each gel electrophoresis experiment. Moreover, internal controls (positive of Ta+/-RBD, negative of Tc+/-RBD, and aptamer+/-non-RBD-protein) should be included and shown in every EMSA experiment.

      Thank you for raising these critical concerns regarding the rigor and completeness of our EMSA experimental data. We highly appreciate your attention to detail, which helps us improve the quality and transparency of our manuscript.

      First, regarding the number of EMSA replicates, we have indeed performed triplicate EMSA experiments for each variant, and all three replicates are provided in the supplementary materials (Fig. S9 of the original manuscript). We have added explicit labels for each replicate in the revised Fig. S9 to avoid confusion, ensuring the reproducibility of our results is clearly demonstrated.

      Second, concerning unedited gel images, we fully agree with the importance of providing uncropped, raw gel images for peer review. In the revised manuscript, all unedited, full-length raw images of each gel electrophoresis experiment have been included in Supplementary Fig. S12, with clear annotations to correspond to the cropped images in the main text.

      Third, with respect to internal controls, we acknowledge the necessity of comprehensive internal controls for EMSA experiments to validate specific binding. For the EMSA assays of RBD with Ta and its variants (Fig. 4E), we have already included the full set of internal controls, namely the Ta-RBD positive control, Tc-RBD negative control, and non-RBD protein control. Notably, the K<sub>d</sub> values of RBD binding to Ta, Tc, and Ta variants are consistent with the signal intensity exhibited in the EMSA images, which further corroborates the reliability of our binding results. In addition, we have supplemented non-specific binding control data in the revised Supplementary Fig. S10, which fully validates the binding specificity between Ta/its derivatives and RBD and effectively rules out non-specific binding.

    1. Author response:

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

      We have addressed all the reviewers’ comments through new experiments, additional analyses, or, in some cases, additional text. Below is a summary of the major changes in the manuscript.

      (1) We have added a considerable amount of new characterization of the biochemical enrichment of the ribosome clusters, including EM of the ribosome clusters, UV absorbance profiles, immunoblots of additional targets, and additional replicates (new Figure 1). In summary, we provide better evidence that (i) the biochemical enrichment is working and (ii) that the loss of FMRP has no effect on this biological enrichment of ribosomal clusters.

      (2) We have now reanalyzed all of the data in Figs. 5-8 using only the data after removing PCR duplicates from the RPFs. Other than the comparison between the nuclease treatments (Fig. 3), only this data is now used. Moreover, we have reanalyzed this data using suggestions from the reviewers, including providing PCA analysis (Fig S5-1), GSEA analysis (Fig 5), and normalizing for group size when comparing significance to total mRNAs, (Fig 6-7). We now also include a new analysis (Fig S7-1) to better explain how the loss of FMRP affects mainly FMRP targets defined by CLIP, but not all mRNAs resistant to run-off.

      (3) We are now more conservative in our nomenclature; we use "pellet" instead of "RNA granule (RG)" and "fraction 5/6" instead of "ribosome clusters (RC)". We have added a section to the discussion about the relationship between the RNA granules measured using imaging of hippocampal neurites and the biochemical purification of ribosome clusters in the pellet, as requested by the reviewers.

      (4) We have made many other minor changes to the text and analysis, which can be found in the specific response to the reviewers.

      (5) One major additional requested change that was not implemented was to repeat our experiments at different time points. We have added a paragraph to the discussion outlining (i) why this was not done and (ii) the caveats of our conclusions without this data being present.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors have investigated the role of FMRP in the formation and function of RNA granules in mouse brain/cultured hippocampal neurons. Most of their results indicate that FMRP does not have a role in the formation or function of RNA granules with specific mRNAs, but may have some role in distal RNA granules in neurons and their response to synaptic stimulation. This is an important work (though the results are mostly negative) in understanding the composition and function of neuronal RNA granules. The last part of the work in cultured neurons is disjointed from the rest of the manuscript, and the results are neither convincing nor provide any mechanistic insight.

      Strengths:

      (1) The study is quite thorough, the methods and analysis used are robust, and the conclusion and interpretation are diligent.

      (2) The comparative study of Rat and Mouse RNA granules is very helpful for future studies.

      (3) The conclusion that the absence of FMRP does not affect the RNA granule composition and many of its properties in the system the authors have chosen to study is well supported by the results.

      (4) The difference in the response to DHPG stimulation concerning RNA granules described here is very interesting and could provide a basis for further studies, though it has some serious technical issues.

      Thank you for these positive comments on the paper.

      Weaknesses:

      (1) The system used for the study (P5 mouse brain or DIV 8-10 cultured neuron) is surprising, as the majority of defects in the absence of FMRP are reported in later stages (P30+ brain and DIV 14+ neurons). It is important to test if the conclusions drawn here hold good at different developmental stages.

      Unfortunately, myelin strongly interferes with the ability to use this protocol to purify ribosome clusters in older brains (See Khandjian et al., 2004). It is possible to redo the ribopuromycylation results at later times in culture, but since we cannot compare this to a comparable time in the brain, we have chosen not to do this experiment. We acknowledge this limitation in the discussion, noting that our results are only a snapshot of development and that different results may be observed at different times.

      (2) The term 'distal granules' is very vague. Since there is no structural or biochemical characterization of these granules, it is difficult to understand how they are different from the proximal granules and why FMRP has an effect only on these granules.

      We agree with the reviewer and have removed all references to distal granules. We clarified that we did not measure RPM puncta close to the neuron because the much stronger RPM signal made defining puncta more difficult, and thus, we cannot determine if there are differences between proximal and distal puncta.

      (3) Since the manuscript does not find any effect of FMRP on neuronal RNA granules, it does not provide any new molecular insight with respect to the function of FMRP

      We would respectfully disagree that the study does not provide molecular insight into the function of FMRP, as disproving that FMRP is important for stalling and determining the position of stalling would remove one of the major hypotheses about the function of FMRP, and showing that a major hypothesis in the literature is unlikely to be correct, is at least to me, providing insight. Moreover, we do show an effect of the loss of FMRP on the RPM puncta that represent neuronal RNA granules containing stalled ribosomes. This also provides insight.

      Reviewer #2 (Public review):

      In the present manuscript, Li et al. use biochemical fractionation of "RNA granules" from P5 wildtype and FMR1 knock-out mouse brains to analyze their protein/RNA content, determine a single particle cryo-EM structure of contained ribosomes, and perform ribo-seq analysis of ribosome-protected RNA fragments (RPFs). The authors conclude from these that neither the composition of the ribosome granules, nor the state of their contained ribosomes, nor the mRNA positions with high ribosome occupancy change significantly. Besides minor changes in mRNA occupancy, the one change the authors identified is a decrease in puromycylated punctae in distal neurites of cultured primary neurons of the same mice, and their enhanced resistance to different pharmacological treatments. These results directly build on their earlier work (Anadolu et al., 2023) using analogous preparations of rat brains; the authors now perform a very similar study using WT and FMR1-KO mouse brains. This is an important topic, aiming to identify the molecular underpinnings of the FMRP protein, which is the basis of a major neurological disease. Unfortunately, several limitations of this study prevent it from being more convincing in its present form.

      In order to improve this study, our main suggestions are as follows:

      (1) The authors equate their biochemically purified "RG" fraction with their imaging-based detection of puromycin-positive punctae. They claim essentially no differences in RGs, but detect differences in the latter (mostly their abundance and sensitivity to DHPG/HHT/Aniso). In the discussion the authors acknowledge the inconsistency between these two modalities: "An inconsistency in our findings is the loss of distal RPM puncta coupled with an increase in the immunoreactivity for S6 in the RG." and "Thus, it may be that the RG is not simply made up of ribosomes from the large liquid-liquid phase RNA granules."

      How can the authors be sure that they are analysing the same entities in both modalities? A more parsimonious explanation of their results would be that, while there might be some overlap, two different entities are analyzed. Much of the main message rests on this equivalence, and I believe the authors should show its validity.

      Thank you for your comments. We have been more conservative in the revised paper, referring to the pellet fraction as the pellet fraction rather than the RNA granule fraction to acknowledge the possibility that these two modalities differ. However, we would respectfully disagree that our main message requires RPM-labeled RNA granules in neurites and the ribosome clusters isolated by sedimentation to be “equivalent”. We do believe they are related and added a section in the discussion on this important point.

      (2) The authors show that increased nuclease digestion (and magnesium concentration) led to a reduction of their RPF sizes down to levels also seen by other researchers. Analyzing these now properly digested RPFs, the authors state that the CDS coverage and periodicity drastically improved, and that spurious enrichments of secretory mRNAs, which made up one of the major fractions in their previous work, are now reduced. In my opinion, this would be more appropriately communicated as a correction to their previous work, not as a main Figure in another manuscript.

      We have removed all discussion of the secretory mRNAs, as our attempts to obtain independent evidence for this finding by examining ribophorin enrichment in the pellet across different Mg<sup>2+</sup> concentrations did not support this interpretation (data not shown in the paper). I understand that the change in nuclease is somewhat out of place narratively, but it is clearly relevant to this work. We would disagree with our previous work requiring a ‘correction’. We believe that the nuclease resistance of the mRNA at the entrance site is important. We reproduce our results from rats with similar nuclease treatment in mice as seen in our previous publication; thus, this work is not wrong. We have a paper in preparation that suggests the secondary structure of the mRNA at this location may be important for stalling and thus feel strongly that this result should remain in the manuscript.

      (3) The fold changes reported in Figure 7 (ranging between log2(-0.2) and log2(+0.25)) are all extremely small and in my opinion should not be used to derive claims such as "The loss of FMRP significantly affected the abundance and occupancy of FMRP-Clipped mRNAs in WT and FMR1-KO RG (Fig 7A, 7B), but not their enrichment between RG and RCs".

      We agree that the changes are small and indeed did not appear in the DEG analysis. However, because we are analyzing a large set of mRNAs in this analysis, the results are highly significant and remain significant when using the new statistical tests suggested by the reviewer below. We now emphasize that these are small changes and remind readers that none of the individual mRNA changes were significant in the DEG analysis.

      (4) Figure 8 / S8-1 - The authors show that ~2/3 of their reads stem from PCR duplicates, but that even after removing those, the majority of peaks remain unaltered. At the same time, Figure S8-1 shows the total number of peaks to be 615 compared with 1392 before duplicate removal. Can the authors comment on this discrepancy? In addition, the dataset with properly removed artefacts should be used for their main display item instead of the current Figure 8.

      We now use only the data after removing PCR duplicates for all the analyses except in Figure 3. The number of peaks observed is determined mainly by the threshold used, as stated in the methods “To be identified as a peak, the zenith of an abundance site for the reads must be 4x higher of the average of the total transcript.” Due the lower number of reads after the PCR duplicates fewer peaks reached this threshold.

      (5) Figure 9 / S9-1, the density of punctae in both WT and FMR1-KO actually increases after treatment of HHT or Anisomycin (Figure S9-1 B-C). Even if a large fraction would now be "resistant to run-off", there should not be an increase. While this effect is deemed not significant, a much smaller effect in Figure 9C is deemed significant. Can the authors explain this? Given how vastly different the sample sizes are (ranging from 23 neurites in Figures S91 to 5,171 neurites in Figure 9), the authors should (randomly) sample to the same size and repeat their statistical analysis again, to improve their credibility.

      The box and whisker plots emphasize the median and not the average. We now also show the averages in Figure S9-1, which indicate a slight decrease for both HHT and anisomycin.

      We apologize for the typo in the figure legend in Figure 9, 171, not 5171. We now use random sampling in Figures 6 and 7, where the sample sizes differ substantially.

      Reviewer #3 (Public review):

      Summary:

      Li et al describe a set of experiments to probe the role of FMRP in ribosome stalling and RNA granule composition. The authors are able to recapitulate findings from a previous study performed in rats (this one is in mice).

      Strengths:

      (1) The work addresses an important and challenging issue, investigating mechanisms that regulate stalled ribosomes that are part of stress granules, and focusing on the role of FMRP. This is a complicated problem, given the heterogeneity of the granules and the challenges related to their purification. This work is a solid attempt at addressing this issue, which is widely understudied.

      (2) The interpretation of the results could be interesting if supported by solid data. The idea that FMRP could control the formation and release of stress granules, rather than the elongation by stalled ribosomes, is of high importance to the field, offering a fresh perspective into translational regulation by FMRP.

      (3) The authors focused on recapitulating previous findings, published elsewhere (Anadolu et al., 2023) by the same group, but using rat tissue, rather than mouse tissue. Overall, they succeeded in doing so, demonstrating, among other findings, that stalled ribosomes are enriched in consensus mRNA motifs that are linked to FMRP. These interesting findings reinforce the role of FMRP in the formation and stabilization of RNA granules. It would be nice to see extensive characterization of the mouse granules as performed in Figure 1 of Anadolu et al., 2023.

      (4) Some of the techniques incorporated aid in creating novel hypotheses, such as the ribopuromycilation assay and the cryo-EM of granule ribosomes.

      Thank you for these positive comments. We have now added a more extensive characterization in Figure 1.

      Weaknesses:

      (1) The RNA granule characterization needs to be more rigorous. Coomassie is not proper for this type of characterization, simply because protein weight says little about its nature. The enrichment of key proteins is not robust and seems not to reach significance in multiple instances, including S6 and UPF1. Furthermore, S6 is the only proxy used for ribosome quantification. Could the authors include at least 3 other ribosomal proteins (2 from the small, 2 from the large subunit)?

      We have increased N to improve the robustness of the enrichment analysis and added several additional RBPs. Along with Coomassie we now include analysis of UV absorbance and include EMs from these fractions showing the presence of 80S ribosomal clusters in the fractions we are using.

      (2) Page 12-13 - The Gene Ontology analysis is performed incorrectly. First, one should not rank genes by their RPKM levels. It is well known that housekeeping genes, such as those related to actin dynamics, molecular transport, and translation, are highly enriched in sequencing datasets. It is usually more informative when significantly different genes are ranked by p-adjust or log2 Fold Change, then compared against a background to verify enrichment of specific processes. However, the authors found no DEGs. I would suggest the removal of this analysis and the incorporation of a gene set enrichment analysis (ranked by p-adjust). I further suggest that the authors incorporate a dimensionality reduction analysis to demonstrate that the lack of significance stems from biology and not experimental artifacts, such as poor reproducibility across biological replicates.

      Thank you for the suggestion. We now use GSEA analysis to examine differences in gene sets between WT and FMR1- mice and find some significant changes (new Fig. 5). The old analysis is still included for comparison to our earlier paper as a supplemental figure. We have now included a PCA analysis (FigS5-1) to show reproducibility across biological replicates.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) RNA sequencing comparison between WT and FMR1 KO mice should be carried out at a later developmental stage, which may provide a better difference between these two groups

      There are a number of studies that have already done this analysis and in specific brain regions 10.1016/j.neuron.2017.07.013; 10.7554/eLife.46919; 10.3389/fnmol.2017.00340; https://doi.org/10.1016/j.neuron.2023.06.009. The main goal of our RNA-seq was to standardize for the RPF studies, not to identify differences in RNA-seq between WT and FMRP. In the response to public review point 1 we explain why we do not look at later developmental timepoints.

      (2) The same is true in characterizing the effect of FMRP on the RNA granules.

      See response to public review point 1, which addresses this point.

      (3) No evidence is provided for the effectiveness of DHPG stimulation in DIV8-10 neurons; this is needed for justification using neurons at this stage.

      We have previously shown that DHPG stimulation in these neurons at this developmental time from cultures made from rat brain is sufficient to decrease the number of RPM puncta and to induce an increase in the synthesis of proteins in an initiation resistant manner (Graber et al, 2013; Graber et al, 2017). This is now more clearly stated in the manuscript. Moreover, here we replicate the result of DHPG in WT mice at reducing the number of RPM puncta.

      (4) In Figure 9 B, it is not clear whether the neurites indicated are axons or dendrites. Since neurons are still in the early stages of dendritogenesis/synaptogenesis, it is important to make that distinction.

      We have previously characterized RNA granules in axons and dendrites in hippocampal cultures from rats at this time (Miller et al, 2009, MCN 40:485-495)) and they are similar. While it is likely that the vast majority of the neurites at this time are dendrites, since we did not use markers, we conservatively just use the term neurites.

      (5) In Figure 1 (and elsewhere), fraction 5/6 is used as a polysome or RNA cluster. The authors have not provided a UV absorption profile and only have s6 as evidence to say this polysome. In the Coomassie gel, this fraction is any different than fractions 7/7 or 9/10; what is the justification for using this fraction?

      The main justification for these fractions is to be consistent with our previous paper (Anadolu et al, 2023) and the Khandian study comparing polysomes to pellet using the same fractionation protocol (El-Fatimy et al, 2016). We now provide a UV absorption profile (Fig. 1C) and EM pictures (Fig. 1D) to show the ribosome clusters in this fraction. We do not believe our results would be fundamentally different from those obtained if we had used other heavy fractions.

      Minor comments

      (1) The font size very small in the figures, please increase it.

      We have worked hard to increase the font size in all the figures.

      (2) In the result section for Figure 3B - it is written 'majority of these mRNA are non-coding mRNA' - this doesn't make sense.

      Corrected

      Reviewer #2 (Recommendations for the authors):

      (1) There are lots of mistakes (e.g. word omissions or duplications, grammatical errors) throughout the text, too many to list here.

      We have carefully edited the text to try to minimize these mistakes.

      (2) In many positions related to their improved nuclease digestion protocol, samples are labelled "M ...", which apparently stands for "high magnesium and high nuclease treatment group". I would suggest switching to something more intuitive, such as "... (improved digestion)".

      We have removed most of the comparisons between these samples. What remains (Figure 3), we just use Low Nuclease when we refer to the sample with low Magnesium and low nuclease.

      (3) Figure 1,3 - It would be tremendously illuminating to see a polysome trace (UV260 absorbance) in addition to Coomassie-stained SDS-PAGE to underscore the interpretation of the different fractions by the authors. As it stands, there is no way of telling whether there are any polysomes present at all. This can also be done by hand using a UV absorption reader if no built-in device is available to the authors.

      We have now done this (Fig. 1C) and also provided EM of this fraction to show the presence of ribosomes in this fraction.

      (4) I don't understand why the authors switched from calling fraction 5/6 the "polysome fraction" in their previous work to calling it "ribosome cluster fraction" in this work. The argument given "[...] due to its structural similarity to ribosomes in RNA Granules (Anadolu et al., 2023), we conservatively call this the ribosome cluster fraction (RC)." does not instill confidence that these two fractions are indeed distinct.

      We agree with the reviewer and regret this decision. We now call the pellet, the pellet and Fraction 5/6, fraction 5/6.

      (5) Figure 1C - There are clear scanning or compression artefacts in the blot images (most prominently in the eEF2 lanes) that should be corrected.

      We have replaced all images in Figure 1 and have increased the N of this experiment considerably.

      (6) Figure 1C - The authors claim that WT mouse RG is enriched in FMRP compared to RC or starter fraction, but there is also a lot more protein loaded in the RG (especially when compared to RC). It is also hard to believe from the Coomassie staining that despite the much stronger presence of low MW bands (which is where ribosomal proteins migrate) in fraction 5/6, the s6 western blot signal is actually comparable between RC and RG. Can the authors please provide more detail on the loading of these fractions and supply quantification of FMRP in all three fractions, normalized by total protein? This might also be the source of their discrepancy, stating that contrary to their expectation, ribosomes (as measured by s6 signal / s6 signal in starter fraction) are actually increased in FMR1-KO brains.

      We have repeated all of these experiments and changed our method of quantification (See methods). We no longer use the starting material in our quantification. Indeed, with the additional data and change in method, we no longer see an increase in S6 in the FMR1- pellet fraction.

      (7) Figure 1 - I believe "D-F)" should only read "D-E)" based on the axis titles, and instead "FG)" should be added before the next sentence. Instead of "Staufen" it should be specified in the Figure that "Stau2" was quantified. "Staufen (59kd)" should read "Stau2 (59 kDa)" and "anti-Staufen (52kb)" should read "anti-Stau2 (52 kDa)" and the same for all other similar instances. It is further hard to believe that e.g., "Staufen2 (59kd)" (see above) is not significantly enriched with N=5, a very low spread, and over 1.5x enrichment. The authors should double-check that the appropriate statistical test was employed.

      Figure 1 has been completely redone, and the two Staufen bands are enriched in this new analysis.

      (8) Figure S4-2 - Most of the detail in the corresponding figure legend should be moved to the Materials and Methods section.

      Details relevant to the methods in this figure legend have been now moved to the Material and Methods section.

      (9) Figure 4A - The displayed/segmented tRNA densities appear unusually distorted. I would recommend displaying segmented densities of the original homogeneous reconstructions, not of separated and later fused partial maps.

      Figure 4 was modified according to the suggestions of this reviewer.’

      (10) Figure 9 C-D, S9-1 B-E - Are not all conditions also including puromycin as in B above? If so, it should be added to both the figure and the figure legend.

      The reviewer is correct and the figure and legend has been changed to reflect this.

      Reviewer #3 (Recommendations for the authors):

      (1) "Loss of FMRP causes Fragile X syndrome. In humans, the loss of FMRP occurs due to the expansion of a CGG repeat in the 5' untranslated region (UTR) of the gene, leading to excessive methylation and transcriptional inhibition."

      Comment: Genes don't have 5'UTR, but exons encoding 5'UTR. I suggest rephrasing this statement.

      This sentence has been rephrased.

      (2) "Several of these functions have been implicated in Fragile X syndrome, including FMRP's regulation of miRNA repression, splicing, translation initiation, and translational elongation".

      Comment: Is this a typo? miRNA instead of mRNA?

      No, this is correct. FMRP has been implicated in the regulation of microRNAs (miRNAs) in a number of studies.

      (3) "elongation rates are also increased in mouse models of FMRP".

      Comment: Mouse models of Fragile X?

      This has been corrected.

      (4) "Parts of this work were included in the Master's thesis of the first author (Li, 2024)."

      This has been removed.

      (5) Comment: Graphs in Figure 1 need proper y-axis labeling. What is the normalization method? What are the values presented in the y-axis?

      Figure 1 has been completely changed and the Y-axes are now clear in this new version.

      (6) "Thus, by looking at the percentage of puromycylation present in the presence of anisomycin, we can estimate the number of ribosomes in this state. "

      Comment: Are the authors really estimating the number of ribosomes in a resistant state? One could argue that they are collecting populational information regarding resistance to anisomycin.

      We have rephrased this sentence to be more conservative about what we are measuring.

      (7) Comment: Page 11 - Why did the authors assume magnesium would affect the conformation state of the ribosomes? What is the rationale behind increasing the [Mg2+]?

      Most preparations using ribosomes use 10 mM MgCl<sub>2</sub>. However, most neuroscientists use physiological buffers that contain 2.5 mM MgCl<sub>2</sub>. In bacteria, this makes a large difference, but evidence from eukaryotes is not clear. Since this is a collaboration between these two schools of thought, we decided to switch to 10 mM MgCl<sub>2</sub>, since in the EM, there were some free 60S ribosomes (Anadolu et al, 2024).

      (8) Page 11- "In other words, high Mg2+ decreased the abundance of mRNAs normally cotranslationally inserted into the ER which are unlikely to be components of transporting RNA granules containing stalled ribosomes and solidified our focus on the M protocol in the analyses below."

      We have removed this from the paper, as additional experiments aimed to solidify this interpretation failed to detect an effect on secretory mRNAs.

      (9) Comment: The whole "abundance", "enrichment", and "occupancy" nomenclature is hard to follow.

      We have rewritten this section.

      (10) Page 13 - "There were only 2 protein coding genes that were significantly different between the abundance of FMR1-KO and WT in protein coding genes - FMR1 and Wdfy1 (Extended Data Table 5-2). There were no significantly different genes between WT and FMR1-KO occupancy and enrichment. Thus, no difference rose to significance, given the large number of mRNAs used in this analysis."

      Comment: It seems like this is repeating the same information three times.

      This has been changed.

      (11) Page 13 - "Similar to previous experiments with rats, the most abundant mRNAs resistant to run off were significantly abundant, occupied and enriched in both WT and FMRP RPFs (Fig 6)"

      The Shah et al dataset we use was based on the most abundant mRNAs resistant to run-off. While we agree it is not surprising that they are also abundant in the pellet we observe, this would not necessarily be true unless the pellet is actually enriched in stalled mRNAs.

      (12) Page 14 - "These mRNAs had been identified by cross-linking FMRP with mRNA, fragmenting the mRNA, immunoprecipitating the mRNA still associated with FMRP and sequencing this mRNA."

      We shortened this description.

      (13) Page 14 - "Interestingly, while still significant, there appeared to be a decrease in the relative abundance of these mRNAs in the FMR1-KO RG (Fig 6B)"

      Comment: It is hard to observe this decrease in the boxplots. Second, the statistical tests for the bioinformatics analyses are not the most appropriate, given the large discrepancy in the number of mRNAs present in the experimental group ("All mRNAs") and the filtered groups.

      We have redone the statistics using multiple random sampling of all the mRNAs such that the total number of mRNAs in the group was the same. This lowered the significance for some groups, but they are mostly still highly significant. This analysis has also been affected by switching to using the data from the PCR-subtracted RPFs. The changes we now observe are more evident in the whisker box plots due to this improvement in the data.

      (14) Page 16 - "To rule out that peaks were due to amplification artifacts in the preparation of RPFs we repeated these analyses after removing PCR duplicates (Fig. S8-1; Extended Data Table S8-3) and found over 95% of the peaks identified without removing PCR duplicates were defined as a peak in at least one of the biological replicates after removing duplicates. More importantly, we found similar results with enrichment of FXS motif and enrichment of negatively charged amino acids in the FMR1-KO only, WT only and both peaks after removing PCR duplicates (Fig. S8-1; Extended Data Table S8-3)."

      Comment: It is unclear why the authors needed to include the analysis without PCR duplicate removal. This is an essential step to guarantee the robustness of ribo-seq findings. I recommend removing the whole analysis from Figure 8 from the manuscript and including only the post-duplicate removal analysis.

      As mentioned above, we completely agree with this statement and now show only this data and moreover have redone all the figures with only this data (except for Fig. 3).

      (15) Figure 9 - I am unsure that the data is convincing enough to demonstrate reinitiation of mRNA granules induced by DHPG. I suggest a colocalization experiment with another protein well known to be localized to RNA granules, such as G3BP1. In addition, repeat the experiment with an additional group where elongation is blocked after the addition of DHPG, which presumably would prevent the reduction in the WT puncta density.

      These are interesting additional experiments, but outside the scope of what we can manage. We have previously shown colocalization of Staufen, FMRP and UPF1 to these puncta (Graber et al, 2013; Graber et al, 2017) and shown that these puromycylated puncta also colocalize with nascent peptides detected using the Sun-Tag technique. While we think doing the experiment in the presence of an elongation inhibitor would be interesting, we disagree that it would prevent the reduction in WT puncta density, since we believe what is happening is the loss of the liquid-liquid phase separation of the ribosome clusters due to dephosphorylation of RBPs like FMRP and UPF1 (Graber et al, 2017), and this would reduce the puncta density whether or not the ribosomes were activated for translation.

      Nevertheless, we have tried to temper the conclusions made from this result, emphasizing what we know (RPM puncta are decreased) as opposed to actual reactivation of stalled polysomes which we are not measuring.

      Discussion - Page 18 - "Nevertheless, if FMRP binding was the critical determinant for presence in neuronal RNA granules, we would have expected to observe more differences." This is not true. If the data is poorly collected, you will not see differences.

      This statement was removed.

      (16) "A proportion of the stalled ribosomes that are not stored in large RNA granules may still be pelleted in the sucrose gradients. This fraction may be greater in the absence of FMRP."

      Comment: The authors are right about this and touch on my original point that the characterization of the biochemical fractionation is not convincing enough. I'd suggest probing against more proteins that are contained in RNA granules.

      We have added several proteins to the biochemical characterization shown in Figure 1. We have added a discussion about the relationship between neuronal RNA granules and the sedimented pellet fraction in the discussion section.

    1. Author response:

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

      We incorporated Reviewer #2’s suggestion to change the name of mll-1 because of overlap with a human gene. We used the updated gene names in our responses below to minimize confusion. Below are the updated gene names for the toxin-antidote system we described.

      tmrl-1 - Toxin-induced Maternal Rod Lethality (formerly mll-1). After we establish that B0250.8 is also a toxin, we refer to this gene as the “N2 tmrl-1 allele”.

      amrl-1 - Antidote of Maternal Rod Lethality (formerly smll-1)

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The article by Zdraljevic et al. reports the discovery of a third toxin-antidote (TA) element in C. elegans, composed of the genes mll-1 (toxin) and smll-1 (antidote). Unlike previously characterized TA systems in C. elegans, this element induces larval arrest rather than embryonic lethality. The study identifies three distinct haplotypes at the TA locus, including a hyper-divergent version in the standard laboratory strain N2, which retains a functional toxin but lacks a functional antidote. The authors propose that small RNA-mediated silencing mechanisms, dependent on MUT-16 and PRG-1, suppress the toxicity of the divergent toxin allele. This work provides insights into the evolutionary dynamics of TA elements and their regulation through RNA interference (RNAi).

      Overall, there are many things to like about this paper and only a few small quibbles, which will not require more than a little rewriting or relatively minor analyses.

      Strengths:

      (1) The discovery of a maternally deposited TA element with delayed toxicity due to delayed mRNA translation of the maternally deposited toxin mRNA is a significant addition to the literature on selfish genetic elements in metazoans.

      (2) Identifying three haplotypes at the TA locus provides a snapshot of potential evolutionary trajectories for these elements, which are often inferred but rarely demonstrated in naturally occurring strains. The genomic analysis of 550 wild isolates contextualizes the findings within natural populations, revealing geographic clustering and evolutionary pressures acting on the TA locus.

      (3) The study employs various techniques, including CRISPR/Cas9 knockouts, FISH, long-read RNA sequencing, and population genomics. The use of inducible systems to confirm toxicity and antidote functionality is particularly robust. This multifaceted approach strengthens the validity of the findings.

      (4) The authors provide compelling evidence that small RNA pathways suppress toxin activity in strains lacking a functional antidote. This highlights an alternative mechanism for neutralizing selfish genetic elements.

      Weaknesses:

      (1) The introduction focuses strongly (for good reason) on bacterial TA systems and then jumps to TA systems in C. elegans. It's unclear why TA systems in other eukaryotes are not discussed.

      We briefly introduced bacterial TA systems because of their ubiquitousness and focused on C. elegans TA systems. We chose certain aspects of previously described Caenorhabditis TA elements that were relevant to the narrative we presented. Furthermore, we have extensively reviewed TA systems previously and have added a citation to that review in the revised manuscript (Burga et al. 2020).

      (2) Similarly, there is a missed opportunity to discuss an analogy between the suppressor mechanism discovered here and the hairpin RNA suppressors of meiotic drive identified by Eric Lai and colleagues. Discussing these will provide a fuller context of the present study's findings and will not affect their novelty.

      Thank you for pointing this out. We added a mention of the Stellate and Dox systems in our discussion.

      (3) While the evidence for RNAi-mediated suppression is strong, the claim that positive selection drove diversification at piRNA binding sites requires further discussion and clarification. The elevated dN and dS are unusual (how unusual relative to other genes in vicinity? What is hyper-divergent statistically speaking?), but there is no a priori reason that there would be selection on piRNA binding sites within the mll-1 transcript to facilitate its recognition by endogenous RNAi machinery; what is the selective pressure for mll-1 to do so? Most TA systems would like to avoid being suppressed by the host. One cannot make the argument that this was motivated by the loss of the antidote because the loss of the antidote would be instantly suicidal, so the cadence of events described requiring hypermutation of the mll-1 transcript does not work.

      We largely agree with the reviewer’s point, which we believe is based on the following sentence in the discussion: “We propose that positive selection for piRNA binding sites in the tmrl-1 transcript drove the diversification of this gene toward the N2 version.” We have removed this argument from the discussion in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      In the manuscript by Walter-McNeill, Kruglyak, and team, the authors provide solid evidence of another toxin-antidote (TA) system in C. elegans. Generally, TA systems involve selfish and linked genetic elements, one encoding a toxin that kills progeny inheriting it, unless an antidote (the second element) is also present. Currently, only two TA systems have been characterized in this species, pointing to the importance of identifying new instances of such systems to understand their transmission dynamics, prevalence, and functions in shaping worm populations.

      Strengths:

      This novel TA system (mll-1/smll-1) was identified on LGV in wild C. elegans isolates from the Hawaiian islands, by crossing divergent strains and observing allele frequency distortions by high-throughput genome sequencing after 10 generations. These allele frequency distortions were subsequently confirmed in another set of crosses with a separate divergent strain, and crosses of heterozygous males or hermaphrodites resulted in a pattern of L1 lethality in progeny (with a rod arrest phenotype) that suggested the maternal transmission of this TA system from the XZ1516 genetic background. By elegantly combining the use of near-isogenic lines, CRISPR editing to generate knock-outs, and a transgene rescue of the antidote gene, the authors identified the genes encoding the toxin and the antidote, which they refer to as mll-1 and smll-1. Moreover, the specific mll-1 isoform responsible for the production of the toxin was identified and mll-1 transcripts were observed by FISH in early and late embryos, as well as in larvae. Inducible expression of the toxin in various strains resulted in larval arrest and rod phenotypes. The authors then characterized the genetic variation of 550 wild isolates at the toxin/antidote region on LGV and distinguished three clades: (1) one with the conserved TA system, (2) one having lost the toxin and retaining a mostly functional antidote, and (3) one having lost the antidote and retaining a divergent yet coding toxin (this includes the reference strain Bristol N2, in which the homologous toxin gene has acquired mutations and is known as B0250.8). Further, the authors show that this region is under positive selection. These data are compelling and provide very strong evidence of a new TA system in this species.

      Weaknesses:

      The question remained as to how one clade, including N2, could retain the toxin gene but not possess a functional antidote. In the second part of the manuscript, the authors hypothesized that small RNA targeting (RNAi) of the toxin transcript could provide the necessary repression to allow worms to survive without the antidote. Through a meta-analysis of multiple small RNA datasets from the literature, the authors found evidence to support this idea, in which the toxin transcript is targeted by 22G siRNAs whose biogenesis is dependent on the Mutator foci protein, MUT-16. They note that from previous studies, mut-16 null mutants displayed a varied penetrance of larval arrest. In their own hands, mut-16 mutants displayed 15% varied larval arrest and 2% rod phenotypes. In an attempt to link B0250.8 to mut-16/siRNAs, they made a double mutant and examined body length as a proxy for developmental stage. Here, they observed a partial rescue of the mut-16 size defect by B0250.8 mutation. Finally, the authors also highlight data from further meta-analysis, which predicts the recognition of B0250.8 by several piRNAs. Also based on existing data from the literature, the authors link loss of Piwi (PRG-1), which binds piRNAs, to a depletion of 22G-RNAs targeting B0250.8 and an upregulation of B0250.8 expression in gonads, suggesting that piRNAs are the primary small RNAs that target B0250.8 for downregulation. The data in this portion of the manuscript are intriguing, but somewhat preliminary and incomplete, as they are based on little primary experimentation and a collection of different datasets (which have been acquired by slightly different methods in most cases). This portion of the study would require subsequent experimentation to firmly establish this mechanistic link. For example, to be able to claim that "the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation" the identified piRNA sites should be mutated and protein and transcript levels analysed in wild-type and in the strain with mutated piRNA sites. At a minimum, the protein levels in wild-type and mut-16, prg-1, and/or wago-1 mutants should be measured by western blot and/or by live imaging (introducing a GFP or some other tag to the endogenous protein via CRISPR editing) to show that the toxin is not accumulated as a protein in wt, but increases in levels in these mutants. mRNA levels in Figure S5A suggest there is still some expression of the B0250.8 transcript in a wild-type situation.

      We thank the reviewer for their thoughtful assessment of our manuscript, and we appreciate that they recognized that the data linking the small RNA machinery to B0250.8 suppression is intriguing. While the reviewer claims our analysis is preliminary and incomplete, we believe we present an appropriate multi-faceted approach for establishing the small RNA-mediated suppression mechanism we describe. 

      First, the reviewer states that we rely on “little primary experimentation”. Our primary experiments show that loss of the N2 tmrl-1 allele partially rescues ∆mut-16 developmental delay and arrest phenotypes. Therefore, we provide direct evidence that the N2 tmrl-1 functionally contributes to the ∆mut-16 phenotype. Furthermore, we overexpressed the N2 tmrl-1 allele to show that this gene is a toxin.

      It is true that we use previously published datasets to establish a small RNA-mediated mechanism that likely explains our observations. The reviewer suggests that our claims are weakened by relying on a “collection of different datasets (which have been acquired by slightly different methods in most cases)”. We believe instead that evidence collected from multiple labs using an array of different techniques strengthens our conclusions. We show that N2 tmrl-1-targeting small RNAs have been identified across multiple datasets (references 26, 32, 33, 34). Taken together, these datasets support a mechanistic framework for the suppression of the N2 tmrl-1 that involves PRG-1-dependent piRNA binding, MUT-16-dependent 22G siRNA, and the secondary Ago WAGO-1 binding. 

      The reviewer suggests several experiments, but we do not view them as essential to support our claims. 

      (a) piRNA site mutatagenesis: we present multiple lines of evidence that the N2 tmrl-1 transcript is post-transcriptionally targeted by small RNAs in a piRNA-mediated manner, not that specific piRNA sites are necessary and sufficient for this silencing. The suggested experiment would be valuable for future work, but is beyond the scope of our study.

      (b) Characterization of TMRL-1 protein levels: We agree that this experiment would provide definitive evidence of complete small RNA-mediated suppression of the N2 tmrl-1 transcript. As we explain above, however, we do show that removing the N2 tmrl-1 allele partially rescues the ∆mut-16 growth defect, demonstrating that when this gene’s regulation is disrupted, it induces toxicity. Importantly, we observed no tmrl-1-induced toxicity when we overexpressed a version of this gene with a stop codon, indicating that it acts as a protein.

      Finally, the reviewer questions our claim that: "the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation."

      We agree that this statement is too definitive given our current data. We have revised it to: "Multiple lines of evidence suggest that the N2 tmrl-1 allele is recognized by piRNAs, leading to MUT-16-dependent 22G siRNA production and post-transcriptional silencing of the transcript."

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The paper suggests that antidote pseudogenization occurred because RNAi replaced its function, but does not explore whether this process is ongoing or complete across all N2-like strains.

      We explored this possibility, but we realize that we did not explicitly state so in the manuscript. The B0250.4 (amrl-1) gene is pseudogenized in all strains within the N2 clade. We have modified the following sentence in the results section to explicitly state this observation:

      “While the previously described C. elegans TA elements are characterized by their absence in susceptible strains (2, 3), all members of the N2-like susceptible clade harbor a divergent allele of tmrl-1 with an intact coding sequence, as well as a pseudogenized version of amrl-1.”

      (2) Some figures (e.g., allele frequency distortions) could benefit from additional annotations to guide interpretation. In general, the figures make the reader work harder than they need to.

      We attempted to add clarity to figure captions for clarity.

      Although mll-1 and smll-1 were identified as toxin and antidote genes, their molecular mechanisms remain unclear and are very interesting.

      We agree that identifying the molecular mechanism associated with the toxin and antidote would be of interest, but is beyond the scope of the current paper.

      Reviewer #2 (Recommendations for the authors):

      (1) Because the rod phenotype was important in identifying the TA system, it seems important to include representative images of this phenotype throughout the paper.

      We added a supplemental figure showing the resulting self progeny from a QX1211/XZ1516 heterozygote: Fig S1B

      (2) In Figure 2A, we were confused as to why there were so few reads of mll-1. We may be misunderstanding something, so could the authors explain this to us? We would have expected more reads of mll-1, given the diagram showing that the breakpoints of the NIL were beyond (closer to the right end of) the mll-1 locus, and the phenotype correlates with the presence of the toxin (frequency of .20 L1 arrest).

      The lack of sequencing depth arises because the sequence divergence between QX1211 and XZ1516 is too high to accurately map short sequencing reads derived from QX1211 to the XZ1516 genome. We added the following sentence to the figure caption to add clarity:

      “The XZ1516 and QX1211 genome are so diverged that short reads derived from QX1211 don’t align to the XZ1516 genome in the 200 bp windows with no corresponding read depth, as indicated by a lack of a gray bar.”

      (3) The use of TOF in Figure 4 as a proxy of animal length instead of directly indicating or measuring animal length hinders the comparison of these results with other studies (i.e., most often in the literature, we see images of worms and measurements of their sizes or use of some other morphological marker to demonstrate the proportion of worms in a particular developmental stage). Nonetheless, we think the approach is clever and certainly enables analysis of a large sample population. However, a wild-type control is missing from these experiments to give a sense of the typical distribution one would expect. Without this, one interpretation of the B0250.8 knock out data shown in B is that loss of B0250.8 results in ~10% arrested larval, which seems higher than would be expected for a wild type N2 strain, and should be explained-but again, if the wild type control showed the same pattern, that would be useful to know. The title for Figure 4 should be revised, as this figure suggests, but does not provide definitive evidence that B0250.8 is suppressed by sRNAs/sRNA pathways. See the next point for providing more definitive data to support this model.

      There is a long list of publications that rely on the large particle sorter to infer how growth rate is affected in various mutants and environmental conditions (See Andersen et al. 2015, ref 28 in the manuscript, and the papers that reference this work). As the reviewer pointed out, the use of time of flight, which is simply the amount of time an object obstructs a laser at a constant flow rate, enables accurate measurement of tens of thousands of individual animals for comparison. 

      The reviewer is correct to point out that without a wild type N2 control, it is impossible to tell what a typical distribution looks like. However, the experiment includes all strains necessary to make the comparisons that enable us to draw the conclusion that the N2 tmrl-1 allele contributes to larval arrest in the absence of MUT-16.

      We agree with the reviewers point that this figure does not provide evidence that B0250.8 is suppressed by small RNAs and we have therefore changed the figure title.

      The new figure title: The N2 tmrl-1 allele contributes to larval arrest in the absence of MUT-16

      (4) To be able to claim that "the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation" the identified piRNA sites should be mutated and protein and transcript levels analysed in wild-type and in the strain with mutated piRNA sites. At a minimum, the protein levels in wild-type and mut-16, prg-1, and/or wago-1 mutants should be measured by western blot and/or by live imaging (introducing a GFP or some other tag to the endogenous protein via CRISPR editing) to show that the toxin is not accumulated as a protein in wt, but increases in levels in these mutants. mRNA levels in Figure S5A suggest there is still some expression of the B0250.8 transcript in a wild-type situation.

      The reviewer makes several good suggestions for experiments to determine whether the conclusions we make from publicly available high-throughput sequencing datasets apply in our context. However, we disagree that the quoted statement “the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation” is not supported by the evidence we present from Reed et al. 2020. The data presented by Reed et al. clearly show that the N2 tmrl-1 transcript is heavily targeted by 22G siRNAs, and that the accumulation of these siRNAs depends on the presence of MUT-16 and PRG-1. The dependence on PRG-1 implicates piRNAs involvement in the mounting of a 22G response.

      (5) Importantly, it is not the mll-1/B0250.8 transcript itself that was not shown to interact with WAGO-1 in the Seroussi et al. eLife paper (Lines 257-259). This study investigated sRNAs associated with every AGO, and computationally inferred the targets of each AGO using those enriched sRNA sequences. Therefore, it is the siRNAs antisense to mll-1/B0250.8 that were detected in association with WAGO-1, making it likely that WAGO-1 is the secondary AGO that targets this transcript. The argument the authors make holds true, but the authors should revise how they describe the evidence supporting that argument to accurately reflect the existing data.

      Thank you for catching this mistake. We have updated the text to accurately reflect the results from the Seroussi et al 2023 publication:

      “Recent work has shown that the N2 tmrl-1 transcript-derived small RNAs co-immunoprecipitated with WAGO-1, providing additional evidence that this transcript is regulated by the endogenous RNAi machinery”

      (6) It seems likely that the authors explored the possibility that another antidote may be present in the third clade. Could they discuss what they did to rule out this explanation in lieu of piRNA/siRNA regulation?

      We did not look for another antidote in the third clade because this clade is defined by the presence of an antidote and the absence of a toxin. Figure 3C shows the result of a cross between a third clade strain (NIC195) and XZ1516. The conclusion we draw from this experiment is that the antidote present in NIC195 provides near complete resistance to the XZ1516 toxin.

      (7) Line 156, legend of Figure S3, and line 273: There was no marker used to indicate that these are the primordial germ cells. Best practices would indicate using a fluorescent marker (e.g., PIE-1 GFP or PGL-1 GFP or PRG-1 GFP, etc.) to definitively identify these as PGCs.

      We agree with the reviewer’s point. As we do not have the perfect experiment, we do not definitively state that tmrl-1 transcripts localize in the primordial germ cells. 

      Minor comments:

      (1) A minor suggestion: incorporating some of the results now shown in the supplementary figures - Figures S1, S3, and S4 - into the main figures may make the manuscript easier to read.

      We constructed the manuscript in a way we thought was straightforward. The figures listed by the reviewer are supplemental to the main conclusions of the manuscript, so we decided to leave them as supplemental figures.

      (2) Line 87, Figure S1A: include numbers in the y-axis.

      The numbers are included on the y-axis and we explain the x-axis tick marks in the figure caption.

      (3) Figures 1B, 2B, 3C, 4B, S1B, S4: statistical analyses missing.

      We have added a summary of the statistical analysis to the captions of Figures 1B, 2B, 3C, and S1B. We added more detail from the analysis of 4A, which is the figure we draw conclusions from. Figure S4 is observational data, and the only conclusion drawn from that figure is that the N2 tmrl-1 gene encodes a toxin. It is toxic in 100% of individuals we looked at and therefore doesn’t warrant statistics. 

      (4) Line 100, "The rod progeny were all homozygous for QX1211 alleles at the locus on the right arm of chromosome V that displayed the allele frequency distortion in the mapping populations". Is this supported by data? While there is strong evidence to suggest it, the way it is currently written makes it seem that the rod progeny have been genotyped (by sequencing or PCR?). Is this the case? If not, the authors should revise the statement accordingly.

      Yes, this is indeed the case and we have updated the text to reflect that we performed PCR of a QX1211-specific indel to verify the genotypes on the right arm of chromosome V.

      (5) Figure 2A: lower panel missing x axis label.

      The top panel is a cartoon representation of a NILs, and the x axis is labeled for the top panel, highlighting the mapped element. 

      (6) Line 140 to 148: The authors should provide data to support these statements.

      Realizing i skipped this one – these are the lines they are referring to -> Long-read RNA sequencing revealed two distinct mll-1 isoforms, a short isoform with three predicted exons and a long isoform with eight predicted exons (Fig. S2A). We constructed plasmids with inducible versions of each mll-1 isoform. When we injected susceptible strains with the short mll-1 isoform array, every F1 individual carrying the array died, with 64% of larvae exhibiting the rod phenotype, indicating that uninduced expression levels of the short mll-1 isoform are sufficient to induce lethality. By contrast, we were able to isolate susceptible strains that maintained the long mll-1 isoform array or a short mll-1 isoform array with a premature stop codon in mll-1. We observed no rod progeny upon induction of these arrays, indicating that the short isoform encodes the functional toxin, and that the toxin acts as a protein.

      (7) Line 193: It would be interesting to see if there is structural conservation between mll-1 and B0250.8 using alpha-fold. Have the authors done this?

      We did attempt to look for structural conservation but we found the confidence in the structural predictions to be very low, which didn’t warrant a comparison.

      (8) Line 206-207: Could the authors explain why the frequency of the rod phenotype is so low when presumably over-expressing B0250.8? Does this indicate that B0250.8 is not as functional a toxin as mll-1, or is it sufficiently repressed by sRNAs and not actually overexpressed? Further, what are "abnormal" phenotypes? This should be clarified for the reader.

      It is likely that the overexpression and misexpression of toxic proteins is causing the abnormal phenotypes. The rod phenotype probably manifests when the gene is expressed at the appropriate developmental stage and tissue to cause the phenotype, whereas abnormal phenotypes manifest when the expression is not in the correct stage or location. A summary of the observed phenotypes is provided in Supplementary Table 7.

      (9) Line 216 and thereafter: indicate that B0250.8 is now referred to as mll-1.

      We incorporated this suggestion.

      (10) Line 228-231: missing to state that this is shown in Figures 4A-B.

      This and the following comment suggests that we did not provide enough clarity in this section. We modified the line to the following:

      Consistent with this report, in an agar plate-based preliminary assay we observed that ~15% of ∆mut-16 progeny arrest at various larval stages, and 2% of progeny are rod, which is suggestive of derepression of tmrl-1 in N2.

      This lets readers know that this initial characterization of the mut-16 knockout strain is different from the data presented in figure 4.

      (11) Line 230: the Figure shows ~25% of arrest for the deletion mutant of mut-16, but the text says ~15%.

      The 15% the reviewer points out was obtained from a preliminary agar plate-based experiment where we attempted to characterize the mut-16 deletion strains. We turned to a more high-throughput approach to screen through more animals for each genotype, which we report in figure 4.

      (12) Line 233: TOF, and not animal length, was compared. The authors should indicate that TOF is used as a proxy for animal length.

      We made the suggested change. The new sentences read:

      To do so, we compared time of flight (TOF) measurements—a proxy for animal length, developmental stage, and growth rate (28)—between a strain with a single knockout of mut-16 and one with a double knockout of mut-16 and the N2 tmrl-1 (a strain with a single knockout of the N2 tmrl-1 served as a negative control). We observed a reduction in TOF and an increase in the fraction of worms in larval stages in the mut-16 knockout strain, and these effects were partially rescued in the double knockout strain (Fig. 4).

      (13) Line 237-239: This claim may be overstated without additional data. Consider adding a "likely" to the statement.

      The line in question: 

      These results indicate that the reduced growth rate observed in the mut-16 knockout strain is partially mediated by derepression of the N2 mll-1 allele.

      We modified it to reflect the reviewer’s concern: 

      These results indicate that the reduced growth rate observed in the mut-16 knockout strain is partially mediated by the presence of the N2 tmrl-1 allele, likely because tmrl-1 is derepressed in mut-16 knockout strains.

      (14) Line 257: Figure S5C should be moved to line 259.

      We made the suggested move. 

      (15) Is the name mll-1 firmly established? We ask because MLL1 is a human mutation commonly associated with leukemia, and it may lead to some confusion in the field. This is a minor point, but we wanted to bring it forth.

      This name was not firmly established. We modified the names to not overlap with known gene names:

      tmrl-1 - Toxin-induced Maternal Rod Lethality

      amrl-1 - Antidote of Maternal Rod Lethality

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In the manuscript "Conformational Variability of HIV-1 Env Trimer and Viral Vulnerability", the authors study the fully glycosylated HIV-1 Env protein using an all-atom forcefield. It combines long all-atom simulations of Env in a realistic asymmetric bilayer with careful data analysis. This work clarifies how the CT domain modulates the overall conformation of the Env ectodomain and characterizes different MPER-TMD conformations. The authors also carefully analyze the accessibility of different antibodies to the Env protein.

      Strengths:

      This paper is state-of-the-art given the scale of the system and the sophistication of the methods. The biological question is important, the methodology is rigorous, and the results will interest a broad elife audience. The authors also establish strong connections to previous literature and acknowledge the limitations of the CT-truncated protein construct, which enhances the manuscript's relevance to the community.

      Reviewer #2 (Public review):

      In this work, the authors elucidate how a viral surface protein behaves in a membrane environment and how its large-scale motions influence the exposure of antibody-binding sites. Using long-timescale, all-atom molecular dynamics simulations of a fully glycosylated, full-length protein embedded in a virus-like membrane, the study systematically examines the coupling between ectodomain motion, transmembrane orientation, membrane interactions, and epitope accessibility. Multiple model variants differing in cleavage state, initial transmembrane configuration, and presence of the cytoplasmic tail are compared to identify general features of protein-membrane dynamics relevant to antibody recognition.

      A major strength of this study is the scope and ambition of the simulations. The authors perform multiple microsecond-scale simulations of a highly complex, biologically realistic system that includes the full ectodomain, transmembrane region, cytoplasmic tail, glycans, and a heterogeneous membrane. The finding that the ectodomain explores a wide range of tilt angles while the transmembrane region remains more constrained, with limited correlation between the two, offers useful conceptual insight into how global motions may be accommodated without large rearrangements at the membrane anchor. The explicit consideration of membrane and glycan steric effects on antibody accessibility further strengthens the study.

      The main limitations relate to sampling and model dependence inherent to simulations of this size and complexity. The analysis of antibody accessibility is based on geometric and steric criteria, which do not capture potential conformational adaptations of antibodies or membrane remodeling during binding; the authors have appropriately noted this as a limitation.

      In the revised manuscript, the authors have addressed all previously raised concerns. Time series plots of the tilt angles have been added, figure captions and visual encodings have been clarified, quantitative descriptions of angular distributions have been strengthened, and the distance metric for MPER exposure is now accompanied by temporal data. The overall presentation is substantially improved, and the conclusions are well supported by the data as presented.

      Reviewer #3 (Public review):

      Summary:

      This study uses large-scale all-atom molecular dynamics simulations to examine the conformational plasticity of the HIV-1 envelope glycoprotein glycoprotein (Env) in a membrane context, with particular emphasis on how the transmembrane domain (TMD), cytoplasmic tail (CT), protomer cleavage, and membrane environment influence ectodomain orientation and antibody epitope exposure. By comparing Env constructs with and without the CT, explicitly modeling glycosylation, and embedding Env in an asymmetric lipid bilayer, the authors aim to provide an integrated view of how membrane-proximal regions and lipid interactions shape Env antigenicity, including epitopes targeted by MPER-directed antibodies.

      Strengths:

      The authors have made a genuine effort to address the concerns raised in the first round of review, and the revised manuscript is substantively improved. The addition of dynamical cross-correlation maps, expanded citation of prior computational work, clarification of the membrane composition rationale, data deposition to Zenodo, and the new discussion contextualizing the independence of ectodomain and TMD motions are all welcome. Several scientifically interesting aspects of the work merit highlighting before the remaining concerns are addressed.

      A key strength of this work remains the scope, scale, and realism of the simulation systems. The authors construct a very large, nearly complete-Env-scale model that includes a glycosylated Env trimer embedded in an asymmetric bilayer, enabling analysis of membrane-protein interactions that are difficult to capture experimentally. The inclusion of specific glycans at reported sites, and the focus on constructs with and without the CT or cleavage, are well motivated by existing biological and structural data.

      The observation that R696 orientation and its interacting partners give rise to asymmetric protomer conformations and distinct TMD tilts is a notable finding. The statement that interactions between R696 and lipid headgroups or CT residues can be strong enough to introduce a kink into the TMD is well-supported by representative snapshots and consistent with prior isolated-TMD simulations. The use of two initialization depths ("high" and "low") to probe R696 leaflet preference is methodologically interesting and the authors' interpretation - that there is a slight bias toward cytoplasmic leaflet interactions, but that these contacts could be highly dynamic over the course of viral entry - is appropriately cautious. It would be valuable to explicitly frame this as a hypothesis with testable predictions that future experimental or enhanced-sampling work could address. Similarly, the equilibration-driven kinking of the TMD core, consistent with prior isolated-TMD studies, represents a useful validation that extends those earlier observations to the intact trimeric context.

      The simulations reveal substantial tilting motions of the ectodomain relative to the membrane, with angles spanning roughly 0-30° (and up to ~40° in some analyses), while the ectodomain itself remains relatively rigid. This framing, that much of Env's conformational variability arises from rigid-body tilting rather than large internal rearrangements, is an important conceptual contribution. The authors also provide interesting observations regarding asymmetric bilayer deformations, including localized thinning and altered lipid headgroup interactions near the TMD and CT, which suggest a reciprocal coupling between Env and the surrounding membrane.

      The analysis of antibody-relevant epitopes across the prefusion state, including the V1/V2 and V3 loops, the CD4 binding site, and the MPER, is another strength. The study makes effective use of existing experimental knowledge in this context, for example by focusing on specific glycans known to occlude antibody binding, to motivate and interpret the simulations.

      Finally, the revised discussion provides more context that situates the study's findings and discrepancies within the broader literature, strengthening the manuscript's clarity and interpretability.

      Weaknesses:

      The revised work is much improved, but still includes substantive issues with writing including organization, such as paragraph run-ons, and citation issues. Improving these would help readers make the most of this important study.

      The revised Introduction now includes a paragraph summarizing prior MD work, which is an Improvement. However, the paragraph remains structured around the limitations and setup of previous studies (e.g., "early studies were constrained by limited computational resources", short trajectory lengths, isolated constructs) rather than their findings. Readers benefit most from understanding what those studies showed - and where the present work confirms, extends, or diverges from those results. The current framing inadvertently positions prior work as deficient scaffolding rather than as independent data points converging on shared conclusions. The Introduction could be revised to briefly summarize the key biological conclusions from prior MD studies alongside their technical context, which could then be revisited in their appropriate place alongside key results.

      The authors have verified that PDB entries are cited at first mention, and this is noted. However, a recurring issue remains: key literature-supported conclusions appear in the Results and Discussion sections without accompanying citations at each point of use. Passages that summarize experimental or computational findings - particularly those used to validate or contextualize the authors' own results - require citation at every point of claim, not only at first introduction of a reference. This is not a minor stylistic preference. Downstream readers, systematic reviewers, and automated tools that map literature to claims (e.g., scite) rely on co-occurrence of claims and citations within the same passage. A citation appearing several paragraphs earlier does not carry attribution forward. As a practical example: the statement that "MPER-targeting antibodies bind effectively only after the gp120-gp41 trimer undergoes major conformational rearrangements toward a fusion-intermediate or post-fusion state (Frey et al., 2008; Alam et al., 2009; Chen et al., 2014; Lee et al., 2016)", which is appropriate. That same standard of inline attribution should be applied throughout - including in Results and Discussion subsections where prior experimental findings are mentioned without citation.

      Additionally, cited literature should be framed to highlight convergence with the authors' conclusions, not primarily to limitations of previous studies. Where prior studies independently support a finding, this should be stated explicitly. Independent replication across methods and systems is one of the strongest arguments for ground truth; treating it as such would improve the manuscript's scientific standing.

      Finally, the dynamical cross-correlation maps assess ectodomain-TMD coupling, and the authors appropriately acknowledge that microsecond simulations capture only the closed ground state. However, the revised manuscript does not address the question raised in the first review regarding CT-TMD and CT-ectodomain correlations. The Results section states that "very weak correlations between the ectodomain and the TMD" were found, but it is not clear whether the CT was included in this analysis or whether analogous correlation maps for CT-TMD and CT-ectodomain pairs were computed for the full-length systems. Additional analyses of the authors' deposited MD trajectories-such as probing for exposure of cryptic epitopes and potential allosteric coupling-could serve as valuable extensions of this work.

      We thank the Reviewer for the further comments and suggestions. We have revised the manuscript accordingly.

      The observation that R696 orientation and its interacting partners give rise to asymmetric protomer conformations and distinct TMD tilts is a notable finding. The statement that interactions between R696 and lipid headgroups or CT residues can be strong enough to introduce a kink into the TMD is well-supported by representative snapshots and consistent with prior isolated-TMD simulations. The use of two initialization depths ("high" and "low") to probe R696 leaflet preference is methodologically interesting and the authors' interpretation - that there is a slight bias toward cytoplasmic leaflet interactions, but that these contacts could be highly dynamic over the course of viral entry - is appropriately cautious. It would be valuable to explicitly frame this as a hypothesis with testable predictions that future experimental or enhanced-sampling work could address. Similarly, the equilibration-driven kinking of the TMD core, consistent with prior isolated-TMD studies, represents a useful validation that extends those earlier observations to the intact trimeric context.

      At the end of the subsection “The energetically unfavorable R696 in the hydrophobic core results in asymmetric, kinked TMD conformations and disrupts membrane integrity” we have added

      “Taken together, these observations suggest that interactions of R696 with lipid headgroups and CT residues may modulate TMD tilt and kink formation during viral entry. However, whether the orientation of R696 dynamically switches between the two leaflets over longer timescales and whether a preference exists for either leaflet remain to be examined in future experimental and/or enhanced sampling simulation studies.”

      The revised Introduction now includes a paragraph summarizing prior MD work, which is an improvement. However, the paragraph remains structured around the limitations and setup of previous studies (e.g., "early studies were constrained by limited computational resources", short trajectory lengths, isolated constructs) rather than their findings. Readers benefit most from understanding what those studies showed - and where the present work confirms, extends, or diverges from those results. The current framing inadvertently positions prior work as deficient scaffolding rather than as independent data points converging on shared conclusions. The Introduction could be revised to briefly summarize the key biological conclusions from prior MD studies alongside their technical context, which could then be revisited in their appropriate place alongside key results.

      We have modified the original fifth paragraph in the Introduction section and subdivided it into two separate paragraphs to emphasize the key biological conclusions in prior simulation studies.

      “Molecular dynamics (MD) simulations have been employed to investigate the stability and conformational properties of monomeric and trimeric TMD. An early study of the trimeric TMD established a foundational understanding of the domain's stability, though it was limited by the computational resources available at the time (Kim et al., 2009). Subsequent work utilizing metadynamics found that the monomeric TMD is characterized by significant conformational plasticity and multiple metastable states, with the individual helix tilting in the bilayer and the midspan arginine (R696) interacting with lipid headgroups in either leaflet (Gangupomu et al., 2010; Baker et al., 2014). Baker et al. also simulated the monomeric TMD on Anton supercomputers, extended sampling to the multi-microsecond time scale, and demonstrated that TMD tilting and the interaction of R696 with lipids lead to local membrane thinning and water defects (Baker et al., 2014). Hollingsworth et al. modeled and simulated trimeric TMD in an asymmetric membrane and observed that TMD tilting and membrane thinning also occurred for the trimeric helical bundle, where water and ions permeated to stabilize the three positively charged R696 residues (Hollingsworth et al., 2018).

      Piai et al. determined the NMR structure of a construct comprising the MPER, TMD, and CT, which currently serves as the only PDB structure to include the majority of the CT residues. They complemented this structural work with MD simulations to assess the structural stability of the trimeric MPER–TMD–CT complex (Piai et al., 2021). Recently, Majumder et al. simulated the same MPER–TMD–CT complex and applied a machine learning-based approach to classify the diverse conformational ensemble of the MPER-TMD-CT (Majumder et al., 2025). Maillie et al. combined conventional MD, steered MD, and coarse-grained simulations to demonstrate that interactions between MPER-targeting antibodies and membrane lipids are critical for effective epitope recognition (Maillie et al., 2025). In addition, MD simulations have been extensively applied to characterize the well-studied ectodomain.”

      The authors have verified that PDB entries are cited at first mention, and this is noted. However, a recurring issue remains: key literature-supported conclusions appear in the Results and Discussion sections without accompanying citations at each point of use. Passages that summarize experimental or computational findings - particularly those used to validate or contextualize the authors' own results - require citation at every point of claim, not only at first introduction of a reference. This is not a minor stylistic preference. Downstream readers, systematic reviewers, and automated tools that map literature to claims (e.g., scite) rely on co-occurrence of claims and citations within the same passage. A citation appearing several paragraphs earlier does not carry attribution forward. As a practical example: the statement that "MPER-targeting antibodies bind effectively only after the gp120-gp41 trimer undergoes major conformational rearrangements toward a fusion-intermediate or post-fusion state (Frey et al., 2008; Alam et al., 2009; Chen et al., 2014; Lee et al., 2016)", which is appropriate. That same standard of inline attribution should be applied throughout - including in Results and Discussion subsections where prior experimental findings are mentioned without citation.

      Additionally, cited literature should be framed to highlight convergence with the authors' conclusions, not primarily to limitations of previous studies. Where prior studies independently support a finding, this should be stated explicitly. Independent replication across methods and systems is one of the strongest arguments for ground truth; treating it as such would improve the manuscript's scientific standing.

      In addition to summarizing the biological conclusions from prior simulation studies in our response to the previous comment, we have also added the following citations.

      “Human immunodeficiency virus type 1 (HIV-1) is the most prevalent strain of HIV responsible for the development of acquired immunodeficiency syndrome (AIDS) (Sharp et al., 2011). The HIV-1 envelop (Env) consists of a host cell-derived lipid membrane and viral glycoproteins that play a crucial role in mediating viral entry into host cells. The Env glycoprotein is initially synthesized in the endoplasmic reticulum (ER) as a precursor gp160 and cleaved by furin into two subunits, gp120 and gp41. The non-covalently associated gp120–gp41 complex is transported to the cell surface in the form of a trimer, where it is subsequently incorporated into the envelope of nascent virions during viral assembly (Wyatt et al., 1998). The exposure of Env protein is essential for binding to the primary receptor CD4 and the co-receptors CCR5 or CXCR4, triggering membrane fusion and viral entry (Dalgleish et al., 1984; Feng et al., 1996; Huang et al., 1996). However, this exposure also renders the virus susceptible to immune attack. In response to host immune pressure, Env is densely coated with N-linked glycans added during post-translational modification in the ER and Golgi apparatus, which effectively shield vulnerable epitopes from immune recognition (Wei et al., 2003).”

      “While MPER plasticity has been linked to its role in virus-host membrane fusion because it enables the ectodomain and TMD to adopt distinct orientations during large-scale structural rearrangements (Salzwedel et al., 1999), our results show that this flexibility is already inherently present in the prefusion state.”

      “However, transition among these three states occur on millisecond-to-second timescales (Munro et al., 2014).”

      Finally, the dynamical cross-correlation maps assess ectodomain-TMD coupling, and the authors appropriately acknowledge that microsecond simulations capture only the closed ground state. However, the revised manuscript does not address the question raised in the first review regarding CT-TMD and CT-ectodomain correlations. The Results section states that "very weak correlations between the ectodomain and the TMD" were found, but it is not clear whether the CT was included in this analysis or whether analogous correlation maps for CT-TMD and CT-ectodomain pairs were computed for the full-length systems. Additional analyses of the authors' deposited MD trajectories-such as probing for exposure of cryptic epitopes and potential allosteric coupling-could serve as valuable extensions of this work.

      We have updated the manuscript to address the correlations involving the CT. Figure 2—figure supplements 12 and 13 display the dynamical cross-correlation maps (DCCM) for the full-length systems (including the CT), which indicate low correlations between the ectodomain and the CT. We have modified the figure captions to explicitly state that the CT is included in these analyses. We have also clarified in the text that we do not further interpret the coupling of the CT with the other domains. As the Reviewer noted, the high structural heterogeneity of the CT makes defining consistent parameters (such as a tilt angle) impractical. Given this variability, along with the inherent uncertainty in the experimental structure of the CT, we believe it is important to avoid over interpreting these observations.

      “Although Figure 2—figure supplements 12 and 13 also show low correlations between the ectodomain and the CT, we do not further interpret the coupling of the CT with the other domains due to its structural heterogeneity and the inherent uncertainty in its experimental structure.”

      We have modified captions of Figure 2—figure supplements 10–13

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      The authors have made meaningful progress in addressing first-round concerns. The remaining issues center on how prior literature is framed and integrated - not just cited - throughout the manuscript, consistent attribution at each point of claim, clarification of the CT correlation analysis, and major writing improvements. Addressing these points would substantially strengthen the manuscript's contribution to the field.

      Abstract

      "knowledge of the cytoplasmic tail (CT) is virtually absent" is overstated. While structural data for the CT are limited and largely uncertain, the CT has been extensively studied functionally and some NMR structural data exist (Piai et al., 2021; Murphy et al., 2017). Suggest revising to reflect that high-resolution structural information for the CT in the context of the intact trimer remains limited

      We have revised the abstract according to the Reviewer’s suggestion.

      “While structural information is available for the membrane-proximal external region (MPER) and transmembrane domain (TMD), these regions remain comparatively understudied. Furthermore, high-resolution structural information for the cytoplasmic tail (CT), particularly within the context of the intact trimer, is limited and largely uncertain.”

      Introduction

      The first paragraph is unreferenced. Foundational claims about HIV-1 biology, Env processing, and glycan shielding should carry at least landmark citations for readers new to the field.

      We have added references to the first paragraph.

      “Human immunodeficiency virus type 1 (HIV-1) is the most prevalent strain of HIV responsible for the development of acquired immunodeficiency syndrome (AIDS) (Sharp et al., 2011). The HIV-1 envelop (Env) consists of a host cell-derived lipid membrane and viral glycoproteins that play a crucial role in mediating viral entry into host cells. The Env glycoprotein is initially synthesized in the endoplasmic reticulum (ER) as a precursor gp160 and cleaved by furin into two subunits, gp120 and gp41. The non-covalently associated gp120–gp41 complex is transported to the cell surface in the form of a trimer, where it is subsequently incorporated into the envelope of nascent virions during viral assembly (Wyatt et al., 1998). The exposure of Env protein is essential for binding to the primary receptor CD4 and the co-receptors CCR5 or CXCR4, triggering membrane fusion and viral entry (Dalgleish et al., 1984; Feng et al., 1996; Huang et al., 1996). However, this exposure also renders the virus susceptible to immune attack. In response to host immune pressure, Env is densely coated with N-linked glycans added during post-translational modification in the ER and Golgi apparatus, which effectively shield vulnerable epitopes from immune recognition (Wei et al., 2003).”

      A paragraph break after "... and cytoplasmic tail (CT), are relatively understudied" would improve readability by separating the general context from the MPER/TMD-specific discussion that follows.

      A paragraph break before "Similarly, there are different conclusions about" would separate the TMD oligomeric state discussion from the MPER conformation discussion and improve navigation.

      A paragraph break after "Despite these advances, it remains challenging to investigate the gp120-gp41 trimer as an intact entity considering its structural complexity" would clearly delineate the literature context from the description of the present work.

      We have introduced paragraph breaks as suggested to improve the flow and readability of the introduction.

      The biological rationale for simulating both cleaved and uncleaved systems should be stated explicitly in the Introduction. Readers unfamiliar with the furin cleavage biology and NFL trimer constructs will benefit from a sentence explaining why this comparison is informative.

      In the middle of the last paragraph in the Introduction section we have added

      “While host furin cleavage of the gp160 precursor into gp120 and gp41 is a prerequisite for viral infectivity (McCune et al., 1988), native virions also incorporate a fraction of uncleaved gp160 (Zhang et al., 2021). Furthermore, many current immunogen designs, such as NFL and UFO constructs, utilize a covalent linker to stabilize the metastable prefusion conformation (Sharma et al., 2015; Kong et al., 2016). Therefore, we simulated both cleaved and uncleaved trimers to explore how the absence of proteolytic cleavage impacts the conformational landscape.”

      The modifier “subsequently” in “Majumder et al. subsequently simulated...” implies temporal sequence and invites the inference that Majumder et al.'s work is less sophisticated or prior. Given that both works are recent and peer-reviewed, a neutral modifier such as “recently” or “independently” is more appropriate.

      We agree that a more neutral modifier is appropriate and have replaced “subsequently” with “recently” to avoid any unintended inference.

      In the beginning of the sixth paragraph in the Introduction section we have modified

      “Piai et al. determined the NMR structure of a construct comprising the MPER, TMD, and CT; to date, this is the only PDB structure including the majority of CT residues. They complemented this structural work with MD simulations to access the structural stability of the trimeric MPER–TMD–CT complex (Piai et al., 2021). Recently, Majumder et al. simulated the same MPER–TMD–CT complex and applied a machine learning-based approach to classify its conformational ensemble (Majumder et al., 2025).”

      The sentence "Moreover, we selected several bNAbs targeting the epitopes across different regions of the Env protein and demonstrate that the simulation trajectories can be used to assess the epitope accessibility" implies that simulations of antibody binding were performed. This should be rephrased, for example: "Moreover, we selected various epitopes across Env that are targeted by bNAbs and demonstrate that the MD simulation trajectories can be used to assess epitope accessibility."

      At the end of the Introduction section we have modified

      “Moreover, by analyzing epitopes targeted by various bNAbs, we demonstrate that the simulation trajectories can be leveraged to assess the epitope accessibility.”

      The revised Methods section now cites van Meer et al. (2008) and Sampaio et al. (2011) as primary experimental sources for plasma membrane composition, which is appropriate. However, the Introduction still contains the statement: "we built a model of full-length gp120-gp41 trimer embedded in a lipid bilayer mimicking the lipid composition of the mammalian plasma membrane (Pogozheva et al., 2022)". This cites only the authors' own prior simulation study. A primary experimental reference (van Meer et al., 2008 and/or Sampaio et al., 2011) should be added here as well, so that readers encountering the claim in the Introduction have direct access to the supporting evidence.

      At the beginning of the last paragraph in the Introduction section we have modified

      “In this work, we built a model of full-length gp120–gp41 trimer embedded in a lipid bilayer mimicking the lipid composition of the mammalian plasma membrane (van Meer et al., 2008; Sampaio et al., 2011; Ingolfsson et al., 2014; Pogozheva et al., 2022) (Figure 1).”

      Additionally, a brief note in the Introduction on the cell type specificity of the plasma membrane model used (or its absence) would be informative, as membrane composition varies substantially across mammalian cell types and the choice has potential consequences for the conclusions.

      We have added a brief note clarifying that differences between the model membrane and the native viral envelope may influence the study's conclusions, particularly regarding protein-lipid interactions.

      “We chose this composition as a representative baseline, though we acknowledge that the native viral envelope may exhibit a distinct lipid profile that could influence protein-lipid interactions.”

      Results

      Connecting the observed accessibility frequencies to known neutralization potency, breadth, or escape propensity for each antibody class (PGT128, PG9, VRC01, 35O22, 10E8, 4E10) would provide a mechanistic framework and substantially increase the impact of this section. Even a brief discussion of how glycan shielding dynamics relate to reported neutralization sensitivity data would add value.

      We have expanded the Results section to include a comparison between our computational accessibility frequencies and established experimental metrics (potency and breadth).

      At the end of each paragraph in the subsection “Ectodomain epitopes are conditionally accessible, whereas MPER epitopes are virtually inaccessible in the closed prefusion state” we have added

      “The high accessibility frequency observed for the PGT128 epitope aligns with its exceptional potency. As demonstrated by Walker et al., PGT128 is capable of neutralizing approximately 72% of global isolates with a median IC<sub>50</sub> of ~0.02 µg/mL. This potency is approximately 10-fold greater than that of PG9 and VRC01, though its breadth is lower than the 93% reported for VRC01 (Walker et al., 2011). This comparatively lower breadth may be attributed to strict sequence dependency. Because PGT128 recognition depends on the N332-centered glycan epitope, loss, truncation, or shifting of the N332 glycan to N334 prevents productive engagement regardless of local steric accessibility.”

      “This is consistent with the lower neutralization potency and moderate breadth of PG9, which exhibits a median IC<sub>50</sub> of ~0.22 µg/mL and a breadth of ~79% (Walker et al., 2009).”

      “This intermediate accessibility is consistent with the biological requirement of the CD4 binding site to remain periodically available for receptor engagement while maintaining a certain degree of glycan shielding to evade neutralization. The potency of VRC01 is even lower than that of PG9, with a reported median IC50 of ~0.32 µg/mL, but it possesses an exceptionally high breadth of ~93% (Wu et al., 2010; Walker et al., 2011).”

      “Altogether, these results demonstrate that epitope accessibility for this antibody is highly sensitivity to the membrane environment, glycan orientation and ectodomain tilting. This complex dependency provides a structural context for the experimental profile of 35O22, which exhibits high potency with a median IC<sub>50</sub> of ~0.03 µg/mL, but a relatively limited breadth of ~62% (Huang et al., 2014).”

      “Though differing in potency — with 10E8 exhibiting a median IC<sub>50</sub> of ~0.35 µg/mL compared to ~1.93 µg/mL for 4E10 — both antibodies demonstrate extremely high breadth of ~98% (Huang et al., 2012). This extensive breadth is primarily attributed to the high sequence conservation of the MPER across global isolates. The negligible epitope accessibility observed in the prefusion trimer supports the conclusion that these antibodies require the transition of the Env trimer into intermediate states to fully engage their epitopes (Frey et al., 2008).”

      The first paragraph of the Results section dives directly into trajectory notation without a brief summary of the simulation systems. A short opening paragraph (2-3 sentences) summarizing the number of systems, the variables tested (cleavage, CT presence, TMD position), and the total number of trajectories would orient the reader before the naming convention is introduced.

      We have moved the original first sentence in the Material and methods — Simulation details subsection to the beginning of the Results section. This sentence summarizes all the configurations we have considered and the number of independent trajectories for each configuration.

      “The combination of cleavage state (cleaved vs. uncleaved), sequence length (full-length vs. CT-truncated), and initial TMD position in the membrane (high vs. low) resulted in eight distinct configurations, and we performed three independent 1-μs all-atom MD simulations for each configuration.”

      The statement "very weak correlations between the ectodomain and the TMD" leaves open the question of CT-TMD and CT-ectodomain correlations. If a tilt angle cannot be defined for the CT due to its structural heterogeneity, this should be stated.

      We have updated the manuscript to address the correlations involving the CT. Figure 2—figure supplements 12 and 13 display the dynamical cross-correlation maps (DCCM) for the full-length systems (including the CT), which indicate low correlations between the ectodomain and the CT. We have modified the figure captions to explicitly state that the CT is included in these analyses. We have also clarified in the text that we do not further interpret the coupling of the CT with the other domains. As the Reviewer noted, the high structural heterogeneity of the CT makes defining consistent parameters (such as a tilt angle) impractical. Given this variability, along with the inherent uncertainty in the experimental structure of the CT, we believe it is important to avoid over interpreting these observations.

      “Although Figure 2—figure supplements 12 and 13 also show low correlations between the ectodomain and the CT, we do not further interpret the coupling of the CT with the other domains, considering its structural heterogeneity and the inherent uncertainty in its experimental structure.”

      We have modified captions of Figure 2—figure supplements 10–13

      Throughout the Results, several long paragraphs could be broken up. In particular, the TMD section and the MPER exposure section each contain dense multi-example run-on paragraphs that would benefit from subdivision.

      We agree with the Reviewer and have introduced multiple paragraph breaks in the Results section to improve the flow and readability. In instances where longer paragraphs remain, they have been intentionally preserved to maintain the logical integrity of closely linked results, ensuring the reader can follow a single cohesive argument without interruption.

      Discussion

      The statement "transition among three states occur on millisecond-to-second timescales" is an important claim that contextualizes the limitations of the microsecond simulations, but it is currently uncited. This should be attributed to the relevant experimental smFRET work (Munro et al., 2014 is cited in the preceding sentence, but not explicitly for this claim) and/or any additional literature that established these timescales for Env conformational switching.

      We have now explicitly attributed the claim regarding the millisecond-to-second timescales of Env conformational transitions to the relevant smFRET literature (Munro et al., 2014).

      In the middle of the second paragraph in the Discussion section we have added

      “However, transition among these three states occur on millisecond-to-second timescales (Munro et al., 2014).”

      The Discussion contains several extended paragraphs that could be subdivided to improve readability and help the reader navigate between distinct topics (e.g., MPER flexibility, CT effects, coupling, lipid composition, antibody accessibility).

      We have subdivided the Discussion section as suggested by the Reviewer to improved readability.

    1. Author response:

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

      In this revised manuscript, we added new analyses of the DNA-binding tail domain of Kid. AlphaFold 3 predictions suggested that dimeric Kid interacts more stably with double-stranded DNA than monomeric Kid. To experimentally test this prediction, we introduced a point mutation into a critical residue predicted to contribute to DNA binding. Consistent with the AlphaFold 3 model, this mutation abolished the interaction between Kid and DNA.

      We also extended our DNA transport assays by testing DNA substrates of different lengths. In addition to 100-bp double-stranded DNA, full-length Kid transported 1,000-bp and 2,000-bp DNA molecules along microtubules in vitro. These findings show that Kid can transport longer duplex DNA substrates than those initially tested, although these substrates do not fully recapitulate the organization of condensed chromatin.

      Furthermore, we performed dual-color imaging using independently purified Kid-mScarlet3 and Kid-mStayGold proteins. We consistently observed co-migration of the two fluorescently labeled Kid molecules along microtubules, supporting the conclusion that Kid forms dimers on microtubules.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Mitotic kinesins carry out crucial roles in intracellular motility and mitotic spindle organization. Although many mitotic kinesins have been extensively studied, a few conserved mitotic motors remain poorly explored, including chromosome-associated kinesins. Here, Furusaki et al reconstitute recombinant chromosome-associated kinesin or chromokinesin (Kid) and reveal processive plus-end motility along microtubules. The authors purify multiple versions of Kid, revealing dimeric organization and their processive microtubule plus-ended motility which depends on their conserved motor domains, neck linkers, and coiled-coil regions. The study reveals for the first time that KID can recruit and transport duplex DNA along microtubules using its conserved C-terminal DNA binding domain. The work provides crucial revised thinking about the mechanisms of Chromokinesins mitosis as physical processive motors that mobilize chromosomes towards the microtubule plus ends in early metaphase.

      Strengths:

      The authors reconstitute multiple chromosome-associated kinesin (KID) orthologs from Xenopus and humans with microtubules and determine their oligomerization. The study shows how coiled-coil and neck linker regions of KID are essential for its function as its deletion leads to non-processive motility. CHimeras placing the KID coiled-coil and neck linker on the KIF1A motor domain led to the production of a processive recombinant motor supporting the compatibility of their motility mechanisms. The KID c-terminal tail binds and transports only double-stranded DNA and its deletion or single-stranded DNA leads to defects in this activity.

      Thank you very much.

      Weaknesses:

      A minor weakness in the studies is that they do not resolve the mechanisms of KID in binding large duplex DNA molecules or condensed chromatin. The authors suggest a model in which KID forms multimers along large chromosomes that lead to their transport, but this model was not directly tested.

      We agree with the reviewer that our study does not directly resolve how Kid binds large duplex DNA molecules or condensed chromatin. In the revised manuscript, we have therefore softened our model and now present the idea that multiple Kid dimers act along chromosomes as a possible mechanism rather than a demonstrated conclusion. To strengthen the mechanistic basis of DNA binding, we added AlphaFold 3-based analysis of the Kid DNA-binding tail domain and experimentally tested a predicted DNA-binding residue. Mutation of this residue abolished Kid–DNA binding, supporting the proposed role of the tail domain in DNA engagement. We also added dual-color imaging experiments showing co-migration of independently purified Kid-mScarlet3 and Kid-mStayGold on microtubules, supporting dimer formation on microtubules. We now explicitly state that future studies using chromatinized DNA or chromosome-like substrates will be required to determine how Kid interacts with condensed chromatin in a cellular context.

      Reviewer #2 (Public review):

      Summary:

      Previous work in the field highlighted the role of the kinesin-10 motor protein Kid (KIF22) in the polar ejection force during prometaphase. However, the biochemical and biophysical properties of Kid that enabled it to serve in this role were unclear. The authors demonstrate that human and xenopus Kid proteins are processive kinesins that function as homodimeric molecules. The data are solid and support the findings although the text could use some editing to improve clarity.

      Strengths:

      A highlight of the work is the reconstitution of DNA transport in vitro.

      A second highlight is the demonstration that the monomer vs dimer state is dependent on protein concentration.

      Thank you very much.

      Weaknesses:

      The authors make several assumptions of the monomer vs dimer state of various Kid constructs without verifying the protein state using e.g. size exclusion chromatography and/or nanophotometry.

      We newly added mass photometry analysis in Figure 3 and Figure 5.

      They also make statements about monomer-to-dimer transitions on the microtubule without showing or quantifying the data.

      We performed dual color imaging to show the assembly of Kid monomers on microtubules.

      The discussion needs to better put the work into context regarding the ability of non-processive motors to work in teams (formerly thought to be the case for Kid) and how their findings on Kid change this prevailing view in the case of polar ejection force.

      We have revised the Discussion to better place our findings in the context of collective motor function and polar ejection force generation. Previous biochemical studies led to the prevailing model that Kid is a monomeric and non-processive chromokinesin. Under this model, sustained chromosome movement would require many Kid monomers distributed along chromosome arms to act collectively. Our findings revise this view. We show that full-length Kid forms homodimers, moves processively along microtubules, and directly transports double-stranded DNA. Thus, the elementary force-generating unit of Kid is unlikely to be a non-processive monomer. Instead, a single Kid dimer may act as a processive DNA-bound motor. In the context of mitotic chromosomes, multiple processive Kid dimers bound along chromosome arms could cooperate to generate chromosome-scale polar ejection forces. We have clarified in the Discussion that our model does not exclude ensemble behavior. Rather, it changes the nature of the proposed ensemble from many non-processive monomers to multiple processive dimers.

      The authors also do not mention previous work on kinesins with non-conventional neck linker/neck coil regions that have been shown to move processively. Their work on Kid needs to be put into this context.

      We thank the reviewer for this important suggestion. We have revised the Discussion to place Kid in the broader context of processive kinesins with non-conventional neck linker or neck coil regions. We now discuss previous work showing that neck-linker length strongly influences kinesin processivity, and that changes in neck-linker length alter the run length and motility properties of kinesin-1, kinesin-2, and other N-terminal kinesins (Shastry and Hancock, 2010; Shastry and Hancock, 2011).

      We also discuss studies showing that longer or non-conventional neck linker regions can provide additional functions beyond supporting processive stepping. For example, kinesin-2 can bypass Tau and other microtubule-bound obstacles by protofilament switching, and the neck linker of the mitotic kinesin KIF18A contributes to obstacle navigation within the mitotic spindle (Hoeprich et al., 2014; Malaby et al., 2019).

      In this context, we now emphasize that Kid has an exceptionally long and flexible neck linker, approximately four times longer than that of kinesin-1. Despite this non-canonical architecture, the Kid neck linker and coiled-coil region support processive motility, as shown by the processive movement of the KIF1A–Kid chimera. We therefore propose that Kid represents a non-conventional processive chromokinesin whose extended neck linker may help it move along crowded spindle microtubules while remaining attached to DNA or chromatin. We have also stated that this possibility remains to be tested directly.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Furusaki et al reconstitute effectively the chromosome-associated kinesin. The studies are well performed and effectively controlled with few minor suggestions

      The studies generally lack a few minor items that would improve the current work:

      (1) Alpha fold or coiled-coil predictions of the c-terminal region characterizing its organization or the nature of its interaction site with DNA. These should aid the presentation of the work and help refine the boundaries for coiled coils and the DNA binding domain.

      We thank the reviewer for this helpful suggestion. In the revised manuscript, we added AlphaFold 3-based structural predictions and coiled-coil predictions for the C-terminal region of Kid (Figure 7). These analyses helped define the predicted DNA-binding tail domain more clearly. The AlphaFold 3 model also suggested a potential DNA-interaction surface within the C-terminal DNA-binding region. We have incorporated these predictions into the revised figure and modified the text to clarify the domain organization of Kid.

      (2) The DNA transport motor activity is quite interesting and extending those studies to cover larger segments of DNA which may bind multiple kid motors would be very interesting.

      We thank the reviewer for this helpful suggestion. In the revised manuscript, we extended our DNA transport assays using longer double-stranded DNA fragments. In addition to the 100-bp DNA substrate, we tested 1,000-bp and 2,000-bp DNA fragments. Full-length Kid was able to transport both 1,000-bp and 2,000-bp double-stranded DNA along microtubules in vitro. These new data are now included in Figure 6F–I. Interestingly, the motile parameters of 1,000-bp and 2,000-bp DNA were comparable to those observed with 100-bp DNA. This result suggests that, under our reconstituted assay conditions, increasing DNA length does not substantially enhance the apparent transport velocity or run length. One possible explanation is that the interaction between Kid and naked DNA is relatively weak, and thus only one or a small number of Kid molecules productively engage each DNA molecule during transport. Alternatively, additional Kid molecules bound to longer DNA may not strongly affect the measured motility parameters under these assay conditions.

      We have added this point to the revised manuscript and now discuss that, in cells, additional factors such as chromatin proteins or chromosome-associated proteins may enhance the avidity or organization of Kid on chromosomes. Future studies using chromatinized DNA or chromosome-like substrates will be needed to determine how multiple Kid molecules engage large chromatin substrates during chromosome congression.

      (3) The final model regarding KID transporting chromosomes is probably oversimplified since there are few experiments with large stretches of DNA or chromatin that were not conducted. I suggest longer segments of DNA be studied or the model be redrawn to scale.

      We thank the reviewer for this important comment. We agree that the original model was oversimplified because naked DNA fragments do not fully recapitulate the size, structure, or mechanical properties of condensed chromatin or mitotic chromosomes. To address this concern experimentally, we extended our DNA transport assays to longer double-stranded DNA fragments. In addition to 100-bp DNA, we tested 1,000-bp and 2,000-bp DNA fragments and found that full-length hKid can transport both substrates along microtubules in vitro. These new data are now included in Figure 6F–I.

      However, we agree that these DNA substrates are still much simpler than condensed chromatin. We have therefore revised the final model to avoid implying that the transport of naked DNA fully explains chromosome-scale movement. The revised model now emphasizes that Kid dimers can directly couple DNA to microtubule-based motility, and that multiple Kid dimers may cooperate on chromosome arms to generate polar ejection forces. We state "This model is not drawn to scale and does not fully represent the structural complexity of condensed chromatin." in the revised legends.

      We also state explicitly in the Discussion that future experiments using chromatinized DNA or reconstituted chromosome-like substrates will be required to determine how Kid engages condensed chromatin and generates chromosome-scale forces.

      Reviewer #2 (Recommendations for the authors):

      Major points:

      (1) The authors state that XKid(1-437), which lacks the coiled-coil domain, did not show any processive runs yet Figure 3D does show short events that look like directed movement. They do not appear to be diffusive events as they are uni-directional. The authors need to quantify these results (motility, mean square displacement) as they are essential to their arguments about monomer vs dimer state and processive motility.

      We thank the reviewer for pointing this out. We agree that, in the original kymographs acquired at lower temporal resolution, some short XKid(1–437) events could appear as directional movements. To address this concern, we repeated the single-molecule motility assays with improved temporal resolution. In the revised manuscript, the kymographs for XKid(1–437) were generated from data acquired at 100 ms per pixel, instead of 3 s per pixel in the previous version. This higher temporal resolution more clearly shows that XKid(1–437) undergoes short, diffusion-like fluctuations rather than sustained unidirectional processive movement.

      We also quantified these trajectories by mean-square displacement analysis. XKid(1–495), which retains the coiled-coil domain, showed superlinear MSD scaling with an α value of approximately 1.6, consistent with persistent, directionally biased movement. In contrast, XKid(1–437), which lacks the coiled-coil domain, showed an α value of approximately 0.8, consistent with hindered or diffusion-like motion rather than sustained processive motility.

      We have added these higher-temporal-resolution data and MSD quantification to the revised Figure 3 and revised the text accordingly. We now state that XKid(1–437) lacks sustained processive runs, rather than implying that it shows no movement at all.

      The authors speculate that the lack of XKid(1-437) processive runs is due to it being unable to form a homodimer. To confirm that the coiled-coil domain is responsible for dimerization, they fuse the coiled-coil to a fluorescent protein. However, the authors should actually show that XKif(1-437) is a monomer by size exclusion chromatography and/or nanophotometry.

      We thank the reviewer for this important suggestion. We agree that directly determining the oligomeric state of XKid(1–437) is essential for interpreting the loss of processive motility. We therefore performed mass photometry to measure the molecular mass of purified XKid(1–437).

      The mass photometry analysis showed that XKid(1–437) was predominantly monomeric, with no detectable dimer population under the conditions tested. In contrast, XKid(1–495), which retains the coiled-coil domain, showed a minor dimer population, similar to full-length XKid. These results support the conclusion that deletion of the coiled-coil domain disrupts Kid dimerization.

      Together with the motility assays and MSD analysis, these data indicate that the coiled-coil domain is required for homodimer formation and sustained processive motility of Kid. We have added these mass photometry data to the revised Figure 3 and revised the text accordingly.

      (2) Likewise, the chimeric protein KIF1AMD-XKidSt shows processive motility (Figure 4), and thus authors conclude that it must be a dimer. This should be verified using size exclusion chromatography and/or nanophotometry.

      We agree that the oligomeric state of KIF1AMD–XKidSt should be directly examined. We therefore performed mass photometry analysis of purified KIF1AMD–XKidSt.

      Mass photometry showed that KIF1AMD–XKidSt behaved similarly to full-length XKid and XKid(1–495). Under the nanomolar concentrations used for mass photometry, KIF1AMD–XKidSt was predominantly monomeric but retained a detectable dimer population. This behavior is consistent with our analysis of full-length Kid and XKid(1–495), which form weak, concentration-dependent dimers. These results indicate that the XKid stalk region in the chimera can support dimer formation, although the dimer is weak under dilute solution conditions.

      (3) Lines 236-239, the authors state "in TIRF-based motility assays, although Kid predominantly dissociates into monomers in solution, its direct interaction with microtubules leads to an increased local concentration of Kid on the microtubule surface. As a result, this would facilitate the formation of Kid dimers on the microtubules, leading to processive motility." This statement implies that monomeric motors diffuse on the microtubule surface until they can associate and begin processive motion. Do the authors see such events (diffuse motion and/or association of single monomers on microtubules and a resulting change to processive motion? The kymograph in Figure 1C shows only static and motile events for XKid but hKid does appear to undergo diffusive motion. What is the percent of static vs diffusive vs processive events and how does this change with increased concentrations of XKid and HKid?

      We thank the reviewer for this important point. We agree that our original statement was too strong, because we did not directly observe monomeric Kid molecules diffusing on microtubules and then associating to initiate processive movement. We have revised the text to clarify that microtubule-dependent dimerization is a model.

      To test this model, we performed dual-color imaging using independently purified hKid–mScarlet3 and hKid–mStayGold. These proteins were mixed at 1 pM each, a concentration at which Kid is expected to be predominantly monomeric in solution. We observed co-migration of the two fluorescently labeled Kid proteins along microtubules, supporting the idea that Kid molecules can associate on microtubules and move together.

      However, because of the limited temporal resolution of our two-color TIRF system, we could not directly capture the transition from two monomers to a processive dimer on the microtubule surface. We therefore do not quantify the fraction of static, diffusive, and processive events as a function of concentration in this revised manuscript. Instead, we have softened the relevant statement and explicitly note this limitation in the Discussion.

      (4) Lines 171-172 - optimal length of neck linker for coordination of the two motor domains has only been shown for kinesin-1 and kinesin-2. In contrast, there are a number of kinesins that do not have typical neck linker domains yet can achieve processivity. The authors need to discuss this work and put their results with Kid into this context.

      As described above, we have revised the Discussion to place Kid in the broader context of processive kinesins with non-conventional neck linker or neck coil regions. We now discuss previous work showing that neck-linker length strongly influences kinesin processivity, and that changes in neck-linker length alter the run length and motility properties of kinesins (Shastry and Hancock, 2010; Shastry and Hancock, 2011).

      We also discuss studies showing that longer or non-conventional neck linker regions, such as those of kinesin-2 and KIF18, can provide additional functions beyond supporting processive stepping (Hoeprich et al., 2014; Malaby et al., 2019). In this context, we now emphasize that Kid has an exceptionally long and flexible neck linker, approximately four times longer than that of kinesin-1. We described a possibility that the extended neck linker of Kid may help it move along crowded spindle microtubules while remaining attached to DNA or chromatin while this possibility remains to be tested directly.

      Minor points:

      (5) Lines 68-69 should note that non-processive motors have been shown to move cargo if they are present in multiple copies of the cargo. This should also be discussed in the Discussion.

      We described it in the revised manuscript:

      “Under this model, sustained chromosome movement would require many Kid monomers distributed along chromosome arms to act collectively.”

      “This model preserves the likely importance of motor ensembles on large chromatin, but changes the nature of the ensemble from many non-processive monomers to multiple processive dimers.”

      (6) For Figure 4, does the KIF1AMD-XKidSt chimeric protein contain both the stalk (coiled-coil?) and tail (DNA binding?) regions of XKid or just the stalk as shown in the schematic?

      We included coiled-coil domain only.

      (7) For Figure 5, please provide a schematic for XKid(delta tail).

      We now added Alphafold 3 data.

      Senior Editor:

      Along the lines of reviewer #2's request to put the results in the context of existing knowledge, please consider whether you want to cite Pike et al. 2018 (https://doi.org/10.1126/scisignal.aaq1060; some evidence for dimerization in Fig. 4) and Walker et al. 2019 (https://pubs.acs.org/doi/10.1021/acs.biochem.9b00011).

      We have cited these papers in the revised manuscript. These are consistent with our finding that Kid can form dimer at higher concentration while dissociate to monomers in lower concentrations.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      This is a well-written and fully documented methods paper.

      The authors have established a clear rationale for their new packages, especially for real-time use, and demonstrate significant speed improvements that will likely appeal to many users of tools like DLC, SLEAP, and LightningPose. The inclusion of a graphical user interface will help make the package more accessible to neuroscientists with limited computational expertise. While it may be challenging to get users to switch from their established workflows for video analysis, the speed gains offered by this package make it worth considering. The hardware aspects of the project are well-documented, and the GitHub repository for this part of the setup is also thorough. Overall, this paper provides a clear summary of the tools, their uses, setup, and benefits.

      We thank this reviewer for the positive comments and have provided responses to the specific and constructive questions listed below.

      I have a few minor questions about the collective set of tools.

      First, the GitHub repository for SqueakPoseStudio appears to be missing a testing routine and associated badge, and the package has not been formally released. This means users would need to download the repository to install it, correct? I suggest the authors consider publishing a formal release of the package, making it installable via pip, and including a basic testing routine to clearly display the package's status on the repository page. Adding a DOI from Zenodo would also be helpful. A testing routine is especially useful when updates are made, as many users avoid repositories with failing tests.

      We thank the reviewer for this helpful suggestion. We agree that visible testing improves user confidence and reproducibility.

      SqueakPose Studio is currently distributed through a repository-based uv workflow rather than through PyPI alone. This is intentional. The application depends on platform-specific deep-learning libraries, and cloning the repository followed by uv sync provides a reproducible environment across Linux, macOS, and Windows while allowing the application to select CUDA, Apple MPS, or CPU execution at runtime. The written installation instructions now clearly describe this workflow.

      In response to the reviewer’s suggestion, we have added a unit-test suite covering the core helper modules used for label handling, dataset export, prediction, inference, and training logic. We have also added an automated GitHub Actions workflow that runs the tests on pushes and pull requests, together with a repository badge that displays the current test status.

      Second, the installation instructions simply state "Create a virtualenv and install:". This may not be sufficient for many researchers, as most neuroscientists are not experienced Python programmers and require clear guidance on the environment specific to this package. The installation instructions should be expanded to provide more detailed guidance and encourage more users. It would also be helpful to verify that the setups work across Windows, Mac, and Linux.

      We agree that installation guidance should be accessible to researchers who may not routinely manage Python environments. In addition to the existing video walkthrough, we have expanded the written GitHub documentation to provide a clearer, step-by-step installation checklist.

      The revised README now distinguishes required components from optional tools, explains the repository-based uv workflow, and provides the minimal commands needed to create the managed environment and launch the application.

      We have also clarified that an integrated development environment is optional. Although Visual Studio Code is used in the tutorial as a convenient interface for demonstrating the workflow, users may launch SqueakPose Studio directly from a terminal and are not required to use Visual Studio Code, Visual Studio, or any other editor.

      We have tested the application on Apple Silicon macOS systems, Windows systems, Linux systems, and NVIDIA GPU-enabled machines. SqueakPose Studio selects CUDA, Apple MPS, or CPU execution at runtime according to availability. Because accelerator support is partly determined by upstream packages such as PyTorch and Ultralytics, we have added links to the relevant compatibility documentation so that users can confirm whether their current hardware and driver configuration are supported.

      Third, the package defaults to UMAP for non-linear dimensionality reduction, which has some known issues. Can the package be modified to allow for alternative mapping methods, such as PaCMAP, PyDiffMap, or the more comprehensive topometry package?

      We agree with the reviewer that UMAP has limitations and that no single nonlinear dimensionality-reduction method is optimal for all pose datasets or behavioral questions.

      In SqueakPose Studio, the UMAP/HDBSCAN workflow is included as an accessible exploratory example for dimensionality reduction and clustering of pose-derived features. Our goal was not to designate UMAP as a preferred or definitive analysis method, but to provide an interpretable starting point that allows users to identify candidate clusters and inspect representative videos to evaluate what the embedding is capturing.

      We agree that supporting additional approaches, such as PaCMAP, PyDiffMap, or related tools, could be useful, and we will consider adding these as modular options in future versions. At the same time, SqueakPose Studio is not intended to replace specialized downstream behavioral-analysis packages or to adjudicate which embedding method is best for a particular dataset. Pose outputs can be exported for downstream analysis in other environments, including CEBRA, Keypoint-MoSeq, and packages implementing alternative clustering or dimensionality-reduction approaches.

      We have clarified in the documentation that the included UMAP/HDBSCAN workflow is intended as an exploratory demonstration rather than as a required or privileged analysis pipeline.

      Finally, what specific GPUs have been tested with the package, and are there any limitations based on the age of the video card or the available libraries for the deep learning component of the package?

      As noted above, GPU compatibility is determined by the deep-learning and hardware-acceleration libraries on which SqueakPose Studio depends, including PyTorch, Ultralytics, CUDA, Apple MPS, and ROCm. Our development ethos is to track current stable versions of these packages rather than maintain separate legacy dependency stacks. This improves performance, simplifies support, and allows users to benefit from ongoing improvements in upstream libraries, but it also means that older GPU architectures may lose support as they are deprecated by those upstream tools.

      For NVIDIA systems, the current package is indexed against CUDA 13.2. CUDA 13.x has deprecated support for some older GPU architectures, so users with older NVIDIA cards may need to use CPU inference or upgrade hardware. However, CUDA 13 is supported on GeForce RTX 20-series, 30-series, 40-series, 50-series, and professional equivalents. We made this clearer in the documentation and provided links to upstream CUDA, PyTorch, and Ultralytics compatibility resources so users can determine whether their hardware is supported.

      For Apple Silicon, the package can use PyTorch MPS acceleration, which supports M-series chips. For AMD GPUs, we do not currently maintain AMD-specific test hardware, but PyTorch supports ROCm on Linux for supported AMD GPUs. ROCm support is more limited on Windows, so AMD users should consult the current PyTorch ROCm compatibility documentation.

      Overall, our support commitment is to maintain compatibility with current upstream deep-learning frameworks rather than to guarantee support for all older or vendor-specific GPU configurations.

      Reviewer #2 (Public review):

      Summary:

      This work presents three tools: SqueakPose Studio, which is used for pose estimation; SqueakView, which is used for real-time video and sensor data capture and analysis; and MouseHouse, which is a behavioral and sensor suite for mouse experiments. Together, these tools provide a comprehensive behavioral platform for acquiring and analyzing video, sensor, and behavioral data. The work is open source and provided as a resource for the field.

      Strengths:

      (1) Squeakpose Studio was relatively easy to install and use. We were impressed that we were able to install it and test our own videos with minimal struggles. The authors provide installation tutorial videos that were very helpful.

      (2) The GUI environment for SqueakPose Studio was very usable, and the authors should be commended on the time and effort that went into improving the useability of their system. The keypoint and skeleton configuration was flexible, allowing us to define custom body part sets without modifying code directly. The pose estimation accuracy on our own videos was good right out of the box, without requiring fine-tuning or retraining. For a tool being evaluated for the first time, this was all very impressive!

      We thank this reviewer for the positive comments and have provided responses to the specific potential weaknesses noted below.

      Weaknesses:

      (1) While we were able to install and test Squeakpose Studio, it was not entirely seamless. The primary installation resource is a tutorial video, and we would recommend supplementing this with a written installation checklist that explicitly lists all required software dependencies (e.g. Python, UV, Visual Studio). The tutorial video was also at times unclear in distinguishing required from optional components. For example, Visual Studio is described as not necessary, yet the tutorial demonstrates the workflow entirely within that environment, so it may be challenging for a user to follow along without that. We recommend that the authors adopt a stricter, step-by-step installation guide that is prescriptive about required software and leaves little room for confusion.

      We thank the reviewer for this helpful feedback and agree that the installation workflow should distinguish more clearly between required and optional components. Our goal with SqueakPose Studio is to place as much functionality as possible in the GUI so that users are not required to rely on command-line tools for additional features or advanced use. For that reason, the command-line surface is intentionally minimal: after the repository is cloned and the UV-managed environment is created, almost all functionality is accessed through the graphical interface.

      We also appreciate the opportunity to clarify the point about Visual Studio. The tutorial video demonstrates the workflow using Visual Studio Code, not Visual Studio. Visual Studio Code is optional and is used in the video only as a convenient editor and interface for demonstrating the workflow. The GUI can also be launched directly from a terminal, and users may use any preferred editor or IDE, including VS Code, Zed, Cursor, Jupyter-based workflows, or no IDE at all.

      We have updated the written README and YouTube walkthrough to make this distinction clearer. Specifically, provided a stricter installation checklist that separates required components, such as Python and UV, from optional tools, such as VS Code or other editors. We also demonstrated launching SqueakPose Studio directly from a terminal so users can follow the workflow without relying on a specific IDE.

      (2) The paper also describes SqueakView and MouseHouse. Unfortunately, we were unable to evaluate these components as both require the MouseHouse hardware platform. Even without directly using MouseHouse, we noticed some incompleteness here, as we could not locate a bill of materials, component pricing, or assembly guide in the paper or associated GitHub repositories. Given that affordability and accessibility are central claims, a consolidated parts list, approximate costs, and a build guide or video would be necessary for most labs to realistically decide whether they plan to replicate the hardware and evaluate this functionality that the paper describes. In this regard, we felt that MouseHouse and potentially SqueakView were not sufficiently documented for publication.

      We agree with the reviewer that MouseHouse and SqueakView are more difficult to evaluate than SqueakPose Studio because they involve dedicated hardware, including an edge-compute platform. This is an unavoidable tradeoff for a system designed not only for offline pose estimation, but also for real-time acquisition and deployment. We recognize, however, that if the manuscript emphasizes affordability and accessibility, then users need a clear way to estimate cost, order components, assemble the system, and reproduce the hardware configuration.

      We have therefore added a consolidated bill of materials to the GitHub repository, including component names, approximate pricing, and suggested sources where appropriate. We now provide a complete guide for connecting the hardware and flashing the required firmware/software to the devices. This documentation makes clearer what is required for MouseHouse-specific functionality versus what can be used independently through SqueakPose Studio.

      We also note that edge-compute devices such as the Jetson Orin Nano are increasingly common in robotics and real-time computer-vision applications, but we appreciate that many behavioral neuroscience laboratories may not yet have this hardware in place. For some users, this paper may be their first exposure to this compute platform. For that reason, we agree that the repository should provide more complete onboarding materials for labs that wish to adopt the hardware ecosystem, and we now provide that.

      (3) The benchmarking comparison to DeepLabCut (DLC) introduced multiple challenges that left us unclear if the head-to-head comparison was appropriate as described. First, the dataset used for benchmarking was small and homogeneous, from the methods they used "10 min open-field tasks of single mice with bilateral photometry cables." As such, the claims about comparisons between SqueakPose Studio and DLC may be too broad, given this single test case. Specifically, this dataset does not test robustness across lighting conditions, coat colors, species, occlusions, different-shaped arenas, etc. Second, the comparison to DLC in Figure 1 does not include any quantitative statistical comparisons, which are needed to evaluate the claims that were made. For instance, the error in Figure 1e looks worse for their system than DLC, although statistical comparisons were not made. Third, there are many settings and optimizations that can be made for both systems. Without more detail, this makes it hard to know if the head-to-head comparison is really fair. Fourth - the metrics are given as very specific numbers from single runs, i.e., an inference time of 71.59 minutes in Figure 1d. This metric would be more meaningful if it reported the mean of multiple runs, with error estimation. Finally, while the code is available, the trained datasets are made available only on "reasonable request". Given the importance of these datasets to evaluating the method and allowing others to benchmark it against other systems, these should be made available on GitHub. Overall, I would recommend toning down the comparison to DLC and focusing on the strengths of Squeakpose Studio on its own merits.

      We appreciate the reviewer’s thoughtful comments about the benchmarking comparison. We agree that no single dataset can establish universal performance across all lighting conditions, coat colors, species, occlusion regimes, arena geometries, or camera configurations. Our intention was not to claim that SqueakPose Studio is superior to DeepLabCut under every possible condition, nor to present a comprehensive benchmark across the full space of pose-estimation use cases. Rather, the benchmark was included as an applied demonstration of performance in a representative behavioral neuroscience workflow involving mouse open-field videos with photometry cables.

      We also agree that users can substantially affect performance in any pose-estimation framework through model selection, training settings, hardware configuration, inference parameters, and optimization choices. For this reason, we view the comparison as a practical workflow benchmark rather than a definitive ranking of all possible DLC and SqueakPose Studio configurations. The primary contribution of SqueakPose Studio is not simply that it is faster in one head-to-head comparison, but that it provides an integrated GUI-based workflow for pose estimation, review, export, and real-time/edge-AI deployment.

      That said, the speed improvements are not incidental. They reflect deliberate architectural and deployment choices, including the use of modern object-detection/pose-estimation architectures and optimized inference workflows. In practice, these choices can substantially reduce inference time relative to workflows that were not designed around the same deployment constraints. We will be careful in our public response and documentation not to overstate this as a universal claim across every dataset or every possible DLC configuration.

      Regarding statistical comparisons and repeated runs, we agree that reporting means and variance across repeated benchmark runs can be useful. However, because this manuscript is primarily an applications and methods resource rather than a large-scale benchmarking study, we do not intend to benchmark every relevant dataset class or hardware configuration. We instead encourage users to evaluate SqueakPose Studio on their own videos and hardware, which is ultimately the most informative test for adoption in a given laboratory.

      Regarding the trained datasets and models, we agree with the reviewer that broad access improves reproducibility and benchmarking. The limitation is practical rather than philosophical: the full benchmark datasets are large and are not well suited for direct hosting in a GitHub repository. We currently make these data available upon reasonable request and have included a Zenodo repo explore more appropriate public hosting options for large files, such as an institutional repository, Zenodo, OSF, or another archival data platform. We will also clarify the availability of trained models and example data so users can more easily reproduce or extend the benchmarking workflow.

      Overall, we agree that SqueakPose Studio is strongest when evaluated on its own merits: accessibility, speed, GUI-based usability, flexible keypoint configuration, real-time deployment, and integration with acquisition and edge-compute workflows. We now frame the DLC comparison as a representative applied benchmark rather than as an exhaustive claim of general superiority.

      (4) The paper at times makes general statements that are beyond what is shown. For instance, discussions of use in human applications are aspirational and should be treated much more conservatively in the discussion, or possibly even removed. As it stands, the discussion implies that this system can already do "zero-shot tracking of human posture and movement", enabling "a bridge between preclinical and clinical behavioral analysis". In principle, this may be true, but even for a Discussion section, this goes far beyond the capabilities that the paper actually shows.

      We appreciate this comment and agree that the manuscript should distinguish more clearly between capabilities demonstrated in the present study and broader potential applications of the software architecture.

      SqueakPose Studio and SqueakView are not intrinsically mouse-specific. Users can define custom classes, keypoints, and skeletons, train compatible pose-estimation models for other organisms or experimental preparations, and deploy those models using the same acquisition and inference workflow.

      To make this technical capability concrete, the SqueakView repository now includes deployment-ready FP16 model packages for both the validated MouseHouse-specific pose model and a stock human-pose model. The included human-pose model demonstrates that the deployment architecture can support zero-shot human posture tracking without requiring changes to the underlying SqueakView pipeline.

      We agree, however, that this technical compatibility should not be interpreted as validation for clinical behavioral analysis. The experimental demonstrations in the present manuscript focus primarily on mouse behavioral datasets. Any clinical application would require separate benchmarking, validation, and domain-specific evaluation beyond the scope of the present manuscript.

      (5) While the comprehensive nature of the system and its 3 parts is impressive, I felt that it also detracted from the main focus of the paper, which was Squeakpose Studio. I might recommend dropping the other two parts, as they also require a much higher bar for a user to evaluate, and only present the Squeakpose Studio in this paper, presenting this as a general resource for pose estimation. This would also allow them more space to more comprehensively benchmark SqueakPose Studio.

      We appreciate this perspective and agree that SqueakPose Studio is the most immediately accessible component of the platform for many users. However, we respectfully disagree that MouseHouse and SqueakView should be removed from the paper. The motivation for developing SqueakPose Studio was not simply to create another offline pose-estimation and analysis tool, but to enable real-time behavioral detection and deployment on edge hardware. SqueakView and MouseHouse provide the acquisition and deployment context that motivated the software architecture and demonstrate how the platform can be used in closed-loop or real-time behavioral workflows.

      In developing the system, we recognized that SqueakPose Studio also functions as a user-friendly general pose-estimation interface, with features that may be useful even for laboratories that do not adopt the full MouseHouse/SqueakView ecosystem. For that reason, we presented it as both a standalone tool and as part of a broader acquisition and deployment platform.

      We agree that this makes the manuscript broader than a paper focused exclusively on pose-estimation benchmarking. However, we view that breadth as important: the paper is intended to serve as a central, peer-reviewed entry point for laboratories interested in deploying real-time pose estimation in behavioral experiments. The manuscript points users to the relevant repositories, documents the design rationale, and provides a source of peer-reviewed validation for the integrated workflow. We have clarified in our response and documentation that users can adopt SqueakPose Studio independently, while MouseHouse and SqueakView support the broader real-time hardware ecosystem.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the role of the insulin receptor and the insulin growth factor receptor was investigated in podocytes. Mice, where both receptors were deleted, developed glomerular dysfunction and developed proteinuria and glomerulrosclerosis over several months. Because of concerns about incomplete KO, the authors generated and studied podocyte cell lines where both receptors were deleted. Loss of both receptors was highly deleterious with greater than 50% cell death. To elucidate the mechanism of cell death, the authors performed global proteomics and found that spliceosome proteins were downregulated. They confirmed this directly by using long-read sequencing. These results suggest a novel role for insulin and IGF1R signaling in RNA splicing in podocytes.

      This is primarily a descriptive study and no technical concerns are raised. The mechanism of how insulin and IGF1 signaling regulates splicing is not directly addressed but implicates potentially the phosphorylation downstream of these receptors. In the revised manuscript, it is shown that the mouse KO is incomplete potentially explaining the slow onset of renal insufficiency. Direct measurement of GFR and serial serum creatinines might also enhance our understanding of progression of disease, proteinuria is a strong sign of renal injury. An attempt to rescue the phenotype by overexpression of SF3B4 would also be useful but may be masked by defects in other spliceosome genes. As insulin and IGF are regulators of metabolism, some assessment of metabolic parameters would be an optional add-on.

      Significance:

      With the GLP1 agonists providing renal protection, there is great interest in understanding the role of insulin and other incretins in kidney cell biology. It is already known that Insulin and IGFR signaling play important roles in other cells of the kidney. So, there is great interest in understanding these pathways in podocytes. The major advance is that these two pathways appear to have a role in RNA metabolism.

      Latest comments:

      The new reviewer raised two major points, whether the KO effect on splicing is specific to IGF1 and whether the interpretation could be developmental rather than due to splicing. The reviewer raises some important issues but the evidence to suggest that this is specific is data in the literature that IR/IGF signaling is already known to regulate splicing and that splicing defects were not detected in other models that they have analyzed. I agree with the reviewer (and authors) that the incomplete floxing of the genes is a major complication. The point that there could be a developmental defect with mice being born with fewer podocytes and perhaps the authors should caveat this point. The fact that they mice are born with normal function, that renal function can be maintained with up to 80% loss of podocytes suggest that they are likely born with a good number of podocytes and the dysfunction that occurs at 6 months is due to a process, induced by the loss of IR/IGF signaling that is detrimental to the podocyte.

      Thank you for these insightful comments. We fully acknowledge that the mouse model will not have had full insulin receptor and IGF1R knockdown and that this is likely the reason it took time to develop and not give a prominent early phenotype. We agree with this reviewer and new reviewer 4 that if the model had facilitated near complete IR and IGF1R knockdown then likely a significant neonatal / embryonic phenotype would have been obvious. We considered using an inducible mouse model to allow normal development before cre-excision but our experience is that the CreER and RtTA-tet-on-cre system is less good at excising genes and hence did not pursue this (we show evidence of reduced excision with an inducible system in supplementary Figure 1D using a reporter mouse system [this was included in a previous response to the reviewers only]). This was rationale for making the immortalised podocyte floxed IR and IGF1R cell line to ensure near complete knockdown. This, not surprisingly, was highly detrimental. We then looked mechanistically for pathways (using agnostic proteomics and phospho-proteomics) and found spliceosomal involvement. From our studies we think this was also involved in our mouse model as SF3B4 was found to be significantly down regulated in the podocytes of double receptor knockdown transgenic mice (Figure 3F).

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, submitted to Review Commons (journal agnostic), Coward and colleagues report on the role of insulin/IGF axis in podocyte gene transcription. They knocked out both the insulin and IGFR1 mice. Dual KO mice manifested a severe phenotype, with albuminuria, glomerulosclerosis, renal failure and death at 4-24 weeks.

      Long read RNA sequencing was used to assess splicing events. Podocyte transcripts manifesting intron retention were identified. Dual knock-out podocytes manifested more transcripts with intron retention (18%) compared wild-type controls (18%), with an overlap between experiments of ~30%.

      Transcript productivity was also assessed using FLAIR-mark-intron-retention software. Intron retention w seen in 18% of ciDKO podocyte transcripts compared to 14% of wild-type podocyte transcripts (P=0.004), with an overlap between experiments of ~30% (indicating the variability of results with this method). Interestingly, ciDKO podocytes showed downregulation of proteins involved in spliceosome function and RNA processing, as suggested by LC/MS and confirmed by Western blot.

      Pladienolide (a spliceosome inhibitor) was cytotoxic to HeLa cells and to mouse podocytes but no toxicity was seen in murine glomerular endothelial cells.

      The manuscript is generally clear and well-written. Mouse work was approved in advance. The four figures are generally well-designed, bars/superimposed dot-plots.

      Methods are generally well described.

      Comments on previous version:

      Coward and colleagues have done an excellent job of responding to all the reviewer comments.

      Thank you.

      Reviewer #4 (Public review):

      Summary and background:

      This report entitled "The insulin/IGF axis is critically important (for) controlling gene transcription in the podocyte" from Hurcombe et al is based on a mouse double knockdown of the IR and IGF1R and a parallel cultured mouse podocyte model. Insulin/IGF signaling system in mammals evolved as three gene reduplicated peptides (insulin, IGF-1, and IGF-2) and their two receptors IR and IGF1R that cross-react to variable extents with the peptides, are ubiquitously expressed, and signal through parallel pathways. The major downstream effect of insulin is to regulate glucose uptake and metabolism, while that of the IGF pathways is to regulate growth and cell cycling in part through mTORC1. The GH-IGF-1-IGF1R pathway regulates post-natal growth. IGF-2 signaling is thought to play a major role in regulating intrauterine growth and development, although IGF-2 is also present at high levels in post-natal life. Thus, one would anticipate that reducing IR/IGF1R signaling in any cell would slow growth and cell cycling by reducing growth factor and metabolic mTORC1-mediated and other processes including the splicing of RNA for protein synthesis.

      Thank you for this clear overview. Of note the podocyte is a terminally differentiated cell so the growth / cell cycling elements may be different from more proliferative cell types in relation IR/IGF1R mediated signalling.

      Comments on revised version:

      The second sentence of the Summary reads "This study sought to elucidate the compound role of the insulin/IGF1 axis in podocytes using transgenic mice and cell culture models deficient in both receptors." The study design and rationale for the proteosome analysis described is predicated on the finding that podocyte-specific knockdown of the IR/IGF-1R in mice is associated with development of proteinuria and reduced eGFR by 20months of life. Since the IR/IGF-1R are critically required for normal development and growth of all cells and organs, the obvious explanation for the observation would be that the model system results in defective podocyte development and deployment (caused by reduced IR/IGF-1) that, in turn, causes subsequent development of proteinuria and glomerulosclerosis (that may be much less dependent on a normal level of IR/IGF-1R expression). Thus, the experimental design does not allow a distinction between podocyte development and steady state function which are different biologic processes. The data provided does not examine podocyte status immediately after birth to confirm that podocyte number and size and structure is normal in mice that subsequently develop proteinuria and glomerulosclerosis. The response to the reviewer suggests that since this would require additional mice it has not been undertaken in order to reduce animal usage. This is not a valid argument, particularly when the investigators have not even used state-of-the-art methods to measure podocyte number, size and density in adult mice, key parameters that would be required to interpret their data. Counting podocyte nuclear number in glomerular cross-sections is simply an inadequate method, even if it is used and reported in other journals, and particularly where the examples given to justify its use can hardly be viewed as representing first rate science.

      Thank you for these comments. As discussed above we agree that the mouse model was not optimal as despite using a good cre driver we did not consistently knock down both receptors. It was the reason that we made the IR/IGF1R knockdown cell line. Importantly we found with both receptors >80% knocked down that this was highly detrimental and evidence that spliceosomal dysfunction was prominent. Thank you for the comment about methodology of assessing podocyte number which we and other investigators use.

      If the absence of studies that would answer the above questions, the investigators should add a sentence to the Discussion dealing with study limitations as follows. "The study design does not allow us to determine whether the primary effect of reduced IR/IGF-1R expression on the phenotype is during in utero and post-natal podocyte development and deployment, during periods of rapid growth when IGF-1 levels are highest, in steady state adult podocytes, or under all of the above conditions".

      Thank you. We have added a section describing that we did not investigate the embryonic neonatal early phenotype for more subtle changes in our model. We have also added a sentence saying we would have liked to have used an inducible model but the cre driven excision is less than constitutional driver and we think would have shown either a very mild or no phenotype due to minimal excision.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The authors address whether theta/beta ratio /TBR) can be used as a clinical biomarker for ADHD.

      Strengths:

      The data were acquired independently from 2 separate datasets, and there are sufficient subjects for adequate statistical power. The authors applied up-to-date EEG data preprocessing, state-of-the-art feature extraction, and statistical analyses, using a multiverse approach. By testing and comparing all meaningful approaches, defined a priori in the previous meta-analysis, the author convincingly demonstrates that TBR cannot be used as a clinical biomarker, and previous positive results can be explained by interactions between different factors (alpha peak frequency, aperiodic component, age).

      Weaknesses:

      There are no apparent issues with data, separate datasets, large sample sizes, and state-of-the-art data analysis.

      We thank Reviewer #1 for their positive evaluation of our manuscript and for the constructive recommendations. The reviewer did not raise additional comments requiring a point-by-point response beyond the recommendations addressed below.

      Reviewer #2 (Public review):

      Summary:

      This manuscript examines whether the theta-beta ratio as derived from EEG data relates to ADHD diagnoses. To do so, it performs a multiverse analysis across a large number of analytical choices, applied to a large EEG dataset, and corroborated in an additional validation set. The results overall show that the TBR is not a reliable indicator of ADHD diagnosis. In discussing the patterns of results across analytical choices, the authors also demonstrate some key points about what appears to be driving the ratio measures, noting that significant results appear to be driven by choices regarding aperiodic-correction and the use of individualized alpha frequencies, suggesting TBR measures can be affected by these features rather than reflecting theta and/or beta activity.

      Strengths:

      This manuscript addresses a clearly posed and important question in the literature, addressing a longstanding discussion on the relationship between TBR and ADHD, and uses a large dataset and an expansive analysis approach to provide a definitive answer. The strengths of the approach allow for a clear answer, providing a notable contribution to the field.

      Weaknesses:

      I find no notable weaknesses in the current manuscript nor any major issues that I think challenge the key findings of this manuscript.

      We thank Reviewer #2 for their positive evaluation of our manuscript and for the constructive recommendations. The reviewer did not raise additional comments requiring a point-by-point response beyond the recommendations addressed below.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, Strzelczyk, Vetsch, and Langer tackle an incredibly important question in clinical neuroscience: the use of the theta/beta ratio as a biomarker of attention deficit hyperactivity disorder (ADHD). The theta/beta ratio is argued to be so reliable as an ADHD biomarker that, in the United States, the Food and Drug Administration has approved its use as a biomarker for ADHD diagnosis. However, there is mounting evidence that the theta/beta ratio is likely not really measuring the relative power between two oscillations - the theta rhythm and the beta rhythm - but rather reflects differences in a singular, non-oscillatory aperiodic process. In this very convincing study, Strzelczyk and colleagues take a "multiverse" analysis approach to show that aperiodic activity differences between healthy controls and people with ADHD are driving the apparent theta/beta ratio differences. While in a vacuum, where a measure is a measure and if it's related to a diagnosis it's still useful no matter what, this distinction might not seem important, from a neuroscientific perspective this is a critical distinction, because the ratio between two oscillations has fundamentally very different underlying physiological mechanisms than aperiodic differences, and this framing has a major impact on guiding research on the diagnosis and treatment of ADHD.

      Strengths:

      While smaller studies and analyses have already hinted at similar results as shown here, the current study's multiverse analysis approach is comprehensive, convincing, and very well done. The large sample size of 1,499 participants is very impressive, as is the use of an independent validation sample of 381 participants.

      Overall, the technical and statistical aspects are very well done: the multiverse approach, the validation set, the resampling methods, and even the shiny apps. The authors should be applauded for being so thorough and making their data and analyses publicly accessible.

      Weaknesses:

      To be clear, I see no breaking weaknesses in the theoretical foundations, methods, statistical analyses, or interpretations. All of my recommendations below are for the sake of clarity, which I believe is especially important because this is such an important paper that many people should read.

      Comments:

      (1) Some figures are mislabeled. For example, Supplementary Figure 1 says (C) are scalp topographies, but those are (A), while (C) shows power spectra, but it's unclear what (C) is. I assume it's only the aperiodic part of the spectrum (oscillations removed)? But it would be better to plot on a log-log scale if so. In fact, I recommend showing all spectra on a log-log scale.

      The reviewer is correct that the figure legend was mislabeled. Panel (A) shows the scalp topographies, panel (B) shows the 1/f-uncorrected power spectra, and panel (C) shows the reconstructed aperiodic signal with oscillations removed. We have corrected the figure legend accordingly. In addition, the power spectra and the reconstructed aperiodic signal are now plotted on log-log scales to improve readability and interpretability.

      (2) Supplementary Figure 6 is also mislabeled, saying (A) shows age (it does not) and so on.

      We thank the reviewer for noticing this error. We have revised the figure legend so that the panel descriptions now match the displayed plots.

      (3) In Supplementary Figure 7, is (B) the aperiodic-removed spectrum? The authors are very inconsistent with what they're showing in these spectral plots, and not actually explaining what they're showing: raw spectra, semi-logged or not, aperiodic-removed or oscillations-removed, etc.

      Panel (B) in Supplementary Figure 7 shows the aperiodic-adjusted spectrum. We have now corrected the figure labeling and revised the figure legend to explicitly state what is shown in each panel.

      (4) For the HBN data, it is said that, "electrode impedances were kept below 40 kΩ, lower than EGI's standard recommendation of 50 (Net Station Acquisition Technical Manual)." For the validation data: "... electrode impedances were maintained below 5 kΩ." These are big impedance threshold differences. Of course, these recommendations differ by recording system, the use of active electrodes, and so on. But such differences can certainly influence signal-to-noise. The fact that the results are so consistent between them is a strength that perhaps should be explicitly called out.

      We appreciate the reviewer’s suggestion. We now explicitly state in the discussion section that the consistency of the results across datasets with different EEG systems and impedance thresholds strengthens the generalizability of the findings. The revised text reads as follows:

      “Our multiverse results thus converge with this broader literature, providing further evidence that TBR lacks the reliability and discriminative validity required for clinical utility. Beyond methodological convergence across analytical frameworks, the consistency of results across two datasets differing substantially in EEG recording systems and impedance thresholds further strengthens the generalizability of these null findings, suggesting they are unlikely to reflect idiosyncrasies of a specific acquisition protocol.”

      (5) The authors cite a lot of foundational / related work here, such as Finley et al, but they should also cite several other highly relevant ones:

      Saad et al., "Is the Theta/Beta EEG Marker for ADHD Inherently Flawed?", J Atten Disord, 2015

      Donoghue, Dominguez, Voytek, "Electrophysiological frequency band ratio measures conflate periodic and aperiodic neural activity", eNeuro, 2020

      Karalunas et al., "Electroencephalogram aperiodic power spectral slope can be reliably measured and predicts ADHD risk in early development", Develop Psychobiol, 2022

      Donoghue, "A systematic review of aperiodic neural activity in clinical investigations", Eur J

      Neurosci 2025

      We thank the reviewer for pointing us to these additional relevant references. We have added the suggested references to the revised manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) "Multiverse analysis was conducted in RStudio (R version 4.4.1) using the multiverse package (version 0.6.1; Sarma et al., 2021). T" Ok, cool, but it would be useful to explain what it does compared to running the standard stat analysis N times.

      We thank the reviewer for this helpful recommendation. We have now expanded the Methods section to clarify this point. The revised text reads as follows:

      “Multiverse analysis was conducted in RStudio (R version 4.4.1) using the multiverse package (version 0.6.1; Sarma et al., 2021). The multiverse framework differs from simply repeating the same statistical analysis multiple times, because it first requires the researcher to define a structured analysis space consisting of multiple defensible analytic decisions. These decisions are then expanded into all valid combinations, with each combination representing one complete analysis specification, or “universe”, providing a transparent and reproducible record of which analytic decisions were considered and how they were combined. In addition, the package reduces the need to manually write, modify, and track separate analysis scripts for each specification, which helps avoid inconsistencies or coding errors across universes. The results can then be extracted and summarized across the full set of universes to evaluate whether the conclusions are robust across reasonable analytic alternatives or depend on specific combinations of choices.”

      (2) I may have missed it, but how many subjects per group do you end up with after all the cleaning (not what is in Table 1, but like in each dataset you describe how many got removed at each step, so we are left wondering the final numbers).

      We thank the reviewer for pointing this out. The final group sizes after all cleaning and exclusion steps were not described in the original manuscript. We have therefore revised Table 1 so that it now reports only the remaining participants included in the final analyses after all exclusions were applied. The revised table shows the final sample sizes separately for the HC (N = 228), ADHD-Combined (N = 429), and ADHD-Inattentive (n = 465) groups, together with the corresponding demographic and clinical characteristics. We have also revised the accompanying text in the result section 3. 1. 1. The same changes were applied to the validation sample, which is reported in the Supplement.

      (3) Missing reference in my opinion. In the discussion, the sentence "as both oscillatory and aperiodic contributions vary systematically across the lifespan" could do with a reference or two about that

      We have now added references showing that developmental changes in EEG spectra involve both periodic/oscillatory and aperiodic components. The revised text reads as follows:

      “These dynamics may account for the recurring Age ’ IAF interactions observed in our multiverse analyses, as both oscillatory and aperiodic contributions vary systematically across the lifespan (Merkin et al. 2023; Tröndle et al. 2022; Tröndle et al. 2021; McSweeney et al. 2023; Hill et al. 2022; Stanyard et al. 2024).”

      (4) Now the big one: this is a cool visualization, and beta estimates from linear modeling do tell us the strength, BUT I would like to see raw effect sizes. It could be in a table or text, to go with the discussion. What was the theta, alpha, beta power raw or adjusted in each group, what about the aperiodic component - even maybe some violin plots to show canonical vs individual - my point is I am convinced from the frequency analysis since an entire subspace become significant and your interpretation that this is spurious is satisfactory but showing that this subspace as tiny effect sizes driven by interactions would be even more convincing in my opinion.

      To complement the regression coefficients from the multiverse models, we now additionally report descriptive standardized effect sizes across representative analytical subspaces. Specifically, we grouped analytical paths according to frequency band definition (IAF-relative vs canonical) and spectral representation (aperiodic signal, 1/f-uncorrected power, and aperiodic-adjusted power). Within each subspace, we computed Cohen’s d values for theta power, beta power, and TBR between ADHD and healthy control groups across all corresponding analytical paths.

      To visualize the distribution of effects across analytical paths, we added violin plots with overlaid individual paths and mean effect sizes with 95% confidence intervals. Importantly, even in subspaces where interaction effects frequently emerged in the multiverse analysis, the corresponding descriptive group differences remained small, supporting our interpretation that the observed significant effects are driven by subtle interactions and analytical choices rather than large underlying group differences.

      The added text in the Results 3. 1. 4. reads as follows:

      “To complement the regression coefficients from the multiverse models, we additionally examined descriptive standardized effect sizes across representative analytical subspaces. Analytical paths were grouped according to frequency band definition (IAF-relative vs. canonical) and spectral representation (aperiodic signal, 1/f-uncorrected power, and aperiodic-adjusted power). Within each subspace, Cohen's d was computed for theta power, beta power, and TBR for both the HC vs. ADHD-Inattentive and HC vs. ADHD-Combined comparisons. To visualize the distribution of effect sizes across the analytical space, violin plots were constructed with each data point representing the Cohen's d value of a single analytical specification (Figure 8). Across all subspaces and outcome measures, Cohen's d values were small for both comparisons, including subspaces in which interaction effects frequently reached statistical significance in the multiverse analysis. This pattern indicates that even where the multiverse revealed reliable significant effects, the underlying group differences in theta power, beta power, and TBR remained small in magnitude. These findings support the interpretation that the significant interactions observed across analytical specifications are driven by subtle moderation effects and analytical choices rather than large, robust group differences in neural activity.”

      Reviewer #2 (Recommendations for the authors):

      (1) As a minor clarification, the manuscript could specify if the calculation of aperiodic-adjusted power values was done as subtraction with linear or log power values.

      The aperiodic-adjusted power values were computed by subtracting the aperiodic fit from the observed power spectrum in log10 power space. Specifically, both the observed power spectrum and the estimated aperiodic component were log10-transformed, and the aperiodic-adjusted signal was obtained as the difference between these two quantities. The result was then transformed back to linear scale. We have clarified this in the revised manuscript. The revised text reads as follows:

      “The aperiodic component was reconstructed based on its fitted parameters and subtracted from the total power spectrum in log10 power space, resulting in an aperiodic-adjusted, 1/f-corrected power spectrum. The resulting values were then transformed back to linear scale and therefore represent power relative to the estimated aperiodic background.”

      (2) The last section of the abstract is a bit repetitive in stating the main finding of what drives the TBR, and this could be edited/condensed.

      We agree that the final part of the abstract repeated the main interpretation regarding the role of aperiodic activity and IAF. We have therefore condensed this section to avoid redundancy while preserving the central conclusion. The revised text reads as follows:

      Across the multiverse, we found that group differences in TBR were highly contingent on analytical choices, with no evidence for robust main effects of diagnosis, indicating no reliable differences between healthy controls, ADHD-inattentive, and ADHD-combined subtypes. Instead, significant effects emerged primarily as interactions with age and individual alpha frequency (IAF), particularly when TBR was derived from aperiodic-uncorrected power or from the aperiodic signal itself. These interaction patterns replicated across both independent samples and were observed using both categorical and dimensional definitions of ADHD. Together, these findings indicate that previously reported TBR effects are largely driven by variability in aperiodic activity and IAF rather than genuine differences in oscillatory theta-beta dynamics. Our results challenge the interpretation of TBR as a reliable standalone biomarker for ADHD and underscore the importance of multiverse approaches for evaluating candidate neurobiological markers in heterogeneous clinical populations.

      (3) As a minor literature note, the finding that ratio measures often largely reflect aperiodic activity rather than oscillatory theta and/or beta per se activity is consistent with a previous (non-clinical) investigation of band ratio measures in a previous report that should perhaps be cited as relevant prior work:

      Donoghue, T., Dominguez, J., & Voytek, B. (2020). Electrophysiological Frequency Band Ratio Measures Conflate Periodic and Aperiodic Neural Activity. eNeuro, 7(6),ENEURO.0192-20.2020. https://doi.org/10.1523/ENEURO.0192-20.2020

      We appreciate the reviewer’s suggestion. We have added this reference to the Discussion section, where we interpret the observed TBR effects as reflecting variability in the aperiodic background rather than genuine differences in oscillatory theta-beta dynamics. The revised text reads as follows:

      “These results suggest that apparent TBR differences may reflect properties of the aperiodic background signal interacting with individual variability in IAF rather than true oscillatory theta or beta activity. This interpretation is consistent with previous work showing that electrophysiological frequency-band ratio measures can conflate periodic and aperiodic neural activity, such that apparent changes in theta/beta or other band ratios may partly reflect changes in the aperiodic spectral component rather than narrowband oscillatory activity (Donoghue et al., 2020).”

      (4) In Figure 3, it may be useful to highlight the theta and beta ranges in panel B.

      We considered highlighting the theta and beta ranges in Figure 3B, but decided against it. In the multiverse analysis, theta and beta were defined using both canonical frequency bands and IAF-relative bands. The IAF-relative bands differ across participants, therefore marking only the canonical ranges could give the impression that these were the only frequency definitions used in the analyses. We therefore kept the spectra unmarked.

      (5) In Figure 5 (and other figures following this motif), it may be useful to color the significant results as green or red based on direction, to match Figure 4.

      We have updated Figure 5 and the corresponding figures so that significant positive effects are shown in green and significant negative effects are shown in red, matching the color scheme used in Figure 4.

      Reviewer #3 (Recommendations for the authors):

      (1) P10, L30: "Individualized bands were centered on the IAF, defined as theta = IAF-6 Hz to IAF-4 Hz"; why is theta defined using such a narrow, 2 Hz band here, when canonical theta is usually defined as a 4 Hz wide, 4-8 Hz band?

      The individualized theta band was chosen to follow the IAF-based frequency-band framework proposed by the seminal work of Wolfgang Klimesch (1999, 2012), rather than to reproduce the width of the canonical 4-8 Hz theta band. In this framework, frequency bands are defined relative to each participant’s individual alpha frequency. Theta is defined as the range from IAF-6 Hz to IAF-4 Hz, while lower alpha occupies the range closer to the individual alpha peak. The narrower individualized theta band is therefore intended to reduce overlap with lower-alpha activity and to account for inter-individual and developmental differences in alpha peak frequency. The 2020 guidelines from the International Federation of Clinical Neurophysiology (IFCN) reaffirmed Klimesch’s division of the alpha and theta bands (Babiloni, 2020). We have explained the frequency bands selection in more detail in the manuscript. The revised text reads as follows in Methods 2. 5. 7. Extraction of power for statistical analyses:

      The selection of these frequency bands is grounded in the seminal work of Wolfgang Klimesch (1999), who demonstrated that the alpha band can be divided into distinct lower and upper sub-bands. The lower alpha band extends up to 4 Hz below the IAF, covering a broader range of approximately 3.5 to 4 Hz, while the upper alpha band, which lies above the IAF, is narrower, spanning about 1 to 1.5 Hz. Klimesch also characterized the theta band as a frequency range that is approximately 2 Hz below the lower alpha band (Klimesch, 1999; Klimesch, 2012). The 2020 guidelines from the International Federation of Clinical Neurophysiology (IFCN) reaffirmed Klimesch’s division of the alpha and theta bands (Babiloni, 2020).

      (2) Figure 3 and Supplementary Figure 1, 7, 8: "Electrodes highlighted on the topographies..." means just the text labels, right? It might be better to show all electrodes as black dots and highlight the others with white dots or something.

      We have revised the figures to display all electrodes as black dots. In addition, we have clarified in the figure legends that the highlighted electrode labels correspond to the regions of interest used in the analyses.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript titled," Sleep-Wake Transitions Are Impaired in the AppNL-G-F Mouse Model of Early Onset Alzheimer's Disease", is about a study of sleep/wake phenomena in a knockin mouse strain carrying "three mutations in the human App gene associated with elevated risk for early onset AD". Traditional, in-depth characterization of sleep/wake states, EEG parameters, and response to sleep loss are employed to provide evidence, "supporting the use of this strain as a model to investigate interventions that mitigate AD burden during early disease stages". The sleep/wake findings of earlier studies (especially Maezono et al., 2020, as noted by the authors) were extended by several important, genotype-related observations, including age-related hyperactivity onset that is typically associated with increased arousal, a normal response to loss of sleep and to multiple sleep latency testing, and a stronger AD-like phenotype in females. The authors conclude that the AppNL-G-F mice demonstrate many of the human AD prodromal symptoms and suggest that this strain may serve as a model for prodromal AD in humans, confirming the earlier results and conclusions of Maezono et al. Finally, based on state bout frequency and duration analyses, it is suggested that the AppNL-G-F mice may develop disruptions in mechanism(s) involved in state transition.

      Strengths:

      The study appears to have been, technically, rigorously conducted with high quality, in-depth traditional assessment of both state and EEG characteristics, with the concordant addition of activity and temperature. The major strengths of this study derive from observations that the AppNL-G-F mice: (1) are more hyperactive in association with decreased transitions between states; (2) maintain a normal response to sleep deprivation and have normal MSLT results; and (3) display a sex specific, "stronger" insomnia-like effect of the knockin in females.

      Weaknesses:

      The weaknesses stem from the study's impact being limited due to its being largely confirmatory of the Maezono et al. study, with advances of importance to a potentially more focused field. Further, the authors conclude that AppNL-G-F mice have disrupted mechanism(s) responsible for state transition; however, these were not directly examined. The rationale for this conclusion is stated by the authors as based on the observations that bouts of both W and NREM tend to be longer in duration and decreased in frequency in AppNL-G-F mice. Although altered mechanism(s) of state transition (it is not clear what mechanisms are referenced here) cannot be ruled out, other explanations might be considered. For example, increased arousal in association with hyperactivity would be expected to result in increased duration of W bouts during the active phase. This would also predictably result in greater sleep pressure that is typically associated with more consolidated NREM bouts, consistent with the observations of bout duration and frequency.

      Reviewer 1 succinctly summarizes the advances of this study beyond the ground-breaking Maezono et al (2020) study of this “humanized” mouse model exhibiting amyloid deposition. Whereas Maezono et al. conducted sleep/wake studies on male App<sup>NL-G-F</sup> mice at 6 and 12 months of age, we had the unusual opportunity to study both sexes of homozygous App<sup>NL-G-F</sup> mice and WT littermates at 14-18 months of age and to conduct a longitudinal assessment of many of the same individuals at 18-22 months. In addition to baseline sleep/wake and EEG spectral analyses, we (1) measured subcutaneous body temperature and activity to obtain a broader picture of the physiology and behavior of this strain at advanced ages; (2) assessed baseline sleepiness in this strain using the murine version of the clinically-relevant Multiple Sleep Latency Test (MSLT); (3) evaluated the response of App<sup>NL-G-F</sup> mice and WT littermates to a 6-h perturbation of the sleep homeostat; (4) compared the sleep/wake characteristics of male vs. female App<sup>NL-G-F</sup> mice at 18-22 months; and (5) to assess the stability of the phenotypes, analyzed these data over a continuous 14-d recording rather than the conventional 24h recordings typical of most sleep/wake studies including Maezono et al. We found that a long wake/short sleep phenotype was characteristic of homozygous App<sub>NL-G-F</sub> mice at these advanced ages which is also evident in the Maezono et al. (2020) study at 12 months of age (but not at 6 months), although the authors do not comment on this phenotype and instead focus on the reduced REM sleep which is particularly evident in female App<sup>NL-G-F</sup> mice in our study. Remarkably, despite being awake ~20% longer per day, we find that App<sup>NL-G-F</sup> mice are no sleepier than WT mice as determined by the MSLT and that their sleep homeostat is intact when challenged by 6-h sleep deprivation. At both advanced ages, the long wake/short sleep phenotype is due primarily to longer Wake bouts and shorter bouts of both NREM and REM sleep during the dark phase. Moreover, hyperactivity develops in older App<sup>NL-G-F</sup> mice, particularly females, which contributes to this phenotype. We agree with Reviewer 1 that “hyperactivity would be expected to result in increased duration of W bouts during the active phase” and that this could result in more consolidated NREM bouts. Accordingly, we have added the following sentence to the Discussion subsection Impacts of pathology on sleep/wake and activity: “Thus, the hyperactivity evident in Figures 4D, 4D’, and 5D’ could drive the longer wake bouts evident in Figure 7A and result in the longer NREM and REM sleep bouts found in male App<sup>NL-G-F</sup> mice (Figure 12A’ and 12A”).”

      The suggestion of greater sleep pressure is not borne out by our MSLT studies as we did not observe the shorter sleep latencies nor increased sleep during the nap opportunities on the MSLT that we have observed in other mouse strains. Moreover, due to their short sleep phenotype, App<sup>NL-G-F</sup> mice should be entering the sleep deprivation study with a greater sleep debt than WT mice, yet we did not observe a stronger homeostatic response (i.e., enhanced EEG Slow Wave Activity) in this strain during recovery from sleep deprivation. Thus, we have suggested that App<sup>NL-G-F</sup> mice are unable to transition from Wake to sleep as readily as their WT littermates. Our observations summarized above set the stage for subsequent mechanistic studies in aged App<sup>NL-G-F</sup> mice, although realistically, mice of this age and genotype are a rare commodity.

      Reviewer #2 (Public review):

      Summary:

      The authors have used a knock-in mouse model to explore late-in-life amyloid effects on sleep. This is an excellent model as the mutated genes are regulated by the endogenous promoter system. The sleep study techniques and statistical analyses are also first-rate.

      The group finds an age-dependent increase in motor activity in advanced age in the NLGF homozygous knock-in mice (NLGF), with a parallel age-dependent increase in body temperature, both effects predominate in the dark period. Interestingly, the sleep patterns do not quite follow the sleep changes. Wake time is increased in NLGF mice, and there is no progression in increased wake over time. NREMS and REM sleep are both reduced, and there is no progression. Sleep-wake effects, however, show a robust light:dark effect with larger effects in the dark period. These findings support distinct effects of this mutation on activity and temperature and on sleep. This is the first description of the temporal pattern of these effects. NLGF mice show wake stability (longer bout durations in the dark period (their active period) and fewer brief arousals from sleep. Sleep homeostasis across the lights-on period is normal. Wake power spectral density is unaffected in NLGF mice at either age. Only REM power spectra are affected, with NLGF mice showing less theta and more delta. There are interesting sex differences, with females showing no gene difference in wake bout number, while males show a gene effect. Similarly, gene effects on NREM bout number seem larger in males than in females. Although there was no difference in homeostatic response, there was normalization of sleep-wake activity after sleep deprivation.

      Strengths:

      Approach (model extent of sleep phenotyping), analysis.

      Weaknesses:

      The weaknesses are summarized below and are viewed as "addressable".

      (1) The term insomnia. Insomnia is defined as a subjective dissatisfaction with sleep, which cannot be ascertained in a mouse model. The findings across baseline sleep in NLGF mice support increased wake consolidation in the active period. The predominant sleep period (lights on) is largely unaffected, and the active period (lights off) shows increased activity and increased wake with longer bouts. There is a fantastic clue where NLGF effects are consistent with increased hypocretinergic (orexinergic) neuron activity in the dark period, and/or increased drive to hypocretin neurons from PVH.

      Although the DSM-5 definition of Insomnia Disorder indeed emphasizes a subjective “complaint of dissatisfaction with sleep quantity or quality”, I think the Reviewer takes an unnecessarily narrow view of the term “insomnia”. Aside from cases of “psychological” insomnia in which there is a mismatch between subjective and objective measures of sleep, most sleep researchers would likely agree that insomnia is objectively characterized by a greater than normal wake time during the sleep period (i.e., low sleep efficiency) due to difficulty in either initiating or maintaining sleep. This view has led to efforts to identify not only the biological causes of insomnia but also animal models in which this disorder can be studied. A PubMed search on the terms “mouse” and “insomnia” retrieves 844 publications, including an authoritative 2023 review in J Sleep Research entitled "Animal Models of Human Insomnia" co-authored by a clinician-scientist who has done human sleep research throughout his career and is an authority on CBT-I, in particular. Similarly, a PubMed search on the terms “fly” and “insomnia” retrieves 18 publications. So, although our intent in the submitted version of the manuscript was to use “insomnia” as an operational term to succinctly mean “less sleep than usual”, in the revised manuscript, we have eliminated use of the term “partial insomnia” and replaced it with the term “insomnia-like phenotype”. In the Discussion section “Impacts of pathology on sleep/wake and activity”, we have revised the opening sentence to read “Insomnia in humans is typically characterized by subjective reports of reduced sleep quality and can be accompanied by objective measures of sleep fragmentation and reduced sleep amounts.”

      (2) Sleep-wake transitions are impaired: This should not be termed an impairment. It could actually be beneficial to have greater state stability, especially wake stability in the dark or active period. There is reduced sleep in the model that can be normalized by short-term sleep loss. It is fascinating that recovery sleep normalized sleep in the NLGF in the immediate lights-on and light-off period. This is a key finding.

      Due to the Reviewer’s objection regarding “impairment”, we have changed the title of the manuscript to “Long Wake/Short Sleep Bouts and Hyperactivity with Advanced Age in a Mouse Model of Early Onset Alzheimer’s Disease”. In Comments (1) and (2), Reviewer 2 suggests a provocative hypothesis to test. In the section “Impacts of pathology on sleep/wake and activity“, we previously stated “A hyperactive hypocretin/orexin or monoaminergic arousal system or a dysfunctional GABAergic sleep onset system could underlie the longer bouts of Wake in App<sup>NL-G-F</sup>mice.” We have now added this additional sentence: “Indeed, Hcrt neurons in aged mice have been shown to exhibit more frequent neuronal activity driving wake bouts and optogenetic stimulation of Hcrt neurons in aged mice results in prolonged wakefulness (Li et al., 2022).“

      Reviewer #3 (Public review):

      Summary:

      In this study, Tisdale et al. studied the sleep/wake patterns in the biological mouse model of Alzheimer's disease. The results in this study, together with the established literature on the relationship of sleep and Alzheimer's disease progression, guided the authors to propose this mouse model for the mechanistic understanding of sleep states that translates to Alzheimer's disease patients. However, the manuscript currently suffers from a disconnect between the physiological data and the mechanistic interpretations. Specifically, the claim of "impaired transitions" is logically at odds with the observed increase in wake-state stability or possible hyperactivity. Additionally, the description of the methods, the quantification, and the figure presentation could be substantially improved. I detail some of my concerns below.

      Strengths:

      The selection of the knock-in model is a notable strength as it avoids the artifacts associated with APP overexpression and more closely mimics human pathology. The study utilizes continuous 14-day EEG recordings, providing a unique dataset for assessing chronic changes in arousal states. The assessment of sex as a biological variable identifies a more severe "insomniac-like" phenotype in females, which aligns with the higher prevalence and severity of Alzheimer's disease in women.

      Weaknesses:

      The study seems to lack a clear hypothesis-driven approach and relies mostly on explorative investigations. Moreover, lack of quantitative analytical methods as well as shaky logical conclusions, possibly not supported by data in its current form, leaves room for major improvement.

      Since this paper studied sleep states, the "Methods" section is quite unclear on what specific criteria were used to classify sleep states. There is no quantitative description of classifying sleep based on clear, reproducible procedures. There are many reasonably well-characterized sleep scoring systems used in rat electrophysiological literature, which could be useful here. The authors are generally expected to describe movement speed and/or EMG and/or EEG (theta/delta/gamma) criteria used to classify these epochs. The subjective (manual) nature of this procedure provides no verifiable validation of the accuracy and interpretability of the results.

      This was an oversight: the “Classification of Arousal States” section has been modified accordingly.

      One of the bigger claims is that "state transition mechanism(s)" are impaired. However, Figure 7 shows that model mice exhibit significantly more long wake bouts (>260s) and fewer short wake bouts (<60s). Logically, an "impaired switch" (the flip-flop model, Saper et al., 2010) results in state fragmentation. The data here show the opposite: the wake state has become too stable. This suggests the primary defect is not in the transition mechanism itself, but possibly in a pathological increase in arousal drive (hyper-arousal), likely linked to the dark-phase hyperactivity shown in Figures 4 and 5. Also, a point to note is that this finding is not new.

      Reviewers 1 and 2 also make comments conisistent with the alternative interpretation that “the wake state has become too stable.” However, I think we are using different words to say the same thing: that the transition from wake to sleep is impaired whether it is due to hyperarousal or to a defect in the flip/flop switch that results in greater Wake stability. I hope the reviewer would agree that a switch can be impaired in two directions: either it could “flicker” as seems to be the case in narcolepsy or it could get stuck in one position, which is what we suggest here based on the data in Fig. 12A, A’ and A” which show longer bouts of all states (Wake, NREM and REM) in older males. Nonetheless, the hyperarousal hypothesis suggested by the Reviewer is certainly a reasonable alternative. Consequently, we have added the following sentence to the Discussion subsection Impacts of pathology on sleep/wake and activity: “Thus, the hyperactivity evident in Figures 4D, 4D’, and 5D’ could drive the longer wake bouts evident in Figure 7A and result in the longer NREM and REM sleep bouts found in male App<sup>NL-G-F</sup> mice.”

      Figure 3 heatmaps lack color bars and units. Spectral power must be quantitatively defined and methods well-explained in the Methods section. Without these, the reader cannot discern if the "reduced power" in females is a global suppression of signal or a frequency-specific shift. Additionally, the representative example used to claim shorter sleep bouts lacks the statistical weight required for a major physiological conclusion. How does a cooler color (not clear what range and what the interpretation is) mean shorter sleep bout in female mice? The authors should clearly mark the frequency ranges that support their claims. In this figure, there is a question mark following the theta/delta range. The authors should avoid speculation and state their claims based on facts. They should also add the theta and delta ranges in the plot, such that readers can draw their own conclusions.

      The Y-axis in the previous version of this figure was labelled 0-25 Hz. This figure was intended to be a descriptive illustration of how unusual the female App<sup>NL-G-F</sup> mice are relative to WT of either sex rather than a quantitative analysis of spectral power. As suggested by Reviewer 2, we have combined this figure with the previous Fig. 14 as the revised Fig. 3 and we have modified the Y-axis labels to more explicitly indicate EEG frequencies. The question mark was legacy text from an earlier version of the manuscript; sorry for the confusion!

      Figure 8 and the MSLT results show that model mice are "no sleepier than WT mice" and have a functional homeostatic rebound. This presents a logical flaw in the "insomnia" narrative. True insomnia in AD patients typically involves a failure of the homeostatic process or a debilitating accumulation of sleep debt. If these mice do not show increased sleepiness (shorter latency) despite ~19% less sleep, the authors might be describing a "reduced need" for sleep or a "hyper-aroused" state, possibly not a clinical insomnia phenotype.

      Both Reviewer 2 and 3 suggest that we are using “insomnia” incorrectly, which we have used as shorthand to denote less sleep per 24h period. Reviewer 2 states that “Insomnia is defined as a subjective dissatisfaction with sleep” per DSM-5 and Reviewer 3 suggests that the mechanism underlying insomnia in AD patients is “a failure of the homeostatic process or a debilitating accumulation of sleep debt” which is not in DSM-5. Our clinical colleagues tell us that this is not established fact; some argue that the homeostat is intact and that the input(s) to the homeostat are defective. We agree that less sleep in these mice could be due to a reduced need for sleep or to hyperarousal. Consequently, we have changed the title of the manuscript to eliminate “Sleep-Wake Transitions are Impaired…” to the more objective “Long Wake/Short Sleep Bouts and Hyperactivity with Advanced Age in a Mouse Model of Early Onset Alzheimer’s Disease”.

      In Figure 9, LFP power shown and compared in percentages is problematic, as LFP power distribution is known to be skewed (follows power law). This is particularly problematic here because all the frequencies above ~20 Hz seem to be totally flattened or nonexistent, which makes this comparison of power severely limited and biased towards the relative frequency in the highly skewed portion of the LFP power spectrum, i.e., very low frequency ranges like delta, theta, and possibly beta. This ignores low, mid, and high gamma as well as ripple band frequencies. NREM sleep is known to have relatively greater ripple band (100-250 Hz) power bursts in hippocampal regions, and REM sleep is known to have synchronous theta-gamma relationships.

      We completely agree with the reviewer. There are at least 3 ways that spectral power data can be presented: (1) absolute power; (2) relative power (normalized to a baseline); and (3) power density. In this study, we intentionally presented results in terms of spectral power density so that our results could be compared to those in Figure 3A and 3B of Maezono et al. (2020). This was important because Maezono et al. recorded from mice of 6 and 12 months of age whereas we recorded from older mice, which allowed us to determine which parameters are likely changing with age (and, presumably, greater Ab deposition).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) A key finding for the AppNL-G-F mouse model is the emergence of hyperactivity that may be responsible for the altered sleep architecture. Further investigation to help determine the mechanism(s) responsible might include cFos expression to help localize or provide evidence for the distributed neuronal activity increase in this model. Additionally, identification of overly active areas might provide targets for their manipulation to test the authors' hypothesis of the mechanism of the altered sleep architecture. Does chronic hyperactivity caused by other mechanisms (DREADDs, LOF of a K channel) mimic the AppNL-G-F mouse model sleep phenotype? These sorts of findings would impact the study's significance.

      We agree with the Reviewer that identifying the mechanism underlying the long wake/short sleep phenotype of aged App<sup>NL-G-F</sup>mice would increase the study’s significance. However, we want to underscore that the opportunity to study both sexes of homozygous App<sup>NL-G-F</sup> mice and WT littermates at 14-18 months of age and to conduct a longitudinal assessment of many of the same individuals at 18-22 months was very unusual. Our observations of the phenotype described in this manuscript set the stage for subsequent mechanistic studies in aged App<sup>NL-G-F</sup> mice, although realistically, mice of this age and genotype are a rare commodity.

      (2) A more technical area of improvement involves the presentation of the results and the associated critical statistical analyses. Relevant tables and statistics are not always reported (in the results) or properly referenced. In the mixed models, the repeated measures are "time of day", I presume.

      Tables 1-6 present statistical results; these 6 Tables are referred to in the Results section a total of 14 times. The text states “The larger sample size in Experiment 2 (N=31 mice) allowed a mixed-effects model ANOVA to be conducted with Genotype, Sex, and Time as factors”. Although “Time of Day” was specified several places in the Results, thank you for pointing out omission of “of Day” from the “Data Analysis and Statistics” section; we have added this information accordingly.

      (3) The model is presented as age-dependent, but there was little statistical support for this. The subjects spanned a considerable age range, and a direct quantifiable correlation between age and the various measured dependent variables could be helpful in this regard.

      The long wake/short sleep phenotype characteristic of homozygous App<sup>NL-G-F</sup> mice that we describe here is also evident in the Maezono et al. (2020) study at 12 months of age but not at 6 months in either the Maezono et al. (2020) or Calafete et al. (2023) studies, although the authors do not comment on this phenotype and instead focus on the reduced REM sleep. Thus, between these studies, there seems to be an age-dependent progression of the phenotype. We have thus added this sentence to the Discussion subsection Sleep/wake and activity phenotypes of 14-18 month vs. 18-22 month old App<sup>NL-G-F</sup> mice: “This long wake/short sleep insomnia-like phenotype is also evident at 12 months of age (Maezono et al., 2020) but not at 6 months (Calafate et al., 2023; Maezono et al., 2020), suggesting a progression in this symptomatology.”

      (4) Would a more advanced age point be helpful? Would sleep fragmentation be likely to appear with more advanced age?

      The text states “Recordings collected throughout the entire 14-day period when Cohort 2 App KI and App WT mice were 21.0-24.3 months of age”. Mice on a C57BL6/J background are considered old at 18-24 months. Fig. 6B’ shows a strong trend (p=0.0558) toward shorter NREM bouts in App KI mice at 18-22 months during the dark phase at the same time that long wake bouts are evident (Fig. 6A’), strongly indicative of sleep/wake fragmentation but not quite significant with the sample size measured.

      (5) How does the onset of sleep-architecture-related symptoms relate to the cognitive impairment onset in AppNL-G-F mice?

      We have added this sentence to the Conclusions: “In a fear conditioning paradigm, impaired learning ability has been correlated with REM sleep duration in 13 month old but not 7 month old App<sup>NL-G-F</sup> mice (Maezono et al., 2020).

      (6) It is importantly concluded that the AppNL-G-F mouse phenotype is "stronger" in females. What is meant here by "stronger" and can this be quantified?

      We have eliminated use of “stronger” and replaced with “more evident” or “more apparent”.

      (7) Would ovariectomized females still show partial insomnia?

      This is an interesting question, particularly because the hyperactivity evident in Figure 7C is most evident in females. The average age of cessation of estrus cyclicity in C57BL6/J mice occurs between 13-16 months of age (Nelson et al., 1982, Biol Reproduction). The female KI mice in Cohort 2 ranged from 21.0 to 23.3 months of age at the time of recording and thus can be expected to be functionally ovariectomized.

      (8) The statement, "...female AppNL-G-F mice exhibited the most wakefulness and the least amount of sleep each day", sounds like a tautology.

      It was an intentional statement to underscore the long wake/short sleep phenotype.

      Reviewer #2 (Recommendations for the authors):

      (1) Introduction:

      The authors might mention in paragraph 3 that because these studies each used a mutant protein on a powerful, and not the endogenous, promoter, the effects on sleep may be skewed by overexpression in specific brain areas. In addition, they might mention that sleep homeostasis and sleep changes relative to brain temp and activity have not been examined longitudinally.

      We have added the following sentences to the Limitations subsection of the Discussion: “Moreover, because studies of this strain used a mutant protein on a powerful exogenous promoter, the effects on sleep described by us and previous investigators may be skewed by overexpression in specific brain areas” and “Neither the present nor previous studies have assessed the effects of age-related changes in brain temperature on sleep/wake, sleep homeostasis or activity.”

      (2) Results:

      Figure 2: Images in 1B and 1B' look like IHC labeling in well over 1 and 2% of the brain for Iba-1. Are these images correct?

      The use of “%” on the Y-axis was inappropriate and has been corrected. Due to variation in Iba1 immunostaining across WT mice, Iba1 measurements were normalized to WT such that the mean Iba1 area coverage for WT mice within each region of interest was set to 1. The negligible 82E1 signal in WT mice obviated the need for normalization.

      Figure 3: I would move to incorporate into Figure 14 with spectra, as this is descriptive but nicely illustrates Figure 14.

      Done -- thank you for this excellent suggestion!

      Figure 10: The figure supports no significant estrus effects in either WT or NLGF. Could run the analysis, but important finding.

      Agreed but, as indicated in the response to Reviewer 1, the average age of cessation of cyclicity in C57BL6/J mice has been reported to occur between 13-16 months of age (Nelson et al., 1982, Biol Reproduction). The female mice in the older cohort that we recorded were 18-22 months of age.

      (3) Discussion:

      Page 11, last paragraph: It is hard to say whether activity caused more wake or response to wake is different in these mice (anxiety and hyperactivity are both seen in Alzheimer's disease).

      Hypocretin MCH is touched on but could be elaborated upon, given light/dark differences.

      We agree that the directionality is difficult to ascertain. As mentioned above, we have added a discussion on hyperactivity but, having not made any assessment of anxiety in the present study, we have refrained from further speculation.

      Reviewer #3 (Recommendations for the authors):

      (1) Figure 9: Y-axis labels are missing on several plots.

      Due to the density of info on this figure, Y-axis labels were intentionally omitted for those panels for which the Y-axis label of the panel to the left applied. Since the reviewer found this to be confusing, we have added Y-axis labels to all panels at the risk of making the figure even more dense!

      (2) Figure 14: x tick labels are perplexing - why would they be labelled in such arbitrary decimal points?

      As stated in the text, “EEG spectra for each state were analyzed in 0.061 Hz bins”. Consequently, X-axis labels are modulo 0.061 Hz.

      (3) Figure S1 is not aligned; some plots cannot even be read.

      Figure S1 has been reformatted to portrait mode from the previous landscape version (although no alignment issues were evident when viewed in landscape mode).

      (4) For some reason, Tables 1-3 are horizontal, which I couldn't read.

      Our apologies, some of the info in Table 1 was omitted during export. We have retained landscape mode for Table 1 and re-formatted Tables 2 and 3 in portrait mode for ease of accessibility.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Freas and Wystrach present a computational model of steering in insects. In this model, the central complex provides an error signal indicating the animal should turn left or right; this error signal biases the function of an oscillator composed of two mutually inhibiting self-exciting units. The output of these units generates a "steering signal" that is used both to set the direction and speed of the ant. Additionally, a separate module induces pauses, and an inverse relation between forward speed and turning speed is externally imposed. Statistics of the trajectories generated by the model are compared to the measured behaviors of ants.

      Strengths:

      While the model is very simple compared to state-of-the-art models, that simplicity makes it a potentially useful guide to researchers studying insect navigation. Some predictions that emerge from the model appear to be experimentally testable, although a more complete description of the model and its parameters, as well as an analysis of how this model's predictions differ from previous models' predictions, would be required to design these experiments.

      Weaknesses:

      I found it difficult to identify evidence in the paper supporting central elements of the abstract. Hopefully, these difficulties can be resolved with a clearer presentation and the addition of supporting detail, especially in the methods.

      (1) The model is not clearly described

      In the Materials and Methods, there is no description of the model, just "The computational model is presented in Figure 1." (This is probably a typo and may refer to Figure 2A-C), and a link to Matlab source code. It is inappropriate to ask readers or reviewers to examine source code in lieu of providing a method, but I attempted to do so anyway. 

      We have now added a full description of the model in the methods.

      To my eye, the source code does not match the model presented in 2A-C. For instance, in 2C, "Steering signal" inhibits "Freeze", but I couldn't find this in the source. "Freeze" is shown to inhibit "steering signal," but as "steering signal" is a signed quantity, it's not clear what this means. Literally, since "ang_speed_raw = L-R," it would seem to indicate the "freeze" would bias towards right turns. In the code, "freeze" appears to be implemented through the boolean variable "speed_inhibition_time." The logic controlled by this variable doesn't appear to inhibit the "steering signal" but instead (depending on control parameters) either reduces the movement speed and amplifies the turning rate, or it turns the angular speed output into a temporal integral of the control signal.

      We understand the confusion. Our neural implementation does not go downstream of the neural steering signal (Left and Right Descending neurons), and the way it is transformed into a movement (ang_speed_raw = L-R) is not modelled neurally (the formula is explicitly shown on the right hand side of Figure 2). Indeed, we did not attempt to put forward any assumption about neural implementation for our freezing signal (see our response to comment 2 below). To avoid confusion, we have now removed the reciprocal inhibition portion as it was previously drawn in Figure 2C, and replaced it by a non neural sign (a cross, indicating that the signal is blocked) acting between steering signal and movement.

      There are a number of parameters in the source code that aren't described at all in the paper, including the internal oscillator parameters.

      We now provide all the parameters in the methods, together with figures showing the dynamics of oscillations across parameter range, and a rationale for their choice (see Supplemental Figure 2).

      Together, these limitations make it difficult to understand what is being simulated, what parts of the model are tied to biology, and where the model improves on or departs from previous work.

      It is absolutely essential that authors fully describe the computational model, that they explain the meaning of all parameters of the model, and that they explain how the particular values of these parameters were chosen.

      This is now done in the methods section under the “Model Overview” subsection.

      (2) The biological inspiration is unclear

      A central claim of the paper is that the model is "biologically grounded." But some elements, for instance, using a signed quantity to represent left-right steering drive, are not biologically possible; at best, these are shorthand for biologically possible implementations, e.g., opposing groups of left-right driving neurons.

      The mechanism that produces fixations and saccades - the "freeze" module - is not tied to any particular anatomy of the insect brain. Initiation of a freeze occurs at a specific time coded into the model by the authors; it is not generated by an internal model signal. Release of a freeze is by drawing a random variable; there is no neural mechanism proposed to generate this signal.

      We now clarified what is neural from is not from the introduction onwards, for instance:

      “Because we did not want to form pre-assumptions for how such a ‘freeze signal’ could be implemented in the insect nervous system; in our model this was achieved using a simple external signal that halts forward motion at random intervals.”

      In some versions of the model, instead of directly controlling the signal, during fixations, the angular drive signal is integrated into a variable "cumul_drive." No neural substrate is proposed for this integrator. In the code, if cumul_drive passes a threshold, the angular heading of the ant changes (saccades), but only if this threshold is passed before the Poisson process ends the fixation. No neural substrate is proposed for any of this logic.

      This has now also be clarified in the introduction:

      “During scanning, real ants display rotational saccades of variable duration and angular magnitude (Figure 1A–C). To replicate this, we introduced a threshold-based mechanism: after each fixation (i.e., zero angular and forward speed), the underlying angular steering signal accumulates until surpassing a threshold, triggering a saccade. The resulting angular magnitude of the saccade corresponds to the sum of the angular drive accumulated during the fixation. Here also we stuck to a non-neural, straight-forward algorithmic level, as we did not want to make assumptions about how such a cumulate-and-release mechanism could be neurally implemented in the insect brain (see discussion for potential implementations).”

      The model steps forward in time by a fixed increment - the actual duration (in seconds) of this time step is not specified. From Figure 4F, G, it appears a simulation time step is meant to be about 10ms. This would imply an oscillator frequency of about 2 Hz (Fig 2B), that the heading oscillates at a similar frequency (2G), and that a forward crawling ant stops moving every 500 ms (2I). Are these plausible? Can they be compared to an experiment? Model parameters, including the ones that control the frequency of the oscillator, are non-dimensionalized. It is not possible to evaluate whether these parameters are biologically plausible or match experimental results.

      We now added a figure showing the oscillatory dynamics of the oscillator across parameter ranges (supplemental figure 2). The step increment (i.e., and thus the sampling rate along an oscillatory cycle) necessarily varies according to the inhibition strength and self decay parameter chosen (e.g., small parameter values will lead to small step increment, and thus a high sampling rate along the oscillatory cycle). We chose oscillatory parameters to ensure that the sampling rate will be high enough to resolve multiple saccades within one oscillatory cycle and that sampling rate is small enough for computation time to remain practical.

      Beyond these constraints, the oscillator parameters can be chosen arbitrarily, and a conversion of time step to actual time (ms) would be equally arbitrary and give the illusion that the model captures the data quantitatively. Because we did not model spiking neural dynamics (or brain region low field potential frequencies), we can not constrain our model through a temporal link between brain clock and behavioural speed. We thus prefer to stick to the true and non-dimensional label ‘time steps’ in our figures.

      (3) Claims that behaviors emerge from the model may be overstated

      The abstract claims that steering correction and fixations/saccades emerge naturally from the same model. But it appears to me that fixations/saccades are externally imposed by the specification of specific times for a "freeze." Faster angular rotation during saccades than during course correction is imposed and does not emerge naturally from neural simulations.

      The abstract now clarifies that what emerges spontaneously is not scannings per se (indeed, the inhibition of movement is externally imposed) but their dynamics. Note that our model captures many aspects of scanning dynamics that are not trivial and which results from the dynamical interactions and contingencies between modules (figure 3 to 7), hence justifying the word ‘emerge’ insofar as these behavioural dynamics cannot be reduced to one module or parameter. Regarding the faster angular rotation during scanning, we agree that its cause is rather straightforward to understand: it results from the added bodily constraints of forward speed to rotational movements. Nonetheless it is not ‘imposed’ during saccades in the sense that 1.) it is biologically/physically evident rather than cherry picked and 2.) it is continuously present in our model, even during forward navigation. We believe the new version of the manuscript now conveys this message in a transparent manner.

      (4) Citations to previous literature are difficult to follow, and modeling results are presented as though they are experimental data

      I would ask the authors to be much clearer in their description and citation of previous work. It should be clear whether the cited work was experimental or computational. To the extent possible, the actual measurement should be described succinctly. Instead of grouping references together to support a sentence with multiple claims, references should be cited for each claim. Studies of computational models should not be presented as proving a biological result.

      Indeed, This we now clearly separated citations referring to experimental evidence vs. modelling. See examples citations below

      For example:

      (a) Lines 141-146:

      "Previous studies have established many key components of insect navigation, including .... the intrinsic oscillatory dynamics in the lateral accessory lobes (LALs) that support continuous zigzagging locomotion (Clément et al., 2023; Kanzaki, 2005; Namiki and Kanzaki, 2016;

      Steinbeck et al., 2020)."

      The first reference is to one author's previous modeling work - it hypothesizes that oscillations in the LAL support zigzagging but includes no data that would "establish" the fact. Kanzaki et al. 2005 describes numerical modeling and simulation with a physical robot. Namiki and Kanzaki, 2016 is a review article that links the LAL to zigzagging behavior. It describes the LAL as a winner-take-all bistable network but does not describe or hypothesize that the LAL has intrinsic oscillatory dynamics. Steinbeck et al. 2020 is a more comprehensive review; it reinforces that the LAL is a winner-take-all bistable network that drives left-right steering, including during zig-zagging behavior. But in my reading, I could not find a statement that the LAL has intrinsic oscillatory dynamics (the closest is Steinbeck et al. saying the activity pattern switches regularly, as does the behavior; this doesn't imply that the LAL is intrinsically oscillatory.)

      It now reads:

      “Previous studies have established many key components of insect navigation, notably, how goal headings are set in the central complex (CX) (Fisher, 2022; Green and Maimon, 2018). Modelling efforts have shown that the CX circuitry can naturally accommodate innate and learnt guidance such as path integration, learn vectors, visual route following or homing as observed in ants and bees. In parallel, oscillatory dynamics in the lateral accessory lobes (LALs) - produced by reciprocal inhibition across both hemispheres and conveyed by so-called descending flip-flopping neurons - were shown to drive the spontaneous zigzags displayed by moths upon losing their pheromone plume (Kanzaki and Mishima, 1996; Mishima and Kanzaki, 1998, 1999; Wada and Kanzaki, 2005; Kanzaki et al., 2005; Iwano et al., 2010). Here also, subsequent modelling efforts have shown how these circuits can equally support the continuous lateral oscillations displayed by a wide range of insect species, including ants.”

      (b) Lines 701-703:

      "In plume-tracking moths, CX output has been shown to modulate LAL flip-flop neurons driving zigzagging (Adden et al., 2022)."

      This reads as though an experimental measurement was made, but in fact, this is modeling work.

      Yes, this could be clearer, it now reads: 

      “In moths, descending neurons in the LALs exhibit characteristic 'flip-flop' activity patterns that correlate with zigzagging maneuvers (Olberg, 1983; Kanzaki and Ikeda, 1994). Computational models suggest that having these LAL neurons modulated by the CX output can explain aspects of the moths’ plume-tracking behaviour (Adden et al., 2022).”

      (c) Lines 703-706:

      "In ants, strong goal signals in the CX - whether elicited by the path integrator or visual familiarity (Wehner et al., 2016; Wystrach et al., 2020b, 2015) do not only sharpen directional accuracy but also increase oscillation frequency (Clément et al., 2023)."

      Here again, modeling results are presented as though they were experimental data.

      Here, we are referring to the experimental part of these works, although this comment demonstrates that our statement should be more clear in stating what are biological results. It now reads: 

      “In ants, behavioural studies show that strong directional drives elicited by the path integrator or visual familiarity do not only gain behavioural weights and sharpen directional accuracy (Wehner et al., 2016; Wystrach et al. 2015, Legge et al. 2014) but also increase the ants’ oscillation frequency (Clément et al., 2023). Assuming that path integrator and visual familiarity modulate goal signals in the CX, as modelled here and elsewhere (Wystrach et al., 2020b, Stone et al., 2017) and that the intrinsic oscillator is in the LAL (Clément et al., 2023, Steinbeck et al., 2020), it suggests that CX output modulates the intrinsic oscillatory activity of the LAL”

      Reviewer #2 (Public review):

      Summary:

      The paper by Freas and Wystrach is an interesting computational study, exploring the detailed mechanisms of how simple neural circuits could explain complex behavioral patterns observed in navigating ants. The authors compare detailed, high-speed video recordings of Australian desert ants (Melophorus bagoti) with predictions made by their new computational model and find convincing similarities between the model and the behavioral data, at a level of detail not previously studied. Particularly interesting are emerging properties of the model, yielding behavioral motifs it was not designed to reproduce, but which occur in natural ant behavior.

      Strengths:

      A strength of the study is that the model is based on previous models, without making major novel explicit assumptions. It combines existing models of the insect central complex with a model of the lateral accessory lobe and adds a stochastic inhibition of forward velocity to the interaction of central complex and lateral accessory lobes. The central complex provides corrective steering signals when the goal direction and the current heading of an insect are not aligned, while the lateral accessory lobes provide an intrinsic oscillator underlying the behavioral oscillations shown by walking ants at all times. These background oscillations are modulated by the steering signals from the central complex. Depending on which phase of the intrinsic oscillations coincides with the corrective signals, and how fast the ant is moving forward during this time, a complex set of behaviors emerges. Most prominently, scanning behaviors, which are regularly carried out by the ants, are recapitulated in great detail by the model. Additionally, other behaviors, such as full loops, emerge naturally from the model. While computational models are not to be seen as definite evidence for any biological reality, they can provide strong support for particular neural implementations. The current study is an excellent example in that it provides evidence for a serial arrangement of central complex circuits upstream of the lateral accessory lobe circuits, modulated by speed-regulating input. While the latter is hypothetical, it yields a clear hypothesis that can be validated by connectomics studies and functional work in the future.

      The study shows that even complex behavioral motifs do not require dedicated neural modules, but can rather emerge from the interplay of already known circuits - highlighting the efficiency of insect brains and possibly providing the path towards embodied hardware solutions of such circuits in autonomous agents.

      Weaknesses:

      There are several weaknesses in the paper as it is.

      Firstly, the model is not described in the methods, but only found when following the link to the authors' GitHub repository. This is clearly not sufficient and prevents readers from evaluating the model's assumptions directly. Most importantly, how natural do the emerging properties indeed emerge from the model? What parameters need to be tuned to generate a match between data and model?

      We have now added a full description of the model in the Methods section.

      These include:

      Mathematical equations for model components

      Complete parameter table along with justifications

      Description of what is fitted vs. what emerges 

      Key assumptions and limitations

      Regarding the emergence of scanning properties: The model has two types of parameters:

      Parameters tuned to match general navigation behavior (independent of scanning):

      Motor gains (g_ang, g_fwd, k): adjusted to produce realistic continuous walking paths and species differences between desert ants and Myrmecia

      CX gain (g_CX = 0.5): set to produce appropriate corrective steering strength during continuous navigation

      Oscillator parameters (α, β, s): are taken from Clément et al. (2023)

      Parameters tuned to match scanning behavior:

      CPG angular threshold (θ_CPG = 2.0): adjusted to generate realistic saccade timing Scan termination probability (p_stop = 0.5/timestep): matched to the Poisson-like distribution of scan durations in M. bagoti

      Properties that emerge without specific tuning:

      Fixation-saccade alternation structure (emerges from angular drive accumulation mechanism)

      Directional reversals (arise from oscillator dynamics competing with CX steering)

      Corrective saccade amplitude increasing with angular deviation (Figure 3)

      Rare full-loop scans (emerge from CX signal shifting oscillator phase)

      The behavioral continuum from straight paths → oscillations → voltes → scans (Figure 8)

      We have clarified this distinction in the Methods section and emphasized that our goal was qualitative demonstration of emergence rather than quantitative parameter optimization.

      Second, it is often not entirely clear what is biological data and what is a computational model. This relates to figures, text, and references. As a reader, this makes it difficult to clearly judge what is new in the current paper, how it adds to previous models, and what the predictions and assumptions are for biology.

      Indeed, we have now clarified the manuscript, clearly separating when we refer to behavioural data, neurobiological data and modelling. In the figures, each panel now clearly indicates if it is model data or biological data so that any reader can immediately tell the data type.

      Third, while neural data from bees and flies are taken to motivate and design the computational model, the discussion and interpretation revolve almost exclusively around ants. For the most part, this is justified, as the behavioral data used to benchmark the model are taken from ants. Nevertheless, more broadly discussing the newly defined circuit in the context of flying insects would give a better idea of the broad relevance of the neural circuits predicted by the model.

      To address this suggestion we have now added two paragraphs in the discussion called: “Scanning in flying hymenopterans”.

      Also happy to add more to this section if requested.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      As mentioned in the public review, I suggest fixing the two concerns I have regarding methods and discussion.

      (1) Include a full description of the model in the methods, so that the model remains reproducible even if the GitHub repo is deleted in the future.

      True, the code’s internal explanations could indeed be removed from GitHub later. The model component overview are now included in text.

      (2) Include the relevance of the model for flying insects in the discussion more prominently. This seems to be an implicit assumption in the model, as neural data from bees and, more prominently, from Drosophila are used to motivate the model to explain ant data.

      Add an “Expression in flying hymenopterans” section at ~line 834.

      Minor points:

      (1) Line 207: I suggest adding the recent review by Collett, Graham, and Heinze (2025, Current Biology), as it proposes interactions between LAL and CX as well.

      Added

      (2) Figure 4: I'm interested in the conversion from steps in the model to real units (ms) in the ants. In Figures 4F and G, it seems that 5 model steps represent circa 100ms. Does this allow us to define the neuronal time constants of the model neurons? If so, are the resulting values biologically plausible? This seems important when describing real-world dynamics being created by a model circuit.

      No the model is time agnostic.

      (3) Figure 7: Font sizes of axis labels are much too small. Also applies to other figures. Please ensure that when printed, labels can be read.

      Enlarged axis labels in all figures. 

      (4) Line 645: proprieties -> properties?

      Fixed. Thanks!

      (5) Figure 7: The figure heading states: "Slow forward speed (Myrmecia) example". This sounds as if real data from ants are shown here, while these are modeling data. It is clear after reading the text and caption in detail, but I was taken off course briefly here. Please make sure that there is no possibility of being misled here.

      We have altered the subtitle to “Slow forward speed (Myrmecia Model) example”. 

      Additionally, we have added a Model tag under each of the model image labels so classification can be done at a glance.

      (6) General discussion: What about search dynamics, i.e., increasing loops when not finding the nest entrance after homing? Are those emerging from this circuit as well? Or would that need to be a separate module? There have been discussions about search emerging from the PI circuit, but as far as I know, this is not settled, and it would be good to know if the current circuit adds something useful to this aspect.

      Because we kept a fixed goal heading, our model does not bring insight about overall trajectories such as search pattern. We now mention in the discussion:

      “In our simulations, the CX goal representation remained fixed in both direction and strength throughout each trial. This simplification allowed us to isolate and compare the effects of different CX strengths on scanning behaviour (Figure 6). However, goal headings in the CX are likely to be updated continuously, including during scans, by novel input from visual recognition in the MB (ref). This would in turn bias saccades direction and duration. Exploring such dynamics lies beyond the scope of the present study but would represent an interesting direction for future work. Notably, our proposed CX-LAL-Body relationship could be implemented downstream of an existing path integration or visual-based model (or both) to form predictions about the occurrence and dynamic of scans along the path, as well as their impact on the emerging trajectories.”

      (7) Line 690: The modulation of PFL3 by PFL2 was presented as a hypothesis in Westeinde et al., consistent with the data, but as far as I know, this is not an established fact.

      You are correct. We have now softened the text, which now reads: “In Drosophila, it has been proposed that PFL2 neurons, which respond maximally when the fly faces away from the goal, modulate steering gain by converging with PFL3 neurons (which drive left or right turns) onto downstream descending neurons (Westeinde et al., 2024).”

      (8) Please ensure that Drosophila is consistently spelled with a capital D and in italics.

      Fixed throughout the text.

      (9) Line 702: Reference Adden et al 2022: This reference is a modeling paper; it sounds as if you are referring to an experimental moth paper, though. Rephrase to clarify.

      You are correct, this could be unpacked much better regarding what is modelled and what has been experimentally shown. Changed to:

      Descending neurons in the LALs exhibit characteristic 'flip-flop' activity patterns that correlate with the zigzagging maneuvers of plume-tracking moths (Olberg, 1983; Kanzaki and Ikeda, 1994). Recent computational models suggest that CX output directly modulates these LAL circuits to coordinate orientation (Adden et al., 2022). 

      (10) Line 761: I would assume that during scans, information is acquired that would decrease uncertainty and thus, as a result change the amplitude of the CX steering signal. Maybe I missed this, but is this closed-loop interaction integrated in the model?

      In our simulation the CX goal representation remains stable in direction and strength throughout the trial. This enabled us to compare neatly the effect of different CX strengths on scanning. However, we fully agree with you that goal headings in the CX might well be continuously updated, both during scans and between scans! The goal heading novel strength or direction may thus bias the scan further left, right, in front or in the back, and also up or down regulate scan duration in both directions. 

      Modelling this would require adding a layer of complexity to determine how the goal heading is updated, which is beyond the scope of the current work, but would form a remarkable project for the future. We now mention this in a dedicated paragraph in the discussion section “Model limitations and future directions”

      (11) Line 814: Please add 'fly' in front of larva. Other insect larvae have a fully developed CX.

      Corrected. Added fly to this sentence 

      (12) Line 815: Maybe add the recent review, Heinze 2025.

      Added this one (Heinze 2024) which seems to fit the best and the 2025 Curr Biol Review doesn't quite fit this line (cited elsewhere though): 

      Heinze, S. (2024). Variations on an ancient theme—the central complex across insects. Current Opinion in Behavioral Sciences, 57, 101390.

      (13) Methods: Subheading formatting should start with capital letters.

      Ah yes, the second level of subheadings got formatted weirdly. Fixed now.

    1. Author response:

      We thank the reviewers for their enthusiasm for the work as well as for their thoughtful and constructive comments, which will lead to many improvements in the manuscript. We will address their concerns/suggestions in the following ways:

      Reviewer 1

      (1) We will revise text to help the reader more intuitively understand how dendritic asymmetry can translate into alterations in receptive field location, as well as provide a better description of the cited portions of the Methods section.

      Reviewer 2

      (1) The simulations in the current version of the manuscript modeled a transient response via a single synaptic conductance in part because one can better visualize the interplay between synaptic inputs and voltage-gated ion channels across both time and dendritic space. However, we agree that it is also important to show how our results are impacted during ongoing trains of synaptic activity exhibiting short-term depression as documented in the literature. We will add an additional figure showing simulations employing realistic statistical patterns of presynaptic excitatory and inhibitory inputs with appropriate short-term plasticity characteristics. These simulations are already complete and show that the increased complexity minimally alters the location of modeled ITD curves of the cell population over a wide range of frequencies (250 Hz – 2 kHz).

      (2) The reviewer’s suggestion of sequentially pruning the different orders of dendritic branches is an excellent one. However, removal of dendrites also alters overall whole cell resistance and capacitance as well as the cable properties of the remaining dendrites. It is thus impossible to disentangle the branch-specific effects of synapse location from changing intrinsic electrical properties. However, the reviewer has inspired us to address their suggestion in a slightly different way: we will add (via a new figure) simulations that take place in the same dendritic arbor, but with inputs restricted to progressively lower orders of dendritic branches. Thus, the relative contributions of synapses onto higher order dendritic branches can be visualized without fundamentally changing the electrotonic structure of the simulated neurons across the different conditions. These simulations will be performed under the “in vivo-like” conditions described in the previous point. We think they will effectively address the essence of the reviewer’s suggestion.

      (3) We will add more specific information about animal ages in relevant figures, including Supplementary Figure 1. We will also indicate that all physiological recordings were performed near physiological temperature (35°C), which was unintentionally omitted.

      Reviewer 3

      (1) We will add more detail about the anatomical assumptions regarding spatial input patterns vs. higher order dendrites. We do not think that VGluT staining with dendritic labeling will be a productive experiment, since the thin sections that provide high quality labeling conditions also preclude following single dendrites for long distances. The distal portions, which are of particular interest, are most difficult to follow because of their smaller diameter and more extensive branching out of the plane of thin sections. Further, the work of Callan and colleagues (2021) has addressed axonal input patterns as well as dendritic coverage, documenting that single axon inputs follow dendrites for variable distances, and typically provide multiple synaptic contacts. This work also highlights the many challenges and large effort involved in documenting synaptic innervation patterns in single cells at the light microscopic level. Thus, we do not think we can improve upon existing anatomical descriptions without excessively expanding the scope of an already long study, which will have 9 figures after revision.

      (2) We have analyzed many other measures of dendritic complexity but for reasons of clarity and focus included the two measures that appeared most intuitive and impactful (length and surface area). We agree that access to other measures would be useful even if some are less intuitive, and thus we will provide a more comprehensive analysis of dendritic structure in a supplementary figure.

      References:

      Callan, A. R., Heß, M., Felmy, F., & Leibold, C. (2021). Arrangement of Excitatory Synaptic Inputs on Dendrites of the Medial Superior Olive. The Journal of neuroscience, 41(2), 269–283. https://doi.org/10.1523/JNEUROSCI.1055-20.2020

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The central pair apparatus of motile cilia consists of two singlet microtubules, termed C1 and C2, each of which is associated with a set of projections, referred to as the C1 and C2 projections. Each projection comprises multiple distinct structural domains, designated a, b, c, and so on. Biochemical studies combined with genetic analyses in Chlamydomonas identified three proteins as the major components of the C2a projection, and subsequent cryo-EM studies confirmed these findings.

      In this paper, the authors aim to study the homologues of these three proteinsCCDC108/CFAP65, CFAP70, and MYCBPAP/CFAP147-using knockout mouse models. Biochemical and cell biological analyses demonstrate that, as in Chlamydomonas, these proteins are components of the C2 projection and form a complex that depends on the presence of each other. In addition, the authors use affinity purification to identify two previously uncharacterized proteins and show that they are central pair apparatus proteins that associate with the aforementioned complex. Knockout mice lacking any of the three core proteins exhibit phenotypes consistent with primary ciliary dyskinesia (PCD).

      Overall, the manuscript is clearly written, and the data are convincing and support the authors' conclusions. However, given the previous findings in Chlamydomonas, this work provides limited conceptual advances to the field. Nonetheless, it represents a useful and well-documented resource for understanding the conserved organization of the central pair apparatus in motile cilia. It will be of interest to cell and developmental biologists, biochemists, and clinicians studying and treating human ciliopathies.

      We sincerely appreciate the positive feedback on our work.

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigates the protein composition and functional role of the C2a projection of the central apparatus (CA) in vertebrate motile cilia. Using three knockout mouse models (Ccdc108, Mycbpap, and Cfap70), the authors demonstrate that these genes - homologs of Chlamydomonas FAP65, FAP147, and FAP70 - are required for normal motile cilia function in ependymal and tracheal multiciliated cells. Specifically, the authors show that:

      (1) Knockout mice for each gene exhibit primary ciliary dyskinesia phenotypes (hydrocephalus and sinusitis), accompanied by abnormal ciliary motion and reduced ciliary beat frequency.

      (2) CCDC108, MYCBPAP, and CFAP70 physically interact and localize to the axonemal central lumen, consistent with the C2a projection.

      (3) Loss of any one of these proteins destabilizes the others and disrupts CA integrity in a tissue-specific manner.

      (4) ARMC3 and MYCBP are C2a-associated proteins.

      Strengths:

      (1) Clarity: the results are presented in a coherent sequence that facilitates understanding of both the rationale and conclusions.

      (2) Genetic rigor: three independent knockout mouse lines that exhibit consistent motile cilia phenotypes provide in vivo support for the proposed role of these proteins.

      (3) Integration of structural and functional analyses: combination of ultrastructural (TEM) and immunofluorescence data with CBF measurements provides convincing correlation between structural defects and impaired ciliary function.

      (4) Mutual dependency model: reciprocal destabilization of CCDC108, MYCBPAP, and CFAP70 supports their interdependence in the C2a assembly.

      (5) Expansion of the vertebrate C2a proteome: the identification of ARMC3 and MYCBP as C2a-associated proteins provides a foundation for future mechanistic studies.

      We appreciate the valuable comments and pertinent suggestions, which provide important guidance for revising and improving this manuscript.

      Weaknesses:

      (1) Mechanistic depth: the data show a convincing correlation between C2a and ciliary function, but the cell type-specificity of CCDC108, MYCBPAP, and CFAP70 knockout effects is underdeveloped. This is an interesting observation that raises mechanistic/structural questions not addressed in the study, such as what is the role of C2a in CP nucleation, maintenance, or mechanical stabilization? Is C2a composition different in different cell types?

      We appreciate this comment. Based on current knowledge, loss of proteins essential for CP nucleation, such as WDR47 and KIF27, typically causes severe CP loss defects [1,2]. However, only mild CP-loss defects were observed in Ccdc108, Mycbpap, or Cfap70 knockout (KO) mouse ependymal cells (mEPCs) serum-starved for 10 days (Figure 2E, F), indicating that C2a proteins are more likely to play a role in CP maintenance or mechanical stabilization. In the revision, we tested this hypothesis by examining the effects of C2a loss on CA ultrastructure in Ccdc108 KO mEPCs serum-starved for 5 days. The percentage of axonemes with defective CA decreased further (Figure 2—figure supplement 1C, D). These results further confirm that C2a proteins play a role in CP maintenance or mechanical stabilization but not in CP nucleation. We have included these results and expanded the related discussion in the revised manuscript.

      To assess whether C2a composition differs across cell types, we performed co-immunoprecipitation using lysates from mouse trachea and mEPCs. We found that, in both tracheal and mEPC lysates, CFAP70, ARMC3, and MYCBP were co-immunoprecipitated with MYCBPAP (Figure 6—figure supplement 6A, B), indicating that at least the C2a core components are conserved in vertebrate motile ciliated cells. We have included these results in the revised manuscript.

      (2) Cell model choice: co-immunoprecipitation was performed using mouse testis lysates. While this is a reasonable source of CA proteins from flagellated cells, the functional analyses in this study focus on ependymal and tracheal multiciliated cells. It would therefore be helpful for the authors to clarify the extent to which these interactions are expected to be conserved across ciliated cell types, and to discuss potential tissue-specific differences in CA assembly.

      We thank the reviewer for the insightful suggestion. Following the reviewer’s suggestion, we performed co-immunoprecipitation using lysates from mouse trachea and mEPCs. We found that, in both tracheal and mEPC lysates, CFAP70, ARMC3, and MYCBP were coimmunoprecipitated with MYCBPAP (Figure 6—figure supplement 1A, B), indicating that at least the interactions among the C2a core components are conserved in vertebrate motile ciliated cells. We have included this result in the revised manuscript.

      (3) Statistical analysis: the manuscript states "Statistical significance was defined as P < 0.5", which is likely a typo, but should be P < 0.05. In general, the statistical methods require more clarification. In several figures (e.g., 2B, 2D, 5J, 5K), multiple knockout genotypes are compared with WT, yet unpaired t-tests are reported. When more than two groups are analyzed, multiple pairwise t-tests inflate Type I error unless appropriately corrected; a oneway ANOVA with post hoc comparisons (e.g., Dunnett's test for WT-referenced comparisons) would be more appropriate. Furthermore, the analysis of ciliary movement modes (Figure 2D) involves categorical data, for which a t-test is not statistically appropriate. These comparisons could instead be evaluated using chi-square or Fisher's exact tests. Addressing these issues is important to ensure accurate statistical inference.

      We thank the reviewer for identifying the error and for their suggestions on the statistical analysis. We performed a one-way ANOVA with Dunnett’s test in Prism to re-evaluate the differences between WT and each KO sample. In the revised manuscript, we have updated the statistical results and revised the Methods section.

      (4) Methods section: does not sufficiently describe how image-based quantifications were performed. For example, the criteria used to define cilia number, basal body number, and rotational beating are not specified, nor is how CBF measurements were analyzed. The authors should also provide details regarding analysis software and imaging parameters used (and whether they were kept constant across genotypes).

      We apologize for omitting a detailed description of image-based quantifications. For counting cilia or basal bodies, cells were immunostained with acetylated α-tubulin and CEP164 antibodies to label cilia and basal bodies, respectively, and imaged using 3D-SIM. Using these super-resolution images, cilia and basal bodies were counted in each multiciliated cell. With highspeed live-cell imaging, ciliary movements were recorded and analyzed using ImageJ. mEPCs in which the majority of motile cilia displayed rotational motility were considered ‘cells with rotational cilia’. The CBF of each cilium was calculated from the total time of 10 beating cycles. In the revised manuscript, we have included these details in the related figure legends and the methods section.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Line 121: "appeared decreased" should be revised to "appeared to decrease."

      We thank the reviewer for the suggestion. In the revised manuscript, we have changed the text accordingly.

      (2) Figure 2 legend: The statement "Arrowheads indicate the C2 projections" is misleading. The arrowheads indicate the positions of the C2 projections, as the C2 projections are absent at the locations marked by the arrowheads.

      We appreciate this comment and have revised the text in accordance with the reviewer’ s suggestion.

      (3) Statistical analysis: For the statistical analyses shown in Figure 2 and the other figures, a t-test was used. In general, a t-test is appropriate for comparisons between two groups. When more than two groups are compared with a single factor, a one-way ANOVA should be used, followed by appropriate post-hoc tests.

      We thank the reviewer for pointing out this issue. In the revised manuscript, we have re-evaluated all statistical analyses in Figures 2 and 5 using Dunnett’s test to compare multiple treatment groups (Ccdc108 KO, Mycbpap KO, and Cfap70 KO) with a single control group (WT). We have also revised the corresponding figure legend and methods section.

      (4) Docking methodology: In Figures 1A and 5L, the molecular model of the C2a projection (PDB: 7SOM) is superimposed onto the cryo-EM density map. I was unable to find a detailed description of the method used for this docking and would appreciate clarification.

      We apologize for omitting a detailed description of the docking methodology. The visualizations in Figures 1A and 5L were generated using the following procedure:

      (1) Generation of the Complete CA Density Map: Following the hierarchical local refinement strategy and map integration methods described in previous high-resolution studies of the Chlamydomonas central apparatus (CA) [3,4], we utilized the published density maps of the C2 microtubule and its associated projections (EMD-24191) and the C1 microtubule and its projections (EMD-24207). These maps were aligned and stitched together in UCSF ChimeraX to reconstruct a complete C1-C2 repeating unit of the central apparatus.

      (2) Superimposition and Fitting (Figure 1A): To generate the molecular model shown in Figure 1A, the atomic model of the Chlamydomonas C2a projection (PDB: 7SOM) was docked into the corresponding region of the integrated C2 density map [4]. The docking was performed as a rigidbody fit using the "Fit in Map" tool in UCSF ChimeraX, which optimizes the correlation between the molecular model and the cryo-EM density.

      (3) Simulation of C2a Loss (Figure 5L): For Figure 5L, we simulated the results of C2a loss observed in our mutation experiments. Using the model established for Figure 1A as a template, we selectively removed the C2a-specific density and the corresponding superimposed atomic model to schematically illustrate the structural consequences of the mutations involved in this study.

      We have updated the Methods section of the revised manuscript to include these details regarding structural visualization and docking analysis.

      Reviewer #2 (Recommendations for the authors):

      (1) Lines 106-107: "frameshift mutation was created by introducing a 458-bp deletion of exons 6-8 in the mouse 107 Cfap70 (ENSMUST00000056073.14) (Figure 1B)". The figure indicates deletion of exons 3-8; please indicate which is correct.

      We apologize for the oversight and confirm that the deletion region encompasses exons 3-8 (as shown in Figure 1B). In the revised manuscript, we have updated the text accordingly.

      (2) Lines 119-121: "Genotyping at postnatal day 0 (P0) revealed that Ccdc108 KO pups, Mycbpap KO pups, and Cfap70 KO pups were all born at the expected Mendelian ratios; however, the ratio of Mycbpap KO mice at P7 appeared decreased (Figure 1E)". The authors can test whether the genotype distribution changes between P0 and P7 to directly support their claim of postnatal lethality.

      We appreciate the reviewer’s comments. The P0 genotyping results were obtained from P0 neonatal mice sacrificed for mEPC culture. Therefore, the P0 and P7 genotyping distributions were from different batches of mice. Re-doing the genotyping distribution analysis would require a large number of mice and considerable time. We hope the reviewer understands the difficulty and allows us to forgo this experiment.

      References

      (1) Liu, H., Zheng, J., Zhu, L., Xie, L., Chen, Y., Zhang, Y., Zhang, W., Yin, Y., Peng, C., Zhou, J., et al. (2021). Wdr47, Camsaps, and Katanin cooperate to generate ciliary central microtubules. Nat Commun 12, 5796. 10.1038/s41467-021-26058-5.

      (2) Park, H., Choi, M., Zhang, Y., Cheung, H.O., Makino, S., Yoshikawa, Y., Qi, H., Liu, Z., Lan, G., Fu, G., et al. (2025). The kinesin-4 protein KIF27 forms a cytoskeletal scaffold at the transi\on zone to promote mo\le cilia structural integrity. Proc Natl Acad Sci U S A 122, e2515392122. 10.1073/pnas.2515392122.

      (3) Han, L., Rao, Q., Yang, R., Wang, Y., Chai, P., Xiong, Y., and Zhang, K. (2022). Cryo-EM structure of an ac\ve central apparatus. Nat Struct Mol Biol 29, 472-482. 10.1038/s41594022-00769-9.

      (4) Gui, M., Wang, X., Dutcher, S.K., Brown, A., and Zhang, R. (2022). Ciliary central apparatus structure reveals mechanisms of microtubule paderning. Nat Struct Mol Biol 29, 483-492. 10.1038/s41594-022-00770-2.

    1. Author response:

      Response to the eLife Assessment

      We thank the Editors and the Reviewers for their helpful suggestions, which will help us strengthen and test the key conclusions of this study of condensate dynamics at atomic resolution. In response to the Editors, we will make clearer in the Results and Discussion how the present work advances beyond our initial study of MUT-16 condensates, the scaffold of Mutator foci (Gaurav K et al., Biophys. J. 2025; 124:3987–4004). That study used a multiscale approach — residue-level (CALVADOS2) and near-atomic (Martini3) coarse-grained simulations together with in vitro experiments — to establish that the foci-forming region (FFR) phase separates whereas the adjacent MUT-8-binding region (M8BR) does not, and used atomistic simulations of that non-phase-separating region to dissect client–scaffold recognition. In this way the multi-scale simulations helped to provide a molecular basis for previous in vivo observations by Uebel et al. (PLOS Genet. 2018; 14(7):e1007542). That study did not, however, resolve with atomic resolution the interactions within the phase-separated FFR condensate itself. The present study addresses precisely this gap: from 10 µs of atomistic molecular dynamics of the FFR condensate, we characterise the sub-µs contact dynamics and the protein–ion and protein–water interactions that govern the condensed phase at atomistic resolution — observables inaccessible to the coarse-grained models used previously, but key to understanding the properties of Mutator foci and ultimately how they underpin biological function in small RNA biology.

      Reviewer 1:

      (1) I have several questions regarding the system preparation that require clarification. The authors state that "65 copies of the coarse-grained MUT-16 FFR were embedded in a slab-shaped simulation," but it is not clear how this initial configuration was generated. Were the molecules randomly distributed in the simulation box, or were they initially arranged in a preformed condensate? Alternatively, were they randomly inserted and allowed to self-assemble into a condensate during NpT simulations? In Figure 1, the atomistic snapshot appears to show a well-defined condensate at the center of the simulation box. It would be important to clarify how this configuration was obtained: Was it generated from coarse-grained simulations starting from random initial conditions? Or was a preassembled condensate used as input? Related to this, how do the authors ensure that the simulations are equilibrated? While 20 μs appears to be a reasonably long simulation time for coarse-grained simulations, it would be useful to demonstrate equilibration explicitly. For example, the authors could plot the center-of-mass positions (in the long axis of the simulation box) of individual proteins over time to show that all molecules reach a steady state and remain within the condensate without systematic drift.

      We thank the reviewer for these important clarifying questions regarding system preparation and equilibration.

      The initial structure for the atomistic simulation was generated by randomly inserting 65 copies of the coarse-grained MUT-16 FFR into a slab-shaped simulation box using the gmx insert-molecules tool. The molecules were therefore not pre-arranged in a condensate; instead, they were allowed to spontaneously self-assemble from this random configuration during NpT simulations using the Martini3-IDP force field over 20 μs. The well-defined condensate visible in Figure 1 is thus the product of this unbiased self-assembly process.

      To make this workflow transparent to the reader, we will revise Figure 1 to include a two-panel illustration of the Martini3 simulation: a snapshot at t = 0 ns showing the randomly distributed chains, and a snapshot at t = 20 μs showing the assembled condensate, connected by an arrow indicating the subsequent backmapping step to the atomistic representation. We believe this will clearly communicate the sequential nature of the pipeline (random insertion → coarse-grained self-assembly → atomistic backmapping).

      We appreciate the concrete suggestion for demonstrating equilibration. We will add a supplementary figure showing the center-of-mass positions of individual protein chains along the long axis of the simulation box as a function of simulation time. This will allow readers to verify that molecules converge into the condensate phase and reach a steady state without systematic drift, providing explicit evidence that 20 μs coarse-grained simulation time is sufficient for equilibration under these conditions.

      (2) The authors experimentally observe UCST behavior for these condensates. Do the coarse-grained or atomistic simulations reproduce this behavior?

      While atomistic simulations may be too computationally demanding to systematically explore temperature dependence, coarse-grained simulations could be used to test whether condensates are stable at lower temperatures and dissolve at higher temperatures. Such an analysis would provide valuable support for the experimental observations.

      We thank the reviewer for this valuable suggestion. In previous coarse-grained simulations we have used a coarse-grained force field that does not capture UCST vs LCST behavior (Gaurav K et al. Biophys. J. 2025; 124:3987–4004). It will be very interesting to revisit these coarse-grained simulations with a coarse-grained simulation force field that can capture UCST and LCST behavior such as the Mpipi-T (Chakravarti & Joseph, Protein Sci 2025;34(10):e70284) and HPS-T models (Dignon GL et al. ACS Cent. Sci. 2019; 5(5):821–830). We plan to perform additional coarse-grained simulations at multiple temperatures using the HPS-T force field. The HPS-T model has been shown to capture UCST versus LCST behavior (Changiarath A et al. bioRxiv 2024) in accordance with previous in vitro experiments. These simulations will allow us to test whether the MUT-16 FFR condensates remain stable at lower temperatures and dissolve at higher temperatures, providing direct computational support for the experimentally observed UCST behavior. We will include this analysis in the revised manuscript.

      (3) Regarding the analysis of ions, several points could be clarified and extended:

      a) It would be helpful to report the total number of ions and quantify how many are located inside vs. outside the condensate. While qualitative trends can be inferred from density profiles, quantitative analysis would strengthen the conclusions.

      b) It would also be interesting to analyze the number of contact ion pairs (e.g., Na⁺-Cl⁻ pairs), as described in J. Chem. Phys. 156, 044505 (2022). It is known that some ion models tend to overestimate ion pairing and underestimate solubility (e.g., J. Chem. Phys. 153, 010903 (2020)).

      c) In this context, the use of scaled-charge models has been shown to improve the description of ionic solutions and biomolecular systems (e.g., J. Phys. Chem. Lett. 2019, 10, 23, 7531-7536). I would suggest that, at least for one trajectory, the authors perform a test simulation using scaled charges (e.g., scaling by ~0.8) to evaluate whether ion distributions and protein-ion interactions are significantly affected.

      We thank the reviewer for these insightful suggestions regarding the ion analysis. We agree that a more quantitative treatment of ion behavior would strengthen the manuscript. To address all three points collectively, we will expand the existing Figure S7 with additional panels. These will include quantitative counts of Na<sup>+</sup> and Cl<sup>-</sup> ions partitioning inside versus outside the condensate complementing the existing density profiles, the Na<sup>+</sup>–Cl<sup>-</sup> radial distribution functions to estimate contact ion pair populations following J. Chem. Phys. 156, 044505 (2022).

      Following the Reviewer suggestion we will run a simulation with scaled charges (~0.8 scaling factor, J. Phys. Chem. Lett. 2019, 10(23):7531–7536) to evaluate the sensitivity of our results to the choice of ion model. We will compare ion distributions obtained with standard versus scaled charges . We will discuss the contact ion pair results in the context of known force field limitations regarding ion pairing (J. Chem. Phys. 153, 010903 (2020)) and assess whether the scaled-charge treatment leads to any qualitatively different conclusions.

      (4) Finally, while the selected water model is known to be accurate, it would be useful to assess its performance for concentrated salt solutions. For example, the authors could estimate the density of a 6 m salt solution and compare it with experimental data or validated models (e.g., J. Chem. Phys. 151, 134504 (2019)). This would help clarify to what extent the conclusions depend on the chosen force field.

      We thank the reviewer for this important suggestion. We agree that while the chosen water model is well established for biomolecular simulations, its performance under concentrated salt conditions is a legitimate concern that is worth explicitly validating in the context of this work. We will perform a short bulk simulation of a 6 m NaCl solution and compute the solution density, comparing it to experimental data (J. Chem. Phys. 151, 134504 (2019)). This straightforward validation will allow us to quantify how well our water and ion force field combination reproduces the thermodynamic properties of concentrated salt solutions, and to transparently discuss any deviations and their potential implications for the ion partitioning and protein–ion interaction results presented in the manuscript. The results will be added to the supplementary information alongside the expanded ion analysis in Figure S7.

      (5) In the Introduction, it would be helpful to elaborate further on the possible driving forces of LLPS in this region. Are there prior hypotheses or evidence pointing to specific interactions (e.g., cation-π, π-π, electrostatic interactions)? While this work addresses these questions, a brief discussion of previous experimental or theoretical insights would provide useful context.

      We thank the reviewer for this helpful suggestion. We will expand the Introduction to briefly discuss the known molecular driving forces of LLPS in IDR-containing proteins. Specifically, we will discuss the role of π–π interactions between aromatic residues (Vernon et al. eLife 2018; 7:e31486), cation–π interactions between aromatic and positively charged residues such as tyrosine–arginine pairs, which have been experimentally demonstrated to drive condensate formation in proteins such as FUS (Qamar et al. Cell 2018; 173:720–734), and the broader sequence-encoded molecular grammar governing these interactions in prion-like RNA-binding proteins (Wang et al. Cell 2018; 174:688–699, Rekhi et al. Nat Chem 2024 16:1113–1124 ). We will discuss previous findings on how ions shape interactions in condensates (MacAinsh et al. eLife 2024; 13:RP100282). We will also note the contribution of electrostatic interactions arising from charge patterning within the IDR, and contextualize how these general principles apply to the specific sequence composition of MUT-16 FFR, motivating the simulation-based investigation presented in this work.

      (6) On page 18, the authors state: "MUT-16 FFR satisfies the length (172 residues), aromatic content (20.35%), and Arg enrichment (85.71%) criteria. Its charge content (10.47%) and charge balance (38.89% positive charge fraction) are slightly below the nominal thresholds." It would be very helpful to include a schematic representation of the protein sequence highlighting these features (aromatic residues, charge distribution, etc.) in the corresponding figure, to provide a more intuitive understanding.

      We thank the reviewer for this helpful suggestion. We will include a figure showing a schematic representation of the MUT-16 FFR sequence, with aromatic residues, charged residues (positive and negative), and arginine content highlighted.

      (7) A question regarding ion hydration: What is the coordination environment of the ions that bridge proteins? Are they still hydrated by water molecules, or does the reduced water content inside the condensate significantly affect their solvation. Typically, Na<sup>+</sup> and Cl<sup>-</sup> ions have coordination numbers around 5-6 in aqueous solution. Do protein interactions and reduced solvent conditions within the condensate alter this coordination? A brief analysis or discussion would be valuable.

      We will calculate the coordination numbers of Na⁺ and Cl⁻ ions that mediate residue–residue bridging interactions inside the condensate and compare them against ions in the bulk dilute phase. This will directly reveal the degree to which bridging ions retain or lose their hydration shell when engaging with protein residues, and whether the condensate environment meaningfully perturbs ion solvation. The results will be presented as an additional figure in the Supplementary Information.

      Reviewer 2:

      (1) The large amount of detail in the results section sometimes makes it difficult to identify the central take-home messages. I encourage the authors to more clearly highlight the principal findings and the physical insights that may generalize to other condensate-forming systems. The authors may also consider streamlining parts of the Results section to improve focus and readability.

      We thank the reviewer for this constructive feedback. We will revise the Results section by adding brief concluding remarks at the end of each subsection that explicitly state the key physical insight emerging from that analysis. We will consider which secondary findings can be moved to the Supplementary Information. We will also strengthen the Conclusion section to more clearly distil the principal findings of the study as a whole and highlight the broader insights that may generalize to other condensate-forming systems, ensuring the central take-home messages are clearly communicated to the reader.

      Reviewer 3:

      (1) In its current form, several technical issues need to be addressed before the main conclusions can be considered robust. Most importantly, the simulated sequence is 172 residues long, while the atomistic slab has box dimensions of only 12 nm in two directions. This length scale is comparable to the expected end-to-end distances of a disordered 172-residue chain. It is therefore not clear whether individual protein chains interact with their own periodic images, which could substantially affect overall chain dynamics and subsequently bias contact lifetimes, residue-residue interaction statistics, and the inferred condensate dynamics. The authors should check, for each chain, histograms of end-to-end distances. For chains for which more than ~2-3% of the end-to-end distances exceed ~11 nm, the authors should explicitly check for self-image interactions (for example, using "gmx mindist -pi") and report whether such interactions occur and for what fraction of the trajectory. Without this control, at least in the Supporting Information, I do not think the simulation-derived contact dynamics are sufficiently trustworthy.

      We thank the reviewer for raising this important point. Indeed the box size in x and y dimensions is only marginal, which may influence the dynamics in our simulations and could affect our conclusions. In response, we will perform a control simulation with a larger box, increasing the x and y dimensions to ~16 nm. We will compare the contact dynamics of the resulting trajectory with our original results. This control simulation is initiated from an independently assembled coarse-grained condensate (see our response to Question 6) and therefore also addresses the replica-independence concern raised there.

      (2) A second major concern is the treatment of ions. The manuscript makes important conclusions about Na<sup>+</sup> association and Na<sup>+</sup>-mediated bridging, but the atomistic ion model is not explicitly stated. This is a reproducibility problem and also affects interpretation - for example, standard Amber ions are known to bind too strongly to the oppositely charged residues. In their results, one acidic residue appears to interact on average with roughly two Na⁺ ions, which is not obviously expected from charge balance alone. The authors should state the exact Na<sup>+</sup>/Cl<sup>-</sup> parameters used, justify their compatibility with TIP4P-D and the protein force field, and explicitly interpret why such a strong Na<sup>+</sup> association with acidic residues is observed.

      We thank the reviewer for raising this important point. We will explicitly state in the Methods section how the Na<sup>+</sup> and Cl<sup>-</sup> ions, including the force field parameters of the ions, were modelled in our setup, and discuss its compatibility with TIP4P-D and the protein force field. In the presented simulations we have used the Joung and Cheatham parameters (Joung et al, J. Phys. Chem. B 2008, 112 (30), 9020–9041) with σ = 0.243934 nm and ε = 0.365846 (kJ mol<sup>-1</sup>) for Na<sup>+</sup> and σ = 0.447766 nm and ε = 0.148913 (kJ mol<sup>-1</sup>) for Cl<sup>-</sup>. While similar setups have been used, these ion parameters have not been optimized for TIP4P-D (originally developed for TIP3P water) and thus a lack of compatibility of the parameters could affect our conclusions.

      In response to the Reviewer and also in response to Reviewer 1 (Question 3), we will perform a sensitivity check by running an additional molecular dynamics simulation with scaled ion parameters as suggested by Reviewer 1 ( J. Phys. Chem. Lett. 2019, 10, 23, 7531-7536). In this way we will assess to what extent the degree of Na<sup>+</sup> association with acidic residues is sensitive to the choice of ion parameters and discuss the implications for our conclusions regarding Na⁺-mediated bridging interactions.

      (3) More generally, because the manuscript is centered on contact lifetimes, the choice of the atomistic force field needs stronger justification. Salt bridges, cation-pi contacts, pi-pi stacking, ion coordination, and water-mediated interactions are all force-field-sensitive. Since there is no direct experimental observable used here to validate the simulations, the authors should discuss the expected limitations of the chosen force field (while I do acknowledge that testing different force fields would be computationally too demanding).

      We thank the reviewer for this fair comment. We will add a short discussion justifying the choice of both TIP4P-D and Amber99sb-star-ILDN-q force field, discussing their performance for disordered proteins. We will explicitly acknowledge that absolute contact lifetime values should be interpreted with caution given the inherent force field sensitivities of salt bridges, cation-π, and π-π interactions, while relative trends and qualitative insights are expected to be more robust. We believe this transparent discussion will strengthen the manuscript and place our findings in the appropriate context for the reader.

      (4) I also find the sequence-comparison section somewhat confusing. The authors compare one specific IDR, MUT-16 FFR, with the average properties of human IDRs and then frame it as more representative than FUS LCD. It is not clear how informative this is because IDR behavior depends strongly on sequence-specific patterning, molecular connectivity, and the particular interaction network of each protein. Averages over human IDRs may provide a broad context, but they do not necessarily define what is physically or biologically representative for phase separation. In addition, FUS LCD is not intended to be a representative human IDR; it is an unusually low-complexity, phase-separating domain. Therefore, the "more representative than FUS" framing should be toned down. At most, this analysis shows that MUT-16 FFR is compositionally less extreme than FUS LCD.

      We thank the reviewer for this valid criticism. We agree that the framing of MUT-16 FFR as "more representative than FUS LCD" is an overstatement, and we will revise the text accordingly. The comparison against human IDR averages was intended to provide broad compositional context rather than make claims about functional or dynamical representativeness, and we will make this distinction explicit. We will reframe the statement to simply note that MUT-16 FFR is compositionally less extreme than FUS LCD, without implying broader representativeness, which as the reviewer correctly points out cannot be inferred from sequence composition alone given the strong dependence of IDR behavior on sequence-specific patterning and interaction networks.

      (5) The ion- and water-bridging analyses are also potentially overinterpreted. A distance-based simultaneous contact with two residues does not by itself establish functional mediation or regulation of condensate dynamics. The authors should either add appropriate controls, such as local-density-normalized baselines or randomized-contact expectations, or soften the language to describe these as geometrically defined co-contact events rather than mechanistic bridging interactions.

      We thank the reviewer for this valid point. We agree that distance-based co-contact events do not by themselves establish mechanistic bridging or functional regulation, and we will revise the manuscript language throughout to describe these observations as geometrically defined co-contact events rather than mechanistic bridging interactions. We will also explore appropriate controls such as local-density normalized baselines or randomized-contact expectations. In this respect we will also consider our results in light of a recent paper that showed that salt-bridges are overestimated in atomistic molecular dynamics simulations (Ivanović et al, JACS Au 2026, 6(3), 1900–1913). We will ensure the interpretation is appropriately cautious and does not overstate the mechanistic implications of these findings.

      (6) Finally, the independence of the atomistic replicas is unclear. The manuscript should state whether all ten all-atom simulations were initiated from the same coarse-grained condensate configuration or from distinct CG frames. If the starting structures came from one CG trajectory, the authors should report how far apart those frames were in simulation time and provide evidence that the initial atomistic configurations are structurally independent. If only velocities differ, the simulations should not be described as fully independent structural replicas.

      We thank the reviewer for this important clarification request. We confirm that all ten atomistic replicas were initiated from the same coarse-grained condensate configuration following backmapping, but were equilibrated independently using different random velocity seeds. Only the last 800 ns of each trajectory was used for analysis, discarding the initial 200 ns as equilibration. We will add these details explicitly to the Methods section and make clearer that these simulations are not fully independent structural replicas. We will report the overlap of residue–residue contact maps between replicas to provide an indication of how the contact statistics have decorrelated, given the shared starting structure.

      In response to this question and also question 1, we are initiating an all-atom simulation from an independently formed CG condensate (16 nm x 16 nm x 60 nm). This will provide a valuable check as to the conclusions from our ten initial simulation trajectories.

      References

      Blazquez S, Conde MM, Abascal JLF, Vega C. J. Chem. Phys. 2022;156(4):044505.

      Chakravarti A, Joseph JA. Protein Sci. 2025;34(10):e70284.

      Changiarath A, Flores-Solis D, Michels JJ, Herrera Rodriguez R, Hanson SM, Schmid F, Zweckstetter M, Padeken J, Stelzl LS. bioRxiv. 2024. doi:10.1101/2024.03.16.585180.

      Dignon GL, Zheng W, Kim YC, Mittal J. ACS Cent. Sci. 2019;5(5):821–830.

      Gaurav K, Busetto V, Páez-Moscoso DJ, Changiarath A, Hanson SM, Falk S, Ketting RF, Stelzl LS. Biophys. J. 2025;124:3987–4004.

      Ivanović MT, Holla A, Nüesch MF, von Roten V, Schuler B, Best RB. JACS Au. 2026;6(3):1900–1913.

      Joung IS, Cheatham TE III. J. Phys. Chem. B. 2008;112(30):9020–9041.

      Kirby BJ, Jungwirth P. J. Phys. Chem. Lett. 2019;10(23):7531–7536.

      MacAinsh M, Dey S, Zhou HX. eLife. 2024;13:RP100282.

      Panagiotopoulos AZ. J. Chem. Phys. 2020;153(1):010903.

      Qamar S, et al. Cell. 2018;173:720–734.

      Rekhi S, Garcia CG, Barai M, Rizuan A, Schuster BS, Kiick KL, Mittal J. Nat. Chem. 2024;16:1113–1124.

      Uebel CJ, Anderson DC, Mandarino LM, Manage KI, Aynaszyan S, et al. PLOS Genet. 2018;14(7):e1007542.

      Vernon RM, Chong PA, Tsang B, Kim TH, Bah A, Farber P, Lin H, Forman-Kay JD. eLife. 2018;7:e31486.

      Wang J, et al. Cell. 2018;174:688–699.

      Zeron IM, Abascal JLF, Vega C. J. Chem. Phys. 2019;151:134504.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors investigated the relationship between physical activity (PA) and both structural (MRI) and cognitive brain health in the LIFE-Adult Study, with total baseline recruitment of 2576. Hippocampal volume, an MRI-derived BrainAGE marker, and scores from the Trail Making Test were used as outcomes, with the majority of participants measured at baseline and subsets also measured in a follow-up session. The key findings were a lack of direct association between PA and outcomes, but longitudinal evidence for a higher BrainAge at baseline leading to lower physical capacity at follow-up. This supports a reverse-causation hypothesis in contrast to the prevailing understanding of the positive effects of physical activity on brain health.

      Strengths:

      The Life-Adult study is a rich and carefully acquired dataset, with multiple follow-up time points. The statistical analyses were conducted carefully with appropriate control for confounds and multiple testing. The study design enables an important assessment for reverse causality. The authors are scrupulous in their consideration of a number of factors that could potentially bias their results, performing an age-stratified analysis, and emphasising discrepancies in PA measurements (specifically, age-reporting bias) across the dataset and other limitations.

      Weaknesses:

      This is an observational study with inconsistent measures of physical activity. Previous studies have used physical activity interventions, and might be more strongly weighted when considering evidence for these effects (specific confounders involved in interventions notwithstanding).

      The model identifying potential reverse causality is relatively limited - it seems possible/likely that brainAge could reflect more general health status, which would expand the potential range of factors underlying this observation.

      The important quantitative actigraphy subset is small (n=227), as are the longitudinal subsets. Along with the discrepancy of physical activity/capacity at baseline and follow-up, and other complexities of the dataset, it is difficult to make firm conclusions. The authors point out that the actigraphy subset was quite inactive.

      We would like to thank the reviewer for their valuable feedback. We agree with the limitations mentioned, and we have extended the discussion section in order to address the drawbacks more effectively. In particular, we agree that the null findings of this study do not suggest that physical activity has no effect on the brain; for such a conclusion, an intervention study would be necessary.

      Furthermore, we agree that BrainAGE might reflect a more general health status. Although we excluded images of individuals with visible acquired brain injuries, we did not control for other medical conditions (e.g. hypertension or diabetes), which may have affected the results.

      Please see the revised discussion parts in the response below.

      Reviewer #2 (Public review):

      Summary:

      This population-based cohort study found no evidence that physical activity, whether self-reported or objectively measured, positively influenced brain structure (hippocampal volume or BrainAGE) or cognitive function (Trail Making Test scores). Notably, longitudinal analyses suggested the opposite temporal relationship: a higher BrainAGE at baseline predicted higher physical capacity at follow-up, more in line with reverse causation rather than a neuroprotective effect of physical activity.

      Strengths:

      The study's statistical approach is thorough and well-documented, and the inclusion of two measurements of physical activity (self-report questionnaire and objective accelerometer data) is a strength. The longitudinal aspect also represents a strength.

      Weaknesses:

      Several aspects of the measurement timing warrant consideration. Physical activity was assessed over 7-day periods, creating a potential mismatch with (commonly less dynamic) brain outcomes examined (hippocampal volume, BrainAGE), which may reflect cumulative exposures over longer timescales. Additionally, the asynchronous measurement protocol (cognitive testing preceding accelerometry, and the MRI occurring weeks after baseline visits) may introduce time lags that attenuate associations. The observed null associations may be influenced by timing misalignment rather than reflecting the absence of consistent effects of physical activity on brain health and cognition.

      Other measurement characteristics also warrant consideration when interpreting the null findings. Physical activity was assessed using short-form self-report questionnaires and averaged accelerometer MET/day values, both of which have limited reliability. Additionally, the modest accelerometer subsample size and low/insufficient variation in activity levels observed in this cohort increase the likelihood of missing effects. These factors collectively raise the possibility that true physical activity-brain health associations may have been obscured.

      The study's conclusions regarding brain health, structure, and cognitive functioning are broad despite the scope of the selection of outcomes examined. The analyses focus on hippocampal volume, BrainAGE (a global aging metric), and Trail Making Test performance (processing speed and executive function), while omitting other important neuroimaging markers such as cortical thickness, functional connectivity, or white matter microstructure. The null findings presented here cannot exclude positive effects of physical activity on broader constructs of brain health or cognitive functioning.

      While the authors appropriately note the use of different physical activity instruments across time points (IPAQ at baseline, VSAQ at follow-up) in the limitations section, the discussion should more explicitly address the interpretive challenges this creates. The observed association between higher baseline brain age gap and lower follow-up physical activity may reflect: (1) a true temporal relationship, (2) an artifact of switching from behavior-focused (IPAQ) to capacity-focused (VSAQ) measurement, or (3) some combination of both. This ambiguity substantially limits causal inference.

      Thank you for a thorough review of the manuscript. We appreciate the opportunity to consider the limitations in more detail. As you highlight, the null findings could be caused by a variety of reasons and changes may have occurred in white matter microstructure or functional connectivity that could not be observed using our chosen measures. We have expanded the discussion to address these and other issues (p. 12):

      “However, our results should be interpreted with caution, due to the limited sample size, potential attenuation of effects resulting from measurement error in the assessment of physical activity/capacity and the shift from an activity-based measure at baseline to a capacity-based measure at follow-up. This change limits the interpretability of longitudinal effects, as observed associations may reflect both changes in the underlying construct being measured and true changes in the relationship over time.

      Strengths and Limitations

      The results of this cross-sectional observational study may be affected by various factors, including bias in self-reported physical activity [48, 49], accelerometer measurement error [59, 60] and reverse causality, among others. Moreover, our results may also be affected by the general medical status of the participants, since we did not control for other diseases within the sample. In fact, BrainAGE may reflect overall health and the cumulative impact of various factors (including previous physical activity) on brain health over an extended period of time. Furthermore, our analysis focused on only a few cognitive and structural brain measures. While we did not observe any changes in hippocampal volume or BrainAGE, this does not exclude the possibility of changes in white matter integrity or functional connectivity. Another limitation of this observational study was the time lag between physical activity measurements and MRI scanning, which may have reduced the observed effects. Although the longitudinal design is a major strength of this study, attrition of participants at follow-up may have affected our estimates. Furthermore, the use of cross-lagged panel model design in the longitudinal setting has frequently been criticised for not distinguishing between within-person changes and between-person differences [61, 62], and our adapted design suffers from these limitations, as well as others arising from the use of different instruments to measure the construct related to physical activity at each time point (IPAQ and VSAQ). Nevertheless, compared to large volunteer-based cohorts such as the UK Biobank, the registry-based recruitment strategy of the LIFE-Adult Study may be less susceptible to healthy volunteer bias, although we cannot entirely eliminate the possibility of volunteer bias among the participants with accelerometry data in our case.

      Direct comparisons are limited in the absence of harmonised recruitment and assessment protocols.”

      Additionally, please note that in the Summary sentence ‘Notably, longitudinal analyses suggested the opposite temporal relationship: a higher BrainAGE at baseline predicted higher physical capacity at follow-up, more in line with reverse causation rather than a neuroprotective effect of physical activity’

      The opposite is actually true; higher BrainAGE at baseline predicted lower physical capacity at follow-up.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The analysis and discussion are somewhat limited. More detail and discussion of the demographic features of the study dataset, and perhaps a stronger concluding position regarding the potential impacts of PA on brain and cognition would be helpful - this might also be integrated into the abstract.

      Thank you for pointing this out. As both of the reviewers have highlighted that the discussion is limited, we appreciate the opportunity to revise it (see also the response above). We hope that it now gives a more comprehensive interpretation of the results.

      We have also updated our abstract to include a bit stronger concluding position:

      “Physical activity is believed to positively influence brain health and cognition and is considered a modifiable lifestyle factor that may protect against cognitive decline and neurodegeneration. In this observational study, we investigated the cross-sectional and longitudinal effects of self-reported total and moderate-to-vigorous physical activity on cognitive scores on the Trail Making Test (TMT-A and TMT-B), hippocampal volume, and BrainAGE, in a large population-based cohort from the LIFE-Adult Study (n = 2576). Furthermore, we examined the effect of objectively measured physical activity on brain structure in a subgroup with available accelerometry data (n = 227). Multiple linear regression analyses did not show any positive effects of self-reported or objectively measured physical activity on hippocampal volume or processing speed and executive function. Longitudinal path analyses suggested a potential for reverse causation, where a higher BrainAGE at baseline was associated with lower physical capacity at follow-up. Additionally, we observed an age-related bias in the self-reporting of physical activity, indicating that older individuals tend to overestimate their level of activity. Future interventions targeting middle-aged adults may be necessary to raise awareness of potential misperception and encourage increased physical activity.”

      There might be more careful inspection of alternative models and dissection of the impact of covariates (e.g. smoking, which is very prevalent in this cohort). For example, did PA show any benefit specifically in the "non-smoker" vs. "smoker" subgroups?

      Thank you for this suggestion. We decided against including analysis of various subgroups, as this would have shifted the focus of the manuscript. However, we do provide the results of the analysis with the interaction term here. There was no evidence that smoking status moderated the association between self-reported physical activity and BrainAGE at follow-up (p = .192). In both non-smokers and smokers, physical activity was not significantly associated with BrainAGE at follow-up (b = 0.038, SE = 0.033, p = .242 and b = −0.028, SE = 0.038, p = .471, respectively).

      The age-dependent reporting bias seems important and should be assessed and discussed in more detail - it could have important implications for other studies. Why might this occur?

      We appreciate your drawing more attention to this point. As you have mentioned, it can have important implications for other studies, suggesting that objective measures of activity should, if possible, be used alongside self-report questionnaires. We have expanded on this topic in more detail in the revised discussion (p. 11):

      “This age-dependent reporting bias was previously demonstrated by other studies, where higher age was associated with overreporting activity levels [51-54]. Overreporting could stem from worsening recall, socially desirable responses, and the subjective nature of self-report questionnaires, which also depend on a person’s physical fitness [51]. Future (observational) studies would greatly benefit from including both accelerometer and self-reported measures of physical activity.”

      The reverse causation result could also be discussed (and possibly analysed) in more detail - what might the neurobiological mechanisms underlying this be? Is general health a factor - were confounds like smoking/health assessed here?

      Thank you for raising this important point. We have not added confounds other than age here, as we did not have enough degrees of freedom to add additional parameters to the model. However, we agree with you that general health might have played an important role here, although we don’t have a specific measure for it. We have expanded upon these limitations in the revised discussion (p. 12):

      “Similarly to Hofman et al. [62] and Rodriguez-Ayllon et al. [63], who found a bidirectional association between physical activity and brain structure, with a more consistent pattern of brain structural measures affecting physical activity, the results of our path analysis partially supported the reverse causality explanation, indicating that baseline brain health influences follow-up physical capacity, rather than baseline physical activity affecting follow-up brain health. Possible mechanisms may involve decreasing health status with age-related mitochondrial dysfunction [64, 65] and potential low-grade inflammation, which could result in fatigue [66] and a possible decline in fitness and physical capacity. Further studies are necessary to investigate this in more detail.”

      Results should contain greater detail; in particular, they should summarise key results from tables and not rely on the reader to carefully look through all figures. Reporting relatively non-informative results (e.g. entirely unadjusted model results) does not add much.

      We appreciate your feedback. We have tried to summarise the results in greater detail, reporting statistical values within the text (e.g., main results, p. 7):

      “The results indicate no statistically significant effects of self-reported total PA on brain structure (β = -0.029, p = .137 and β = 0.035, p = .137 for hippocampal volume and BrainAGE, respectively). There is a statistically significant effect of total self-reported PA on cognitive function, indicating that higher levels of PA lead to higher time scores on TMT-B (β = 0.053, p = .042). Similar results can be observed for MVPA, however, the results do not survive the correction for multiple comparisons (β = 0.045, p = .072). The analysis of objectively measured PA indicated no statistically significant effects on brain structure (β = -0.036, p = .582 and β = -0.076, p = .393 for hippocampal volume and BrainAGE, respectively).”

      We report the results of the unadjusted model to provide greater transparency, in line with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines.

      Reviewer #2 (Recommendations for the authors):

      Please review the manuscript for consistent use of abbreviations and definitions (e.g., write out BDNF line 49). Specifically, definitions and language to describe BrainAGE, brain age, brain age gap, neuroimaging-derived biomarker of brain ageing, Brain Age Gap Estimate, BA, BrainAGE (BA), etc. would benefit from consistency.

      Thank you very much for this observation. We have revised the manuscript in the hope that it is now more consistent. Specifically, we spelled out the ‘brain-derived neurotrophic factor’ and replaced the abbreviation 'BA' in Figure 2 with BrainAGE. However, we acknowledge that there are already many naming inconsistencies within the field. We therefore tried to follow the different authors' notations, which were established within the field: we used 'brain age gap' when referring to James Cole's model (or the concept in general), and 'BrainAGE' for our own.

      We thank both reviewers for their helpful feedback, which has improved our manuscript.

    1. Author response:

      We thank the reviewers for their careful and constructive assessment. We are glad they found the theory well motivated, that they recognised it unifies the previously unexplained center–surround suppression and facilitation in MT, and that they appreciated the methodological innovation in mapping ideal-observer predictions onto neural responses. We will make the manuscript more self-contained and mathematically explicit.

      To clarify our central claim and the connection to neural data: Our model can account for both what people perceive and what neurons do. Specifically, we take a Bayesian causal-inference model that was built and fitted to human behaviour (Shivkumar et al., 2025), and use it to derive neural predictions for center–surround interactions in area MT during motion perception. We then compare these predictions to previously reported MT single-neuron responses – qualitatively, but without any further parameter fitting.

      The reviewers are correct that there are two types of latent variables in our model, which imply two different sets of neural predictions. While one might conjecture relationships to other neural properties like classic center-surround suppression, a separate determination of which latent variable a neuron corresponds to is a simple matter of model comparison after fitting its responses to both. If the responses of a recorded neuron correspond to one of these predictions (as many existing neurons appear to do as we show in our paper), then this constitutes evidence in favor of them representing the corresponding posterior in our model. On the other hand, if they do not, then this can be due to a number of factors: our generative model being wrong, the neural encoding assumption (sampling or LDC) being wrong, or the Bayesian brain hypothesis being wrong (also see Lengyel et al. 2023; Haefner et al. 2024).

      Furthermore, we’d like to also clarify that both types of latents support each of the perceptual states (including integration and segmentation) and that there is no 1-1 correspondence between them. Importantly, the related velocity latent represents the velocity in the inferred reference frame – which may be the surround, or the retinal, or an intermediate reference frame (see Fig. 5 in Shivkumar et al. 2025). As a result, the same neuron can show both suppressive and facilitatory effects (yellow and blue regions in the difference panels in Fig. 6 of our paper).

      Finally, while specifying both the likelihood and the prior constitutes our model definition, we have made reasonable assumptions about the shape of each. The physics of the world — for instance, that objects tend to be stationary or to move slowly — motivates a spike-and-slab prior (Knill & Richards, 1996), and the likelihood is well described by a unimodal form (Stocker & Simoncelli, 2006). Our qualitative predictions do not depend on the exact specification of the prior and likelihood; other unimodal likelihoods yield similar results.

      We will make corresponding edits throughout the text to clarify each of these points.

      References:

      Haefner, R. M., Beck, J., Savin, C., Salmasi, M., & Pitkow, X. (2024). How does the brain compute with probabilities? arXiv.

      Knill, D. C., & Richards, W. (Eds.). (1996). Perception as Bayesian inference. Cambridge University Press.

      Lengyel, G., Shivkumar, S., & Haefner, R. M. (2024). A general method for testing Bayesian models using neural data. In Proceedings of UniReps: The First Workshop on Unifying Representations in Neural Models (Proceedings of Machine Learning Research, Vol. 243).

      Shivkumar, S., DeAngelis, G. C., & Haefner, R. M. (2025). Hierarchical motion perception as causal inference. Nature Communications, 16, Article 3868.

      Stocker, A. A., & Simoncelli, E. P. (2006). Noise characteristics and prior expectations in human visual speed perception. Nature Neuroscience, 9(4), 578–585.

    1. Author response:

      We would like to express our sincere gratitude for your time and constructive feedback. We are highly encouraged by the positive assessment highlighting the solid evidence and convincing methods of our study. We also deeply value the insightful and constructive comments regarding our conceptual framing, the integration with established ecological theories, and the underlying dynamic mechanisms. We believe that incorporating these excellent suggestions will substantially enhance the conceptual clarity and theoretical depth of our manuscript. To achieve this, we are fully committed to conducting a comprehensive revision to address all the points raised. Below, we outline our main strategies for the forthcoming revision:

      (1) Structural Reorganization

      We fully agree with the reviewers and the Editor that the manuscript's structure requires improvement. We are especially grateful to Reviewer 1 for providing such a detailed and constructive roadmap for the revision. We will adopt all of the suggested changes. Specifically, in the revised manuscript, we will:

      (1.1) Rewrite the Abstract: provide a clearer introduction to the "Tragedy of the Commons" and a more accessible description of our modeling framework.

      (1.2) Establish a dedicated Methods section: move the core model equations, key assumptions, parameter choices, and the detailed explanation of our graph-theoretic framework (the Benefit Transfer Graph) from the Supplementary Information (SI) into the main text.

      (1.3) Restructure results and figures: We will reorganize the Results section to improve the logical flow. As suggested, we will split the current Figure 2, move critical diagrams from the SI into the main text, and expand our figure captions to ensure all data representations are immediately clear.

      (2) Reframing the Conceptual Framework and Terminology

      We thank Reviewer 1 for the insightful critique regarding the use of the term “cheating.” We have reflected on our previous phrasing and fully agree that "cheating" introduces an unnecessarily humanized judgment and conflates pure exploitation with metabolic generalism. To ensure mechanistic accuracy and alignment with recent ecological literature, we will systematically update our terminology throughout the text, from title to supplement:

      (2.1) Species strategies: "Pure-producers," "partial-producers," and "pure-cheaters" will be redefined as "single-receptor producers," "multi-receptor producers," and "non-producers," respectively.

      (2.2) Receptor types: "Cheating-receptors" will be renamed to "exogenous-receptors" (or foreign-receptors, exploitative-receptors) to objectively describe the uptake of siderophore types that are not produced by the focal microbe.

      (2.3) Updating the key parameter: To avoid ambiguity regarding synthesis versus uptake, we will rename "Cheating Breadth (CB)" to "Siderophore Exploitative Breadth (SEB)," defined strictly as the number of distinct exogenous-receptors expressed by a species.

      (2.3) Updating the core paradigm: We will reframe "The Paradox of Cheating" to "The Paradox of Siderophore Exploitation." We will clarify that the transition to high-diversity coexistence is not driven by "cheating", but by the topological connectivity of the mBTG.

      (3) Contextualizing within BQH and Hypercycles

      We sincerely thank the Editor and Reviewer 2 for highlighting the connections between our work, the Black Queen Hypothesis (BQH), and Hypercycle theory. We will dedicate a new section in the Discussion to thoroughly compare our siderophore-mediated network with these established frameworks.

      We will explicitly discuss the key similarities and differences. While the exploitation of siderophores in our model resembles the producer-beneficiary dependency described in BQH, the evolutionary drivers are distinct, in that BQH is primarily driven by the adaptive loss of costly genes (reductive evolution), whereas siderophore exploitation is driven by the acquisition of exogenous-receptors (e.g., via horizontal gene transfer). More importantly, the high diversity and lock-and-key specificity of siderophore-receptor interactions, renders each siderophore a "mixed good." This dynamic can actually drive the community into a Red Queen-like arms race, as suggested by the high probability of oscillatory dynamics observed in our simulations. Although we did not explicitly consider genetic mutations in the current ecological framework, unidirectional exploitation typically drives the involved species to extinction; consequently, the system naturally selects for communities where exploitation is reciprocated, organically giving rise to closed, distributed loops of benefit transfer.

      In the revised text, we will cite recent theoretical progress on structured and multi-goods BQH networks. We will also discuss how our topological loops link to Eigen's Hypercycle theory by illustrating how specific structures of exploitative interactions foster community diversity.

      (4) Addressing Siderophore Exploitative Breadth (SEB) Interpretations

      (4.1) The biological realism of the SEB range

      Both reviewers raised insightful questions regarding the settings and impacts of SEB (previously "CB"). While some of these questions will be addressed through new control simulations, we would like to immediately clarify the biological realism of the SEB parameter, particularly addressing Reviewer 1's concern about the simultaneous expression of multiple receptors.

      We completely agree that possessing a vast genomic repertoire of siderophore receptors does not mean a microbe expresses all of them simultaneously. Receptor expression in nature is a highly regulated and substrate-specific process. In Gram-negative bacteria like Pseudomonas, the expression of exogenous-receptors is tightly regulated by cell-surface signaling pathways (e.g., ECF sigma/anti-sigma factor systems). Under iron-limited conditions, a specific receptor is upregulated only when it detects its corresponding siderophore in the environment. Based on our literature review, while a bacterium may not express 30 receptors at once, expressing a substantial subset (e.g., 5–15) is biologically realistic. Therefore, in our model, SEB does not represent a static genomic capacity, but rather the number of active receptors that actually have corresponding siderophore producers present within the local community. We extended the SEB axis up to 30 in our initial figures primarily to capture the complete theoretical phase transition. However, following the reviewer's excellent suggestion, we will adjust the x-axis in our primary revised figures to highlight the more realistic regime (e.g., SEB 0–15) and add a dedicated paragraph detailing these biological regulatory mechanisms, with appropriate citations.

      (4.2) Disentangling the receptor allocation trade-off

      We highly appreciate Reviewer 2’s perceptive insight regarding the confounding effect: under a normalized allocation scheme, increasing SEB inevitably decreases the expression level of the self-receptor, thereby reducing self-reliance. We completely agree that explicitly addressing this trade-off is crucial.

      Biologically, this strong trade-off is realistic: receptor operations are energetically costly, and the initiation of their expression requires competing for a finite pool of RNA polymerase core enzymes. Therefore, investing in the capacity to exploit heterologous siderophores inherently incurs a cost to self-reliance. To rigorously test whether our central paradox is merely an artifact of this specific trade-off, we immediately initiated a series of control simulations. In these new models, we mathematically decoupled the variables by fixing the allocation fraction of the self-receptor as a constant.

      We are encouraged to report that our preliminary results support the core of the original paradox. Even when self-reliance is mathematically maintained, community-level extinction risk and the biodiversity of surviving communities remain positively linked. Interestingly, these controlled simulations exhibit an even clearer non-monotonic pattern, where both diversity and extinction risk peak at a biologically realistic SEB of approximately 5. This suggests that the paradox is fundamentally driven by network topology changes rather than the allocation trade-off alone:Viewed through our maximal Benefit Transfer Graph (mBTG) framework, a higher probability of non-self-directed edges in the mBTG forces the community to "gamble" between collapsing into a Sink Core or surviving in a high-diversity Cyclic Core. We are currently performing exhaustive simulations to gather detailed statistics on this decoupled model, particularly the non-monotonic behavior, which will be prominently featured in the revised manuscript.

      (5) Evolutionary Stability and Topological Resilience

      We also deeply appreciate Reviewer 2’s insightful critique regarding the evolutionary stability of our proposed cyclic networks, particularly their potential vulnerability to self-serving or short-circuit mutants that bypass intermediate species in a loop.

      To rigorously address this, we are currently conducting invasion simulations in which established communities are challenged by randomly generated mutant species. While the exhaustive computational analysis is ongoing, our preliminary results suggest the absence of a strict, static Evolutionarily Stable Strategy (ESS). Instead, the topological space fosters complex, intransitive competition. Intriguingly, these early data suggest that communities exhibiting oscillatory dynamics are actually more robust against invaders than those at a stable equilibrium. We intend to explore this phenomenon fully.

      Furthermore, we will expand our Discussion to address the implications of longer evolutionary timescales. When true structural mutations occur (e.g., the appearance of novel siderophore-receptor pairs to evade existing exploitation), the system will likely transition into a continuous Red Queen regime of ongoing molecular arms races. We will thoroughly discuss these evolutionary horizons and present our complete invasion simulation data in the revised manuscript.

    1. Author response:

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

      eLife Assessment

      Amyotrophic lateral sclerosis (ALS) affects nerve cells in the brain and spinal cord. The authors' approach to use genetic code expansion to tag two ALS proteins associated with stress granules has value and should be useful in the ALS field. Parts of the work are well done, but there are concerns that the evidence is incomplete overall, and additional controls would strengthen the study.

      We thank the editors and reviewers for their thoughtful assessment and for highlighting the potential value of applying genetic code expansion (GCE) to study ALSassociated proteins involved in stress granule biology. Our goal in this work was to establish and validate a minimally perturbative labeling strategy using the noncanonical amino acid Anap to monitor the localization and stress-dependent behavior of TDP-43 and G3BP1.

      We agree that additional controls can further strengthen the conclusions. In the revised manuscript, we have clarified the experimental design and added essential controls to better support the reliability of the Anap labeling approach (Supplementary Fig. 1).

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors utilize genetic code expansion to tag TDP-43 and G3BP1, and evaluate this protein tagging system (ANAP) compared to antibodies, and evaluate protein trafficking and stress granule formation in response to stress with sodium arsenite treatment. They find similar staining to antibodies in HeLa cells, mouse embryonic stem cells, and primary mouse cortical neurons. This is a useful study that demonstrates the utility of ANAP tagging to evaluate ALS proteins.

      We sincerely thank the reviewer for the positive assessment of our work and for recognizing the utility of the Anap-based GCE system for studying ALS-associated proteins.

      Strengths:

      Rescue of cell survival by ANAP-tagged TDP-43 is compelling

      We appreciate the reviewer’s highlighting of this point. Demonstrating that TDP43-Anap can rescue cell survival was an important validation in our study, as it indicates that incorporation of the noncanonical amino acid does not substantially disrupt the biological function of TDP-43. Additionally, we also tested the RNA splicing function recovery potency of TDP-43-Anap. As shown in Fig. 1K and 1L, a recovery of expression of PFKP, a protein undergoing cryptic exon when TDP-43 lost its function [1], was observed when expressing TDP-43-Anap in TDP-43 knockout Hela cells.

      Weaknesses:

      While the ANAP-tagged proteins had similar distributions to antibody staining, there were some discrepancies that may be more explained by the technique than by novel findings, as the authors suggested. The inclusion of additional controls to evaluate this would be helpful.

      This is a helpful suggestion. To ensure that the fluorescence signal observed in our experiments was specifically derived from site-specific Anap incorporation rather than background fluorescence, we performed three control conditions. Specifically, we tested: (1) cells cultured with Anap supplement, (2) cells expressing the Anap incorporation system with the addition of Anap, and (3) cells expressing both the TAG-mutated protein plasmid and the Anap incorporation system but without the addition of Anap. These control experiments were performed for both TDP-43 and G3BP1, and no observable fluorescence signal was detected under any of these conditions (Supplementary Fig. 1). We have clarified this control experiment in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Chen and colleagues describe a novel means of labeling two RNAbinding proteins, G3BP1 and TDP-43, using genetic code expansion. Overexpressed constructs that incorporate the intrinsically fluorescent non-canonical amino acid Anap redistribute to cytoplasmic granules upon application of external stressors such as sodium arsenite. Similar labeling and redistribution of overexpressed G3BP1 and TDP43 were observed in cultures of mouse primary neurons.

      We are grateful for the reviewer’s accurate summary of our study and recognition of the value of GCE strategy for labeling the RNA-binding proteins G3BP1 and TDP-43.

      Strengths:

      Genetic code expansion and non-canonical amino acid labeling have quite a few advantages over traditional fusion proteins for tracking protein redistribution in living cells. The authors show that they are able to label exogenous G3BP1 and TDP-43 with the non-canonical amino acid Anap and follow labeled proteins in living cells with and without stress.

      We acknowledge the reviewer’s comment on the advantages of GCE-based noncanonical amino acid labeling for studying protein dynamics in living cells.

      Weaknesses:

      The authors do not convincingly leverage the advantages of genetic code expansion in the current study. There is no specific question posed by the authors that can be or is answered using this approach, and several of the experiments lack critical controls. This is also not the first example of TDP-43 labeling by genetic code expansion (see PMID: 38290242). As a result, the study as a whole adds little to our understanding of protein trafficking and behavior under stress.

      We thank the reviewer for raising these important points. Although as reviewer mentioned, genetic code expansion has previously been applied to TDP-43 [2], it mainly employed the photocaged lysine incorporation system to optogenetic control of TDP-43 translocation, and the protein was still labeled by mRubby. Our paper has totally different goal, to establish and validate a minimally perturbative labeling strategy using the intrinsically fluorescent noncanonical amino acid Anap to monitor the localization and stress-dependent behavior of both TDP-43 and G3BP1. And our work extends this approach in several important ways.

      First, we demonstrate that Anap incorporation enables visualization of stress-dependent redistribution of both TDP-43 and G3BP1, two key proteins involved in stress granule biology. Importantly, we validate this approach across multiple cellular systems, including HeLa cells, mouse embryonic stem cells, and primary mouse cortical neurons, which broadens the applicability of this labeling strategy.

      Second, we provide functional validation of the Anap-tagged protein, showing that TDP43-Anap rescues both cell survival and RNA splicing activity in TDP-43 knockout cells, including restoration of PFKP expression, a known cryptic exon target of TDP-43. These results support that Anap incorporation does not substantially disrupt protein function.

      We performed additional control experiments to ensure the specificity of the labeling system. Specifically, we tested three control conditions: (1) cells cultured with Anap supplement, (2) cells expressing the Anap incorporation system with the addition of Anap, and (3) cells expressing both the TAG-mutated protein plasmid and the Anap incorporation system but without the addition of Anap. These control experiments were performed for both TDP-43 and G3BP1, and no observable fluorescence signal was detected under any of these conditions (Supplementary Fig. 1).

      We agree that the manuscript would benefit from clearer articulation of the advantages of genetic code expansion in this context. Accordingly, we have revised the manuscript to more explicitly emphasize how Anap labeling provides a minimally perturbative alternative to large fluorescent protein fusions, which can alter the phase behavior and localization of stress granule proteins.

      “Conventional fluorescent protein tags have enabled visualization of TDP-43 and G3BP1 in living cells; however, these approaches can perturb the native biophysical properties of the proteins being studied. For example, GFP or other fluorescently tagged TDP-43 usually requires additional modifications, such as deletion of the nuclear localization signal (NLS) [3, 4], to induce cytoplasmic inclusion formation. Such manipulations introduce non-physiological conditions that may alter the native trafficking and aggregation behavior of TDP-43. As for G3BP1, tags like GFP may also cause unexpected effects on the phase separation or other dynamics of the protein. In contrast, Anap based GCE strategy allows the minimally perturbative labeling and visualization of protein localization and stress-induced redistribution while preserving native protein architecture and function of both proteins. Importantly, the approach provides a generalizable genetically encoded platform for quantitatively examining the behavior of ALS-associated proteins in living cells. By enabling faithful monitoring of protein trafficking and stressgranule dynamics without extensive protein engineering, Anap-based GCE can offer a powerful strategy for probing molecular-scale mechanisms underlying ALS-linked proteinopathies”.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 1A

      The authors report that the nuclear staining of G3BP1 by ANAP labeling shows the presence of nuclear pools of G3BP1 that aren't detected with antibody staining. However, unspecific nuclear staining by aminoacylated tRNAs bound to synthetases has been described. It would be important to have a control to evaluate for this possibility.

      This is an important point. We agree that the nuclear ANAP signal should be carefully controlled to exclude the possibility of nonspecific staining arising from the Anap incorporation machinery itself, such as aminoacylated tRNAs and/or synthetases.

      To address this concern, in methods and material part, we note that after DPBS washes to remove excess Anap, cells were incubated in fresh medium for 2 hours to allow sufficient time for the decay of unstable aminoacylated tRNAs, which are generally cleared within minutes to tens of munites [5].

      Also, we performed three control conditions for both TDP-43 and G3BP1: (1) cells cultured with Anap supplement, (2) cells expressing the Anap incorporation system with the addition of Anap, and (3) cells expressing both the TAG-mutated protein plasmid and the Anap incorporation system but without the addition of Anap. Under all three conditions, we observed no detectable fluorescence signal (Supplementary Fig. 1).

      In addition, as shown in Fig. 1I, the nuclear signal of G3BP1-Anap partially colocalizes with the nuclear signal of TIA-1 in several condensate-like structures. This observation further supports that the nuclear Anap signal reflects protein-associated localization rather than nonspecific fluorescence, as it overlaps with a known RNA-binding protein that can form nuclear condensates under certain conditions.

      (2) Figure 1A, 1B

      Anap labeling appears to stain fewer cytoplasmic structures compared to antibody staining for both G3BP1 and TDP-43 after sodium arsenite treatment. Quantification would be useful to address whether this is the case. If so, might this be due to unincorporated/truncated proteins competing with Anap-labeled proteins?

      We appreciate the reviewer’s helpful suggestion. To address this point, we performed quantitative colocalization analysis using Fiji/ImageJ, calculating the Pearson correlation coefficient (R) for regions of interest between the Anap signal and antibody staining. These analyses indicate a strong overall agreement between the two detection methods under stress conditions, supporting that Anap labeling reliably reports the localization of both G3BP1 and TDP-43 (see Fig1. A, B).

      Regarding the possibility that truncated or unincorporated proteins could influence the observed signal, we note that fluorescence from Anap depends on successful amber suppression and incorporation of Anap at the engineered TAG site. Proteins that fail to incorporate Anap, such as truncated products generated by premature termination, would not produce fluorescence, and therefore would not contribute to the Anap signal. Thus, the Anap fluorescence selectively reports the population of successfully labeled full-length proteins, whereas antibody staining detects both labeled and unlabeled protein pools. This difference may partially explain why antibody staining appears to label a larger number of cytoplasmic structures.

      (3) Figure 1F

      FRAP of G3BP1-GFP in stress granules is slower than in previous publications. The underlying reasons for this should also be addressed.

      We thank the reviewer for this important observation. Differences in FRAP recovery kinetics of G3BP1 in stress granules may arise from several experimental variables that are known to influence stress granule dynamics. These include differences in cell type, expression levels of G3BP1-GFP, and imaging or photobleaching parameters. In our experiments, FRAP measurements were performed under specific conditions optimized for our experimental system, which may lead to recovery kinetics that differ from those reported in previous studies.

      (4) Figure 1H

      A full-size Western blot would be useful to evaluate for amount of truncated protein for G3BP1 and TDP-43. Could truncated proteins be competing with and altering ANAPtagged G3BP1 and TDP-43 localization in response to stress? This should be addressed.

      We acknowledge this important point. Full-size Western blotting can provide information on the overall presence of truncated species in the transfected population; however, it represents a bulk measurement and does not capture cell-to-cell variability in amber suppression efficiency at the single-cell level. We therefore cannot exclude the possibility that truncated products are present at varying levels in individual cells and may contribute, directly or indirectly, to differences between antibody staining and Anap fluorescence.

      Importantly, we observe that cells with successful Anap incorporation consistently exhibit strong antibody staining for TDP-43 or G3BP1, indicating that full-length protein is the predominant species in these cells. Because Anap fluorescence depends on successful amber suppression, it selectively reports the full-length protein population, whereas truncated products are not detected in the imaging assay. The concordance between Anap fluorescence and antibody staining therefore argues against a major contribution of truncated species to the observed localization patterns (Supplementary Fig. 1).

      Accordingly, we interpret the Anap signal as reflecting the localization of successfully labeled full-length protein, while acknowledging that heterogeneity in suppression efficiency is an important limitation of the current approach.

      (5) Figure 3

      This is a well-designed diagram.

      We are grateful for the reviewer’s positive feedback on the diagram and are pleased that the schematic effectively illustrates the experimental design and the principles of the genetic code expansion strategy used in this study.

      Reviewer #2 (Recommendations for the authors):

      The authors present a one-sided viewpoint concerning the connection between stress granules and disease (lines 45-46). A more balanced discussion is recommended, including data arguing against a role for abnormal stress granules in neurodegeneration.

      This is an important suggestion. We agree that the relationship between stress granules and neurodegeneration remains an active area of investigation and that evidence both supporting and questioning a causal role of stress granules in disease has been reported. In the revised manuscript, we have modified the Introduction to provide a more balanced discussion of this topic.

      “Altered stress-granule dynamics have been associated with ALS/FTD [6, 7]; however, whether stress granules directly drive neurodegeneration remains debated, as several studies suggest that stress granules primarily function as protective stress responses [8].”

      (1) A central rationale for the study is missing. The authors state only that G3BP1 and TDP-43 'undergo dynamic stress-dependent redistribution, making them ideal candidates for minimally invasive, site-specific fluorescent labeling.' Is there a controversy or question that can be resolved using these approaches?

      We thank the reviewer for raising this important point. The central motivation of this study is that the dynamic behavior and phase separation properties of stressgranule proteins are highly sensitive to protein modifications and tagging strategies.

      “Conventional fluorescent protein tags have enabled visualization of TDP-43 and G3BP1 in living cells; however, these approaches can perturb the native biophysical properties of the proteins being studied. For example, GFP or other fluorescently tagged TDP-43 usually requires additional modifications, such as deletion of the nuclear localization signal (NLS) [3, 4], to induce cytoplasmic inclusion formation. Such manipulations introduce non-physiological conditions that may alter the native trafficking and aggregation behavior of TDP-43. As for G3BP1, tags like GFP may also cause unexpected effects on the phase separation or other dynamics of the protein.”

      (2) Related to this, there is little context for how or why genetic code expansion is utilized for these studies

      We agree that the rationale for using genetic code expansion should be more clearly explained. In this study, genetic code expansion was employed to enable sitespecific incorporation of the small fluorescent noncanonical amino acid Anap, allowing minimally perturbative labeling of proteins of interest.

      “Anap based GCE strategy allows the minimally perturbative labeling and visualization of protein localization and stress-induced redistribution while preserving native protein architecture and function of both proteins. Importantly, the approach provides a generalizable genetically encoded platform for quantitatively examining the behavior of ALS-associated proteins in living cells. By enabling faithful monitoring of protein trafficking and stress-granule dynamics without extensive protein engineering, Anapbased GCE can offer a powerful strategy for probing molecular-scale mechanisms underlying ALS-linked proteinopathies.”

      (3) The justification for the criteria for selecting the site for incorporation of non-canonical amino acids in G3BP1 or TDP-43 is missing.

      We acknowledge this important comment and agree that the rationale for selecting the incorporation sites should be stated more clearly.

      “For TDP-43, the incorporation site was selected to avoid the major functional domains involved in RNA binding, nuclear localization, and aggregation-related behavior, thereby reducing the likelihood that Anap incorporation would perturb its native trafficking or function. For G3BP1, the selected site was chosen to minimize interference with domains important for stress granule assembly, RNA binding, and protein-protein interactions. More generally, we aimed to place the ncAA at positions likely to be solventaccessible and tolerant of substitution, while avoiding highly conserved or functionally essential residues.”

      (4) Studies in Figures 1 and 2 lack essential controls, including background signal from Anap in non-transfected cells, or those transfected with plasmids lacking the tRNA or tRS.

      This is an important point, also raised by Reviewer 1. To evaluate potential background fluorescence arising from Anap or the labeling system, we performed several control experiments. Specifically, we examined three conditions: (1) cells cultured with Anap supplement, (2) cells expressing the Anap incorporation system with the addition of Anap, and (3) cells expressing both the TAG-mutated protein plasmid and the Anap incorporation system but without the addition of Anap. Under all three conditions, we observed no detectable fluorescence signal (Supplementary Fig. 1).

      (5) Another marker of stress granules should be used for confirming the identity of G3BP1-Anap (+) or TDP-43-Anap (+) structures, including TIA1, TAF15, or polyA RNA.

      We appreciate this helpful suggestion. To further confirm the identity of the stress granule structures observed in our experiments, we performed colocalization analysis with TIA-1, a well-established marker of stress granules. The results have been included in revised manuscript.

      “Additionally, we examined the colocalization of G3BP1-Anap with TIA-1, another established stress granule marker. Under stress conditions, G3BP1-Anap largely colocalized with TIA-1 within stress granules. Interestingly, under basal conditions, the nuclear signal of G3BP1-Anap, which was not detected by antibody staining, appeared to partially colocalize with TIA-1 in several condensate-like structures. (Fig. 1I).”

      (6) There is no information on the number of granules bleached or the number of cells selected for FRAP studies. There is no information on the shaded areas in Figure 1F or 1G, and no information on statistical comparisons between regressions in Figure 1F.

      We thank the reviewer for pointing out these omissions. We have revised the figure legends to clarify these details.

      “One granule from each of three independent cells was selected and photobleached for FRAP analysis.”

      “Here, error bars with filled area are used for better data presentation. FRAP recovery curves were compared using two-way ANOVA.”

      (7) Protein dynamics measured by FRAP are highly dependent on the concentration and/or expression level of each protein. Because of this, the authors need to control for expression level in all FRAP studies.

      We agree that protein concentration and expression level can influence FRAP recovery kinetics. Since Anap incorporation is based on amber suppression, and the suppression rate in each cell varies, so it is difficult to control the expression of Anap labeled proteins, however, to minimize this potential effect, we performed FRAP measurements on cells exhibiting comparable fluorescence intensities, which served as a proxy for similar expression levels of the labeled proteins. In addition, FRAP analyses were conducted on individual granules within cells expressing moderate levels of the protein, avoiding cells with unusually high fluorescence intensity that might reflect overexpression.

      Furthermore, fluorescence recovery was normalized to the pre-bleach intensity of the selected granules, which reduces variability arising from differences in overall expression levels between cells.

      (8) There is no point of reference for TDP-43-Anap FRAP results in Figure 1G. Additional studies using variants harboring a mutated NLS (mNLS) can be used in place of TDP43-YFP.

      This is a helpful suggestion. In response, we have performed additional FRAP experiments using TDP-43<sup>ΔNLS</sup>, a commonly used construct that promotes cytoplasmic localization and facilitates analysis of TDP-43 granules. The results from TDP-43<sup>ΔNLS</sup> have now been included as a reference for the FRAP measurements of TDP-43-Anap in the revised manuscript (Fig. 1D, 1G).

      “We then used YFP-tagged nuclear localization signal (NLS)-deleted TDP-43 (TDP43<sup>ΔNLS</sup>-YFP) as a reference and performed FRAP analysis to compare the mobility of TDP-43-Anap and TDP-43<sup>ΔNLS</sup>-YFP. Fluorescence recovery of TDP-43-Anap reached ~45% within 20 s after photobleaching, consistent with liquid-like dynamics. In contrast, TDP-43<sup>ΔNLS</sup>-YFP showed only ~22% recovery, suggesting more solid-like dynamics (Fig. 1D, 1G). These results are consistent with previous reports describing relatively immobile aggregates formed by TDP-43<sup>ΔNLS4</sup>and illustrate the advantage of Anap-based labeling, which preserves native protein properties and enables real-time assessment of protein dynamics without introducing disruptive mutations.”

      (9) There is no point of reference for comparing FRAP results from G3BP1-GFP to G3BP1-Anap. What is the 'gold standard'? Without this, it is difficult to conclude that "... Anap labeling better preserved the native mobility and biophysical properties of G3BP1 than the conventional GFP tag."

      We acknowledge this important point and agree that there is currently no definitive gold standard for measuring the native mobility of endogenous G3BP1 within stress granules in living cells. Our intention was not to claim that the Anap-labeled protein definitively represents the native state, but rather to compare the relative effects of different labeling strategies.

      Thus, we rewrite the sentence as “These results suggest that G3BP1-Anap displays higher mobility compared with G3BP1-GFP, indicating that Anap labeling may provide a less perturbative approach for monitoring G3BP1 dynamics.”

      (10) The WB in Figure 1H is overexposed, making it difficult to compare expression levels between WT and V100Anap-transfected cells. In addition, there is no similar assay for confirming G3BP1-Anap expression.

      Thank you for pointing this out. In the revised manuscript, we have replaced the image with a properly exposed Western blot to allow clearer comparison of protein expression levels.

      In addition, we have now included a corresponding western blot analysis to confirm the expression of G3BP1-Anap in G3BP knockout U2OS cell (Fig. 1H). These results verify that the Anap-labeled proteins are expressed at detectable levels and support the interpretation of the imaging and FRAP experiments.

      (11) Although survival studies in Figures 1I and J are promising, a more convincing demonstration of functional replacement of TDP-43 would involve an assessment of cryptic exon splicing, comparing WT to TDP-43 KO, V100Stop- and V100Anaptransfected cells.

      This is a valuable suggestion.

      “We also evaluated TDP-43-dependent RNA splicing activity by examining the expression of PFKP, a well-established target that undergoes cryptic exon inclusion upon loss of TDP-43 function17. As shown in Figures 1K and 1L, expression of TDP-43Anap in TDP-43 knockout HeLa cells restored PFKP expression, indicating that the Anap-labeled protein retains functional RNA splicing activity. These results demonstrate that TDP-43-Anap is capable of functionally compensating for endogenous TDP-43, supporting that the incorporation of Anap does not substantially disrupt the protein’s biological function.”

      (12) Tuj1 staining in Figure 2 is inconsistent and often fails to confirm neuronal identity.

      We thank the reviewer for this important comment. We acknowledge that Tuj1 staining in Figure 2 is variable and, in some cases, does not clearly delineate neuronal identity. Notably, the reduced Tuj1 signal is primarily observed in neurons that express Anap-labeled proteins under sodium arsenite treatment, which likely reflects the combined effects of transfection-associated stress and oxidative stress on neuronal morphology and cytoskeletal integrity.

      In addition, transfection efficiency in primary neurons is inherently low and variable, and cells that successfully express the constructs may represent a more stress-sensitive subpopulation, further contributing to variability in staining quality. Despite optimization efforts, these technical constraints limit the consistency of Tuj1 labeling under these experimental conditions.

      (13) Close-up images and correlation scatter plots in Figures 1 and 2 do not add very much information.

      We thank the reviewer for this comment. To address the reviewer’s concern, we have revised the figure legends to better clarify the purpose of these panels and how they support the quantitative analysis presented in the manuscript.

      For scatter plot, “Colocalization threshold analysis was performed in Fiji/ImageJ to calculate the Pearson correlation coefficient (R) for each region of interest (A, B, I, J). The X- and Y-axes represent the fluorescence intensity values of the red and green channels, respectively. When signals are colocalized, pixels with high intensity in one channel correspond to high intensity in the other, forming a diagonal distribution. In contrast, non-colocalized signals cluster along the axes. A higher R value indicates a greater degree of colocalization. Scale bar, 3 μm.”

      Same information was added to figure legend of figure 2.

      For the scheme, please see line 412-413 in the revised manuscript.

      Reference:

      (1) Rothstein, J.D. et al. Sporadic ALS induced pluripotent stem cell derived neurons reveal hallmarks of TDP-43 loss of function. Nature Communications 16, 7092 (2025).

      (2) Shadish, J.A. & Lee, J.C. Genetically encoded lysine photocage for spatiotemporal control of TDP-43 nuclear import. Biophys Chem 307, 107191 (2024).

      (3) Gasset-Rosa, F. et al. Cytoplasmic TDP-43 De-mixing Independent of Stress Granules Drives Inhibition of Nuclear Import, Loss of Nuclear TDP-43, and Cell Death. Neuron 102, 339–357.e337 (2019).

      (4) Yan, X. et al. Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates. Cell 188, 4123–4140.e4118 (2025).

      (5) Walker, S.E. & Fredrick, K. Preparation and evaluation of acylated tRNAs. Methods 44, 81–86 (2008).

      (6) Kassouf, T. et al. Targeting the NEDP1 enzyme to ameliorate ALS phenotypes through stress granule disassembly. Science Advances 9, eabq7585 (2023).

      (7) Van Nerom, M. et al. C9orf72-linked arginine-rich dipeptide repeats aggravate pathological phase separation of G3BP1. Proceedings of the National Academy of Sciences 121, e2402847121 (2024).

      (8) Wolozin, B. & Ivanov, P. Stress granules and neurodegeneration. Nat Rev Neurosci 20, 649–666 (2019).

    1. Author response:

      eLife Assessment

      This important study provides evidence that plateau pikas, at moderate densities, can facilitate yak nutrition by suppressing a poisonous plant, offering a helpful perspective on reciprocal interactions between small mammal ecosystem engineers and large herbivores. The evidence is solid, supported by a manipulative field experiment and appropriate measurements of intermediary ecological processes, although some claims about density dependence, competition, and stress-gradient mechanisms are not fully supported by the experimental design. The work will be of interest to ecologists, conservation biologists, and rangeland managers, particularly those studying grassland herbivore interactions and livestock management on the Qinghai-Tibetan Plateau.

      Thank you very much for these positive assessments of our work, below we provided the point-by-point responses to the comments from the 2 peer reviewers, and we hope these revisions are satisfied.

      Reviewer #1 (Public review):

      Summary:

      This is important and significant work because it helps describe the complexity of interactions between system components where two herbivores interact with vegetation. Whereas other studies have shown that the larger ungulate (yaks, Bos grunniens, in this case) can facilitate the abundance and population growth of the smaller (the semi-fossorial lagomorph, Ochotona curzoniae, plateau pika hereafter), this study flips the tables and shows that, at least under some conditions, moderate densities of the plateau facilitate the nutritional condition of yaks.

      The study was not designed to investigate the reasons that pikas clip Stellera chamaejasme. That said, based on other studies and general knowledge of the ecology of these pikas, it is likely that they clip (although do not eat) this plant because its relatively large size hinders predator detection. This species of pika does better where vegetation height is low than where it is higher.

      Strengths:

      Notably, the strong inference the authors can claim for their results is supported by the careful experimental design. A weaker paper would have simply noted correlations between pika burrow density and yak feeding efficiency without experimental removal. This paper, to its credit, not only used experimental removals but also documented the various intermediary results that support the ultimate conclusions. The statistical approaches used appear to be appropriate. (Readers are encouraged to read the full Materials and Methods, which are available in the Supplementary Materials section.)

      We appreciate these positive comments on our work.

      Weaknesses:

      Although the study was well designed and executed, and its conclusions appear strongly supported, readers interested in the management implications of the Qinghai-Tibetan Plateau should be mindful of its limitations. First, the study site, at approximately 3,200 m elevation, was relatively low by Qinghai-Tibetan Plateau standards. Stellera chamaejasme becomes less common at elevations > 4,000 m, where a majority of livestock grazing occurs. Thus, it would be instructive to learn, through follow-up studies, whether similar facilitation occurs where unpalatable (and mildly poisonous) species in such genera as Astragalus, Oxytropis, and Thermopsis replace S. chamaejasme as the problematic plant for pastoralists.

      Agree! We will acknowledge this limitation in the Discussion, by adding the paragraph below (see the Third point):

      “Despite of these, several questions remain deserve further investigation. First, our study examined pika–yak interactions only during the summer period, when food resources are most abundant. Whether such facilitative effects weaken or even shift toward competition under more stressful conditions—for example, when forage becomes limited during autumn or winter—remains to be tested. Second, if pika facilitation of yak nutrition at the densities documented results in herders increasing yak density, might the increased herbivory from the domestic animals provide the conditions for the pika population to increase beyond the densities observed here, and thus toward the levels where facilitation yields to competition (Yang et al., 2026)? Third, our study site located at approximately 3,200 m elevation, was relatively low by Qinghai-Tibetan Plateau standards. Stellera becomes less common at elevations > 4,000 m, where a majority of livestock grazing occurs. It would be instructive to learn, through follow-up studies, whether similar facilitation occurs where unpalatable (and mildly poisonous) species in such genera as Astragalus, Oxytropis, and Thermopsis replace Stellera as the problematic plants for pastoralists (Lu et al., 2012; Li and Zhao, 2025). Finally, it is unclear whether similar facilitation as observed here applied to the other principal livestock species in the area, such as domestic sheep and goats.”

      Second, the authors make no mention of wild ungulates, so it is unclear what, if any, role they may have played in this system. At least one study in Qinghai Province, albeit at a slightly higher elevation, showed that not only pikas, but also Tibetan gazelles (Procapra picticaudata), which were commonly observed on grazed pastures, grazed more frequently on some dicots avoided by domestic sheep than did the livestock themselves (Harris et al. 2015). Citation:

      Harris RB, Wang, WY, Badinqiuying , Smith AT, Bedunah DJ (2015) Herbivory and Competition of Tibetan Steppe Vegetation in Winter Pasture: Effects of Livestock Exclosure and Plateau Pika Reduction. PLoS ONE 10(7): e0132897.

      doi:10.1371/journal.pone.0132897

      Agree! We will add more details about the study site, particularly regarding wild ungulates, in the Methods section. Specifically, we will include the following sentence: “Wild ungulates, such as Tibetan gazelles (Procapra picticaudata) (Harris et al., 2015), and other small mammals such as rabbits and zokors, occur rarely in the area.” This key reference will also be cited in this section.

      It would also be instructive to learn if similar facilitation as observed here applied to the other principal livestock species in the area, domestic sheep (which are often herded together with smaller numbers of domestic goats).

      Agree! The same as mentioned above. We will acknowledge this limitation in the Discussion, by adding the paragraph below (see the Final point):

      “Despite of these, several questions remain deserve further investigation. First, our study examined pika–yak interactions only during the summer period, when food resources are most abundant. Whether such facilitative effects weaken or even shift toward competition under more stressful conditions—for example, when forage becomes limited during autumn or winter—remains to be tested. Second, if pika facilitation of yak nutrition at the densities documented results in herders increasing yak density, might the increased herbivory from the domestic animals provide the conditions for the pika population to increase beyond the densities observed here, and thus toward the levels where facilitation yields to competition (Yang et al., 2026)? Third, our study site located at approximately 3,200 m elevation, was relatively low by Qinghai-Tibetan Plateau standards. Stellera becomes less common at elevations > 4,000 m, where a majority of livestock grazing occurs. It would be instructive to learn, through follow-up studies, whether similar facilitation occurs where unpalatable (and mildly poisonous) species in such genera as Astragalus, Oxytropis, and Thermopsis replace Stellera as the problematic plants for pastoralists (Lu et al., 2012; Li and Zhao, 2025). Finally, it is unclear whether similar facilitation as observed here applied to the other principal livestock species in the area, such as domestic sheep and goats.”

      Finally, as suggested by this study, the interactions between all components of the system are complex and interactive. If pika facilitation of yak nutrition at the densities documented results in herders increasing yak density, might the increased herbivory from the domestic animals provide the conditions for the pika population to increase beyond the densities observed here, and thus toward the levels where facilitation yields to competition?

      Agree! The same as mentioned above. We will acknowledge this limitation in the Discussion, by adding the paragraph below (see the Second point):

      “Despite of these, several questions remain deserve further investigation. First, our study examined pika–yak interactions only during the summer period, when food resources are most abundant. Whether such facilitative effects weaken or even shift toward competition under more stressful conditions—for example, when forage becomes limited during autumn or winter—remains to be tested. Second, if pika facilitation of yak nutrition at the densities documented results in herders increasing yak density, might the increased herbivory from the domestic animals provide the conditions for the pika population to increase beyond the densities observed here, and thus toward the levels where facilitation yields to competition (Yang et al., 2026)? Third, our study site located at approximately 3,200 m elevation, was relatively low by Qinghai-Tibetan Plateau standards. Stellera becomes less common at elevations > 4,000 m, where a majority of livestock grazing occurs. It would be instructive to learn, through follow-up studies, whether similar facilitation occurs where unpalatable (and mildly poisonous) species in such genera as Astragalus, Oxytropis, and Thermopsis replace Stellera as the problematic plants for pastoralists (Lu et al., 2012; Li and Zhao, 2025). Finally, it is unclear whether similar facilitation as observed here applied to the other principal livestock species in the area, such as domestic sheep and goats.”

      Reviewer #2 (Public review):

      Summary:

      This study uses a combination of field sampling and manipulative experiments to test for facilitative impacts of pikas on yaks via suppression of a poisonous forb. The authors found that, when Stellera forbs were present, yak weight increases over the growing season were greater in the presence of pikas compared to in their absence. This occurred because, although pikas do not consume Stellera, they clip it and use it in nest/burrow construction, thereby decreasing its relative abundance in the plant community. Thus, overall, the study contributes to our understanding of how herbivores of different size classes indirectly affect each other via the use of shared resources.

      Strengths:

      It is well known that large herbivores on grasslands impact smaller animals, but the reciprocal interaction is rarely tested. Thus, this study asks a valuable question, and the experiment is well-designed to test it. The authors also do a good job of demonstrating the potential conservation impacts of their research.

      We appreciate these positive comments on our work.

      Weaknesses:

      What the authors tested is really cool, but their claims go far beyond what they can say based on their experimental design. For example, the authors claim to show that pika impacts on yaks display density-dependent transitions from competition to facilitation. However, their experiment only looked at the presence (at moderate densities) and absence of pikas, and they only tested for facilitation, not competition. The paper would also benefit from changes to the framing in the introduction and discussion. For example, the authors pitch the work as a test of the stress-gradient hypothesis. However, there is no abiotic stress gradient in the study, which is an essential component of the SGH. They also pitch the work in terms of density dependence, but there is no significant variation in population densities beyond the presence-absence binary. The paper would be stronger if they focused their framing around the literature on facilitative interactions across mammals of different size classes, especially indirect facilitation via use of shared resources, which is what this paper is really about.

      We agree that our work had explored only the facilitative effects of pikas on yaks, rather than the density-dependent balance between competition and facilitation, and the Stress Gradient Hypothesis (SGH).

      We plan to make the major revisions below to address this important concern.

      (1) We will revise the title as “Moderate density of small mammalian herbivores facilitates livestock growth in grasslands ”.

      (2) We will delete all the statements about density-dependent transition of facilitation and competition and the SGH in the Abstract, Introduction, Discussion, and the References sections.

      Finally, the paper has significant weaknesses in the experimental and statistical methodology. Most importantly, there are inconsistencies in what is visualized in the figures compared to the model results. For example, the results section in several places notes a lack of significant interaction terms in the model but shows interactions in the p-values on the figures.

      In the Results section, there are only two locations where we discussed non-significant interactions: Line 148–149 “Pikas and Stellera had no interactive effects on abundance of sedges, forbs, and neutral detergent fiber (NDF) of total forage for yaks (Fig. 3F,I, fig. S1, table S3,5).” and Line 161–162 “Pikas and Stellera had no interactive effects on yaks’ foraging efficiency on forbs (fig. S2, table S7).”.

      We have cross-checked both the manuscript as submitted and the website, and in every instance we are consistent in not reporting interactions as non-significant when the model output shows significance.

      We will confirm these details in the revised version as “Pikas and Stellera had no interactive effects on abundance of sedges, forbs, and neutral detergent fiber (NDF) of total forage for yaks (Fig. 3F,I, Fig. S1, Table S5, S8). ”; and “Pikas and Stellera had no interactive effects on yaks’ foraging efficiency on forbs (Fig. S2, Table S10).” in the Results section.

      The authors also plot smoothed lines rather than their model results and then draw interpretations from those lines that cannot be tested in the models that they used.

      Agree! There are only two figures in which we used generalized additive models (GAMs) to plot smoothed lines: Figure 2C and Figure 3C.

      For Figure 2C, the supplementary table for the GAMM associated with the smoothed line was not originally included, but we will add it as Table S4 in the revised version. For Figure 3C, we explicitly fit a GAMM corresponding to the plotted line, and the model results will be reported in the Table S7 in the revised version.

      There are also missing details that are important for model interpretation, including the distributions used and the sample sizes.

      Agree! We will provide the Table S13 to summarize all statistical models used in the study, including the distributions used and the sample sizes in the Supplementary Materials. We will also add a sentence of “A summary of all statistical models used in the study is available in table S13.” in the Statistical analyses section to indicate this information.

      Another major concern with experimental design is in the forage nutrient analyses. The authors picked plants along a grazing trail, then measured nutrient content without standardizing based on plant species, so any differences across treatments could be because of what they happened to grab rather than overall forage quality.

      We will revise this section to provide more details on how forage samples were collected and their quality were analyzed. Specifically, five forage samples were collected per grazing plot, focusing on the two dominant plant species —one sedge and one grass—that were most frequently grazed by yaks. To ensure comparability across plots and treatments, we mixed the two species at equal dry mass (5 g). We will revise this section as below.

      “To assess forage quality, five forage samples were collected from each grazing plot to quantify their nutritive values. To obtain samples that reflect the forage actually consumed by yaks, we tracked the animals along their grazing paths and collected the plant tissues of the two most frequently consumed species: the dominant sedge Kobresia humilis and the dominant grass Elymus nutans (Fig. 2B; Pan et al., 2019). The collected tissues of each species were dried in a forced-air oven at 60 °C for 48 h, then ground through a 1-mm mesh. Subsequently, 5 g of each dried and ground species were combined in a 1:1 dry mass ratio, and the resulting mixture was stored in plastic bags for subsequent analyses.”

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      This manuscript used deep learning to highlight the role of inhibition in shaping selectivity in primary and higher visual cortex. The findings hint at hitherto unknown axes of structured inhibition operating in cortical networks with a potentially key role in object recognition.

      The multi-species approach of testing the model in macaque and mouse is excellent, as it improves the chances that the observed findings are a general property of mammalian visual cortex. However, it would be useful to delineate any notable differences between these species, which are to be expected given their lifestyle.

      The overall performance of the model appears to be excellent in V1, with over 80% performance, but it falls substantially in V4. It would be important to consider the implications of this finding; for example, in the context of studying temporal lobe structures that are central to recognizing objects. Would one expect that model performance decreases further here, and what measures could be taken to avoid this? Or is this type of model better restricted to V1 or even LGN?

      While the manuscript delineates novel axes of inhibitory interactions, it remains unclear what exactly these axes are and how they arise. What are the steps that need to be taken to make progress along these lines?

      Reviewer #2 (Public review):

      The classic view of sensory coding states that (excitatory) neurons are active to some preferred stimuli and otherwise silent. In contrast, inhibitory neurons are considered broadly tuned. Due to the gigantic potential image space, it is hard to comprehensively map the tuning of individual neurons. In this tour de force study, Franke et al. combine electrophysiological recordings in macaque (V1, V4) and mouse (V1, LM, LI) visual cortex with large-scale screens based on digital twin models, as well as beautiful systems identification (most/least activating stimuli). Based on these digital twins, they discover dual-feature selectivity (which they validate both in macaques and mice). Dual-feature selectivity involves a bidirectional modulation of firing rates around an elevated baseline. Neurons are excited by specific preferred features and systematically suppressed by distinct, non-preferred features. This tuning was identified by excellently combining advances in AI & high-throughput ephys.

      The study is comprehensive and convincing. Overall, this work showcases how in silico experiments can generate concrete hypotheses about neuronal coding that are difficult to discover experimentally, but that can be experimentally validated! I think this work is of substantial interest to the neuroscience community. I'm sure it will motivate many future experimental and computational studies. In particular, it will be of great interest to understand when and how the brain leverages dual-feature selectivity. The discussion of the article is already an interesting starting point for these considerations.

      Strengths:

      (1) Using computational models to predict neuronal responses allowed them to go through millions of images, which may not be possible in vivo.

      (2) The cross-species and cross-area consistency of the results is another major strength. Pointing out that the results may be a fundamental strategy of mammalian cortical processing.

      (3) They show that the feature causing peak excitation in one neuron often drives suppression in another. This may be an efficient coding scheme where the population covers the visual manifold. I'd like to understand better why the authors believe that this shows that there are low-dimensional subspaces based on preferred and non-preferred stimulus features (vs. many more, but some axes are stronger).

      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. Overall, we agree with the assessment of the reviewers. We have performed the following changes to the text to clarify and strengthen the manuscript, without introducing new analyses or altering the conclusions. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Page 3: The authors state that RFs were mapped using sparse noise, with the goal to ensure that the RFs align with the visual stimulus, but no data appear to be shown regarding this alignment. It would be important to provide a full analysis of the sparse noise-mapped RFs for both V1 and V4. Also, is it correct that the V4 data analyzed here came from a single animal? This could potentially be problematic and would need to be addressed, for example, by performing analyses also in V1 for participant animals separately. Please elaborate.

      We have added a sentence to the Results section clarifying the sparse noise RF mapping procedure, noting that probe insertions were targeted orthogonal to the cortical surface so that neurons sampled along the probe depth share overlapping receptive fields, allowing a single stimulus configuration to adequately drive the entire recorded population. We have also corrected the text to clarify that V4 data were collected from 2 animals (not 3 as previously stated in an earlier draft), consistent with the Methods section.

      (2) Page 4: Only half the neurons in V4 are "high confidence" in terms of test image performance, which seems a little low and probably significantly lower than the corresponding value for V1 of 84%. It is unclear how to interpret this confidence, but it seems to suggest that half of the V4 neurons are not well captured by the model. If true, this fraction appears large enough to cast doubt on the validity of the V4 results. Please elaborate.

      We have expanded the text to explicitly discuss the lower proportion of high-confidence in-silico neurons in V4 relative to V1. We attribute this to the greater complexity of V4 tuning compared to V1, as well as missing contextual information such as image surrounds and sequential image context—factors that likely limit model performance in higher visual areas. We note that our restriction of analyses to high-confidence neurons provides resilience against these limitations, and that the goal was not to maximize predictive performance per se but to identify response patterns—dual-feature selectivity—that are robust across neurons, areas, and species.

      (3) Page 5: It seems that identical L2 norms are valid for discounting contrast variations, particularly if the neural responses are linear, since the L2 norm is computed on the entire RF. It might be judicious to attenuate the claim that contrast variation has no effect.

      We have softened the claim that contrast variation has no effect. The revised text now states that L2 normalization controls for root-mean-squared contrast but does not fully equate effective contrast in nonlinear cells, whose responses depend on the spatial structure of the stimulus beyond its total energy. We note that residual contrast dependent effects, particularly in the suppressive regime, cannot be entirely excluded.

      (4) Page 6: The authors acknowledge that, at least for simple cells, a phase shift in the grating and concomitant ON-OFF overlap is an inhibitory axis, which is correct. It does not really become clear what other axes were found, and whether any of these represent a novel discovery about V1.

      We have clarified the description of inhibitory axes in V1, noting that while phase-shifted stimuli represent a well-established suppressive axis for simple cells reflecting linear On-Off subfield structure, and complex cells exhibit no coherent suppressive pattern due to phase pooling, neither model class accounts for the multidimensional suppressive structure we observe. We have made explicit that our unbiased approach reveals suppressive structure spanning simultaneous changes across orientation, spatial frequency, phase, and texture, exceeding what any single known suppressive mechanism predicts.

      (5) Page 7: Dreamsim is based on human similarity judgements, whereas the data is from macaques. Is there any evidence suggesting that macaque similarity judgements might be similar to those of humans?

      We have added a paragraph to the Discussion acknowledging that DreamSim was trained on human perceptual similarity judgments while our neuronal data are from macaques. We note that this cross-species application is supported by the deep homology between primate ventral visual streams, and that natural-image similarity judgments have been found to be highly consistent across macaques and humans. Importantly, we clarify that we deploy DreamSim not as a model of macaque perception but as an image feature embedding to test whether stimuli that cluster in perceptual space evoke similar neuronal responses—a use that is robust to the precise calibration of the metric. We also note that we are developing custom macaque-specific embeddings for future work.

      (6) Page 7: How many images were in the test set?

      We have added the number of test images to the relevant text (n=75 for V1, n=150 for V4) and to the Figure 1 caption.

      (7) Page 8: As mentioned above, performing the analysis on V1 data of individual subjects and demonstrating similar digital twins might be an additional way to confirm the models' accuracy.

      We have added text noting that for V4, 1digital twin models were fit independently per neuron without sharing information across animals, and that extreme image sets identified by the model elicited correspondingly extreme responses in neurons from the other animal, confirming that identified selectivity patterns are not idiosyncratic to individual subjects.

      (8) Page 11: The mouse data is presented very briefly only, and the authors seem to imply that there is a high degree of coding similarity between this rodent species and macaques and, by extension, humans. Were there any notable differences between the mouse and macaque data?

      We have added text explicitly noting that while macaque and mouse visual cortex differ substantially in their functional organization and the complexity of neuronal selectivity, the broader principle—that non-sparse neurons are jointly defined by distinct excitatory and suppressive feature sets—generalizes across mammalian visual systems. We clarify that this does not imply that mouse and macaque visual cortex share similar functional organization or equivalent complexity of neuronal selectivity; rather, within the representational regime of each area, neurons are organized such that excitatory and suppressive feature sets are jointly structured and distinct.

      (9) Page 13: One main finding of the study is that inhibition appears to operate along additional dimensions that had not been previously recognized, but what is the nature of these dimensions, how do they arise and relate to known inhibitory effects in V1 such as centre-surround effects? The fact that suppression is tuned in response to natural images or other complex objects is not a new finding, and there is plenty of published work along these lines; the authors may want to cite Tamura et al 10.1152/jn.01267.2003. I am not sure introducing the term "dual feature selectivity" is really a major conceptual advance.

      We have added a citation to Tamura et al. (2004) in the Discussion, alongside other prior work documenting suppression by non-optimal stimuli. We have also expanded the Discussion to more carefully position our findings relative to existing work on feature-selective suppression, noting that while prior work has established that inhibition can be structured and feature-selective, our results suggest a broader organizing principle: within each visual area, there exists a set of feature combinations from which individual neurons draw both their excitatory and suppressive preferences.

      (10) Page 14: The authors enumerate a number of technical limitations, which is to be commended. It would be useful for them to comment on the particular advantages of the digital twin model, compared to a more traditional analysis of the responses to the thousands of natural images that were experimentally obtained. It seems likely that the main finding, i.e. tuned inhibition, is also evident directly in this population (?). While the digital twin is to some degree validated by the test images, its responses to the much larger set of images studied are not validated, and one must trust that the ResNet50 indeed captures V4 selectivity. It would be useful to discuss some of these points, and highlight a potential way that digital twins (maybe as a shared model between laboratories) can learn from a large number of animals and datasets, and maybe even be used to generate novel visual stimuli suitable to test emergent hypotheses.

      We have added a paragraph to the Discussion explicitly contrasting the advantages of digital twin models with direct analysis of experimentally recorded responses, noting that digital twins enable screening of more than one million images per neuron in silico, gradient-based synthesis of stimuli precisely optimized to drive or suppress individual neurons, and cross-model verification of identified selectivity patterns—a test that has no analog when working with fixed experimental image sets.

      Reviewer #2 (Recommendations for the authors):

      Minor comments:

      (1) Call out Figure 1/b in the main text. 

      We have added a callout to Figure 1b in the main text

      (2) Can you make a supplementary figure illustrating more examples with skewness around the middle (e.g. 1.5, 2, 2.5)? Namely, you state that 2 is a good threshold for deciding if it is non-sparse, but you only present clear-cut cases in Figure 2 (with <0.75 and >3.5). I am wondering if 2 is a good threshold?

      We have revised the text to clarify that the skewness threshold of 2.0 is adopted purely for analytical convenience to focus subsequent analyses on neurons with sufficiently graded response distributions, and that the key findings are not dependent on the exact threshold chosen. We explicitly note that the underlying distribution of sparsity is continuous, consistent with recent findings (Gondur et al., 2025).

      (3) The reference "A tale of two tails: Preferred and anti-preferred natural stimuli in visual cortex." Has no authors. I know it's anonymous, but maybe put that for now? I also congratulate including a paper that is anonymously under review at ICLR 2026. I don't find Unk, 2025 in the list of references. Perhaps related?

      We have updated the reference “A tale of two tails” to include the authors (Gondur et al., 2025) and ensured it appears consistently in the reference list. We have also resolved the missing “Unk, 2025” citation, which now correctly refers to this same work.

      (4) Why do you use a different model for the analysis in Figure 8?

      We have added text to the Methods and Results clarifying why a distinct architecture was used for the V4 evaluator model in Figure 8. Specifically, the V4 generator model uses a fixed, pretrained ResNet50 backbone whose weights are deterministic; any re-trained model sharing this backbone would not constitute a genuinely independent evaluation. By contrast, for V1, the ConvNeXt core is fine-tuned from different random initializations, producing architecturally equivalent but computationally independent models. A truly independent V4 evaluator therefore required a fundamentally different architecture.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The study by Raiola et al. conducted a quantitative analysis of tissue deformation during the formation of the primitive heart tube from the cardiac crescent in mouse embryos. Using the tools developed to analyze growth, anisotropy, strain, and cell fate from timelapse imaging data of mouse embryos, the authors elucidated the compartmentalization of tissue deformation during heart tube formation and ventricular expansion. This paper describes how each region of the cardiac tissue changes to form the heart tube and ventricular chamber, contributing to our understanding of the earliest stages of cardiac development.

      Strengths:

      In order to understand tissue deformation in cardiac formation, it is commendable that the authors effectively utilized time-lapse imaging data, a data pipeline, and in silico fate mapping.

      The study clarifies the compartmentalization of tissue deformation by integrating growth, anisotropy, and strain patterns in each region of the heart.

      Weaknesses:

      The significance of the compartmentalization of tissue deformation for the heart tube formation remains unclear.

      While it is obvious that the patterns of deformation should be relevant to model the cardiac crescent into the primitive cardiac tube, we do not provide direct evidence that changing these patterns affects heart tube formation. In this sense, the Reviewer is correct and this is a limitation of the study.

      Reviewer #1 (Recommendations for the authors):

      (1) It is interesting that growth rate and anisotropy are anticorrelated. However, the functional significance of this anticorrelation in heart formation remains unclear. It may be worthwhile to analyse the importance of the relationship between the two by adding inhibitors to cultured embryos or using mutant mouse models.

      We appreciate this thoughtful suggestion and agree that such experimental approaches, involving inhibitors or mutant mouse models, could provide powerful validation of the proposed relationship. However, generating the appropriate lines and performing the necessary quantifications would represent a substantial effort that extends beyond the scope of the current study. Our focus here is to establish the correlation and its potential implications, leaving these more in-depth mechanistic investigations for future work.

      (2) The authors claim to have analysed tissue deformation at the cellular level. Although cell labelling of specific regions using Tat-Cre and DiI injection and tracking of their fate have been performed, this still gives the impression of tissue-level analysis. An analysis "at the cellular level" would be expected to describe morphology, proliferation, polarity, etc., at the single-cell to multi-cell level.

      We thank the reviewer for the comment. Our analysis does not involve single-cell characterization (e.g., morphology, proliferation, polarity) but focuses on quantifying tissue motion. The motion extracted from the images achieves cellular-level precision, as demonstrated by testing the registration algorithm and validating it against cellular tracking experiments. The accuracy of the method is therefore at the cellular scale. The goal of our study is to describe tissue dynamics during heart development, not to perform detailed cellular analyses. The novelty of our approach is that it enables tissuescale quantification in developmental mouse heart imaging, where cell density and image resolution make automated single-cell tracking unfeasible. By using fluorescence labelling as markers, we obtain cellular-level accuracy in tissue motion quantification.

      (3) It is stated that cardiomyocytes, cardiac mesodermal cells, and SHF cells were labeled with Nkx2.5-GFP/Nkx2.5-Cre, Mesp1-Cre, and Islet1-Cre, respectively; however, the results of the labeling using these mice are not presented, and the reason for using different mouse strains is not apparent. Information on these mouse strains is missing in the Materials & Methods section. In particular, attention must be paid to mice of the same name but different strains. Islet1-Cre mice are not SHF-specific and exhibit activity in part of the left ventricular progenitors. Sparse labeling induced by low-dose tamoxifen administration is also unclear regarding the timing and concentration of tamoxifen administration. The authors should provide data on labeling efficiency and region, and also discuss the usefulness of analyses using different mouse strains.

      We thank the reviewer for raising these important points. In this study, the use of different mouse strains was not driven by a biological comparison or lineage-specific analysis, but by the availability of high-quality cardiac imaging datasets generated in the laboratory. The primary goal of this work is methodological: to demonstrate that developmental cardiac imaging data can be reused within an engineering framework to quantify tissue deformation. For this purpose, we do not track individual cells but instead use fluorescence labelling as a versatile strategy to follow tissue motion without requiring a strain- or lineage-specific labelling.

      We acknowledge that Islet1-Cre mice are not SHF-specific and exhibit activity in part of the left ventricular progenitors. However, this limitation does not affect our analysis, as the specificity of the labelled cells is not used in the image processing or deformation quantification pipeline.

      Regarding tamoxifen, we clarified the dosage and administration in the revised Experimental workflow section. Importantly, tamoxifen treatment does not influence the proposed image analysis framework, since labelled cells are employed solely as fiducial references to provide ground-truth validation of the tissue motion estimated from image registration.

      We made these points clearer in the Results section and in Materials and Methods.

      (4) It is noteworthy that the authors have utilized many new analytical methods that they have developed. In the analysis presented in this paper, it is understandable that the methods described in another paper by the authors (Raiola M et al., 2025) are utilized; however, it is important to note that this causes some overlap. It is necessary to clearly distinguish and describe whether the novelty of the methods is based on those developed in this paper or those described in the paper by Raiola M et al. (2025).

      We thank the reviewer for this important observation. We agree that it is essential to clearly separate the methodological developments reported in Raiola M et al. (2025) from the present work. As described in Raiola M et al. (2025), the methods have already been fully developed and validated. In this paper, our focus is to apply these approaches to cardiac development in order to generate and describe the new biological insights. In the revised version, we made this distinction more explicit in the Results and Discussion, highlighting the methodological continuity with our previous work and the biological contribution of the present study.

      Minor points

      (1) In Figure 4, the labels and legends for A, A', B, and B' are reversed. Similar colours are used for C through F, making it difficult to distinguish between them.

      We thank the reviewer for noticing this error. We have corrected it.

      (2) In Figure 5, the labels start with B.

      We thank the reviewer for noticing this error. We have corrected the labels in Figure 5.

      Reviewer #2 (Public review):

      The authors address an important challenge in developmental biology: the quantitative description of tissue deformation during organogenesis. They have developed a new pipeline to quantify early heart tube morphogenesis in the mouse, with cellular resolution. They adopt an elegant approach by integrating multiple 3D time-lapse datasets into a dynamic atlas of cardiac morphogenesis in order to compute spatio-temporal deformation patterns. The main findings highlight a strong compartmentalization of cell behaviors, with tissue growth and anisotropy exhibiting complementary and spatially segregated patterns. Using these data, the authors developed an in-silico fate mapping tool to interrogate cell displacement within the myocardium. This virtual model provides new mechanistic insights into how the bilateral cardiac primordia converge and transform into a three-dimensional heart tube. The authors identify "belt-like" constraints at the arterial and venous poles that prevent tissue expansion and thus shape the ventricular barrel morphology.

      The computational framework is highly innovative and impressive, providing an unprecedented 3D model of tissue deformation during heart morphogenesis. It also opens avenues for testing hypotheses regarding tissue growth and the forces that cause cell motion. However, the proposed model of ventricular chamber formation with the two constraining belts remains hypothetical, lacking biological validation and requiring strengthening or modulation.

      Overall, this carefully performed study provides a new model for exploring tissue deformation during organogenesis and will be of broad interest to computational and developmental biologists.

      We agree with the Reviewer on the limitations of the proposed model due to limited experimental validation. In the revised version of the manuscript we provide further experimental evidence that strengthens the biological validation of the proposed barrel model with two transversal “belts” generating the barrel shape of the primitive ventricle.

      Reviewer #2 (Recommendations for the authors):

      (1) The study proposes a new model of heart morphogenesis by identifying two regions of tissue contraction at the arterial and venous poles. Although the fate map tool has been validated using two ex vivo approaches (DyeI microinjection and TAT-Cre genetic labelling), the conclusions regarding the two belts still need to be demonstrated using in vivo/ex vivo experiments and quantification of cell movements.

      We thank the reviewer for this important suggestion. We agree that experimental validation of the two contraction belts is essential to strengthen the conclusions of the study. In the revised manuscript, we have addressed this point by adding new experimental data directly supporting the existence and dynamics of both D1 and D2 contraction boundaries.

      Specifically, we performed microinjection experiments in which four anchor points, two along D1 and two along D2, were labeled in living embryos and tracked after 10–14 hours (Figure 5C–E, Table S2). For D2, the Euclidean distance between the two anchor points was computed from multiphoton microscopy images acquired at t0 and tfinal (voxel size: 0.57 × 0.57 × 2.5–6.0 µm). In all three embryos analyzed, the D2 anchor points converged over time, with the segment retaining on average 0.27 ± 0.14 of its initial length (range: 0.13–0.40), confirming the lateral compression predicted by the model. For D1, the in-plane geodesic distance between anchor points was measured at t0 and after 10–14 hours. Given the difficulty of imaging the arterial pole at high resolution by whole-mount microscopy, cryosections were used for these measurements (pixel size: 0.65 × 0.65 × 0.042 µm). The D1 segment similarly underwent contraction, retaining on average 0.50 ± 0.22 of its initial length (range: 0.23–0.77). Together, these results provide direct experimental evidence that both boundaries undergo compression during heart tube formation, consistent with the contraction dynamics predicted by the virtual model and supporting the existence of the two belts described in the study.

      We acknowledge that the quantitative values show variability across embryos, which reflects two main sources of uncertainty: (i) the exact position of microinjection along D1 and D2 could not be perfectly standardized; (ii) embryos were not staged at exactly stage 2 at t0 nor did they all reach exactly stage 8 at tend, introducing stage-dependent variability. The primary goal of this experiment was therefore not to precisely quantify compression rates, but to demonstrate that tissue contraction along both boundaries occurs in vivo, consistent with the barrel model predictions. The fact that contraction was observed in all six embryos analyzed, despite the inherent variability of the experimental setup, supports the robustness of this conclusion. These points have been discussed in the revised manuscript.

      (2) The region labelled as OFT appears to correspond instead to the right ventricle primordium, as demonstrated previously by cell labelling of the anterior heart field (Zaffran et al., 2004, PMID: 15217909). The nomenclature should be corrected in the figures and the text. Alternatively, the term "arterial pole" may be useful.

      We thank the reviewer for this observation. We aligned our nomenclature with the literature, correcting the labelling in figures and text.

      (3) The integration of 12 different time-lapses into the model is very impressive. However, while the early stages (2 to 5) are very well covered, the number of replicates for the later stages is much lower. Figure S4 highlights variability between some of the samples, but this is not commented on in the results or the discussion. How does this impact the averaging of tissue deformation patterns and the subsequent model predictions? We thank the reviewer for this comment. We acknowledge that the number of specimens is lower and more variable at later stages. This limitation primarily arises from technical constraints associated with long time-lapse imaging. Because embryo positioning could not be actively tracked during growth, manual repositioning was required, and since embryo development proceeded overnight, maintaining perfect alignment throughout the acquisition was challenging. As a result, several embryos gradually drifted out of the imaging volume and had to be excluded due to incomplete coverage. In addition, at later stages the onset of uncoordinated and subsequently coordinated cardiomyocyte contractions introduces motion-related blurring, which further limits image quality at the acquisition frequency used. These technical limitations were already discussed in the context of the imaging methodology and Limitation and Future Directions section in Raiola et al. (2025).

      As shown in Figure S4, variability between embryos is present and reflects natural biological diversity. Figure S4 also indicates that this variability is highly localized, whereas the regions identified as anticorrelated growth and anisotropy zones remain consistently preserved across embryos. The variability observed in Figure S4, we note that while inter-embryo variability is present, it mainly affects the magnitude of tissue deformation rather than the spatial pattern of deformation. As shown in the additional analyses presented in Figures S5 and S6, the overall organization of deformation, both in terms of growth and anisotropy, is consistently preserved among embryos within the same stage group, within the expected range of natural intra-embryonic variability.

      Finally, regarding the in-silico fate map, our model was not constructed as a statistical average but as a descriptive framework obtained from the concatenation of selected representative embryos. Constructing a statistical model was not feasible due to the limited number of embryos at later stages and the frequent occurrence of incomplete datasets (e.g., randomly missing inflow or arterial pole regions). Under such conditions, only the left ventricular primordium and the inner curvature would have been consistently preserved, thereby limiting the analysis to a very restricted and less informative region. We emphasized these points more clearly in the revised Result section.

      (4) Since the growth rate appears to be highly regionalized, could the authors provide a molecular mechanism for one of these growth patterns?

      We thank the reviewer for this insightful suggestion. Although correlating growth patterns with specific molecular mechanisms would greatly enhance the study, such an effort necessitates extensive additional experimentation, including spatial transcriptomics and detailed molecular analyses. As this falls outside the scope of the present work, we have chosen not to incorporate molecular mechanism data in this manuscript, reserving it for future research.

      (5) Could the model be used to predict new experimental outcomes? For example, could the author simulate a perturbation and validate it through in vivo experiments using mouse mutants?

      We thank the reviewer for this interesting suggestion. At this stage, the model cannot be used to predict new experimental outcomes, as it was designed as a descriptive rather than a statistical or predictive framework. The predictive potential of the model, including the simulation of perturbations, was discussed in detail in Raiola et al. (2025), where this aspect was indicated as a direction for future work.

      We clarified this more explicitly in the revised Results and Discussion sections.

      Minor points

      (1) The readership of eLife is diverse. The methodology and figures could be further annotated, and the axes (A/P, D/V, L/R) could be labelled in all figure panels.

      We thank the reviewer for this helpful suggestion. We revised the figures to include clearer annotations and ensure that the axes (A/P, D/V, L/R) are consistently labelled across all panels.

      (2) It is sometimes difficult to follow without reference to the companion paper. For example, machine learning is mentioned in the summary but is not described in this paper.

      We thank the reviewer for this comment. We clarified in the revised manuscript that the staging system is machine learning-based, using morphometric features to align specimens over time, and indicate that full methodological details are provided in Raiola et al. (2025). This will help readers understand the approach while keeping the focus on the biological findings.

      (3) The authors state the versatility of the model in the introduction, but this is not really addressed in the manuscript; please modulate.

      We thank the reviewer for this feedback. We agree that the versatility of the model was not sufficiently demonstrated throughout the manuscript. In the revised version, we rephrased the Summary to ensure that our claims are aligned with the descriptive scope shown in the current study.

      (4) The authors describe a rightward rotation of the ventricle in stage 9, which they relate to the arterial pole rotation described by Le Garrec et al., 2017. However, this event was reported to occur at E8.5f (which would be equivalent to stage 7). Please modulate or modify.

      We thank the reviewer for this observation. Heart tube rotation is a gradual process that begins at earlier stages, including stage 7, depending on embryo developmental variability. In our study, using the Atlas-based framework described by Esteban et al. (2022), this rotation becomes clearly detectable and morphologically prominent at stage 9, as illustrated in Figure 6d of Esteban et al. At this stage, rightward rotation of the ventricle emerges as the dominant feature in terms of tissue deformation and associated growth patterns, providing a robust reference point to describe and quantify the process. Thus, the description of stage 9 does not indicate the initiation of ventricular rotation, but rather the stage at which the process is most evident and measurable. We moderated it into the revised manuscript to avoid potential ambiguity.

      (5) Some rationales are missing. Why aren't all of the initial 16 time-lapses used for the cumulative deformation pattern analysis? Please explain the impact on the virtual fate mapping of using either labelling of cell clusters or cell continuums. Explain how the Strain Agreement Index neighborhood size (6-7 cells) was chosen, and whether the results are robust at other scales.

      We thank the reviewer for raising these important points. We agree that this section requires clarification and will expand it in the revised Results and Discussion. Not all 16 time-lapses could be included in the cumulative deformation analysis, as this approach relies on concatenating individual embryos into the Atlas framework while preserving the largest possible overlap of tissue. A technical limitation of our recordings was the nonsystematic loss of cardiac tube extremities (inflow tract or arterial pole) due to embryo drift during acquisition. Consequently, several time-lapses provided incomplete tissue coverage and were excluded to avoid an inconsistent assessment of cumulative deformation. In fact, some regions of the tissue would have reflected the contribution of multiple embryos, whereas others would not. Moreover, the registration required to align anatomical regions across stages and embryos would have yielded inaccurate correspondences. For these reasons, we decided to exclude such cases. We commented on this point in more detail in the revised manuscript. For the Strain Agreement Index, the choice of a 6–7 cell neighbourhood size represented a balance between local resolution and robustness. This scale was small enough to allow the tissue to be computationally flattened, while larger neighbourhoods would have included folded regions and created artefacts during the flattening step. Conversely, smaller neighbourhoods would have produced fragmented, “salt-and-pepper” patterns lacking generalization. We commented on this point in more detail in the revised manuscript.

      (6) Figure 5: The panels are mislabelled (B-C versus A-B).

      We thank the reviewer for noticing this mistake. We have corrected the panel labels in Figure 5 to ensure consistency.

      (7) Figure 5C: The red region in stage 2 within the IFT is missing.

      We thank the reviewer for this observation. We have corrected Figure 5C accordingly.

      (8) Typo in Figure 1 legend (p.5): "Our dataset includes multiple specimens raging from E7.75 to E8.25" - should be "ranging".

      We thank the reviewer for pointing this out. We have corrected the typo in the Figure 1 legend.

      (10) Figure S3 legend should state: "Deformation analysis for stage 7, stage 8, and stage 9."

      We thank the reviewer for pointing this out. We have revised the Figure S3 legend accordingly.

      Reviewer #3 (Public review):

      Summary:

      The manuscript by Raiola and colleagues entitled "Quantitative computerized analysis demonstrates strongly compartmentalized tissue deformation patterns underlying mammalian heart tube formation" takes a highly quantitative approach to interrogating the earliest stages of cardiogenesis (12 hours, from early cardiac crescent to early heart tube) in a new and innovative way. The paper presents a new computational framework to help identify both regional and temporal patterns of tissue deformation at cellular resolution. The method is applied to live embryo imaging data (newly generated and from the group's previous pioneering work). In the initial setup, the new model was applied directly to raw time-lapse data, and the results were compared to actual cell tracks identified manually, showing close correlations of the model with the manual tracking. Next, they integrated spatial and temporal information from different embryos to generate a new model for tissue movement, driven by parameters such as tissue growth and anisotropy. Key findings from their model suggest that there are distinct compartments of tissue deformation patterns as the bilateral cardiac crescent develops into the linear heart tube, and that the ventricular chamber forms by a defined expansion pattern, as a 'hemi-barrel shape', with the aterial and venous poles (IFT and OFT) acting as the harnessing belts constraining the expansion of the chamber further. Lastly, the model is tested for its ability to predict future residence of cardiac crescent cells in the heart tube, which it seems to be able to do successfully based on fate tracking validation experiments.

      Strengths:

      The manuscript provides an exceptionally careful analysis of a critical stage during heart development - that of the earliest stages of morphogenesis, when the heart forms its first tube and chamber structures. While numerous studies have interrogated this stage of heart development, few studies have performed time-lapse imaging, and, to my knowledge, no other report has performed such in in-depth quantitative analysis and modeling of this complex process. The computational model applied to normal heart development of the myocardium (labelled by Nkx2-5) has revealed multiple new and interesting concepts, such as the distinct compartments of tissue deformation patterns and the growth trajectories of the emerging ventricle. The fact that the model operates at cellular resolution and over a nearly continuous time period of approximately 12 hours allows for unprecedented depth of the analysis in a largely unbiased manner. Going forward, one can imagine such models revealing additional information on these processes, performing analyses of subpopulations that form the heart, and maybe most importantly, applying the model to various perturbation models (genetic or otherwise). The manuscript is very well written, and the data display is accessible and transparent.

      Weaknesses:

      No major weaknesses are noted with the study. It would have been very exciting to see the model applied to any kind of perturbation, for example, a left-right defect model, or a model with compromised cardiac progenitor populations. However, the amount of live imaging required for such analyses renders this out of scope for the current study.

      We agree with the Reviewer on the relevance of applying this pipeline to mutant conditions. We are engaged on those experiments but they represent a major effort beyond the scope of this manuscript, as also indicated by the Reviewer.

      Reviewer #3 (Recommendations for the authors):

      (1) Application of the model to defective heart development:

      While including perturbation models seems out of scope for the present work, some discussion on how the model might benefit our understanding of early cardiac defects, or any currently unknown mechanisms acting at this stage of development, could be included in the discussion of the manuscript. This would help highlight the enormous power that this new model could bring to understanding these critical steps during heart development, in a quantitative and unbiased manner.

      We thank the reviewer for this insightful comment. Our approach is a deterministic, descriptive framework that integrates individual tissue motion into a common spatiotemporal Atlas, providing a quantitative description of early HT morphogenesis. The primary goal of this framework is to establish a robust baseline of normal HT development under wild-type conditions.

      This baseline is essential for studying heart defects, as deviations from normal tissue motion and deformation patterns can reveal developmental defects like altered growth or aberrant morphogenetic trajectories. Currently, the limited number of embryos per developmental stage (typically 2-4) does not allow the construction of statistically robust inferential models. Nevertheless, by mapping all embryos into a unified reference system and providing quantitative descriptors of tissue motion, our framework already enables meaningful comparisons between normal and abnormal development.

      We have clarified this point in the Discussion section.

      (2) Confusion with Raiola et al., 2025:

      The manuscript frequently references an accompanying manuscript, which is currently a preprint on bioRxiv. The relationship of these two papers is not clear from the description. Not only is the majority of the data shared between the reports, but some figures seem to overlap quite substantially. The methods state that "the computational workflow is detailed in Raiola et al 2025". Any clarification on this would be helpful.

      We thank the reviewer for raising this important point and we appreciate the opportunity to clarify the relationship between the two manuscripts. The two studies indeed rely on the same underlying dataset; however, their aims and scope are fundamentally different. Raiola et al. (2025) is a purely methodological study, whose sole objective is to describe, validate, and benchmark a computational framework for spatiotemporal alignment, motion integration, and in-silico fate mapping. That work deliberately avoids biological interpretation, as the proposed approach is designed to be general and transferable to other organs or developmental systems.

      In contrast, the present manuscript represents the biological application of this validated framework. Here, the computational model is used as a tool to extract, characterize, and interpret biologically meaningful information about early heart morphogenesis, including myocardial motion patterns, regional growth and anisotropy, and fate relationships, supported by experimental validation.

      To avoid any ambiguity, we revised the Introduction and Materials and Methods to explicitly state this distinction and clarify why the methodological details are provided in Raiola et al. (2025), while the current manuscript focuses on biological insight rather than computational development.

      (3) Additional point:

      Concerning overlap with the authors' related manuscript in Bioarchive on the computational workflow: the number of specimens analysed should be noted without referral to the second manuscript (as currently mentioned in the figure legends). Is the "b" necessary when referring to the second manuscript?

      We thank the reviewer for this suggestion. We included the number of specimens analysed directly in the revised manuscript to improve clarity for the reader. Regarding the citation format, the "b" in Raiola et al. (2025) is used to distinguish between two manuscripts from the same group published in the same year.

    1. Author response:

      The following is the authors’ response to the previous reviews

      eLife Assessment

      This study presents valuable findings on the differential effects of RNA on the phase separation, aggregation dynamics, and bioactivity of PSMα3 and LL-37. The authors provide solid evidence from complementary biophysical and cell-based experiments that RNA influences peptide assembly and associated in vitro activities. The study is of interest for understanding interactions between amyloidogenic peptides and nucleic acids, although the physiological significance and some aspects of the mechanistic interpretation would benefit from further clarification.

      We are grateful for the positive assessment. The two outstanding concerns about physiological significance and mechanistic interpretation are addressed in detail below through Reviewer #2's comments. We have made targeted revisions throughout the manuscript, and have been careful to distinguish genuine clarifications from reframing that would misrepresent what the data show.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Rayan et al. aims to elucidate the role of RNA as a contextdependent modulator of liquid-liquid phase separation (LLPS), aggregation, and bioactivity of the amyloidogenic peptides PSMα3 and LL-37, motivated by their structural and functional similarities.

      Strengths:

      The authors combine extensive biophysical characterization with cell-based assays to investigate how RNA differentially regulates peptide aggregation states and associated cytotoxic and antimicrobial functions.

      Weaknesses:

      While the study addresses an interesting and timely question with potentially broad implications for host-pathogen interactions and amyloid biology, some aspects of the experimental design and data analysis require further clarification and strengthening.

      We thank Reviewer #1 for the positive assessment. Previous revision round incorporated all major quantitative additions requested:

      Quantitative EMSA binding analysis with Kd values and Hill coefficients (Fig. S1)

      Quantitative FRAP recovery curves with mobile fractions and half-times (Figs. S4, S8, S12)

      Colocalization metrics — Pearson's correlation coefficient and Manders' overlap coefficients (Fig. S5)

      Quantification of AmyTracker630 amyloid signal intensity (Fig. S6)

      Explicit acknowledgment of limitations regarding phase diagram boundaries and csat

      Revised interpretation clarifying nucleolar localization as phenomenological, not causal

      Reviewer #2 (Public review):

      In this paper, Rayan et al. report that RNA influences cytotoxic activity of the staphylococcal secreted peptide cytolysin PSMalpha3 versus human cells and E. coli by impacting its aggregation. The authors used sophisticated methods of structural analysis and describe the associated liquidliquid phase separation. They also compare to the influence of RNA on aggregation and activity of LL-37, which shows differences to that on PSMalpha3.

      That RNA impacts PSM cytotoxicity when co-incubated in vitro becomes clear. However, I have two major problems with this study:

      The premise, as stated in the introduction and elsewhere, that PSMalpha3 amyloids are biologically functional, is highly debatable and has never been conclusively substantiated. The property that matters most for the present study, cytotoxicity, is generally attributed to PSM monomers, not amyloids. The likely erroneous notion that PSM amyloids are the predominant cytotoxic form is derived from an earlier study by the authors that has described a specific amyloid structure of aggregated PSMalpha3. Other authors have later produced evidence that, quite unsurprisingly, indicated that aggregation into amyloids decreases, rather than increases, PSM cytotoxicity. Unfortunately, yet other groups have in the meantime published in-vitro studies on "functional amyloids" by PSMs without critically challenging the concept of PSM amyloid "functionality". Of note, the authors' own data in the present study that show strongly decreased cytotoxicity of PSMalpha3 after prolonged incubation are in agreement with monomerassociated cytotoxicity as they can be easily explained by the removal of biologically active monomers from the solution.

      In their revision and in the rebuttal, the authors have further described their concept regarding what they call "functionality" of PSMalpha3 amyloids. They now admit that monomers are the active cytolytic form, like other researchers have stressed, whereas amyloids are not. This represents a considerable difference to earlier papers in which they ascribed functionality, i.e. cytolytic capacity, to PSMalpha3 amyloids, a claim that has raised considerable controversy. Now, they use the term "functional " to describe that PSMalpha3 amyloids, while not cytolytic, can be reversed to a cytolytic monomeric state, calling them a "dynamic reservoir". There is no evidence that such a reservoir is necessary for the cytolytic activity of the monomers to be established; also, there is no evidence that in a biological system, such an amyloid reservoir exists. To continue calling PSMalpha3 amyloids "functional" based on this - considerably changed - concept of the authors appears inappropriate, given the finally admitted absence of cytolytic activity of the PSM amyloids in addition to the continuing complete lack of evidence of any biological relevance of PSM amyloid formation.

      That RNA may interfere with PSM aggregation and influence activity is not very surprising, given that PSM attachment to nucleic acids - while not studied in as much detail as here - has been described. Importantly, it does not become clear whether this effect has biologically significant consequences beyond influencing, again not surprisingly, cytotoxicity in vitro. The authors do show in nice microscopic analyses that labeled PSMalpha3 attaches to nuclei when incubated with HeLa cells. However, given that the cells are killed rapidly by membrane perturbation by the applied PSM concentrations, it remains unclear and untested whether the attachment to nucleic acids in dying cells makes any contribution to PSM-induced cell death or has any other biological significance. Overall, the findings can be explained in a much more straightforward way with the common concept of cytotoxicity being due to monomeric PSMs, and the impact of nucleic acids on cytotoxicity being due to lowering of the concentration of that active form by RNA attachment. Further limiting the significance of the findings, whether this interaction has any biological significance on the physiology or infectivity of the PSM producer remains largely unexplored.

      We thank the reviewer for the detailed comments. We appreciate the opportunity to further clarify our interpretation of the relationship between PSMα3 assembly, cytotoxicity, and RNA-mediated regulation. In the revised manuscript, and building on the previous revision round, we substantially expanded and refined the Discussion and Introduction to more clearly distinguish between mature fibrils, transient assembly intermediates, and broader assembly state-dependent mechanisms. We also incorporated additional literature representing different perspectives from the field. The revised manuscript presents a model in which biological activity is governed by dynamic assembly pathways and membrane-associated intermediates whose formation, persistence, and structural organization are modulated by environmental conditions, including RNA.

      A central point raised by the reviewer is the suggestion that the RNA effects observed here can be explained simply by sequestration of active monomeric PSMα3. We respectfully disagree that this interpretation can account for the data. A monomer-depletion model makes a clear experimental prediction: conditions that promote aggregation should proportionally reduce activity by reducing the free monomer pool. However, our data show the opposite behavior. RNA promotes PSMα3 aggregation, induces liquid–liquid phase separation, and reshapes fibril morphology into distinct polymorphic assemblies, yet preserves cytotoxic and antimicrobial activity over incubation periods during which peptide alone progressively loses activity. Thus, activity does not correlate with suppression of aggregation or maintenance of soluble peptide. Instead, the data indicate that assembly trajectory and supramolecular organization are functionally relevant parameters. We state this point explicitly in the section “RNA preserves PSMα3 bioactivity,” where we added text clarifying that RNA does not prevent aggregation but redirects the assembly pathway toward structurally and functionally distinct states.

      To further clarify our interpretation, we substantially revised the section “PSMα3 cytotoxicity arises from dynamic assembly intermediates.” This section now integrates multiple independent lines of evidence supporting an assembly-state-dependent model. Together, these observations argue against a simple binary model in which either monomers alone or mature fibrils alone determine activity. Instead, they support a framework in which transient intermediates formed along the assembly pathway contribute to membrane disruption and cytotoxicity. Consistent with this interpretation, our confocal and super-resolution microscopy experiments directly show PSMα3 accumulation and aggregation at bacterial and cellular membranes (Figs. 5, 6C, S10), supporting a model in which assembly occurs in direct association with membrane interfaces rather than exclusively in bulk solution prior to membrane contact. We expanded the Discussion accordingly.

      We acknowledge the reviewer’s alternative interpretation that the nucleolar/nucleic-acid association observed in HeLa cells may reflect post-lysis binding following membrane permeabilization. We agree that this is a valid consideration at the cytotoxic concentrations used here, where membrane disruption is rapid (Figs. 5–6, Movies S1–S2). The Discussion therefore clarifies that nucleolar localization under these conditions is unlikely to represent a distinct intracellular toxic mechanism, but instead reflects the intrinsic nucleic-acid binding capacity of PSMα3 after cellular entry. We accordingly do not claim that intracellular nucleic-acid interactions contribute causally to cell death in these experiments. The potential biological relevance of PSMα3–nucleic acid interactions at sub-cytotoxic concentrations, where membrane disruption does not dominate, remains an important question for future investigation.

      We additionally revised the manuscript to clarify the significance of the EGCG comparison. We agree with the reviewer that the EGCG data alone do not demonstrate “amyloid-mediated cytotoxicity,” and we do not make that claim. Rather, the comparison between EGCG and RNA provides evidence that different assembly trajectories produce different functional outcomes. EGCG redirects PSMα3 into amorphous, non-fibrillar assemblies that lose activity, whereas RNA promotes aggregation while preserving activity and generating distinct supramolecular morphologies. If activity depended solely on monomer concentration, both conditions would be expected to reduce activity similarly through sequestration. Instead, the divergent outcomes support the conclusion that assembly architecture and assembly pathway are functionally important.

      In response to the reviewer’s concern that the manuscript overstates the concept of “functional amyloid,” we explicitly distinguish between mature fibrils and dynamic assembly processes, and we avoid wording that could be interpreted as implying that mature fibrils themselves are the active cytotoxic entities. At the same time, we note that the broader concept of functional amyloid-like assembly pathways is widely used in biology to describe assemblies whose formation regulates storage, localization, stabilization, or timing of bioactive states, including hormone-storage amyloids, RNA-binding protein assemblies, and bacterial curli systems. Within this framework, our interpretation is that PSMα3 assembly dynamics modulate the availability and lifetime of bioactive species rather than that mature fibrils themselves are directly toxic.

      Importantly, we also broadened the manuscript substantially by incorporating independent studies from multiple unrelated systems supporting the principle that supramolecular organization influences biological function. These additions include: studies showing that structured fibrillar assemblies of LL-37 are required for specific antibacterial activities; work demonstrating that the nanoscale organization of β-defensin–nucleic acid complexes governs immunostimulatory potency; studies correlating α-helical solid-state conformations with cytotoxicity across fibril-forming antimicrobial peptides; salt-induced PSMα3 polymorphism studies showing distinct toxicities for amorphous versus fibrillar assemblies; and real-time AFM work demonstrating that membrane-associated protofibrillar intermediates are more disruptive than mature fibrils. We also added discussion of recent cryo-EM structures showing that RNA acts as a structural cofactor shaping tau fibril polymorphism at atomic resolution, as well as two-dimensional infrared spectroscopy studies demonstrating coexistence of cross-α and cross-β PSMα3 polymorphs. Together, these orthogonal observations from multiple systems support the broader principle that assembly architecture is a major determinant of biological behavior.

      We also addressed the reviewer’s concern regarding biological relevance. We agree that direct in vivo validation remains an important future direction and state this explicitly in the revised Discussion. However, we respectfully submit that establishing the mechanistic principle that RNA regulates PSMα3 assembly state and functional output is itself a meaningful contribution independent of immediate in vivo confirmation. To better contextualize potential physiological relevance, we expanded the “Biological and therapeutic implications” section to discuss biologically plausible extracellular environments in which PSMα3 may encounter nucleic acids, including biofilms enriched in extracellular RNA, extracellular vesicles, damaged host tissues, inflammatory milieus, and host-derived extracellular RNA released as DAMPs.

      Overall, the revised manuscript reflects a substantially expanded discussion of PSMα3 assemblystate-dependent activity, the role of RNA in modulating assembly trajectories, and the broader conceptual implications for membrane-active peptide assemblies.

      Further remarks:

      (1) Circumstantial evidence based on the "amyloid inhibitor", EGCG: The results with EGCG, which has been shown to have a moderate amyloid-reducing effect on PSMalpha 1 and PSMalpha4, should not be taken as evidence for amyloid-based cytotoxicity. While increased concentrations of EGCG reduced the cytotoxic effect of PSMalpha3, it is not convincingly shown that this is due to a lower concentration of amyloid vs. monomeric PSM.

      We agree that the EGCG data alone should not be interpreted as evidence that mature amyloid fibrils are the directly cytotoxic species. Our interpretation is more limited and focuses on the effect of assembly redirection. Specifically, EGCG redirects PSMα3 into amorphous, non-fibrillar assemblies that lose activity, whereas RNA promotes aggregation while preserving activity and producing structurally distinct assemblies. The key conclusion is therefore that functional outcome depends on the nature and trajectory of assembly rather than on aggregation versus non-aggregation alone. We clarified this distinction in the revised Discussion section addressing RNA- versus EGCG-mediated modulation of PSMα3 assembly.

      (2) It is appreciated that the authors refrain from presenting the unsubstantiated concept of "functional" PSM amyloids in the discussion. However, wording in that direction must also be removed from other parts of the manuscript (e.g. "bioactive fibrillar polymorphs". "The formation of cross-alpha amyloids has been correlated with toxic activity", etc.), generally refraining from uncritically implying that amyloid formation underlies PSM biological activity, and rather discussing that the much more likely explanation of the findings is a lowering of cytolytically active, monomeric PSM concentration.

      In the Introduction, the phrasing 'may enable dynamic switching' has been used to soften the mechanistic claim regarding cross-α assemblies. The phrase 'bioactive fibrillar polymorphs' was revised in the previous round. At the same time, statements such as “cross-α amyloid formation has been correlated with toxic activity” are retained because they describe experimental observations reported in multiple studies (including Tayeb-Fligelman et al., 2017, 2020; Malishev 2018), without implying direct causality (correlation is not causation). We now explicitly frame these observations within a broader discussion of transient assembly intermediates and assembly-state-dependent toxicity.

      (3) Discussion: "PSM alpha3 interaction with nucleic acids within human cells ...supports a comparable mechanism...". Delete. Unsubstantiated.

      This sentence was removed in the previous revision round and remains absent from the current manuscript.

      (4) The authors should cite papers that have argued against their hypothesis and not only their own manuscripts.

      We appreciate this suggestion and agree that alternative interpretations should be represented explicitly. In the revised manuscript, we added and discussed studies including Zheng et al. (2018) and Yao et al. (2019) (already cited in both earlier versions), which support models in which advanced amyloid formation reduces cytotoxicity and active species are prefibrillar. These studies are now discussed substantively in both the Introduction and Discussion alongside our own work and that of others.

      More broadly, we revised the manuscript to present the current understanding of PSMα3 toxicity as an actively debated question in the field rather than as a settled model. At the same time, we note that citing our prior studies remains necessary where the present work directly builds upon previously reported structural, biophysical, and mechanistic observations.

      If the reviewer has additional specific references in mind, we welcome them and will incorporate them.

    1. Author response:

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

      In preparation for release of the analysis code used in the paper, we made many analyses more parallel to one another in their exact preprocessing. This resulted in very slight changes to many panels, but these changes are nearly invisible and conclusions did not change. In one case, though, we realized that the way we were presenting data was potentially misleading (the timing plot in Figure 3A). The original plot was of the distribution of pixel values from the spatially smoothed map instead of distributions over individual neurons. We have now swapped it out for better interpretability and changed the accompanying text accordingly.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Here, the authors address the organization of reach-related activity in layer 2/3 across a broad swath of anterodorsal neocortex that included large subregions of M1, M2, and S1. In mice performing a novel variant water-reaching task, the authors measured activity using two-photon fluorescence imaging of a GECI expressed in excitatory projection neurons. The authors found a substantial diversity of response patterns using a number of metrics they developed for characterizing the PETHs of neurons across reach conditions (target locations). By mapping single-neuron properties across the cortex, the authors found substantial spatial variation, only some of which aligned with traditional boundaries between cortical regions. Using Gaussian mixture models, the authors found evidence of distinct response types in each region, with several types prominent in multiple cortical regions. Aggregating across regions, four primary subpopulations were apparent, each distinct in its average response properties. Strikingly, each subpopulation was observed in multiple regions, but subpopulation members from different regions exhibited largely similar response properties.

      Strengths:

      The work addresses a fundamental question in the field that has not previously been addressed at cellular resolution across such a broad cortical extent. I see this as truly foundational work that will support future investigation of how the rodent brain drives and controls reaching.

      The quantification is thoughtful and rigorous. It is great that the authors provide an explanation for and intuition behind their response metrics, rather than burying everything in the Methods.

      The Discussion and general contextualization of the results are thorough, thoughtful, and strong. It is great that the authors avoid the common over-interpretation of classical observations regarding cortical organization that are endemic in the field.

      All things considered, this is the best paper regarding spatial structure in the motor system I have ever read. The breadth of cellular resolution activity measurement, the rigor of the quantification, and the clear and open-minded interrogation of the data collectively have produced a very special piece of work.

      Thank you! We really, really appreciate this!

      Weaknesses:

      The behavioral task is very impressive and an important contribution to the field in its own right. However, given that it appears substantially different from the one used in the previous paper, the characterization of the behavior provided in the Results is too brief. More illustration of the behavior would be helpful. For example, it is rather deep into the paper when the authors reveal that the mice can whisk to help localize the target location. That should be expressed at the outset when the behavior is first described. Other suggestions for elaborating the behavior description are included below.

      Thank you. Although the task will be treated in greater detail in the next paper (where we more closely relate neural activity to the kinematics), we have added more exposition of the task here. In particular, we now include a figure with a characterization of the trial-to-trial variability across reaches to the same target versus across reaches to different targets (Figure 2-figure supplement 1B). This supports the idea that the mice aimed their reaches. We have also expanded that text.

      Regarding whisking, we have now revised that text to make clear that we do not know how the mice localize the spout. The original work by Galinanes and Huber argued that they find the spout by sniffing the water; they may do the same here, or may find it via whisking. It is also possible that the whisking they do is simply because the spout moves in and they are excited, or startled, or do it by reflex. We simply have no evidence one way or another. We have therefore revised the text to make it clearer that whisking-related activation could have occurred for a variety of reasons.

      Statistical support for key claims is lacking. For example, "The five areas of interest varied in the fraction of neurons that were modulated: M2 had 14%, M1 had 23%, S1-fl had 30%, S1-hl had 25%, and S1-tr had 27%" - I cannot locate the statistical tests showing that these values are actually different. Another example is Figure 7, where a key observation is that distributions of PETH features are distinct across regions. It is clear that at least some distributions are not overlapping, but a clearer statistical basis for this key claim should be provided.

      Good idea. For the proportions, we have now added first a Chi-square test for homogeneity to show that there is variation in the proportions, then shown the results of pairwise two-proportion Z tests (Bonferroni-corrected for multiple comparisons) as a binary matrix in Figure 3-figure supplement 1B. For the area distributions in the t-SNE space (Figure 7), we have added a 2-dimensional Kolmogorov-Smirnov test, again corrected for multiple comparisons, with p-values quoted in the text.

      I understand that the authors are planning a follow-up study that addresses the relation between activity patterns and kinematics. One question about interpreting the results here though, is how much the activity variation across target locations may relate to the kinematic differences across these different conditions, as opposed to true higher-order movement features like reach direction.

      We agree this is a very important question. However, having done many of the analyses to examine the question for the next paper in the series, we do not know of a shortcut to the right answer. This question requires thorough treatment, and so we leave it to be covered in subsequent work. Instead, after our speculation about how responses suggest function, we are now explicit that these hypotheses needs testing:

      “In each of these cases, determining the relationships of the observed activity patterns to function will require specific attempts to link the activity to kinematics, target location, sensory feedback, and more; these relationships will be addressed in future work.”

      Reviewer #2 (Public review):

      Summary:

      The functional parcellation of cortical areas is a critical question in neuroscience. This is particularly true in frontal areas in mice. While sensory areas are relatively well characterized by their tuning to sensory stimuli, the situation is much less clear for motor areas. This has become even more ambiguous since recent studies using large-scale neuronal recordings consistently report mixed sensory and motor-related activity throughout the brain, and motor mapping studies have shown that movements evoked by cortical stimulation are by no means limited to motor areas alone. Here, the authors use a correlation approach combining large-scale functional imaging at cellular resolution with movement-tracking in mice executing a reaching task. Across multiple recording sessions in the same animals, the authors have imaged a large portion of the sensorimotor cortex at cellular resolution in mice performing a reaching task, recording the activity of nearly 40,000 neurons. By aligning the calcium signal of each neuron to three task events-the Go cue triggering the reach, the onset of paw lift, and the contact between the paw and the target-for different target positions, the authors identified different response patterns distributed differently across cortical areas. They defined a set of features that describe the neurons' response pattern, representing the temporal dynamics and tuning properties for the different target positions. These features were used to construct cortical maps, and the authors show that, interestingly, gradient maps obtained from the first derivative of the feature maps reveal sharp discontinuities at the boundaries between anatomically defined cortical areas. Using dimensionality reduction of the neuronal response features, the authors found that, despite clear differences in their average response properties, individual neurons from the same cortical areas do not form distinct clusters in the reduced-dimensional space. In fact, most areas contain heterogeneous neuronal populations, and most neuronal populations are present in multiple areas, albeit in different proportions. Interestingly, the authors identified four neuronal subpopulations based on the distance between the components of the Gaussian mixture model used to model the distribution of neurons within each area. One of these subpopulations is almost exclusively represented in the anterior M2 cortex, while another is broadly distributed across the different areas.

      Strengths:

      This article is based on an impressive dataset of nearly 40,000 neurons covering a large portion of the sensorimotor cortex and on innovative analytical approaches. This study is likely the first to clearly demonstrate boundaries between cortical areas defined based on the responses of individual neurons. This innovative approach to functional mapping of cortical areas potentially opens up new perspectives for higher-resolution mapping of frontal cortical areas, using a broader repertoire of sensory and motor evoked responses.

      Thank you!

      Weaknesses:

      The second part of the article, which presents multimodal responses in the cortical areas, seems to be a perhaps overly complicated way of showing what has already been demonstrated in numerous recent publications, but these new analyses expand upon these previous observations by revealing an interesting functional organization of the sensorimotor cortex, highlighting interesting similarities and differences between certain areas.

      We understand the concern: a number of recent papers have also noted different neuron response characteristics distributed throughout the motor system. We compare and contrast in greater detail following the more specific comments on this below, but we briefly summarize here. The way previous work handled the data – for example, starting with PCA – mixes what neurons are tuned for and when they are tuned for it with what we refer to as the “response format”: properties like tuning sharpness, response duration, etc. We focused primarily on this response format, and designed our features to be mostly independent of tuning preferences or peak response timing. We therefore pick up on different properties of neurons’ responses than those prior works. In addition, no previous work we know of examined these properties across large swathes of cortex at single-cell resolution in the context of forelimb control. Together, these aspects of our work allowed us to produce high-resolution mapping of response properties in a way we have not seen in any prior work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In addition to addressing the weaknesses stated above, I suggest the authors also consider the following.

      The one big question left unresolved here is whether we should be thinking about these four subpopulations as distinct types with a biological basis and importance, or just reflections of activity pattern heterogeneity. The authors say that "we did not observe tight clusters in feature space separated by gaps," but their discussion here is light and a bit unclear, and their engagement with the issue of types versus heterogeneity, in my view, could be improved. We do not need "gaps" where the density goes to zero in parameter space, but we do need reproducible troughs between peaks. The authors should clarify if there are substantial and reproducible troughs in the parameter space between their four subpopulations.

      This is a great idea, and we have added three analyses and additional text to address it. We break this concern down into two more specific questions, based on the next comment by this reviewer.

      (1) Are the clusters well separated / do they have troughs between them? (Note that even with troughs, clustering might not be stable if the clustering algorithm is poorly matched to the shapes of the clusters.)

      (2) Is the clustering stable? (It can be stable even without troughs, if, for example, the distribution has a long tail and a GMM needs one Gaussian for the body of the distribution and a second for the tail.)

      First, to directly address the presence or absence of troughs between clusters, we have added Figure 9-figure supplement 2A and 2B. For each pair of subpopulations, we trained a logistic regression classifier to separate the 5D feature vectors of the neurons in one subpopulation from the feature vectors of the neurons in the other subpopulation, then projected the feature vectors onto this axis. Note that because the subpopulations are defined by GMMs, which have nonlinear boundaries, the (linear) logistic classifier does not typically produce perfect classification. Nevertheless, this analysis provides a window onto how well separated each cluster is from each other cluster in feature space. In 5 of the 6 pairwise comparisons, it is obvious that the distributions are different and have at least some dip in the distribution density at the boundary. The one pair of clusters without a trough between them were the forelimb somatomotor and hindlimb somatomotor subpopulations. This was surprising to us, given that their likelihood maps are so strongly distinct, but this presumably reflects trying to capture a nonlinear classifier boundary with a linear one (see below). Overall, this analysis argues that the clusters do have fuzzy edges that blend into one another, but reflect concentration of mass near the centers of the clusters we identified.

      Second, to address the same question with a different nonlinear method, we have added a version of the t-SNE plot from Figure 7 that is instead colored and contoured by subpopulation identity instead of area (Figure 9-figure supplement 2B). Agreement with the GMMs is not a given here either, because t-SNE is a fundamentally different and independent nonlinear transform from that performed by the GMM classification. Nevertheless, the subpopulations were again nicely separated – though not with troughs, possibly thanks to the inherent difficulty of interpreting point density with t-SNE. Interestingly, here the hindlimb somatomotor subpopulation was the best separated from the other subpopulations, supporting the idea that the lack of separation we observed above with the logistic projections was indeed due to a nonlinear boundary. This analysis again argues that neurons are more likely to have features that lie near the center of a cluster, but that the edges of the clusters run into one another. Additionally, this analysis makes clear that treating the hindlimb somatomotor subpopulation as a second cluster can be supported by other analyses, even if not by the logistic regression projection.

      Third, to address the question of cluster stability, we have performed random splits of our data, GMM clustered the two halves independently, applied the GMM from one half to the other, and asked how similar the clusterings are using the Adjusted Rand Index. This produced a value of 0.856, which for this sensitive measure argues that the clustering is rather stable (at least for the three clusters that can be found with all data together, which does not include the smaller-in-size Anterior subpopulation). Note that we did not perform this analysis on the more complicated version where we fit a GMM to each area separately then cluster those; in our main analysis, the hierarchical clustering agreed with what we found by eye, but determining the number of clusters for hierarchical clustering is in general very unstable and so we did not have an objective way to determine the “true” number of clusters.

      In addition to these new analyses, we note that three analyses we had already included bore strongly on this issue. Regarding separability of the clusters, the fact that our likelihood maps (Figure 9C-F) were quite distinct for different subpopulations argues that we picked up on ‘real’ differences. Second, Figure 9B found that when clustering non-overlapping data – different cells from different areas – we obtained clusters that were nearly identical in their feature distributions. Third, Figure 10E used the clusterings from different areas’ data to create likelihood maps, and found that they were extremely similar. These analyses together argue strongly that we are finding ‘types’ in a meaningful sense; given that we know the areas do have different distributions of properties, if there weren’t types then clustering would yield different clusters for different areas. Given the importance of the question, however, we are grateful that the reviewer encouraged us to find additional ways to make this point!

      The original t-SNE plot is beautiful and quasi-fractalic, but it does not show clear signs of four cell types. The single-neuron activity profiles are clearly heterogeneous in very interesting ways, but heterogeneous does not imply a strong or reproducible multimodality that would indicate meaningful cell types. Clustering algorithms will always spit out an answer. If you just have elements uniformly distributed across a parameter space, plus some noise, when you ask for X clusters, you will get X clusters that have different centroids. When you ask an algorithm to cluster without defining the number of clusters, noise can lead the algorithm to produce a particular number of clusters that again will have distinct centroids. The salient question, though, is whether in the present case there is a parameter space in which the clusters are substantially and or reproducibly distinct. Distinct here would mean that peaks in the density across some parameter space are separated by troughs - again, we don't need true gaps. The more substantial the differences between clusters are (again, not the differences between centroids but the prominence of the density troughs between them), the more biologically meaningful the clustering is likely to be. Reproducibility here could be addressed with resampling methods (e.g., how often do two separate halves of the cells produce the same clusters?).

      Please see the reply above, which includes our addressing of this concern.

      The Introduction is generally good, but it could further develop existing ideas about how function is distributed across cell types and regions. We would like to be able to imagine different answers to the question of how activity patterns are organized that might have divergent implications for how the circuit works. I understand we have very little to go on in terms of data, but I think it would be helpful for readers to be given more of a sense of what *could* be important.

      Good idea. We have added such a paragraph to the Introduction:

      “To frame possible outcomes, consider that single neuron responses can vary along many dimensions. Cells could differ according to which movements or time periods they are recruited for (tuning), what movement parameters their activities reflect (encoding), or how their responses are structured across different movements (e.g., nonlinear encoding structure). Further, differences in these response properties across cells could be distributed over the cortical sheet in a variety of ways. Cells could form distinct “categories” or clusters that are spatially well-aligned to the boundaries of anatomically defined regions. Or, categories of neurons might span area boundaries in spatial footprints that do not relate obviously to area boundaries, and that either abut or overlap. At a fine-grained scale, cells with similar responses could be physically located near one another as in primate and feline visual cortex, or similarly-responsive neurons might be salt-and-pepper intermingled as seen in rodent visual cortex or in primate motor cortices during reaching behaviors.”

      It should be clarified in the Results how the cue relates to the target location. Most would assume a different cue for each location, but this does not appear to be the case. The authors should clarify whether there was some amount of searching for the precise target location after the reach, or else how the block structure or other sensory information allowed mice to learn where exactly the target would be. In the absence of target-specific cues, some sense of how the mice achieved target-specific reach trajectories should be offered.

      Related to this, in Figure 1, it would be good to see some individual trajectories, as they all overlap near the target in the current plot. Clearly, the reaches were targeted, but it is unclear how targeted. Some of the adjustments at the end may reflect searching or palpation to resolve the precise spout location. It is very much ok if the mice were not reaching with micron precision each time to each of 15 different targets, but it would be good to provide the reader a better sense of what the mice were doing.

      These are important points. First, to clarify, the Cue is just a Go cue, and was the same for all targets. It is now described in the Results as “non-target-specific”. For additional explanation about supplemental analyses to assess “aiming”, see replies to Reviewer #1 Public Review comments above. Finally, regarding how the mice locate the target: we just don’t know. As discussed above, Galiñanes and Huber found evidence for the mice using stereo sniffing, but whisking, listening to the motors, or some other strategy are also conceivable. We simply don’t have data to weigh in on this. We now make this limitation clear where we describe the task.

      In Figure 1A, CFA does not look well aligned with Tennant et al. (2011). CFA should only extend to +1 AP. The overlap of CFA and RFO seems strange. RFO also does not totally align with the injection coordinates used in An et al, biorxiv 2022.

      Thank you for your attention to these points. Our designation of the name CFA to the red dashed outline in Figure 1A was consistent with an earlier version of our previous work (Grier et al 2026) wherein we referred to the anatomical outline “MOp-ul” from Munoz-Casteneda et al 2021 as CFA. We have since revised that nomenclature to now refer to the outline as M1-fl, or the forelimb representation of primary motor cortex.

      Our placement of RFO was obtained by aligning the Allen CCF from Figure 1K of An et al 2022 to our version of the Allen CCF and outlining the hotspot of RFO with a circle. We have slightly adjusted the location of RFO posterior and medial to more closely align with the injection coordinates reported in the methods of An et al. 2022 of “1.5-1.88 mm anterior from Bregma, 2.25-2.63 mm lateral from the midline.” Because (as far as we understand) the injection coordinates and the map are not perfectly in register, we show a compromise between the two.

      We stress that the Figure 1A map is meant to be descriptive in its illustration of the variety of organizational zones that have been identified across mouse sensorimotor cortex.

      Discrepancies in the alignment procedure, animal strain, and mapping modality all introduce heterogeneity across mapping attempts that we do not aim to reconcile or resolve here.

      Related to this, aspects of the results do seem consistent with the distinction between RFA and CFA, but this is not acknowledged or discussed. For example, the barriers in Figure 6H that lie along the M1/M2 border - these seem consistent with the gap between RFA and CFA. The same could be said for the dim trough along the M1/M2 boundary that appears to separate RFA and CFA in Figure 3B. A slightly more rostral and lateral location of CFA compared to Tennant's definition or the regions backlabeled from cervical spinal injections (see Wang, Maunze et al. J Nsci, 2018) could be expected if flattening the brain under the coverslip for imaging effectively stretches the ML axis, and Bregma (notoriously hard to define reliably at this spatial scale) was defined a bit more caudally here than in other studies. Related to this, it would be better for the field if people described their method for defining Bregma in the Methods. I suggest the authors do this here.

      We appreciate the suggestion and have acknowledged the suggested correspondence in the discussion. Given the difference in our approach from those that originally characterized RFA (through ICMS and deep layer projection tracing) we have avoided making overly strong conclusions about this correspondence in our data. See the quoted text below.

      “The spatial distribution of modulated cells in Figure 3 suggests a distinction between the caudal forelimb area (CFA, involving M1 and S1-fl) and the rostral forelimb area (RFA) in M2, while the feature gradient boundaries suggest a distinction between M1 and M2 more generally. The absence of a clearly delineated RFA was surprising, given its distinct projection patterns (Carmona et al. 2024; Hira et al. 2013b; Wang et al 2018) and functional differences from CFA (Kristl et al. 2025; Morandell and Huber 2017; Saiki-Ishikawa et al. 2025), but our results might suggest that the activity in layer 2/3 of RFA does not differ markedly from other nearby subregions of M2.”

      Regarding bregma, we did not use it for atlas alignment here. Alignment was accomplished through a combination of paw vibration mapping and the location of the central sinus. Bregma’s location was only relevant for our injection of tdTomato labeling, and that labeling was used here only to stabilize the image plane. We include an estimate of it on the map solely in an attempt to be helpful, but we cannot claim we have the most reliable method for defining it.

      The authors focus on activity aligned to cue timing. This is sensible, but it could be meaningful to know how this choice affects the definition of organization. If response clustering is largely different across time, it would seem important. I understand that addressing this question may be beyond the scope of this paper. I just wanted to raise the issue with the authors for their future consideration.

      We agree that this is important to address directly. There are two aspects to this comment: (1) does it matter if activity from approximately the same time period is aligned to the paw lift or contact instead of the cue? (2) What changes if we use data from a different period of time?

      Regarding the first question (alignment), if we switch to aligning our data based on lift or contact, we have more statistically modulated neurons (see Figure 3C), but everything else is qualitatively similar with one exception: the GMM optimization doesn’t separate out the Anterior subpopulation from the Forelimb Motor subpopulation. The Anterior subpopulation only has a relatively small number of members, and they mostly exhibit the strongest peaks in their PETHs when Cue-aligned, so this makes sense. We now show the modulation maps for all of the locking events (Figure 3-figure supplement 1).

      The issue of the time window is a little more complicated. There are many choices we made in this work, of course, not least of which are the task we used and the features we chose based on hand-inspection of thousands of PETHs. As we noted in the Discussion, different tasks or different features would likely distinguish more subpopulations from one another. We think of the time window as a feature choice, albeit an implicit one. We chose not to include later time points because this begins to strongly include reward signals, which are known to be large (Levy et al 2020) and can dominate other aspects of the responses. The largest differences we noted when trying time windows that extended later are that mouth-related areas are separated out in the subpopulation analyses, perhaps because of later licking/consummatory responses, but we have not explored fully enough to speak confidently on this point without much more work and another 10 figures. To keep the scope of the paper manageable, we now call out this choice explicitly (see text below). We thank the reviewer for raising these important points.

      “Crafting additional PETH features, or using end-to-end neural network approaches to discover other features, might enable the discovery of additional structure (Minderer et al. 2019; Wang et al. 2023b). For example, our PETH features were chosen to be invariant to the onset time of activity, but these onset times were markedly later in lateral M1 than in adjacent M2 or S1-fl. Including onset times, using a wider window of time that includes more of the reward/licking period, aligning data to other behavioral events, or adding other PETH features would presumably result in finer subdivisions of sensorimotor cortex.”

      The map in Figure 4 is very cool, and the spatial structure is quite striking. In terms of the actual values of the onset times in each region, I am a little concerned with a dependence on the level of reach-related activity modulation, especially relative to the level of background activity (potentially related to posture). Less reach-related activity and more background activity, which we might expect for trunk and hindlimb regions, could seemingly skew the onset times earlier. We could be getting the right answer, or an answer that makes intuitive sense, for the wrong reason. Can this potential confound be excluded with some sort of control analysis?

      The previous text wasn’t clear. We have now clarified what we meant, very much in line with the reviewer’s thoughts. In addition, note that our change to what is displayed in the histogram (now neurons, previously pixel values) makes clearer that there is a multi-peaked distribution of onset times and it is mostly the prevalence of each peak in each area that varies. The text now reads:

      “These distributions over neurons revealed clear differences in the overall profile of activation: early onsets were more prevalent in S1 trunk and hindlimb regions, perhaps due to activity related to the animal stabilizing itself even if the neurons became more active later; then M2, and finally S1-fl and M1. Nevertheless, each area contained neurons activated at any given time in the trial.”

      The "Peak time variation" metric could potentially vary with activity level, with lower, noisier activity levels making cells appear less persistent. Perhaps a control analysis, based on SNR or some reasonable assumptions of the linkage between calcium signals and spiking, could be performed to measure the extent to which this could be creating differences between regions.

      Good idea. We have now performed this analysis, and the reviewer was correct: the correlation between peak time variation and a simple metric of SNR (assessed as range of PETH / max s.e.m.) was substantial: ⍴=-0.53. We now report this correlation and describe in the Results that this metric is driven by both true peak time variation and trial-by-trial variation. Thank you for this!

      “Peak time variation. To quantify whether a neuron’s firing peaked at the same time for every target or varied by target, we found the peak firing rate of the response to each target, then computed the standard deviation of these peak times across targets. This value is therefore higher if the peak time varied and nearly zero if the timing was consistent. Notably, this measure correlated substantially with overall signal-to-noise ratio of a neuron’s PETH (Spearman’s ⍴=-0.53; Methods), and thus partly measures trial-to-trial variability, not just true peak timing variability. This metric was quite low in M1, indicating highly consistent timing of the activity peak (and reliable responses), and was highest in the posteromedial part of M2 (presumably corresponding to the hindlimb representation) and the posterior tip of S1-hl (Figure 5B).”

      One could argue that the likelihood calculations illustrated in Figure 8 are biased higher for neurons within each region since they were used for defining the likelihood for that region. I think these likelihood calculations should be done for separate neurons other than the ones used to compute the mixture model for each region.

      We agree with the point about bias: the by-area GMM in Figure 8 is biased toward cells within the area, though the effect is probably quite mild given the large numbers of neurons and modest number of parameters. However, this model was intended to make the point that even if you give an area an unfair advantage, you still can’t cleanly isolate it. This was intended to help motivate the following analysis of subpopulations, and we have now made this logic clearer. Doing it this way has the advantage that the GMM components are identical between Figures 8 and 9, while if we held out the test neurons it would not be possible to make them the same without some complicated version of bagging on the GMM components. The reviewer is right that we should make this bias explicit, though, and we have now done so:

      “This mapping approach is explicitly biased toward finding feature differences between areas, allowing for a direct test of the hypothesis that response profile distributions are area-specific.”

      To me, the last Results section (Spatial overlaps between subpopulations indicate intermingled members) does two things: it shows you get the same results when you map each cell to a subpopulation independently of its area, and it shows that defining the subpopulations with cells from each area gives you essentially the same results, arguing against spatial variation of properties within subpopulations. I worry that these two points are getting merged together or not made clearly enough here, especially the first one. In general, the logic of this section does not seem well conveyed.

      Thank you for the feedback. In particular, your first point is made by Figure 9-figure supplement 4 when we fit an area-agnostic GMM to all modulated cells in the five main areas. However, your second point is one of the two main goals of the last Results section, along with the demonstration of the spatial distributions of cells after hard-clustering them by subpopulations. We have tried to clarify these main points further through substantial edits of the results section for Figure 10.

      One set of ideas that is highly relevant and should be raised concerns an ethological organization of the motor cortex. Since the observations of Graziano, there has been a steady stream of results describing ethological organization in rodents as well. This literature is briefly reviewed in Kristl et al., Nature Communications, 2025. For example, because of the potential for a differential involvement of grasping movements across different target locations, some of the variation in neuronal tuning described in the present manuscript may stem from a region preferentially involved in grasping.

      We agree that the Graziano literature, and the substantial literature in rodent that was inspired by Graziano’s work, is highly relevant to understanding the organization of motor areas. Kristl 2025 handles these issues very thoughtfully. The challenge here is that there are many possible different reconciliations of the stimulation results with ours, and some seriously unresolved challenges in doing so. To name a few:

      Our subpopulations and high-gradient boundaries both give quite different pictures than microstimulation does in rodent motor and sensory cortices. In particular, microstim produces more subregions that evoke different movements than we identify, and the borders don’t generally line up. This implies that the mapping between the two approaches is probably complicated.

      There is a completely alternative possibility to explaining the Graziano-like results: microstimulation is thought to preferentially hit axons, and some of these projections reach the medullary motor regions. Given that the medullary motor regions have known topography in the movements they evoke (Yang et al 2023) – but may or may not be driving the movements during flexible behavior – the two approaches may not be reconcilable. Or, it may require a much deeper understanding of medulla as driving the primary movement and cortex acting as a residual controller. This is an exciting set of ideas, but as yet very underdeveloped in our understanding.

      We don’t know if the subpopulation structure exists at all in L5, or in the PT cells, and if it does whether it differs. This is crucial given the frequent targeting of deep layers by ICMS stimulation protocols.

      As we caution in the Discussion, it is possible that our subpopulation findings are at least partly specific to the task we used.

      Although it is beyond the scope of this paper and will be addressed thoroughly in separate work, we have spent significant time with encoding models for joint angles and high-level target encoding in these same data. Given those results, we are fairly confident that the reviewer’s reasonable guess, of tuning variation due to intersections between body parts, does not seem to be the main driver of the subpopulation structure we find.

      After careful thought and discussion amongst the authors, we did not think that including this discussion in the paper was likely to improve interpretability of the present results for most readers. We very much agree with the point, though, and when we can narrow down the possible explanations in the future (likely in our next paper on this topic, which will address encoding) we plan to address it. We thank the reviewer for encouraging us to think through this.

      Minor:

      (1) Page 3: "densely shared" - perhaps "broadly shared"? Dense implies most/all the neurons get the same signals, which may not be true.

      Changed to “widely”.

      (2) Page 4: "data-driven approaches" - could be more specific - isn't everything we do data-driven?

      Changed to “bottom-up”.

      (3) Page 4: "spanned areas" - perhaps "spanned multiple cortical areas", since everything spans an area.

      Changed to “spanned multiple areas” (we mention cortex just a few words earlier).

      (4) Page 5: "intervals were generally fast" - awkward, "short" perhaps.

      Agreed, changed.

      (5) Page 5: "which asks whether the activity for a neuron changes over time consistently in relation to any target" - Rephrase to disambiguate between consistent temporal variation in firing for all targets and variation across targets in the firing patterns. In other words, are we talking about cells that are just modulated during reaching, or cells whose firing patterns differ across targets?

      Changed ending to “to any given target”. The ZETA measure really does simply ask whether there is a change in firing rate over time that is consistent across trials, for each target independently. A neuron that exhibits an identical bump for all targets would register as modulated. We chose this measure in part because of the number of temporally-modulated but untuned cells. This wasn’t very clear as we had written the text, so we now note this explicitly in the Methods. Thank you for pointing out that this wasn’t clear.

      “For all analyses, only neurons modulated by the relevant locking event were included. Note that this measure looks for modulation over time to any target; it is indifferent to whether the neuron exhibits tuning across targets.”

      (6) Figure 1: It seems like some of the abbreviations used in 1A have not been defined yet in the paper.

      Yes. It’s a long list, and we wanted to put the citations for the description of each area together with the definition of the acronym. Moreover, we wanted all this info together with the description of how we aligned these area descriptions from others’ work with one another on the Allen atlas. This was impractical in the caption, and would be a long digression for what is intended as a simple point in the Results, which is why we refer to the Methods here.

      (7) Page 8: "Given that these areas have known spatial organization within them and structure was apparent by eye in the spatial scatterplot of modulated neurons (Fig. 3A)," - it is not clear what spatial structure we are supposed to see in 3A.

      Good point. We have changed the parenthetical to: “(for example, the less modulated band along the M1/M2 border in Fig. 3A)”

      (8) Page 8-10: The region-wide onset analysis breaks up the flow from PETHs to the metrics used to quantify them. I suggest moving this section (Onset of neural activity varied with somatotopy and subregion) to later in the manuscript.

      We appreciate the reviewer’s input on organization. We went back and forth many times in how to organize the many results in this paper. The reviewer is right that this analysis breaks the flow, but the reason we included it where we did was threefold. First, it uses an easily-understood metric to introduce the reader to how we made maps from single-neuron features. Second, it easily introduces the power of making such maps. Finally, it makes clear that if we are not careful with how we handle time in the feature design, timing will dominate.

      All these things said, this has helped inspire us to add a result in which we re-examine timing broken down by subpopulation (Figure 9-figure supplement 2C). It shows that subpopulations timing distributions appear more distinct than distributions for areas, but there is still substantial heterogeneity in timing that is explained by location in cortex and not subpopulation membership alone.

      (9) Page 12, Target tuning linearity: This metric should be clarified in the Results. It is not clear how the 2D of targets is turned into 1D. Also, the plot in the figure has correlation on the y-axis, and it is not clear how each target location gets its own correlation value. The phrase "optimized anchor target" is unclear.

      Agreed this needed to be clearer. The text in the Results now reads: “To quantify how linearly a neuron’s activity related to target location in physical space, we correlated the 15D vector of mean activity of the neuron for each target with the 15D vector of the targets’ ordinal distances from the neuron’s preferred target (Methods).” In agreement with your suggestion, we have dropped use of the phrase “anchor target” in favor of “preferred target”, which should be clearer. We have also revised the Methods text accordingly to clarify.

      To directly answer your question, we turn the targets from 3D positions into 1D by computing the ordinal distance of each target from a preferred target. (Note that the preferred target is actually the one that maximizes the resulting correlation; this is detailed in the Methods). There therefore aren’t 15 correlations; we’re correlating two 15D vectors, where each has one element per target and the “ordinal distance” vector has a zero for the preferred target. Hopefully the new description makes this clearer.

      The figure schematic was unclear, thank you for catching that. We have updated the Y axis to read “mean activity” and the X axis now reads “dist. to pref. target.”

      (10) Page 12, paragraph beginning "We also compared our metric maps simply using the top 20 PCs." - This paragraph is unclear, since both sentences refer to using the metrics. I would guess the authors mean that the metric maps were compared with and without PCA and basis rotation, but this is not clearly stated.

      Thank you, this was unclear as written. We have changed it to:

      “We also compared our metric maps with maps generated from the top 20 PCs of the PETHs (Methods), rotated using VARIMAX to identify a sparser basis (Musall et al. 2019).”

      (11) Page 18: "These results make clear that the working hypothesis - of areas with well-separated feature distributions - is incorrect." This is the clearest statement of the impact of the results. The authors could consider including this in the Abstract or Introduction.

      Thank you for pointing this out. We agree, and have added a similar phrase to the Abstract.

      (12) Figure 9: It would be great to also just see the average PETHs for each of the four clusters to get a better sense of how their time series differ.

      Good idea. The feature computations are a many-to-one mapping, so it’s not possible to literally generate a PETH from the mean of the cluster, but we have added PETHs from well-modulated neurons that are near the means of their subpopulations (Figure 9-figure supplement 1).

      (13) Figure 9B: Colorbar has no label.

      Fixed, thanks.

      (14) Figure 9C: Need a colorbar - need to see the difference in density for locations.

      The color map is the same Figure 8B, which is now noted in the caption for Figure 9C. The scaling of likelihoods is almost totally uninformative; they’re not well-behaved like probability distributions, so you’ll note that even on Figure 8B the labels are simply “max likelihood” and “min likelihood”. The important pieces of information here are that these are log likelihoods (noted in the Figure 8 caption), and the visualization of the color map itself (from the color bar). Given these considerations, we have elected to keep the maps themselves a little larger by not trying to squeeze in a minimally-informative colorbar to all of the plots, but thank you for noting that the reference to 8B was needed.

      (15) Page 22: "additional spatial structure could be present" - The nature of the additional spatial structure here is a bit opaque. The authors could clarify what additional structure may be present.

      Good idea. This paragraph now reads:

      “The overlaps in the subpopulation likelihood maps above imply that members of different subpopulations are spatially intermingled, but it is less clear whether each subpopulation has homogeneous response profiles across space. In particular, the use of likelihoods mixes two properties: the fraction of neurons in a given neighborhood that are members of each subpopulation, and the heterogeneity of response profiles amongst members of that subpopulation. These properties could vary systematically with respect to one another, and the spatial structure shown by the likelihood map does not disentangle them.”

      (16) Figure 10E, legend: "GMM component" - I think this should be "GMM subpopulation" to avoid confusion with the previous use of "component" above, referring to the components of the GMM models for each region.

      Thank you – good catch. Changed to “Likelihood map”.

      (17) Page 24: "Note that this consistency also validates the use of clustering to combine components and identify the subpopulations in the first place." - I don't totally get this, and how this result validates the method of combining components, as opposed to just clustering all the cells from all regions at once. Perhaps the implied opposing strategy is not clear here.

      We have changed this sentence to:

      “Note that this consistency mirrors the low Bhattcharyya distances between corresponding GMM components in Figure 9B, and further validates the use of clustering to combine components from different areas.”

      Regarding the reviewer’s larger point, we have three thoughts. First, we do also show the result of fitting the GMM to all cells together (Figure 9-figure supplement 4).The result is similar, but the Anterior subpopulation is lost because its membership is low and so the ICL criterion can’t justify a fourth cluster. Second, because we imaged more neurons in some areas than others, fitting the GMMs to each area separately put their representations on a more equal footing. Finally, doing the analysis this way allowed us to most directly compare our two hypotheses, as illustrated in Figures 8A and 9A.

      (18) Page 25: "in the zones where different subpopulations overlapped" - I would omit this, since "intermingled" seems to mean exactly this.

      We included this phrase to prevent quickly-skimming readers from incorrectly concluding that the subpopulations overlapped entirely and were therefore intermingled everywhere. The reviewer is right that it’s unnecessary for a careful reader, but we aimed to prevent misinterpretation by readers that might skip to the Discussion for a results summary.

      (19) Page 25: "content of the activity, but also its format" - the difference between content and format is not entirely clear. Metaphor not quite metaphoring here. Agreed. We have added examples to clarify.

      “This makes clear that there are potentially important differences not just in the content of the activity (e.g., encoding target vs. movement commands (Grier et al. 2026)), but also its format (e.g., linear encoding vs. nonlinear, persistent vs. brief responses).”

      (20) Page 30, bottom: In the description of the behavior, more details should be provided, especially since the paradigm is new. For example, it says the block size was reduced - what was the ultimate block size?

      Targets were cued randomly in the behavior performed during neural recordings. Blocked trials were used during training and were phased out incrementally as performance improved. This and various other details have been added. Please let us know if there are other specific details you would like to see in the final version.

      (21) Page 39, citation of An, Mulcahey et al.: There is a biorxiv version with a different author list that could be cited.

      This was an error with our citation manager, and has been corrected. Thanks for catching it.

      Reviewer #2 (Recommendations for the authors):

      Overall, this is a remarkable study with well-designed in-depth analyses, and I only have some minor suggestions that could help improve the clarity of the paper.

      Thank you!

      General:

      It is not immediately clear to me why the GMM approach used in this study is more interesting than a clustering approach based on single-neuron response patterns (See Esmaeli et al., Neuron 2021 or Oryshchuk et al., Cell Report 2024). But my impression is that it led to the same observation that most clusters are widely distributed across cortical areas, with different proportions, but a few clusters are quite specific to a few areas. A noticeable difference perhaps is the number of clusters - or response profile - that seems particularly low (only 4) in the current study. Could the authors clarify and comment on that, maybe?

      The reviewer brings up an interesting point: at heart, these works ask related questions, albeit about different effectors, tasks, recording modalities, and types of information encoded. Those differences probably mean that results cannot be directly compared, but we can certainly discuss the methodological tradeoffs. The two papers mentioned take a more traditional first step, using PCA on the vectorized PETHs to reduce dimensionality, then layer on a spectral approach to improve clusterability. These are good methods; we use something similar as our alternate method, applying VARIMAX to the PCs instead of spectral methods to preserve linearity of transforms. For the kinds of responses both they and we have, PCA will tend to most strongly pick up two aspects of the responses: tuning and timing. This is because vectorized PETHs will have large values in the rows corresponding to the target/condition and time points where the high activity is, and the alignment of these profiles with those of the other neurons will capture a large fraction of the variance. For data like either theirs or ours, this would tend to cluster apart left-tuned cells from right-tuned, and (more importantly here for revealing spatial structure) early-response cells from later response cells. That intuition is consistent with what those papers report, and examining our VARIMAX’ed PC plots closely (which have sharpened in the latest version thanks to improved normalization), we can see that they break apart sub-regions largely based on timing. In our feature approach, we intentionally chose our features to be largely invariant to both tuning preferences and timing. Instead, we chose our features to pick up on what we call the single cell “response format”: response duration; peak time variation (but not absolute timing); and tuning sharpness, persistence, and linearity. These different methods pick up on different aspects of responses.

      To double-check that the PCA-then-spectral approach reveals similar structure to our use of VARIMAX on the PCs, we tried applying the suggested method to our data. We applied spectral clustering to the N x 20 PETH PC feature matrix, then fit an area-agnostic GMM to the spectral features. We plot the likelihood map for the components of a GMM with 10 modes. The GMM components did not display clear spatial structure beyond that observed in the VARIMAX’ed PCs (Figure 5-figure supplement 1) and were less interpretable than those identified by area-agnostic clustering of our response features (Author response image 1). As noted, the number of subpopulations identified by the clustering of our hand-engineered features is lower than what would be obtained from clustering the PCs of the PETHs. This is likely the result of the substantial heterogeneity in activity onset and preferred target that is preserved by PCA. Because our central approach is largely agnostic to these two sources of variation, the number of identified clusters reflects the dominant patterns of variation beyond these two sources.

      Author response image 1.

      GMM fit to spectrally transformed PETH PCs, agnostic to anatomical areas. One GMM was fit to the spectrally-embedded PC feature vectors of cells from all 5 main areas. Each component of a 10 component model is shown.

      Also, I think it would greatly help the reader to return to PETHs at some point, if possible, to show the response profiles of each identified neuronal subgroup (page 20). To what extent are they similar or different across the cortical areas (for the same neuronal subgroup)?

      This is a good idea. We have added a figure to address this question and the related question by R1 (Figure 9-figure supplement 1). In short, given the wide variety of PETHs we observed, there is of course still substantial variation within subpopulation, and some mild but systematic differences in the distribution of what we observe across areas. We now discuss the conclusions from this plot in the Results:

      “As a qualitative depiction of the response profiles identified with each subpopulation, we plotted the two highest-likelihood cells for each area/subpopulation combination (Figure 9-figure supplement 1). These examples reveal stereotypy in the subpopulation responses across areas, but also show variation across areas, especially for the two somatomotor subpopulations.”

      Specific:

      (1) Figure 2B and M&M: the 3D spatial organization of the target locations is not immediately clear. What is the spacing between target locations? What is the 'final azimuthal spacing'?

      Added, thanks. The pairwise horizontal distances between targets were between 1.72 and 6 mm apart and the vertical spacing within a column was 1 mm. “Final azimuthal spacing” just referred to the targets being closer together during training and our gradually spacing them apart to their final locations. We have also added some relevant details about the training.

      (2) Figure 2C: It would help to have a scale bar (mm).

      Added, thanks.

      (3) Figure 2C: It would be easier to appreciate the variability of the trajectories across trials to plot an overlay of trajectories to one target only (could be a Supplementary Figure).

      The reviewer has a good point: the variability and accuracy of aiming was hard to ascertain from the plot. We experimented with a few options for making this clearer most effectively. We have now added Figure 2-figure supplement 1 that shows in the third subpanel of panel A the finger centroid trajectories for one of the 15 targets highlighted for the mouse shown in Figure 2C, mouse 3. The centroid trajectories for all other mice are shown as well to illustrate similarities and differences across animals as well as the overall variability. As noted elsewhere we have also included an analysis of the variability of the centroid trajectories, showing that reaches to a given target were more similar than reaches to different targets. We think this provides a fuller picture of the behavior and intend to provide still more detail in future work. Thank you for suggesting additional detail here!

      (4) Figure 4: It would be nice to also show the amplitude-normalized grand-average PETHs for the different areas.

      This is an interesting suggestion. After careful consideration, we think that this analysis is not as effective for depicting overall timing and modulation profiles as the current ones, given the strong amount of target selectivity and response time heterogeneity (now better visible in the revised Figure 4A). When computing the grand mean of all cells within each area, the dominant features distinguishing areas are onset time and response duration. The differences across areas in these two features are better supported by the analyses of Figures 4 and 5 due to the large amount of heterogeneity in responses within each area. We thank the reviewer for encouraging this exploration; more complicated spin-offs will likely inform additional timing analysis in the next paper on these data.

      (5) Figure 7C: figure legend - although it is quite self-explanatory, please explicitly indicate which pattern corresponds to the 'Three contour levels (98%, 95%, 90%)'.

      We have now added this as a legend on the figure panel itself (here and on similar plots). Thanks for pointing this out.

      (6) Figure 8: Is there also an interesting asymmetry between sensory are motor areas, with neurons in sensory areas being more likely associated with motor areas (B and C), whereas neurons in motor regions are less likely to arise from the distribution of sensory areas (dark blue color in frontal regions in D, E, and F)?

      This is an interesting observation, but we understand it to be an artifact of colormap scaling. As mentioned above, likelihoods are not well-behaved like probability distributions are: for example, they are not bounded at 1, and their sums over a dataset can have any positive value. The only things that can be interpreted are their relative values. This makes their scaling functionally arbitrary – you’ll notice we used “min likelihood” and “max likelihood” instead of numbers, which would be nearly meaningless – and therefore presents a problem for scaling the colormaps. We don’t know of a principled way around this problem. To deal with it, we simply put the ends of our colormap at the extreme pixel values. It so happens that both the M1 and M2 maps had a handful of neurons in a less-sampled spot at the bottom of M2 that were very low-likelihood, which results in what you noticed. We debated removing those neurons for this purpose, but we had no basis on which to do that kind of manipulation, so we left it as the most honest representation of the data we could produce.

      To clarify this, we now mention in the caption “The ends of the colormap were set to the maximum and minimum likelihood values for each map.”

      (7) Figure 9B: there are two-time 'S1-hl: 1' indicated at the two bottom rows of the distance matrix. I suppose one of them should be 'S1-tr: 1' instead?

      Fixed, thanks for catching it.

      (8) Page 20: 'This hinted at a second hypothesis: that some of the 'modes' (groups of neurons) discovered separately in each area might correspond.' ???

      We had meant “mode” as in “multimodal”, but it was very unclear. We have rewritten the sentence:

      “This hinted at a second hypothesis: that a peak in the multimodal distribution from one area might correspond to a peak in the multimodal distribution of a different area.”

      (9) Figure 9S2: Please indicate for which area each map is computed.

      The caption was not clear enough about what we were doing here: we fit the GMM on all neurons together, ignoring which area they came from. We have now clarified it in the caption:

      “One GMM was fit to the feature vectors of cells from all 5 main areas. Each map plots the likelihood for all cells to each of the three components of this area-agnostic GMM.”

      (10) M&M, Subjects and surgical procedures: 'ambient temperature of 71.5 {degree sign}F', please use international units.

      Done.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      It was nice to see that the authors could distinguish differences between the OFC signals that they observed and those in the visual regions based on changes through the session. However, the linkage between these brain activations and a functional role in generating behavior was left unexplored. Without further exploration, it is hard to tell exactly what role the signals might be playing, if any, in the behavior of interest.

      To link the behavioral with the fMRI data, we now correlated fMRI decoding accuracy with behavioral performance. We studied behavioral performance in two ways: the difference in high versus low noise environment learning rates, and mean accuracy (i.e., absolute prediction error). We correlated both measures with the decodability of the environment in the central OFC. Each correlation was calculated either in the full experiment, or only the second half. However, none of these correlations were significant (all p > .1). Given the difficulty of interpreting this result, and our lack of statistical power for doing individual difference analyses, we decided not to report these analyses in the final paper.

      Reviewer 2 (public review):

      (1) The authors make the distinction between meta-learned "global" learning rates and within environment learning rate adaptation in response to "local" fluctuations/observations. Though the experimental paradigm is novel, there are certainly links to prior work - for instance, though change point structures don't entail revisiting unique environments, they do require meta-learning from environmental statistics that is distinct from transient local adaptation to prediction errors. This tendency to increase one's learning rate after large prediction errors is appropriate in change point environments, though, as is true in this study, the amount of increase should be dependent on. This represents a similar kind of slower-timescale learning or reuse of more "global" parameters, and can be seen to different extents in prior work. It might benefit readers if the authors were to link the current work to previous research more explicitly to draw clearer connections between the approaches and findings.

      We thank the reviewer for their very helpful literature suggestions and now contextualize and discuss our findings in light of relevant literature.

      (2) Throughout much of the paper, the authors refer to the distinctions between environments primarily as differences in "initial learning rates" or "environment-specific learning rates." This is particularly prominent when discussing fMRI results. Though the optimal initial learning rate did differ across environments, this was the result of differences in underlying task statistics. It will be important to clarify this throughout the text, because of the confounds between task statistics and initial learning rate (and to some extent, the position on the screen), it is not possible to separate the impact of these specific variables. This is also relevant to understanding the justification for using methods like RSA to test whether brain regions represent task states similarly. If the main hypothesis is that neural activity reflects the (initial) learning rate itself, then a univariate analysis approach would seem more natural.

      We agree that task statistics are not the same as differences in learning rates. However, we do not consider this as a confound: The point of the differences in task statistics is exactly to generate differences in learning rates. With our paradigm, we deliberately tried to dissociate variations in learning rate that were induced by learned environmental differences versus local task statistics. We tried to make this dissociation more clear, especially when discussing the fMRI results.

      (3) For the neuroimaging results in particular, the specificity of some of the results (e.g. ventral striatum showing an effect of prediction error only in the low noise condition in the second half of task experience, only on the first trial) is a bit surprising. Additional justification of or context for these results would be useful to help readers gauge how expected or surprising these findings are.

      We agree some of these findings were unexpected. We now also highlight that while we expected the ventral striatum to be involved in prediction error processing, we had no strong a priori expectations regarding these further modulations by time and environment. We also tried to contextualize these interactions more.

      (4) There are some methodological details that are unclear (e.g., how were the positions of the crabs selected relative to the location they emerged from? Looking at Figure 1C, it looks like the crabs spread out unevenly, and that the single position they emerge from is not necessarily at the center of the crab locations.) Additional detail and clarity would help address some unanswered questions (more details below).

      We clarified the experimental procedure at several places, and now added a video that helps illustrate the trial timeline better.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) With regards to the primary weakness mentioned above, it would be nice to have some link between the brain signals of interest and upcoming behavior. For example, can you read something out of OFC that enables you to better predict what the participant will do next? Or even better, do so beyond any behavioral variability that is explained by the computational model?

      To link the behavioral with the fMRI data, we now correlated fMRI decoding accuracy with behavioral performance. We studied behavioral performance in two ways: the difference in high versus low noise environment learning rates, and mean accuracy (i.e., absolute prediction error). We correlated both measures with the decodability of the environment in the central OFC. Each correlation was calculated either in the full experiment, or only the second half. However, none of these correlations were significant (all p > .1; see plots in Author response image 1). Given the difficulty of interpreting this result, and our lack of statistical power for doing individual difference analyses, we decided not to report this analysis in the paper.

      Author response image 1.

      (2) A number of the learning analyses are based on splitting the session into halves. As a first pass, this seems like a reasonable thing to do, but I certainly wonder what the dynamics of the meta-learning actually look like, and it seems like the data collected would be sufficient to gain some insight into those dynamics through some sort of sliding window analysis.

      We thank the reviewer for this interesting suggestion, which was also raised by Reviewer 2. We now calculated the learning rate in a sliding window of 20 trials (i.e., trial x to x + 19), and provide revised figures for each experiment separately (Fig. 2E and Fig. 4E, respectively).

      (3) The model selection procedures described make sense, but it would still be useful if the authors justified them by showing that they work in synthetic data (ie, generate a confusion matrix). I may be confused about what delta-SE is, but I'm confused about why two models with very different fits have the same value (211) for that metric.

      We report model recovery on synthetic data, which yielded model recovery rates of 100%, and added these to our Methods section. To clarify the Reviewer’s second point, ∆SE is the standard error of the difference between a model’s LOOIC and the top ranked model’s LOOIC. There is no one-to-one mapping between the ∆SE and a model’s LOOIC.

      (4) Was the central OFC anatomical ROI overlapping with the cluster surviving in the whole brain analysis? I didn't see this mentioned in the text, and it certainly would be important for interpreting the two results together.

      The central OFC indeed overlapped with the cluster surviving whole brain analysis, which we report on page 17-18.

      (5) The authors found regions that reflected learning rate at the "island presentation" phase of the task - it could be distinguishing this analysis and its meaning from other work that has focused on representations of learning rate at the time of feedback.

      We agree that this is an important distinction worth emphasizing. Therefore, we added the following lines to our discussion paragraph: 

      “Importantly, previous studies examined neural correlates of learning rates during outcome evaluation, where learning rates may be adjusted online as a function of locally experienced prediction errors (e.g., (Behrens et al., 2007; Browning et al., 2015; Nassar et al., 2012). In contrast, our RSA analysis targeted neural activity at island presentation, before any outcome information was available. At this moment, learning rates cannot be updated based on current feedback and instead reflected the retrieval of a previously learned, environment-specific learning-rate settings. This difference reflects our hypothesis that the OFC represents the latent states in a cognitive map of the task (Knudsen & Wallis, 2022; Moneta et al., 2024; Schuck et al., 2018; Wilson et al., 2014), which are expected to activate as soon as the agents can infer which task state it is in. Several studies have identified such “partially observable” task states in the medial OFC (Bradfield et al., 2015; Schuck et al., 2016; Tan et al., 2025; Wimmer & Büchel, 2019), in line with the region identified here (but see e.g., (Ongur & Price, 2000), for important anatomical distinctions between medial and lateral OFC and (Tan et al., 2025) for an example of related functions in lateral OFC). Our finding extends this notion by suggesting a link between OFC and meta learning, wherein meta-learned information becomes encapsulated in task states (Hattori et al., 2023; Moneta et al., 2024).”

      (6) "Specifically, it showed a more negative response to larger (location) prediction errors, which is consistent with its documented role in showing a more positive response to more positive reward prediction errors (Calderon et al., 2021) - keeping in mind that being closer to the centre of where the crabs appeared (i.e., smaller location prediction errors) is less negatively or more positively surprising (i.e. smaller negative or larger positive reward prediction errors)."

      I found this sentence very hard to parse. Do PE responses in the high noise environment get "compressed" in their representation over time (ie, it takes a larger error to get the same BOLD response)? If so, this relates to claims made in Diederen 2016... but see also Mah 2024 Cell Reports, who fails to see learning rate encoded in DA system in striatum of rodents that appear to adjust their learning rates.

      Thank you for pointing to this. We agree that this sentence was hard to parse, and so we now split it in three revised sentences. We also agree with the Reviewer’s interpretation, and would like to thank the Reviewer for their useful literature suggestions which we now added to our discussion. 

      (7) Figure 7 should use a different color scheme because many of the activations just appear black, and I can't tell whether they are positive or negative. It was also notable in Figure 7A that regions are not visible, including ACC, which is typically thought to encode prediction errors in such paradigms. It would probably be useful for the authors to include a table of all clusters exceeding multiple comparisons correction and to on differences to other work examining absolute prediction errors. ACC does appear on the second trial, which made me wonder whether there were changes in the prediction error coding from first to subsequent trials. 

      Thank you for pointing this out. We now revised our color scheme which we agree makes it much clearer now. Although the ACC is frequently implicated in prediction error–related signals (e.g., Behrens et al., 2007), models suggest that ACC responses more strongly reflect unsigned prediction errors, surprise, or the need for control and model updating (Alexander & Brown, 2019; Hayden et al., 2011; Silvetti et al., 2018). In our task, ACC activity only emerged on the second trial, when participants had formed an initial estimate and prediction errors could meaningfully signal the need to update internal models or control settings. We now added a to the Discussion highlighting this distinction and relating our findings to this prior work emphasizing prediction errors and control-related signals in ACC.

      (8) The authors suggest that fast learning would presumably occur in a neural activation space, whereas slow learning would occur through weight adjustments. This makes sense, but activity-based dynamics have been suggested to do rapid adjustments by encoding a "latent state" though (Razmi 2022 j neurosci) -- and such a latent state has been shown in OFC (Schuck etc)... but here OFC is more implicated in the slow learning. I am curious about whether authors could on this a bit in the discussion. 

      Thank you for bringing up this interesting question. We can only speculate but a crucial factor is on which level of resolution tasks states operate. On the one hand “detailed” trial-level states are needed that map a specific sensory input onto a specific latent state and its value. Such states would change quickly, possibly through activation dynamics, and are in line with how they have been operationalized in Razmi or Schuck etc. On the other hand, successful task performance also needs “higher level” states that describe entire task phases or full tasks, as in the present experiment. Due to the different speeds of learning, it appears plausible that these would be learned with synaptic changes. We expand on this in the discussion as follows: 

      “Our finding extends this notion by suggesting a link between OFC and meta learning, wherein meta-learned information becomes encapsulated in task states (Hattori et al., 2023; Moneta et al., 2024). Consistently, OFC has been shown to represent task states (Moneta et al., 2024; Stalnaker et al., 2015; Wilson et al., 2014). While earlier evidence shows that the OFC represents concrete aspects of task states, such as task-relevant stimulus features (Schuck et al., 2016), we hypothesized that the OFC also represents more abstract aspects, such as learned, environment-specific learning rates. Indeed, we showed that the central OFC gradually came to represent these environment-specific learning rates (or the environment-specific statistics that drive them). While previous work speculated that these different levels could have different neural underpinnings (Sharpe et al., 2019), our findings indicate OFC might signal states on multiple levels. This does not imply identical learning dynamics; fast-changing trial-specific states might be learned through activity dynamics, while higher-level contextual states could involve synaptic plasticity.”

      (1.9) Also, as a more minor point in the same section, the sentence about blocking synaptic plasticity in OFC sounded interesting, but should have a reference.

      Thank you for noticing, we now added the reference (Hattori et al., 2023).

      Reviewer #2 (Recommendations for the authors):

      (1) Additional links to prior literature: In terms of prior work in which there is something akin to more "global" adaptation, some examples of potentially relevant prior work include:

      McGuire, Nassar, Gold, & Kable (2014) Neuron 

      D'Acremont & Bossaerts (2016) Cerebral Cortex 

      Lee, Gold, & Kable (2020) Decision 

      Bakst & McGuire (2021) JEP: General 

      Bakst & McGuire (2023) Cognition

      We would like to thank the reviewer for pointing us to these different literature suggestions which we agree help us contextualize and discuss some of our findings better. We now refer to McGuire et al. (2014) when discussing the fMRI results, and d'Acremont & Bossaerts (2016) when discussing potential alternative strategies in the high noise environment (the Reviewer’s last point). Finally, we integrated the clearly relevant works of Bakst & McGuire (2021; 2023) and Lee et al. (2020) in our discussion of meta-learning different adaptive strategies. 

      (2) Individual differences: Though not always the focus of work on predictive inference, one common finding has been that there are pronounced individual differences in behavior (see, e.g., coefficients in Figure 2 in Nassar et al. 2019 eLife, or Figure 2 McGuire et al. 2014 Neuron, or Bakst & McGuire 2023 Cognition). There appears to be substantial variability between individuals in your data as well (i.e., Figure 2B, 4B, and the modeling figures). It would be interesting to see some direct exploration of this variability: baseline learning rate appears to differ between participants to a large extent, does their rate of adaptation (across trials within a block) also differ? Does their metalearning occur at different rates (in fact, do some participants not show evidence of appropriate meta-learning at all)? 

      Relatedly, your computational modeling approach fits the six candidate models hierarchically, and therefore the reported results show the overall best fit for the group. It might be worthwhile to determine whether individuals have different best-fitting models. This could be another way to characterize the variability between individuals. 

      In concert with this, it could be a useful complement to determine whether either the strength of the OFC neural similarity results or their time course reflects aspects of behavior. Put another way, is it the case that not only does OFC activity and behavior both come to reflect task structure, but that these changes happen to a similar extent and over a similar time course across individuals?

      We agree it would be highly interesting to investigate meaningful individual differences in both fast and slow adaptations in learning rate. However, our sample was not set up and is underpowered to conduct such analyses. In response to a similar by Reviewer 1, we did run correlational analyses between differences in learning rate, performance accuracy, and the responsiveness of the OFC. However, none of these analyses yielded a significant effect. We decided to not include these results in the paper, for reasons of statistical power, but we report them in Author response image 1.

      (3) fMRI:

      (3a) The primary finding in OFC is restricted to the central OFC. The manuscript would benefit from additional explanation regarding this specific subregion. 

      Thank you for bringing up this important distinction. In the discussion we now clarify as follows: 

      “This difference reflects our hypothesis that the OFC represents the latent states in a cognitive map of the task (Wilson et al., 2014; Schuck et al. 2018; Knudsen & Wallis, 2022; Moneta et al, 2023), which are expected to activate as soon as the agents can infer which task state it is in. Several studies have identified such “partially observable” task states in the medial OFC (Schuck et al., 2016; Bradfield et al., 2015; Wimmer et al., 2019; Tan et al., 2025), in line with the region identified here (but see e.g., Öngur & Price, 2000, for important anatomical distinctions between medial and lateral OFC and Tan et al., 2025, for an example of related functions in lateral OFC).”

      (3b) Though the main clusters visible in Figure 6 are the occipital and OFC clusters, there appear to be others. Did other clusters indeed rise to statistical significance in the whole-brain analysis? If so, is there a reason they aren't included or discussed? 

      All clusters visible in Figure 6C survived FDR correction. However, we refrained from interpreting these other clusters, because we had no prior hypotheses about them like we did for the OFC.

      (3c) Why do you posit that the ventral striatum becomes less sensitive to RPE on the second trial over time? And why is the ventral striatum only sensitive to RPE in the low noise environment generally?

      We reasoned the ventral striatum should be more responsive to more positive reward prediction errors. While we further assumed this response could be modulated by both time and environment, we would like to emphasize that we had no specific hypotheses about the direction of this modulation. We now also make this clearer in the manuscript. This being said, we believe both the pattern that its responsiveness to the second trial decreases over time, and the pattern that it was most sensitive to the low noise environment, can be considered fitting with its broader involvement in coding behaviorally relevant reward prediction errors. Namely: 

      First, we believe that as the participants learn more about the global reward structure of the task, they should obtain a better understanding of the fact that, per round, all crabs always center around a fixed mean. Therefore, the first RPE is most behaviorally relevant, and every later RPE has an exponentially decreasing relevance. As participants obtain more experience with this aspect of the task over time, the VS should show a lower responsiveness to the second RPE over time.

      Second, as participants learn more about the local differences between the three different environments, they should learn that especially in the low noise environment, RPEs are most behaviorally informative. That is, in this environment it makes most sense to have a high learning rate and thus let the RPEs substantially inform the placement of the cage on the next trial. Accordingly, participants showed that the ventral striatum was most responsive to RPEs in these environments.

      (4) Methods

      (4a) This section could generally benefit from some proofreading. 

      We now proofread the method section. 

      (4b) The main results text states that 49 participants performed Experiment 1, while the methods section reports 50 participants. Which is correct? 

      (4c) Following this, on page 8, statistical results are reported with a df = 49 (which would be appropriate only if n=50). 

      The correct sample size was actually 50, we adjusted the text and degrees of freedom where incorrect accordingly (note: only text is in track changes, but degrees of freedom were also changed accordingly). 

      (4d) Additionally, I am a bit surprised by the Experiment 1 findings that learning rates on the second trial were significantly different between low and high noise conditions, in that the effect size found using all trials was stronger than both the first half of trials (no significant effect) and the second half (significant but weaker than all trials). Are these all the same type of statistical test? Double-checking the statistics might be worthwhile. 

      It is not the effect size that is larger across the full experiment, but the t-statistic. This is possible because a t-statistic depends on both effect size and noise estimate, and the latter is smaller with more data. 

      (4e) The methods and results both state that the five crabs always emerged from one position in the sand. How were the locations of the crabs selected relative to this position? Looking at Figure 1C, it looks like the crabs spread out unevenly, and that the single position they emerge from is not necessarily at the center of the crab locations. 

      The crabs did indeed spread out evenly. However, we can see how the graphic in Figure 1C can be confusing, as two crabs are shown to be caught, which breaks the symmetry of the dispersion (because some crabs can run away after the even spreading phase, see Methods). We emphasized the even spreading more clearly in the new version of the paper. We think the flow of events will be much clearer with our newly added animation (Video 1).

      (4f) The methods section states that the crabs "spread out to cover the same proportion of the screen width as the cage (18.75%)" (page 23). The corresponding visual in Figure 1C appears to show something different. 

      This looks different because the graphic illustrates the last 500 msec, where crabs can run away (see also response to 4e, and the novel animation that was added).

      (4g) Information on the timing of the trials would be useful to include in Figure 1C or similar. 

      The reader can find this information in the Methods section. We chose not to include it in the caption to avoid information overload.

      (4h) The methods section specifies that there was a 3-7s ITI after the first and second trials of each block. How was the ITI selected for each trial? Were there ITIs between the other trials? If so, what were they? 

      The ITIs were selected from a truncated exponential distribution. This selection was not random, but rather a distribution was carefully constructed for each environment (and event of interest: boat presentation, first trial of each block, second trial of each block) separately to ensure that enough longer ITIs were selected for each environment (and event of interest). Of course, the order in which the ITIs were used across blocks, was random. The same approach was used to determine the duration of the presentation of the boat at the start of each block. There were no ITIs after later trials.

      (4i) Please provide a link to the data and analysis materials on OSF in the text. 

      We now provide a link to the data and analysis materials in our methods section.

      (4j) In the methods section, there are some references to information provided "below" (page 26: "The two approaches resulted in different posterior densities (see below) for estimate uncertainties, but in similar posterior densities (see below) for learning rates..."). Where in the paper is this referencing? 

      We indeed did not detail this further as we considered it not further relevant to our main study, and now removed the references to “below”.

      (4k) The methods section specifies using uniform priors between the lower and upper bounds of the relevant parameters. This seems likely to be 0 and 1, but should be listed explicitly. 

      Thank you for noticing. We now added this to our manuscript.

      (4l) For parameter recovery, correlations are provided to indicate effective recovery. These correlations are indeed high and suggest excellent recovery, but correlations wouldn't reveal if there was systematic over- or underestimation occurring. It might be useful to provide some visualizations of the parameters and their estimates to speak to this potential issue. 

      We now visualize the parameter recovery results in Author response image 2, which show that, indeed, there was a slight underestimation of the decay rates, but not the learning rates. Importantly, our main analyses and results all pertain to the learning rates, and we never made hypotheses or conclusions about the decay rates.

      Author response image 2.

      (4m) The methods section ends with a reference to a reward localizer (page 32). This localizer doesn't appear to be mentioned/used elsewhere. 

      Indeed. We implemented the localizer because we wanted to independently identify reward processing areas. However, this localizer did not succeed in localizing a reward area (no significant results), possibly due to the fact that (1) it was performed by the end of the experiment when participants may have been fatigued, and (2) there was no learning component in this localizer task. For these reasons, we did not use it after all.

      (5) Analysis: 

      (5a) Did you consider fitting a Bai model that only allowed for environment-specific initial learning rates (with a non-environment-specific decay rate)? Given that the data (e.g., Figure 2, Figure 4) seems to support differences in initial learning rate but not necessarily a difference in the rate of change, it might be worthwhile to see whether a model like that fits best. 

      We now fitted this extra model, which we called the semi-environment-specific Bai model. See Author response tables 1 and 2 for result in experiments 1 and 2, respectively) for the results. This new model has the best (in Experiment 2) and second-to-best (in Experiment 1) LOOIC. In a way, this is not surprising, because the model formulation is entirely based on the data. We think that we can draw the same substantive conclusions with or without this extra model, so for simplicity we did not include this new model in the paper itself.

      Author response table 1.

      Note. Models are ranked in descending order according to how well they fit the data. LOOIC refers to a model’s approximated expected log pointwise predictive density. Higher values indicate higher out-of-sample predictive fit. SE refers to the standard error of a model’s LOOIC. ∆LOOIC refers to the difference between a model’s LOOIC and the top ranked model’s LOOIC. ∆SE refers to the standard error of the difference between a model’s LOOIC and the top ranked model’s LOOIC.

      Author response table 2.

      Note. Models are ranked in descending order according to how well they fit the data. LOOIC refers to a model’s approximated expected log pointwise predictive density. Higher values indicate higher out-of-sample predictive fit. SE refers to the standard error of a model’s LOOIC. ∆LOOIC refers to the difference between a model’s LOOIC and the top ranked model’s LOOIC. ∆SE refers to the standard error of the difference between a model’s LOOIC and the top ranked model’s LOOIC.

      (5b) If part of the goal is to investigate whether there is a distinct local change in LR between conditions (dependent on prediction errors), then there might be more direct ways of doing so as a complement to the modeling approach. One potential way could be to visualize the LR or change in LR as a function of PE. 

      We agree that it’s beneficial to use a direct (model-free) approach to represent learning rate as a function of condition; that is also part of our approach. For example, see Figures 2, 4, which shows learning rate as a function of condition, but in a model-free manner. We think learning rate as a function of prediction error is less informative, because the idea is that prediction error can (in Kalman-filter terminology) be indicative of either noise variance or process variance, and participants are able to distinguish between them. This is also why we constructed the conditions in such a way that on the very first trial, prediction errors were on average the same across conditions. The fact that participants did respond appropriately to prediction errors on the very first trial (i.e., larger updates or learning rates in the low noise condition), suggested they are able to assign the prediction error to process variance (in the low noise condition) versus noise variance (in the high noise condition).

      (5c) In addition to looking at the evolution of LR across trials within a block separated by task epoch (i.e., Figure 2C-D & Figure 4C-F), the structure of the task would lend itself very nicely to visualizing the evolution of the second trial LR on its own across instances. This could provide additional insight into the meta-learning process.

      We thank the reviewer for this interesting suggestion, which was also raised by Reviewer 1. We now calculated the learning rate in a sliding window of 20 trials (i.e., trial x to x + 19), and provide revised figures for each experiment separately (Fig. 2 and 4, respectively).

      (6) The environment-specific Bai model appeared to become less good at capturing participant behavior with increased environmental noise. Why do you think this is?

      We thank the reviewer for raising this point. In this environment, individual outcomes are considerably less indicative of the latent mean, which may reduce the usefulness of the trial-by-trial, prediction-error–driven learning-rate adjustments that we see in the other environments. Under such extreme conditions of variability, people may rely less on delta-rule updating and more on alternative strategies (D'Acremont & Bossaerts, 2016; Reynders et al., 2026), such as exploratory adjustments or heuristics that are not explicitly captured by the Bai model but also outside the scope of the present paper.

    1. Author response:

      Reviewer #1 (Public review):

      Summary:

      Hüppe and colleagues characterized the network of neurons in the central nervous system of Antarctic krill that contained pigment-dispersing hormone (PDH), an important output factor in the circadian clock of insects. These neurons in the brain are putative clock neurons since a subset also expressed the clock genes period and cryptochrome 2. As one of the ocean's major contributors to biomass, krill is an ecologically important marine species that experiences challenging daily and seasonal environmental fluctuations in its high-latitude habitat. A comprehensive study of krill's internal clock may help to understand the extent of its resilience to the rapidly changing climate.

      The authors used antibody staining against PDH across the whole central nervous system and additional in situ hybridization for cry2 and per mRNA, with a focus on the supraesophageal ganglion. There, they identified the major neuropils in the eye stalks and central brain of Antarctic krill. The resulting staining pattern aligns with the identified circadian clock network in insects and PDH-expressing networks in other crustaceans, making these neurons highly likely candidates for krill clock neurons.

      Strengths:

      (1) This study provides the first clues about the circadian clock architecture in a non-model organism in chronobiology, Antarctic krill, with a clear 3D reconstruction of the putative clock network.

      (2) The authors effectively place their results within the extensive body of literature on arthropod circadian clock networks to argue that the neurons they describe are likely the circadian clock in krill.

      Weaknesses:  

      (1) The data presented here are not sufficient to support the claim that the described network is the circadian clock because functional evidence is missing.

      (2) Additionally, the study falls short of identifying any elements of the positive limb of the canonical circadian clock transcriptional-translational feedback loop, e.g., clk or cyc, in the PDH-expressing neurons.

      (3) No sample sizes are reported, making it difficult for readers to assess the generalizability of the presented data.

      We thank the reviewer for recognizing the contribution of this study to advancing our understanding of clock systems in non-traditional model organisms. We acknowledge that definitive functional evidence would require the generation of null mutants of core clock components, which is currently not feasible in this species. In a revised version, we will adjust our claims to more precisely reflect the evidence presented and include sample sizes to allow the reader to better assess the representativeness of the results.

      Reviewer #2 (Public review):

      Summary:

      This study advances our understanding of the neuronal basis of the circadian clock in pancrustaceans. It extends our knowledge on the pigment-dispersing hormone system and provides links to information on the expression of core clock components, cryptochrome 2, and period. The data are sound and well-documented.

      Comments:

      The neuronal components of the arthropod circadian clock system have been analysed extensively in insects. Much less information on this system is available on malacostraca crustacea crustaceans. However, considering that malacostracan crustaceans and insects go back to a common pancrustacean ancestor and considering that we know that the brain architecture in these two groups shares many commonalities (see, e. g., extensive reviews by N. J. Strausfeld), we have to expect that crustaceans and insects share many of the characteristics of the circadian system. This is the case, e. g., for the network of pigment-dispersing hormone-positive neurons. The authors cite these studies, although late in the paper (discussion, line 339ff), and I suggest to move this info into the introduction: "339 ff: The arborization pattern of the PDH-network has been described in various malacostracan crustaceans, including Carcinus maenas (Alexander et al., 2020; Mangerich & Keller, 1988; Mangerich et al., 1987), Cancer productus (Hsu et al., 2008), Orconectes limosus (de Kleijn et al., 1993; Mangerich & Keller, 1988; Mangerich et al., 1987), Homarus americanus (Harzsch etal., 2009), Cherax destructor, Procambarus clarkii (Sullivan et al., 2009), and Procambarus virginalis (Luna et al., 2010)."

      The strength of this paper is that it extends our knowledge on the PDH system and brings together neuroanatomical information on PDH-positive neurons with information on the expression of core clock components, cryptochrome 2, and period. That way, it advances our understanding of the neuronal basis of the circadian clock in pancrustaceans. The data are sound and well documented, and the authors are to be applauded for the superb dissection presented in Figure 1.

      Below, please find some essential suggestions on how to further improve the paper.

      (1) Framing of the study:

      I know that krill is a key element of the Southern Ocean's food webs, but my sense is that discussing the current findings in a context of resilience of this species to global ocean change means largely overselling this study:

      Lines 47, 48: "and the resilience of this key species in a rapidly changing Southern Ocean."

      Lines 70 ff: "Hence, understanding the mechanisms of adaptation, including biological clocks, is crucial for predicting how species, populations, and whole ecosystems will respond to climate change."

      154 ff: "The Southern Ocean environment experiences rapid change (Abram et al., 2025; Meredith et al., 2019; Thomalla et al., 2023). To assess krill's resilience to environmental changes, understanding the mechanisms that govern daily and seasonal timing in krill is essential."

      325 ff: "The rhythmic adaptation of krill to its high-latitude environment is key to its success in the Southern Ocean, which in turn represents a cornerstone for the well-being of the whole krill centred ecosystem. To predict krill's resilience to rapid environmental changes, it is essential to understand the mechanisms that govern daily and seasonal timing in krill."

      597 ff: "A detailed mechanistic understanding of the flexibility of clock-based processes is therefore essential to predict krill resilience in a changing Southern Ocean."

      My understanding is that duration of day length is one of the most predictable environmental drivers, and - despite the seasonal changes of day length - nevertheless a very stable one compared to fluctuations of environmental drivers such as temperature or salinity (see, e.g. this recent review on environmental driver fluctuations on nervous system functioning in crustaceans: Stein W, Harzsch S (2021) The Neurobiology of Ocean Change - insights from decapod crustaceans. Zoology: 125887. https://www.sciencedirect.com/science/article/pii/S094420062030146X).

      I do not see how global ocean change may significantly change day length, and what this study has to do with understanding this species' resilience against ocean change. I suggest that you explain in more detail why the light day length will change in the future or strongly tone this aspect. Statements such as Line 76 ff: "Due to their disproportionate importance for ecosystem function, understanding the resilience of ecological key species is essential in assessing the fate of ecosystems in the future." are completely out of focus here and, again, trying to oversell the current study.

      (2) Uncited essential studies of crustacean neuroanatomy, missing connection to contemporary crustacean neurobiology:

      Line 157: "despite the ecological importance of E. superba, only very little is known about its neurobiology".

      Line 329: "However, so far, little was known about the neurobiology of krill in general."

      I agree that this species' brain is understudied, but this makes it even more important to cite the little information that IS available. Please consider this essential reading for any crustacean neurobiologist: "Sandeman, D.C., Scholtz, G., Sandeman, R.E., 1993. Brain evolution in decapod crustacea. J. Exp. Zool. 265, 112-133." to find information on the basic brain anatomy in E. superba.

      The manuscript in many places seems to reinvent the wheel and raises the impression that our knowledge of crustacean brain morphology is close to zero. The authors in places seem to operate in a vacuum, and I find it disturbing that in a study on the crustacean brain, very few references are provided to studies on crustacean brain anatomy, such as the following essential book chapter: "Schmidt, M., 2016. Malacostraca. In: Schmidt-Rhaesa, A., Harzsch, S., Purschke, G. (Eds.), Structure & Evolution of Invertebrate Nervous Systems. Oxford University Press, Oxford, pp. 529-582. https://www.researchgate.net/publication/315366157"

      In terms of brain anatomy, I would like to know if the authors have a hypothesis on whether and how their target species' brain structure may be similar or different to the brains of other "shrimps" as described, e. g., in the following studies. If so, please elaborate in the introduction:

      Krieger J, Hörnig MK, Sandeman RE, Sandeman DC, Harzsch S (2020), Masters of communication: The brain of the banded cleaner shrimp Stenopus hispidus (Olivier, 1811) with an emphasis on sensory processing areas. Journal of Comparative Neurology 528(9): 1561-1587.

      Meth R, Wittfoth C, Harzsch S (2017) Brain architecture of the Pacific White Shrimp Penaeus vannamei Boone, 1931 (Malacostraca, Dendrobranchiata): correspondence of brain structure and sensory input? Cell and Tissue Research 369(2): 255-271.

      (3) Lacking rigor and command of crustacean brain nomenclature

      I suggest that for their brain nomenclature, the authors should rigorously stick to that laid out by Sandeman et al. 1992 (not yet cited in the ms): Sandeman, D.C., Sandeman, R.E., Derby, C.D., Schmidt, M., 1992. Morphology of the brain of crayfish, crabs, and spiny lobsters: a common nomenclature for homologous structures. Biol. Bull. 183, 304-326.

      More specifically, in lines 41, 163, 199, 204, 207, and throughout the paper, the authors use the terms "Optic lobes" or "optic lobe neuropils". To the best of my knowledge, "optic lobe" is not a term used in crustacean neuroanatomy at all (as opposed to insects). Lamina, medulla, and lobula are collectively referred to as "visual neuropils" (see Krieger, J., Hörnig, M. K., Sandeman, R. E., Sandeman, D. C., & Harzsch, S. (2020). Masters of communication: The brain of the banded cleaner shrimp Stenopus hispidus (Olivier, 1811) with an emphasis on sensory processing areas. Journal of Comparative Neurology, 528(9), 1561-1587. https://doi.org/10.1002/CNE.24831). The medulla terminalis and mushroom bodies are referred to as "lateral protocerebrum". All afore-mentioned neuropils are summarized as "eyestalk neuropils" (compare nomenclature in Schmidt 2016 as referenced above).

      Line 170, 172, 175 ff, and Figure 1. "abdomen", "abdominal ganglia": Contra the book chapter by Siegel 2016 "Introducing Antarctic Krill Euphausia superba Dana, 1850", his Fig. 1.2, the "tail" of crustaceans in most books on crustacean anatomy is not called "abdomen" but instead "pleon"; hence the name "pleopods" for the appendages of the pleon (instead of "abdomipods"). What is more, I suggest using the terms "pleon ganglia" instead of "abdominal ganglia", following the terminology suggested in "Harzsch S, Sandeman D, Chaigneau J (2012) Morphology and development of the central nervous system. In: Forest J and von Vaupel Klein JC (Eds.). Treatise on Zoology - Anatomy, Taxonomy, Biology. The Crustacea Vol. 3. Brill, Leiden pp. 9-236."

      Line 174: "thoracic ganglia". In Figure 1, there is a labelling mistake as these ganglia are named "thoracaic ganglia".

      Line 176, and throughout the paper: "supraesophageal ganglion". Following the standard nomenclature for crustaceans (see, e. g., Schmidt, M., 2016. Malacostraca. In: Schmidt-Rhaesa, A., Harzsch, S., Purschke, G. (Eds.), Structure & Evolution of Invertebrate Nervous Systems. Oxford University Press, Oxford, pp. 529-582. https://www.researchgate.net/publication/315366157", this structure (as in insects) is typically called a "brain". For terminology, also consult the following nomenclature paper: "Richter, S., Loesel, R., Purschke, G., Schmidt-Rhaesa, A., Scholtz, G., Stach, T., Vogt, L., Wanninger, A., Brenneis, G., Döring, C., Faller, S., Fritsch, M., Grobe, P., Heuer, C. M., Kaul, S., Møller, O. S., Müller, C. H. G., Rieger, V., Rothe, B. H., Stegner, M., Harzsch, S. (2010). Invertebrate neurophylogeny: Suggested terms and definitions for a neuroanatomical glossary. Frontiers in Zoology, 7. https://doi.org/10.1186/1742-9994-7-29".

      Line 212, and throughout the paper - hemielliposoid body: please refer to Harzsch Krieger 2011 and the numerous references to studies by Strausfeld cited therein in crustaceans. Strausfeld has provided compelling evidence that the crustacean hemiellipsoid body is equivalent to the insect mushroom body, so this term should be replaced. Harzsch, S., & Krieger, J. (2021). Genealogical relationships of mushroom bodies, hemiellipsoid bodies, and their afferent pathways in the brains of Pancrustacea: Recent progress and open questions. Arthropod Structure & Development, 65, 101100. HYPERLINK "https://doi.org/10.1016/J.ASD.2021.101100" https://doi.org/10.1016/J.ASD.2021.101100.

      Legend, figure 2, and others, and throughout the paper: "The olfactory neuropiles comprise the lateral antennal neuropile (LAN, ochre), the olfactory lobes (OL, yellow), and the antennal neuropile (AnN, green)." This is a strange terminological mix that you should urgently revise according to the standard terminology by Sandeman et al. 1992 (as referenced above). The LAN is the lateral antenna 1 neuropil. The AnN is the antenna 2 neuropil. The AnN is NOT deutocerebral but tritocerebral.  

      We thank the reviewer for acknowledging this paper's contribution to our understanding of the neuronal basis of the circadian clock in Pancrustaceans, as well as for the positive evaluation of the data documentation and presentation.

      We would like to clarify that we are aware of the existing body of literature on crustacean neuroanatomy and did not intend to present our data as a first in this field. This study intersects multiple communities (e.g., chronobiology, crustacean neurobiology, krill ecology), and the current focus of the manuscript arose from an attempt to make the paper as accessible to these communities as possible. We acknowledge, however, that the current version falls short in its engagement with the existing literature on crustacean brain anatomy. We therefore thank the reviewer for the input on crustacean neuroanatomy and its nomenclature, which will help us improve the manuscript in these respects. In a revised version, we plan to adjust the framing of the study to more precisely reflect the data presented. This will include better situating the present findings within the existing literature on crustacean neuroanatomy and its specific nomenclature, while toning down the emphasis on ecological importance and implications.

      Reviewer #3 (Public review):

      Summary:  

      A solid and very descriptive study of gene expression of three factors in krill, PDH, per, and cry2 that are important for circadian rhythms in insects. The results reveal optic areas in which PDH colocalises with each or per and cry2, and central brain areas where it does not. The authors speculate on the functional implications of their results for biological rhythms.  

      Comments:

      This manuscript describes a detailed anatomical study of the brain of krill in a circadian gene expression context. The results are well described, and the work is well done considering the obvious technical/practical difficulties of working with this species. Having stated that, the authors in their Methods write that the animals, after being caught, were placed in constant darkness. Is there any idea at all of when in ZT these brains were processed? Are the representations of gene expression taken at random around the clock? Perhaps the authors might make this explicit somewhere in the ms as it is an important point.

      The manuscript focuses mostly on PDH and its overlap or not with per or cry2. I found Figures 5 and 6 particularly confusing. The panels show PDH colocalising (or not-filled or unfilled arrows) with cry2 or with per. What they do not show (to me) is that per and cry2 colocalise. Now, of course, they probably do, but Figure 5 does not show this - or am I misinterpreting it? In Figure 6 again, I cannot see any panels with per and cry2 overlaid. Seems different sections were used for each probe? Is that what 'Areas with high per/ cry2-expression are marked by white arrowheads' means? I see that lines 493 and 494 confirm my suspicions that per/cry were not shown to be colocalised. Perhaps the authors could make this clearer up front than halfway through the Discussion, and clarify this in their legends, which are a little misleading in this respect?

      We thank the reviewer for his positive evaluation of our work, acknowledging the difficulty when working with this organism, and for the constructive comments. In a revised version of the manuscript, we will clarify the sampling time in the Methods. We will also state upfront — and in the figure legends — that per and cry2 were assessed on separate sections and their direct co-localization was therefore not demonstrated. However, as both components were independently shown to co-localize with PDH, their spatial overlap is nevertheless suggested by the shared co-localization with PDH. We will make this reasoning explicit earlier in the manuscript to avoid any misleading implications.

    1. Author response:

      We agree that the manuscript would benefit from a more clearly articulated conceptual framing, stronger model validation, more explicit statistical and ERP comparisons, and improved transparency regarding task design, sample inclusion, and preregistration. In the revised manuscript, we plan to address these points through substantial revision of the Introduction and Discussion, along with additional robustness and validation analyses, and more cautious interpretation of the main findings.

      Reviewer #1 raised important points about the framing of the cooperation task, the interpretation of betrayal, the standard statistical analyses, the modelling, and the ERP analyses. In response, we plan to clarify that the present task captures betrayal-related social risk or anticipated partner defection, rather than betrayal in its full interpersonal and emotional sense, and to better motivate this operationalization with reference to the betrayal-aversion and trust-game literature. We will moderate our claims regarding “emotional costs,” incorporate a more explicit task overview and accompanying schematic into the main text, and frame individual differences as a key avenue for future research. In addition, we will streamline the standard behavioral analyses, make the expected-value structure of the task explicit, add EV-based analyses of choice and reaction time, strengthen the ERP analyses, clarify that the study was not preregistered, and provide a complete report of data-quality checks. For the modelling section, a central revision will be to simplify the model structure and refit the models using a Bayesian hierarchical approach.

      Reviewer #2 emphasized the need for stronger theoretical framing and more specific distinctions between related constructs. In the revised manuscript, we will substantially revise the Introduction to better situate the present task in relation to the Trust Game literature and prior work comparing social and non-social decision-making under matched payoff structures. We will also define risk aversion, loss aversion, anticipated partner defection, and betrayal-related aversion more explicitly, and clarify that the distinction between betrayal-related aversion and loss aversion is inferred through computational modelling rather than directly manipulated as separate experimental factors. We also plan to introduce the computational model earlier in the manuscript, clarify how the key constructs are operationalized, replace unclear wording such as “impersonal losses,” strengthen the rationale for our hypotheses, and acknowledge the lack of preregistration more clearly.

      Reviewer #3 highlighted the need to align our conclusions more closely with the current evidence. In the revised manuscript, we will moderate the interpretation of the betrayal-related parameter, acknowledging that the cooperation task differs from the non-social risk task not only in social versus non-social uncertainty, but also in partner outcome, intentionality, and potential inequity structure. We therefore plan to avoid treating this parameter as a pure betrayal-specific construct and to describe it more cautiously as capturing betrayal-related social risk or aversion to anticipated partner defection. We also plan to report robustness analyses excluding participants who expressed doubts about the social interaction, as well as participants with poor catch-trial performance or otherwise low-quality data, and to clarify the sample sizes and exclusion criteria used for behavioral, modelling, and ERP analyses. Finally, we will strengthen model validation and ERP reporting, including broader validation analyses and more cautious interpretation if the evidence for temporal dissociation between betrayal-related aversion and loss aversion proves weaker than currently stated.

      Across these revisions, we also intend to simplify the model structure and use Bayesian hierarchical fitting to strengthen model validation, while avoiding overly strong claims if the additional analyses provide only modest support for a single preferred model.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Demeshkina and Ferré-D'Amaré showed that extrachromosomal circular DNA (eccDNA) and chromatin-associated proteins are present in stress granules, based on proteomic and sequencing analyses. Using HCR-FISH combined with imaging, the authors showed the colocalization of eccDNA with stress granule proteins. Furthermore, they found that CRISPR machinery targeting the eccDNA component of stress granules disrupts stress granule assembly, and that this effect is largely independent of Cas9 endonuclease activity. Notably, expression of cytoplasmic chromatin factors restores stress granule formation in the presence of CRISPR machinery in yeasts. This also rescues the growth defect caused by hypoxic stress, which correlates with impaired stress granule formation. Together, this manuscript provides insight into the presence of eccDNA in cytoplasmic membraneless organelles, specifically stress granules, and suggests a functional role for eccDNA within these structures under stress conditions.

      Strengths:

      The authors used a panel of ribonucleases to demonstrate that stress granule cores isolated from yeast and HEK293 cells are resistant to plasmid-safe DNase, an enzyme that does not degrade circular double-stranded DNA. To further support the presence of extrachromosomal circular DNA (eccDNA) in stress granules, they performed Circle-Seq on stress granule cores. The gel electrophoresis and sequencing experiments complement each other well, providing consistent evidence for eccDNA within these granules. Overall, this study provides insight into potential cytoplasmic roles for eccDNA, an area that remains largely unexplored.

      Weaknesses:

      (1) Figure 1F suggests that stress granule cores are susceptible to DNase I but not to plasmid-safe DNase (psDNase). However, its smearing pattern in the psDNase condition appears similar to that in the DNase I treatment shown in Figure 1E, although psDNase produces more discrete bands. The authors should comment on these differences between Figures 1E and 1F, or consider revising Figure 1F to improve consistency with Figures 1E and 1D.

      We suggest that the appropriate comparisons are between the DNase I and psDNase treatments within each figure panel, and not between panels (e.g., Figures 1E vs. 1F). The electrophoretic gels in the different panels were run for different lengths of time, and therefore the comparison between gels would be spurious. In Figure 1E, electrophoresis after DNase I treatment results in a characteristic smear, while after psDNase treatment yields discrete bands (lanes 2–3 vs. 4–5). Electrophoretic conditions for this figure were optimized to minimize diffusion and allow quantitative evaluation. The electrophoresis shown in Figure 1F, which compares yeast and mammalian stress granule core nucleic acids, was run for a longer period — as evidenced by the greater migration distance from the loading wells — yet still clearly shows the same qualitative difference between DNase I (smear, lane 3) and psDNase (discrete bands, lanes 1–2) treatments for the yeast samples. The apparent discrepancy noted by the referee therefore simply reflects the difference in electrophoretic conditions between the gels shown in the two separate figure panels.

      (2) The authors should clearly define "colocalization". Does it refer to complete spatial overlap between two signals (i.e., VCP and T30), or partial overlap (i.e., AHNAK DNA and G3BP)? Figure 3 and the associated text are descriptive. Quantitative analysis would strengthen the conclusions. For example, the authors could analyze the fraction of molecules localized to stress granules or provide Pearson's correlation coefficient or similar measurements.

      In our considered opinion, categorizing colocalization as either "partial" or "complete" implies a level of molecular precision that is physically unattainable at the resolution limits of any current light microscopy modality, and would therefore be misleading. Our approach employs super-resolution confocal laser scanning microscopy (Airyscan) with hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) or with immunofluorescence. The detection method used offers higher spatial resolution and signal-to-noise ratio than single-point detector/physical pinhole confocal (or widefield epifluorescence) microscopy used in most prior stress granule studies. Despite these enhancements, the system retains inherent diffraction-imposed limits: a lateral (XY) resolution of ~130 nm and an axial (Z) resolution of ~350–400 nm, defining the minimum separable distance between two fluorescent signals. Structures smaller than these thresholds remain unresolved within a single point spread function (PSF) maximum – a volume sufficiently large to simultaneously accommodate multiple stress granule cores or tens of thousands of individual proteins (such as G3BP) and dozens of nucleic acid molecules several thousand nucleotides in length. Consequently, any detected fluorescence signal may represent the superimposition of a large and indeterminate number of individual molecules or particles. True molecular interaction analysis remains for future studies using technologies with angstrom resolution (e.g., cryo-electron tomography, cryo-EM, X-ray crystallography, smFRET, EPR, NMR, etc.). Metrics such as Pearson's correlation coefficient report solely on the degree of signal overlap at the PSF scale (hundreds of nanometers) and would not provide any insight beyond what is already conveyed by our data.

      (3) The authors used a CRISPR-based approach to target the Ty1 LTR retrotransposon, an abundant stress granule eccDNA, and they observed a loss of stress granule formation. However, this phenotype may be specific to Ty1 eccDNA rather than representative of all eccDNA species present in granules. In particular, the title "Cytoplasmic circular DNA is a key constituent of stress granules" implies a broader role. To support this claim, the authors should consider approaches that more globally deplete eccDNA rather than targeting a single eccDNA.

      We respectfully disagree with the referee that further depletion of eccDNA would alter our conclusions. A central finding of our study is that stress granules can be abrogated cytoplasmically by co-expressing a Cas9 endonuclease, active or inactivated by point mutations (D10A /H840A), and a gRNA (which is itself a fusion of the crRNA and trcrRNA, natively separate RNAs in the source bacterium). We show in Figure 4 that when the gRNA targets the Ty1 sequences, endonucleolytically active holoenzyme co-expression in the cytoplasm results in loss of the corresponding eccDNAs, as assayed by sequencing of the relevant cytoplasmic fractions. Critically, when a catalytically inactive Cas9 protein (dCas9) is co-expressed with the gRNA instead of the wild-type endonuclease, depletion of the eccDNAs containing Ty1 sequences no longer takes place (Figures 4D and 4E), but stress granule formation is still abrogated (Figure 4C).

      In our manuscript, we indicated (as "data not shown”) that co-expression with Cas9 of a gRNA "targeting" a sequence that is absent from the S. cerevisiae genome still results in abrogation of stress granule formation. These data are shown in Author response image 1. The gRNA is targeted to the sequence 5’-agaatcgatgcattt, which is absent in the genome of the yeast strain used.

      Author response image 1.

      It follows from our experiments that stress granule abrogation (1) is not a result of the catalytically active Cas9 endonuclease; (2) is not a result of the presence of a gRNA-directed but catalytically inactive Cas9 holoenzyme, but (3) is the result of the presence of a CRISPR holoenzyme (as defined above) in the cytoplasm.

      To reiterate, abrogation of stress granules occurs when a Cas9-gRNA complex is present in the cytoplasm, regardless of whether the nuclease activity exists, or the gRNA targets a sequence that is present in the genome. Importantly, the holoenzyme is required for this phenomenon: presence of the endonuclease or the gRNA alone does not abrogate stress granule formation (Figures S5).

      It is because of this unexpected observation that we next hypothesized that activities of the Cas9-gRNA complex other than sequence-specific gRNA-targeted endonucleolytic activity is driving the suppression of stress granule formation. The best documented such activity is DNA sequence sampling (1-dimensional diffusion). We think that 1-dimensional diffusion of the Cas9-gRNA holoenzyme is displacing from the cytoplasmic eccDNA interactors whose association with the DNA is required to drive stress granule assembly. The fact that the stress-granule suppressive effect of cytoplasmic Cas9-gRNA expression can itself be suppressed by two completely unrelated proteins whose only shared feature is action on chromatin (CHD1 and GCN5) strongly supports this hypothesis (Figures 4G, 4H and S6; also response to point 4, below), in addition to confirming that cytoplasmic eccDNA is packaged by histones in a conformation that CHD1 and GCN5 can both recognize.

      (4) The authors should provide additional experimental evidence to support the claim that eccDNA is packaged in a chromatin-like state. The rescue of stress granule formation by ectopic expression of modified chromatin-associated proteins (CHD1NES and GCN5NES) following CRISPR treatment does not necessarily demonstrate that eccDNA is packaged like chromatin under basal conditions.

      We would like to reiterate the temporal order in our experimental design (detailed in full in Methods and summarized in Results). Cas9<sub>NES</sub>-gRNA and CHD1<sub>NES</sub> (or GCN5<sub>NES</sub>) were expressed simultaneously (not sequentially) in the cytoplasm. This was intentional, so as to give each player ample opportunity to engage its preferred substrate under non-stress conditions, prior to the brief oxidative stress. The referee appears to believe that cytoplasmic eccDNA was pre-exposed to Cas9<sub>NES</sub>-gRNA, and then the bound endonuclease challenged with chromatin-modifying enzymes.

      Our experimental design accounts for the contrasting substrate specificities of CRISPR and chromatin-modifying enzymes. Cas9-gRNA (holoenzyme) binds to nucleosome-free DNA with sub-nanomolar dissociation constant (Kd 0.1–1 nM) but its association with chromatinized DNA is impeded 5- to 100-fold (Isaac et al., 2016; Yarrington et al., 2018; Strohkendl et al., 2021). In contrast, whereas CHD1 binding to DNA is strictly nucleosome-dependent — its chromodomains actively block engagement with protein-free DNA (Hauk et al., 2010), and its productive binding (Kd 10–200 nM) relies on obligate multivalent contacts with the histone octamer, H4 tail, and wrapped DNA (Farnung et al., 2017; Sundaramoorthy et al., 2018).

      Our observation that stress granule formation was unperturbed following oxidative stress is most parsimoniously interpreted as CHD1<sub>NES</sub> outcompeting the CRISPR machinery for cytoplasmic binding to eccDNA by virtue of the latter existing in a histone-bound state that is recognized as chromatin by CHD1 –simultaneously favoring CHD1<sub>NES</sub> engagement and impeding Cas9 access. Thus, our experiment in effect employs stress granule formation as a readout for differential binding to chromatin or chromatin-like eccDNA.

      Farnung, L., Vos, S.M., Wigge, C., and Cramer, P. (2017). Nucleosome-Chd1 structure and implications for chromatin remodelling. Nature, 550(7677), 539–542.

      Hauk, G., McKnight, J.N., Nodelman, I.M., and Bharat, T.A.M. (2010). The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol Cell, 39(5), 711–723.

      Isaac, R.S., Jiang, F., Doudna, J.A., Lim, W.A., Narlikar, G.J., and Bhatt, D.L. (2016). Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Nature Struct Mol Biol, 23(12), 1097–1103.

      Strohkendl, I., Saifuddin, F.A., Gibson, B.A., Bhatt, D.L., Russell, R., and Bharat, T.A.M. (2021). Inhibition of CRISPR-Cas9 by bacteriophage-encoded proteins. Mol Cell, 81(8), 1665–1679.

      Sundaramoorthy, R., Hughes, A.L., Singh, V., Wiechens, N., Ryan, D.P., El-Mkami, H., Petoukhov, M., Svergun, D.I., Treutlein, B., Sproll, P., and Owen-Hughes, T. (2018). Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife, 7, e35720.

      Yarrington, R.M., Verma, S., Schwartz, S., Trautman, J.K., and Carroll, D. (2018). Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo.PNAS, 115(38), 9450–9455.

      Reviewer #2 (Public review):

      Summary:

      The authors report the presence of extrachromosomal circular DNAs (eccDNAs) within the core of stress granules purified from both yeast and mammalian cells.

      Strengths:

      This study is important for understanding the molecular mechanisms underlying stress granules containing eccDNAs and is likely to have a major impact on future research. A major strength of the study is the extensive experimental validation performed in yeast cells. In particular, cytoplasmic CRISPR-mediated targeting of eccDNAs suppresses stress granule formation and impairs recovery from hypoxic stress in yeast cells.

      Weaknesses:

      The conclusions would be further strengthened by validating the functional findings in an additional model system, such as mammalian cells.

      Comments:

      (1) Section: "Stress granule cores contain eccDNA"

      (a) The presence of eccDNAs would be more convincingly demonstrated using an orthogonal validation approach, such as DNA FISH targeting MYC and Centromere 8 (CEN8) on metaphase spreads from HEK293T cells (as performed in PMID: 34819668).

      The relationship between eccDNA dynamics and stress granule assembly across distinct cell cycle phases remains an important and poorly explored question. To our knowledge, no published data currently describe how stress response mechanisms are regulated during mitotic division, particularly in metaphase. Our identification of eccDNA as a component of stress granule cores can provide a first tractable framework to investigate this relationship. However, a systematic and in-depth characterization of this phenomenon warrants a dedicated future investigation.

      (b) The study would also benefit from assessing the presence of eccDNAs in the extracellular medium. For example, DNA could be extracted from conditioned media and analyzed by PCR using primers spanning eccDNA breakpoint junctions (as performed in PMID: 40074906; PMID: 36123406).

      We agree with the referee that eccDNA biology represents a fascinating and rapidly evolving area of research, particularly given the emerging role of eccDNA in oncogenesis. In this context, our identification of eccDNA as a core structural component of stress granules opens a novel avenue for exploring the connection between stress-dependent translational regulation and disease-associated eccDNA dynamics. While we acknowledge the importance of this direction, a rigorous investigation of this relationship requires extensive multifaceted experimentation that falls beyond the scope of the current study.

      (2) Section: "eccDNA-CRISPR abrogates stress granules"

      These findings should be further validated under additional stress conditions, such as drug-induced stress (like methotrexate) or nutrient deprivation in the cell medium. In addition, the same set of experiments should be performed in HEK293T cells to support the broader relevance of the observations.

      We agree with the referee that the composition and dynamics of stress granules arising from different stressors is an important endeavor. However, given the range of stressors documented to result in stress granule formation, those studies fall well beyond the scope of this manuscript. We will note however that the presence of eccDNA in stress granules of yeast and human cells is strong evidence for conservation of function(s). We think that exploration of the role of eccDNA in stress granule formation across the kingdoms of life (stress granules were first observed in heat-shocked tomato plants), cell cycle stages, stressors, etc. will be important research programs for the future.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Figures 3D and 3I: The use of magenta and red makes it difficult to distinguish between the two labeled signals. Consider using more contrasting colors to improve visual clarity.

      We appreciate the comment regarding color choices in the figures. In our view, magenta and red are sufficiently distinguishable as nucleic acid labels, particularly when combined with the green signal representing G3BP in these panels.

      (2) Figures 3F and 3G: Do the authors have an explanation for why AHNAK or MAPT DNA (white) does not colocalize with the anti-DNA immunofluorescence signal?

      Immunofluorescence (IF) is standard for detecting protein antigens but has limitations when the target is a non-protein molecule such as DNA, owing to its compacted chromatinized state. Anti-DNA antibodies can miss a significant fraction of their targets because the DNA backbone remains largely inaccessible, a limitation that DNA-FISH overcomes by directly hybridizing probes to denatured DNA sequences with high specificity. The fixation step required for both IF and FISH imaging can introduce additional steric barriers that disproportionately restrict antibody access compared to small nucleic acid probes. Even under optimized conditions, the IF signal with anti-DNA antibodies is inherently reflective of a subset of the total cellular DNA content.

      (3) Adding a subtitle on page 12 ("The abundant histones in purified stress granule...") would improve the overall structure and readability of the manuscript.

      We think that an additional subtitle would not substantially improve the readability of what is, admittedly, a very dense manuscript that employs a diversity of experimental approaches.

      (4) It would strengthen the analysis if statistical significance were included for the different time points in Figure 5C.

      We appreciate the reviewer’s suggestion. Figure 5C shows the largest difference at 40–45 hours after stress recovery, which is statistically significant between Cas9NES-gRNA (or dCas9NES-gRNA) and Cas9NES or gRNA only (two-tailed Student’s t-test, *, p ≤ 0.05). All primary experimental data are publicly available (FigShare) so further analyses can be performed by interested future parties.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      Eroglu and Hobert demonstrate that injecting CRISPR guides and repair constructs to target three genes at a time, tagging each with a different fluorescent protein, and selecting which gene to tag with which fluorophore based on genes' expression levels, can improve efficiency of gene tagging.

      Strengths:

      This manuscript demonstrates that three genes can be targeted efficiently with three different fluorophores. It also presents some practical considerations, like using the fluorophore least complicated by agar/worm autofluorescence for genes with low expression levels, and cost calculations if the same methods were used on all genes.

      Weaknesses:

      Eroglu has demonstrated in a previous publication that single-stranded DNA injection can increase efficiency of CRISPR in C. elegans, while inserting two fluorescent proteins and a co-CRISPR marker into three loci, and Paix et al 2015 demonstrated simultaneous insertion of two fluorescent tags. The current work is valuable and incremental advance. In general, I applaud the authors' willingness to strategize about how whole proteome tagging might be accomplished. I predict that the advance here will be one of many small advances that will get the field to that goal. The title oversells the advance presented, in my view, since seems like one among many key advances, and the first sentence of the Discussion seems a more apt summary of the key advance here.

      Some injections targeted genes on the same chromosome together, which will create unnecessary issues when doing crossing that will be useful for some future experiments. This made me wonder if injecting 3 together really is helpful vs targeting each gene separately, since only 5 worms need to be injected. It cuts time down by 2/3, but perhaps avoiding targeting the same chromosome with two tags would be useful.

      The limited utility of current blue fluorescent proteins makes me wonder if it's worth using at this stage, before there are better blue fluorescent proteins, or better yet, far red, to avoid issues with live imaging under phototoxic UV or near-UV illumination.

      These comments are a repeat of the original comments, and we refer the reader to our response to the original comments.

      Reviewer #2 (Public review):

      Original Review:

      The manuscript by Eroglu and Hobert presents a set of strains each harboring up to three fluorescently tagged endogenous proteins. While there is technically nothing wrong with the method and the images are beautiful, we struggled to appreciate the advance of this work - who is this paper for?

      As a technical method, the advance is minimal since the first author had already demonstrated that three mutations (fluorophore insertion and co-CRISPR marker) could be introduced simultaneously.

      As a pilot for creating genome-scale resources, it is not clear whether three different fluorophores in one animal, while elegantly designed and implemented, will be desired by the broader community.

      Finally, the interpretation of the patterns observed in the created lines leaves much to be desired. A Table with all the observations must be included and can replace the tedious (and often wrong) descriptions of the observations with the different lines. It would be too much to point out every mistaken expectation of protein expression. Two examples include:

      The expectation that ACDH-10 is enriched in the intestine and epidermal tissues (hypodermis) is naïve - there are multiple paralogs of this protein (look at WormPaths or WormFlux) that may share functions in different tissues. There is also no reason to assume that fatty acid metabolism does not occur in other tissues (including the germline). Finally, there are no published studies about this enzyme, so we really don't know for sure what it's doing.

      The expectation that HXK-1 is ubiquitously expressed is similarly naïve. There are three paralogous enzymes that are all associated with the same reaction, and we have shown that these three function redundantly in vivo, perhaps in different tissues (PMID: 40011787). Moreover, single cell RNA-seq data (PMID: 38816550) also shows enrichment of hxk-1 in gonadal sheath cells.

      The table should have at least the following information: gene/protein name - Wormbase ID - TPM levels of single cell data assigned to tissues for L2, L4 and adult (all published) - tissues in which expression is observed in the lines presented by the authors.

      Other points:

      (1) We would encourage the authors to provide systematic validation of the reported insertions. The manuscript reports that 24 of 30 tags were isolated and visible but does not clearly state whether each isolated line was confirmed by sequence‑level validation to be correctly in‑frame and free of unintended mutations at the target locus.

      (2) The manuscript presents aggregated success counts (e.g., 8/10 mTagBFP2 tags, 9/10 mStayGold, 7/10 mScarlet3) and useful narrative descriptions of injection outcomes. We suggest also to include per‑locus success rates.

      (3) For pools that required re‑injection after initial failures, we would like to see a description of the specific changes that were made to the injection mixes or procedures (e.g., new repair template prep, different Cas9 reagent lot, guide redesign). This will be useful troubleshooting information for others.

      (4) The authors states that the fluorophore sequences are codon-optimized for C. elegans. We suggest they provide the exact donor/tag sequences used specifically state whether the fluorophore sequences contain any synthetic/artificial introns or other sequence modifications (e.g., silent PAM‑disrupting mutations) were included in the donor templates.

      (5) Page 3: Include a reference for "The C. elegans genome encodes around 20,000 genes"

      We hope these comments are useful.

      Comments on Revised Version:

      Overall, we found the responses to be quite recalcitrant.

      We have one remaining composite concern about the comparison between observed expression patterns with the new strains versus published data.

      First, the authors only report patterns for one stage while it should be not too much effort to image the different life stages. However, since this is a revision, we are not formally requesting they do this.

      Second, in the now provided Table (thank you) 'observed expression' (last column) is lacking for 9 of the 30 proteins, and for 6 of these the procedure was not successful. Why not report patterns for the other three? It is confusing also because on page 5, the authors say that "overall, 24 of 30 tags ...all of which were visible with fluorescence stereomicroscopy" - are we missing something? Also, they then said that they "obtained 6/9 of the originally failed tags"; why are the corresponding patterns not included in table 1, and are 9 proteins still labeled as "no" in the "success?" Column?

      We appreciate the chance to clarify this matter: There are only 6 “no” in the “success” column. In two cases, HAT-1 and CBP-1, expression was dim at F1 but still sufficient to pick positive worms and quantify success rate at the locus. We noted these as “dim” on the table to indicate that if expression was lower, we likely would not have been able to isolate them at F1. In one case, COX-6B, expression was too dim at F1 to be isolated but was sufficient at F2 to be visualized and isolated from parents that were positive for the other two tags. We now clarified this distinction in the table and accompanying text: “Fluorescent signals of HAT-1::mScarlet3 and CBP-1::mScarlet3 in F1 progeny were dim but still sufficiently visible for quantification of knock-in efficiency, indicating that they are at the lower end of detectability for mScarlet3.”

      We imaged worms that had multiple tags as proof of principle and are happy to provide strains to those who would like to image/study them. At this point we are not convinced that imaging more worms would add to the conceptual framework.

      Third, we strongly feel that the response to our comments about expression patterns is not adequate. On page 5 the authors say that "all proteins were expected to be ubiquitously expressed" and that "scRNA-seq indicated that transcript abundance was ubiquitous and without strong tissue-specific enrichment with few exceptions". However, in their rebuttal, the authors now argue for tissue-specific expression for proteins with paralogs, turning around their own argument! Moreover, their Table indicates that many genes show tissue-enriched expression by RNA-seq while many of their tagged proteins exhibit ubiquitous expression.

      We respectfully disagree that there is contradiction. In our response, the discussion on paralogs was added as a clarification in response to the referee’s original comments (e.g., regarding ACDH-10): “There is also no reason to assume that fatty acid metabolism does not occur in other tissues (including the germline).” We wanted to make it clear that we were not concluding fatty acid metabolism (or other processes) does not occur in other tissues.

      We wish to stress that we never argued that paralogs could not fulfil the same essential function across tissues. The proteins were selected because their biological functions (e.g., glycolysis, fatty acid β-oxidation, translation) are broadly required, and that scRNA seq generally predicted broad expression with few exceptions as detailed in the text. Paralogs with similar activities (e.g., hxk-1, -2, -3) may overlap broadly in expression, or individual paralogs may carry out the process in different tissues provided one carries out the reaction in each tissue. For acdh-10 and hxk-1 specifically, both appear broadly expressed across tissues by scRNA-seq, with no consistent enrichment or depletion across datasets. So, our central point is that: for a specific gene involved in an essential process, transcript data alone are not sufficient to accurately predict tissue specific enrichment. Not that the processes do not occur in tissues where one paralog is absent. The possibility that a paralog may compensate for lack of expression is in no way contradictory with our conclusion.

      The table does not generally show tissue-enriched expression: it simply lists three tissues with the highest quantitative value in the respective dataset. For instance, taking the first gene from the list (Y82E9BR.3) and looking at the Ghaddar dataset, the top 3 tissues (log2(TPM)) are: pharyngeal muscle (13.4), gonadal sheath (12.9), marginal cells (12.9). The next 3 tissues are: body wall muscle (12.9), pharyngeal epithelium (12.8), and intestine (12.3). Even when there were apparent enrichments among the top 3 tissues, there were significant disagreements between datasets, and beyond top 3 even greater disagreements (the datasets agreed on the top tissue only 4 times over the 30 genes). These indicate that much of the variation is attributable to experimental noise rather than true predicted enrichment. The referee points to HXK-1 being correctly gonadal sheath enriched in one scRNA dataset; however, the other two datasets actually show different sites as being highest, and the same dataset misses effects in other cases. This is precisely why protein level data is needed.

      We further clarified this issue in the text: “We thus selected 30 genes across a variety of bulk transcript expression ranges which are generally predicted to be broadly expressed based on molecular function or, where molecular function was unknown (e.g., ZK632.9), single cell RNA sequencing (scRNA-seq) data (Table 1, Fig. 2A, B) (Gao et al., 2024; Ghaddar et al., 2023; Taylor et al., 2021).”

      Overall, this indicates that both the overall accomplishment of generating tagged protein strains and analyzing their expression is oversold.

      We have tried to make clear that our contribution is not a handful of new tagged strains added to the many that already exist. Rather, as stated in the abstract and elsewhere, we propose a strategy and provide proof-of-concept for scaling up tagging efforts. We believe the importance of this cannot be oversold.

      Reviewer #3 (Public review):

      Summary:

      The authors argue that establishing the expression pattern and sub-cellular localisation of an animal's proteome will highlight hypotheses for further study. This claim is probably accepted by many in the community. This manuscript seeks to confirm the feasibility of establishing such a resource, by using current transgenic methods to knock in DNA encoding different colored fluorescent tags into C. elegans genes.

      Strengths:

      The authors make the points above. For example, they provide evidence that the C. elegans germline harbors two populations of mitochondria that differ qualitatively in the proteins they express. They also confirm that labelling the whole proteome is an achievable goal with relatively limited resources and time.

      Weaknesses:

      The work is somewhat incremental in that it uses existing transgenic technology. Cell biology in C. elegans is challenging because of the small size of many of its cells, notably neurons. This can make establishing the sub-cellular localisation of a fluorescently tagged protein, or co-localizing it with another protein, tricky. The authors point out in their introduction that advances in light microscopy such as diSPIM, STED and ISM (a close relative of SIM), have increased the resolution of light microscopy. They also point out that recent advances in expansion microscopy can similarly help overcome the resolution limit. However, they do not use these technologies to characterize their transgenic strains.

      Reviewer #4 (Public review):

      Summary:

      Tagging the entire proteome of a metazoan would be a landmark achievement, providing a powerful complement and extension to existing "omic" catalogs in model systems. Here, Eroglu and Hobert argue that efficiently tagging multiple loci in a single "batch" would make the community-based achievement of this goal realistic. They provide rigorous evidence that such an approach is indeed feasible, exploring issues related to efficiency, design and screening strategies, disruption of gene function, and the potential for endogenously tagged alleles to reveal unexpected aspects of protein expression and localization. While the work has some minor gaps that are important to rigorously assess the feasibility of the proposed effort, the detailed and valuable insights that emerge should provide impetus to the community to coordinate efforts to make this ambitious goal a reality.

      Strengths:

      The work has numerous strengths. The authors provide compelling evidence that:

      Three distinct loci can be efficiently targeted with three distinct fluorescent tags in a single injection.

      Thoughtful targeting design can reduce the likelihood of disruption of function by the tag.

      Systematic design principles based on expression level and predicted localization/function can be used to optimize tagging strategies.

      The resulting tags can provide unexpected insight into patterns of protein production and subcellular localization.

      Not all of these advances are novel in themselves, but taken together, they represent an important technical and conceptual advance. The most important strength comes from the exceptionally high value of the goal itself, in that the work is that it has the potential to spur a community-wide effort toward achieving the ambitious goal of proteome-wide tagging.

      We appreciate the referee’s enthusiasm and hope that this will engage members of the community in a collective effort.

      Weaknesses:

      The work's shortcomings are minor.

      One concern has to do with the feasibility of the proposed screening strategies. The experimental design cleverly coinjects tags for three loci in different gene expression 'zones'; this expression level determines which tag will be used. As the authors allude to, there is an important distinction between genes with the same overall FKPM value between those that are expressed broadly and those focally expressed in a specific tissue. The proposed strategy claims that there are a sufficient number of highly expressed genes "to be used as visible markers" for recovering successfully edited animals. It would be useful for the authors to discuss the issue of broad vs focused expression among this set of genes a bit more thoroughly, with an eye toward the issue of how likely it is that these genes could indeed consistently be used as visible markers, particularly for those at the low end of this limit.

      To give two examples, this principle aided us with screening F54C8.1 and HAT-1. We added additional discussion on this to the first paragraph of the discussion: “For instance, we could clearly visualize F54C8.1::mScarlet3 in adult sperm by fluorescence stereomicroscopy despite a bulk FPKM of 16. Similarly, nuclear localized proteins will likely be easier to detect even at low expression levels, given the concentration of signal in small subcellular compartments. Indeed, this helped us detect HAT-1::mScarlet3 (56 bulk FPKM), which may have been too dim if distributed more broadly within cells.”

      What fraction of the proteome (on a per-gene basis) is secreted proteins? How difficult will it be to screen these for successful tags? Are there specific tags that would be more optimal for secreted proteins? (The authors mention the use of an SL2 or T2A cassette to label the cells in which these proteins are expressed but note that there are technical challenges associated with doing this at scale.)

      We added some of these points to the discussion: “Moreover, around 17% of the C. elegans genome (3,484 genes) may encode for secreted proteins (Suh and Hutter, 2012). Endogenous tagging of a substantial fraction of these proteins could reveal spatial patterns of secretion, distinguishing components that remain near their cell of origin from those that disperse to distal sites (Keeley et al., 2020). Tagging secreted proteins can also reveal sites of secretion – such as apical or basolateral membranes, or neurites – as has been observed for specific insulins (Sural et al., 2025) and for neuropeptides that localize selectively to synaptic regions (Toker et al., 2025).”

      Various tags have been used for secreted proteins including Venus, TagRFP, and mNeonGreen. The pH of secretory vesicles is ~5.0-5.5, so chosen FPs should have a pKa below this range to avoid denaturation. All 3 fluorophores used here (mStayGold, mScarlet3 and mTagBFP2) have pKa’s below this range and would likely be fluorescent within secretory vesicles.

      For secreted and/or weakly expressed genes, it would be useful for the authors to estimate for what fraction of these would successful insertions need to be screened by PCR, and what resources (time and money) this would likely entail. 

      We think that the bulk of ECM proteins would likely be visualizable without PCR due to their broad and stable expression, and as mentioned a good portion of these have been already tagged. However, it is likely that most of the secreted small peptides will have to be screened by PCR. We use homemade Taq, which makes material cost of the reagents minimal. A pair of genotyping primers costs ~$8 (~$27,872 for all secreted genes).

      Hands on time for lysis of 48-96 worms is approximately 20-30 minutes, with time to set up PCR around 5-10 minutes per target, and time to load a gel of 10 mins. In a given pool, 2/3 could be a putative secreted protein; thus, the same lysed population would enable screening for two targets at once. Collectively, around 40-60 mins of hands-on time would be required for two genes (around 20-30 mins per gene). Given 18 targets are injected per day, if 12 are screened by PCR, the screening could be done in 6 hours per day without affecting throughput. Most of the time spent on PCR would be replacing fluorescence screening time and would not overlap with the rate limiting injection step, performed by a separate specialist.

      For how many genes would a single tag not capture all predicted isoforms?

      Around 25% of C. elegans genes are thought to undergo alternative splicing (PMID: 21177968), with on average, ~2 isoforms per transcript. Among our selected genes, we only had one case where a single tag would not capture all isoforms (flad-1). We examined an additional 30 random genes and found no more examples by chance. So, in our view, this will be rare though we recognize in some cases a practical decision will need to be made, which could involve consideration of expression levels of each terminal exon.

      Finally, some readers might object to the authors' assertion in the abstract that this work is "a first step in this direction" (presumably referring to designing a strategy for whole-proteome tagging). There is no concern that the authors are disregarding the extensive work of other groups, as they explicitly mention the contributions of other groups to the foundation that enables the present work. However, the spirit of the abstract could be misinterpreted by a well-intentioned reader.

      We appreciate the referee’s perspective and have reworded this phrase in the abstract to: “As proof-of-principle for scalable pooled tagging, we undertook a pilot study in the nematode C. elegans, in which we set out to tag 30 different genetic loci with three different fluorophores, with 3 tags being introduced at a time.”

    1. Author response:

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

      eLife Assessment

      This study uses the yeast two-hybrid assay to identify proteins that may interact with yeast Set1 and other subunits of COMPASS/Set1C, the histone H3K4 methyltransferase, providing also some evidence for Set1 sumoylation and a role of SET1C methylating other factors in vitro. The results are valuable, and they should contribute to understanding the functions of the conserved SET1C complex, as they suggest potential functional connections with RNA biogenesis, chromatin remodeling, and non-histone methylation, whose implications would yet need to be explored. Nevertheless, apart from the fact that only a small subset of the Y2H interactions is further examined, the validating experiments are only partial or inconclusive, the strength of evidence being at this point incomplete.

      We present a systematic SET1C interaction map that provides a structured resource for generating and testing new hypotheses on SET1C function. We emphasise that these interactions represent a hypothesis generating resource rather than a set of validated protein–protein interactions. To reflect this, the manuscript has been carefully revised to distinguish clearly between observation and interpretation, and to avoid overstatement of the data. Accordingly, we have revised the title and the abstract. Selected examples are explored further to illustrate how candidates from the dataset can be followed up, but the primary contribution of this work is to provide a structured framework and resource that can guide future mechanistic studies of SET1C function.

      We thank the reviewers for their thoughtful comments. We have followed their recommendations by modifying the structure of the manuscript, removing distracting results and relocating some figures to the supplementary materials to improve the readability of the manuscript. At the same time, the reviewers acknowledge that the dataset is extensive and that aspects of the validation work are valuable.

      The changes made to the manuscript's structure in accordance with the reviewers' recommendations are as follows:

      (1) Figure 1 is accompanied by a table (Table S2) with the raw data describing all the interactions from the ten 2H screens. This table also lists common interactors found in the independent screens. I'm afraid Table S2 was omitted from the initial submission of the manuscript

      (2) Figure 2 has been modified to include an AlphaFold modeling of a seven-subunit Set1C complex (Set1– Bre2–Sdc1<sub>2</sub>–Swd1–Swd3–Spp1) together with Kap104. Figure 2D has been moved to a new Figure S2

      (3) The initial figure S2, which was problematic, has been removed, along with the accompanying text.

      (4) Figure 3 of the original paper has been moved to the supplementary material and is now shown as a new Figure S3.

      (5) Figure 5 in the original paper becomes Figure 3 in the revised version

      (6) Figure S3 (Co-IP between Set1 and Prp22), which serves as validation data, has been moved to the main figures and is now presented as Figure 4.

      (7) Figure 6 in the original paper becomes Figure 5 in the revised version

      (8) Figure 4 from the original paper has been repositioned as the first figure (new Figure 6) of the biochemical characterization of the interaction between Snf2 and Set1C.

      (9) Figure 7 has been removed from the manuscript. We have kept the original Figure 7E as a new Figure S6.

      (10) Figures 8, 9, 10 become Figures 7, 8, 9.

      Public Reviews:

      Reviewer #1 (Public review):

      We thank Reviewer 1 for the careful and thoughtful evaluation of our manuscript. We fully agree that yeast two hybrid screening provides candidate interactions that require cautious interpretation, and we recognise that our original version did not always make this sufficiently explicit.

      In the revised manuscript, we have made substantial changes to address this central concern. All Y2H interactions are now consistently presented as candidate or potential interactions, and speculative statements have been either removed or explicitly framed as hypotheses. Our intention is that the reader can clearly separate the dataset itself from any proposed biological implications.

      Second, we have refocused the manuscript to better reflect its primary contribution. We now present the Y2H screens as a comprehensive resource that defines a set of candidate interactions for SET1C, rather than as a set of validated functional relationships. In line with this, we have reduced the emphasis on speculative models and removed sections where the connection to experimental evidence was not sufficiently strong. This includes the removal of Fig. S2 and Fig. 7 and the associated text, as well as the relocation of several figures to the supplementary material. Where appropriate, we have added statements highlighting the limitations of the approaches used and the need for future work to establish physiological relevance.

      More generally, we agree with the reviewer that the value of Y2H data lies in generating testable hypotheses rather than establishing conclusions. We have therefore revised the manuscript throughout to ensure that the interpretation remains proportionate to the strength of the evidence.

      We hope that these changes address the reviewer’s concerns and result in a clearer and more appropriately balanced presentation of the data.

      The manuscript by Luciano et al is a collection of experiments about the yeast histone 3 lysine 4 methyltransferase, Set1, starting with 10 yeast two-hybrid screens (Y2H). Y2H screens were briefly popular 20+ years ago, but the persistently unfavourable false-to-true positive ratios limited their utility, and the conclusion emerged that Y2H is an unreliable approach for gathering protein-protein interaction data. Y2H outcomes are candidate interaction lists at best, strongly contaminated by false positives. Here, the authors employed a company (Hybridomics) to perform the Y2H screens.

      The primary data is not presented, and the outcomes are summarized using the Hybridomics in-house quality scoring system in Figure 1A. It is not possible to evaluate these data, and the manuscript presents cartoon summaries that the reader must accept as valuable.

      Hybrigenics brings extensive experience from conducting numerous screens, enabling the team to recognize recurring false positives that commonly arise in screening assays. In their detailed analysis, Hybrigenics reports the number of clones recovered and the extent of overlap among interaction regions, both of which contribute to the confidence scores they assign. Table S2, provided in the revised version, more accurately reflects the raw data obtained by Hybrigenics. Nevertheless, we agree that false positives contaminate the list of potential interactors. Some interactions may also be indirect through a common interactor and do not reflect a physiological interaction.

      (1) Based on the extensive knowledge about Set1C/COMPASS acquired from genetics and biochemistry by many labs (including the Geli lab), the results presented here from the 10 Y2H screens are notably patchy. Of the 7 subunits of this complex, only one (Spp1) was identified using Set1 as bait. Conversely, as baits, Swd2, Spp1, Shg1, captured Set1, and the Bre2-Sdc1 interaction was reciprocally identified. These interactions were scored at the highest confidence level, which lends some confidence to the screens. However, the missing interactions, even at the third confidence level, indicate that any Y2H conclusions using these data must be qualified with caution. The authors do not appear to be cautious in their lengthy evaluations of these candidate interactions, which are illustrated with cartoons in Figures 2 and 3, with some support from the literature but almost without additional evidence. Snf2 is a particularly interesting candidate, which the authors support with pull-down experiments after mixing the two proteins in vitro (Figure 4). After Y2H, this is the least convincing evidence for a protein-protein interaction, and no further, more reliable evidence is supplied.

      We thank the reviewer for raising this important point regarding the strength of the evidence supporting the Set1– Snf2 interaction. We agree that the current data do not establish a definitive physiological interaction. In the discussion, we explicitly note the limitations of the current data.

      For Figure 2, as recommended by referee 2, we performed AlphaFold modeling of a seven-subunit Set1C complex (Set1–Bre2–Sdc1<sub>2</sub>–Swd1–Swd3–Spp1) together with Kap104. Consistent with the Y2H data, the model recapitulates binding of the Kap104 SID to the PY-NLS region of Set1 (residues 40–90).

      We have moved Figure 3 in the supplementary materials.

      (2) Figure 5 continues the cartoon summary of extrapolations from the Y2H screens, again without supporting evidence, except that the authors state.

      Figure 5 is now Figure 3. We have added the statement in the text: “It is not feasible to validate all of these interactions within the limits of this manuscript, and their validity should therefore be interpreted with caution. Nonetheless, these findings provide a useful basis for future research”.

      "We have refined the interaction region between Set1, Prp8 and Prp22, showing that Prp8 and Prp22 interact strongly with Set1-F4 (n-SET). Prp22 interacts in addition with Set1-F1 (Figure S2)." However, Figure S2 does not show this evidence and is incoherent.

      When we say that we have refined the interaction region between Set1, Prp8, and Prp22, we mean that we have restricted the interaction regions according to Y2H criteria. Indeed, we have not shown the spots illustrating the results. This statement has been deleted as well as Fig. S2

      The figure legends for Figure S2B and C do not correspond to the figure.

      (B) Expression of the F1-F5 fragments in yeast cells. Fusion proteins were detected with an anti-GAL4 monoclonal antibody. TOTO yeast cells (Hybrigenics) were transformed with the different pB66-Set1-F1 to F5 plasmids and subsequently with either P6, pP6-Snf2 762-968, pP6-Prp8 37-250, or pP6-Prp22 379-763 that were identified in the Y2H screens. Transformed cells were incubated 3 days at 30{degree sign}C on SD-LEU-TRP and then restreaked on SD-LEU-TRP-HIS with 3AT. Cell growth was monitored after 2 days at 30{degree sign}C.

      (C) Solid and dotted arrows indicate that transformed TOTO cells transformed with pB66-Set1-F1 to F5 and the indicated prey (Snf2, Prp8, and Prp22) are growing in the presence of 20 mM and 5 mM of AT, respectively.

      Figure S2D is two almost featureless dark grey panels accompanied by the figure legend D) Control experiment showing that TOTO cells transformed with p6 and pB66-Set1-F4 are not gowing (sic) in the presence of 5 mM or 20 mM AT.

      We agree that the legend for Figure S2 was unclear and does not accurately describe the panels shown in the figure. Fig; S2 has been deleted in the revised version. The results shown in the original Fig. S2 add limited information and may detract from the clarity of the main points.

      In the revised version, we have moved the CoIP analysis demonstrating the interaction between Set1 and Prp22 (previously shown in Figure S3) into the main figures (now Figure 4) to further support and validate the two-hybrid screening results presented there.

      Line 343. Interestingly, the two-hybrid screens reveal that Set1 1-754 interacted with Gag capsid-like proteins of Ty1 (Figure S5), raising the possibility that Set1 binding to Ty1 mRNA is linked to the interaction of Set1 1-754 with Gag.

      This is another example of the primary mistake repeatedly made by the authors -Y2H interactions are candidate results and not conclusive evidence.

      This statement is supported by our previous findings showing that Set1 binds Ty1 mRNA independently of its dRRM domain and represses Ty1 mobility at a post-transcriptional stage (Luciano et al., Cell Discovery, 2017; PMID: 29071121). One possible explanation for Set1 association with Ty1 mRNA is its interaction with the Gag capsidlike protein. In this context, the observed interaction between Set1(1–754) and Gag capsid-like proteins is consistent with this model.

      To further illustrate this point, the authors highlight the candidate interaction between Nis1 and 3 Set1C subunits.

      While we agree that the Nis1-Set1C interaction has not been demonstrated beyond doubt, we feel that our Y2H and in vitro binding experiments provide reasonable evidence that the interactions may be relevant. It is important to consider that any interaction assay can provide negative (and false positive) results, this includes Y2H, in vitro binding and mass-spec analysis of purified complexes from cells. We feel that it is not appropriate to only trust protein interactions that are strong and stable enough to be demonstrated via purified complexes. It is clear that some protein interactions do occur in transient and weak manner and therefore are not compatible with biochemical purification approach. This indeed is the strength of alternative methods like Y2H and in vitro binding assays, that interactions can be identified and tested even if the physiological context of the interaction may be more complex.

      (3) After multiple speculations based on the Y2H candidates, the authors changed to focus on sumoylation of Set1, which has previously reported to be sumoylated. Evidence identifying two sumoylation sites in Set1, in the N-SET and SET domains, is valuable and adds important progress to the role of sumoylation in the regulation of H3K4 methyltransferase, relevant for all eukaryotes. This illuminating part of the manuscript is only tenuously connected to the preceding Y2H screens and concomitant speculations.

      We thank Referee 1 for their comment. While it is true that there is only a modest connection between Set1 interactors involved in direct or indirect sumoylation and the characterization of Set1 SUMOylation sites, we believe that this does not constitute a weakness of the manuscript.

      (4) The manuscript then describes a red herring exercise involving Set1 methylation of Nrm1. In an already speculative and difficult manuscript, it is exasperating to read a paragraph about a failed idea. Apart from panel E, Figure 7 is a distraction, and I believe it should not be shared.

      (5) However, despite the failure with Nrm1, Line 443 - The H3K4-like domain in Nrm1 raised our attention to other yeast proteins that carry such sequences.

      This line of thinking is even less connected to the Y2H screens than the sumoylation work.

      However, the authors present a reasonable evaluation of the yeast proteome screened for six amino acids similar to the known H3K4 motif ARTKQT (Figure 7e).

      (6) However, this evaluation goes nowhere and has no connection with the next section of the manuscript, which is entirely speculation about the regulation of metabolism and stress responses based on the Y2H results and selected evidence from the literature.

      In response to comments 4 and 5, we have removed Fig. 7 and the paragraph titled “The transcriptional corepressor Nrm1 interacts with SET1C.” Part of this paragraph and the section describing the screen of the yeast proteome for six–amino acid sequences resembling the H3K4 motif (ARTKQT) has been kept as Fig. S6.

      In the abstract, we have removed the sentence: We demonstrate that the transcriptional corepressor Nrm1 is methylated by SET1C in vitro suggesting that H3K4-like domains may represent a class of non-histone substrates for SET1C.

      At the end of the introduction, we have deleted “the transcriptional corepressor Nrm1” in the sentence: In addition, we demonstrate that the transcriptional corepressor Nrm1 and the Snf2 AT-hook are both methylated by SET1C in vitro

      (7) The manuscript then describes more failed experiments regarding lysine methylation of Snf2 by Set1C, which unexpectedly reports arginine methylation rather than lysine. The manuscript does not currently meet the standard expected for this type of paper - the composition is somewhat incoherent and there are no previous reports of arginine methylation by SET domain proteins.

      We have integrated extensive in vitro reconstruction experiments with complementary in vivo studies, all conducted according to the rigorous standards expected by leading journals. These approaches have allowed us to reach the conclusions presented in this manuscript. While some of these findings are unexpected, they are supported by the data. We have carefully discussed the results and their limitations to provide a comprehensive interpretation.

      The manuscript presents a very experienced grasp of the literature and a sophisticated appreciation of the forefront issues, but a surprising failure to eliminate uninformative failures and peripheral distractions. The over interpretation of Y2H results is a dominating failure. There are some valuable parts within this manuscript, and hopefully, the authors can reformat to eliminate the defects and appropriately qualify the candidate data.

      We thank Referee 1 for these insightful comments. In the revised version, we have followed the advice to remove non-informative failures and peripheral distractions. Additionally, we exercise greater caution to avoid over-interpreting the Y2H results.

      Reviewer #2 (Public review):

      Summary:

      This paper starts with a large-scale yeast two-hybrid (Y2H) screen using Set1 (full-length and smaller parts) and other Set1C/COMPASS subunits as bait. There are hundreds of possible interactions identified, but only a small number are given any follow-up. While it's useful to document all the possible interactions, the unfocused and preliminary nature of the results makes the paper feel scattered and incomplete.

      Strengths:

      The Y2H screen was very comprehensive, producing lots of interesting possible leads for further experiments.

      Weaknesses:

      The results are useful but incomplete because only a small subset of the Y2H interactions is further examined. Even in the case of those that were further tested, the validating experiments are only partial or inconclusive.

      Referee 2’s comments align in some respects with those of Referee 1. In the revised version, we have followed the detailed Referee 2 suggestions to reduce the scattered nature of the manuscript. In addition, we include an AlphaFold model of the interaction between the Set1 N-term 1-754 with the SID domain of Kap104 that involves the proposed Set1 PY-NLS sequence.

      Reviewer #3 (Public review):

      The SET1C/COMPASS complex is the histone H3K4 methyltransferase in Saccharomyces cerevisiae, where it plays pivotal roles in transcriptional regulation, DNA repair, and chromatin dynamics. While its canonical function in histone methylation is well-established, its full interactome remains poorly defined. Moreover, whether SET1C methylates non-histone substrates has been an open question. In this study, Luciano et al. employ systematic yeast two-hybrid (Y2H) screening to uncover novel interactors and functions of SET1C. Their findings reveal potential functional connections to RNA biogenesis, chromatin remodeling, and non-histone methylation.

      The authors performed multiple Y2H screens using Set1 (full-length, N-terminal, and C-terminal fragments) and each of its seven subunits as baits. They identified high-confidence interactors that link SET1C to diverse cellular processes, including chromatin regulation (e.g., the SWI/SNF complex via Snf2), DNA replication (e.g., Mcm2, Orc6), RNA biogenesis (e.g., spliceosome components Prp8 and Prp22; polyadenylation factors Pta1 and Ref2), tRNA processing (e.g., Trm1, Trm732), and nuclear import/export (e.g., importins Kap104 and Kap123). Some of these interactions were further validated by immunoprecipitation or in vitro assays.

      Given the interaction of Set1 with Slx5 and Wss1 - proteins involved in SUMO-dependent processes - the authors investigated and convincingly demonstrated that Set1 is sumoylated. This modification may influence the function and regulation of the SET1C complex.

      Finally, the authors provide evidence that SET1C methylates proteins beyond histone H3K4, notably Nrm1, a transcriptional corepressor, and Snf2, the catalytic subunit of the SWI/SNF chromatin remodeling complex. Although Nrm1 contains a domain resembling the H3K4-methylated sequence (H3K4-like domain), this region does not appear to be required for its methylation. The search for other proteins containing similar domains as potential methylation candidates (p.12, first paragraph) seems less justified, given the lack of evidence supporting the requirement for the H3K4-like domain in methylation.

      This study offers valuable insights into the interactome of SET1C, suggesting potential links between the complex and a wide range of cellular processes. However, the functional implications of the Y2H interactions remain to be explored further. Additionally, the study provides intriguing information on the possible regulation of Set1 by sumoylation. The discovery of Nrm1 and Snf2 as methylation substrates could significantly expand the known targets and functions of SET1C.

      The results are supported by high-quality data.

      We thank referee 3 for their positive comments

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Restructure the manuscript into at least two papers.

      We thank the reviewer for this suggestion. In the revised manuscript, we have addressed this concern by substantially restructuring and streamlining the presentation. We consider the dataset, validation experiments, and functional observations to be closely integrated, and we believe that presenting them together provides the most coherent and impactful account of the work.

      Minor points

      There are several basic flaws in the manuscript that I feel indicate the co-authors have not proofread the manuscript sufficiently - 4 examples from early in the manuscript are listed below.

      (1) The reference for Hybridomics is (73) - obviously from an earlier version that used a different referencing system that has not been corrected.

      Thank you. This has been corrected.

      (2) Line 194 - 197. These screens have proven their power and effectiveness. In particular, they identified ...... the CTD of Rpb1 as an interactor of the N-terminal region of Set1 (Bae et al, 2020) (Figure S1). Rbp1 interaction is not identified in the screens presented here, and Figure S1 is a cartoon and not primary evidence.

      The interaction between the CTD of Rpb1 (Rpo21) and Set1 is reported in Table S2. The detailed characterization presented in Bae et al. (2020) was subsequently carried out as a direct follow-up to this screen.

      (3) Line 205-211. The highly confident interactors of the seven SET1C subunits are shown in Figure 1C-E. We found that Spp1, Shg1 and Swd2 interact alone with Set1 (Figure 1C). The minimum Set1 region for which an interaction is found for each of these 3 subunits is shown in Figure 1C. The high confidence interactors of the seven SET1C subunits are shown in Figure 1C-E. We found that Spp1, Shg1 and Swd2 display Y2H interactions with Set1 (Figure 1C). The high confidence interactors of Spp1, Shg1 and Swd2 are indicated in Figure 1D (see also Table S2).

      It is possible that Table S2 was omitted from the original submission, as it was requested during the production stage.

      (4) Line 335. We have classified all Set1 and subunit interactors according to these SET1C roles (Figure S5). However, this refers to Figure S4 - many further references to Figure S5 are also to Figure S4.

      Thank you. This has been corrected.

      Reviewer #2 (Recommendations for the authors):

      General recommendations:

      (1) Figures 1, 2, 3, and 5 and their associated main text are essentially just lists of interactors, put in graphic form and grouped to allow speculation about possible biological functions for the interactions. But almost none of the ideas are tested, so these sections take much more space than warranted. Having so much preliminary Y2H data actually distracts attention from the follow-up experiments that are shown. I would move most or all of this to the supplement, consolidating the Y2H results into fewer figures (or even just the Table).

      As mentioned earlier, the manuscript has been reorganized and Table S2 is provided.

      (2) The Snf2 interaction gets the most follow-up, so separating Figure 4 from Figures 8-10 broke the flow of that story. I would group these figures together since all are related to the Snf2 AT hook story.

      This was done accordingly.

      (3) I understand that it's impossible to validate all the possible interactions, particularly if resources are limited. However, at least for the interactions that get further attention, it could be very useful to try some AlphaFold multimer predictions. A high confidence AlphaFold score would provide a second orthogonal piece of evidence to support the Y2H results.

      We generated an AlphaFold model (Figure 2C) that recapitulates the key predictions for the Set1-Kap104 Y2H interaction.

      Comments on specific sections:

      (1) Y2H results. The text says Figure 1 shows all the high-confidence interactors. But the Set1 NTD interaction with the Rpb1 CTD is not shown here (it's in the supplement).

      In Table S2, an interaction is observed between full-length Set1 and the Rpb1-CTD (14 repeats), where Rpb1 is referred to as Rpo21.

      Figure 2 shows additional high-confidence interactors that do not appear in Figure 1, while others (like the Shg1Mog1 interaction) are shown in both Figures 1 and 2. It's confusing to scatter the data like this, which is why I recommend consolidating into a single figure or table.

      In Figure 2, the high-confidence interactors of Set1 (1–754) are highlighted in red and green (Snf2, Gbp2, and Kap104), and all are also present in Figure 1. Dbp1, identified as a high-confidence interactor of Spp1, likewise appears in Figure 1. Table S2 summarizes all of these interactions.

      (2) Line 219. How does a "high confidence" Set1-Kap104 Y2H interaction suggest the interaction is direct? Couldn't an indirect interaction also be tight and reproducible? This is an example where it would be worth seeing if AlphaFold also predicts an interaction and, if so, whether it involves the proposed NLS sequences.

      Y2H screening indicated that Kap104 binds to the N-terminal region (aa 1–754) of Set1 via its Set1 interaction domain (SID). To validate this, we used AlphaFold to model the seven-subunit Set1C complex (Set1-Bre2-Sdc1(x2) Swd1-Swd3-Spp1) with Kap104. The resulting model showed borderline confidence for the overall fold (pTM = 0.53) and low confidence in subunit positioning (ipTM = 0.5). Visualization in PyMOL confirmed Kap104 SID binding to Set1(1–754), consistent with Y2H results. The structure highlights Kap104 SID interaction with Set1’s PY-NLS at residues 40–90; the second PY-NLS is neither visible nor engaged in this model.

      (3) In the discussion of nuclear import interactors, what does it mean to say the Shg1-Mog1 interaction is "along the same line" as Set1-Kap104?

      We meant that the interaction between Shg1 and Mog1 represents another example of an interaction between a Set1C subunit and a protein involved in nuclear import. Along the same line has been deleted in the revised version.

      (4) To follow up on the Swd1-Nrm1 Y2H interaction, the paper shows that Nrm1 is methylated by Set1 in vitro (Figure 7), but it's not clear whether this has any biological significance. Without any in vivo follow-up, this figure is probably more appropriate for the Supplement.

      As noted above, Figure 7 has been removed, only panel E of Figure 7 is retained in the revised version.

      (5) Figures 6 and S8 show that Set1 is SUMOylated. Although it's not clear what this does to Set1 function or which E3 is responsible, the modification data looks convincing. The legend to Figures 6A and B says the Elutes samples are purified on nickel columns. Why are the Myc-Set1 and GB-Set1 proteins without the his-SUMO modification also binding to the nickel column? That's not happening in panels C and D. In the blots on the right for his-SUMO, is there any way to show that one of those bands is Set1? Maybe IP for MYC and then probe for the His tag?

      We thank the reviewer for this observation. His-SUMO purification using Nickel beads was used to purify HisSUMOylated proteins. Purified proteins were analyzed by Western blot using anti-MYC or anti-GAL4 antibodies to detect SET1-His-SUMO, as well as anti-His antibodies to confirm the presence of purified His-SUMOylated proteins. As mentioned by the reviewer, we detected unmodified MYC-Set1 and GAL4-Set1 in both the (-) and (+) His-SUMO eluates. This phenomenon is most likely due to the stickiness of unmodified Set1 to the beads. This is a commonly observed phenomenon in this type of biochemical assay, particularly when analyzing large proteins such as Set1 (124 kDa). This stickiness behavior has been observed in similar SUMOylation assays, e.g., for Hpr1 (88 kDa) (Bretes H, 2014. PMID: 24500206), Nup1 (114 kDa), and Nup2 (78 kDa) (Folz H, 2019. PMID: 30837289). This stickiness was not observed when using Set1 fragments (panels C and D), most likely because the fragments lost the stickiness to the beads, a characteristic belonging only to the full-length Set1. We mention this point in the legend of the new figure 5.

      (6) The Snf2 interaction gets the most follow-up. The GST pulldown validation of Set1 interaction with Snf2 AThook looks pretty good. However, the RGG repeats are necessary for the Set1 interaction with recombinant Snf2 proteins, but not for the co-IP of in vivo material. Again, AlphaFold could lend further support here.

      Thank you for this helpful suggestion. We agree that structural modelling could, in principle, provide an additional and orthogonal line of support for the Set1-Snf2 interaction. We did explore this using AlphaFold. However, both Set1 and Snf2 contain extensive intrinsically disordered regions, including the regions implicated in the interaction, and none of the models we obtained provided interpretable structural insight into the interaction interface. In particular, the predicted complexes showed low confidence in relative domain positioning, which limits their usefulness for supporting or refining the interaction model. One possible explanation is that additional components are required to stabilise a meaningful interaction in silico. While we modelled Set1 within a seven-subunit Set1C complex, Snf2 was necessarily included in isolation from its native context. Given that Snf2 functions as part of multiple, heterogeneous chromatin remodelling complexes, the absence of its physiological binding partners may prevent AlphaFold from resolving a relevant interaction interface. In light of these limitations, we have not included the AlphaFold models in the manuscript, as we felt they would not provide reliable or informative support. Instead, we have focused on the experimental evidence presented. We have clarified this point in the revised discussion to acknowledge both the potential and the current limitations of structural prediction approaches in this context.

      (7) The Snf2 methylation by Set1 is less convincing, and its biological significance is still unclear. I think it's pretty unlikely that Set1 could methylate arginine. The mass spectrometry is used for in vivo validation (mass spec), but mutating the lysines (Figure S11, S12) or Set1 deletion (Figure S14) doesn't seem to affect the signal. Could there be quantitative differences? Is there any way to quantitate the mass spec data to estimate the modified/unmodified ratio?

      We thank the reviewer for highlighting the unexpected nature of the methylation results. We agree that the observation of arginine methylation in this context is surprising, particularly given that SET domain proteins are classically associated with lysine methylation. This is why we performed multiple in vitro and in vivo experiments, and careful interpretation data that were clear led us to conclude that Set1C methylates the arginines within the ARTSTRGR motif of the AT-hook. We agree that the biological significance of this modification remains unclear. We obtained data showing that deletion of the SID domain of Snf2 impairs yeast growth on lactate, whereas this mutant grows normally on glucose and galactose, in contrast to the Snf2Δ mutant, which exhibits poor growth on both glucose and galactose. In comparison, deletion of the RG motif of Snf2 does not affect growth on lactate. These results provide insight into the interaction between Set1 and Snf2 but do not shed light on the potential importance of methylation of the RG motif. We therefore chose not to include them. In the discussion, we acknowledge the limitations of the current evidence. Our intention is to retain these findings as potentially interesting observations while ensuring that their interpretation remains appropriately cautious.

      Minor comments:

      (1) Lines 153 and 163: Stress response is listed twice, but with different references. Maybe these need to be further defined or else combined?

      We have deleted stress response line 163 and moved the references “Deshpande et al, 2022 and Nadal-Ribelles et al, 2015” line 153.

      (2) Line 193: better to say the proteins were fused to the C- or N-terminus (rather than upstream/downstream). It would be worth mentioning if there was a reason why Swd2 was fused to the N-terminus, unlike all the others.

      This has been done accordingly. In our hands, C-terminal fusions of Swd2 are not functional.

      (3) Is the scoring scheme (highest, high, good) that produces the colors in Figure 1 shown in the table? It doesn't say what the tan color (two of the Bre2 interactors) means.

      It is a mistake, Tea1 should be blue and Swi1 should not appear here. This has been fixed.

      (4) Line 206. It's not clear what it means to say that three of the subunits "interact alone with Set1". It can't mean they only interact with Set1, since other interactors are shown in Figure 1B. If it meant to say the interactions don't require other COMPASS subunits? I don't see how you can tell that from the Y2H assay. Please clarify.

      It means that these 3 subunits interact directly with Set1 without the need of another subunit, unlike of the other subunits.

      (5) Line 252. While discussing the Set1 - Snf2 interaction, the paper cites Hirschhorn et al. That paper talks about Swi-Snf, but doesn't mention Set1 anywhere. Maybe the authors meant to cite a different paper?

      We agree, this reference is not appropriated. It has been deleted.

      (6) Figure S2 panels A and C are redundant and could easily be combined.

      Figure S2 has been deleted.

      (7) Figure S4: Should the green category also include transcription? Ssl1 is a TFIIH subunit, which could be involved in either transcription initiation or NER. Sen1 and Nrd1 are transcription termination factors, although Sen1 may also function in R-loop resolution.

      We agree but it is already complicated as it is.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors identify and investigate a specific population of PVNOT neurons (oxytocin neurons of the paraventricular hypothalamus) that seem to be involved in both behavioral and autonomic thermoregulation. These cells are activated by social thermoregulatory behaviors, but can influence thermoregulation in both social and nonsocial contexts, specifically during transitions and when mice are at low core body temperature (Tb).

      Strengths:

      The manuscript has many strengths.

      This is a novel study, with a clear question that is addressed using an array of well-designed experiments employing integrative methods. Most of the figures are well-developed, and the analysis is generally rigorous and well-detailed. The authors are clearly very experienced in this field, and indeed, their scholarly introduction and discussion sections are to their credit.

      We are grateful for the reviewer’s careful reading and positive assessment, including their remarks on the clarity of the question, experimental design, and analysis.

      The link between thermoregulation and the oxytocin system is well established, as is the link between social behavior and the same broad system. However, the link between these three things is novel, if it can be well substantiated. I am not persuaded that was achieved here, but I do think this manuscript has many novel and useful offerings.

      We thank the reviewer for this thoughtful comment and for recognizing the novelty of the study. We wish to clarify the central goal of the manuscript: while social thermoregulation provided the initial influence for studying PVNOT neurons, our principal finding is that PVNOT activity during rest-to-arousal transitions is independent of social context. As stated in the manuscript, "To our surprise, these peaks were observed in both social and non-social contexts." Thus, our study demonstrates a broader role for PVNOT neurons in state-dependent thermoregulatory transitions—one that includes, but is not limited to, social contexts. We have revised the text to make this emphasis clearer throughout.

      We also added a short piece to the Discussion on this point. This is the fourth and final paragraph of the Discussion section called “State-dependent PVNOT activity during thermo-behavioral transitions.”

      The authors use a cooling floor, and only go down to 10 degrees Celsius. This is fine, but I would like to see the effects using ambient temperature also. This is not a crucial issue, as it is not necessary for the authors' interpretations, but it could improve measurement sensitivity.

      Both Reviewer 1 and Reviewer 2 raise important and related points: manipulating floor temperature provides a thermal stimulus that is distinct from manipulating whole-chamber ambient air temperature, and these modalities could engage partially different sensory pathways and circuits. (Note this response is copy-pasted to other relevant comments).

      We intentionally used floor cooling/heating because it provides a reliable, well-controlled stimulus that elicits thermoregulatory behaviors while keeping the experimental environment stable (e.g., avoiding changes in airflow/humidity that can accompany ambient cooling). To prevent conflation of these modalities, we revised the manuscript to consistently describe the manipulation as “floor temperature” (and not “ambient temperature”), and we added to the Discussion acknowledging that conductive floor temperature changes may differentially recruit peripheral thermoreceptors compared to ambient air temperature.

      While extending these experiments to whole-chamber ambient temperature changes could be informative in future work, it is not required for the central interpretations here, which focus on PVNOT activity dynamics during thermoregulatory behavior under controlled thermal conditions.

      Through an elegant behavioral experiment in Figure 1, the authors identify c-Fos patterns in the PVN that are activated by active social huddling, and they show that at the RNA level these cells overlap with oxytocin, indicating that they are oxytocin-producing cells. But this is not well discussed or indeed quantified.

      We thank the reviewer for catching this; Reviewer 2 made a similar comment. A typo in the figure legend led to this confusion. Figure 1I is in fact a quantification of the percent Oxytocin:Fos colocalized cells (not Fos:DAPI, as was written) in dorsal and ventral subregions of the PVN during active huddling and quiescent huddling. We have corrected the legend and clarified the quantification in the revised manuscript.

      The authors engage in a deep analysis of fiber photometry experiments, first by observing PVNOT neuron overall activity during a variety of different behaviors in the context of three different temperatures. Activity was associated with nesting, quiescence, and both types of huddling (when social opportunities exist). Social situations did not strongly affect this, nor did temperature conditions. These analyses indicate that the PVNOT neurons are involved in mediating specific behavioral outputs.

      With more detailed analysis, the authors investigated how PVNOT neuronal activity relates to behavioral state transition. They found that the probability of peak PVNOT neural activity strongly predicts the offset of quiescence or quiescent huddling, and therefore can be argued to signal an increase in physical activity, and as such, increased metabolism. However, the opposite pattern was observed for huddling and nesting (onset being associated with PVNOT activity), again arguing for increased thermogenesis as a function.

      What is particularly compelling is that these peaks of activity tend to occur during low Tb, again arguing for the function in increasing body warmth.

      The authors then employ an impressive setup where they image brown adipose tissue (BAT) in tandem with DeepLabCut (DLC) based animal tracking. Crucially, BAT activity and surface temperature correlated with the calcium peak of PVNOT neurons.

      Lastly, optogenetic activation of PVNOT neurons increased Tb when it was in the lower range, but not when in the higher range. It also affected BAT and rump temperature, again at low Tb. However, there is no real effect on behavior, except a trend in activity.

      The authors do some interesting tracing work at the end, though this is not functionally explored. That is not a criticism, as it does seem like this would be a whole follow-up study.

      Weaknesses:

      While novel and valuable, the manuscript feels incomplete in its current form.

      The main evidence lacking is a loss of function of the experiment. Ideally, the authors would chronically and/or acutely inhibit PVNOT neurons to establish their necessity. I know this seems obvious, but I think it is important.

      We agree with the reviewer that loss-of-function experiments are a valuable component of circuit mapping and we appreciate this suggestion. For transparency, we did attempt a chronic chemogenetic inhibition experiment using DREADDs in PVNOT neurons. However, the results were inconclusive, primarily owing to the confounding effects of pharmacological injections: both drug and vehicle-treated animals exhibited stress-induced hyperthermia following injection, and because inhibition could not be delivered while animals were asleep/resting the experimental conditions did not recapitulate the low-Tb quiescent state during which PVNOT peaks naturally occur. Given these confounds, we do not believe these data meet the standard required for inclusion in this manuscript.

      We did consider acute optogenetic inhibition. However, a clear prediction about inhibition was not as apparent in our model. Our photometry data identified a, testable hypothesis for activation: PVNOT peaks precede the exit from quiescence, therefore activation during quiescence should increase the transition, which it did (Figures 5 and 6).

      That said, new analyses of our data, driven by these reviews, have now uncovered what might be inhibition of PVNOT neurons during the approximate 60 seconds prior to entry to resting states (i.e., quiescence and quiescent huddling); see the new Fig. S3I-L. This raises the possibility that an appropriately timed photoinhibition of PVNOT neurons could facilitate the establishment of resting states. We believe that, in light of our chemogenetic and optogenetic activation experiments, for an inhibition experiment to be done appropriately would require a real-time, closed loop setup that is currently not available in our laboratory.

      We have added a caveat to the Discussion acknowledging the lack of LOF data as a limitation and have identified this as an important direction for future investigation.

      The relative lack of behavioral analysis following optogenetic activation of PVNOT neurons is puzzling. The authors must surely want to study what this intervention does to behavioral state transitions. I feel that the current level of analysis limits the overall conclusions of this study to a large extent.

      We appreciate this concern and wish to clarify two points.

      First, our decision to perform optogenetic activation in isolated (solo-housed) animals was driven by our initial finding that PVNOT activity profiles are mostly social-context independent during the transition from rest to arousal (Figures 2 and 3). By studying isolated animals, we could test the fundamental relationship between PVNOT activation and the rest-to-active transition without confounding social feedback. Additionally, we encountered technical challenges when using the SGBS thermographic model in paired contexts: the high thermal intensity at the point of contact between huddling mice created a thermal merging artifact that prevented accurate segmentation of individual body regions (BAT vs. rump).

      Second, we did examine the post-stimulation behaviors of solo-housed animals (Fig. S5B). While PVNOT activation significantly increased the probability of exiting quiescence, it did not trigger a singular, stereotyped behavioral output. Instead, it facilitated a generalized transition to an active state, within which animals engaged in various context-appropriate actions (nesting, grooming, locomotion). We note in the discussion that “Analysis of manually- annotated behaviors suggested that PVNOT stimulation did not activate a specific motor pattern output but instead resulted in combined increases in the time spent in nesting (linear mixed model estimate coefficient of ChR2+ stimulation: +38.0 sec), locomotion (+54.0 sec), and grooming (+14.5 sec), but not in eating/drinking (-0.4 sec) (Fig. S4B).”

      That photostimulation had relatively larger effects on nesting and locomotion is consistent with our model.

      Last, in the Discussion we acknowledge that future experiments should seek to disentangle the effects of PVNOT light simulation in the non-social vs social context (last paragraph of the Discussion section called “State-dependent PVNOT activity during thermo-behavioral transitions”).

      A broader criticism is that the social dimension of this manuscript seems overplayed. Naturally, oxytocin signaling can be implicated in social behavior based on a large literature. However, the focus on social thermogenesis seems like a crude integration of social behavior and thermogenesis. Given that the authors see their effects in both social and nonsocial cases of thermoregulation, I am not sure the attempts at integrating social functions and thermogenic functions of PVNOT neurons are warranted. That is, unless the authors have further experiments or analysis that can convincingly justify this link.

      We thank the reviewer for this comment. We understand the concern and wish to reframe our position. We argue that the equivalence of PVNOT signals across social and non-social contexts is itself a central finding. While the oxytocin system is widely regarded as a mediator of social bonding, and therefore a candidate mechanism underlying huddling, our data demonstrate that PVNOT neurons provide a signal for state-dependent thermoregulatory transitions that is unbiased by social context. Rather than overplaying the social dimension, we believe our study contextualizes the social function within a broader homeostatic role: PVNOT neurons facilitate transitions from rest to thermogenesis and arousal regardless of whether the resting state involves social huddling or solitary quiescence.

      While the thermoregulatory transitions are present in both contexts, we note that social context appears to modestly enhance some PVNOT downstream effects. Specifically, peak probability and frequency were slightly higher in the paired compared to solo context (Fig. 3F-I, Fig. S2D), and peaks were associated with a somewhat stronger increase in physical activity when a cagemate was present (Fig. 3B-E). Additionally, quiescent huddling (paired) bouts were associated with stronger body temperature regulation compared to solo quiescence (Fig. S3Q-V). This nuance supports that the social dimension is not overplayed but rather situated within a broader homeostatic function.

      We have revised the manuscript to ensure that this framing is consistent and clear. We emphasize that our goal was to uncover neural mechanisms underlying physiological transitions across behavioral and arousal states, using our social thermoregulation assay as a starting point (based on our previous publication). Counter to our initial hypothesis, the PVNOT signals generalized beyond the social setting.

      In addition, the analysis of virgin females and lactating mothers seems out of place in Figure 4.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this. (Note this response is copy-pasted to the other reviewers).

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of nonoxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      The c-Fos/oxytocin overlap needs to be quantified.

      We thank the reviewer for catching this; Reviewer 2 made a similar comment. A typo in the figure legend led to this confusion. Figure 1I is in fact a quantification of the percent Oxytocin:Fos colocalized cells (not Fos:DAPI, as was written) in dorsal and ventral subregions of the PVN during active huddling and quiescent huddling. We have corrected the legend and clarified the quantification in the revised manuscript. (Note this response is copy-pasted to other relevant comments).

      The methods section could be improved by explaining how the authors exclude animals that exhibit both types of huddling, if they occur within a 90-minute time window. This seems like it could cause significant confounds.

      We have clarified in the Methods that animals were not excluded if they exhibited both active and quiescent huddling during the recording session. Importantly, a prerequisite for inclusion in the FOS study was that animals had to be continually engaged in the target behavior for a minimum of 15 consecutive minutes from behavior onset, an established approach for behavior-driven immediate early gene mapping. The 90-minute window was then counted from that same onset for FOS IHC. Because active huddling frequently transitions directly into quiescent huddling (and vice versa), excluding such animals would have eliminated the majority of recordings. The heterogeneity of behavioral states within the FOS integration windows is precisely why we turned to fiber photometry, a technique with the temporal resolution necessary to dissociate neural signals associated with each behavioral state.

      The computer vision model is not well-explained. The authors need to be far more explicit here about how it was validated.

      We thank the reviewer for this comment and agree that the original manuscript did not sufficiently detail the validation framework. We have revised both the Methods and Results to explicitly detail how SGBS was evaluated.

      First, we now clearly describe model validation on a held-out dataset (20% of manually annotated images not used for training), reporting standard segmentation metrics (per-class IoU and Dice/F1) and directly comparing SGBS to an unmodified Mask R-CNN trained under identical conditions (same backbone initialization, dataset split, and training schedule). As shown in Fig. 5D, the skeleton-guided model converged more rapidly and achieved a lower final loss than the baseline network, demonstrating improved segmentation performance in occlusion-rich thermographic recordings.

      Second, we more explicitly describe an independent physiological validation step. SGBS-derived surface temperature trajectories were temporally aligned with simultaneously recorded implanted thermologger measurements, which were not used during model training. As shown in Fig. 5E, SGBS-derived signals strongly corresponded with core body temperature dynamics and reproduced expected thermophysiological relationships (e.g., BAT warming preceding core temperature rise). This establishes external validity beyond pixel-level segmentation metrics.

      The authors should cite and consider this preprint: https://www.biorxiv.org/content/10.1101/2024.09.17.613378v1

      We have cited this preprint (Raam et al., 2024) in the revised manuscript and integrated relevant findings into the Discussion, in the section called “Limitations and caveats”.

      Reviewer #2 (Public review):

      Summary:

      This is a very interesting study from Vandendoren and colleagues examining the role of PVN oxytocin neurons during thermoregulatory behaviors, in particular during thermoregulatory huddling. The findings are important and compelling, and have implications for the thermoregulation field as well as the social/naturalistic behavior field.

      Strengths:

      The study is very creative and tackles a challenging task to examine how natural and social behavior influences neural circuits for a homeostatic system such as thermoregulation. The authors use a combination of state-of-the-art tools (photometry, optogenetics, automated behavior tracking, thermal imaging, and core body temperature measurement), often in combination with each other, to produce a rigorous and high-dimensional dataset. Carrying out tightly temperature-controlled experiments and examining natural behavior, neural activity, and body physiology simultaneously is quite a feat. I applaud the authors for taking this on in a rigorous and detailed manner. This paper will be valuable for both the thermoregulation field as well as for researchers interested in naturalistic social behaviors. The conclusions are supported by the data.

      We appreciate the reviewer’s careful read and positive assessment of our integrated behavioral, neural, and physiological measurements and their relevance to both thermoregulation and social behavior.

      Weaknesses:

      I have a number of questions and suggestions for clarification that would help improve the interpretation of the findings.

      (1) Figure 1D-F: It would be helpful to include representative images of cFos expression in the PVN, LS, and DMH during both quiescent and solo huddling conditions, to better illustrate the reported differences.

      We have now addressed this in the revised manuscript. We had originally shown active huddle FOS expression in Fig. 1D-F and quiescent huddle in Fig. S1A-C. We have now added solo groom FOS expression to Fig. S1D-F.

      (2) Figure 1C: The data suggest a general suppression of neural activity during sleep-associated quiescent huddling, which somewhat complicates the interpretation of what specifically the active huddling cells are responding to. A more informative control might have been a comparison between huddling and a more generic form of social engagement (e.g., dyadic sniffing) to assess whether huddling-responsive neurons are broadly tuned to social stimuli. While it may not be feasible to add this experimentally at this time, a brief discussion of this limitation in the main text would be valuable.

      We thank the reviewer for this thoughtful suggestion. We agree that comparing huddling-responsive neurons with a more generic social engagement is an important consideration.

      We first note that the FOS study required animals to be continuously engaged in the target behavior for a minimum of 15 consecutive minutes, ensuring that FOS expression reflects sustained behavioral engagement rather than brief social contact. Furthermore, we believe the FOS association with active huddling in Figure 1C is likely driven by preceding bouts of quiescent huddling. Because these experiments were conducted during the light phase, active huddling bouts were almost always preceded by bouts of quiescent huddling.

      Given that FOS protein often integrates neural activity over ~60-90 minutes, the FOS signal during active huddling may reflect cumulative PVNOT activity during the quiescent to active transition, rather than active huddling by itself. This interpretation aligns with our fiber photometry data, which show that PVNOT peaks are concentrated at the offset of quiescent states and the onset of active states. Moreover, a broad-scale analysis of calcium data driven by these reviews, now shows there is a local minimum of PVNOT neurons during the transition into quiescent states and a local maximum of calcium activity during the offset of resting states and the onset of nesting and active huddling (Fig. S3I-L).

      To directly address whether PVNOT neurons are broadly tuned to social engagement or specifically associated with thermoregulatory state transitions, we examined neural activity during "Contact Initiated" (ConI) and "Contact Received" (ConR) events—brief social interactions (e.g., dyadic sniffing) that occur outside the context of huddling. These interactions, which typically last less than one second, did not trigger the large-amplitude calcium peaks observed during rest-to-arousal transitions. Specifically, there was no significant association between ConI or ConR events and PVNOT peak frequency or amplitude (Fig. S2H; Table S1; p = 0.505, p = 0.575, respectively). This reinforces our conclusion that PVNOT peaks are not a generic response to social stimuli but are specifically aligned with the coordinated autonomic and behavioral transitions required to exit a low-temperature quiescent state. We have added a clarifying paragraph to the Discussion.

      (3) Figure 2H-J vs. Figure 1: The fiber photometry data suggest increased PVN activity during quiescent huddling vs active huddling, which appears to contrast with the cFos results from Figure 1. It would be helpful for the authors to comment on possible reasons for this discrepancy-e.g., methodological differences, temporal resolution, or cell-type specificity.

      We agree that this apparent contrast deserves explicit discussion. The difference arises from the dramatically different temporal resolutions of the two techniques. Fiber photometry captures real-time neural dynamics at subsecond resolution, revealing that PVNOT neurons exhibit high-amplitude bursts primarily during the offset of quiescence (and to a lesser extent the onset of post-quiescence behaviors) (Figs. 3 and 5). Because these peaks occur while the animal is categorized as "quiescent," they appear as quiescence-associated activity in the photometry ethogram.

      Conversely, FOS integrates neural activity over ~30–90 minutes. In retrospect, and in light of our photometry data, an animal categorized as "Active Huddling" in the FOS study is one that has likely experienced PVNOT bursts and subsequently transitioned to an active state. The higher FOS signal in active animals therefore likely represents the cumulative activity of the transition itself and sustained activity in the active state.

      We have added a clarifying statement to the Discussion section, in the section called “State-dependent PVNOT activity during thermo-behavioral transitions”.

      (4) Figure 2O: A comparable linear regression for active huddling would be informative to assess whether the observed relationships extend across behavioral states.

      We agree. We have added linear regression analyses for active huddling and nesting to Fig. S2K-N including rsquared values, to complement the resting analyses in Figure 2O and 2L.

      This analysis shows that active huddling peak counts are also positively correlated with active huddle duration (but not nesting duration). The text has been updated accordingly.

      (5) Temperature manipulation: The use of floor temperature changes presents a distinct physiological and sensory experience from, for example, manipulation of ambient temperature. A discussion of how this choice may affect neural circuit engagement or interpretation of thermoregulatory responses would be beneficial.

      Both Reviewer 1 and Reviewer 2 raise important and related points: manipulating floor temperature provides a thermal stimulus that is distinct from manipulating whole-chamber ambient air temperature, and these modalities could engage partially different sensory pathways and circuits. (Note this response is copy-pasted to other relevant comments).

      We intentionally used floor cooling/heating because it provides a reliable, well-controlled stimulus that elicits thermoregulatory behaviors while keeping the experimental environment stable (e.g., avoiding changes in airflow/humidity that can accompany ambient cooling). To prevent conflation of these modalities, we revised the manuscript to consistently describe the manipulation as “floor temperature” (and not “ambient temperature”), and we added Discussion acknowledging that conductive floor temperature changes may differentially recruit peripheral thermoreceptors compared to ambient air temperature.

      While extending these experiments to whole-chamber ambient temperature changes could be informative in future work, it is not required for the central interpretations here, which focus on PVNOT activity dynamics during thermoregulatory behavior under controlled thermal conditions.

      (6) Correlations with behavior: Across the manuscript, it would be informative to see correlations between huddle duration and neural activity (e.g., cFos expression, calcium signal magnitude). Similarly, do longer huddles produce greater thermogenic effects?

      This is a great suggestion. The first point about huddle duration and neural activity echoes the Reviewer’s comment (4) above. For this point, we now show that the duration of active huddling is positively correlated with PVNOT peak count (Fig. S2K), which is similar to what we had shown for quiescence and quiescent huddling (Fig. 2K-P).

      Next, the point about huddle duration and thermogenic effects is also helpful. We have now added new analysis and panels to address this (Fig. S3M-R). We find that the duration of quiescent huddle bouts is negatively correlated with Tb (Fig. S3V). The other behaviors examined did not show correlations between duration and Tb. This finding supports our previous demonstration that quiescent huddling is an energy saving state in mice (Landen et al., 2024).

      Finally, we note that longitudinal correlations between bout length and peak counts are already reported in Fig. S3A-H.

      (7) Lactating vs. virgin mothers: The inclusion of maternal data is intriguing but feels somewhat disconnected from the central huddling-thermoregulation narrative. If these experiments are to remain, additional explanation of their rationale and how they fit into the broader story would help clarify their relevance.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this.

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of non-oxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      (8) Optogenetic manipulation: Have the authors tested the effect of PVN OT neuron stimulation or inhibition during huddling? Even a negative result would be of interest to the field. If these data exist (main or supplementary), I apologize for missing them. If not, the authors might consider including them or commenting briefly on any attempts or challenges in carrying out these experiments.

      We thank the reviewer for this question. We have not performed optogenetic manipulation during huddling. Our decision to perform optogenetic activation in solo-housed animals was driven by our fiber photometry finding that PVNOT activity profiles during the rest-to-arousal transition are social-context independent (Figures 2 and 3). Had the GCaMP data suggested that PVNOT peaks were specific to social huddling, optogenetic manipulation during huddling would have been the natural next experiment. However, because peaks aligned with thermoregulation broadly, rather than social behavior specifically, we designed our functional experiments to test the circuit's role in driving the autonomic and behavioral arousal transition.

      We also note that our experience with chemogenetic manipulation suggests that pharmacological approaches to study the rest-arousal transitions during huddling are not currently feasible. As described to our response to Reviewer 1, our DREADD inhibition experiments were confounded by stress-induced hyperthermia following injection, and because drug delivery could not occur while animals were asleep and resting, the experimental conditions failed to recapitulate the low-Tb quiescent state during which PVNOT peaks naturally occur. We share this experience because we believe it will be informative for others in the field considering similar approaches.

      Additionally, as described above (Reviewer 1, #5), the SGBS thermographic model encounters artifacts in paired contexts due to thermal merging between huddling mice. We have added a note in the Discussion addressing this, in the section called “Limitations and caveats”.

      Reviewer #3 (Public review):

      Summary:

      The authors aimed to elucidate the relationship between physiological state (i.e., behavioral status and thermogenic sympathetic activity) and the activity of hypothalamic paraventricular oxytocin (PVNOT) neurons in female mice. They studied this by combining automated classification of mouse behavior via video-based analysis with calcium imaging of PVNOT neuron activity. Sympathetic thermogenesis was inferred from surface temperature changes captured by infrared thermography, and the authors provided their custom analysis scripts in the manuscript. Notably, they found that a strong, pulsatile activation of PVNOT neurons was "occasionally" observed immediately before the animals transitioned from a resting to an active state. This pulsatile activity was observed in both pair-housed and individually housed animals. While PVNOT neurons are often associated with social behaviors, this finding suggests that the oxytocinergic system is also engaged during naturalistic behaviors, even in the absence of social interactions. If experiments were more convincingly performed and presented, the results would point to a broader physiological role of central oxytocin, including in the regulation of fundamental brain states and homeostatic processes, and offer a new perspective on the functional significance of central oxytocin signaling.

      Strengths:

      The oxytocinergic neural system is believed to subserve a wide range of physiological functions, and elucidating these roles requires monitoring PVNOT neuronal activity under various behavioral contexts, as well as manipulating this activity to establish causal links. In the present study, the authors show a technically sound experimental framework that integrates behavioral tracking in both individually and group-housed mice with the observation and manipulation of PVNOT neuron activity. This experimental setup represents a valuable methodological resource for researchers investigating the physiological functions of oxytocin.

      We thank the reviewer for the thoughtful review and for recognizing the value of our integrated framework for monitoring and manipulating PVNOT neuronal activity across behavioral contexts.

      Weaknesses:

      While this study successfully established a new experimental setup for simultaneous analyses of behavior and PVNOT neuronal activity, there are several concerns regarding the interpretation of the results and the robustness of the conclusions, which should be more thoroughly addressed.

      (1) The study relies on the assumption that calcium imaging and optogenetic manipulation were restricted only to PVNOT neurons. However, the specificity of AAV-mediated gene expression was not verified quantitatively. A fair number of cell bodies in the PVN expressed GCaMP8s, but not OT, indicating potential off-target expression (see Figure S2A, B). The lack of quantitative validation weakens confidence in the causal interpretation of the results.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this.

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of nonoxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      (Note, we have updated Figure S2A,B to more accurately reflect the extent of co-localization in this image).

      (2) The study focuses on the transition from rest to active states following pulsatile activity of PVNOT neurons. However, the physiological significance of this pulsatile activity remains unclear. According to the authors, pulsatile activity occurred with an approximately 20% probability within 100 seconds prior to the end of the resting state. This implies that, in the remaining 80% of rest-to-active transitions, pulsatile PVNOT activity did not occur, suggesting that it is not essential for initiating the transition. A comparative analysis of behavioral and thermogenic changes between transitions with and without pulsatile PVNOT activity would help to further clarify the functional relevance of this phenomenon and strengthen the authors' interpretation of the findings.

      These are excellent points, and here we address them separately.

      (1) probability of transitions.

      We agree that our wording could be misread and we have revised the text for clarity. The “~20%” value is not the fraction of rest-to-active transitions that exhibit pulsatile PVNOT activity within a 100-s window. Instead, Fig. 3F,H report an instantaneous (per-second) probability of observing a calcium peak as a function of time-to-bout offset (logistic regression). In other words, the probability of a peak increases sharply as the animal approaches rest offset (e.g., from ~2–3%/s near onset to ~14%/s for quiescence and ~25%/s for quiescent huddling near offset), indicating a strong state-dependent increase in peak likelihood rather than an all-or-none trigger.

      We further clarify in the Discussion that we do not claim PVNOT peaks are essential for initiating every transition; rather, PVNOT activity biases or enhances the probability of transition toward thermogenesis and behavioral arousal (added to section called “State-dependent PVNOT activity during thermo-behavioral transitions”).

      (2) the effect of peaks on transitions

      This is a very helpful suggestion and we agree that directly comparing transitions with vs. without pre-offset pulsatile PVNOT activity could strengthen interpretation of the functional relevance of these events. We have therefore added a new transition-aligned analysis of thermogenic dynamics at rest-to-active transitions (new Fig. 3P&S; and corresponding text in the Results and Statistics sections).

      Briefly, we extracted peri-transition body temperature (Tb) traces (−300 to +300 s) aligned to the offset of quiescence and quiescent-huddling bouts and classified each transition as Peak+ if it contained one or more calcium peaks in the 100 s preceding bout offset, and Peak− otherwise. To account for inter-individual differences in “balance point,” Tb was z-scored within mouse. We then quantified the post-offset thermogenic rise for each transition as the change in scaled temperature from a pre-offset baseline (−60 to 0 s) to the post-offset interval (0 to 300 s) and tested Peak+ vs Peak− differences using linear mixed-effects models. This revealed that Peak+ transitions exhibited significantly larger post-offset increases in scaled Tb than Peak− transitions for both quiescence offsets and quiescent-huddling offsets.

      Together, these results indicate that while pulsatile PVNOT activity is not present prior to every rest-to-active transition, when it occurs it is associated with a stronger thermogenic rise, consistent with a probabilistic modulatory role in promoting the transition rather than being strictly required to initiate it.

      We are grateful for this suggestion as this new data is very informative in the context of our model.

      (3) The study identifies a correlation between pulsatile activity of PVNOT neurons and rest-to-active transitions, and tests for a causal relationship using optogenetic stimulation. However, since PVNOT neurons are known to co-release other neurotransmitters such as glutamate, it remains unclear whether the observed effects are mediated specifically through oxytocin receptor signaling. To address this question, functional intervention experiments using oxytocin receptor antagonists or receptor knockout mice are necessary.

      We agree with the reviewer that PVNOT neurons co-release glutamate and that isolating the specific contribution of oxytocin signaling versus co-transmitted signals is an important question. However, our study was designed to identify the functional role of the PVNOT cell type during thermoregulatory state transitions, not to dissect the molecular mechanism of signaling at downstream targets. By demonstrating that the endogenous activity of this specific population aligns with the rest-arousal window and that their activation is sufficient to drive the phenotype, we provide an anatomical and functional framework for future mechanistic investigations.

      We also note that we provide anatomical evidence supporting a possible peptidergic mechanism: PVNOT neuron projections to the rostral medullary raphe (rMR), a key thermogenic control site, alongside oxytocin receptor mRNA expression in this region (Fig. S5). This anatomical link suggests a plausible pathway for oxytocinergic modulation of thermogenesis, but of course does not rule in/out glutamatergic signaling. We acknowledge this limitation in the Discussion and frame pharmacological and receptor knockout studies as important next steps.

      We address these points in the Discussion, in the section called “Limitations and caveats.”

      (4) The authors attempted to detect BAT thermogenesis and skin vasomotion using infrared thermography. This technique measures only skin hair temperatures (since the skin was not shaved), but does not measure "BAT temperature" or "vasomotor tone". As seen in Figure 5E, the temperatures of the body surface areas ("BAT", "Rump", and "Dorsal surface") mostly changed in parallel, indicating that these temperatures are strongly affected by body core temperature. Therefore, the thermographic measurements in this study did not provide convincing information on BAT thermogenesis or skin vasomotion. To avoid misleading reports, the authors need to use other techniques to directly measure temperatures, such as telemetry.

      We agree that infrared thermography measures surface radiance rather than internal tissue temperature. We have revised the manuscript to use more precise language (e.g., "surface temperature over the interscapular BAT region" rather than "BAT temperature"). However, surface measurements are not merely passive reflections of core temperature. Here we add background and explanation about our thermography data:

      Background on our approach

      Infrared thermography provides a non-invasive readout of heat emission over the interscapular region and has been validated as reporting UCP1-dependent BAT thermogenesis in mice under adrenergic stimulation (Crane et al., 2014). That said, there are known confounds (insulation/adiposity, blood flow, protocol variability) and standardized protocols are needed (Law et al., 2018). Direct telemetry or implanted thermocouples offer superior precision for measuring BAT temperature, so long as the probe is sutured to BAT itself or to Sulzer’s vein–a technical challenge because probes tend to drift over time (e.g., (Dodson et al., 2024)).

      Our BAT findings in context:

      Using SGBS, we demonstrate that the interscapular BAT region is significantly warmer than the adjacent rump surface (Fig. 5C). If surface temperature were purely a reflection of uniform core temperature, this consistent regional hotspot would not be observed.

      Our cross-correlation analysis from the photometry (Fig. 5E) shows the rise in BAT surface temperature precedes changes in other body regions by approximately 90 seconds, suggesting that BAT acts as a primary heat source during rest-to-arousal transitions rather than passively following core temperature. This finding is consistent with another study, using telemetric probes placed in BAT, finding that episodic onset of BAT temperature started to increase 3 minutes before body temperature (Ootsuka et al., 2009).

      Based on this Reviewer’s comment here and the subsequent one (5), we have now added a new analysis of the temporal patterning of arousal and thermogenesis in the optogenetic cohort of animals; see below for details.

      Vasomotor tone

      We agree that infrared thermography does not directly measure vasomotor tone. We have revised the text to remove language implying that our measurements directly quantify vasomotor tone, vasodilation or vasoconstriction.

      We note that the established approach for non-invasive assessment of vasomotion uses glabrous skin of the tail and ears (Garami et al., 2011; Meyer et al., 2017; Škop et al., 2020). Rump surface temperature measured over hairy, non-glabrous skin correlates more closely with core body temperature than with cutaneous vasomotor tone (Meyer et al., 2017; Škop et al., 2020) and is used in the literature as a reference point for calculating BAT thermogenesis.

      In our data, rump surface temperature decreased following PVNOT calcium peaks while BAT and dorsal surface temperatures increased (Fig. 5L-M). This pattern is consistent with sympathetically-driven thermogenesis in which peripheral heat loss is reduced while BAT drives core temperature upwards. We now acknowledge that our rump measurements do not isolate vasomotor contributions. We have revised the manuscript accordingly, replacing references to rump vasoconstriction with language describing the observed thermal pattern while avoiding attribution to a specific thermoeffector mechanism.

      Finally, we note that telemetry would strengthen deep-body temperature interpretation, but telemetry does not itself quantify vasomotor tone; the same distal heat-loss readouts described above would be required regardless of core Tb methodology.

      In sum, infrared thermography enables non-invasive, simultaneous tracking of multiple thermal features in freely moving, undisturbed animals—a requirement for studying the naturalistic state transitions central to this study. We have added a section to the Discussion acknowledging the limitations of surface infrared thermography.

      (5) Photostimulation of PVNOT neurons increased Tb after 400 sec (6.6 min) (Figure 5). This latency is too long to conclude that the neuronal stimulation elicited BAT thermogenesis. A more reasonable explanation is that the increase in Tb was caused by the induction of physical activity (Figure S4C), which slowly generates heat and contributes to the elevation of Tb. However, this view contradicts the authors' claim. To address this concern, the authors should directly measure BAT thermogenesis and compare it with the rate of Tb elevation. If BAT thermogenesis occurs, the rate at which the BAT temperature increases must exceed the rate at which Tb rises.

      We thank the reviewer for this thoughtful critique. With this response we first provide additional context about the timeline of temperature increases, and second add a new analysis addressing the relative contributions of activity and BAT-surface to Tb changes.

      (1) Additional context on the temporal progression

      First, the observed timescale does not, per se, rule out a contribution of BAT thermogenesis. While the kinetics of BAT activation and associated Tb increases can operate on a fast timescale in anesthetized animals, in vivo activation of BAT thermogenesis pathways can take several minutes to yield a statistically detectable difference. For example, activation of DMH→rMR glutamatergic signaling, a canonical thermogenic command pathway, takes several minutes to produce a significant increase in both Tb and BAT using telemetric temperature probes (Kataoka et al., 2014).

      This timescale could also be consistent with peptidergic neuromodulation by PVNOT neurons, which are more likely to be modulators (and not drivers) of the canonical thermogenic pathway. Oxytocin is known to act via volume transmission and metabotropic receptor signaling, which operate on slower timescales than ionotropic neurotransmission (Ludwig and Leng, 2006). Downstream recruitment of sympathetic outflow and BAT thermogenesis is likewise a multistep autonomic process, not an immediate synaptic event.

      Next, the thermal dynamics reported in Figure 5 and Figure S4 are not consistent with activity-induced heat production alone. Specifically:

      - Thermal increases were spatially localized to interscapular/dorsal regions corresponding to BAT depots before generalized surface warming.

      - Importantly, photostimulation-induced warming was observed even during behavioral states characterized by low baseline activity, suggesting that thermogenic activation was not simply a byproduct of movement.

      While we did not directly measure BAT sympathetic nerve activity, our surface thermography approach was designed specifically to resolve regional temperature dynamics over the interscapular BAT area. The spatial specificity and temporal profile of the warming are consistent with BAT thermogenesis rather than uniform musclegenerated heat.

      We acknowledge that direct measurement of BAT sympathetic activity or oxygen consumption would provide additional mechanistic resolution. However, given (i) the known role of PVN oxytocin neurons in autonomic regulation, (ii) the spatially localized dorsal temperature increase, and (iii) the temporal dissociation between stimulation onset and gradual systemic Tb rise, we conclude that BAT thermogenesis remains the most parsimonious explanation.

      We have revised the Discussion to more explicitly acknowledge these temporal dynamics by clarifying that photostimulation likely follows the timescales of peptidergic neuromodulation.

      (2) New analysis

      We have added a new analysis to address the relationship between Tb and BAT-surface temperature and locomotion the optogenetic cohort. In short, we show that across all mice changes in BAT typically precede changes in Tb, and that the effect of optogenetic stimulation on core Tb can’t be explained by physical activity (nor can it be explained by BAT-surface temperature).

      First, cross-correlation of derivatives suggested BAT surface temperature changes typically precede changes in dTb/dt across mice, whereas physical activity changes did not consistently precede dTb/dt. This result, now shown in Fig. S5G, is consistent with our cross-correlation analysis of the fiber-photometry cohort.

      Next, we used a lagged regression analysis to test whether photostimulation-evoked increases in core temperature are fully mediated by physical activity. Specifically, we modeled the derivative of core Tb (dTb/dt) using an impulseresponse representation of photostimulation, while controlling for distributed lags (0–120 s) of physical activity and BAT surface temperature derivative, with random effects for mouse and trial. Photostimulation remained a significant predictor of dTb/dt while controlling for activity and BAT-surface (likelihood ratio test, χ<sup>2</sup>=7.66, p=0.0056), indicating that the relationship between stimulation and Tb is not fully explained by activity.

      Recommendations for the authors:

      Editors note:

      We suggest including key statistical support for the claims in the main text (e.g., results or figure legends).

      We have added statistical support for key claims in the main text results. We have also added references to Table S1 where appropriate (e.g., where there is a long list of statistical results); we hope this aids the readability of the report.

      Reviewer #1 (Recommendations for the authors):

      See above - the authors should decide what to prioritize, but I only mention significant concerns above. The manuscript could be improved to 'Convincing' or even 'Compelling' with sufficient effort.

      Thanks for the careful reading of the manuscript. We’ve addressed many of these points, and feel the manuscript has been strengthened as a result.

      There were also some text errors here and there.

      Several text errors were identified and fixed. Thank you.

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1I: The quantification shown here is a bit unclear from the figure and legend - are the authors reporting the percentage of cFos+ cells within the OXT+ population, or within the general DAPI+ population? If the latter, including a co-localization analysis to estimate the proportion of OXT+ cells activated would strengthen the interpretation.

      We thank the reviewer for catching this; Reviewer 1 made a similar comment. A typo in the figure legend led to this confusion. Figure 1I is in fact a quantification of the percent Oxytocin:Fos colocalized cells (not Fos:DAPI, as was written) in dorsal and ventral subregions of the PVN during active huddling and quiescent huddling. We have corrected the legend and clarified the quantification in the revised manuscript. (Note this response is copy-pasted to other relevant comments).

      (2) PVN cell types: It would be useful to briefly discuss the potential involvement of other PVN populations (e.g., CRF, AVP neurons) in huddling, given their known roles in social behavior, stress, and thermoregulation.

      Thank you for the insightful comment. We address these points in two parts.

      (1) PVN cell types and huddling

      Regarding the specific connection between these cell types and huddling: to our knowledge, no study has directly tested the effect of PVN CRF or PVN AVP neuron manipulation on huddling behavior. The most relevant data come from Bendesky et al. (Bendesky et al., 2017), who found that intracerebroventricular administration of AVP in Peromyscus inhibited nest building but had no effect on huddling, licking, or pup retrieval (though this pharmacological approach does not isolate PVN AVP neurons specifically). Their chemogenetic manipulation of PVN AVP neurons in Mus musculus confirmed the nest-building effect but did not assess huddling. For CRF, the available evidence suggests an opposing role to OT in social care contexts: chemogenetic activation of PVN CRF neurons impairs maternal behavior in postpartum mice (Melón et al., 2018), and intracerebroventricular CRF administration suppresses maternal care and can induce pup-killing in virgin rats (Pedersen et al., 1991).

      That said, PVN AVP neurons do promote wakefulness via lateral hypothalamic orexin neurons (Islam et al., 2022) and a recent preprint has implicated PVN AVP neurons in temperature-dependent maternal thermoregulatory behaviors, including co-nesting and shepherding, via projections to the central amygdala (Adahman et al., 2025). Notably, while that study focused on AVP neurons, their c-Fos data also revealed significant temperature-dependent modulation of PVNOT neurons (Fig. 3B), with suppressed activity at thermoneutrality relative to cooler conditions, a pattern suggesting that OT neurons are active under conditions where thermoregulatory effort is required. This data is consistent with our findings on PVNOT neuron involvement in rest-to-arousal transitions driven by thermoregulatory need.

      Additionally, Inada et al. (Inada et al., 2025) used an elegant series of viral-genetic experiments to demonstrate that PVN AVP neurons facilitate paternal caregiving behaviors via AVP to oxytocin receptor crosstalk in the preoptic area. Critically, their fiber photometry and circuit mapping data showed that chemogenetic activation of PVN AVP neurons did not recruit PVN OT neurons (Fig. 4), indicating that these populations operate independently in this context. We believe this finding is consistent with our interpretation that the thermoregulatory signals we observe reflect a cell-type specific property of PVNOT neurons. Future work examining how PVNOT, AVP, and CRF population interact during thermoregulatory state transitions would be valuable.

      (2) PVN cell types and stress and thermoregulation

      PVN CRF and AVP neurons have established roles in stress responses and social behavior, and future studies examining their involvement in huddling would be valuable. However, their direct roles in thermoregulation are limited. PVN CRF neurons are primarily stress-axis regulators whose thermoregulatory influence is mediated indirectly through downstream targets such as the DMH (reviewed in (Morrison and Nakamura, 2019)). AVP's thermoregulatory role is principally as an endogenous antipyretic acting via preoptic area neurons (Tabarean, 2021), rather than through PVN magnocellular AVP neurons.

      Importantly, the synchronized pulsatile bursting pattern that is characteristic of OT neurons during lactation (which serves as a key validation benchmark for our PVNOT calcium peaks), appears to be specific to OT neurons and does not generalize to other PVN populations. One study (Popescu et al., 2019) directly demonstrated that lactation-induced IPSC burst upregulation occurs selectively in OT magnocellular neurons, with no change in VP neurons within the same nucleus. VP neurons do exhibit phasic bursting, but these patterns are asynchronous, of longer duration, and serve antidiuretic rather than neuroendocrine-pulsatile functions (De Mota et al., 2004; Poulain et al., 1977; Wakerley et al., 1978). To our knowledge, no studies have reported synchronized burst activity in PVN CRF neurons during lactation or at rest. We have added a brief discussion of these points to the manuscript.

      (3) Figure 2B: Several behavioral abbreviations (e.g., LMA) are not intuitive and are missing from the legend. Spelling them out or including schematic illustrations would improve clarity.

      We have expanded the figure legends to define all behavioral abbreviations: LMA (Locomotor Activity), EaDr (Eating or Drinking), Groom (Grooming), Nest (Nesting or Nest Building), Quies (Quiescence), Sta (Stationary), ConI (Contact Initiated), ConR (Contact Received), AHud (Active Huddle), QHud (Quiescent Huddle).

      Reviewer #3 (Recommendations for the authors):

      (1) Figures 1D-F and S1A-C: The current magnification is insufficient to clearly resolve the distribution of FOS signals. FOS fluorescence is generally expected to be localized within cell nuclei. However, particularly in Figure 1F, the signals exhibit punctate or fibrous staining in addition to nuclear localization.

      This raises concerns about the quality of the tissue staining and the reliability of subsequent analyses. Including higher-magnification images would strengthen the credibility of the data presented.

      Thanks for the careful observation. We used a well-validated FOS protocol (see Methods; c-Fos (9F6) Rabbit mAb, Cell Signaling, 14609, 1:1000 dilution in block solution).

      To address this issue, in Figure 1 we have included better images of the regions of interest (DMH, LS, and PVN). We also show an inset with DAPI and the FOS IHC. These inset images show that the FOS signal does co-localize with nuclei.

      The reviewer notes that there is a fibrous staining in the PVN. We too noted this type of staining, due to clusters of bright dots in the PVN but not in other regions. This pattern was reproducible across several histological experiments. Fortunately, these bright dots were easily removed in our image processing routine using a selective median filter (pixel radius < 2.0 and and pixel intensity > 50).

      (2) Figures 2A, 4C, and 6A: As mentioned in the Public Review, the specificity of AAV-mediated gene expression is critical for the strength of the conclusions. Quantitative data demonstrating the expression specificity should be included.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this. (Note this response is copy-pasted to the other reviewers).

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of non-oxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      (3) Figure 2D: The authors should show an expanded view of a representative "PVNOT peak" from the spikes presented.

      We have added a representative peak to Fig. 2D.

      (4) Figure 2E-J: All the abbreviations of the behavioral states must be defined in the figure or legend.

      We added these abbreviations to the legend, and a text box reading “See legend for abbreviations” to the schematic.

      (5) Figure 2F, G, I, and J: The units on the y-axis should be indicated to facilitate interpretation.

      We have added these units. Thanks.

      (6) Figure 3A: Three large PVNOT peaks occurred between 01:30 and 02:00. However, these peaks did not cause an obvious transition in behavioral states or an increase in Tb within several minutes. Therefore, statements such as "PVNOT neurons predict transitions towards thermogenesis and behavioral arousal" in the text and subheading (pages 7 and 9) are questionable.

      We thank the reviewer for this careful observation. The three peaks between 01:30 and 02:00 that do not immediately lead to a behavioral transition illustrate a key aspect of our findings: the relationship between PVNOT activity and state transitions is probabilistic and state-dependent, not deterministic. Our logistic regression analysis (Fig. 3F, H, J, L) demonstrates that peaks increase the probability of a transition (up to ~20% per second) rather than acting as an obligatory "on switch." While individual variability exists in any single trace, the group-level analysis reveals a statistically significant increase in physical activity following PVNOT peaks (Fig. 3B–E).

      We therefore use ‘predict’ in a probabilistic sense: PVNOT peaks increase the conditional probability of impending state transitions in a manner that depends on behavioral context, rather than acting as an obligate trigger in every instance. We have taken care to not claim that PVNOT neurons are a necessary causal factor for transitions towards thermogenesis and arousal.

      We have updated the figure legend to clarify that Figure 3A shows an individual example trace, and revised the subheading on page 7 to more accurately reflect the probabilistic nature of this relationship: "PVNOT neurons predict increased likelihood of transitions towards thermogenesis and behavioral arousal in social and non-social contexts".

      We qualified the word “predicts” with “probabilistically” in the third paragraph of this section.

      Finally, this comment is related to the Reviewer’s comment-2 in the Public Reviews. To address that comment, we added a new analysis (now Fig. 3P&S) which shows that the presence of a peak in a bout of rest increases the thermogenic trajectory compared to bouts without a peak.

      (7) Figure 3F and H: If PVNOT peaks contribute to the initiation of transitions into the active state, the probability of peak occurrence should reach its maximum prior to the quiescence offset. However, the figures do not present the probability trajectory after the offset, which limits the ability to evaluate the authors' interpretation. Reanalysis extending to 150 seconds post-offset would be needed to clarify this issue.

      Thank you for this suggestion. We agree that examining PVNOT dynamics around the period following quiescence (and quiescent huddling) offset can further inform how PVNOT activity relates to rest-to-active transitions, and this has led to new insights within the manuscript.

      For background, in the original analysis (Fig. 3F,H), we used logistic regression to quantify how peak probability differs between bout onset versus near bout offset. We focused these analyses on the the timeframe of the bouts themselves (plus a small margin) because, in freely behaving animals, the pre-onset and post-offset period is heterogeneously composed of multiple potential subsequent behaviors (e.g., brief re-entry into quiescence, nesting, active huddling, locomotion, etc), which would confound a single post-offset probability trajectory (unless offsets are stratified by the identity of the subsequent behavioral state–beyond the scope of this paper).

      To address this concern, we now expand our peri-event baseline calcium analysis to include three minutes before and three minutes after both bout onset and bout offset for all four behaviors (new Fig. S3I–L). These extended traces show that for the two resting states (quiescence and quiescent huddling), baseline PVNOT calcium reaches a minimum near bout onset and a maximum near bout offset, whereas for the two active states (nesting and active huddling) baseline calcium shows the opposite pattern (maximum near onset, minimum near offset). Thus, the expanded post-offset analyses provide a more complete view of PVNOT calcium dynamics across the requested post-offset epoch and further support the conclusion that PVNOT activity is aligned with (and elevated around) behavioral transitions in a state-dependent manner. We have updated the Results text accordingly and now explicitly reference these new extended peri-event baseline analyses.

      (8) Figures 4H and I: Figure 4H shows that the waveform in the PPD2-7 group has a narrower FWHM than the Virgin group, which is the opposite of the group data in Figure 4I. Presenting scaled waveforms in parallel would allow for a clearer comparison across groups.

      Thank you for pointing out the inconsistency between the representative waveform in Fig. 4H and the group summary in Fig. 4I. You were correct: the PPD2–7 and Virgin waveforms in Fig. 4H had been mislabeled. We have corrected the labeling. (We verified that the underlying data are correct).

      As suggested, to enable visual comparison of waveform width across groups independent of amplitude differences, we derived peak-normalized average waveforms using a normalization procedure for every peak prior to averaging. Specifically, for each peak we (1) baseline-subtracted the trace by subtracting the mean fluorescence in a pre-peak baseline window, and then (2) divided the baseline-subtracted waveform by its own maximum value to scale the event amplitude to 1. We then computed the mean ± SEM of these peak-normalized waveforms across events within each group.

      We believe these changes resolve the discrepancy and improve the clarity of the figure, consistent with your suggestion.

      (9) Figure 5: In studies of thermoregulatory processes, tail blood flow or temperature is commonly used as an indicator of vasomotor responses. Is it feasible to track tail temperature using the SGBS system? If not, it may be helpful to acknowledge this as a technical limitation.

      We agree that tail temperature is a commonly used indicator of vasomotor responses. While SGBS could in principle be trained to segment the tail, the current model was optimized for dorsal body regions viewed from an overhead perspective. Reliable tail tracking presents substantial technical challenges in our configuration of homecage recordings. The tail’s thin geometry and rapid, multidirectional movement frequently result in partial or complete occlusion (e.g., beneath bedding or the animal’s body). In addition, during vasoconstriction the tail temperature approaches ambient floor temperature, reducing thermal contrast and making segmentation unreliable with the current thermal resolution limited by our camera. We have acknowledged this as a technical limitation in the Discussion, in the section called “Thermal tracking and validation of PVNOT recording specificity”.

      (10) Figure S5: Please describe the reason and histological background for the intravenous injection of FluoroGold.

      Intravenous injection of FluoroGold (FG) was used to histologically differentiate between magnocellular and parvicellular oxytocin neurons in the PVN. Because the posterior pituitary is located outside the blood-brain barrier,

      i.v. FG is selectively taken up by terminals of magnocellular neurons and retrogradely transported to their cell bodies. This allows us to infer the neuroanatomical identity (magno- vs. parvicellular) of the PVNOT neurons of interest. We have updated the Methods with a detailed description of the FG injection protocol as follows:

      “To distinguish between peripheral-projecting magnocellular and central-projecting parvicellular neurons, mice received 15 uL intravenous injection of 4% Fluoro-Gold (Fluorochrome) diluted in 100 uL of sterile saline. Prior to injection, mice were given an analgesic dose of carprofen (20 mg/kg, s.c.). Mice were briefly restrained using a modified 50 mL conical tube, in which holes were drilled to allow for proper air flow and respiration. Mouse tails were interposed between two heating pads to enhance visibility of the tail vein. Tails were wiped down with 70% ethanol and FG was administered via either right or left lateral tail vein using a 0.5 mL 28G syringe. Mice were sacrificed 24- 48 hours post-FG administration.”

      The following are minor points.

      (11) Figure 2E-G, Figure 3F,G, Figure S2G,I, Figure S3A: "quiesence" > "quiescence". This typo may appear elsewhere in the manuscript as well.

      Thanks. These edits have been made.

      (12) Page 7, line 14: Peaks were NOT significantly increased at 29{degree sign}C in Figure 2N.

      Thanks for the very careful read. By way of explanation: this difference had been significant in an earlier draft; however, when we added more replicates, the difference went away. We have corrected this sentence.

      (13) There are mislabeled figure numbers in the main text. The authors should carefully check this throughout the manuscript.

      We found mislabeled figure numbers and have corrected them.

      (14) Page 13, lines 1- 2: To make the description clearer, it might be better to rephrase the part that says, "some blue light stimulations occurred." As it stands, it could give the impression that the stimulations happened spontaneously. Using a phrase like "were delivered" would more clearly indicate that these were intentional, experimenter-controlled events.

      Agreed. Thanks. The edit has been made.

      Additional comments:

      The oxytocin system is thought to support a wide range of physiological and behavioral functions, and the circuits involving oxytocin neurons are likely to be regulated in complex and dynamic ways. As oxytocin research continues to expand, the growing body of evidence not only deepens our understanding but also highlights the system's complexity. In this context, the development of an approach that enables the observation of oxytocinergic neuron activity in parallel with naturalistic behavior represents a promising methodological contribution. It is likely that similar experimental frameworks will become increasingly common in future studies. While reading this manuscript, as a reader rather than a reviewer, I was wondering how OXT neurons detect or define the "rest balance-point," and how they might contribute to shifting the brain toward an "awake balance-point" (Figure 7). Given that eLife allows authors to include an "Ideas and Speculation" subsection within the Discussion, it would be appreciated - though not essential - if the authors could briefly share their perspective on this point. I believe such mechanistic insight would make the manuscript more intellectually stimulating.

      This is a great suggestion. We have added a new “Ideas and Speculation” section of the Discussion.

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    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In the submitted manuscript, Steinbach et al describe the formation of a detergent-resistant "cloud" around the Legionella-containing vacuole (LCV) that functions as a protective barrier. The authors show that formation of the "cloud" barrier is contingent upon the phosphoribosyl-ubiquitination activity of the SidE/SdeABC effector family, and is temporally regulated, with the assembly and subsequent disassembly of the "cloud" coinciding with replication and vacuolar expansion. The authors postulate a model of "cloud" barrier formation that relies upon a wave of initial ubiquitination by the SidC effector family, after which the SidE/SdeABC family expands the ubiquitination and forms cross-links that render the ubiquitin cloud resistant to harsh detergents. Additionally, Steinbach et al. also demonstrate that Rab5 is recruited to the LCV and remains associated for a considerable period.

      Strengths:

      This manuscript is very well written, with clear justification provided for experiments that make it very easy to follow along with the experimental logic. The figures have clearly been designed with much thought and are easy to interpret. Steinbach et al have also done a commendable job of addressing the previous reviewers' comments, even though some may suggest that some of these comments could be viewed as slightly unreasonable. This work would be of interest to both the Legionella and ubiquitin fields. Legionella researchers would potentially be interested to explore the proposed barrier model as the function for the ubiquitin "cloud," whereas ubiquitin researchers may be interested in exploring the mechanisms underlying SidE's crosslinking ability.

      Weaknesses:

      While the work is important and describes the physical nature of the ubiquitin cloud on the Legionella vacuole, it is somewhat descriptive in nature and does not dig deeply into what purpose this cloud serves. This is a complicated topic that will certainly stimulate additional research in this area.

      We thank Reviewer #1 for positive assessment of our work. We acknowledge that our study leaves many mechanistic questions open and, as suggested by Reviewer #1, we hope that our data is thought-provoking for researchers studying Legionella, ubiquitin signaling, or both. We are greatly looking forward to the results of future experimentation on the role of the “cloud” surrounding the bacterial vacuole.

      Reviewer #2 (Public review):

      Summary:

      The manuscript "Canonical and phosphoribosyl ubiquitination coordinate to stabilize a proteinaceous structure surrounding the Legionella-containing vacuole" by Steinbach et al. is well written and presents strong evidence that satisfactorily supports the main hypothesis and research objectives. The authors have clearly demonstrated the presence of cloud-like, detergent-resistant GTPase Rab5 surrounding the LCV, and formation of the structure is dependent on the SidE family of effectors. The study provides insights into the relevant (associated with described phenotype) ubiquitination pathways. The findings advance our understanding of Legionella pneumophila vacuole remodeling during intracellular infection and open directions for future research to establish broader implications of this structure on Legionella pathogenesis.

      Strengths:

      The manuscript convincingly demonstrates the presence of a cloud-like, detergent-resistant GTPase Rab5 surrounding the LCV through elegant microscopy. The experimental evidence about the dependence of the observed phenotype on the SidE family of effectors is compelling and presented with strong scientific rigor. The introduction is well-written, and the discussion is thorough and satisfactory. The article is thought-provoking and shows preliminary evidence for ubiquitin-mediated protection and spatial organization of the LCV.

      Weaknesses:

      The manuscript is well-organized and detailed, and it is hard to find weaknesses under the set goals of the research. A few weaknesses are that the molecular determinants or the regulatory mechanisms that drive selective versus non-selective incorporation of host proteins into this structure are unclear, and, as the authors mentioned, further work is required to establish the precise biophysical basis of the detergent resistance and expansive morphology of the ubiquitinated GTPase "cloud". Currently, the function or purpose of the structure is completely speculative. The effects or importance of the structure on bacterial replication is also not established in the current study. Figure 2D, right panel, Western blot results, the authors suggested the signal present in all four lanes between 37 and 25 kDa is 'nonspecific', which is probably a 'too intense' signal to be called so. Mass spec analysis would be interesting in order to identify sources of such intense signals. With these few limitations, the research presented in this manuscript is experimentally rigorous and opens avenues for future research.

      We thank Reviewer #2 for their positive assessment and constructive criticism of our study. We agree that the degree of selectivity of incorporation of proteins into the “cloud” is of great interest, as are the molecular details of the cloud structure, and we expect that future experimentation in this area will provide insight into these key questions.

      Reviewer #2 rightly points out that our study did not address the role of the LCV associated “cloud” in supporting bacterial replication. We note that previous studies have reported growth defects for knockout strains lacking SidC/SdcA (PMID 24483784) and the SidE family (PMID 27049943). However, given the multiple roles that these effector families appear to play during infection, we cannot ascribe these defects in bacterial growth solely to the absence of the LCV associated “cloud”.

      As for the band present in the four lanes in Fig 2D, we suggest that this band is non-specific (most likely detection of the light chain of the antibody used for immunoprecipitation) because we do not observe this band in the input lanes, and we also see this band in the IP samples in Fig 2C (uninfected samples), including the vector control in which no PR-ubiquitination is observed. In Fig 2C, the non-specific bands in the IP samples appear lower intensity because the HA signal is relatively intense in comparison to the infection experiment in 2D, as overexpression of SidE family effectors results in far more PR-ubiquitination than in infection.

      Reviewer #3 (Public review):

      Summary:

      This manuscript by Mukherjee and colleagues extended earlier studies on the coordination of the SidC and SidE effector families on the generation of a unique ubiquitin layer on the surface of the vacuoles containing the bacterial pathogen Legionella pneumophila (LCV).

      Strengths:

      The main strength of the manuscript is the identification of the small GTPase Rab5 as a major "carrier" of these differently modified ubiquitin and ubiquitin chains, which was nicely quantified.

      Weaknesses:

      (1) The results are mostly descriptive, based on mechanistic studies from earlier works.

      (2) The majority of the work was dedicated to the characterization of the unique ubiquitin layer on the LCV. One important question was ignored: what is the role of Rab5 in this process? Is the GTPase activity of Rab5 required for its ubiquitination by SidC and SidE? The authors should create a Rab5 KO cell line, complement the line with different mutants of Rab5, and examine their ubiquitination and association with the LCV.

      (3) The finding that Rab5 is associated with the LCV supports the notion that the LCV has characteristics of endo- or/late endosomes. The positioning of the LCV in the endocytic pathway should be discussed in the context of earlier studies (e.g.,PMID: 38739652; PMID: 11067875; PMID: 11067875).

      We thank Reviewer #3 for their constructive criticism of our work. While we appreciate this reviewer’s interest in Rab5, our data is not consistent with Rab5 being a primary “carrier” of ubiquitin species; many more LCVs are ubiquitin-positive than Rab5-positive during early infection, and in our live imaging experiments we observe many ubiquitin-positive, Rab5-negative LCVs. We used Rab5 as a model substrate in this study because it allowed us to compare modification at the LCV membrane between the WT and avirulent dotA strain. Our data is more consistent with a model in which Rab5 is one of many small GTPases, and likely other host proteins, caught in a crosslinked mesh around the LCV. However, we agree that discussing the interaction of the LCV with the endolysosomal system is relevant; while this is discussed at length in our previous publication (PMID 38117589), we have expanded the discussion in this study to include new publications and contextualize our latest findings.

      We agree with Reviewer #3 that assessing the role of nucleotide binding state in Rab5 ubiquitination is of interest. While creating a Rab5 KO cell line was not feasible given time and technical constraints, we conducted overexpression experiments with nucleotide binding mutants that exhibit dominant phenotypes (Q79L and S34N) and find that these mutants are still recruited to the LCV and ubiquitinated during infection (see new figure S1).

      Recommendations for the authors:

      Reviewing Editor Comments:

      There are suggestions from the reviewers to further address the role of Rab5 in LCV-associated ubiquitination, including whether its GTPase activity is required for modification by SidC and SidE, and the mechanism underlying the dissolution of the ubiquitin cloud during vacuolar expansion.

      Reviewer #1 (Recommendations for the authors):

      To improve upon the manuscript and its impact, the authors could consider the following:

      Major concern:

      The temporal regulation of the ubiquitin cloud is fascinating. The authors nicely demonstrate that SidE- and SidC-type ligases cooperate to form the cloud, but how is it dissolved during vacuolar expansion? They demonstrate that ectopic expression of DopA can do this, but do DopA and DopB regulate this process natively?

      We thank Reviewer #1 for their suggestions. While we agree that this line of experimentation is absolutely of interest, it is not feasible for our lab to carry out these experiments on a reasonable timeline to include in the current work.

      Minor concern:

      A syntax error on line 267 of the manuscript should be addressed.

      This has been corrected.

    1. Author response:

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

      Reviewer #1 (Public Review):

      Summary:

      This study presents valuable data on diurnal patterns in aphid (Rhopalosiphum padi) feeding behavior and transcriptome profiles. The authors measured honeydew production by the aphids on plants and artificial diet during the day and night and conducted a comprehensive feeding behavior study using EPG with many biological replicates at 6 time-points in 24 hours. They also conducted transcriptome analyses of three samples of each 30 aphids at these time points. Differentially expressed transcripts were grouped into four clusters with distinct expression patterns. The expression of two genes found to be diurnally rhythmic was knocked down with RNAi and these aphids did less well, especially at night. They also analyzed the differential expression of candidate effector genes and found rhythmic ones to be enriched for more expression in aphid heads versus bodies - this pattern is expected given that effectors are most likely expressed in the salivary glands. Knockdown of a known effector (C002) that is diurnally rhythmic, and a novel effector gene, was found to alter aphid feeding dynamics and performance.

      Thank you for your thoughtful review and summary of our study. We would like to clarify one aspect of your summary regarding our clustering analysis. We did not cluster differentially expressed transcripts. Instead, our clustering analysis was performed exclusively on transcripts that were significantly diurnally rhythmic, as identified in our time-course transcriptomic analysis. This approach allowed us to reveal patterns of gene expression that exhibit robust rhythmicity over the 24-hour cycle, rather than grouping transcripts based solely on differential expression at individual time points.

      Strengths:

      The manuscript was highly accessible, with clear writing, and the figures provided were both comprehensive and of good quality. The datasets generated from this research are valuable to the research field, especially the findings for honeydew secretion, EPG analysis, and transcriptome experiments.

      The datasets generated in this study will be useful to scientists working on aphids and aphidplant interactions and will inform similar studies on other insect species.

      Weaknesses:

      The weaknesses mainly relate to the (depth of) analyses and interpretation of the data. Also, some methods require more explanation, as follows:

      In Figure 1, data show that aphids produce more honeydew at night than during the day. This suggests that the aphids ingest more phloem (E2 phase). However, in Figure 1d the duration of the E2 phase does not show obvious differences among the time points in the 24 hours. The authors contribute the explanation that the aphids may osmoregulate more during the night, leading to more honeydew secretion at night. This may be the case, but there could be other explanations. For example, the physiology, including regulation of water transport, of plants is known to change during night/day. The authors may focus this section more on the differences in the E1 phase, as this involves the delivery of aphid saliva and effectors into the plant phloem.

      Thank you for your constructive feedback. As noted, aphids excreted more honeydew at night, although the duration of the E2 phase did not differ significantly across time points. We agree that host plant physiology, particularly the composition of the phloem and its osmotic quality, also influences the observed osmoregulatory patterns in R. padi. However, a similar diurnal pattern of honeydew excretion was also observed on artificial diets (Fig. 1b), in which host-derived cues have been eliminated. This strongly suggests that increased nighttime honeydew excretion is primarily driven by enhanced aphid osmoregulation rather than plant factors alone. Nonetheless, we acknowledge that plant-derived factors may also contribute and cannot be entirely ruled out. We have revised the text in the discussion of the revised manuscript to reflect this broader interpretation. As suggested, we have also added further details to highlight the important role of the E1 phase in aphid salivation.

      Transcriptome data shown in Figure 2 (and the experimental procedure of Figure 5b) appears to be based on three biological replicates. However, these replicates appear to have been harvested at the same time in the experiment, and this makes them technical replicates, not biological replicates. The inclusion of true biological replicates that include samples from time series experiments done on different days should be considered.

      Thank you for your concern regarding the biological replication in our transcriptome analysis. Our experimental design included multiple independent pools of aphids collected at each time point. Specifically, each replicate consisted of a unique group of aphids collected from different leaf positions across multiple host plants, such that no individuals were shared among replicates. As a result, these samples represent biologically independent populations rather than technical replicates, which are defined as repeated measurements of the same biological sample used to estimate technical noise. Although all samples were collected within the same experimental time course, this approach is commonly used in time-series transcriptomic studies to minimize confounding variation associated with differences in insect age, entrainment history, or environmental conditions, all of which can obscure rhythmic gene expression patterns. By maintaining tightly controlled and consistent conditions across the sampling period, we aimed to ensure that observed transcriptional differences primarily reflected diurnal regulation rather than uncontrolled day-to-day variability.

      We acknowledge that conducting time-series experiments on different days could provide additional insight into biological variability. However, our approach aimed to reduce potential confounding effects caused by day-to-day environmental fluctuations – such as minor changes in temperature or humidity - which could significantly influence gene expression in insects. By maintaining consistent conditions, we sought to ensure that observed transcriptional differences were due to diurnal rhythms rather than uncontrolled variation. Similar designs or strategies have been employed in studies examining diurnal and circadian gene expression in both insects and plants. We have revised the Methods section to clarify our replication strategy.

      The authors conducted knockdown experiments targeting aquaporin 1 and gut sucrase 1 in aphids, resulting in reduced nymph production and decreased honeydew secretion. It is concluded that these results indicate significant roles of aquaporin 1 and gut sucrase 1 in diurnal regulation. However, it is essential to consider that these genes likely play crucial roles in aphid physiology beyond diurnal rhythms. Consequently, reduced expression would naturally impair aphid performance. The dsAQP1 and dsSUC1 aphids consistently produced less honeydew, regardless of the time of day, indicating a broader impact of gene knockdown. The observed increase of the phenotype at night may not be attributable to the specific roles of these genes in diurnal regulation but rather due to heightened aphid activity during that time (as evidenced by increased honeydew secretion) that could magnify the impact of the knockdown effect, making it easier to observe. Therefore, the knockdown of aquaporin 1 and gut sucrase 1 may exert a general negative influence on aphid fitness, independently of diurnal factors.

      We agree that these genes likely play fundamental roles in aphid physiology beyond diurnal rhythms, and that reduced expression may affect overall aphid performance. However, it is important to highlight that if the observed effects are solely due to general fitness impairments, we would more likely expect a comparable reduction across time points rather than a disproportionately stronger impact at night. We agree that the increased honeydew excretion at night is likely due to heightened aphid excretory activity. However, since this excretory behavior is downstream of osmoregulatory functions, such as water cycling to the midgut and digestion, polymerization, and excretion of oligosaccharides, the increased nighttime phenotype is likely a result of an increased nighttime regulation of osmoregulation in aphids. This hypothesis is further supported by our functional analysis, where the knockdown of AQP1 and SUC1 resulted in a loss of diurnal variation in honeydew production (Fig. 2h), indicating that the observed effects are not merely a general impact on aphid fitness but are likely tied to the genes' roles in regulating diurnal physiological processes. We have revised the discussion to clarify that our findings do not exclude general physiological roles for these genes but instead suggest that their functions intersect with diurnal rhythms to influence aphid feeding and excretion patterns.

      To analyze the roles of genes in diurnal regulation, additional controls should be incorporated. This could involve the knockdown of genes with essential functions that are not influenced by diurnal rhythms, providing a baseline comparison. Furthermore, consider including genes known to be involved in diurnal regulation in other insects, as documented in the existing literature, in the experimental design.

      We agree that incorporating appropriate controls in the RNAi experiments would provide a useful baseline for comparisons, helping to distinguish between general physiological effects and specific diurnal effects. Unfortunately, given the current limited knowledge on rhythmic genes in aphids, particularly in the context of aphid-plant interactions, it is challenging to identify appropriate rhythmic and non-rhythmic controls that can be definitively linked to or unaffected by diurnal regulation within aphids. We will ensure to consider this valuable suggestion in our future experiments.

      The same arguments as for aquaporin 1 and gut sucrase 1 above may be made for knockdown of effector genes (Figure 4). It has already been shown that knockdown of C002 impacts aphid performance, and the data herein may be explained by a general lower performance of aphids rather than a specific function of these effectors in diurnal regulation. It is also expected that knockdown of the effectors has less impact on aphids feeding from artificial diets. This does not necessarily indicate the role of the effectors in diurnal regulation.

      Our response to this comment mirrors that expressed in our earlier response regarding AQP1 and SUC1.

      In the abstract and elsewhere, the authors assert priority by stating, "...the first evidence of...". However, it's important to note that priority claims are often challenging to verify across many fields. Instead of relying solely on claims of precedence, the evidence presented in the research could stand on its own merit.

      We understand that priority claims can be difficult to substantiate across various fields, and we appreciate the importance of allowing the evidence to speak for itself. Considering this, we have revised the language in the abstract.

      Conclusion:

      The study presents intriguing new findings, particularly in the realms of honeydew analysis, EPG, and transcriptome analysis. However, the interpretation of subsequent studies employing gene knockdowns needs further consideration.

      We thank the reviewer for the thoughtful and constructive feedback. We appreciate the positive assessment of our findings on honeydew analysis, EPG, and transcriptome profiling. We have carefully revised the section on gene knockdown experiments to provide clearer interpretation and additional context, and we hope the concerns raised have now been appropriately addressed.

      Reviewer #2 (Public Review):

      Summary:

      The authors conducted a time-course of whole-body transcriptional analysis of a pest aphid, Rhopalosiphum padi, and identified four major clusters of the genes that show diurnal rhythmicity in transcription. In addition, they conducted the analysis of aphid feeding behaviour and showed that aphids salivate longer from the end of the day toward the beginning of the night while their phloem feeding time does not change throughout the day. The genes upregulated at night time were enriched with the genes involved in metabolic activities, collaborating with the results showing a higher number of honeydew excretion at night. The authors identified the list of candidate salivary genes that show diurnal rhythmicity in the transcription and silenced a salivary gene C002 and the candidate salivary gene E8696. Silencing of these genes reduced aphid fecundity and survival rate on the host plant but not on the artificial diet.

      Thank you for your thoughtful review and valuable comments on our study.

      Strengths:

      The time-course transcription study and its analysis will be of interest to researchers studying diurnal rhythms in insect biology. Also, the analysis of aphid feeding behaviour at different times of day is interesting. This study provides variable resources for those who study insect biology.

      Weaknesses:

      It is not clear to me which data was used to define the putative salivary effectors for R. padi, but the candidate salivary gene list made by Thorpe et al consists of the aphid genes encoding secreted proteins that are up-regulated in the head samples compared to the body samples. Although some proteins were confirmed to be secreted into the aphid saliva, many genes in the list are not confirmed to be expressed in the aphid salivary glands, and their products are not confirmed to be secreted into the saliva and the plant. Is E8696 expressed in the aphid salivary glands and secreted into its host plant? Without the data confirming the expression of the gene in the salivary glands and its secretion into the saliva and into the host plant, we cannot call the protein a salivary protein. Furthermore, without the observation that E8696 has some effect on plant biology, we cannot call it an aphid effector. Therefore, I cannot agree with the parts of the manuscript that refer to E8686 as an aphid salivary effector.

      We have revised the text in the Methods to clarify the database used for defining putative salivary effectors. We have also added a sentence in the discussion to indicate that these are putative effectors. The putative effector E8696 was confirmed to be expressed in the salivary glands; however, its secretion into saliva and the host plant remains undetermined due to the lack of E8696-specific antibodies. Over the past year and a half, we have been creating an antibody for E8696. However, the antibody we generated is non-specific, and as a result, we are still unable to demonstrate that E8696 is secreted into host tissue and functions as an effector. While our functional analysis provided strong evidence of E8696’s impact on aphid fecundity and mortality on host plants but not on artificial diets, we agree that without further confirmation of its secretion and effect on the host plant, E8696 should be considered only a putative salivary effector. We expect to address these important questions in future research. To prevent any confusion, we have revised our manuscript to reflect that E8696 is only a putative effector.

      It is interesting to know that some candidate salivary gene expression showed a diurnal rhythm. However, without the knowledge of the functions of the salivary effectors, especially their targets, it is not possible to conclude that the rhythmical expression is important for the aphid performance. In addition, I wonder whether the increase in gene expression is directly correlated with the increase of protein secretion into the saliva and the plant.

      The primary goal of this study was to determine whether aphid genes, particularly those associated with osmoregulation and salivary effectors, exhibit diurnal patterns of expression and whether disrupting these rhythms affects aphid performance. While we agree that the precise molecular targets of these effectors in host plants remain to be identified, our functional assays provide evidence that rhythmic expression is biologically relevant for aphid physiology. Our results demonstrate that silencing rhythmic effector genes resulted in increased aphid mortality, reduced fecundity on host plants, and, more importantly, the disruption of diurnal honeydew excretion patterns, especially for C002. As honeydew excretion is a critical physiological process for aphids, the alteration of this behavior suggests that the rhythmic expression of these genes is functionally important for aphid physiology. We believe our results provide compelling evidence that rhythmic expression plays a critical role in aphid biology. We agree that rhythmic transcript abundance does not necessarily imply proportional changes in protein secretion into saliva, and direct measurements of effector protein dynamics will be an important direction for future work. However, the observed physiological and performance consequences of disrupting rhythmic gene expression support the conclusion that temporal regulation of these salivary genes is functionally important for aphid biology, even in the absence of detailed target identification.

      Finally, the authors examined aphid survival, fecundity, and feeding behaviour. Those are important for overall aphid performance, but they do not "shape" aphid colonization. Aphid colonisation is shaped by the mechanisms by which aphids find and select their host plant and start to feed on it. Therefore, I do not agree with the title of this manuscript and some parts of the discussion.

      We agree with your perspective and have revised the title and discussion to more precisely reflect the scope of our findings, focusing on aphid performance rather than colonization. The revised title now reads “Diurnal rhythmicity in metabolism and salivary effector expression shapes aphid performance on host plants”.

      I would like the authors to develop how the knowledge of the diurnal rhythm of aphid feeding can contribute to optimise pest management. I see that there are some differences in aphid metabolism and feeding behaviour between day and night, but I would like to hear how such knowledge can optimise pest management strategies.

      We have expanded the Discussion to address how knowledge of diurnal rhythms in aphid physiology and feeding behavior could inform the optimization of pest management strategies. Specifically, we discuss how time-of-day variation in aphid feeding activity and metabolism may influence the efficacy of control measures and how chronobiological insights could be integrated into future pest management frameworks.

      Recommendations for the authors:

      Reviewing Editor:

      Based on comments from two reviewers, here are the six key areas that need to be addressed to improve the manuscript.

      Clarity and Specificity:

      (1) Salivary effectors: The manuscript defines "salivary effector" loosely. The reviewer argues for stricter criteria - a protein can only be called a salivary effector if it's confirmed to be produced in the salivary glands and/or secreted into the plant with saliva and function in or around the plant.

      We have addressed this comment and clarified the definition in the revised manuscript.

      (2) Diurnal rhythm: The paper finds a daily rhythm in aphid gene expression, but doesn't explain how these genes affect the plant. The reviewer argues that without understanding the function of these genes, the significance of the rhythm is unclear.

      We have addressed this comment and clarified that the scope of our study is to elucidate diurnal rhythmicity in aphid gene expression and to evaluate the functional importance of rhythmic genes for aphid performance. We agree that understanding how these genes interact with host plants is essential for fully elucidating their molecular functions under diurnal regulation; however, this is beyond the scope of the current study and will be pursued in future research.

      (3) Knockdown experiments: The reviewer suggests the observed effects of knocking down certain genes (aquaporin, sucrase, effectors) might be due to their general importance, not necessarily their role in the day-night cycle. They recommend including control genes and genes known to be involved in circadian rhythms for a more robust comparison.

      We have addressed this comment and clarified the interpretation of these experiments in the revised manuscript.

      Technical Issues:

      (4) Honeydew production: The explanation for nighttime honeydew production needs more exploration. Plant changes at night might also play a role, and the daytime saliva delivery phase deserves more attention in the analysis (Figure 1).

      We expanded the description and interpretation of the salivation phase by incorporating additional detail in the revised manuscript.

      (5) Gene expression data: The current data (Figure 2 & Figure 5b) lacks proper biological replicates. Replicates collected at different times are essential for stronger conclusions.

      We have addressed this comment and clarified the experimental design and replication strategy in the manuscript.

      (6) Priority claims: The reviewer advises against focusing on claiming novelty ("first evidence"). The research should be impactful based on its own merit, not just being the first to find something.

      We revised the sentences to avoid making claims of priority throughout the manuscript.

      Reviewer #2 (Recommendations For The Authors):

      Figures 2 f,g, and h : according to the legend, these experiments seemed to have a low number of replicates (n=3-5). However, Figure 2h has many data points. I understood that here n means the number of experimental replications, but it may be better to show the number of aphid samples examined.

      You are correct that the n refers to the number of experimental replicates, with each replicate comprising multiple individual aphids. Because our analyses were performed on replicate-level averages across multiple days, rather than on individual aphids, we believe this notation most accurately reflects the experimental design. To improve clarity, we have revised figure legends to explicitly state that each replicate includes several individual aphids.

      Are the orthologous proteins of E8696 expressed in aphid salivary glands or detected in saliva? Such data will strengthen the claim that E8696 is a salivary protein of R.padi.

      E8696 is expressed in aphid salivary glands, but it is not confirmed to be secreted into saliva or host plants due to the lack of specific antibodies. We have revised our manuscript to reflect that E8696 is only a putative effector. We will address this question in future research.

    1. Author response:

      The following is the authors’ response to the previous reviews

      We thank the reviewers for their additional feedback. Below, we provide detailed responses to each reviewer’s major concerns. In addition, we identified an error in the previously submitted Fig. 6C and have corrected the X-axis labels accordingly.

      Public Reviews:

      Reviewer #1 (Public review):

      Motion-related signal in ACC: the new Fig. 2E looks good, but it is hard to visualize how it is just a reordering of the old Fig. 5C.

      We thank the reviewer for this feedback. Fig. 2E and the original Fig. 5C do bear resemblance. The primary difference is the temporal window and organization of the data. In the original Fig 5C, the time window was only ± 5 sec whereas Fig. 2E is ± 30 sec. The main objective we aim to highlight is that ACC shows both activation and inhibition in response to shuttle on an extremely prolonged order, up to 30 sec. Data is sorted to separate inhibition and activation to illustrate the sustained activity persists for both populations.

      All categories in the new Fig. 4D appear to respond to shuttle initiation, with less than 1s latency. For example, type 2a/2b consists of 40% of the population and their response to movement onset is apparent. Thus, it is not clear whether most neurons respond to shuttle crossing as described in the manuscript.

      We thank the reviewer for drawing attention to this discrepancy. It was not our intention to strike comparison between shuttle initiation versus shutting crossing responses across neurons, and we do not dispute that ACC responds to both events. While shuttle initiations and crossings provide a consistent temporal alignment point, they do not define the temporal focus of much of our analyses. Given that most shuttle responses terminate within ~2 sec, the extended windows analyzed (i.e. ± 5 sec; Fig. 4) largely reflect post-action ACC activity. Overall, although ACC neurons show mixed responses to initiations or crossings, the most consistent feature is prolonged modulation that persists beyond shuttle termination. We have revised the text to reflect this focus.

      Given this and the reviewer’s feedback, we further examined whether ACC activity is more strongly aligned with shuttle initiation, crossing, or termination. To determine which shuttle event (initiation, crossing, or termination) captured the most acute changes in ACC neuronal firing, we conducted an event-locked modulation analysis (Fig. S4). Our results showed that shuttle crossing was associated with the largest fraction of significantly modulated ACC neurons (Fig. S4). These findings suggest that shuttle crossing represents the most prominent event for ACC engagement during shuttle behaviors.

      Could the authors use relatively simple analysis, such as comparing spike rate before and after crossing, or before and after initiation, to quantify the response properties of each neuron? This could also help validate the classification analysis performed in Fig. 4.

      As mentioned above, we have added a new supplemental figure to directly address this question (Fig. S4).

      Reviewer #2 (Public review):

      I think the authors did a very admirable job revising the manuscript. It is much improved. However, I believe a formal analysis of action-state versus action-content neurons on A-->B versus B-->A crossing is still warranted. I appreciate the fact that this analysis may not be as reliable with smaller ensemble sizes, but with careful pseudo-ensemble and resampling approaches, such an analysis would go a long way towards increasing the strength of evidence.

      At present, we are not sure what the reviewer means as “formal analysis”. Below is our best effort in addressing this concern.

      Firstly, in our first revised manuscript, we implemented a generalized linear model-based classification of action-content and action-state neurons using direction specific regressors. Specifically, this analysis classified neurons as action-content or action-state based on coefficient contrasts (Δβ), with appropriate statistical testing and multiple comparison correction (see Methods; Fig. 7 C–E). Neurons were classified as action-content neurons if the corrected p-value for Δβ was significant and the absolute effect size exceeded a predefined threshold (|Δ β |> 0.5). Neurons were classified as action-state neurons if Δβ was not significant but both β1 and β2 were individually significant after correction. We believe our generalized linear model-based classification offers a sophisticated and formal classification of these two neurons classes.

      Subsequently, we performed an SVM decoder to distinguish A→B from B→A shuttles. Decoding accuracy depended on action-content neurons, as their removal drastically decreased decoding accuracy, whereas removal of non-action-content neurons had no effect, further strengthening the conclusion that these populations encode distinct information.

      In the updated revision, we performed an additional SVM decoding analysis while controlling for unequal neuronal population sizes between action-state and action-content neurons (Fig. S8). Specifically, we constructed pseudo-ensembles by randomly resampling neurons within each category and training SVM decoders on size-matched ensembles. Decoder performance was evaluated across repeated resamples to generate distributions of accuracy. We found that only decoders using action-content neuronal activity predicted shuttle content with high accuracy (>95%), whereas decoders trained using non-action-content neurons performed at chance levels (Fig. S8).

      Reviewer #3 (Public review):

      The only remaining comment that was not addressed pertains to anatomy and recording details. Some electrodes appear to be clearly in M2 (Fig 2A), and the tetrodes were driven each day. I would strongly suggest that this be included as a further limitation, particularly given the statement on line 178.

      We thank the reviewer for this feedback. In the previous revision, we added a supplemental figure showing tetrode locations for each mouse (Fig. S2) and described recording details in the Methods (Lines #481–488). We agree that this should also be noted as a limitation, and we have now added this to the Discussion (Lines #384–388).

    1. Author response:

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

      As the reviewers noted, the evidence we provide is the strongest on the mechanistic link between hepatic cardiolipin deficiency and electron leak from the electron transport chain. This narrative is supported by our assessment of site-specific electron leak as well as reconstitution of exogenous cardiolipin in the small unilamellar vesicles deficient with CL. On the other hand, as pointed out by the Reviewer 2, the mechanistic link between cardiolipin to MASLD/MASH is less robust. At this moment, we have not experimentally demonstrated that the MASLD/MASH induced by CLS deletion can be rescued by replacement of mitochondrial CL in vivo. Taken together, our current narrative makes an incomplete loop between CL deficiency, electron leak, and MASLD/MASH. Nevertheless, as indicated by all the reviewers, this manuscript highlights a previously undescribed role that CL potentially plays in MASH pathology, particularly with the data that human MASH coincides with reduction in liver mitochondrial CL. We focused this revision primarily on additional descriptive experiments in CLS-LKO mice that were requested by the reviewers. Even though it is not a component of the current manuscript, we have recently successfully developed mice with hepatocyte-specific CLS overexpressing mice and began performing experiments to test causality of CL deficiency to MASLD/MASH which we hope to complete in a few years. We are hopeful that the MASLD/MASH research community will still find evidence on CL contained in this manuscript plausible, and that it provides critical information to our understanding of mechanisms for MASH pathogenesis.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Brothwell and colleagues describes a central role for hepatic cardiolipin deficiency in MASH. The authors identify cardiolipin as a mediator of two long-standing problems in the field: how dysregulated lipid metabolism relates to altered mitochondrial metabolism during MASLD, and what the innate changes are in the steatotic liver that cause the increased respiration. The authors identified reduced liver cardiolipin in humans with MASH and in a variety of mouse models with MASH. When they knocked out hepatic cardiolipin synthesis, mice developed steatosis and inflammation. These mice also recapitulated the elevated hepatic oxidative metabolism and oxidative stress found in obese humans with MASLD. Some of the in vivo functional data related to glucose homeostasis and substrate metabolism could be stronger, and interpretation of the in vitro flux data needs some clarification, but in both cases, the data are not essential to the main conclusions of the manuscript. Overall, the study offers compelling evidence that cardiolipin is reduced in MASLD and that impaired cardiolipin synthesis is sufficient to recapitulate many features of MASLD.

      We thank the reviewer 1 for the positive feedback emphasizing novel and important findings in our manuscript.

      Strengths:

      The main strengths of the study are:

      (1) The identification of reduced cardiolipin levels in the liver of humans with MASLD and in a variety of mouse models of MASLD.

      (2) The finding that loss of cardiolipin synthesis recapitulates steatosis and inflammation in MASH.

      (3) The finding that loss of cardiolipin increases mitochondrial respiration, ROS production, and fat oxidation (in a separate hepatocyte cell line), again recapitulates several previous studies in obese humans with MASLD.

      (4) Evidence, though less definitive, that cardiolipin deficiency promotes electron leak by disrupting respiratory supercomplexes and preventing CoQ reduction.

      Weaknesses:

      (1) Figure 3A-D tries to make the point that liver CLS KO causes defects in substrate handling in vivo, based on glucose and pyruvate tolerance tests. The KO mice have a blunted response to a glucose tolerance test, but the pyruvate tolerance test showed very little (almost no) effect on glucose levels in either WT or LKO mice. The small blunting of the response in the LKO is impossible to interpret (if it's real), since the ability to clear glucose is also increased, and no tracers were used. It might be useful to monitor pyruvate and lactate levels during the experiment. However, this reviewer doesn't think the data is essential to prove the authors' main points.

      Thank you for pointing this out. We have now revised our manuscript to correctly reflect our findings on GTT and PTT. In our initial submission, we failed to clearly articulate that CLS deletion appeared to increase systemic glucose handling, which is the opposite of what one might expect in liver with steatosis. We agree that additional experiments would be helpful to better understand the systemic substrate handling in the CLS-LKO mice. As the reviewer indicates, we decided to focus this particular manuscript on intracellular and mitochondrial metabolism because of cardiolipin’s known localization to mitochondria, and the central role that this organelle plays in the pathogenesis of MASLD.

      (2) After presenting convincing evidence that respiration is elevated in isolated mitochondria from CLS KO liver, the authors follow up the findings by investigating whether 13C-palmitate and 13C-glucose oxidation are altered by CLS knockdown in murine Hepa1-6 cells (Figure 4).

      A few comments are worth mentioning about Figure 4:

      (a) It is not clear why the authors chose to use a hepatoma cell line rather than primary hepatocytes from LKO mice. The latter would be more convincing, since there could be important differences in metabolism between hepatoma cells and hepatocytes (e.g., preference for fatty acids vs glucose). Nevertheless, I think the approach is sufficient to test the general effect of loss of CLS on substrate metabolism.

      We appreciate the sentiment and agree that primary hepatocytes would have been a better model. We simply have not had prior expertise to culture primary hepatocytes and do not have the system working. We completely agree that it’s important to discuss the limitation of hepa1-6 cells as a hepatoma cells and now discuss this in our manuscript.

      (b) The authors use the M+2 enrichments of TCA cycle intermediates to infer rates of oxidation of [U-13C] palmitate or [U-13C] glucose. It is important to note that this kind of data reports fractional carbon sources (i.e., substrate preference) rather than rates of oxidation. For example, data from the 13C-palmitate experiment indicates that the CLS KD cells increase the fractional contribution from 13C palmitate (compared to glucose, for example) to the TCA cycle, but the actual rate of palmitate oxidation is not implicit in the data. However, it is reasonable to suggest that, in combination with the increased rates of O2 consumption observed in isolated mitochondria, this data supports increased fat oxidation.

      We agree with the reviewer that the nuances are important: that M+2 enrichments from [U-13C] palmitate or [U-13C] glucose reflects the fractional contributions of labeled substrates to the TCA cycle rather than oxidation. We have now revised the text to clarify that the data represent carbon incorporation patterns.

      (c) I have some concern that the [U-13C] glucose experiment is more complicated to interpret than the description implies. I'm not sure what happens in this cell line, but in the liver, most labeling from pyruvate (i.e., originating from glucose in this case) enters the TCA cycle via pyruvate carboxylase, with smaller amounts entering via PDH (depending on the nutritional state). Since one could expect pyruvate carboxylase to contribute M+3 labeled TCA cycle intermediates initially, and M+2 on the first turn of the cycle, it's hard to conclude what the data indicates about glucose oxidation. The authors could generalize the conclusion by framing the TCA cycle enrichment data as the contribution of glucose carbons and noting in Figure 4A that pyruvate carbons can enter the TCA cycle via PDH or pyruvate carboxylase, without attempting to assign their relative contributions. There are better ways to do it, but it's a small nuance here since the authors aren't making a critical point about the pathways.

      This expert comment is much appreciated. We have revised the text to more broadly describe glucose carbon entry into TCA cycle through PDH and PC. We also revised the schematic to reflect this notion.

      Reviewer #2 (Public review):

      In this study, the authors show that alterations in the lipid composition of the inner mitochondrial membrane, particularly changes in cardiolipin (CL) content, lead to defects in electron transport, supercomplex formation, and oxidative stress. Using liver-specific CLS knockout mice, which are characterized by dysfunctional capacity for cardiolipin synthesis, the authors highlight an underappreciated role for CL in MASH pathology. Overall, this is an interesting study highlighting the importance of functional/physiological electron transport (and in this context, electron leakage) in MASH pathophysiology. Despite that, this manuscript has several weaknesses that require attention.

      We thank the reviewer 2 for the constructive criticisms and identifying areas of weakness were additional data or explanations can improve the manuscript.

      (1) For all LKO studies, it is stated that the decrease in hepatic CL is causal for the observed phenotype. However, it is evident that many other lipids are impacted by CLS KO, including a marked increase in hepatic PG. In this respect, the authors show no evidence that the observed metabolic phenotype is indeed due to the reduction in CL and not to other accompanying changes.

      Thanks for this comment. We agree that because deletion of CLS promotes changes in mitochondrial lipids other than CL, we cannot conclusively attribute phenotypes we observed to CL and not to other lipids such as PG. In our experience, rescuing mitochondrial phospholipids by exogenous supplementation is problematic as they most certainly are not exclusively destined to the tissue of interest, nor to the organelle of interest, and often metabolized to produce other lipids, etc, making it difficult to interpret the data. We now have mice that conditionally overexpress CLS, which could be used to address this question, but the study is in its early phase and are outside the scope of the current study.

      The one experiment we performed is the ex vivo CL supplementation by SUV fusion to mitochondria, which has an ability to rescue electron leak. While they do not demonstrate the role of CL in all phenotypes found in the CLS-LKO mice, we think that bioenergetic phenotype associated with CLS deletion is therefore likely due to the reduction in CL. We now provide these additional discussions in lines.

      (2) In the results, the authors highlight that 'MASLD has been shown to alter the total cellular lipidome in liver.' Given that this study focused on CL, it would be useful to include specific studies that pointed to changes in hepatic CL content in MASLD/MASH/fibrosis.

      We now provide citations for these studies (PMID: 30042157, PMID: 34257827).

      (3) The initial human mitochondrial lipidomics studies show a reduction in mitochondrial CL and PG content. What was the content/expression of CL synthase and PGP synthase in these samples? If this cannot be assessed, is there any association of CLS or PGPS expression and MASLD/fibrosis (etc) in publicly available databases (e.g, GEP liver) that may explain the reduction in mitochondrial PG and CL content?

      Thanks for this suggestion. Quantification of mitochondrial lipidome require a good amount of tissue, and we do not have sufficient biomaterials left to quantify gene expression. Upon our survey of publicly available database (including GepLiver), we did not find that human MASLD was associated with an increase in CLS or other enzymes of CL biosynthesis compared to healthy controls.

      (4) The validation of MASH in patients (Figure 1B) is not convincing (ie., no quantification/scoring provided). NAS /fibrosis scoring (according to Kleiner) would help to define if all patients have indeed MASH, and what subset has fibrosis. Could the reduction in CL/PG content be (also) associated with fibrosis? In addition, Masson's Trichrome should be added to Figure 1B.

      The diagnosis was based on obvious bridging fibrosis and/or regenerative nodules on H&E staining (see additional zoomed-out images in Figure 1 – figure supplement 1). Due to the severity of these cases, formal NAS scoring was not applied. We do not have the Trichrome staining available but all MASH samples had fibrosis. Thus, it is possible that reduced CL/PG is related to fibrosis. We now added more descriptions on this point.

      (5) In human lipidomics, the authors suggest that reductions are observed in tetralinoleoyl CL (Figure 1C). However, Figure 1C only shows the combined FA acyl chain length + unsaturation, therefore not allowing for FA-specific ID (unless such data are available from the LC/MS analysis).

      Thanks for pointing this out. Per lipidomic nomenclature guideline we assign combined FA acyl chain length + unsaturation when MS2 is not performed. We have validated that our 72:8 peak corresponds to TLCL, but we do not perform MS2 on every lipid species for every sample. We now clarify this point in our manuscripts.

      (6) Figures 1 J/K/I. It is obvious that the background in all murine immunoblotting analysis has been altered. The authors should provide unaltered images for these immunoblots.

      We apologizes with the confusion. In Figure 1J/K/L/M, each panel actually represents two western blots (not one, similar to Figure 3H). The above represents a western blot with OXPHOS antibody cocktail (CV, CIII, CIV, CII, and CI), while the bottom represents the second western blot with citrate synthase (CS). Thus, we had not manipulated parts of the western blot to look different. To clarify, we now place an outline in each of the western blot to clearly demarcate individual blots to avoid confusion (new Figure 1J-M).

      (7) For Figure 1, it is unclear what is meant by 'we performed all mitochondrial lipidomic analyses by quantifying lipids per mg of mitochondrial proteins'. Was the murine lipidomics carried out on fractionated mitochondria or whole liver? If whole liver, then how were the data corrected, particularly given that PG is not a mitochondria-specific lipid?

      The data are all from lipidomic analyses performed in isolated mitochondria.

      (8) While total CL content seems indeed decreased across the different mouse models, this is mostly due to 1-2 CL species showing a pronounced reduction, with the remainder being unaltered. This should at least be acknowledged in the results. This is similarly the case in the LKO livers.

      Thanks for pointing this out. We now provide additional clarification in the text.

      (9) Figure 2. A secondary biochemical analysis of changes in lipid content should be provided, e.g., total triglyceride content, particularly given that the histology analysis does not show any major changes in hepatic lipid droplets/steatosis. In addition, the Masson's Trichrome staining shows almost no collagen deposition.

      We now provide a quantification of triglycerides in Figure 2J.

      (10) Figure 3. 'CLS deletion modestly reduced glucose handling' should be reworded. The LKO mice show improved glucose tolerance (despite the MASH phenotype), which is not evident from the above wording.

      We modified our text accordingly.

      (11) Looking at the mechanism behind the increase in hepatic steatosis, the authors state that lipid accumulation can occur due to increased lipogenesis, or dysfunctional VLDL secretion or beta oxidation, and subsequently assessed the relevant proteins/pathways. What about fatty acid uptake, which is also one of the four major pathways impacted in MASLD? This should be included in this assessment in Figure 3.

      Thank you for this comment. We now provide data for genes involved in fatty acid uptake, which was not reduced with CLS deletion (Figure 3E).

      (12) For Figure 5A, it is simply stated 'CLS deletion promotes liver fibrosis in standard chow-fed condition', and it is unclear what is highlighted within the selected EM images and what the arrows refer to. The authors should clarify this within the text.

      We have modified the text accordingly.

      Reviewer #3 (Public review):

      Summary:

      Mitochondrial oxphos causes lipid accumulation, leading to MASH, although the mechanism has been poorly understood. In this study, Funai and colleagues identify that reductions in cardiolipin in the mitochondria cause disruptions in the electron transport chain. Knockout of cardiolipin synthase was sufficient to drive MASH phenotypes, increase respiratory capacity, and cause electron leak at complexes II and III. It is well established that loss of cardiolipin increases ROS. Studies to date have been performed on whole tissue lysates, but to rule out which changes in mitochondrial lipids are driven by changes in mitochondrial number versus lipid synthesis/turnover, the authors uniquely purified mitochondria from human and mouse livers in MASH and NASH models for this study. This study provides critical information to the field that will inevitably help us better understand the mechanisms underlying MASH and NASH onset. The evidence provided is both convincing and compelling. With further suggested revision experiments, this study has the potential to change our understanding of MASH and NASH pathogenesis.

      We would like to thank the reviewer 3 for the highly-encouraging feedback.

      Strengths:

      The authors use a unique approach of lipidomics on purified mitochondria. They also analyze many distinct MASH models and provide a unique resource for the field of comprehensive lipidomics analysis of the different ways in which MASH can be induced. The use of human tissue elevates the impact/significance of the findings.

      Weaknesses:

      The data on the super complexes was the least compelling, and frankly, I do not think the authors needed those data to make a compelling argument! The authors should shift their focus more to the compelling electron leak data they have collected. If possible, it would also strengthen the work to include cardiolipin rescues on more of the experiments. Finally, expanding their explanations of the model systems would be very helpful for the readership.

      Thank you for this comment. We have now revised our argument to highlight the electron leak data and less emphasis on the supercomplexes.

      Reviewer #4 (Public review):

      Summary:

      Here, the authors wish to shed light on factors that contribute to the development of liver disease in what used to be called 'the metabolic syndrome'. This is a human-health problem of considerable significance, and the insights they provide, namely the implication of a defect in mitochondrial cardiolipin (CL) content to the progression from metabolic dysfunction associated steatotic liver disease to steatohepatitis, are plausible.

      We would like to thank the reviewer 4 in an encouraging feedback.

      Strengths:

      The experimental evidence proffered is derived from the observation of lower levels of (CL) in mitochondria from the liver of patients undergoing liver transplant or resection due to endstage steatohepatitis compared with mitochondria derived from livers of patients with other conditions. This correlation is buttressed by observations made in mice with liver-selective compromise in CL synthesis and which suggest a pathological environment associated with mitochondrial dysfunction and enhanced oxidative stress, features deemed to play a role in the progression from steatotic liver disease to steatohepatitis.

      The paper is well written, and the findings are well explained and superficially convincing.

      Weaknesses:

      It is unclear how much can be learned from compromising a key enzyme that produces a key mitochondrial lipid in a busy metabolic organ like the liver - isn't the discovery of a mitochondrial defect in such a context rather trivial? And how reliably can these findings be related to the human observations? Most importantly, the chain of causality implied by the title is unproven: the key question of whether or not (somehow) preventing the drop in cardiolipin content affects the course of steatohepatitis remains unanswered.

      We agree with the reviewer that the current manuscript does not directly provide evidence that reduction in CL causes MASLD in humans, which as the reviewer describes, must be tested by rescuing CL content in the context of MASLD. We have now obtained mice with conditional overexpressor and have begun the experiments, but findings from these mice are beyond the scope of the current study. We have modified our title to “Cardiolipin deficiency disrupts electron transport chain AND drives steatohepatitis” to reduce the implication for causality.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The manuscript states that loss of mitochondrial respiration is expected in MASLD. Forexample, line 187 "MASLD is known to be associated with reduced mitochondrial oxidative capacity". A more accurate statement is that "MASH" is known to be associated with reduced mitochondrial oxidative capacity and increased ROS production in humans. As you correctly cite later for an ex vivo human mitochondrial respiration study, early MALSD, especially with obesity, is associated with elevated mitochondrial respiration (40). Since those measurements are maximal respiration rates, which might not reflect actual in vivo flux, you might also make readers aware that your data is consistent with in vivo human studies that found increased hepatic oxidative flux (TCA cycle flux) in obese subjects with moderate steatosis (PMID: 22152305), which appears to wane with severe steatosis and/or inflammation (PMID: 31012869, PMID: 40272888).

      Thank you for these suggestions. We have made the suggested changes to the text.

      Reviewer #3 (Recommendations for the authors):

      (1) Throughout the manuscript, the authors refer to the inner mitochondrial membrane, although they never perform assays to distinguish the inner vs outer mitochondrial membrane. It would be better to just refer to the cardiolipin being measured as "mitochondrial."

      Thank you. We made these changes.

      (2) In figures showing changes in cardiolipins, not all of them change; only a handful of them are reduced in NASH. Could the authors add commentary in the manuscript about what is known about these different cardiolipin species, and speculate as to why certain CLs are changing while others are not?

      Thank you. Reviewer #2 had similar comments and we provided additional discussions.

      (3) In the human tissues, what do the other mitochondrial inner membrane lipids (PC, PE, PI, PS, LPC, LPE) look like in the healthy vs NASH patients (Figure 1A-D)?

      Thank you for this request. We did not include these data in the manuscript as we have a separate ongoing study (the second author is the lead author on this paper) where we are following up on hepatic mitochondrial PS and PE, which we found to be decreased in human MASH samples compared to healthy livers. This turned out to be a convoluted story so we decided not to include it in the paper.

      (4) The descriptions of the different MASLD/MASH models are a little sparse. Especially needing more detail is the model for carbon tetrachloride injection, causing NASH. The authors should explain how each of these models typically induces MASLD/MASH.

      We now provide these details.

      (5) In figures 2E and F, total body mass is unchanged in CLS-LKO mice, but liver mass is decreased; yet on the chow diet, there appears to be lipid accumulation in the liver as well; I am wondering what the authors' reasoning is for this decreased liver mass.

      It is difficult to say conclusively, but we suspect it is due to cell death evidenced by fibrosis. It’s important to note that while there is lipid accumulation in the liver, steatosis is relatively mild and the increase in liver triglyceride is quite marginal (Figure 2J).

      (6) The lipidomics analysis and comparison of livers in these different models is a wonderful dataset that needs far more depth in terms of unpacking and describing the findings. For example, all the models of MASH show similar changes in most of the lipid species analyzed. NASH appears to be quite different than MASH. This, among other trends, is certainly worth highlighting as it will be of interest to the field.

      Thanks for this comment. We agree that while CL phenotype were common to mouse and human MASH samples, there were other changes that we observed in other lipids that may be biologically significant. As described above, we have an ongoing study pursuing mitochondrial PS in the liver.

      (7) Figure 2B - It is interesting that the CLS KO only impacts certain CLs. The 72:8 CL, which is regulated by CLS, is also a CL that appears to change in the human patient samples. The information on the specific CL that is changing seems critical to the mechanism of the role of the CL in the disease. Throughout the manuscript, it is important to specify which specific CL is being referred to, instead of broadly characterizing the changes to cardiolipins, especially since most of the cardiolipins shown do not change; only a handful of them do.

      Thank you for this suggestion. We have included additional discussions on 72:8 CL in the manuscript.

      (8) One potential non-specific mechanism whereby CLS knockout can cause MASH would be if the mice change their overall food consumption. It is an important control to test if the total food intake is different in WT vs KO mice to formally rule out this possibility.

      The food intake was not different between the group (Figure 2E).

      (9) To determine the extent to which de novo cardiolipin synthesis underlies the change in MASH/fatty liver observed in the HFD, GAN, and CCl4 models in Figure 1, the authors should also put the CLS KO mice on these diets and perform liver histology, analysis of inflammation markers, and analyze immune cell infiltration. Alternatively, the authors could try to rescue the CLS KO model by supplementing cardiolipin in the diet or by injection.

      Thank you. We have an ongoing experiment to examine the effect of hepatocyte-specific CLS overexpression on protection from GAN-induced MASLD.

      (10) Figure 3F shows a decrease in UQCRC2 by RNA but no change at the protein level in Figure 3H. The authors should comment a bit more on this disparity, and the data in Figure 3F don't mean much for the main point of the study if the levels of the proteins are unchanged.

      The reviewer is correct. We initially performed RNAseq in trying to broadly capture how CLS knockout influences liver health, which implicated that transcriptional program for mitochondrial proteins were downregulated. Nevertheless, gold standard measurements of mitochondrial content (mitochondrial protein or mtDNA) did not show change in the abundance with CLS deletion.

      (11) The increase in respiration and spare respiratory capacity upon CLS KO shown in Figure 3J is extremely interesting! The explanation of the experiment and its meaning should be significantly expanded upon.

      Thank you. We included additional discussion on this point.

      (12) Figure 4 - It is interesting that the fraction of the TCA cycle metabolites labeled is increasing with the palmitate tracer and decreasing with the glucose tracer. This implies a "fuel switch," such that more of the TCA cycle carbons originate from fatty acids than glucose upon loss of CLS. The authors should make note of this point. Also, to understand if the total molar quantity of labeling in the TCA cycle from palmitate and glucose is changing, the authors should also report the relative abundance (instead of just the fraction labeled) of the labeled metabolites and unlabeled metabolites.

      Thanks for this suggestion, we have now added this discussion.

      (13) In Figure 5C-F, the authors show that CLS deletion can activate the caspase pathway, but do not see any change in cytochrome c localization. Can the authors clarify if CLS deletion is sufficient to induce apoptosis?

      CLS deletion certainly causes cell death that induces tissue fibrosis. Activation of the caspase pathway suggests that the cell death may be due to apoptosis but we did not see changes in cytochrome c localization. Our lab is currently performing additional experience to test the possibility that CLS deletion may induce ferroptosis.

      (14) Figure 6A-C- The authors discuss the I + III2 + IV supercomplex substantially and consistently decreasing in the CLS-KO mice, however, the quantifications do not look statistically significant. Can the authors confirm if these changes are or are not significant and adjust the text accordingly?

      The reviewer is correct. Abundances of I+III2+IV supercomplexes are decreased in CLS-LKO mice compared to control mice when quantifying with supercomplex antibody cocktail or with UQCRSF1 (complex III subunit) antibody, but not with complex I antibodies. The discrepancy for these results are not entirely clear but it’s likely a combination of antibody sensitivity and a tricky nature to dissolve high molecular weight protein complexes.

      (15) The most compelling data to indicate electron leakage increasing upon CLS knockout is in Figures 7A-E. I would suggest the authors decrease their emphasis on the rearrangement of the supercomplexes and focus their discussion on the very compelling results of Figure 7.

      Thanks for this suggestion. We have modified our text.

      (16) Figure 7D shows that a major site of electron leak is from site II, and these results also fit with the profound succinate-induced respiration observed in earlier experiments. It would be nice if the authors could test the ability of cardiolipin to rescue these phenotypes, similar to the assay in Figure 5I. Assessing this rescue on the CoQ redox state would also strengthen the claims.

      Thank you for this comment. We are encouraged with your suggestions. We have thought about this quite extensively during the preparation of the manuscript but we refrained from making conclusive statements regarding complex II because the magnitude of the increase in electron leak is equally elevated at complex II and III. It’s true that CLS deletion increases succinate-induced respiration, but this might also be because succinate elicits the highest increase in respiration even in wildtype mice (see values in Figure 3K and L compared to other substrates). It would be intriguing to examine the influence of CLS deletion on complex II/III electron leak as well as succinate-induced respiration in tissues where succinate is not a preferred substrate. We have attempted cardiolipin rescue in SUV but unfortunately, we could not get this assay to work for site-specific electron leak measurements.

      (17) In Figure 7G-H, it would be nice to see a ratio of oxidized to reduced CoQ, in the CLS deletion mice and in human NASH livers, if samples are available.

      Thanks for this suggestion. Data shown (Figure 7- figure supplement 1P-S).

      (18) CoQH2 can also deliver electrons to complex II (via its reversal). Complex II shows a remarkable contribution to the electron leak phenotype (Figure 7D). Also, as the complex II monomer showed much larger changes in the native gels of Figure 6 than the complexes involving complex III. A more likely model is that oxidized CoQ accumulates in the CLS knockout model because of increased CoQH2 leak via complex II.

      Perhaps. We also thought about this but we are not sure if this fits with the observation that CLS deletion increases succinate-induced respiration, which suggests increased succinate to fumarate conversion, a notion that I am not sure can be congruent with increase CoQH2 reversal to complex II. Overall, I think we lack the tools or evidence to conclusively implicate whether CLS deletion primarily acts on complex II or III. Nevertheless, we appreciate the reviewer’s enthusiasm on these topics as we perform additional experiments on the mechanism of interactions between CL and the ETC.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      Cruz-Gonz´alez and colleagues draw on DNA methylation and paired genetic data from 621 participants (n=308 controls; n=313 participants with Alzheimer’s Disease). The authors generate a panel of epigenetic biomarkers of aging with a primary focus on the Horvath multi-tissue clock. The authors find weaker correlations between predicted epigenetic age and chronological age in subgroups with higher African ancestry than within a subgroup identified as White. The authors then examine genetic variation as a potential source for between-group differences in epigenetic clock performance. The authors draw on a large collection of publicly available methylation quantitative trait loci datasets and find evidence for substantial overlap between clock CpGs located within the Horvath clock and methQTLs. Going further, the authors show that methQTLs that overlap with Horvath clock CpGs show greater allelic variation in African ancestral groups pointing to a potential explanation for poorer clock performance within this group.

      Thank you for this summary.

      Strengths:

      This is an interesting dataset and an important research question. The authors cite issues of portability regarding polygenic risk scores as a motivation to examine between-group differences in the performance of a panel of epigenetic clocks. The authors benefit from a diverse cohort of individuals with paired genetic data and focus on a clinical phenotype, Alzheimer’s disease, of clear relevance for studies evaluating age-related biomarkers.

      Thank you.

      Weaknesses:

      While the authors tackle an important question using a diverse cohort the current manuscript is lacking some detail that may diminish the potential impact of this paper. For example:

      (1) Information on chronological ages across groups should be reported to ensure there are no systematic differences in ages or age ranges between groups (see point below).

      Thank you for pointing out this omission. The distributions are now presented in Supplementary Figure 1. While there is some variation in median age, the age ranges are similar across cohorts (median 73.1 to 79.3). The small differences do not explain the differences in accuracy between the cohorts, e.g., the median age of the African Americans (76.4) is lower than the median age for the White cohort (77.7).

      (2) The authors compare correlations between chronological age and epigenetic age in sub-groups within to correlations reported by Horvath (2013). Attempting to draw comparisons between these two datasets is problematic. The current study has a much smaller N (particularly for sub-group analyses) and has a more restricted age range (60-90yrs versus 0-100 yrs). Thus, is an alternative explanation simply that any weaker correlations observed in this study are driven by sample size and a restricted age range? Reporting the chronological ages (and ranges) across subgroups in the current study would help in this regard. Similarly, given the lack of association between AD status and epigenetic age (and very small effect in the white group), it may be of interest to examine the correlation between chronological age and epigenetic age in each group including the AD participants: would the between-group differences in correlations between chronological age and epigenetic be altered by increasing the sample size?

      Our conclusions about the reduced accuracy of the clock in admixed individuals are based on the comparison within the MAGENTA cohorts, not a comparison of MAGENTA to previously published studies. We find significantly reduced accuracy in the admixed cohorts compared to the White MAGENTA cohort. Further supporting this conclusion beyond he MAGENTA cohort, we analyzed three independent whole blood methylation datasets. Two focused on African American individuals—the Grady Trauma Project (n = 422) and the GENOA study (n = 1,394)—and one focused on White Swedish individuals (n = 729). As observed in MAGENTA, the Horvath clock had significantly lower accuracy for the African American cohorts (Figure 3 than for the White Swedish cohort.

      When comparing results across studies, the reviewer is correct that lower correlations are generally seen for older cohorts. Indeed, other studies applying the Horvath clock have seen similar correlations in older cohorts to those observed in MAGENTA (Marioni et al., 2015, Horvath 2013, and Shireby et al., 2020). We now also include the chronological age distributions of the cohorts in this study, along with their mean and standard deviations (Supplementary Figure 1). This shows that the distribution of chronological ages for White individuals is similar to the cohorts where the clocks did not perform as well. Finally, as suggested, we correlated chronological and epigenetic age with the inclusion of AD cases in each cohort for the Horvath clock. The significantly lower performance of the clock on Puerto Ricans and African Americans, relative to White individuals, remains even after including all individuals in each cohort. Thus, combining cases and controls did not qualitatively change the performance relationships for the African Americans and Puerto Ricans relative to the Whites (Supplementary Figure 3).

      (3) The correlation between chronological age and epigenetic age, while helpful is not the most informative estimate of accuracy. Median absolute error (and an analysis of MAE across subgroups) would be a helpful addition.

      We used correlation because it is commonly used to evaluate the performance of epigenetic age clocks, but we agree that other error quantification metrics provide a complementary perspective. We now include MAE and MSE comparisons across sub-groups in the revision (Supplementary Table 1). We find that across all accuracy metrics, the African American and Puerto Rican cohorts perform worse than the White and Peruvian cohorts. Interestingly, the Cubans show relatively high error despite a high correlation between predicted and chronological age. However, there are only 21 non-demented Cuban controls. In addition, we evaluated the same metrics in three replicate datasets (two African American cohorts and one for White Swedish individuals) and found the same patterns of lower accuracy across metrics in African ancestry individuals, albeit with some variation in accuracy between cohorts (Supplementary Table 2). Notably, as discussed above, this is not driven by differences in chronological age distributions: when we subset to older individuals (≥ 55 years old) in order to facilitate comparisons to MAGENTA study individuals, the median age for the White Swedish individuals (70 years old) is higher than that of the GENOA (62.7 years old) and Grady (58 years old) individuals. Despite the difference in median ages, the clock performs better on White Swedish individuals across all accuracy metrics than the African ancestry cohorts with younger individuals.

      (4) More information should be provided about how DNAm data were generated. Were samples from each ancestral group randomized across plates/slides to ensure ancestry and batch are not associated? How were batch effects considered? Given the relatively small sample sizes, it would be important to consider the impact of technical variation on measures of epigenetic age used in the current study. The use of principal Component-based versions of these clocks (Higgins Chen et al., 2023; Nature Aging https://doi.org/10.1038/s43587-022-00248-2) may help address concerns such concerns.

      Thank you for pointing out the need for additional context on data generation. We have added details to the Methods. All omics data from the MAGENTA study were generated using standard protocols that ensure minimal technical artifacts and batch effects. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch. We also performed a principal components analysis of the normalized methylation data used as inputs for all MAGENTA analyses. We found that the samples did not stratify by sample plate, cohort, ethnicity, or ascertainment center along the principal components (Supplementary Figure 2).

      We also thank the reviewer for their suggestion to apply the principal component clock to account for potential technical variation. As outlined in the new section “Principal component versions of the methylation clocks also have lower age prediction accuracy for genetically admixed individuals,” using the principal component version of the Horvath clock did not result in consistent improvement in age prediction accuracy or generalization across MAGENTA cohorts (Supplementary Figures 4 and 5). The lower accuracy for age prediction in individuals with substantial African ancestry was present for the PC clock in the replication cohorts, just as in the MAGENTA cohorts (Supplementary Figure 6).

      (5) Marioni et al., (2015) found a very weak cross-sectional association between DNAm Age and cognitive function (r∼0.07) in a cohort of >900 participants. Given these effect sizes, I would not interpret the absence of an effect in the current study to reflect issues of portability of epigenetic biomarkers.

      We agree that previous links between DNAm Age and AD or cognitive function have been relatively small in magnitude. For example, the PhenoAge paper (Levine et al., 2018) and a study using the Horvath clock (Levine et al., 2015) found age acceleration of less than a year in AD patients relative to non-demented individuals. Similar results have also been observed in studies with smaller sample sizes (e.g., 700 for Levine et al. 2015 and 604 for Levine et al. 2018). Given these small effect sizes, we agree that accounting for statistical power is essential for interpretation of our results. We performed power calculations based on an effect of the size observed in previous studies (0.5 year acceleration). We have 86% power in the full MAGENTA data set to detect an effect of this size. Stratifying by cohorts, we have 75% power for the African Americans, 72% for the Puerto Ricans, 72% for the Whites, 65% for the Peruvians, and 47% for the Cubans. Thus, we believe we have high enough power that the consistent lack of association outside of the White cohort in MAGENTA is likely meaningful. Based on these calculations, there is only a 1% chance that we would not observe an effect in any of the other cohorts if the effect was present across cohorts. Nonetheless, we have added caveats about power and the small sample size to our suggestion that the reduced accuracy of the clocks contributes to the lack of AD association outside of Whites.

      (6) The methQTL analyses presented are suggestive of potential genetic influence on DNAm at some Horvath CpGs. Do authors see differences in DNAm across ancestral groups at these potentially affected CpGs? This seems to be a missing piece together (e.g., estimating the likely impact of methQTL on clock CpG DNAm).

      We agree. Thank you for this suggestion. We have added Figure 6 in the main text to address this gap. In short, we analyzed additional whole blood methylation data from inidividuals with African ancestry and found that a substantial proportion of the CpGs in methylation clocks are differentially methylated in African ancestry individuals relative to European ancestry individuals. In the case of the Horvath clock, we find that 84/353 (23.8%) of the clock CpGs are differentially methylated between ancestries. In parallel, we found that 56 of these differentially methylated clock CpGs are also affected by meQTL, many of which are at different frequencies between populations. We also investigated whether the meQTL-affected clock CpGs are associated with increased clock error in the MAGENTA individuals. We found 56 clock CpGs whose methylation levels associated with increased clock error, and 42 of these have at least one meQTL. Thus, while meQTL are not the only factor to affect the portability of methylation clocks across global populations, we suggest that they are a significant contributor, especially in the case of the Horvath clock.

      Reviewer #2 (Public review):

      Summary:

      This paper seeks to characterize the portability of methylation clocks across groups. Methylation clocks are trained to predict biological aging from DNA methylation but have largely been developed in datasets of individuals with primarily European ancestries. Given that genetic variation can influence DNA methylation, the authors hypothesize that methylation clocks might have reduced accuracy in non-European ancestries.

      Strengths:

      The authors evaluate five methylation clocks in 621 individuals from the MAGENTA study. This includes approximately 280 individuals sampled in Puerto Rico, Cuba, and Peru, as well as approximately 200 self-identified African American individuals sampled in the US. To understand how methylation clock accuracy varies with proportion of non-European ancestry, the authors inferred local ancestry for the Puerto Rican, Cuban, Peruvian, and African American cohorts. Overall, this paper presents solid evidence that methylation clocks have reduced accuracy in individuals with non-European ancestries, relative to individuals with primarily European ancestries. This should be of great interest to those researchers who seek to use methylation clocks as predictors of age-related, late-onset diseases and other health outcomes.

      Thank you for this summary.

      Weaknesses:

      One clear strength of this paper is the ability to do more sophisticated analyses using the local ancestry calls for the MAGENTA study. It would be valuable to capitalize on this strength and assess portability across the genetic ancestry spectrum, as was recently advocated by Ding et al. in Nature (2023). For example, the authors could regress non-European local ancestry fraction on measures of prediction accuracy. This could paint a clearer picture of the relationship between genetic ancestry and clock accuracy, compared to looking at overall correlations within each cohort.

      Thank you for this suggestion. To model portability across genetic ancestry as a spectrum, we regressed the Horvath clock error on the proportions of African ancestry in the genomes of the MAGENTA individuals, adjusting for chronological age. The proportion of African ancestry is significantly associated with increased Horvath clock error (p = 0.039), with the clock making less accurate age predictions by 1.46 years for individuals with full African ancestry compared to no African ancestry. We have added this new analysis to the Results.

      The authors present two possible reasons that methylation clocks might have reduced accuracy in individuals with non-European ancestries: genetic variants disrupting methylation sites (i.e., ”disruptive variants”) and genetic variants influencing methylation sites (i.e., meQTLs). The authors conclude disruptive variants do not contribute to poor methylation clock portability, but the evidence in support of this conclusion is incomplete. The site frequency spectrum of disruptive variants in Figure 4 is estimated from all gnomAD individuals, and gnomAD is comprised of primarily European individuals. Thus, the observation that disruptive variants are generally rare in gnomAD does not rule them out as a source of poor clock portability in admixed individuals with non-European ancestries.

      In the revision, we now additionally report ancestry-specific allele frequencies to demonstrate the rarity of CpGclock disrupting variants (Supplementary Figure 9). The global allele frequencies were so low that even if they all occurred in individuals of non-European ancestries, they would still be extremely rare.

      It is also unclear to what extent meQTLs impact methylation clock portability. The authors find that the frequency of meQTLs is higher in African ancestry populations, but this could reflect the fact that some of the analyzed meQTLs were ascertained in African Americans. The number of meQTL-affected methylation sites also varies widely between clocks, ranging from 6 to 271; thus, meQTLs likely impact the portability of different clocks in different ways. Overall, the paper would benefit from a more quantitative assessment of the extent to which meQTLs influence clock portability.

      We agree that the meQTL likely influence the clocks in different ways and that the ascertainment of the meQTLs in different populations makes direct comparisons challenging. To more directly link meQTL to clock performance, we identified 56 Horvath clock CpG sites whose methylation levels significantly associate with increased clock error in the MAGENTA study individuals. Of these, 42 (75%) are affected by an meQTL, including nine that are affected by an African ancestry-differentiated meQTL. As such, meQTL, and specifically meQTL that were likely not present in the training data of the Horvath clock, associated with both the methylation of CpG sites and clock error. However, as the reviewer suggests, determining causality among these factors is challenging. Given our incomplete knowledge of meQTL in different ancestries, we have added caveats to our conclusions about the effect of meQTL on clock portability.

      The paper implies that methylation clocks have an inferior ability to predict AD risk in admixed populations relative to white individuals, but the difference between white AD patients and controls is not significant when correcting for multiple testing. This nuance should be made more explicit.

      We agree that the signal is not strong in the white cohort; however, it is similar in magnitude to previous studies. As outlined in response to Reviewer 1’s Point 5, we have now added power calculations that indicate reasonable power (≥72%) to detect small effect sizes (0.5 year increase) in the white, Puerto Rican and African American cohorts. We now interpret the AD association tests in the context of these power calculations and multiple testing correction.

      Finally, this paper overlooks the possibility that environmental exposures co-vary with genetic ancestry and play a role in decreasing the accuracy of methylation clocks in genetically admixed individuals. Quantifying the impact of environmental factors is almost certainly outside of the scope of this paper. However, it is worth acknowledging the role of environmental factors to provide the field with a more comprehensive overview of factors influencing methylation clock portability. It is also essential to avoid the assumption that correlations with genetic ancestry necessarily arise from genetic causes.

      We entirely agree and have now clarified the scope of our analyses and importance of environmental factors in the revision. We intersected clock CpGs with enviromental-factor-associated CpGs from multiple epigenome-wide association studies (EWAS) and found overlaps that suggest an environemtnal contribution to differences in clock CpG methylation. However, given the lack of environmental data on the MAGENTA study individuals, as well as the lack of datasets for replication, we cannnot directly compare the environmental and genetic contributions to clock accuracy. Nevertheless, the new analyses in the revision highlight the contribution of both genetic and environmental factors to lack of portability for certain methylation clocks.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 64: An association between methylation patterns and genetic ancestry does not presuppose that meQTLs vary in frequency between genetic ancestries; environmental factors could also play a role. It would be nice to comment on this further in the Introduction.

      We agree that environmental factors likely play a role in the decrease in methylation clock performance in admixed populations. We have added text highlighting this in the revised Discussion. Regarding meQTL, we agree that associations between methylation patterns and genetic ancestry do not necessarily imply that meQTL will vary in frequency between genetic ancestries. However, our new analyses in the revision find African-ancestry differentiated meQTL that associate with Horvath clock CpG methylation levels and overall clock error (Figure 6E-F and Supplementary Figure 13).

      (2) Line 116 implies Puerto Ricans have “substantial amounts of African ancestry” but the median ancestry is 15% (which is not much more than the Peruvian and Cuban cohorts).

      Thank you for pointing this out. We have clarified this statement in the text. While the median proportion of African ancestry in Puerto Ricans is 15% (vs. 6% and 2% for the Peruvian and Cuban individuals in MAGENTA), there are many individuals with substantially higher African ancestry. The upper quartile is >25% and several Puerto Ricans have >50% African ancestry.

      (3) In Figure 2B, Puerto Ricans have worse accuracy than Peruvians but a higher proportion of inferred CEU ancestry, which is interesting and defies intuition - is there any hypothesis for why this might be the case?

      In light of our new meQTL analyses, we hypothesize that the African ancestry differentiated meQTL that affect Horvath clock CpGs drive the increase in clock error for these individuals, despite having more European ancestry across their genome. Given that the Peruvians (and Cubans, for that matter) hold very little African ancestry, and also very few of the African-differentiated meQTL, this could explain some of the large difference in clock errors for the cohorts.

      (4) Figure 2C would be improved with confidence intervals.

      We thank the reviewer for this suggestion and have added confidence intervals for Figure 2C.

      (5) It’s interesting that the correlation with Cubans is positive in Figure 3B (for one clock, significantly so). Is there any rationale for this?

      We noticed this as well, but have not been able to come to a definitive conclusion. It is possible that environmental factors contribute. However, the Cuban cohort is the smallest in MAGENTA (22 cases and 21 controls) and the none of the differences are statistically significant, so more investigation in a large cohort is required.

      (6) Line 231: Which population(s) is allele frequency estimated in?

      This is the global frequency reported in gnomAD, which is calculated across all populations in gnomAD v3.0. As noted above, we now also report allele frequencies by gnomAD population (Supplementary Figure 9).

      (7) Were the meQTLs pruned? How many independent variants are there per methylation site? It would be nice to see a distribution for the sites in the Horvath clock.

      We now report the distribution of meQTL across clock CpG sites. The mean number of variants is 108; the median is 36; and the maximum is 1,699. We have now included a plot of the distribution for all 271 (out of 353) Horvath clock CpG sites (Supplementary Figure 14). We did not perform any pruning in these initial results for several reasons. First, we sought to demonstrate the great potential for meQTL to influence these CpGs and to compare the distributions of these common meQTL across populations (based on gnomAD data). Second, identifying the causal variant or variants is challenging. Given that many of these meQTLs likely reflect redundant signals, for the new analyses of African-differentiated meQTL, we restrict to a single variant per clock CpG site. We focus on the variant with the greatest absolute beta, as reported by the original meQTL study from which the variant originates.

      (8) Figure 5C might benefit from a geom density rather than overlapping bar plots; the trends are hard to see.

      We appreciate the reviwer’s suggestion and have now reworked the figure and based it on just the density curves so that readers may better appreciate the differences in allele frequencies.

      (9) Several figures would be more legible with larger font sizes.

      We appreciate this recommendations and have made the font sizes for all plots larger and more legible.

      Reviewer #3 (Public review):

      This manuscript examines the accuracy of DNA methylation-based epigenetic clocks across multiple cohorts of varying genetic ancestry. The authors find that clocks were generally less accurate at predicting age in cohorts with large proportions of non-European (especially African) ancestry, compared to cohorts with high European ancestry proportions. They suggest that some of this effect might be explained by meQTLs that occur near CpG sites included in clocks, because these variants may be at higher frequencies (or at least different frequencies) in cohorts with high proportions of non-European ancestry relative to the training set. They also provide discussions of potential paths forward to alleviate bias and improve portability for future clock algorithms.

      The topic is timely due to the increasing popularity of DNA methylation-based clocks and the acknowledgment that many algorithms (e.g., polygenic risk scores) lack portability when applied to cohorts that substantially differ in ancestry or other characteristics from the training set. This has been discussed to some degree for DNA methylationbased clocks, but could of course use more discussion and empirical attention which the authors nicely provide using an impressive and diverse collection of data.

      Thank you for this summary.

      The manuscript is clear and well-written, however, some key background was missing (e.g., what we know already about the ancestry composition of clock training sets) and most importantly several analyses would benefit from being taken one step further. For example, the main argument of the paper is that ancestry impacts clock predictions, but this is determined by subsetting the data by recruitment cohort rather than analyzing ancestry as a continuous variable. Extending some of the analyses could really help the authors nail down their hypothesized sources of lack of portability, which is critical for making recommendations to the community and understanding the best paths forward.

      Thank you for this suggestion. As noted in our response to Reviewer 2’s Point 1, we have analyzed ancestry as a continuous variable and found that the proportion of African ancestry in the genomes of the MAGENTA individuals significantly associates with increased difference in chronological and predicted age, even after controlling for chronological age (1.46 years more error for 100% vs. 0% African ancestry; p = 0.039). As outlined below, we have also added details on the training of previous clocks and the important additional previous work highlighted by the Reviewer.

      Reviewer #3 (Recommendations for the authors):

      Major comments

      There is previous literature addressing who is in the training set for methylation clocks. To my knowledge, this work has been primarily led by Nancy Krieger. It would be a valuable addition to discuss her work (and any similar work by other investigations) in the introduction. In other words, what do we currently know about the degree of bias in the training sets for methylation-based clocks? The assumption of the introduction is that the training sets are overwhelmingly European ancestry (which I assume is true) but I think some quantitative information about this would be helpful for understanding the source and magnitude of the problem.

      We thank the reviewer for bringing the work of Dr. Nancy Krieger to our attention. It directly supports the rationale for this study: the sociodemographic characteristics of the individuals used to train these clocks are poorly reported, limited to outdated population descriptors (for example, the use of “Caucasians” to describe some of the individuals used to train the Horvath and the Hannum clocks) or race and ethnicity labels. Moreover, where labels are available for training individuals, they tend to underrepresent the individuals of diverse backgrounds, as in the Horvath clock. We have incorporated Dr. Krieger’s work into the Introduction, including details of how this supports the rationale and purpose of our study.

      Related to the above comment, there has been pretty extensive previous work on the effects of race and ethnicity on epigenetic clock estimates (e.g., https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1030-0), and that seems like it could be more explicitly weaved into the introduction and discussion.

      We thank the reviewer for highlighting this relevant article. We have added discussion of it into the Introduction. Several factors make direct comparison with our results challenging. First, the grouping of individuals based on race and ethnicity without consideration of genetic ancestry complicates comparisons. Race and ethnicity commonly do not match genetic ancestry components (see Gouveia et al., 2025 https://www.cell.com/ajhg/fulltext/S00029297(25)00173-9). Second, the study reports differences in epigenetic age accelerations (intrinsic and extrinsic) in individuals from various race and ethnic groups. It does not directly evaluate the accuracy of the epigenetic age predictions in these groups. Thus, it is challenging to interpret whether the differences in acceleration are driven by biological factors or biases in the performance of the clocks themselves.

      The main analysis that felt like it was missing was asking whether the age deviations are larger for individuals with greater proportions of African ancestry. The authors have the ability to analyze ancestry as a continuous variable, but instead performed analyses in various a priori subsets of the data; the subsets do have average differences in ancestry, but also there is heterogeneity within groups. Given that the authors calculated admixture proportions already, it seems like a missed opportunity not to use these estimates. This would also sidestep the issue of the problematic labels applied to the subsets, which mix ancestry, nationality, and race terms (note that I thought the legacy reasons why these labels are used were well-explained, but they are nevertheless problematic for biological explanations that center on ancestry/genetic information as the driver of bias).

      We appreciate the reviewer’s suggestion to investigate clock accuracy in the context of African ancestry proportions. As noted in the response to Reviewer 2’s Point 1, we modeled the clock error as a function of the fraction of African ancestry of each individual, adjusting for an individual’s chronological age. The proportion of African ancestry is significantly associated with increased Horvath clock error (p = 0.039), with the clock estimated to give less accurate age predictions by 1.46 years for individuals with 100% African ancestry compared to no African ancestry. We now report this in the Results.

      Another missed analysis opportunity occurs in lines 259-261, where the authors state “Thus, the clock with the largest decrease in performance in admixed cohorts (in terms of predicting chronological age and identifying age acceleration in AD) has the most and largest fraction of meQTLs influencing its CpGs.” This is another place where the authors make generalizations about a given cohort based on average ancestry rather than testing the claim empirically on an individual basis (e.g., by examining the number of meQTL variants a given individual is heterozygous for or has the non-European allele for).

      We thank the reviewer for this comment. This feedback motivated us to evaluate the relationship between differences in meQTL frequencies and methylation clock error. We found differences in meQTL frequency in the MAGENTA individuals, specifically many of the clock CpG affecting meQTL are most common in the African American cohort, consistent with our theory (Figure 6E,F). Nonetheless, there are 84 Horvath clock CpGs (24%) that are differentially methylated in AFR individuals, and 56 of these are affected by an meQTL, including 11 that are affected by an African ancestry-differentiated meQTL (Figure 6G). Finally, we find that 42 Horvath clock CpG sites in MAGENTA individuals with methylation levels that are significantly associated with increased clock error, and that are also affected by an meQTL (Figure 6B). However, at the individual level we do not find a clear relationship between the number of meQTL or ancestry-differentiated meQTL and methylation clock error. In light of these data, we have reframed our conclusions to state that meQTL likely contribute to clock error, while also being clear that they are not the sole cause.

      Can the authors explain or offer an investigation into why predicted age is often better in Cubans than Whites? They gave much attention to the opposite effect (of similar magnitude) in African Americans and Puerto Ricans but didn’t really discuss the surprisingly accurate prediction in Cubans.

      We did not focus on the results in the Cuban cohorts for several reasons. As discussed in response to Reviewer 2’s comment, the Cuban cohort had the smallest sample size (22 cases and 21 controls). Thus, while the correlation between methylation age and chronological age is similar to Whites, and in a few cases higher, the differences were not statistically significant. Second, looking at other error metrics, like mean absolute error, the clocks are comparatively less accurate in Cubans than on the White cohort (Supplementary Table 2). Finally, the clocks consistently find that Cubans with AD have lower predicted age than controls, though this is only significant for the ZhangEN clock. However, given these inconsisencies and the very small sample size, we caution against over-interpretation of these results. We clarify this in the manuscript and suggest that more work is needed on larger Cuban cohorts before any clear conclusions can be made.

      I was not a conceptual fan of the ensemble clock. The clocks are trained on very different things (e.g., chronological age versus clinical biomarkers) and are designed to capture different aspects of biology. Without more validation and motivation, I don’t think it makes sense to average values that are not designed to measure the same thing.

      We agree that combining the first and second-generation clocks for the task of age prediction is not sensible. However, for AD risk stratification, combining values from multiple clocks that capture different aspects of biology and aging could be beneficial. As mentioned in the main text, we took inspiration from approaches in polygenic risk scores, as well as the broader machine learning field, where ensembling often makes for better predictors. Nonetheless, consistent with the Reviewer’s intuition, we do not see improvement here.

      Minor comments

      (1) Typo in line 91.

      Thank you for bringing this to our attention. Fixed.

      (2) Lines 111-115, sample sizes would be helpful.

      We have added the sample sizes of the non-demented controls that were used to calculate these correlations in each cohort.

      (3) Line 137-138, the correlation stats would be helpful here. This is a common issue throughout the paper, more in-text statistics would help readers to evaluate the authors’ claims. For example, lines 249-251 as well. The authors refer the reader to Figure 5C, which itself has no statistics, this has two plots so it’s unclear which the authors are putting forward as the primary evidence.

      We have added more statistical details in the text and figures to address this comment. In this instance, we have removed the referenced figure.

      (4) Lines 258 and 261, I believe the authors report the same result in both these lines.

      Thank you for pointing out this lack of clarity. These lines report different, but related, results about the frequency of clock-affecting meQTL in different ancestral contexts. The first reports the frequency of clock CpGaffecting meQTL in individuals of African ancestry across all of gnomAD. The second result gives the frequency of those meQTL in different local ancestry backgrounds in admixed individuals. This is distinction is relevant since admixed individuals’ genomes are mosaics of multiple genetic ancestries. As such, a genetic variant might be present in haplotype whose ancestry is not in line with expectations based on global ancestry (e.g., an African American individual inherits a genetic variant within a European ancestry block). This local ancestry difference could modify the effect of the variant or obscure causal variants. Given the potential for confusion and similar results considering global and local ancestry context in this case, we have focused on the first result in the Main Text.

      (5) Somewhere, it would be helpful to provide the distribution/range of ages broken by cohort. Similarly, I didn’t see the breakdown of AD versus control cases within each cohort. Both of these features will impact power within a given cohort for certain analyses.

      We have added the distribution of ages by cohort in Supplementary Figure 1. Table 1 provides a breakdown of cases versus controls for each of the cohorts in the MAGENTA study.

      (6) Figure 3 is pretty hard to read. It would also be helpful if the authors put the white cohort in Figure 3A as a ’baseline’ comparison, as they use this as the baseline comparison in the text.

      We have made these changes to the figure and used larger text overall.

      (7) The various acronyms in the labels in Figure 5 are not explained. For Figure 5C - this is over-plotted and therefore hard to see.

      We have added the full population descriptors from gnomAD to the boxplots showing allele frequencies (Figure 6E). In addition, what used to be Figure 5C has been simplified and moved to Supplementary Figure 12.

      (8) The authors correct for cell type heterogeneity, which is known to vary across populations and can impact clock estimates. However, as far as I can tell, the cell type proportion estimates are coming from the DNA methylation data. The deconvolution algorithms for cell type proportions also have the same problem as the clocks of being trained on a very specific subset of human genetic and environmental diversity. Do the authors have any empirically derived estimates of cell type heterogeneity to sanity-check these deconvolution estimates? At the very least, it would be helpful to acknowledge this limitation.

      We thank the reviewer for commenting on this. There are no empirically derived estimates of cell type counts for the samples in the MAGENTA study. This is an inherent limitation of our study, and we have included text to make note of this.

      (9) There are very different sample sizes for each group, did the authors consider that their null results for the AD analyses in different cohorts are just a lack of power? This could be evaluated with power analyses or by comparing against sample sizes from similar studies in the literature.

      We agree that this is an important analysis and have added it to the manuscript. Given these small effect sizes, accounting for statistical power is essential for interpretation of our results. We performed power calculations based on an effect of the size observed in previous studies (0.5 year acceleration). Considering the full study, we have 86% power to detect an effect of this size. Stratifying by cohorts, we have 75% power for the African Americans, 72% for the Puerto Ricans, 72% for the Whites, 65% for the Peruvians, and 47% for the Cubans. Thus, we have high enough power that the consistent lack of association observed outside of the White cohort in MAGENTA is likely meaningful. Based on these calculations, there is only a 1% chance that we would not observe an effect in any of the other cohorts if the effect was present across cohorts. Nonetheless, we have added caveats about power and the small sample size to our suggestion that the reduced accuracy of the clocks contributes to the lack of association outside of Whites.

      (10) There has been a fair amount of discussion recently that single CpG-based clocks are much more variable than clocks that combine information across CpG sites, either using PC-based or window-based approaches. For example, the PC clock R package from the Levine Lab (https://github.com/MorganLevineLab/PC-Clocks) is very easily implemented and generally gives much less variable age estimations than site-level clocks. It would be nice to consider integrating or discussing these later-generation clocks as ways to improve clock performance in diverse human groups.

      We thank the reviewer for their suggestion to apply the principal component clock to account for potential technical variation. As outlined in the new section “Principal component versions of the methylation clocks also have lower age prediction accuracy for genetically admixed individuals,” using the principal component version of the Horvath clock did not result in consistent improvement in age prediction accuracy or generalization across MAGENTA cohorts (Supplementary Figures 4 and 5). The lower accuracy for age prediction in individuals with substantial African ancestry were present for the PC clock in the replication cohorts, just as in the MAGENTA cohorts (Supplementary Figure 6)

    1. Author response:

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

      Thank you very much for handling our revised manuscript and for the careful and constructive comments from the reviewers. We are grateful for the detailed feedback, which has helped us improve both the experimental presentation and the framing of the study. In response to the comments, we have substantially revised the manuscript, updated the figures and supplementary figures, and clarified several points in the text. We have also added new experimental analyses, which were essential to strengthen the manuscript.

      We would like to highlight the major changes in the revised version:

      Added the late phenotype analysis of the ror2 mutant, including loss of nasal and maxillary barbels and altered adult jaw morphology by microCT, strengthening the disease-model relevance.

      Added new data on a further target locus (wls) showing 46 bp attP insertion by PEn and comparison with HDR-mediated knock-in at the same site.

      Expanded the analysis of insertion performance at adgrf3b and clarified comparison with previously reported PE2 data.

      Added the analysis of HDR-mediated knock-in and prime editing substitution to generate ror2 W722X allele.

      Added comparative off-target analysis for PE2, PEn and HDR at three predicted off-target sites for the ror2 target.

      Resolved the cloning/NGS inconsistency for ror2 by increasing clone analysis

      We have also moderated several statements in the manuscript, for example, that editing efficiency is locus- and edit-dependent, and that broader comparison of germline transmission efficiencies between prime editing systems will require future work.

      A few reviewer suggestions would have required substantial additional experimental work that is technically demanding and beyond the immediate scope of the present methods-focused resubmission, for example, a direct side-by-side germline comparison of PE2 and PEn across several loci, or systematic cost benchmarking against HDR across multiple edit classes. Rather than overstate these points, we have acknowledged these limitations directly in the revised manuscript and narrowed our claims accordingly.

      Public Reviews:

      Reviewer #1 (Public review):

      From the work presented, it is unclear how prime editing could be used to transiently model human pathogenic variants, given the low frequency of precision edits in somatic tissue, or to isolate stable germline alleles of variants that are potentially dominant negative or gain-of-function in nature. Without a direct comparison with CRISPR/Cas9 nuclease HDR-based methods that use oligonucleotide templates to introduce edits, the advantage of prime editing is unclear. A cost comparison between prime editing and HDR methods would also be of interest, particularly for integration of longer DNA sequences

      We thank the reviewer for this important comment. In response, we added a direct comparison between PEn-mediated editing and HDR-mediated knock-in at the ror2 locus and the wls locus using insertion of a 46 bp attP sequence. This new dataset shows that PEn can achieve programmed insertion at a higher efficiency in ror2 and comparable efficiency in wls to HDR at the same target site, thereby providing a more direct benchmark within zebrafish embryos. We also revised the Discussion to better position prime editing as a practical donor DNA-free approach rather than as a universally superior method. We agree that a formal cost comparison would be informative; however, such an analysis would depend strongly on locus, edit size, optimisation burden, and local reagent production pipelines, and we believe this is beyond the scope of the present manuscript. Instead, we now discuss these practical considerations more cautiously in the revised Discussion.

      (1) In Figure 3, the data indicate a significant increase in precise edits of the 3 bp TGA using PE2 RNP (11.5%) vs. PE2 mRNA (1.3%). At the adgrf3b locus, only PEn mRNA was tested for introducing the 3 bp and 12 bp insertions. The previous study testing PE2 for 3 and 12 bp insertions was mentioned, but the frequency was not listed, and the study wasn't cited (lines 204 - 207). A comparison of germline transmission rates using PE2 vs. PEn would support the conclusion that PEn allows precise integration of longer templates and recovery of germline integration alleles.

      We appreciate this point. We revised the adgrf3b section to include the relevant reference and explicitly state the previously reported PE2 frequencies, allowing clearer comparison with our PEn data. We added our own experimental data to compare PE2 and PEn with mRNA or RNP form in adgrf3b locus (Figure 3i and j). We also refined the wording of our conclusions so that we do not imply a direct germline comparison between PE2 and PEn where such data are not available. In the revised manuscript, we now state that our germline transmission results apply to PEn-mediated insertions in the loci tested here. A full side-by-side germline comparison between PE2 and PEn across multiple loci would indeed be valuable, but this would require substantial additional animal work and time and is beyond the scope of the present resubmission.

      (2) Figure 4 shows the results of introducing a TGA stop codon that is predicted to result in nonsense-mediated decay. Testing the ability to also isolate different substitution mutations in the germline would be useful information for identifying the most effective approach for generating human disease variant models.

      We agree that this would be useful. In the present study, we focused experimentally on establishing stable lines for the insertion-based edits, while the substitution experiments were used to compare PE2 and PEn performance in somatic editing at the crbn locus. We also tested the generation of ror2 W722X allele by prime editing substitution (Supplementary Figure 3). We have therefore revised the manuscript to clarify the scope of the disease-modelling claim and now state more explicitly that our data support the generation of disease-relevant alleles in cases where short, programmed substitutions or insertions are sufficient.

      A comparison with the prime editing variant knock-in frequencies reported in the recent publication by Vanhooydonck et al., 2025, Lab Animal should be included in the Discussion.

      We have added this study to the revised manuscript and now discuss our findings in relation to the frequencies reported by Vanhooydonck et al. (2025).

      Reviewer #2 (Public review):

      The comparative analysis between PE2 and PEn systems suffers from limited evidentiary support. The comparison relies on single loci for substitutions (crbn) and insertions (ror2), raising concerns about generalizability. Additional validation across multiple loci is necessary to support broad conclusions about PE2/PEn performance

      We appreciate this concern. To strengthen the manuscript, we added new experimental data at an additional target locus, wls, where we tested insertion of a 46 bp attP sequence and compared PEn with HDR-mediated knock-in. We also included the adgrf3b insertion data more prominently. At the same time, we revised the wording throughout the manuscript so that our conclusions are more carefully limited to the loci tested here.

      Reviewer #3 (Public review):

      (1) The logic for introducing two nucleotide changes (at +3 and +10) to change a single amino acid (I378) should be explicitly explained in the main body of the manuscript. It is indeed self-explanatory when looking at Supplementary Figure 1. One way of doing it could be to include Supplementary Figure 1a in Figure 1.

      We thank the reviewer for pointing this out. We have now explained this directly in the main text. Specifically, we state that one nucleotide change introduces the desired missense mutation, whereas the second was included to reduce potential pegRNA misfolding caused by complementarity between the spacer and the PBS/RT template region.

      (2) It is not clear why a 3-nucleotide insertion was used to generate W722X. The human W720X is a single-nucleotide polymorphism, and it should be possible to make a corresponding zebrafish mutant by introducing two nucleotide changes.…

      We agree that this point and have now explained in the main text that the 3 bp stop-codon insertion was chosen as a proof-of-principle strategy for generating a precisely truncated protein through programmed insertion, a type of edit that can be broadly applied to target loci. We also tested the generation of ror2 W722X allele by prime editing substitution (Supplementary Figure 3). We also clarify that prime editing substitution was tested separately here.

      (3) Lines 137-138: T7 Endonuclease assay used in Figure 2d detects all polymorphisms, both precise changes and indels. Thus, if this assay were performed on embryos shown in Figure 1c-d, the overall percentage of modified alleles would be similarly higher for PEn over PE2 (add up precise prime edits and indels). The conclusion in the last sentence of the paragraph is, therefore, incorrect, I believe.

      We agreed with this point and revised the sentence accordingly. The text now states that no obvious cleavage was observed with the PE2/pegRNA condition, suggesting fewer editing events compared with PEn, rather than implying greater precision from the T7E1 result alone.

      (4) Use of terminology. "Germline transmission" is typically used to refer to the fraction of F0s transmitting desired changes (or transgenes) to their progeny, while "germline mosaicism" refers to the fraction of F1s with the desired change in the progeny of a given F0. "Germline transmission" in line 217 should be replaced with "germline mosaicism".

      We have replaced the terminology accordingly in the revised manuscript.

      (5) Lines 253-255: The fraction of injected embryos that had mosaic nuclear expression of GFP, indicative of NLS insertion, should be clarified. It should also be clarified whether embryos positive for nuclear GFP were preselected for amplicon sequencing and germline transmission analyses. This is extremely important for extrapolation to scenarios like epitope tagging, where preselection is not possible.

      We agree and have clarified this in the revised manuscript. We now state the fraction of injected embryos showing mosaic nuclear GFP expression, and we explicitly note that embryos were not preselected prior to sequencing or founder analysis. We further explain that preselection was not practical because the transgene is multicopy and individual fibres showed variable ratios of nuclear to cytoplasmic GFP, which made reliable scoring difficult.

      (6) Statistical analyses. It would be helpful to clarify why different statistical tests are sometimes used to assess seemingly very similar datasets (Figures 1c, 1d, 2b, 2c, 2f).

      We have clarified this in the Materials and Methods section and now state that the choice of statistical test depended on the normality and variance structure of the experimental data.

      (7) Discussion. Since authors suggest that PEn might be especially beneficial for insertion of additional sequences, it is important to stress locus-to-locus variability of success. While the precise +3 insertion was indeed tremendously efficient at both tested loci (ror2 and adgrf3b), +12 addition into adgrf3b was over 10 times less efficient. In contrast, +30 into smyhc:GFP using the shorter pegRNA was highly efficient again. Longer pegRNA did not work nearly as well. As dangerous as it is to extrapolate from small datasets, perhaps these observations indicate that optimization of RT template and PBS may be needed for each new locus in order to significantly outperform oligonucleotide-mediated HDR? If so, would the cost of ordering several pegRNAs and the effort needed to compare them factor in when deciding which method to use?

      We fully agree and have substantially revised the discussion to reflect this point. We now emphasise more clearly that editing efficiency is locus- and edit-dependent and likely influenced not only by insertion length but also by spacer sequence and pegRNA complexity. We cite the relevant literature on prime editing determinants and discuss that locus-specific optimisation may be required. We also softened our concluding claims so that the manuscript presents PEn as a practical donor DNA-free approach rather than as a universally high-efficiency solution.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Because this is a genome editing methods paper, including frequency or percentages of somatic and germline editing in the abstract, in comparison to previously published studies, it would be useful information for the intended audience

      We agree and revised the abstract to include concrete editing frequencies. We now indicate the strongest insertion efficiencies observed. We also retained the statement that edited alleles were transmitted to the next generation.

      Reviewer #2 (Recommendations for the authors):

      (2) Please include additional loci for substitutions and insertions to strengthen conclusions about PE2/PEn efficiencies.

      In response, we added further substitution data at the ror2 (Suppl. Data 3) and insertion at the wls locus (Suppl. Data 6) and strengthened the presentation of the adgrf3b insertion data: first, by adding new locus data where feasible; and second, by narrowing the wording of our conclusions so that they are explicitly limited to the loci tested here.

      (3) Please provide direct comparisons between zebrafish ror2 W722X phenotypes and human Robinow syndrome symptoms to support disease modeling claims.

      We addressed this by adding analysis of the late ror2 phenotype. In the revised manuscript, zygotic and maternal-zygotic mutants are reported to lack nasal and maxillary barbels, and one-year-old mutants show altered jaw morphology with a less protrusive lower jaw (Figure 4).

      (4) The substitution of two nucleotides (+3 G→C and +10 A→G) to target residue I378 of crbn is not justified. It is unclear why two substitutions were required to model thalidomide sensitivity or validate editing efficiency. Please explain why dual nucleotide substitutions were necessary in the crbn experiments and whether single substitutions would suffice.

      We now explain in the main text that the second substitution was introduced to reduce potential inhibitory intramolecular interactions within the pegRNA, while the primary substitution generated the intended amino-acid change. This clarification is now stated explicitly in the Results.

      (5) The reported 10.3% precise editing efficiency for PEn/pegRNA at ror2 conflicts with Supplementary Figure 2, where none of the 20 clones from PEn/pegRNA showed precise edits, while one clone from PEn/springRNA did. Please address the inconsistency between NGS and cloning results at ror2, possibly by increasing sample size or reanalyzing sequencing data.

      We addressed this directly by repeating and expanding the clone analysis. The revised Supplementary Figure 2 now includes the updated clone dataset, and the result is in much better agreement with the NGS-based frequency estimates.

      (6) Figure 3d highlights edits from PEn/springRNA but omits PEn/pegRNA results, despite the latter being described as superior. This creates ambiguity about the relative performance of pegRNA vs. springRNA. Please include PEn/pegRNA results in Figure 3d to fairly represent pegRNA performance.

      We agree. We therefore revised Figure 3e so that it now includes alignment data for PE2/pegRNA, PEn/pegRNA and PEn/springRNA, allowing more direct visual comparison of the editing outcomes.

      (7) The study does not specify the version of PEn used, or introduce some background of PE2 and springRNA. Comparisons to prior PE work in zebrafish, base editing, or HDR efficiencies are absent, obscuring the novelty of this approach. Please specify the PEn variant used, describe springRNA/PE2 structures, and compare results to prior zebrafish PE studies, BE, and HDR efficiencies for similar edits, contextualizing where PE2/PEn offers unique advantages.

      We thank the editors for this helpful suggestion. We have clarified the PEn and PE2 systems in the manuscript, specified the nuclease-based PEn used, and improved the background text introducing these editing strategies. We added the data to directly compare prime editing and HDR in the ror2 locus (Figure 3). We also expanded the Discussion to place the current findings in the context of prior zebrafish prime editing, HDR-based knock-in and base-editing work. We did not test all alternative systems experimentally in the current study, but we now discuss their relevance and clearly define the specific contribution of the present work.

      (8) The manuscript does not explore advanced PE variants (e.g., PE3, PEmax), codon optimization, or scaffold modifications to improve efficiency. Please discuss whether codon optimization, PE3/PEmax systems, or pegRNA modifications were tested or could improve outcomes.

      We agree that this should be discussed and we added recent work on zebrafish prime editing optimisation, codon optimisation, pegRNA engineering and related advances to the discussion, and explain that these are promising avenues for improving efficiency in future studies.

      (9) No data compares the off-target effects of PE2 and PEn, a critical consideration for evaluating specificity and safety. Please perform comparative off-target analyses for PE2 and PEn to assess specificity.

      In response, we performed comparative off-target analysis for the ror2 target and analysed three predicted off-target sites. These data are now included in Supplementary Figure 3 and show no significant increase in non-specific editing for the prime editing conditions tested.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Strengths:

      Great care was taken in selecting and cleaning the data, and in making sure that intramural vs. extramural projects were compared appropriately. The data has statistical validation. The trends are clear and convincing.

      We thank the reviewer for highlighting the strengths of the manuscript.

      Weaknesses:

      The Discussion is too short and descriptive, and needs more perspective - why are the findings important and what do they mean? Without recommending policy, at least these should discuss possible implications for policy.

      The Discussion has been substantially expanded. We added several new paragraphs discussing: the 2024 Senate HELP Committee proposal for NIH reform; implications for portfolio management (positioning extramural for basic research, intramural for clinical translation); generalizability to other agencies (DoD, NSF FFRDCs, DoE national labs); and the extramural program's role in workforce training as a societal benefit distinct from research outputs.

      The biggest problem I have with this submission is Figure 3, which shows a big decrease in clinical-related parameters between 2014 and 2019 in both intramural and extramural research (panels C, D and E). There is no obvious explanation for this and I did not see any discussion of this trend, but it cries out for investigation. This might, for example, reflect global changes in funding policies which might also influence the observed closing gaps between intramural and extramural research.

      We added an explicit explanation in the Results: because the dataset is truncated at 2020, clinical citations naturally approach zero near the window's end, consistent with the ~7-year lag for clinical citations to accrue documented in prior work (Hutchins et al., 2019). The APT metric declines less steeply because it uses the forward citation network for predictions.

      Reviewer #2 (Public review):

      Strengths:

      The authors leveraged publicly available data (including RePORTER and the iCite repository) and used robust validated metrics (RCR, APT, clinical citations). They carefully considered a large number of confounders, including those related to the PI, and performed several well-described regression analyses.

      We thank the reviewer for highlighting these strengths of the manuscript

      Figure 3A shows intramural projects producing about 2.75 papers per year in 2009, whereas extramural projects are producing just over 1 paper per year. Extramural projects appear to catch up over the next five years. While the authors attempt to explain the difference in their figure legend, another explanation is that the intramural projects started well before 2009 but, as the authors state, intramural data only became available in 2009.

      We added a methodological note acknowledging that some intramural projects may have had start dates prior to 2009 that are not captured in the data, and that the ramp-up of new intramural projects is slower because they are more tied to new PI hiring. We also note the exclusion of projects matched in 2008 as possible continuations. However, the slow ramp-up of Intramural costs in Supplemental Figure 3 is consistent with hiring-associated lagged investment suggesting that our filtering of continuing projects was very successful. Nevertheless, because we cannot completely rule out some continuing projects made it through despite our efforts, we have made the caveats mentioned above in the “Comparison of research topics” section of the Results and the Data section of the Methods.

      As the authors note, funding information is often complex and difficult to characterize for an analysis like this. How did the authors handle: i) publications linked to multiple extramural grants; ii) publications linked to intramural and extramural grants; iii) publications linked NIH grants and non-NIH grants?

      I would think it necessary to somehow apportion credit, as otherwise it would appear that extramural projects are more productive than they truly are.

      We have now explicitly stated that papers with both intramural and extramural funding links were excluded, while papers with multiple links within the same funding type were retained. A new Supplemental Figure 6 was added showing the distribution of papers by number of funding sources for both extramural and intramural grants, demonstrating that the vast majority acknowledged only one project. These changes are in the Methods, Data section and Supplemental Figure 6

      Apportioning credit among a many-to-many graph like the ones used here is indeed a high value problem to solve, but one with many researcher-degrees-of-freedom about analytical design decisions that impact the results. We are working on a rigorous methodology for this, but the amount of time required to do this well is its own research project, and out of scope for manuscript revisions.

      Also, it is not clear if the authors took account of the indirect costs paid by the NIH to universities that have received extramural grants.

      We added explicit language clarifying that all cost comparisons use inflation-adjusted total costs (direct + indirect) for extramural grants. We also added a new sensitivity analysis (Supplemental Figure 4) inflating extramural indirect costs by 30% to approximate unrecovered university expenditures, with the finding that the fundamental pattern holds even under this adjustment. These are found in the “Comparison of funding” and “Comparison of cost effectiveness” sections of the Results, as well as Supplemental Figure 4.

      Reviewer #3 (Public review):

      Strengths:

      The authors clearly presented their methods for processing the NIH project data and classifying projects into either intramural or extramural categories. The limitations of the study are also well-addressed.

      We thank the reviewer for highlighting these strengths of the manuscript

      Weaknesses:

      The article would benefit from a more thorough discussion of the literature, a clearer presentation of the results (especially in the figure captions), and the inclusion of evidence to support some of the claims.

      The Introduction was updated with more specific framing of prior literature (e.g., explicit mention of risk management, funding disparities, and diminishing marginal returns as the focus of prior work). New references were added throughout, including Sampat (2012) on mission-oriented NIH research, Ioannidis et al. (2019) on grant competition inefficiencies, Drummond et al. (2005) on health economic evaluation methods, and the Cassidy (2024) Senate report, throughout the introduction and discussion.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The article would benefit from a more detailed analysis/discussion about the recovery of indirect costs for extramural research.

      I note that the authors are from the University of Wisconsin, which is part of the IRIS network (https://iris.isr.umich.edu/iris-members-map/). They could work with IRIS (also called UMETRICS) to get a better sense as to the true costs of extramural research for each project (e.g., all labor costs, all equipment costs). The IRIS data are extraordinarily robust. Here's an example of an IRIS / UMETRICS paper: https://www.science.org/doi/10.1126/sciadv.abb7348.

      They could, for example, re-do the analyses assuming that the recorded indirect cost covers only 70% of the true indirect costs. Thus, if they get $700,000 indirect costs from RePORTER, they should assume that the true indirect costs were $1,000,000. Similarly, they can add the costs of the time the PI spent writing the grant proposal, using the Bergstrom paper as a guide.

      Another option would be to conduct sensitivity analyses taking into account ~30% incomplete indirect cost recovery (see https://docs.house.gov/meetings/AP/AP07/20171024/106525/HHRG-115-AP07-Wstate-DroegemeierK-20171024.pdf) and lost efficiency due to excess time writing grant proposals (see https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000065).

      We conducted a sensitivity analysis as requested inflating extramural indirect costs by 30%, citing the Droegemeier (2017) Congressional testimony as the basis for this estimate. The cost of grant-writing time is now acknowledged in the Discussion as an unreimbursed hidden cost of the extramural system, citing Ioannidis et al. (2019). This narrowed the gap between extramural research and intramural research, but did not close it completely. In addition, our updated regression (Supplemental Figure 4) showed similar trends as our main Figure 4, but with the Intramural advantage heightened and the Extramural advantage diminished. Both remained significant. We have also added to the discussion that there are additional costs and benefits that may not be fully captured in an analysis such as ours.

      The authors appear to have used an agency-perspective for their cost-effectiveness analyses. Generally, it is preferable to use a wider societal perspective. While that may be difficult, the article would benefit from some discussion from the perspective of the government and universities.

      We added a new paragraph explicitly acknowledging the agency-centered perspective and its limitations, noting that it does not capture the full economic cost borne by universities (startup costs, philanthropy, endowments, state contributions, graduate student training, faculty retention, infrastructure). The extramural program's contribution to the US workforce pipeline is specifically highlighted as a societal benefit not captured by the cost-effectiveness metrics.

      Reviewer #3 (Recommendations for the authors):

      Line 84-87: "The overrepresentation of viral research is likely because of the outsize investment toward the intramural Vaccine Research Center, and the cancer/genetics overrepresentation due in part because National Cancer Institute intramural investigators conduct research at that institute as well as at the NIH Clinical Center for their human genetics work." What evidence is there to support this claim?

      A citation to the NCI Center for Cancer Research website was added to support the claim about NCI intramural investigators working at the Clinical Center and Center for Cancer Research, where vaccine research is extensively discussed.

      Lines 107-109. "Given that NIH funding for intramural research has remained relatively constant as a percent of total funding over the years, this indicates larger single awards for intramural research while extramural investigators may increasingly require multiple concurrent grants to sustain their labs." Authors may consider adding a panel to Figure 2 showing the percentage of total funding of intramural vs. extramural funding.

      Rather than adding a panel to Figure 2, we added a new Supplemental Figure 3 showing the cost breakdown and intramural percentage of total funding by year.

      Discussion section: Are any of the findings of this study relevant to other funding agencies in the US (such as the National Science Foundation, the Department of Energy, and the Department of Defense)?

      A new paragraph to the Discussion was added discussing implications for the Department of Defense (including the Congressionally Directed Medical Research Programs), NSF FFRDCs, and the Department of Energy's national labs and FFRDCs, arguing that the incentive-alignment logic likely generalizes across agencies.

      Methods section: Please add an explanation of the technique used for propensity score matching.

      A detailed step-by-step description of the PSM procedure was added, covering propensity score estimation, within-year matching, matched cohort construction, outcome regression on matched data, and visualization of results.

      Figure 1: Please clarify if the relative ratio of intramural projects is calculated from the numbers of grants (as suggested in lines 95-96 and 98-100) or the numbers of publications (as suggested in lines 82-83 and 97-98).

      Also, this figure would be more intuitive if, for each topic, it showed the relevant intramural number (as it currently does) and also the relevant extramural number.

      The caption and Methods were updated to clarify that clustering and ratio calculation are based on projects/grants, not publications. A formula was added to the Methods to make the ratio calculation explicit. The figure itself was not modified to add extramural bars, though the ratio calculation already implicitly encodes both.

      Figure 2: Please change "(red)" to "(blue)" in the caption, and remove the A as there is only one panel in this figure

      Figure 4: Please change "(red)" to "(blue)" in the caption.

      These changes have been made.

      Lines 19-21: I suggest rewriting this sentence as follows:

      "We find that extramural awards are more cost-effective for producing outputs commonly used for academic evaluation, such as publications and citations per dollar, while intramural awards are more cost-effective for generating research that influences future clinical work, more closely in line with agency's health goals."

      The sentence was rewritten substantially in line with the reviewer's suggestion, now reading more clearly with "per dollar" removed as a parenthetical and the structure of the comparison clarified.

      Lines 31-34: Please rewrite this sentence along the following lines to provide more context on previous research into the grant funding system:

      Certain aspects of the grant funding system have been the focus of research, such as AAAA (Azoulay et al., 2009), BBBB (Goldstein and Kearney, 2020), CCC (Hoppe et al., 2019), DDDD (Lauer et al., 2017), EEEE (Wahls, 2018a) and FFFF (Wahls, 2018b), but the relative merits of intramural and extramural funding have received little attention to date.

      The sentence was rewritten to name specific contributions of each cited paper (e.g., risk management, funding disparities, diminishing marginal returns), replacing the generic list of citations.

      Lines 41-44: Please explain "merit score" and please add a reference to an article or website that explains the review process at the NIH.

      "Merit score" was revised to "percentile ranking of overall impact merit score" and a citation to the NIH CSR website ("What happens to your application during and after review?," 2025) was added.

      Lines 53-54: Please change Intramural to intramural (two instances, and also in line 284), and Extramural to extramural.

      "Intramural" and "Extramural" were corrected to lowercase throughout.

      Line 65-67: This sentence ("Potential advantages of the intramural approach are that researchers in the NIH's own laboratories allow the NIH to hire researchers whose research agendas more closely align with its mission.") reads awkwardly. Please clarify.

      The sentence was rewritten to read more clearly: "An advantage of the intramural approach are that NIH has the direct ability to hire scientists whose research closely aligns with agency goals, and researchers do not need to devote time and effort on preparing and submitting grant applications."

      Line 95-97: Authors should consider including an equation to help explain the following sentence: "The relative ratio of intramural projects for each topic was calculated by taking a ratio of the proportions of total grants a topic represented in the intramural vs. extramural portfolios. A relative ratio >1 signifies a higher share of intramural project publications on that topic relative to their share across all topics."

      A formula was added to the Methods defining the topic-level ratio calculation explicitly.

      Line 143: The phrase "may reflect the extra attention intramural investigators are afforded" reads awkwardly - please reword.

      Reworded to "may reflect the extra time intramural investigators save because they do not have teaching and grant writing responsibilities."

      Lines 303-304: This sentence ("First, as the renewal of project contracts may alter the topic and arrangement of the projects, we dropped 70,297 projects with renewal records in our data.") reads awkwardly. Please clarify.

      Reworded to "Since the scientific focus of a study may drift over time, we dropped 70,297 projects with renewal records in our data."

      Line 378-379: Please specify the model of ChatGPT used.

      Done.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      Weakness:

      The diversity of neurons mediating these projections and their targeting within the BLA and NAc is not explored. These are not homogeneous structures and so one possibility is that some of the diversity within their findings may relate to targeting of different sub-structures within BLA or NAc or the diversity of projection neuron subtypes that mediate these pathways. This is an important future direction for this work but does not detract from the main finding as reported. The electrophysiological data in Figure 7 have some experimental confounds that makes their interpretation challenging.

      We thank the reviewer for these thoughtful comments. We fully agree that targeting different substructures within the BLA or NAc, as well as the diversity of projection neuron subtypes mediating these pathways, represents an important direction for future investigation. We will certainly explore these possibilities in future studies.

      We have also removed the optogenetics and electrophysiology data, as they may introduce confounds. The removal of these data and figures does not affect our main conclusions.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (a) The authors have improved the manuscript somewhat by refining their description of the results. However, the normalized EPSC experiments still do not make much sense. If you have a higher light intensity or LED duration the curve of the EPSC response will saturate earlier. Similarly, if you are in a highly, or poorly labeled slice or subregion of a slice then you will see responses emerge at different intensities based on the number of synapses labelled. There is no standardization in the way these experiments were performed, so performing some arbitrary post hoc normalisation does not correct for this. Similarly, they also place the fibreoptic manually above the slice each time. This makes it much harder to determine the actual light intensity delivered to the slice on a cell by cell and group by group basis.

      I have reduced my public statement from significant experimental confounds, to some experimental confounds. But the way the experiments were performed does not allow the normalized data to really be interpretable. They still argue that normalized EPSCs are relatively larger. I don't even really understand what this means biologically.

      The subsequent rise/decay and other measures is now better described. However, they note that the decay constant is larger. This means that the kinetics are slower, not enhanced, as they describe.

      Again, we thank the reviewer for the careful advice. We recognize the limitations of the optogenetics and electrophysiology data and have therefore removed them to avoid potential confounds.

    1. Author response:

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

      In the revised version, our primary focus has been to more clearly demonstrate the unique contribution of the brain-cognitive gap (BCG) beyond what is captured by cognitive performance alone, and to show that the BCG is not trivially driven by the observed cognitive scores. Additional analyses now demonstrate that the BCG provides complementary and nuanced information regarding factors associated with cognitive resilience, above and beyond the cognitive measures themselves.

      In response to the comment regarding the inclusion of a baseline predictive model, we would like to clarify that the central aim of our study is to compare predictive utility across different cognitive states (resting state, movie watching, and n-back), rather than to establish a single universally optimal prediction model. Several previous studies have already systematically compared deep learning approaches with more traditional machine learning methods for functional connectome-based prediction. In contrast, the goal of the present study is to examine how brain state modulates the ability of AI-based functional connectome models to capture individual differences in working memory and episodic memory.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors attempted to identify whether a new deep-learning model could be applied to both resting and task state fMRI data to predict cognition and dopaminergic signaling. They found that resting state and moving watching conditions best predict episodic memory, but only movie watching predicts both episodic and working memory. A negative 'brain gap' (where the model trained on brain connectivity predicts worse performance than what is actually observed) was associated with less physical activity, poorer cardiovascular function, and lower D1R availability.

      Strengths:

      The paper should be of broad interest to the journal's readership, with implications for cognitive neuroscience, psychiatry, and psychology fields. The paper is very well-written and clear. The authors use two independent datasets to validate their findings, including two of the largest databases of dopamine receptor availability to link brain functional connectivity/activity with neurochemical signaling.

      Weaknesses:

      The deep learning findings represent a relatively small extension/enhancement of knowledge in a very crowded field.

      It's unclear from these results how much utility the brain gaps provide above and beyond observed performance. It would be helpful to take a median split of the dataset on observed performance and plot aside the current Figure 3 results to see how the cardiovascular and physical activity measures differ based on actual performance. Could the authors perform additional analyses describing how much additional variance is explained in these measures by including brain gaps?

      We thank the reviewer for raising this important point. In response to their request, we first examined the relationship between the BCG and the cognitive measure itself. We did not find any significant relationship in either the DyNAMiC sample (r =0.01, p =0.939) or the COBRA sample ((r =0.01, p=0.894) (see Author response image 1).

      Author response image 1.

      We then conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular disease (CVD) risk scores. We found no significant difference in physical activity (DyNAMiC: p =0.56, 95% CI: –14.99 - 8.13; COBRA: p =0.29, 95% CI: –3.54 - 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, 95% CI: –1.08 - 10.72; COBRA: p =0.41, 95% CI: –1.86 - 4.58) between high and low EM perfprmers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCG provides unique information, beyond the observed cognitive measure (episodic memory score), regarding factors that contribute to cognitive resilience. These results have been added to Section 2.4, and Figure 3 has been updated.

      Some of the imaging findings require deeper analysis. For Figure 1f - Which default mode regions have high salience? DMN is a huge network with subregions having differing functions.

      Grad-CAM provides a coarse, gradient-based attribution that reflects how the learned feature maps contribute to the model output. It is not designed to produce specific input-level interpretations, such as symmetric edge-wise importance values. Therefore, the primary interpretation remains at the network level rather than at the level of individual FC edges.

      Along the same lines, were the striatal D1R findings regionally specific at all? It would be informative to test whether the three nuclei (Accumbens, Caudate, Putamen) and/or voxelwise models would show something above and beyond what is achieved from averaging D1R across the striatum. What about cortical D1R, which is highly abundant, strongly associated with cognitive (especially WM) performance, and has much unique variance beyond striatal D1R? https://www.science.org/doi/full/10.1126/sciadv.1501672. The PET findings are one of the unique strengths of this paper and are underexplored. It's also unclear if the measure of brain entropy should simply be averaged across all regions.

      In this study, we focused on D1DR/ D2DR averaged across the caudate and putamen, which has been reported in our previous work to be more strongly associated with cognitive functions (Johansson et al., 2023, Nyberg et al., 2016), compared to the nucleus Accumbens, which tends to show lower D1DR/D2DR levels and limited association with these cognitive domains. Following the Reviewer’s suggestion, we examined regional variations and found that while both caudate and putamen D1DR showed significant associations with BCG, there were no significant associations for D1DR in the nucleus accumbens or DLPFC with BCG. For D2DR, we observed a significant association between caudate/putamen D2DR and BCG.

      D1DR:

      Partial correlation between:

      Caudate_Bilateral vs. NegGap, (r =0.37, p =0.02

      Putamen_Bilateral vs. NegGap, r =0.34, p =0.03

      Accumbens_Bilateral vs. NegGap, r =0.07, p =0.69

      Mean (LRCaud, LRput, LRacc) vs NegGap, r =0.35, p =0.03

      DLPFC_Bilateral vs NegGap, r =0.21, p =0.21

      Striatum_Bilateral (Mean (LRCaud, LRput)) vs. NegGap, r =0.40, p =0.01

      Caudate_Bilateral vs. PosGap, r=–0.37, p=0.02

      Putamen_Bilateral vs. PosGap, r=–0.53, p=0.02

      Accumbens_Bilateral vs. PosGap, r=–0.25, p=0.31

      Mean (LRCaud, LRput, LRacc) vs PosGap, r=–0.41, p=0.08

      DLPFC_Bilateral vs. PosGap, r=–0.30, p=0.21

      Striatum_Bilateral (Mean (LRCaud, LRput)) vs. PosGap, r=–0.49, p=0.03

      Author response image 2.

      D2DR:

      Correlation between:

      Caudate_Bilateral vs. NegGap, r=0.36, p=0.0003

      Putamen_Bilateral vs. NegGap, r=0.22, p=0.03

      Accumbens_Bilateral vs. NegGap, r= –0.01, p=0.91

      Mean (LRCaud, LRput, LRacc) vs PosGap, r= –0.24, p=0.01

      Striatum_Bilateral vs. NegGap, r=0.39, p=0.0001

      Caudate_Bilateral vs. PosGap, r= –0.34, p=0.004

      Putamen_Bilateral vs. PosGap, r= –0.37, p=0.002

      Accumbens_Bilateral vs. PosGap, r= –0.21, p=0.09

      Mean (LRCaud, LRput, LRacc) vs PosGap, r= –0.38, p=0.001

      Striatum_Bilateral vs. PosGap, r= –0.49, p=0.0001

      We have added the following sentence to the Results section to highlight these regional differences in D1DR/D2DR in relation to BCG.

      “Both D1DR and D2DR availability in the striatum were associated with BCG, such that lower dopamine receptor availability was linked to a greater behavioral-cognitive gap. However, these associations varied by region. For D1DR, significant correlations with BCG were observed in the caudate (positive gap: r = –0.37, p =0.02; negative gap: r= 0.37, p =0.02) and putamen (positive gap: r = –0.53, p=0.02; negative gap:r=0.34, p=0.03), but not in the nucleus accumbens (positive gap: r= –0.25, p= 0.31; negative gap: r =0.07, p=0.69) or the DLPFC (positive gap: r = –0.30, p=0.21; negative gap: r =0.21, p=0.21). For D2DR, both caudate (positive gap: r = –0.34, p=0.004; negative gap: r =0.36, p=0.0003) and putamen (positive gap: r = –0.37, p=0.002; negative gap: r =0.22, p=0.03) showed significant associations with BCG.”

      Author response image 3.

      It is not clear from the text that the authors met the preconditions for mediation analysis (that is, demonstrating significant correlations between D1R and entropy, in addition to the correlation with brain gap. The authors should report this as well.

      This is a fair question. We recalculated entropy in the striatum, given that D1DR is more strongly expressed in this region and, therefore, reduced striatal D1DR may have a more pronounced impact on local entropy (as the reviewer suggested, it may not be appropriate to compute entropy across all brain regions). Our analyses showed that lower D1DR/D2DR levels were associated with higher entropy, which in turn was related to higher BCG.

      DyNAMiC; negative gap:

      Partial correlation between:

      Entropy and D1DR, r = –0.33, p=0.04.

      Entropy and NegGap, r = –0.36, p=0.03.

      DyNAMiC; positive gap:

      Partial correlation between:

      Entropy and D1DR, r = –0.56, p=0.01.

      Entropy and PosGap, r r =0.47, p=0.04.

      COBRA; negative gap:

      Correlation between:

      Entropy and D2DR, r = –0.22, p=0.03.

      Entropy and NegGap, r = –0.27, p=0.007.

      COBRA; positive gap:

      Correlation between:

      Entropy and D2DR, r = –0.26, p=0.03.

      Entropy and PosGap, r = 0.25, p=0.03.

      We have added these results under the result section 2.6. We have further updated Figure 4 in the revised manuscript, reporting these correlation results.

      Was age controlled for in the mediation analysis? I would not consider this result valid unless that is the case.

      We utilized the mediation package in R, and to control for a covariate age in the mediation analysis, we added age as a covariate in both the mediator model and the outcome model. The following information has been added in the method section in the revised version of the manuscript.

      “To assess the statistical significance of this mediation effect, we employed the bootstrapping method as outlined by Preacher and Hayes (145) and age has been controlled for in all statistical analysis.”

      The discussion section is long, but the authors would do better to replace some less helpful sections (e.g., the paragraph on methodological tweaks to parcellations and model alignment) with a couple of other important points, including:

      (1) Discuss the 'sweet-spot' of movie watching for behavior prediction in the context of studies showing that task states 'quench' neural variability: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007983. This may not be mutually exclusive of the discussion on dopamine and signal-to-noise ratio, but it would be helpful for the authors to discuss their potential overlap vs. unique contributions to the observed findings.

      Thank you for the comment. We have now eliminated the section about methodological tweaks and extended the discussion on the sweet-spot of the task for behavioral prediction by referencing the paper that the reviewer suggested. Here comes the paragraph discussing this topic:

      “Additionally, previous research showed that movie-watching alters the propagation of activity across cortical pathways (105), particularly within and between regions involved in audiovisual processing and attention. These alterations lead to a less segregated and more integrated network organization (106). Similarly, the n-back task has been associated with increased integration of task-positive cortico-cortical connectivity (104, 107) and striato-cortical connectivity (102). Our findings also suggest that certain task contexts strike an optimal balance between reducing neural variability and maintaining sufficient richness to capture individual differences. Prior work shows that task states quench neural variability, leading to a more reliable and predictable neural signal (108). In this context, movie watching may represent such a sweet spot constraining neural dynamics through shared audiovisual stimulation, while simultaneously engaging a broad range of cognitive processes that preserve individual differences.”

      (2) The argument that dopamine signaling increases signal-to-noise ratio is based on some preclinical data as well as correlational data using fMRI with pharmacological challenges. It is less clear how PET-derived estimates of D1R and D2R availability equate to 'dopamine signaling' as it is thought of in this context. Presumably, based on these data, higher D1R or D2R availability would be related to greater levels of tonic dopaminergic signaling. However, in the case of the COBRA dataset with D2R estimates, those are based on raclopride -- which competes with endogenous dopamine for the D2 receptor. Therefore, someone with higher levels of endogenous dopamine signaling should theoretically have lower raclopride binding and lower D2R estimates. I'm not arguing that the authors' logic is flawed or that D1R and D2R are not good measures of dopamine signaling, but I'd ask the authors to dig into the literature and describe more direct potential links for how greater receptor availability might be associated with greater dopamine signaling (and hence lower entropy). Adding this to the discussion would be very valuable for PET research.

      Thank you for raising this important point. We agree that D1R and D2R availability should not be taken as direct proxies of dopamine signaling. However, prior work has suggested meaningful associations between pre- and post-synaptic markers. For instance, a well-powered study demonstrated a significant correlation between D2R availability and dopamine synthesis capacity measured by FMT (Berry et al., 2018). This finding supports the idea that postsynaptic receptor markers may, under certain conditions, serve as an indirect proxy for dopaminergic signaling. Moreover, the number of dopamine-producing neurons innervating the striatum during development has been proposed to shape the structural maturation and arborization of dendrites (McAllister, 2000; Whitford et al., 2002), potentially providing a structural and functional basis for observed associations between pre- and post-synaptic measures.

      At the same time, smaller-scale studies have yielded mixed findings, reporting either non-significant associations (Heinz et al., 2005; Kienast et al., 2008) or negative correlations (Ito et al., 2011). Importantly, the latter studies employed [18F]FDOPA to index dopamine synthesis, which has been argued to provide a less reliable estimate of synthesis capacity compared to FMT, as used in Berry et al. (2018). These inconsistencies underscore that the relationship between pre- and post-synaptic markers is not straightforward and requires further examination in larger, well-powered samples. The following paragraph has been added to the discussion.

      “An important caveat is that D1DR and D2DR availability do not provide a direct measure of dopamine signaling. Instead, they reflect receptor availability, which interacts with endogenous dopamine in a complex manner. PET measures of D1R and D2R availability reflect the density of unoccupied dopamine receptors and the degree to which endogenous dopamine competes with radioligand binding. D2R binding potential is sensitive to competition from synaptic dopamine, such that higher ambient dopamine generally reduces tracer binding; D1R binding, however, is less affected by endogenous dopamine under physiological conditions, reflecting more directly receptor expression levels. Previous studies demonstrated a significant association between D2R availability and dopamine synthesis capacity measured by FMT (117, 118), suggesting that postsynaptic receptor markers may, under certain conditions, serve as a proxy for dopaminergic signaling. Developmental factors, such as the number of dopamine-producing neurons innervating the striatum, may further influence the structural and functional relationship between pre- and post-synaptic markers. By contrast, smaller studies have reported non-significant (119, 120) or negative (121) associations, although these studies relied on [18F]FDOPA, which is considered a less precise index of dopamine synthesis than FMT. Taken together, these reports indicate that the relationship between pre- and post-synaptic markers is complex and not necessarily linear. Accordingly, our observation that lower receptor availability is associated with greater neural variability should not be interpreted as direct evidence of weaker dopaminergic signaling, but rather as reflecting the interplay between receptor density and endogenous dopamine occupancy, particularly in the case of D2DR.”

      Reviewer #2 (Public review):

      Summary:

      The authors developed a deep learning model based on a DenseNet CNN architecture to predict two cognitive functions: working memory and episodic memory, from functional connectivity matrices. These matrices were recorded under three conditions: during rest, a working memory task, and a movie, and were treated as images for the CNN algorithm. They tested their model's performance across different conditions and a separate dataset with a different age distribution (using the same MRI scanner, scanning configurations, and cognitive tests). They also calculated the "brain cognition gap" based on the model trained on resting functional connectivity to predict working memory. Extending from the commonly used index "brain age," the brain cognition gap was defined as the difference between the working memory score predicted by their model (predicted working memory) and the working memory score based on the working memory test itself (observed working memory). This brain cognition gap was found to be associated with physical activity, education, and cardiovascular risk. The authors also conducted additional mediation tests to examine whether regional functional variability mediated the relationship between PET-derived measures of dopamine and the brain cognition gap.

      Strengths:

      The major strength of this manuscript is the extensive effort the authors have put into creating a new 'biomarker' that links deep learning with fMRI, PET, physical activity, education, and cardiovascular risk across two studies. This effort is impressive.

      Weaknesses:

      There are several weaknesses in the current methods and results, making many of the claims unconvincing. These weaknesses include:

      (1) The lack of baseline models to benchmark the predictive performance of their DenseNet models.

      (2) The inappropriate calculation of the brain cognition gap due to the lack of control for regression-toward-the-mean and the influence of the working memory itself (a common practice in brain age studies).

      (3) The lack of benchmarking of the brain cognition gap against the 'corrected' brain age gap and the direct prediction of physical activity, education, and cardiovascular risk.

      (4) Minimal justification for their PET mediation analysis.

      We appreciate the reviewer’s constructive comments on the strengths and weaknesses of our study. In this revised version, we’ve addressed the concerns regarding the calculation of the brain-cognitive gap, clarified the unique variance that the brain-cognitive gap contributes beyond cognition itself, and provided additional justification for the PET mediation analysis. For the lack of a baseline model, it is important to highlight that our aim has never been to compare the predictive power of different deep learning or machine learning approaches. Therefore, the text in the introduction and discussion has been amended to avoid miscommunication on this topic.

      Regarding the impact of the work on the field and the utility of the methods and data to the community, I see its potential. However, addressing all the weaknesses listed above is crucial and likely to change the conclusions of the results.

      It is important to note that many statements in the manuscript are overstated, making the contribution of the manuscript seem exaggerated.

      We have run additional analysis based on the reviewer’s suggestions. The effect sizes and statistical values were adjusted due to the corrections; the overall conclusions remain largely consistent. The relationships between the brain-cognition gap and key factors such as physical activity, and cardiovascular risk persisted. We have updated the manuscript accordingly and revised the relevant sections to reflect these refinements and the resulting interpretations.

      For instance, the abstract claims "there is a lack of objective biomarkers to accurately predict cognitive function," and the discussion states, "across various studies, the correlation between predicted and actual fluid intelligence typically hovers around 0.25 (98-100)." However, a meta-analysis by Vieira and colleagues (2022 https://doi.org/10.1016/j.intell.2022.101654) found over 37 studies up to 2020 predicting cognitive abilities from fMRI with machine learning, with 24 studies published in 2019-20 alone. Since 2020, with the rise of machine learning and AI, even more studies have likely been published on this topic, all claiming to show objective biomarkers to accurately predict cognitive function. Vieira and colleagues also found an average performance of these objective biomarkers in predicting general cognition at r = .42, similar to what was found in this manuscript. Based on this alone, it is unclear how novel or superior their method is without a proper systematic benchmark.

      We appreciate the opportunity to clarify our study’s contribution relative to prior work. We have revised the introduction and discussion to highlight the contribution of other methods when it comes to biomarkers. As for the comment related to the work by Vieira and colleagues, Vieira et al. (2022) indeed present a comprehensive meta-analysis of studies predicting general and fluid intelligence using neuroimaging and machine learning. However, there are two critical differences between ours verus previous work:

      Target Cognitive Domains:

      Our study does not focus on general or fluid intelligence, but rather on comprehensive EM (3 tests) and WM (3 tests), two distinct cognitive domains that are critically important for aging research. These distinct abilities, in this context (measured by three independent tests to boost the reliability) are less frequently studied as predictive targets in the existing fMRI-ML literature, particularly using deep learning methods.

      Critically, our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.

      Our primary objective is to test how brain state influences the ability of functional connectivity to predict domain-specific cognitive performance, using a deep learning framework. As now stated explicitly in the revised manuscript, this objective is operationalized through three clearly defined aims:

      (1) To compare the predictive utility of functional connectomes derived from different brain states (resting state, movie watching, and n-back task) for EM and WM;

      (2) To introduce and evaluate a brain-cognition gap as a marker of individual differences beyond chronological age; and

      (3) To examine the contribution of dopaminergic integrity to variability in connectome uniqueness and brain-cognition gaps.

      We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework for some of the prediction models, we did not conduct a comprehensive benchmark across all available machine learning methods nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological/biomarker superiority beyond the scope of our analyses.

      Modeling Approach:

      While Vieira et al. show that the majority (76%) of prior studies used linear modeling approaches, including CPM and penalized regressions, these models are often vulnerable to overfitting, especially when applied to high-dimensional fMRI data. Our use of a DenseNet-based CNN architecture is motivated by the need to leverage inductive biases suited to functional connectivity data, and we evaluate this approach across multiple cognitive tasks and independent datasets.

      Vieira and colleagues report that studies predicting general intelligence from fMRI (particularly from the HCP dataset) average around r =0.42, while those predicting fluid intelligence average around r =0.15. Our original claim about the correlation hovering around 0.25 is therefore not incorrect – and aligns with the Vieira meta-analysis. We have, however, nuanced this statement in the manuscript, now stating that correlations are higher for general intelligence than fluid intelligence.

      Altogether, we considered the reviewer’s comments and therefore conducted a careful revision of the manuscript text to moderate and clarify statements that may have come across as overstated. We have refined the language throughout the Introduction and Discussion sections to better align with the strength of the evidence and the scope of our contributions. A few examples are:

      “Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      Also in page 14.

      “Our study introduces a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30).”

      Similarly, the authors claim superior performance of deep learning and mischaracterize machine learning algorithms: "In particular, deep neural networks (DNN) methods have been successfully applied to behavioral and disease prediction (24-26), and have been found to outperform other machine learning approaches (27-29)," and "Deep learning approaches overcome the limitation of predictive techniques that solely rely on linear associations between connectivity and behavioral phenotypes (17)." However, the superiority of deep learning is debatable. Studies show comparable performance between machine learning (such as kernel regression) and deep learning (such as fully-connected neural networks, BrainNetCNN, Graph CNN (GCNN), and temporal CNN), e.g., He and colleagues (2019) and Vieira and colleagues (2024) https://doi.org/10.1016/j.neuroimage.2019.116276 and Vieira and colleagues' https://doi.org/10.1101/2024.03.07.583858.

      We agree that the performance gap between traditional machine learning models and deep learning (which is a subcategory of machine learning) in neuroimaging is debatable and task-dependent. Indeed, both He et al. (2019) and Vieira et al. (2024) offer evidence that kernel regression can achieve performance on par with deep learning models, applied to appropriate datasets.

      We have therefore nuanced the statements in the revised version of the manuscript as follows:

      Introduction:

      “In particular, deep neural networks (DNN) methods have been successfully applied to behavioral and disease prediction (24-26), and were initially expected to outperform other machine learning approaches (27-29). However, this superiority remains debatable, as recent studies have reported comparable performance between DNNs and traditional methods (He et al.,2019; Vieira et al.,2024). Accordingly, the present study does not aim to benchmark deep learning against traditional machine learning approaches, but instead uses a consistent predictive framework to examine how brain state influences the utility of FC for cognitive prediction.”

      “Deep learning approaches offer a flexible modeling framework capable of capturing complex non-linear associations in high-dimensional data with potentially less sensitivity to training on a smaller subsample (Vieira et al., 2024)”.

      Discussion:

      We agree that traditional methods, such as kernel-based models, tree ensembles, and non-linear SVRs, can also effectively capture such relationships. The relative performance of our model and other non-linear approaches depends on several factors, including data size, model architecture, and domain-specific considerations. We have included additional explanations in the discussion to address this.

      Moreover, many non-deep learning predictive techniques are non-linear, e.g., XGBoost, CatBoost, random forest, kernel ridge, and support vector regression with non-linear kernels (such as RBF and polynomial). Thus, stating that machine learning can only model linear relationships is incorrect. Moreover, for the small amount of data the authors had, some might argue that a linear algorithm might be more appropriate to balance the bias-variance trade-off in prediction. Again, without a proper systematic benchmark, it is unclear how well their DenseNet algorithm performs compared to other algorithms.

      Thank you for bring this up. We have now removed statements implying that machine learning can only model linear relationship.

      Regarding the Brain Age literature, the authors also misinterpreted recent findings: "However, a recent study suggests that brain age predictions contribute minimally compared to chronological age for explaining cognitive decline (65), implying that cognitive predictions are more reliable." In this study, Tetereva and colleagues (2024) (https://doi.org/10.7554/eLife.87297.4) showed that non-deep-learning machine learning can make good predictions from MRI on both chronological age (with r up to .88) and fluid cognition (with r up to .627). Using the combination of functional connectivity matrices across rest and tasks to predict fluid cognition, they found performance at r = .565, comparable to what was found in the current manuscript with deep learning. Nonetheless, while brain age predicted chronological age well (and brain cognition predicted fluid cognition well), it was problematic to predict fluid cognition from brain age. They showed that, because brain age, by design, shared so much common variance with chronological age, brain age and chronological age captured the same variance of fluid cognition. When chronological age was controlled for in the prediction of fluid cognition, brain age no longer had high predictive ability. In the case of the current manuscript, the brain cognition gap is not appropriately controlled for cognition (to be more precise, a working memory score). I expect the performance in predicting physical activity, education, and cardiovascular risk will drop dramatically once cognition is controlled for. There are at least two ways to control cognition according to Tetereva and colleagues' study (see more in the recommendations).

      We thank the reviewer for breaking down the findings in the study by Tetereva and colleagues (2024). It was not our intention to suggest that Tetereva et al. showed brain age has little predictive value in general. Our understanding of the findings reported in that study is on par with the reviewers’ clarifications. We have now revised the introductions to avoid any misunderstanding:

      “A recent study demonstrated that while brain age can predict chronological age with high accuracy from MRI, its utility for predicting cognition is limited. Specifically, Tetereva and colleagues (2024) showed that brain age strongly tracks chronological age and that brain cognition (using functional connectivity) can predict fluid cognition. Yet, when used to predict cognition, brain age largely overlapped with chronological age, such that controlling for chronological age eliminated the predictive contribution of brain age. This finding suggests that brain-age models may provide little unique explanatory power for cognitive decline beyond what is already captured by chronological age. Building on this observation and extending the concept of a brain-age gap to a brain-cognition gap (BCG, defined as the discrepancy between predicted and observed cognitive performance), we propose that a BCG may serve as an informative marker of individual differences.”

      In addition, in response to the first comment from Reviewer 1, we have extended our results in the manuscript. We first showed that BCG is not significantly associated with cognition itself (see Author response image 1). Moreover, we conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular risk scores. We found that no significant difference in physical activity (DyNAMiC: p =0.56, 95% CI: -14.99 – 8.13; COBRA: p =0.29, 95% CI: -3.54 – 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, 95% CI: -1.08 – 10.72; COBRA: p =0.41, 95% CI: -1.86 – 4.58) between high and low EM performers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCP provides unique information, beyond cognitive measures, regarding factors that contribute to cognitive resilience. This text has been added into the result section, and Figure 3 has been updated in the manuscript.

      The authors mentioned, "The third aim of the current study is to uncover the contribution of dopamine (DA) integrity to brain-cognition gaps." However, I fail to see how mediation analysis would test this. The authors also mentioned, "Insufficient DA modulation can affect neurocognitive functions detrimentally (69, 74, 76-78)." They should test if DA levels are related to working memory scores in their study, and if so, whether the relationship is mediated by the "corrected" brain-cognition gaps. Note see more on the recommendation for the calculation of the "corrected" brain-cognition gaps.

      Our mediation was not designed to test whether DA predicts episodic memory performance directly, nor whether BCG mediates such a relationship. Instead, we specifically investigated whether the effect of DA on BCG operates through functional variability, the theoretical framework emphasizing the role of DA on neuronal grain and signal-to-noise ratio (see our recent work in Korkki et al., 2025). We agree that future work could extend our approach by directly examining whether BCG mediates the link between DA and cognitive outcomes. However, in the present study, our primary focus was on testing the mechanistic pathway of DA → entropy → BCG.

      In line with this aim, we found that lower DA receptor availability was associated with larger BCGs (Figure 4). We then asked whether this relationship is mediated by functional signal variability, such that lower DA is linked to reduced signal-to-noise ratio (i.e., greater entropy), which in turn contributes to less reliable prediction of cognition and, consequently, larger BCGs. Our mediation analysis supports this pathway (please see also our reply to Reviewer 1, Comment 6).

      Reviewer #3 (Public review):

      Summary:

      This paper by Esmaeili and co-authors presents a connectome prediction study to predict episodic memory and relate prediction errors to other phonotypic variables.

      Strengths:

      (1) A primary and external validation dataset.

      (2) Novel use of prediction errors (i.e., brain-cognitive gap).

      (3) A wide range of data was investigated.

      Weaknesses:

      (1) Lack of comparisons to other methods for prediction.

      (2) Several different points are being investigated that don't allow any particular one to shine through.

      (3) Some choices of analysis are not well-motivated.

      (4) How do the n-back connectomes perform for prediction if the authors do not regress task activations from the n-back task?

      We thank the reviewer for raising these important points. For the lack of comparisons to other methods, it is important to highlight that our aim has never been to compare the predictive power of different deep learning or machine learning approaches. Rather, our primary objective was to test how brain state influences the ability of functional connectivity to predict domain-specific cognitive performance, using a deep learning framework.Therefore, the text in the introduction and discussion has been amended to avoid miscommunication on this topic.

      We chose to regress out task-evoked activations based on prior work demonstrating that failing to do so can produce spurious but systematic inflation of task functional connectivity estimates (Cole et al., 2019). In that study, as well as subsequent reports (e.g., Gao et al., 2020; Gonzalez-Castillo & Bandettini, 2018), connectomes derived without activation regression tended to capture task-evoked coactivations rather than background task functional interactions, which can artificially boost predictive performance but limit interpretability (whether it is co-activation or intrinsic connectivity during an entire goal-oriented task) and generalizability. For this reason, our analyses focused on the more conservative approach of regressing out task activations. Accordingly, we compared predictive performance only under this preprocessing strategy.

      We have added the following sentence to clarify this in the method: “To avoid spurious inflation of task functional connectivity by task-evoked activations, we regressed out task activation patterns from the n-back data prior to estimating functional connectivity, following recommendations by Cole et al. (2019) and related work.”

      (5) I am a little concerned about overfitting with the convolutional neural net. For example, the drop-off in prediction performance in the external sample is stark. How does the deep learning approach used here compare to something simpler, like a connectome-based predictive model or ridge regression?

      (6) It may be nice to try the other models in the validation dataset. This would also provide a sense of the overfitting that may be going on with overfitting.

      We thank the reviewer for raising this point. The prediction performance indeed dropped for episodic memory when models trained on the DyNAMiC sample were applied to the COBRA sample, whereas performance for working memory remained nearly identical across datasets. Moreover, our prediction power is on par with previous studies reporting reliable prediction of intelligence using deep learning approach (Vieira et al., 2021; Fan et al.,2020). While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods nor was this the aim of the present study.

      We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. Finally, We have added the following paragraph to the discussion:

      “Our study used a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30). Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back) to identify the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      (7) While predictive models increase the power over association studies, they still require large samples to prevent overfitting. Do the authors have a sense of the power their main and external validation sample sizes provide?

      We thank the reviewer for this important point. Our main sample size, together with the external validation in COBRA, is moderate for deep learning applications. To reduce the risk of overfitting, we employed several strategies, including external validation, early stopping, dropout, and regularization. As noted, performance for episodic memory decreased in the external sample, which we acknowledge, but key associations such as the link between BCG and resilient factors remained significant. Importantly, prediction of working memory was maintained across datasets, reducing the likelihood that the observed findings are driven by overfitting. We have added a statement in the Discussion to reflect on the limitations of sample size and the implications for generalizability.

      We added the following sentence to the discussion:

      “We acknowledge that our main and validation samples are moderate in size for deep learning, which constrains statistical power and generalizability. Although external validation, early stopping, dropout, and regularization help mitigate overfitting, larger samples will be needed in future work to fully establish the robustness of these predictive models.”

      (8) I am not sure that the Mann-Whitney is the correct test for comparing the distributions of prediction performances. The distributions are dependent on each other as they are each predicting the same outcomes. Using the typical degrees of freedom formula would overestimate the degrees of freedom.

      We appreciate the reviewer’s comment and agree that applying statistical tests directly to bootstrapped samples can lead to inflated or misleading p-values, as the degrees of freedom are determined by the number of bootstrap iterations rather than the actual number of independent observations.

      In our analysis, the Mann-Whitney U test was applied to 1000 bootstrapped correlation coefficients (r) for each model. While this number is relatively low and was chosen to limit overestimation of significance, we recognize that these bootstrapped samples are not independent, and thus the use of a Mann-Whitney U test can still be problematic. To address this concern, we have revised our statistical analysis. Rather than applying the Mann-Whitney U test to the bootstrapped r distributions, we now compute the difference in correlation coefficients (Δ r = r<sub>actual</sub> − r<sub>rest</sub>) for each bootstrap iteration. We then calculate a 95% confidence interval for Δr. If this interval does not include zero, we consider the difference statistically significant. This approach avoids artificially inflating the sample size and adheres more closely to proper statistical inference.

      We have updated the Methods (the following text) and Results sections accordingly and clearly stated the limitations regarding the degrees of freedom for all tests.

      “For the bootstrap-based comparison of model performance (bootstrap resampling with 1000 iterations), no test statistic with an associated degree of freedom is reported. Instead, statistical inference is based on the bootstrap distribution of the difference in correlation coefficients (Δr) and its 95% confidence interval. As bootstrap confidence-interval–based inference does not rely on an analytic sampling distribution, degrees of freedom are not defined for this procedure.” This has now been explicitly stated in the Methods section to avoid ambiguity.

      In the result section, we have reported with corresponding CI.

      (9) The brain cognition gap is interesting. It is very similar conceptually to the brain age gap. When associating the brain age gap with other phenotypes, typically age is regressed from the brain age gap and the other phenotype. In other words, age is typically associated with a brain age gap as individuals at the tail ages often show the largest gaps. Is the brain cognition gap correlated with episodic memory and do the group differences hold if episodic memory is controlled for?

      We thank the reviewer’s comment regarding the relationship between the brain cognition gap and episodic memory.

      Since this question was raised by all reviewers, we have conducted additional analyses. We did find that BCG is independent from the cognitive measure and provided additional information, beyond cognition alone, about factors contributing to resilience. Please visit our response to the first comment of Reviewer 1.

      (10) I have the same question for the dopamine results. Particularly, in the correlations that are divided by brain cognition gap sign. I could see these types of patterns arise due to a correlation with a third variable.

      For dopamine results, we explored whether age or cognition alone might confound the dopamine–brain cognition gap relationships. However, neither was significantly correlated with the brain cognition gap groups. The associations remained significant after controlling for age, suggesting that the observed patterns are not likely due to these potential third-variable confounder. This is also inline with our observation of significant associations between DA and GAP in an age-homogeneous COBRA sample. That said, we found that entropy, indeed, mediates the direct link between DA and BAG, suggesting that individuals with lower DA exhibit greater regional variability, and in turn larger BCG.

      These results have now been embedded into the manuscript. We also highlighted that age has been controlled for in reported correlation and mediation analyses.

      Recommendations for the authors:

      Reviewing Editor Comment:

      We particularly recommend that the authors: (a) compare the performance of their deep learning model with other baseline models, and (b) adjust for cognitive performance within the brain-cognition gap. These steps would strengthen the evidence base.

      We thank the editor for their comments. As for the first comments, our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach. We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods, nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological superiority beyond the scope of our analyses. Finally, we have added the following paragraph to the discussion:

      “Our study used a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30).

      Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back) to identify the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      As for the second comment, we followed the instructions by Reviewer 1. In response to their request, we first examined the relationship between the Brain-Cognitive Gap (BCG) and the cognitive measure itself. Surprisingly, we did not find any significant relationship in either the DyNAMiC sample (r =0.01, p =0.939) or the COBRA sample (r =0.01, p =0.89) (see Author response image 1).

      We then conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular disease (CVD) risk scores. We found no significant difference in physical activity (DyNAMiC: p =0.56, 95% CI: –14.99 - 8.13; COBRA: p =0.29, 95% CI: –3.54 - 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, 95% CI: –1.08 - 10.72; COBRA: p =0.41, 95% CI: –1.86 - 4.58) between high and low EM perfprmers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCG provides unique information, beyond the observed cognitive measure (episodic memory score), regarding factors that contribute to cognitive resilience. These results have been added to Section 2.4, and Figure 3 has been updated.

      Reviewer #1 (Recommendations for the authors):

      (1) The top and bottom triangles of the saliency maps, particularly in Figure 2, do not look symmetrical (this is most notable in the hotspot representing the between-network correlation of DMN and FPN). What is going on here? Was the image compressed or altered in some way, or is this a visual artifact of the interpolation method?

      We appreciate the reviewer’s insightful comment. Minor differences in the saliency maps between the upper and lower triangles of the FC matrix can arise due to several factors. For instance, Grad-CAM generates saliency maps at the resolution of the convolutional feature maps, which are then upsampled to match the input matrix dimensions. We initially used the default bilinear interpolation, which may have introduced slight asymmetries or blurring, resulting in interpolation artifacts. In response, we have reprocessed the saliency maps using spline interpolation in MATLAB. The updated saliency figures have been included in the revised version of the manuscript.

      (2) Pages 11-12. Please make it explicit in the text that the brain gap-education association was not significant in the COBRA dataset.

      Thanks for pointing this out. We added the following sentence to the discussion.

      “Note that the association with education was significant only in the DyNAMiC sample and did not reach significance in the COBRA dataset.“

      (3) Please overlay individual data points onto the boxplots in Figure 3 so that we can appropriately evaluate the data distributions.

      Figure 3 has now been updated.

      (4) Section 2.6: Was entropy calculated on movie-watching data, resting data, or all fMRI data? Please specify.

      We thank the reviewer for pointing this out. We have updated the text (Section 2.6) to clarify that entropy was calculated from the resting-state data. We intended to examine the mediating role of regional variability in the relationship between dopamine and the BCG of the winning model for episodic memory. Because resting state and movie-watching were the winning conditions for EM prediction, but movie-watching was not available in COBRA, we focused on entropy during rest, which exists in both datasets.

      (5) Was entropy during the resting state correlated with entropy during the task state, across individuals?

      We agree this is an interesting question. However, investigating the correlation of entropy between rest and task states goes beyond the scope of the present study. Our aim here was to test whether regional variability mediates the effect of dopamine on the BCG. Specifically, we examined whether individuals with lower striatal D1DR show higher local variability, which in turn relates to less accurate prediction and a larger gap. We assessed both the relationship between D1DR and entropy and the association between entropy and the gap, and these results have now been added to the manuscript (see also our response to Reviewer 1’s public comment).

      Reviewer #2 (Recommendation for authors):

      (1) The lack of baseline models to benchmark the predictive performance of their DenseNet models makes their results hard to interpret. This problem is quite common across ML literature. For instance, many DL-based algorithms were developed for tabular data without proper benchmarking against other ML algorithms. When they were properly tested, most weren't better than many tree-based ML algorithms (e.g., https://proceedings.neurips.cc/paper_files/paper/2022/file/0378c7692da36807bdec87ab043cdadc-Paper-Datasets_and_Benchmarks.pdf). I can see that a similar problem might happen here.

      For this particular manuscript, the authors made strong statements without doing a proper benchmark, e.g., from the discussion, "Indeed, the predictive power in the current study is stronger than for CPM-based predictions reported before." And "Unlike the BrainNet convolutional neural network, which focuses on staged transformations, our densely connected model promotes extensive feature reuse, possibly leading to more robust feature extraction." I hope to see the performance of the proposed algorithm against 1) other DL algorithms (e.g., fully-connected neural networks, BrainNetCNN, Graph CNN (GCNN), temporal CNN, GRU, and LSTM, see https://doi.org/10.1016/j.neuroimage.2019.116276 and https://doi.org/10.1002/hbm.26415), 2) ML algorithms (e.g., SVR with linear, RBF and polynomial kernels, Elastic Net, XGBoost, random forest, CPM), 3) data reduction algorithms (e.g., PCA regression, Partial Least Square). The results of this benchmark will substantiate the claims made by the authors.

      Our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach. We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods, nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological superiority beyond the scope of our analyses. Finally, we have added the following paragraph to the discussion:

      “Our study used a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30). Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back) to identify the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      (2) From Figure 6b, it looks like the functional connectivity matrices were converted to different images, and each of the four images (in grey, blue, yellow, and red) was treated as a separate channel. What are these grey, blue, yellow, and red images?

      In our study, the inputs to the deep learning models were subject-specific FC matrices of size 273×273. To augment the data, we created different versions of each FC matrix by reordering specific brain networks within the matrix. To visualize that the inputs were augmented, we used different color codings (grey, blue, yellow, and red) in Figure 6b. These colors were intended solely to represent different augmented versions of the same subject’s FC matrix. They were not treated as separate channels in the model. To avoid any confusion or misinterpretation, we have revised this part of the figure and now use only grey coloring to represent the augmented FC matrices.

      (3) The differences in performance between within vs. outside studies might simply be due to the fact that the models trained from DyNAMiC captured the brain variation due to age, which is also related to cognitive abilities. I was wondering if age is controlled for, would performance be more similar across the studies? The authors should provide the performance of models that are controlled for age.

      We initially conducted partial correlation between FC features and cognitive measures while controlling for age. This is further supported by the fact that the model trained on the age-heterogeneous DyNAMiC sample provided a fairly reasonable prediction in the age-homogeneous COBRA dataset, particularly for working memory (see figure 2d). Moreover, in our post hoc analyses, we additionally controlled for age when examining associations, for example, between GAP and dopamine measures.

      (4) Related to point (3), from the discussion, "Validation outcomes thus affirm that the models, particularly those constructed from rest data, are robust to the particulars of the dataset." The performance dropped around half, so I am not sure if this conclusion is warranted.

      We thank the reviewer for raising this point. The prediction performance indeed dropped for episodic memory when models trained on the DyNAMiC sample were applied to the COBRA sample, whereas performance for working memory remained nearly identical across datasets. Although both EM and WM are sensitive to age, the divergence in cross-dataset performance suggests that factors beyond age alone may contribute to these differences. To address this, we have revised the discussion as follows:

      “Differences between the DyNAMiC and COBRA datasets make cross-dataset prediction a harder problem, as the age ranges of samples significantly vary, and prior studies highlight the importance of individual characteristics like age in predicting behavior from FC (33). In line with this, model performance decreased when predicting EM in the COBRA sample whereas prediction of WM remained largely unchanged. Thus, validation outcomes suggest that the models, particularly those predicting WM, show robustness across datasets, whereas the reduced EM performance highlights potential data-specific influences that limit generalizability.”

      (5) Please report the degree of freedom in all of the statistical analyses. Was the Mann-Whitney U test done on the bootstrapped r? If so, the degree of freedom was arbitrarily set by the number of bootstrapping, and hence the p-value can be higher or lower depending on the number of bootstrapping. This could lead to misleading conclusions.

      We appreciate the reviewer’s comment and agree that applying statistical tests directly to bootstrapped samples can lead to inflated or misleading p-values, as the degrees of freedom are determined by the number of bootstrap iterations rather than the actual number of independent observations.

      In our analysis, the Mann-Whitney U test was applied to 1000 bootstrapped correlation coefficients (r) for each model. While this number is relatively low and was chosen to limit overestimation of significance, we recognize that these bootstrapped samples are not independent, and thus the use of a Mann-Whitney U test can still be problematic. To address this concern, we have revised our statistical analysis. Rather than applying the Mann-Whitney U test to the bootstrapped r distributions, we now compute the difference in correlation coefficients (Δr = r<sub>actual</sub> − r<sub>rest</sub>) for each bootstrap iteration. We then calculate a 95% confidence interval for Δr. If this interval does not include zero, we consider the difference statistically significant. This approach avoids artificially inflating the sample size and adheres more closely to proper statistical inference.

      We have updated the Methods (the following text) and Results sections accordingly and clearly stated the limitations regarding the degrees of freedom for all tests.

      “For the bootstrap-based comparison of model performance (bootstrap resampling with 1000 iterations), no test statistic with an associated degree of freedom is reported. Instead, statistical inference is based on the bootstrap distribution of the difference in correlation coefficients (Δr) and its 95% confidence interval. As bootstrap confidence-interval–based inference does not rely on an analytic sampling distribution, degrees of freedom are not defined for this procedure.” This has now been explicitly stated in the Methods section to avoid ambiguity.

      In the result section, we have reported with corresponding CI.

      (6) For predictive performance, the correlation was reported in the table, while R<sup>2</sup> is reported in the text. This is confusing. Also, could you clarify if the R<sup>2</sup> is calculated using the sum square definition, not Pearson r squared? If Pearson r squared was used, then R<sup>2</sup> of a negative Pearson r would be positive, which is misleading (see 10.1001/jamapsychiatry.2019.3671). Also, other performance indices apart from Pearson r and R² should be reported (e.g., MSE and MAE, again see 10.1001/jamapsychiatry.2019.3671). This will allow a better understanding of the models' performance.

      We thank the reviewer for this helpful comment. We acknowledge the inconsistency in reporting predictive performance metrics and have revised the manuscript for clarity. In the text, we have reported the r value, whereas in the table, we have reported r<sup>2</sup> using the sum-of-squared definition. Specifically, we now consistently report Pearson correlation (r), mean squared error (MSE), and mean absolute error (MAE) across both the text and Tables 1 and 2.

      Regarding r<sup>2</sup>, we confirm that it was calculated using the sum-of-squares definition (i.e.,

      rather than as the square of the Pearson correlation coefficient. This ensures that negative correlations do not result in misleading positive R<sup>2</sup> values, as pointed out by the reviewer and discussed in Poldrack et al. (2020). All performance metrics (r, r<sup>2</sup>, MSE, and MAE) are now reported in Tables 1 and 2 to allow a more comprehensive and interpretable comparison of model performance.

      We have included a description of the method under section 4.9. Statistical significance analysis.

      (7) Could you clarify how data are standardized across training, validation, and tests (including Z-standardization for the cognitive tests)? This is to prevent data leakage.

      Thanks for the comments. We did standardization the cognitive test from both training and test, separately.

      We have added the following paragraph to the method section:

      “A composite score of performances across the three tests was calculated and used as the measure of the cognitive domain in question (i.e., episodic memory, working memory). For each of the three tests, scores were summarized across the total number of trials. The three resulting sum scores were z-standardized and averaged to form one composite score for each domain. The standardization has been carried out independently for the training (DyNAMiC) and test (COBRA) samples.”

      (8) There is really no ground truth to confirm that Grad-CAM provides actual feature importance used by the models. Perhaps the authors should compare that with Haufe transformation, which is commonly used in the predictive model for cognition (e.g., https://doi.org/10.1016/j.neuroimage.2021.118648 and https://doi.org/10.1016/j.neuroimage.2023.120115).

      We appreciate the reviewer’s comment and the suggested references. The Haufe transformation is primarily applied in traditional machine learning models, particularly in cognitive neuroscience, to interpret linear predictive models by mapping classifier weights back to the input space. However, its direct applicability to deep learning models, especially convolutional neural networks, remains an open research area with no widely established methodologies. Furthermore, the Haufe transformation does not provide feature importance in the same manner as Grad-CAM. Grad-CAM highlights spatial regions within an image that contribute to a model’s decision, making it particularly useful for interpreting convolutional networks in vision tasks. In contrast, the Haufe method offers a weight transformation that is more suited for understanding linear models and may not be as intuitive for feature attribution in complex hierarchical representations such as those learned by deep neural networks.

      While we acknowledge that Grad-CAM, like other interpretability methods, does not provide absolute ground truth validation for feature importance, it remains one of the most widely used and validated techniques for deep learning interpretability, particularly in medical imaging applications. Given its integration with frameworks such as Keras and TensorFlow and its ability to provide spatial attributions aligned with domain knowledge, we believe it is a suitable choice for our study. Future work may explore additional interpretability techniques, including adaptations of the Haufe transformation if applicable to deep learning architectures.

      We have added more details on Grad-CAM implementations in the Method.

      (9) Related to Grad-CAM, "These edges, indicated by a salience intensity of {greater than or equal to}.5, exert a significant influence on the model (Figure 1f)." What does 'significant' in this context mean? And how did the authors come up with the .5 threshold? Is it based on permutation or bootstrapping tests?

      We appreciate the reviewer’s comment and the opportunity to clarify our approach. In this context, the term "significant" refers to the regions' relative contribution to the model’s decision, as shown by the Grad-CAM saliency map. However, to avoid implying statistical testing, we will revise the term to "highly contributing."

      Regarding the 0.5 threshold, this value was selected empirically based on the normalized Grad-CAM activation values, where saliency scores range between 0 and 1. A threshold of 0.5 was used as a heuristic to highlight regions with relatively strong activation. However, this was not determined through statistical methods such as permutation or bootstrapping tests. We recognize the importance of rigorous threshold selection and will clarify this in the text. Future work could incorporate statistical methods to define thresholds more objectively.

      We have included the following text in the Method section:

      ”Grad-CAM saliency maps were interpreted qualitatively, with a heuristic threshold (≥ 0.5) applied to highlight regions with relatively higher contribution to the model’s predictions. These values do not reflect statistical significance and should therefore be interpreted descriptively.”

      (10) Still related to the saliency map, I believe the upper and lower triangles of the functional connectivity matrix are the same. If so, why are there some differences in saliency? While the difference is not prominent, this might affect the accuracy of Grad-CAM.

      Minor differences in the saliency maps between the upper and lower triangles of the FC matrix can arise due to several factors. For instance, Grad-CAM generates saliency maps at the resolution of the convolutional feature maps, which are then upsampled to match the input matrix dimensions. We initially used the default bilinear interpolation, which may have introduced slight asymmetries or blurring, resulting in interpolation artifacts. In response, we have reprocessed the saliency maps using spline interpolation in MATLAB. The updated saliency figures have been included in the revised version of the manuscript.

      (11) Why did the authors only report the cross-study for EM on rest, and for WM on n-back? This is a bit unexpected since COBRA has both rest and n-back. If there is no good justification, please report both.

      We focused on reporting cross-study results for EM using rest because rest was the winning condition for predicting EM in the DyNAMiC sample. Importantly, n-back did not significantly predict EM in DyNAMiC, and rest did not significantly predict WM. For this reason, we highlighted only the conditions that showed meaningful predictive power in the original analyses.

      (12) Are codes, trained models, and data available? To ensure transparency and reproducibility, I hope to see the code from preprocessing to modeling and statistical analyses.

      The analysis code is openly available on our GitHub page https://github.com/MorEsm/AI-based-Prediction-of-Cognitive-Function. Due to ethical considerations and GDPR restrictions in the European Union, we are not permitted to publicly share the raw data. However, we can provide detailed information about preprocessing steps and analysis pipelines to facilitate reproducibility.

      (13 &14) The authors did not appropriately control for regression-toward-the-mean and the influence of the working memory itself when calculating the brain cognition gap. This is commonly done to brain age (see https://doi.org/10.7554/eLife.87297.4https://doi.org/10.1002/hbm.25533https://doi.org/10.1016/j.nicl.2020.102229https://doi.org/10.3389/fnagi.2018.00317). Otherwise, the brain cognition gap still depends on the cognition/working memory score itself. Based on Tetereva et al., "If, for instance, Brain Age was based on prediction models with poor performance and made a prediction that everyone was 50 years old, individual differences in Brain Age Gap would then depend solely on chronological age (i.e., 50 minus chronological age)." Because of this, Tetereva and colleagues found that the 'uncorrected' brain age gap that predicted chronological age the worst became the best index to predict fluid cognitive abilities. This shows the pitfall of the 'uncorrected' brain age gap. You can apply the same logic to the brain cognition gap.

      (14) Additionally, another way to show the unique contribution of brain cognition, over and above cognition per se, is to add both brain cognition and cognition together to predict physical activity, education, and cardiovascular risk.

      We thank the Reviewer for raising this important point. In response to their request and also the request from Rev. 1, we first examined the relationship between the Brain-Cognitive Gap (BCG) and the cognitive measure itself. Surprisingly, we did not find any significant relationship in either the DyNAMiC sample (r =0.01, p =0.939) or the COBRA sample (r =0.01, p =0.894) (see Author response image 1).

      We then conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular risk scores. We found that no significant difference in physical activity (DyNAMiC: p =0.56, CI: -14.99 – 8.13; COBRA: p =0.29, CI: -3.54 – 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, CI: -1.08 – 10.72; COBRA: p =0.41, CI: -1.86 – 4.58) between high and low EM perfprmers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCP provides unique information, beyond cognitive measure, regarding factors that contribute to cognitive resilience. These results have been added to Section 2.4, and Figure 3 has been updated.

      (15) Related to the brain age gap, the brain cognition gap is actually just another way to quantify how generalizable models are to another sample, similar to MAE or MSE. If the models built from DyNAMiC don't fit well with samples from COBRA, you will get a higher (i.e., wider) brain cognition gap, which means a poor fit. The authors should discuss this interpretation - should your biomarker's performance be due to a fit of the model?

      We appreciate this insightful comment. We agree that BCG can be interpreted not only as a marker of individual differences and resilience factors but also as a measure of model fit, analogous to error metrics, such as MAE or MSE. A higher gap may, in part, reflect poorer generalizability of models across samples. We have now revised the Discussion to explicitly acknowledge this alternative interpretation and to emphasize that BCG should be viewed both as a candidate biomarker and as a reflection of model performance.

      We added the following paragraph in the discussion:

      “An important caveat is that BCG can also be conceptualized as an error metric, similar to mean absolute error or mean square error, reflecting the extent to which models trained in one sample generalize to another. From this perspective, a larger gap may not only indicate individual differences related to resilience factors and dopaminergic function, but also reduced model fit or generalizability across datasets. Thus, BCG likely reflects a combination of meaningful biological variability and methodological variance.”

      (16) It is unclear why the authors binarized the brain cognition gap when predicting physical activity, education, and cardiovascular risk, and not doing so with the striatal D1DR. It is rarely a good idea to binarize a continuous variable (see 10.1136/bmj.332.7549.1080). In this case, people who had a bigger negative brain cognition gap were treated equally to people who had a smaller negative brain cognition gap. I also do not think it is necessary to separately analyze positive and negative gaps. Perhaps the authors should correlate the corrected brain cognition gap with physical activity, education, and cardiovascular risk and provide scatter plots and effect sizes.

      Following the reveiwer suggestion, we directly correlated BCG with physical activity and cardiovascular risk. Our results confirmed our initial analysis that individuals with a negative gap exhibited lower physical activity and higher Framingham CVD risk across both COBRA and DyNAMiC datasets. We have reported these results on page 10.

      Author response image 5.

      (17) Given that the motivation is to move away from brain age, the authors should benchmark the corrected brain cognition gap against the corrected brain age gap, as well as against the performance when directly predicting physical activity, education, and cardiovascular risk from the functional connectivity metrics.

      Author response image 6.

      We agree that benchmarking BCG against BAG in predicting lifestyle and vascular risk factors would be valuable. We have calculated adjusted BAG and related it to lifestyle and vascular risk factors. Interestingly, we did not find any significant association, suggesting that BCG might be more sensitive to cognitive resilience. However, this investigation was beyond the scope of the present study. Our aim was not to compare BCG with BAG, but rather to examine whether BCG provides information beyond cognition itself. We also note that introducing BAG would open a separate line of investigation, namely, which cognitive state (rest, movie-watching, n-back) best estimates biological age. While this is an interesting question in its own right, addressing it here would considerably broaden the scope and complexity of an already dense manuscript. To prevent misunderstanding, we have clarified this point in the Discussion and added a caveat noting that future work should explicitly benchmark these approaches. That said, if the Reviewer and/or the Editor incline to add these additional findings into the manuscript, we are open to doing so in a revision.

      We have added the following sentence to the Discussion.

      “While our focus was to investigate whether the brain–cognition gap provides information about factors contributing to cognitive resilience, we acknowledge that benchmarking BCG against the brain-age gap in predicting lifestyle and vascular risk factors would be valuable. However, addressing this question lies beyond the scope of the present study, and future work should systematically compare these approaches.”

      (18) Why was only the working memory score used to create brain cognition, and not episodic memory as well? Including both could provide a more comprehensive measure.

      We initially attempted to predict both episodic memory (EM) and working memory (WM). However, EM prediction was only reliable within and across samples for the resting state, whereas WM prediction generalized most strongly from the movie-watching condition. Because COBRA does not include a movie-watching paradigm, we could not evaluate WM prediction across datasets. For this reason, we focused on EM when examining the brain–cognition gap.

      (19) The PET mediation analysis seemed to come out of the blue. Is there existing literature showing the relationship between striatal D1DR and cognition? If so, did the authors find a similar relationship in the current data? I also suggest rewriting this section to strengthen the justification for the PET mediation analysis.

      We have previously conducted studies in which DA found to be associated with memory (Johansson et al., 2023, Nyberg et al., 2016).

      The third aim of our study was to examine whether DA integrity is implicated in brain–cognition gaps (BCG), which we propose as a marker of cognitive resilience. In line with this aim, we found that lower DA receptor availability was associated with larger BCGs (Figure 4). We then asked whether this relationship is mediated by functional signal variability, such that lower DA is linked to reduced signal-to-noise ratio (i.e., greater entropy in functional connectivity), which in turn contributes to less reliable prediction of cognition and, consequently, larger BCGs. Our mediation analysis supports this pathway (see also our reply to Reviewer 1, Comment 6).

      Thus, our mediation was not designed to test whether DA predicts episodic memory performance directly, nor whether BCG mediates such a relationship. Instead, we specifically investigated whether the effect of DA on BCG operates through functional variability. We agree that future work could extend our approach by directly examining whether BCG mediates the link between DA and cognitive outcomes. However, in the present study, our primary focus was on testing the mechanistic pathway of DA → entropy → BCG.

      Minor recommendations:

      (1) Task-based connections are not truly task-based, as they are around 70-80% related to the resting state, capturing non-task-specific functional connectivity. Task-based connections should refer to techniques that derive task-related connectivity, such as psychophysiological interaction and beta-series correlation. Perhaps use terms like "functional connectivity during tasks."

      Thank you. This has been corrected throughout the manuscript.

      (2) Are there really two studies? The same MRI was used with the same configurations, and participants were from the same city. The only difference is the age range. It may be more appropriate to refer to this as "across age groups" rather than "cross-datasets."

      Thank you for this comment. While the two samples share some similarities, there are also several marked differences beyond age range. For example, Movie-watching was administered in DyNAMiC but not collected in COBRA. The resting-state fMRI sequence was 12 minutes in DyNAMiC but only 6 minutes in COBRA. Moreover, DyNAMiC included dopamine D1-receptor PET, whereas COBRA assessed dopamine D2-receptor availability. Even the questionnaires used to measure physical activity differed between the two studies. Given these methodological and measurement differences, we believe that referring to them as “cross-datasets” rather than “across age groups” more accurately captures the distinction.

      (3) What kind of movie is "Cockpit"? Can you explain? Different movies may elicit different patterns of connectivity.

      We apologize for not providing information about the movie, which has been presented in our recent work (Johansson et al., 2023).

      The participants’ reactions to the content of the movie were not monitored, but the clips were selected to be as neutral in their content as possible. The content of the movie: Following his termination as a pilot and the end of his marriage, Valle embarks on a quest to secure new employment. Faced with desperation in the job market, he resorts to disguising himself as a woman with the intention of obtaining a position at a company specially seeking a female pilot.

      This information is added to the method section.

      “During the fMRI session, participants viewed a 12-minute segment from the Swedish comedy film Cockpit (2012). We did not monitor participants’ responses to the movie, and the chosen clips were selected to be relatively neutral in emotional content. The storyline follows Valle, a recently fired pilot whose marriage has ended, as he struggles to find new employment. In a desperate attempt to secure a job at an airline specifically recruiting a female pilot, he presents himself as a woman.”

      (4) There is a typo in the equation numbering (i.e., two equations are designated as #1).

      We have now corrected the typo.

      (5) From the discussion: "Importantly, this prediction generalizes across conditions." This is not surprising given the similarity between conditions, with around 70-80% variance.

      We agree with the reviewer that the high similarity of FC across states likely increases the chance of cross-condition generalizability. However, this generalization is not guaranteed for all models. For example, the model trained on FC during movie-watching successfully predicted episodic memory during rest, but it did not generalize to episodic memory during the n-back condition, although movie-watching and n-back FC patterns are themselves highly correlated. Thus, the observed generalization is meaningful in demonstrating that not all models transfer equally well across states.

      That said, we have added the following sentence to the Discussion:

      “Importantly, this prediction generalizes across conditions and datasets, suggesting that features derived from resting state FC serve as a relatively stable marker of individual differences in EM, though with reduced strength in COBRA. While such generalization is partly facilitated by the similarity of functional connectivity across states, it is not a trivial outcome. For instance, the model trained on movie-watching data generalized to EM prediction during rest but failed to do so for the n-back condition, even though movie-watching and n-back connectivity patterns are themselves highly correlated. This indicates that successful generalization depends not only on shared variance across states but also on the cognitive processes most relevant to the target behavior.”

      (6) It might be helpful to include some figures for the cognitive tasks used. The description is a bit hard to follow without visual aids.

      Thanks for the comment. We have had a figure describing this in the initial paper about DyNAMiC (Nordin et al., 2022). We have added the Supplementary Figure (Fig S3) in the manuscript.

      Fig S3. Overview of the cognitive tests included in the DyNAMiC study. Adopted from Nordin et al. with permission.

      (7) It may not be appropriate to use the term "cross-validation" here, as one dataset was used for testing and the other for training, but not vice versa (so no "cross" per se).

      We thank the reviewer for pointing this out. We agree that the term “cross-validation” is not precise in this context, since we trained the model in one dataset and tested it in another without performing the reverse. We have revised the manuscript to use the term “external validation” instead of “cross-validation” to more accurately describe our cross-dataset approach.

      (8) I don't have access to the supplementary materials or code/data, so all of the comments here are based on the main text.

      We have added the supplementary materials and inserted the GitHub link to the code.<br />

      Reviewer #3 (Recommendations for the authors):

      I suggest benchmarking against other simpler algorithms and controlling for memory in the brain cognition gap analyses.

      The authors might also want to simplify some aspects of the paper. There is a lot going on, which leaves less space to go into enough details for some analyses to warrant claims in the discussion. For example, the authors only compare the deep net to CPM and kernel ridge based on the literature. Direct comparisons would be needed.

      Thanks for the comment. We have made an attempt to address the concerns outlined in the public recommendation. Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach. We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods, nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological superiority beyond the scope of our analyses. Furthermore, we have controlled for memory as suggested by the reviewer and outlined in response to reviewer 1.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study used whole genome data to investigate Beefalo ancestry for the first time, filling the gap in the field of Beefalo ancestry. The authors used preserved semen samples to generate genomic data on 47 registered Beefalo and 3 bison hybrids, further questioning the ABA's stated goal of ⅜ bison ancestry. In addition, the authors also show that ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species, demonstrating the value of genomic information in examining gene flow between species in the genus Bison. This is an interesting study that still has some major weaknesses that exist, but overall, the work demonstrates the utility of genomic information in validating specific breeding claims for a more complete understanding of gene flow and genetic variation among bovine species.

      We thank the reviewer for their thoughtful assessment of our work.

      Strengths:

      Numerous genetic analysis methods such as PCA, ADMIXTURE, F4 ratios, and local ancestry inference techniques revealed that no single Beefalo set meets the ancestry requirements set by the American Beefalo Association (ABA) and some beefalo had detectable indicine cattle ancestry.

      Weaknesses:

      While this study contributes to our knowledge of Beefalo ancestry, there are some key issues that need to be addressed in terms of analysing the specific results as well as writing the article.

      We have followed the reviewer’s suggestions for improving our study in detail (specified below), and appreciate their close reading of the manuscript.

      Reviewer #2 (Public review):

      Summary:

      Shapiro et al. set out to verify the American Beefalo Association's claim that Beefalo cattle possess 37.5% bison ancestry. They employ a comprehensive range of well-established population genomics methods to estimate ancestry in these hybrid populations, including PCA, ADMIXTURE, D and F statistics, and local ancestry inference. Their findings conclusively demonstrate that most Beefalo lack the claimed bison ancestry, with only 8 out of 47 samples showing any detectable bison ancestry, ranging from 2 - 18%.

      We thank the reviewer for their thoughtful assessment of our work.

      Strengths:

      The primary strength of this analysis lies in the comprehensive dataset available to the authors, which includes important foundational Beefalo individuals and various reference populations. The rigorous and multi-faceted methodological approach employs several well-established techniques in population genomics for detecting and measuring admixture. Each method used has a firm basis in the field, providing consistent and robust results. The authors' approach of using PCA to initially assess the data within a global context, followed by more specific analyses using ADMIXTURE and D-statistics, provides a clear and logical progression of evidence. The presentation of these results in figures is particularly effective, clearly illustrating the key findings of the study. Additionally, the examination of both autosomal and sex chromosome ancestry offers a more complete understanding of Beefalo genetic composition and the mechanics of bison-cattle hybridisation.

      Weaknesses:

      One limitation of this analysis is the relatively low coverage (~2x) of many Beefalo samples. However, the authors have taken steps to mitigate biases that may arise from this. Another weakness is the limited sampling of contemporary Beefalo populations, as the study focuses primarily on historical samples. This may limit our understanding of how Beefalo genetics may have changed over time.

      The reviewer is correct that the low coverage obtained for many Beefalo is one potential limitation, although we believe that the downsampling experiment we performed (Fig. S4) shows that this level of coverage is appropriate for summarizing species-level ancestry across Bos, as the reviewer notes.

      Sampling contemporary Beefalo individuals would be valuable, though as the focus of our study was to understand the origins of bison ancestry in Beefalo, we prioritized sampling individuals which played an important role in establishing the breed. We also note that contemporary Beefalo breeding involves crossing between Beefalo individuals or backcrossing to cattle, with no additional bison ancestry input since the formation of the Beefalo. As such, sampling individuals that existed close to the breed’s founding should provide the most insight into bison ancestry in Beefalo.

      Appraisal:

      The authors have clearly achieved their primary aim using a rigorous and comprehensive methodology. Their extensive dataset and multi-faceted analytical approach provide strong support for their conclusions. The study not only addresses its main research question but also reveals unexpected insights into Beefalo genetics, particularly the presence of zebu ancestry.

      Discussion:

      This study is valuable for several reasons beyond its primary findings. First, it definitively addresses and refutes the claim of 37.5% bison ancestry in Beefalo, providing crucial information for those studying these interspecies hybrids and the viability of their offspring. Second, it reveals the unexpected presence of zebu ancestry in many Beefalo, raising intriguing questions about the breed's development and the potential role of zebu cattle in achieving desired traits. This finding suggests that the distinctive appearance of Beefalo may be due in part to zebu admixture rather than bison ancestry. Third, the study highlights the significant barriers to admixture between bison and cattle, both in controlled breeding programs and potentially in wild populations. This has important implications for conservation genetics and our understanding of gene flow between these species. Lastly, the study demonstrates the power of genomic analysis in verifying breed claims and understanding the complex history of domestic animal breeds. These findings open new avenues for research in bovine genomics, breed development, and the dynamics of interspecies hybridisation.

      Reviewer #3 (Public review):

      Summary:

      I really like this topic and study. But I think much can be more focused and tightened up. All the components are here - just some more refining to really make the storyline clear, the journey of discovery, and the impact of such knowledge.

      We thank the reviewer for their thoughtful assessment of our work.

      Strengths:

      The authors dive directly into the question of genomic ancestry as compared to the breed club's reported ancestry with heavy, quantitative data and critical analytical methods. The questioning line is direct and does not meander. The reader learns about the challenges of breeding associations, and values of understood ancestry, and presents a clear need of re-evaluating the breed standards and expectations of beefalo (if ancestry is indeed the primary goal instead of a phenotype-driven breed mission).

      Weaknesses:

      Much of the quantitative results are only referred to in the main text with qualitative language. Please incorporate more written quantitative results to highlight evidence that underlines the study narrative because it is quite an interesting study!

      The reviewer highlights an important point, and we agree that the qualitative language used to describe the results was generally lacking. We have now described the results quantitatively throughout the manuscript where possible.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) This study is not the first to question claims surrounding bison ancestry in the breed and is the sample size too small to be representative of the entire genetic structure of Beefalo?

      The reviewer correctly points out that this study is not the first to address uncertainty in the amount of bison ancestry present across beefalo. All earlier studies, to our knowledge, have been highlighted in the introduction and discussion (Lenoir and Lichtenberger, 1978 and Stormont et al, 1986). However, these studies examined a narrow range of Beefalo sources and used older methods (karyotyping and blood typing), such that comprehensive statements about the proportion of bison ancestry in Beefalo could not be made.

      We also agree that an appropriate sampling scheme is crucial for making definitive statements about Beefalo ancestry across the breed. As Beefalo breeding typically involves breeding select “full-blood” individuals with cattle, the ancestry across contemporary Beefalo is likely complex, with the cattle component coming from a wide range of breeds. Therefore, our sampling emphasized “full-blood” representatives, especially those that were involved in the founding of the breed and from which later Beefalo descend. This involved an exhaustive survey of the Beefalo individuals contained within the USDA’s National Animal Germplasm Program. Although we did not extensively evaluate current Beefalo diversity, we believe this approach is most suited for characterizing bison ancestry within Beefalo, as bison ancestry is maintained primarily through the continued use of genetic material from these “full-blood” individuals rather than repeated hybridization between bison and cattle.

      (2) Although genomic information is important for breeding research, this requires quality of data. The coverage of the data used in this study was mainly ~2X, and although multiple methods of analysis gave similar results, the ability to identify rare variants (e.g. insertions or deletions of long segments of the genome) may be limited at low coverage, affecting the confidence of the results.

      This is an important consideration, and we agree with the reviewer that the sequencing depth obtained for most individuals in our study precludes accurate genotype calling. Therefore, we did not attempt to perform traditional genotype calling. Rather, we used a pseudohaploid calling approach in which a random base was selected to represent the genotype at each position for each individual, using a pre-ascertained set of variants discovered in gaur, a closely related outgroup to bison and cattle. This pseudohaploid approach is common in other situations where coverage is low, for example in analyzing ancient DNA.

      Furthermore, our ancestry analyses focused on biallelic SNPs which were discovered in gaur and we did not attempt to call structural variants, given the limitations in coverage. As this outgroup ascertainment approach seeks to target SNPs which were polymorphic in the ancestor of both bison and cattle, which should yield unbiased results in population genetic analyses, we were less interested in discovering rare variation within the species and populations we examined here.

      Finally, we performed downsampling experiments comparing low coverage read data to genotypes called from high coverage data, and obtained consistent results between low and high coverage analyses using read-level data and called genotypes (Fig. S7).

      (3) Missing from the conclusions is the very important presentation of the results of genomic calling, the basics of what these data look like, coverage histograms, number of SNPs, categorization, annotations, and so on. These are necessary prerequisites for subsequent population analysis.

      The reference to “5.29M” on page 14 has been replaced with the exact number of SNPs used in analyses (5,291,534). The average sequencing depth for each sample is also included in Table S1.

      (4) The manuscript mentions "most" in a number of places, but can the authors give an accurate number based on the current data? "Most" is not a rigorous description. Based on the simulations of genomic data, how many Beefalo cattle were not detected as hybridized? This may be related to both sample size and where the authors sampled.

      We thank the reviewer for this important suggestion. We have now replaced vague summaries of results with precise numbers. However, we are unsure what “simulations” means in this context, as all results were obtained by analyzing empirical data from Beefalo, bison, cattle, and other bovines, rather than simulations.

      (5) The information in the third and fourth paragraphs of the Introduction is not sufficiently coherent and could be further consolidated into a more logical presentation.

      We have now condensed these paragraphs and edited them for clarity.

      (6) "For some analyses we also incorporated published genomes from outgroups". The description here is unclear as to what criteria were used to select these data, and it is possible that the choice of outgroups could lead to different conclusions from the analyses. In addition, ancient DNA data from cattle may be useful for this study and the authors are encouraged to consider it.

      Outgroup choice can certainly have a large impact on population genetic analyses. For the species examined in our study, we considered other Bos species, including yak, gaur, and banteng, as suitable outgroups, along with water buffalo, which is the closest outgroup outside of Bos. We have added comparisons of D-statistics using yak as an outgroup as a supplementary figure (Fig. S4), in addition to those using water buffalo as the outgroup which were presented in Figure 2.

      As we were examining species-level ancestry, and given the high level of divergence between bison and cattle, relative to that between published ancient and modern cattle genomes, we believed that it was most appropriate to use high quality modern cattle data, rather than poorer quality ancient cattle genomes, for analyses. Additionally, as any hybridization which took place between bison and cattle in the formation of Beefalo would have occurred within the past ~50 years, modern cattle are likely to be the most appropriate proxy for the cattle ancestry in Beefalo, especially given the lack of published historical North American cattle genomes.

      (7) The coordinates of the PCA plot need to be further supported by providing values.

      We have now updated axis labels for the PCA in Fig. 1A to include the proportion of variance explained for the first two components.

      (8) In Figure 1, Beefalo has one individual, NAGP9109, which belongs exclusively to the indicine group. For this individual, wouldn't it be nicer to label it separately in the PCA and ADMIXTURE plots, like Joe's Pride (JP), to make the presentation of the results clearer?

      This individual was one which was determined to be mislabeled as Beefalo within the NAGP and is actually a Brahman cattle. Therefore, we have relabeled it as zebu, rather than Beefalo, throughout the figures.

      (9) As the sex chromosome data do not fully support the authors' claims, some caution may be needed in describing the results.

      We interpret the sex chromosomal results as being fully consistent with patterns seen in the autosomes. However, they do shed some light on the dynamics of bison-cattle hybridization, and suggest male-mediated gene flow in which bison ancestry in Beefalo was introduced primarily through bison bulls.

      (10) Would it be appropriate to analyse the results at K = 3 only? The admixture analysis of all bison, cattle, bison hybrids, and buffalo individuals at different K values should further refine the results.

      We now also show ADMIXTURE results at K=2 and K=4 (Fig. S2) and present the cross-validation results from ADMIXTURE (Fig. S3).

      (11) The conclusions of this article about bison ancestry in Beefalo individuals are completely inconsistent with the American Beefalo Association, and should a description of possible reasons for this discrepancy be added to the discussion?

      Our analyses make it clear that there was much less hybridization between bison and cattle leading to the formation of the Beefalo that was previously believed. As the genetic data does not provide insight into exactly why this might be the case, we can only speculate on the precise reasons bison-cattle hybridization did not take place, which we have avoided here.

      Reviewer #2 (Recommendations for the authors):

      The manuscript is well written, the figures are easily understandable, and the claims made are justified by the results obtained.

      It is need to clarify cattle breeding terminology, particularly concerning breeds like the Brahman. While often described as zebu-taurine hybrids, Brahman cattle typically show over 90% zebu ancestry when analysed using ADMIXTURE against panels including European Bos taurus, African Bos taurus, and Bos indicus animals. This context would help explain why "NAGP9109" clusters with the Zebu group.

      We thank the reviewer for this useful context, and agree that most Brahman cattle have a high proportion of zebu ancestry. In fact, the zebu group we included primarily consists of Brahman individuals, which we have now clarified in the text, which now reads:

      “The reported pedigree in the NAGP for this animal lists its composition as 1/2 Brahman, 1/4 Charolais, 1/8 bison, 1/16th Hereford, and 1/16th Shorthorn, but the American Brahman Breeders Association records this animal (#309519) as purebred Brahman, which is a zebu breed (5 of the other 6 zebu individuals analyzed here are Brahman cattle).”

      I suggest three other improvements:

      (1) Standardise terminology: The manuscript alternates between "zebu" and "indicine" when referring to these cattle. While both terms are correctly defined in the introduction as "indicine (zebu; Bos indicus)" using one term consistently throughout would improve readability. I prefer "zebu" but leave this choice to the authors.

      We agree that this mixed terminology was confusing and have replaced all instances of “indicine” with “zebu.”

      (2) Add PCA metrics, including the percentage of variance explained by each principal component would demonstrate the genetic distinctiveness between bison and cattle, and between Taurus and zebu cattle. This would also support the selection of K=3 for the ADMIXTURE analysis.

      The axis labels for the PCA have been updated to include the proportion of variance explained for each component. We now also show ADMIXTURE results at K=2 and K=4 (Fig. S2) and present the cross-validation results from ADMIXTURE (Fig. S3).

      (3) Improve quantitative precision: The authors could improve precision by replacing qualitative statements with exact counts. For example "39 of 47 Beefalo showed no detectable bison ancestry." The same suggestion applies when describing how many Beefalo had zebu ancestry.

      We thank the reviewer for this useful suggestion, and agree that the manuscript used imprecise language in describing the results of certain analyses. We have now added quantitative detail throughout the Results section.

      Reviewer #3 (Recommendations for the authors):

      (1) Introduction

      The introduction sets a tone that is heavily focused on the genetic revelation that the economics of beefalo are somewhat of a facade. Beefalo are indeed not part-buffalo (bison). It is unclear to me if the introduction also could benefit from motivating this with more of a theoretical framework based on evolution, inheritance, or trait transmission. If this is really meant to be an economics-focused article, then lean more heavily into that. As it stands, it straddles a bit of economics, a bit of legacies that appear false (beefalo are not part bison at all!), and a bit of admixture genetics theory.

      We intended the focus of this study to be on documenting the species-level ancestry of Beefalo, and concentrated the information presented in the Introduction on this topic. Given that less hybridization between bison and cattle appears to have taken place to form the Beefalo breed than was previously described, we believe that broader theoretical statements about admixture are less relevant here, beyond highlighting examples of successful and failed interspecies hybridization in Bos. We also avoided speculating on the history of the establishment of the breed beyond what could be understood from the genetic data.

      Can the authors give a bit more details about beefalo breeding? Did the breeders select for any quantitative traits and is there a targeted phenotype for beefalo they used as a standard?

      Limited information exists about the precise origins of Beefalo, which were never publicly shared—possibly in part for reasons this manuscript addresses. The only criteria defining Beefalo is the proportion of bison ancestry, and so no quantitative traits or specific phenotypes are related to breed standard.

      Can the authors provide a few examples of what is known about the incompatibilities and reproductive challenges? What is known from past research or from the Beefalo Association documenting the breeding history?

      We provided a general summary of hybridization and incompatibility across Bos, but unfortunately cannot provide details about incompatibilities in Beefalo specifically. Though there is a long history of challenges interbreeding bison and cattle (referenced in the third paragraph of the Introduction), to our knowledge no examination has been carried out of Beefalo specifically and little is known about Beefalo pedigrees (again, perhaps for reasons related to information presented in this study).

      (2) Results Section Sequencing Beefalo genomes

      Please report the number of polymorphic sites to accompany the genomic read depth averages. It seems the authors could include a larger summary of the genomic data that was used for downstream analyses (like the PCA in the next section). Also, does this dataset include the sex chromosomes? How many variants that are retained for analyses are autosomal, sex-linked, or haploid? Please provide more characteristics of the data that was generated after QC and filtering.

      We have now replaced “5.29M” on page 14 with the exact number of SNPs (5,291,534) and added a description of genotype calling to the Results section. We have also included the number of SNPs used for sex chromosomal analyses.

      (3) Results section Estimating bison ancestry in beefalo

      What is a "foundational" individual? Is this a beefalo pedigree founder, a common sire, or an individual with remarkably high bison content? I see in the introduction Joe's Pride was the "most expensive cattle" but there are surely other aspects of "foundational" that the reader should understand as the results are presented.

      We agree that this terminology was imprecise, and have now clarified that we use foundational to mean an early individual that was important in the founding of the Beefalo breed, such as those that were first bred by Bud Basolo.

      For the sentence "The reported pedigree in the NAGP for this animal [NAGP9109] lists its composition as 1⁄2 Brahman, 1⁄4 Charolais, 1⁄8 bison, 1/16th Hereford, and 1/16th Shorthorn, but the American Brahman Breeders Association records this animal (#309519) as purebred Brahman.", this is difficult for a reader with limited cattle breed knowledge to infer significance of this. What is the origination of Brahman breed cattle? Does Brahman ancestry come from another mixed origin that could explain this discrepancy? Does the PCA have references to resolve the origin of Brahman? I realize this may sound extraneous but if membership to a breed that is recently formed from several other lineages or breeds, could you be seeing the deeper parts that compose Brahman cattle? How could one validate that the contributors erroneously labeled this individual as a beefalo?

      We have now noted that the Brahman breed has primarily zebu ancestry. The placement of this individual in the PCA supports the American Brahman Breeders Association metadata, and suggests that the NAGP labeling is incorrect:

      “The reported pedigree in the NAGP for this animal lists its composition as 1/2 Brahman, 1/4 Charolais, 1/8 bison, 1/16th Hereford, and 1/16th Shorthorn, but the American Brahman Breeders Association records this animal (#309519) as purebred Brahman, which is a zebu breed (5 of the other 6 zebu individuals analyzed here are Brahman cattle). We believe NAGP9109 was erroneously labeled as Beefalo by the contributors.”

      Figure 1A: Please add % explained by each PC.

      We have now updated axis labels for the PCA to include the proportion of variance explained for each component.

      Figures 1B and 1C are identical except for the Y axis. Please combine them into a graph with 2 Y-axes (one for PC1 and one for ADMIXTURE). Also, please include the bison in this panel as well.

      We have now updated these panels to include bison, although have kept the labeling so that they may be referenced separately in the text.

      I see that the authors did both unsupervised and supervised. Can the main text have the supervised graphical result instead of the unsurprised? That is more relevant for ancestry proportions via an assignment probability to ancestry groups. Or, if possible, could the authors consider STRUCTURE to also obtain the probability of assignment to a prior defied parental up to 2-generations back? This is by far the best way to leverage the ancestry information of the cattle and bison parental references in addition to the known F1/bison hybrids. Swap the Supplementary Figure 1 with Figure 1D!

      The supervised and unsupervised ADMIXTURE results are highly consistent, as could be expected given the high levels of divergence between species. We prefer to show the unsupervised results in the main text, as this makes the fewest assumptions about the ancestry of the examined individuals, and so also shows that the panels used to represent each species (taurine cattle, zebu cattle, and bison) do not contain individuals which were themselves highly admixed, which could have influenced the supervised ADMIXTURE analyses.

      For the unsupervised ADMIXTURE analyses, what were the cross-validation values per K value tested? How did the authors decide that K=3 was the best one to show?

      We now also show ADMIXTURE results at K=2 and K=4 (Fig. S2) and present the cross-validation results from ADMIXTURE (Fig. S3).

      Regarding "D-statistics ..... are consistent with 0 for most individual Beefalos....", I have two comments. First, by "consistent with", do you mean "are not significantly different from 0", indicating that (explain what this means in your words). Next, "most individual beefalos" means how many? Please provide numbers and values to highlight points or specific findings.

      The interpretation of the D-statistics has been clarified and Z-scores and numbers of individuals to quantitatively describe these results have been added. The text now reads:

      D-statistics of the form D (taurus, Beefalo; bison, water buffalo), which test whether Beefalo share more alleles with bison than taurine cattle, again show 39 Beefalo have no excess affinity with bison compared to taurine cattle (-13.04 < Z < 3.14), although the same eight Beefalo identified in PCA and ADMIXTURE as having bison ancestry also have an excess of bison alleles (6.16 < Z < 34.86), confirming their bison ancestry (Fig. 2A).”

      "In Beefalo with bison ancestry, that ancestry tends to be present in large contiguous blocks, often tens of megabases in size, indicative of recent admixture (Figure 3A, B)". Please display the quantitative results (mean, max, range, standard deviation, etc.) in the main text and point the reader to the table that contains the values for each individual. The rest of this paragraph also uses the words "most' or "always" - please provide numbers. Is most 30/46 beefalo? Is it always exactly all 47 beefalo? Readers want to see numbers!

      The reviewer is correct that this section lacked specificity. We have now provided the exact number of individuals identified with bison and zebu ancestry.

      The section starting "Several lines of evidence attest to the efficacy of using these source panels..." could realistically come first in the Results section and before beefalo results are presented. This would build confidence for the reader that this panel of samples passes a QC and will indeed be able to resolve ancestry-based questions.

      This section specifically refers to the local ancestry analyses, which we have now clarified in the text.

      Figure 3A-C: Please include on each of these figure panels the documented (breeder association) ancestry percentage and the percentage of bison ancestry you obtained from your genomic analyses. Moving it from the legend to the figure is more immediately powerful for the reader. If the authors dated the admixture events as well, please include the meta-data of the association pedigree reporting when bison entered the target individual's genome versus the genome-estimated number of generations since admixture.

      Figure 3 has now been updated to include the reported bison ancestry. No attempt was made to date the admixture event or compare with reported pedigrees, as documented Beefalo pedigrees are typically very sparse (and may be unreliable, as our results suggest).

      Figure 3 legend: Move the following text from the figure legend to the Results section: "Three bison hybrids are inferred to have ~75% bison ancestry, while eight Beefalo have detectable bison ancestry, ranging from 2-18%. Indicine ancestry is detected in most Beefalo at variable levels, ranging from 2-38%, with most Beefalo having between 2-18%.".

      This sentence has been removed from the legend and is now worked into the main text. The corresponding paragraph in the results now reads:

      “Local ancestry inference across individual Beefalo and bison-cattle hybrid genomes provides similar estimates of overall Beefalo ancestry, inferring an absence of bison ancestry across the 37 Beefalo that lacked evidence for such ancestry in previous analyses (Fig. 3). Three bison hybrids are inferred to have ~75% bison ancestry, while eight Beefalo have detectable bison ancestry, ranging from 2-18%. Zebu ancestry is detected in 38 Beefalo at variable levels, ranging from 2-38%, with all but two of Beefalo having between 2-18%.”

      (4) Results section Beefalo sex chromosome ancestry

      Check that the authors do not reference Figure 4B before Figure 4A.

      Thank you to the reviewer for noticing this, it has now been corrected.

      Figure 4A: Could this panel be considered to merge with the autosomal admixture plot? It helps with comparison. Not a firm request - but it is nice to see what is consistent versus what is discordant.

      To avoid cluttering the figure with two highly similar plots, we preferred to separate the autosomal and sex chromosomal results.

      Figure 4C: Could this panel be merged with the autosomal ancestry bar graph to help the reader with visual comparisons?

      We thank the reviewer for this suggestion, but do not understand exactly which figures they are suggesting to be merged.

      (5) Materials and Methods: Modeling Beefalo ancestry:

      The language used in this sentence "This approach allows for directly understanding the ancestry of Beefalo individuals relative to these three groups while mitigating the effects of the low sequencing depth obtained for many Beefalo." conflicts with a sentence later in this paragraph which called PCA a model-free analysis. Please correct.

      Unfortunately, we are unsure what the reviewer refers to here and believe that this sentence does not conflict with the characterization of PCA as a model-free analytical approach.

    1. Author response:

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

      Reviewer #1 (Public review):

      (1) The inferred relationships between neural clusters and specific drift‑diffusion parameters (e.g., bound height, scaling factor, non‑decision time) are intriguing but inherently correlational. The authors should clarify that these associations do not necessarily establish distinct computational mechanisms.

      We agree and have revised the text to avoid any mention of a causal relationship.

      (2) While the k‑means approach is well described, it remains somewhat heuristic. Including additional cross‑validation (e.g., cluster reproducibility across monkeys or sessions) would strengthen confidence in the four‑cluster interpretation.

      We took several steps to increase our confidence in the clustering results. First, we made improvements in how we used the k-means method, primarily by using activity vectors with finer time resolution and filtering out “outlier” neurons (details in Methods) that were dissimilar to other neurons to reduce spurious clustering results. Second, we performed a new set of clustering procedures based on the linkage method, in addition to the k-means method that we originally used. The two clustering methods generated very similar neuron groupings, with a Rand index of 0.93. We now present k-means results in the main figures and linkage results as supplements (e.g., compare Fig 5 and Fig 5-S2). Third, following the reviewer’s suggestion, we performed clustering based on the two monkeys’ data both combined and separately (new Fig 5-S3). Clustering of data from both monkeys combined, compared to each monkey considered separately, had rand index values of 0.94 and 1 for monkeys C and F, respectively (i.e., neurons from one monkey tended to be assigned to the same cluster regardless of whether the clustering was based on data from that monkey alone or both monkeys together), indicating comparable cluster boundaries for the two monkeys. Lastly, we performed clustering based on pseudo-vectors derived from sampling a subset of trials for each neuron and found that the clustering results were stable and robust based on as low as 40% of the trials (new Fig 5-S4).

      Because most neurons were recorded in separate sessions, we cannot perform session-based cross validation.

      (3) The functional dissociations across clusters are clearly described, but how these subgroups interact within the STN or through downstream basal‑ganglia circuits remains speculative.

      We agree and have made sure any speculative claims we make are clearly described as such.

      (4) A natural next step would be to construct a generative multi‑cluster model of STN activity, in which each cluster is treated as a computational node (e.g., evidence integrator, bound controller, urgency or evaluative signal).

      (5) Such a low‑dimensional, coupled model could reproduce the observed diversity of firing patterns and predict how interactions among clusters shape decision variables and behavior.

      (6) Population‑level modeling of this kind would move the interpretation beyond correlational mapping and serve as an intermediate framework between single‑unit analysis and in‑vivo perturbation.

      We agree that such a model would be extremely useful. However, given that designing, implementing, and testing a model like that would require a good deal of speculation about functional and anatomical interactions that we did not measure, it is also well outside the scope of the current study.

      That said, we appreciate the suggestions, which spurred us to go further in terms of providing a summary of our findings (new Figure 9) with a bit of informed speculation about how the different functionally defined subgroups of STN neurons that we characterized might relate to not only different computations but also different pathways through the basal ganglia (i.e., the hyperdirect versus indirect pathway, both of which include the STN). We hope that this summary, along with our more detailed findings, will inform new modeling studies by us and others.

      (7) Causal inference gap - Without perturbation data, it is difficult to determine whether the identified neural modulations are necessary or sufficient for the observed behavioral effects. A brief discussion of this limitation - and how future causal manipulations could test these cluster functions - would be valuable.

      As suggested, we have added the following to the Discussion (line 365): “The exact contributions of these subpopulations are challenging to elucidate, as their intermingled localization make common perturbation techniques, such as electrical microstimulation or optogenetic manipulations, not suitable. It would be interesting to examine if these subpopulations differ in molecular or connectivity properties (e.g., as we speculated above) that can be capitalized to precisely target each subpopulation.”

      Reviewer #1 (Recommendations for the authors):

      (1) Develop or outline a generative multi‑cluster model:

      Consider constructing, even at a conceptual level, a generative network model in which the identified STN clusters serve as interacting computational nodes (e.g., evidence integration, bound modulation, urgency, or evaluative nodes).

      Such a framework could reproduce the simultaneous presence of ramping, transient, and context-sensitive activity patterns observed across clusters.

      Even a simulated or schematic implementation - showing how parameter coupling among these clusters gives rise to the reported firing diversity and behavioral effects - would help clarify the mechanistic implications of your findings.

      As noted above, we believe that a full modeling study is well outside the scope of the present work. However, we have provided a conceptual framework, shown in Figure 9, summarizing our findings and providing some informed speculation about how different subgroups of STN neurons could provide different functions along distinct anatomical pathways.

      (2) Strengthen the link between cluster activity and computation:

      Use cross‑validated or hierarchical regression models to verify the robustness of correlations between cluster‑specific firing measures and fitted drift‑diffusion parameters. This would make the mapping between neural activity and model components more statistically grounded.

      We appreciate the suggestion and thought hard about how we might implement it but ultimately decided our approach is most appropriate, given the strengths and limitations of our dataset. The fundamental issue is that it takes many trials to obtain reliable estimates of DDM parameters. Our approach of creating twelve “pseudo-sessions” for each neuron (half of those for trials with high firing rates, half for trials with low firing rates) balances our ability to obtain those estimates while testing for relationships with firing rate. Any further subdivision of the data for cross validation yields unreliable parameter estimates (i.e., with big error bars). We also chose not to use a hierarchical model and instead took a more unbiased approach by considering how all of the DDM parameters relate to firing rate.

      Despite the simplicity of our approach, we believe that these results are statistically grounded. It is possible that more complex regression models may reveal additional (e.g., non-linear) relationships, but those results would also be less intuitive to interpret. We therefore decided to retain our analysis choice.

      (3) Assess cluster reproducibility:

      Report or include in the supplement the degree of correspondence of cluster identities across monkeys or across independent subsets of trials. Cluster stability metrics (e.g., bootstrap or split‑half analysis) would reassure readers that cluster structure is not dataset‑specific.

      Please see our response above to the main comment #2 regarding the robustness and stability of clustering results.

      (4) Explore population interactions directly:

      You could analyze pairwise or population‑level covariations (e.g., principal components or canonical correlation analysis) to test whether inter‑cluster interactions correspond to model‑predicted dynamics such as competition or normalization.

      Because most of the neurons were recorded in separate sessions and not simultaneously, the suggested population analyses are not feasible.

      Discuss briefly how the proposed generative or dynamical multi‑cluster model could be empirically tested-e.g., using selective perturbation (microstimulation, optogenetic, or pharmacological) in future studies-to evaluate interactions inferred from the current dataset. If feasible, mention how this framework might generalize to other decision contexts beyond oculomotor tasks, such as effort‑reward tradeoffs or inhibitory control, reinforcing the broad relevance of STN computations.

      As suggested, we have added the following to the Discussion (line 366): “The exact contributions of these subpopulations are challenging to elucidate, as their intermingled localization make common perturbation techniques, such as electrical microstimulation or optogenetic manipulations, not suitable. It would be interesting to examine if these subpopulations differ in molecular or connectivity properties (e.g., as we speculated above) that can be capitalized to precisely target each subpopulation.”

      Reviewer #2 (Public review):

      One criticism I would make is that the authors sometimes seem to assume that readers are familiar with their previous work. Indeed, the motivation and choices behind some analyses are not clearly explained. It might be interesting to provide a little more context and insight into these methodological choices. The same is true for the description of certain results, such as the behavioral results, which I find insufficiently detailed, especially since the two animals do not perform exactly the same way in the task.

      We apologize for the lack of detail regarding the behavioral results and analysis choices. To address this issue, we substantially revised the text, particularly in Results and Methods.

      The differences in behavior for the two monkeys were the subject of an entire published study (Fan Y, Gold JI, Ding L, 2018, Ongoing, rational calibration of reward-driven perceptual biases. Elife 7: e36018.). That study showed that these differences most likely arose from the monkeys’ individual sensitivity to the motion stimulus, combined with a heuristic-based strategy to gain satisficing rewards that they all seem to use. We revised the text to acknowledge the individual differences and refer readers to our previous study (line 78): “Both monkeys showed consistent biases toward the large-reward choice (Figure 1B, C). The individual differences in their choice and RT performance reflect individual differences in sensitivity to motion stimulus and a common heuristic-based satisficing strategy, as we demonstrated in a previous study (Fan et al., 2018).”

      Another criticism is the difficulty in following and absorbing all the presented results, given their heterogeneity. This heterogeneity stems from analytical choices that include defining multiple time windows over which activities are studied, multiple task-related or monkey behavioral factors that can influence them, multiple parameters underlying the decision-making phenomena to be captured, and all this without any a priori hypotheses. The overall impression is of an exploratory description that is sometimes difficult to digest, from which it is hard to extract precise information beyond the very general message that multiple subpopulations of neurons exist and therefore that the STN is probably involved in multiple roles during decision-making.

      In response to the three reviewers’ comments on data inclusion and the clustering analysis we presented, we have substantially improved the objectivity and robustness of our approaches, by: 1) applying a data-driven criterion for identifying neurons with robust task-relevant modulation (Figure 4C), 2) removing “outlier” neurons that appear not to share activity profiles with any other neurons in our sample (note that these outlier neurons would be at the outskirts in the cluster space instead of between clusters), 3) increasing the temporal resolution for generating firing rate vectors, and 4) comparing clustering results based on two methods (k-means and linkage). These improvements both sharpened the cluster boundaries and allowed us to observe more robust and distinctive subpopulation-specific relationships between neural activity and computational components in the DDM framework (new Figures 5–7 and their supplementary figures). We believe these updated results clearly demonstrate that: 1) there are different STN subpopulations, and 2) each of the subpopulations encodes a distinct set of functions.

      It would also have been interesting to have information regarding the location of the different identified subpopulations of neurons in the STN and their level of segregation within this nucleus. Indeed, since the STN is one of the preferred targets of electrical stimulation aimed at improving the condition of patients suffering from various neurological disorders, it would be interesting to know whether a particular stimulation location could preferentially affect a specific subpopulation of neurons, with the associated specific behavioral consequences.

      We have added a new Figure 8 to show the localization of neurons with and without task modulation and of neurons from different subpopulations. Consistent with our previous demonstration of intermingled distribution of STN subpopulations, we did not observe any activity pattern-based segregation.

      To relate the activity patterns to previously reported stimulation effects, we added the following to the Discussion (line 307): “This functional diversity, along with a lack of clear anatomical organization, is consistent with the multiple effects of STN stimulation in patient populations on decision-making and out previous results in monkeys, including reductions in response times, a weaker dependence on evidence, and changes in the maximal value and trajectories of the decision bound (Frank et al., 2007; Cavanagh et al., 2011; Coulthard et al., 2012; Green et al., 2013; Zavala et al., 2014; Herz et al., 2016; Pote et al., 2016; Branam et al., 2024).”

      Therefore, this paper is interesting because it complements other work from the same team and other studies that demonstrate the likely important role of the STN in decision-making. This will be of interest to the decision-making neuroscience community, but it may leave a sense of incompleteness due to the difficulty in connecting the conclusions of these different studies. For example, in the discussion section, the authors attempt to relate the different neuronal populations identified in their study and describe some relatively consistent results, but others less so.

      We hope that our revised Results and Discussion clarify the conclusions that can be drawn from this and other related studies.

      Reviewer #2 (Recommendations for the authors):

      (1) Introduction, l. 47-48: It would be interesting to provide more details on these three populations in order to better understand why we need additional experiments to more comprehensively define their roles.

      We now give more details in the Introduction about the remaining questions we aimed to address in this study (line 50): “However, the specific computational roles that these different subpopulations play in decision-making and other cognitive functions remain not well understood. For example, two of the subpopulation had overall activity patterns that were consistent with two different models in which the STN modulated the decision bound (Ratcliff and Frank, 2012; Wei et al., 2015), but the exact nature of this modulation is not known. The other subpopulation’s general activity patterns were consistent with a model of STN mediating evidence accumulation (Bogacz and Gurney, 2007), but it is unclear if and how this activity contributes to how evidence is weighed, biased, or accumulated.”

      Our previous attempt to distinguish these alternatives using electrical microstimulation was unsuccessful because that manipulation likely affected highly intermingled subpopulations with different functions.”

      (2) Results, l. 71-73: A slightly more detailed description of the behavioral results would be appreciated, especially since the two monkeys do not behave exactly the same way in the task, particularly in terms of reaction times (Figure 1B top-right versus bottom-right).

      We revised the text to acknowledge the individual differences and refer readers to our previous study (line 78): “Both monkeys showed consistent biases toward the large-reward choice (Figure 1B, C). The individual differences in their choice and RT performance reflect individual differences in sensitivity to motion stimulus and a common heuristic-based satisficing strategy, as we demonstrated in a previous study (Fan et al., 2018).”

      (3) Figure 2G-I: Were the multiple linear regressions performed only in the asymmetric reward condition?

      Yes. We added in Methods (line 487): “All analyses were performed on activity from the asymmetric-reward task.”

      (4) Very often in the text, the authors use terms that refer to concepts or methods that are difficult to grasp on the first reading, especially if we are not familiar with the team's previous publications. This is the case, for example, with "joint modulation," "reward context," "reward expectation," "k-means clustering," "tSNE," "Silhouette score for neurons," "Rand index," etc. All the explanations are minimal, and it would be helpful to clearly define these terms and provide some justification and insight to support the use of the analyses and the resulting variables, all of which would facilitate the reading of the manuscript.

      We now define these terms explicitly in the text (emphasis added here for clarity):

      (Results, line 129): “Using a previous definition of “joint modulation” (Doi et al., 2020), including modulation separately by motion coherence and reward context or reward size and modulation by the interaction of motion coherence and reward size, we found that ~40% of the neurons showed joint modulation during motion viewing.”

      (Results, line 71): “… for which we separately manipulated the noisy evidence (motion direction and strength) and reward context (a larger juice reward for a correct choice associated with one of the two directions).”

      (Results, line 250): “Choice accuracy describes the probability that a choice is correct given the evidence. Reward expectation describes the the expected reward given a choice.”

      (Methods, line 550): “To quantify the consistency between two runs of clustering, we computed the Rand index as the number of neuron pairs with consistent grouping (i.e., they were placed in the same cluster for both runs or they were placed in different clusters for both runs), normalized by the total number of possible neuron pairs. A value of 1 indicates that the two clustering runs produce identical results, and a value of 0 indicates that the two runs do not agree on any pairs of neurons.”

      To quantify the separation of clusters, we computed silhouette scores as the difference between mean intra-cluster distance and the mean nearest-cluster distance, normalized by the maximum of the two values. A positive score indicates that the member is closer to its same-cluster neighbors than different-cluster neighbors. Clustering runs with high mean silhouette score were considered to have better cluster separation.

      We no longer use tSNE visualization.

      (5) Figure 5A, caption: A quick description of the parameters would be useful.

      We added the description of DDM parameters in the caption of new Figure 4.

      (6) Results l. 222: Why does the analysis only concern epoch 5? I suggest justifying this choice. Also, the text indicates a "trend" but Figure 5C shows a significant result (p=0.0129).

      These statements have been removed from the updated manuscript.

      (7) Methods, l. 443: The authors should report more details about how they decided that neurons were task-related or not. "Visual inspection" sounds like a very vague and subjective criterion.

      We now apply a more objective criterion for identifying neurons with task-relevant modulation:

      (Results, line 145): “To focus on neurons with the most robust task-relevant activity, we measured firing rates during a baseline period (300 ms before motion onset) and sliding 100 ms windows from motion onset to 150 ms after saccade onset in 50 ms steps. We identified the maximal and minimal z-scores, representing the peak activation and suppression, respectively, for each neuron across all trial conditions (Figure 4C). We applied a threshold of z-score >1.5 for either activation or suppression and focused further analyses on the 87 neurons that met this selection criterion (n = 62 and 25 for monkeys C and F, respectively).”

      (8) A map of the location of the different STN neuron clusters found in this study within the structure would be very interesting.

      We have added a new Figure 8 to show the localization of neurons with/without task modulation and of neurons from different subpopulations.

      (9) Unless I am mistaken, there is no mention of data availability in this manuscript.

      The data availability statement was/is on the submission form.

      Data Availability: All electrophysiological data and the code for the analyses presented in the paper will be deposited in a publicly accessible domain when the paper is published.

      Previously Published Datasets: Source data for Figure 3-S2 in eLife paper:

      https://doi.org/10.7554/eLife.60535.: Fan, Doi, Gold, Ding, 2020,

      https://cdn.elifesciences.org/articles/60535/elife-60535-fig3-data1-v1.csv,

      https://cdn.elifesciences.org/articles/60535/elife-60535-fig3-data1-v1.csv

      Reviewer #3 (Public review):

      The primary weakness of the paper lies in the claim that STN contains multiple sub-populations with distinct involvements in decision making, which is inadequately supported by the paper's methods and analyses.

      First, while it is clear that the ~150 recorded neurons across 2 monkeys (91, 59 respectively) display substantial heterogeneity in their activity profiles across time and across stimulus/reward conditions, the claim of sub-populations largely rests on clustering a *subset of less than half the population - 66 neurons (48, 15 respectively) - chosen manually by visual inspection*. The full population seems to contain far more decision-modulated neurons, whose response profiles seem to interpolate between clusters. Moreover, it is unclear if the 4 clusters hold for each of the 2 monkeys, and the choice of 4-5 clusters does not seem well supported by metrics such as silhouette score, etc, that peak at 3 (1 or 2 were not attempted). From the data, it is easier to draw the conclusion that the STN population contains neurons with heterogeneous response profiles that smoothly vary in their tuning to different decision variables, rather than distinct sub-populations.

      In response to the three reviewers’ comments on data inclusion and the clustering analysis we presented, we have substantially improved the objectivity and robustness of our approaches, by: 1) applying a data-driven criterion for identifying neurons with robust task-relevant modulation (Figure 4C), 2) removing “outlier” neurons that appear not to share activity profiles with any other neurons in our sample (note that these outlier neurons would be at the outskirts in the cluster space instead of between clusters), 3) increasing the temporal resolution for generating firing rate vectors, and 4) comparing clustering results based on two methods (K-means and linkage). These improvements both sharpened the cluster boundaries and allowed us to observe more robust and distinctive subpopulation-specific relationships between neural activity and computational components in the DDM framework (new Figures 5–7 and their supplementary figures). We believe these updated results clearly demonstrate that: 1) there are different STN subpopulations, and 2) each of the subpopulations encodes a distinct set of functions.

      We performed additional analysis to assess the robustness of the clustering results. First, following the reviewer’s suggestion, we performed clustering based on the two monkeys’ data both combined and separately (new Fig 5-S3). Clustering of data from both monkeys combined compared to each monkey considered separately had rand index values of 0.94 and 1 for monkeys C and F, respectively (i.e., neurons from one monkey were assigned to the same cluster regardless of whether the clustering was based on data from that monkey alone or both monkeys together), indicating comparable cluster boundaries for the two monkeys. Second, we performed clustering based on pseudo-vectors derived from sampling a subset of trials for each neuron and found that the clustering results were stable and robust based on as low as 40% of the trials (new Fig 5-S4). Third, we generated a new figure (Figure 5-S1), using dendrograms to visualize how the neurons relate to each other. The dendrogram in Figure 5-S2 is more consistent with (at least) three distinct subpopulations of neurons than with the null hypothesis of a continuous distribution with smoothly-varying response profiles.

      Second, assuming the existence of sub-populations, it is unclear how their time- and condition-varying relationship with DDM parameters is to be interpreted. These relationships are inferred by splitting trials based on individual neurons' firing rates in different task epochs and reward contexts, and regressing onto the parameters of separate DDMs fit to those subsets of trials. The result is that different sub-populations show heterogeneous relationships to different DDM parameters over time - a result that, while interesting, leaves the computational involvement of these sub-populations/implementation of the decision process unclear.

      The improvements we made of the clustering procedure both sharpened the cluster boundaries and allowed us to observe more robust and distinctive subpopulation-specific relationships between neural activity and computational components in the DDM framework (new Figures 5-7 and their supplementary figures). These updated results demonstrate that: 1) there are different STN subpopulations, and 2) each of the subpopulations encodes a particular set of functions.

    1. Author response:

      eLife Assessment

      This valuable study raises the intriguing possibility that crickets use bat-associated odors as cues of predation risk, extending the classic bat-insect arms race beyond its usual acoustic framework. The authors combine fecal metabarcoding, behavioral assays, electrophysiology, chemical analyses, and field observations to show that Loxoblemmus equestris avoids the odor of the insectivorous bat Scotophilus kuhlii, and that synthetic (-)-limonene can elicit antennal responses, avoidance in the laboratory, and reduced calling activity in the field. However, the evidence is currently incomplete because the identity, biological source, natural concentration, and ecological specificity of limonene as a bat-derived predator cue require stronger support, including clearer quantification, contamination controls, individual-level odor data, and evidence that crickets can distinguish bat-associated limonene from common environmental sources. The work will be of interest to researchers in sensory ecology, chemical ecology, predator-prey interactions, and bat-insect coevolution.

      We thank the editors for recognizing the novelty and significance of our work.

      The central aim and contribution of this study is to provide direct evidence that an insect can detect a phylogenetically distant vertebrate predator, an insectivorous bat, via olfaction and initiate avoidance behavior. Our dietary analysis of bats and survey of potential prey in foraging habitats established a predator–prey relationship between the Asiatic lesser yellow house bat (Scotophilus kuhlii) and the cricket Loxoblemmus equestris. In addition, behavioral assays showed that the crickets strongly avoid air carrying bat body odor, and electrophysiological recordings using GC-EAD confirmed that volatiles from S. kuhlii body odor are detected by L. equestris antennae. Together, these results provide strong evidence that this insect can perceive and avoid the body odor of its predator, S. kuhlii. We are grateful that the editors and reviewers acknowledged the main conclusions.

      We also investigated the sources of bat body odor, its major volatile components, and the behavioral, physiological, and ecological responses of the crickets to limonene. The purpose of these studies was to test the hypothesis that elemental perception—detection of a single compound—could serve as a mechanism by which crickets perceive bat odor. We found that limonene was present in bat odor, elicited antennal responses in crickets, induced avoidance behavior in olfactometer assays, and reduced calling activity in the field. Together, these results support the idea that elemental perception is a plausible and efficient strategy for initiating anti-predator behavior against bats.

      We appreciate the editors’ constructive comments. The editors and Reviewer #1 suggested that limonene, as a bat-derived predator cue, requires more evidence, mainly for two reasons:

      (1) Limonene is common in plants but rare in mammals; the reviewer raised the possibility that the limonene identified in our study may have been introduced as exogenous contamination during handling.

      (2) The ability of crickets to distinguish bat-associated limonene from limonene originating from common environmental sources (e.g., plants) remains unclear.

      Below we address these points and describe the revisions we will make to strengthen the manuscript.

      On the potential contamination origin of limonene

      We agree that limonene is common in plants and human-associated products, and we carefully considered this possibility. However, several lines of evidence suggest that contamination is highly unlikely. First, we followed strict experimental protocols: all instruments were cleaned with ethanol and oven-dried before each use; bats were held in stainless-steel cages and cloth bags made of degreased bleached cotton washed with purified water. Second, limonene was not detected in any blank controls (empty-chamber air samples for whole-body odor collection, nor blank cotton swabs for secretion analysis), whereas it was consistently identified in multiple bat snout-secretion samples. Third, previous studies have independently reported limonene in the secretions of several bat species (Faulkes et al., 2019, PeerJ; Zhang et al., 2022, Ann. N.Y. Acad. Sci.). Moreover, recent work suggests that skin-associated microorganisms can contribute to bat volatile profiles (Sun et al., 2026, BMC Biology), and some microbes possess enzymes involved in limonene biosynthesis. Therefore, we are confident that the limonene we detected originates from the bats themselves (either endogenously or via their microbiota), not from exogenous contamination.

      On how crickets might distinguish bat-derived limonene from environmental sources

      This is an insightful question. As discussed in our original manuscript (Discussion section), crickets may not rely exclusively on limonene as a standalone cue. First, our GC-EAD analyses showed that cricket antennae respond to multiple bat volatiles beyond limonene, suggesting that additional compounds, either alone or in synergistic blends, may contribute to predator recognition. Elemental perception via (–)-limonene therefore likely represents one effective strategy within a broader olfactory toolkit, rather than the sole mechanism. Second, under natural conditions, crickets could also integrate olfactory information with non-chemical ecological signals, such as temporal patterning (bats are active at night) and spatial patterning (specific foraging habitats), to further reduce false alarms.

      However, fully testing these hypotheses would require substantial additional work. It would be necessary to quantify natural limonene concentrations in bat odors versus various plant sources, conduct choice experiments with ecologically relevant concentrations and blends, and perhaps manipulate the olfactory landscape in the field. It would also be necessary to examine how other volatile compounds in bat body odor interact with limonene, alone or together, to shape cricket recognition. After all, bat body odor contains dozens of compounds, and it is challenging to determine the necessity and sufficiency of each. These kinds of difficulties are not unique to our study; they are widespread in chemical ecology. Problems like how animals distinguish identical compounds from different biological sources are common in chemical ecology, and they are rarely solved in a single study. These lines of investigation, from quantifying natural concentrations to examining compound interactions, are important, but they are not the focus of the present study. So we have put this forward as an important direction for future research.

      Revisions we will make:

      (1) In the Methods section, we will add detailed descriptions of contamination controls and report blank-control results to demonstrate that exogenous contamination is very unlikely.

      (2) In the Discussion section, we will expand the discussion of the possible biological sources of limonene (including microbiota) in light of our results and the literature.

      (3) In the Discussion and Conclusion, we will state more cautiously the role of limonene as a bat-derived cue, acknowledging that while it is sufficient to trigger avoidance, additional work is needed to establish its ecological specificity.

      We believe these revisions will address the editors’ and the reviewers’ concerns while preserving the main conclusion that olfaction can mediate bat detection by crickets.

      Reviewer #1 (Public review):

      The manuscript examines whether insects can use bat odor as a cue of predation risk. The authors focus on the insectivorous bat Scotophilus kuhlii and the cricket Loxoblemmus equestris. They first use fecal DNA metabarcoding to show that crickets are part of the bat's diet, and field surveys to show that L. equestris is abundant at local foraging sites. In laboratory Y-tube assays, the authors show that crickets strongly avoid air carrying bat body odor. Gas chromatography coupled with electroantennographic detection showed that cricket antennae respond to components of bat odor. Chemical analyses identified several volatile compounds, with 2,2-dimethylheptane and (−)-limonene associated with antennal responses. Further analyses suggested that snout secretions are likely to contribute to the bat's body odor. The authors then tested individual compounds. Among the commercially available candidates, (−)-limonene elicited a strong antennal response and was sufficient to cause avoidance in the olfactometer. In field plots, spraying (−)-limonene reduced cricket calling activity relative to pre-exposure levels, whereas calling increased in control plots treated with hexane. Overall, the study argues that crickets can detect a vertebrate predator through olfactory cues and that a single bat-associated volatile can trigger antipredator behavior.

      This is an interesting and enjoyable study that addresses an understudied aspect of predator-prey interactions. The manuscript is clearly written, the experiments are presented in a logical sequence, and the figures are crisp and easy to follow. I really appreciated the combination of behavioral assays, electrophysiology, chemical analysis, and field observations.

      My main issue concerns the identity and biological origin of the proposed bat odor cue, (−)-limonene. Limonene seems like an unusual compound to be emitted endogenously by a mammal, particularly by an insectivorous bat. It would be helpful if the authors could clarify whether mammals are known to synthesize this compound de novo, and, if not, what the likely source of this plant-associated terpene would be in S. kuhlii. Possible sources could include environmental exposure, diet, roosting material, handling, or temporary housing conditions.

      I do not doubt that crickets avoid synthetic (−)-limonene. Indeed, this result is quite plausible given that limonene is widely used in insect repellent or repellent-associated fragrance products. However, this also makes contamination an important issue to address explicitly. How did the authors exclude the possibility that limonene entered the samples from human-associated sources, such as insect repellents, soaps, cleaning products, field equipment, cloth bags, cages, gloves, or other materials used while handling wild-caught bats? It would strengthen the manuscript to report limonene levels for individual bat odor collections, all relevant blanks, and any handling or housing controls.

      More broadly, given the common occurrence of limonene in plants and human-associated products, I am not yet convinced that it would function as a reliable "keystone kairomone" as suggested around line 253. How would crickets distinguish bat-associated limonene from limonene emitted by a mint leaf, citrus peel, pine material, or other non-threatening environmental sources? The authors may wish to soften this interpretation or provide additional evidence that crickets respond to limonene in a bat-specific context, perhaps through concentration, temporal patterning, co-occurring volatiles, or enantiomeric composition.

      We thank Reviewer #1 for the positive evaluation and for recognizing the study as “interesting and enjoyable.” We greatly appreciate the endorsement of our integrative approach combining behavioral assays, electrophysiology, chemical analysis, and field observations. The core conclusion that crickets can detect and avoid bats via olfaction is well supported by our data, and we are pleased that the reviewer has recognized this central finding.

      We are grateful for the reviewer’s constructive comments on the biological source and ecological specificity of limonene. In our response to the editor above, we have already responded to both aspects in detail; here we will briefly restate the key points.

      On the biological origin of limonene and potential contamination

      We agree that limonene is common in plants and human-made products, but relatively unusual for a mammal to emit endogenously. We have carefully examined the possibility of contamination and believe it is highly unlikely for the following reasons:

      (1) Strict experimental protocols: All experiments were conducted in a dedicated space. Instruments were cleaned with ethanol and oven-dried before and after each use. Cloth bags used to hold bats were made of degreased bleached cotton and washed with purified water; holding cages were stainless steel.

      (2) Blank controls: Limonene was not detected in any blank control samples, neither in the empty-chamber air controls for whole-body odor collection nor in the blank cotton swabs used for secretion analysis. In contrast, limonene was consistently identified in multiple bat snout-secretion samples.

      (3) Independent reports: Limonene has been previously identified in the secretions of several bat species (Faulkes et al., 2019, PeerJ; Zhang et al., 2022, Ann. N.Y. Acad. Sci.), indicating that its presence is not unique to our study or handling conditions.

      (4) Potential microbial origin: Even if bats do not synthesize limonene de novo (a capacity for which there is currently no evidence), recent work shows that skin-associated microorganisms can substantially shape bat volatile odors (Sun et al., 2026, BMC Biology). Some of these microbes possess enzymes involved in limonene biosynthesis, making bat-associated microbiota a plausible biological source of this compound.

      (5) Thus, the limonene we detected is highly likely to originate from the bats themselves (directly or via their microbes) rather than from contamination.

      On how crickets distinguish bat-associated limonene from environmental sources

      This is an excellent and important question. As we briefly discussed in the original manuscript, crickets may not rely exclusively on limonene as a bat-specific cue. Under natural field conditions, they could integrate olfactory information with other ecological cues, for example, temporal and spatial patterning (bats are active at night in specific foraging habitats), co-occurrence with other bat-specific volatiles (the full odor blend contains many compounds), or even concentration thresholds that differ between bat emissions and plant sources. We hypothesize that such context-specific integration could minimize false alarms.

      However, we also recognize that fully testing these hypotheses would require substantial additional work: quantify natural limonene concentrations in bat odors versus various plant sources, conduct choice experiments with ecologically relevant concentrations and blends, and perhaps manipulate the olfactory landscape in the field. These are important questions, but they are not the central focus of the present study, whose primary aim is to provide evidence that olfaction—and elemental perception of a single compound—can function in this predator-prey system. We have therefore framed this as an important direction for future research.

      Revisions we will make:

      (1) In the Methods section, we will add detailed descriptions of contamination controls and present blank-control results to demonstrate that exogenous contamination is very unlikely.

      (2) In the Discussion section, we will expand the discussion of limonene’s biological sources (including microbial contributions) and explicitly acknowledge the need for future work on how crickets might discriminate bat-derived from plant-derived limonene.

      (3) In the Conclusion, we will more cautiously characterize limonene’s ecological role, emphasizing that it is sufficient to trigger avoidance but that its natural specificity requires further investigation.

      We thank the reviewer again for these insightful comments, which will help us improve the manuscript.

      Reviewer #2 (Public review):

      Summary:

      Many insects possess extremely sensitive olfactory systems that can detect chemical signals from distances of several kilometers. For decades, the arms race between bats and insects has served as a prime example of acoustic co-evolution. The auditory adaptations of insects to echolocation have been well documented. Cricket has a multi-sensory predator recognition system with keen olfactory, tactile, and auditory senses. However, whether crickets can use the scent of bats to avoid them remains unknown at present. The authors hypothesized that cricket prey (Loxoblemmus equestris) might eavesdrop on predator bat (Scotophilus kuhlii) VOCs as an early warning. L. equestris is one of the prey species of S. kuhlii, and the authors demonstrated that the body odor of the insectivorous bat S. kuhlii triggers robust avoidance and electrophysiological responses in the cricket L. equestris, and that a single compound, (-)-limonene, is sufficient to elicit this avoidance in the laboratory and suppress calling in the field. Overall, this paper has a complete chain of evidence and should be a highly praised study.

      Comments:

      (1) Olfactory eavesdropping can transcend the evolutionary divide between vertebrate predators and invertebrate prey, enabling invertebrates to trigger defensive avoidance behaviors in response to predator-derived volatile odors. This phenomenon is empirically well-documented and requires no excessive emphasis.

      (2) Without quantitative analysis and without knowing the relative content of this key substance limonene, I don't quite understand how to determine the concentration of limonene standard for EAD, as well as the concentration in field experiments. How is the concentration of limonene determined in field spraying, and is this actually the case in the wild environment?

      (3) Figures 1C and D should compare the GC-EAD response of L. equestris to the odor of bat body and the odor of bat nasal secretions. It should not be compared with the air control group. Figure 1D has the same problem.

      We sincerely thank Reviewer #2 for the high praise (“complete chain of evidence,” “highly praised study”) and for the constructive suggestions to further improve the manuscript.

      On the novelty of olfactory eavesdropping across the vertebrate–invertebrate divide

      We agree with the reviewer that “olfactory eavesdropping can transcend the evolutionary gap between vertebrate predators and invertebrate prey” and that such phenomena have been documented. However, we would like to note that empirical examples remain relatively scarce, especially those that combine chemical identification, electrophysiology, behavioral assays, and field validation within a confirmed predator–prey relationship. We will adjust the wording in the Introduction and Discussion to more accurately reflect this current state of knowledge, acknowledging prior work while clarifying the added value of our study.

      On quantitative analysis and concentration choices for limonene in EAG and field experiments.

      EAG concentration gradients: The concentrations used in our EAG experiments (including the 1% and 10% v/v dilutions of (−)-limonene) were selected based on standard practices in insect chemical ecology and on previous studies investigating dose-dependent antennal responses to volatile compounds (e.g., Tang et al., 2024, Int. J. Biol. Macromol.). The goal was to determine whether L. equestris antennae are capable of detecting limonene across a range of concentrations, not to precisely match natural emission levels or to determine behavioral thresholds. Our data clearly show concentration-dependent antennal responses, establishing physiological sensitivity.

      Field spray concentration: We acknowledge that the concentration used in the field experiment (10% v/v limonene sprayed over 25 m²) does not represent the exact amount of limonene naturally emitted by bats. Natural odor plumes are highly complex; the diffusion, dilution, and persistence of volatiles depend on multiple factors (airflow, turbulence, temperature, humidity, vegetation structure, etc.). Accurately reconstructing such dynamics would require detailed quantitative measurements and possibly fluid-dynamic modeling, which were beyond the scope of this study. The aim of the field experiment was functional: to test whether limonene, as a single bat-associated volatile, could alter cricket calling behavior under semi-natural conditions, not to establish the concentration threshold for this effect. Therefore, we did not design experiments to determine the exact concentration at which crickets begin to respond. The positive result supports the ecological relevance of limonene as an avoidance cue, but we do not claim that the applied concentration matches natural levels. We will clarify this point in the revised Methods and Discussion sections and acknowledge that quantitative characterization of natural bat-odor compositions and their diffusion dynamics is an important direction for future research.

      On Figures 1C and 1D comparing bat body odor with air control rather than with snout secretions.

      We thank the reviewer for this suggestion. The comparison between bat body odor and snout secretions is indeed novel and informative, and we agree that it could help identify anatomical sources of active volatiles. However, the purpose of Figures 1C and 1D in the current manuscript is to answer a more fundamental question: whether bat body odor (as a whole) contains volatile components that elicit antennal responses in crickets, compared to an odor-free control. This establishes the basic phenomenon of olfactory detection. The identification of snout secretions as the primary source of body odor is addressed separately in Figure 2, using HS-SPME-GC-MS and PCA. In the revised manuscript, we will clarify this rationale in the Methods and Results sections to avoid confusion. We also note that the reviewer’s idea, directly comparing GC-EAD responses to snout secretions versus whole-body odor, is an excellent suggestion for future experiments and would further strengthen the source attribution.

      Revisions we will make:

      (1) In the Introduction and Discussion, we will adjust the wording to more accurately reflect the current state of knowledge on olfactory eavesdropping across the vertebrate-invertebrate divide, acknowledging prior work while clarifying the added value of our study.

      (2) In the Methods and Discussion, we will clarify the rationale for our concentration choices in the EAG and field experiments, acknowledging that our aim was functional (testing sufficiency) rather than determining quantitative thresholds.

      (3) In the Methods and Results, we will clarify the rationale for comparing bat body odor with air controls in Figures 1C and 1D, and note that the reviewer’s suggestion of comparing with snout secretions is an excellent direction for future work.

      We thank Reviewer #2 again for the thoughtful comments, which have helped us improve the manuscript.

    1. Author response:

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

      Reviewer #1 (Public review):

      I am not fully convinced about the responses from authors, so I would like to retain my original assessment of the paper. The same may be made available for public viewing, along with the responses of the authors. Readers can go through both and form their opinion.

      Unfortunately, this response from Reviewer 1 impacted the Assessment Statement but did not provide specific points for us to address. In the first round, the concerns of Reviewer 1 were: 1) the validity of the WLC prediction; 2) the claim that catch-bond measurements are generally made with superstall loads; 3) the role of vertical forces for dynein and a question about the orientation of the forces for kinesin; and 4) a request that we repeat the study using dynein. In rereading our responses to points 2-4 following our first revision, we felt that there were no unresolved issues around those points that affect our conclusions in any way. However, for point 1 regarding the validity of the WLC prediction, we had responded only in the reviewer response letter, and both reviewer 2 and the editors felt that there were points that we had addressed in the response letter that should be incorporated into the revised manuscript. Therefore, to clarify Reviewer 1’s question, we revised the text to address why we were justified to approximate the dsDNA force-extension curve using a WLC model with a 50 nm persistence length and why the precise shape of the force-extension curve has no impact on our conclusions.

      Reviewer #2 (Public review):

      The authors extensively entered into a scientific debate with the reviewers in their Response Letter. This led to a few changes and some (limited) new data in the manuscript. This is great and did improve the manuscript.

      However, in the view of this reviewer, (i) a significant number of responses fall short of actually addressing the concerns of the three reviewers (e.g. wrt using the same kinesin-1 neck-coil domains for all motors) and or (ii) a significant number of arguments now only occur in the response letter but not in the manuscript. The authors may check themselves critically for both. In principle, each longer discussion in the response letter warrants mentioning the appropriate facts and arguments in the main text of the manuscript.

      Based on this feedback, the first change we made was to rewrite the section justifying our choice of using a common coiled-coil dimerization domain for the three motors. Secondly, we went through our responses to all three reviewers to identify any instances where we either didn’t fully address the reviewer concerns or we provided arguments in the response letter but did not add corresponding text in the manuscript.

      Reviewer #3 (Public review):

      The authors attribute the differences in the behaviour of kinesins when pulling against a DNA tether compared to an optical trap to the differences in the perpendicular forces. However, the compliance is also much different in these two experiments. The optical trap acts like a ~ linear spring with stiffness ~ 0.05 pN/nm. The dsDNA tether is an entropic spring, with negligible stiffness at low extensions and very high compliance once the tether is extended to its contour length (Fig. 1B). The effect of the compliance on the results is not fully considered in the manuscript.

      In our first revision we added a paragraph in the ‘Geometry Calculations section of the Supplementary Methods addressing the dsDNA stiffness and comparing it to an optical trap. We considered moving this paragraph to the main text but decided against it because we felt it interrupted the flow of the Discussion. Instead, we expanded and clarified this paragraph to more specifically address the stiffness question. The paragraph with revised text now reads as follows:

      “Another consideration when comparing the DNA tensiometer to optical trap measurements is the relative stiffness of the trap and dsDNA. Optical traps stiffnesses are generally in the range of 0.05 pN/nm [13,14]. To calculate the predicted stiffness of the dsDNA spring, we computed the slope of theoretical force-extension curve in Fig. 1B. The stiffness is highly nonlinear and is <0.001 pN/nM below 650 nm extension. We compare motor performance under this low stiffness regime to the unloaded case in Fig. 3. In contrast, at the predicted stall force of 6 pN (960 nm extension), the dsDNA stiffness is ~0.2 pN/nm, which is stiffer than most optical traps, but it is similar to the estimated 0.3 pN/nm stiffness of kinesin motors themselves [13,14]. An 8 nm step at the 0.2 pN/nm stiffness of the dsDNA leads to a 1.6 pN jump in force and at the 0.05 pN/nm stiffness of an optical trap leads to a 0.4 pN jump in force; this is important because it means that in both cases the motors are likely dynamically stepping at stall. Because both experimental approaches allow for dynamic stepping at stall and because the stiffnesses of the instrument in both cases are less than the motor stiffness, there is no reason to expect that differences in stiffness between optical traps and the dsDNA spring lead to different motor detachment kinetics.”

      In the main text, we now address this compliance point in the ‘Comparison to previous work’ section of the Discussion:

      “stiffness differences are an unlikely explanation because at stall the stiffness of the DNA tether (~4 fold stiffer than optical tweezer) is still sufficiently low to allow for dynamic motor stepping at stall, and in any case it is still below the estimated motor stiffness (see Geometry Calculations in Supplementary methods).”.

      There were two points the reviewer felt we had sufficiently addressed. They were presented in the second review as a reiteration of the first review comments with a sentence appended, and are reproduced here. We added no new text based on these two points:

      In the single-molecule extension traces (Fig. 1F-H; S3), the kinesin-2 traces often show jumps in position at the beginning of runs (e.g. the four runs from ~4-13 s in Fig. 1G). These jumps are not apparent in the kinesin-1 and -3 traces. What is the explanation? Is kinesin-2 binding accelerated by resisting loads more strongly than kinesin-1 and -3? In their response, the authors provide an explanation of the appearance of jumps due to limited imaging speeds. The authors state that the qualitative difference in the kinesin-2 traces compared to the kinesin-1 and -3 traces may be due to the specific rebinding kinetics of kinesin-2.

      When comparing the durations of unloaded and stall events (Fig. 2), there is a potential for bias in the measurement, where very long unloaded runs cannot be observed due to the limited length of the microtubule (Thompson, Hoeprich, and Berger, 2013), while the duration of tethered runs is only limited by photobleaching. Was the possible censoring of the results addressed in the analysis? The authors addressed this concern by applying a Markov model to estimate the duration parameter.

      There was one final point from Reviewer 3 in the first round of reviews that we had addressed in the reviewer response (and that the reviewer was satisfied with), but we did not incorporate into the manuscript. Based on the suggestion from Reviewer 2 and the editors that we incorporate more from our responses to reviewers into the manuscript, we added new text on this point. That point (with the new sentence in the second review underlined), our response from first revision, and our response for this second revision are given below:

      The mathematical model is helpful in interpreting the data. To assess how the "slip" state contributes to the association kinetics, it would be helpful to compare the proposed model with a similar model with no slip state. Could the slips be explained by fast reattachments from the detached state? In their response, the authors addressed this question by explaining that a three-state model is required to model the recovery time distributions.

      In the model, the slip state and the detached states are conceptually similar; they only differ in the sequence (slip to detached) and the transition rates into and out of them. The simple answer is: yes, the slips could be explained by fast reattachments from the detached state. In that case, the slip state and recovery could be called a “detached state with fast reattachment kinetics”. However, the key data for defining the kinetics of the slip and detached states is the distribution of Recovery times shown in Fig. 4D-F, which required a triple exponential to account for all of the data. If we simplified the model by eliminating the slip state and incorporating fast reattachment from a single detached state, then the distribution of Recovery times would be a single-exponential with a time constant equivalent to t<sub>1</sub>, which would be a poor fit to the experimental distributions in Fig. 4D-F.

      Reviewer 3 noted that they were satisfied with our explanation of this point. However, based on Reviewer 2’s suggestion that we incorporate more of our responses into the text of the manuscript, we added the following clarification point in the model section of the Results:

      “We note that recapitulating the tri-exponential restart time distribution in Figure 4D-F required this slip/detached formulation and that lumping all events into a single detached state resulted in a single-exponential distribution of recovery times.”

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      The pupil traces in Figure3 (main results) are heavily pre-processed (per-participant demeaned), loosing any feature besides the effect of interest. As I argued in my first review, I worry that this format gives unrealistic expectations about the effect (the perception of dark/bright colors do not generate a net dilation/constriction of the pupil; perception-related modulations of pupil size are always relative and generally small compared to the numerous other effects registered in pupil size; these include a pupil dilation that is more prominent in the controls and that gets analyzed later on in the manuscript; I do not think that eliminating one of the effects of interests from a main results figure helps the reader understand the results). In the revised manuscript, the authors addressed this concern by adding a Supplementary Figure 4, where a more complete representation of the results is shown (traces from individual trials are baseline corrected and averaged, resulting in more informative timecourses). I would strongly recommend that Supplementary Figure 4 is brought to the main text (Figure 3 could be presented in Supplementary).

      We agree that it is important to counter unrealistic interpretations of the effect. However, figures in the main article are the ones that are depicting the effects. Instead, it seems that additional clarification on these effects is needed. First and foremost, Figure 3 in the main manuscript visualizes the core effect: pupil size reveals that synesthesia is a sensory process and the phenomenology of the synesthetic experience can be measured physiologically. Secondly, this allows to advance synesthesia (and phenomenology) research as a new and powerful method.

      No doubt, our effect is relative in nature (as almost any pupillometry, fmri, eeg effect etc.). Including variation that is unrelated to the effect would increase rather than decrease confusion, as individual differences (i.e., how the pupil of an individual responds irrespective of the synesthetic experience) are unmeaningful to the question we set out to answer. Individual variations in pupil response shape irrespective of synesthetic color brightness are removed in Figure 3 but still present in Supplementary Figure 4. Thus, Figure 3 is better suited to illustrate our core effect than Supplementary Figure 4, as individual average responses (illustrated on the right) cannot be meaningfully related to the core effect anymore, only the difference can be.

      At the same time, the reviewer is correct that this may, not so much among researchers as among a general audience, create the expectation that the pupil will always net dilate when experiencing a dark synesthetic percept. This is clearly not the case, but only over its counterfactual (i.e., not seeing that dark synesthetic percept). We now counter such an unrealistic expectation:

      “Note that the effects here are visualized as counterfactuals. So while the pupil dilated for dark relative to bright experienced colors in synesthetes, this does not mean that the pupil net dilates and constricts to dark and bright experienced colors relative to baseline, but only relative to the counterfactual (see Supplementary Figure 4 for net pupil size changes).”

      We updated the caption of Supplementary Figure 4 as follows:

      "Supplementary Figure 4: Pupil size change to graphemes, split by 0.5 reported color lightness (dark gray = low lightness; light gray = high lightness) without demeaning (i.e., removing the average pupil response shape in the 4s stimulus interval per individual irrespective of brightness perception). (…)"

      Responses to physical brightness modulations were only measured in the synesthethes group, not in controls. The authors point out that pupillary light responses have been thoroughly characterized in previous studies, and conclude that synesthethes' responses were in line with the expectations both in terms of amplitude and latency. However, as we are not dealing with standardized measurements, subtle differences in pupil reactivity across the two populations remain a possibility. I recommend that this possibility is mentioned in the discussion.

      We agree with the reviewer, if there were any differences in the PLR between the two groups, they must be minor given that the responses follow those reported in the literature so closely. Yet, subtle differences cannot be ruled out fully unless tested and it doesn’t hurt mentioning this in the discussion, which we now do as follows:

      Finally, pupil light responses in Block 2 were only assessed in synesthetes. While these closely match such of control populations [50,51], subtle between-group differences cannot be excluded and could ideally be assessed in future and replication work.

      Reviewer #2 (Public review):

      Synesthesia is a neurological condition where stimulation of one sensory channel leads to involuntary, automatic, and consistent experience of another, unrelated percept. For example, Sir Francis Galton (1880, Nature) famously described the robust tendency of some individual (synesthetes) to associate numerals with a distinct color. Ever since, synesthesia keeps attracting a broad interest in the cognitive neurosciences in light of its implications for the study of domains such as perception, consciousness, and brain connectivity, among others.

      Strauch, Leenaars, and Rouw measured pupil size in a group of 16 grapheme-color synesthetes and two matched control groups. The participants were presented with gray digits - that is, visual stimuli having identical physical properties in terms of brightness. Each participant subsequently rated the corresponding evoked color and brightness: unlike controls, synesthetes did so in a very consistent and reliable fashion. Accordingly, this was also shown in their pupils: despite the same objective luminance, digits associated with brighter percepts caused their pupils to constrict and digits associated with darker percepts caused their pupils to dilate more than controls. These results highlight how crossmodal correspondences are deeply rooted in synesthetes, and puts forward pupillometry as a particularly appealing biomarker for some phenomenological experience (at least those grounded in "brightness").

      Further strengths of the technique are its temporal resolution and its responsiveness to several constructs. Across several tasks, the authors show for example that responses to synesthetic light are somewhat slower than responses to real light (i.e., they are likely mediated), but at the same time faster than responses to mental imagery. The role of mental imagery can also be reasonably dismissed when considering the second feature of pupil size: its responsiveness to mental effort and cognitive load. The pupils tend to dilate with demanding, challenging tasks, and this was the case when control participants were asked to report the color of a digit for which they did not consistently experience a synesthetic association. The same task was, instead, seemingly effortless for synesthetes, again speaking in favor of the automaticity of number-color correspondences in their case.

      Overall, the findings by Strauch, Leenaars, and Rouw are highly significant for the field and likely to be impactful. The strength of their evidence, when accounting for the relatively small sample size and the inherent variability of both phenomenology (color perception and subjective reporting) and physiology (pupil size), is adequate and sufficiently convincing.

      Comments on revisions:

      I thank the authors for addressing all my comments in a satisfactory way. I think that the paper has improved, especially in terms of transparency of the reporting and clarity of the results.

      We thank R1, R2, and R3 for their very useful input to improve our manuscript.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This retrospective study provides new data regarding the prevalence of pain in women with PCOS and its relationship with health outcomes. Using data from electronic health records (EHR), the authors found a significantly higher prevalence of pain among women with PCOS compared to those without the condition: 19.21% of women with PCOS versus 15.8% in non-PCOS women. The highest prevalence of pain was conducted among Black or African American (32.11%) and White (30.75%) populations. Besides, women with PCOS and pain have at least a 2-fold increased prevalence of obesity (34.68%) at baseline compared to women with PCOS in general (16.11%). Also, women with PCOS had the highest risk for infertility and T2D, but women with PCOS and pain had higher risks for ovarian cysts and liver disease. Regarding these results, the authors suggested the critical need to address pain in the diagnosis and management of PCOS due to its significant impact on patient health outcomes.

      Strengths:

      (1) The problem of pain assessment in PCOS patients is well described and the authors provided a clear rationale selection of the retrospective design to investigate this problem.

      (2) A large number of analyzed patient records (76,859,666 women) and their uniformity increases the power of the study. Using the Propensity Score Matching makes it possible to reduce the heterogeneity of the compared cohorts and the influence of comorbid conditions.

      (3) Analysis in different ethnic cohorts provides actual and necessary data regarding the prevalence of pain and its relationship with different health conditions that will be helpful for clinicians to make a diagnosis and manage PCOS in women of different ethnicities.

      (4) Assessment of the risk of different health conditions including PCOS-associated pathology as other common groups of diseases in PCOS women with or without pain allows to differentiate the risk of comorbid conditions depending on the presence of one symptom (pelvic or abdominal pain, dysmenorrhea).

      We would like to thank the Reviewer for their positive feedback on this manuscript. Pain assessment in women with PCOS is of paramount interest and because of a gap in this research area, we are trying to address it.

      Weaknesses:

      (1) Although the paper has strengths in methodology and data analysis, it also has some weaknesses. The lack of a hypothesis doesn't allow us to evaluate the aim and significance of this study.

      We would like to thank the Reviewer for their valuable feedback regarding the hypothesis of this study. We understand that the hypothesis may not have been written clearly under the objectives and we have corrected this in the formal revision.

      The primary hypothesis of this study is that women with PCOS experience a higher prevalence to pain (including dysmenorrhea, abdominal pain and pelvic pain) compared to women without PCOS, and this prevalence varies by racial groups. Our hypothesis aims to explore the relationship between PCOS and pain, the associated health risks, and the potential racial disparities in pain prevalence and long-term health outcomes. Additionally, we seek to assess the effect of treatment on reducing pain symptoms in women with PCOS. This study not only examines the immediate burden of pain but also investigates its long-term consequences, including risks of infertility, obesity, and type 2 diabetes.

      To enhance clarity for readers, we explicitly stated this hypothesis in the revised manuscript and have ensured that its connection to the study’s objectives is clearly articulated. We appreciate the Reviewer’s insights and have incorporated these refinements to strengthen the manuscript.

      (2) The exclusion criteria don't include conditions, that can lead to symptoms similar to PCOS: thyroid diseases, hyperprolactinemia, and congenital adrenal hyperplasia. Thyroid status is not being taken into account in the criteria for matching. All these conditions could occur as on prevalence results as on risk assessment.

      We would like to thank the Reviewer for highlighting the need to include these additional conditions that mimic PCOS. After excluding hypothyroidism, hyperprolactinemia, and adrenal hyperplasia from the PCOS and PCOS and pain cohorts, we observed that 7,690 patients (1.65%) with PCOS and 1,854 patients (1.36%) with PCOS were removed. Based on this observation, we added these three conditions to our exclusion criteria and reran all our analysis for disease for our resubmission. The manuscript, figures, and tables have been updated to reflect these exclusions. Additionally, we have added rationale for excluding these conditions to the Discussion. With these major changes to the analysis, we aim to improve transparency and provide more accurate results and precise interpretations of our findings to the field.

      (3) The significant weakness of the study is the absence of a Latin American cohort. Probably the White cohort includes Latin Americans or others, but the results of the study cannot be extrapolated to particular White ethnicities.

      We appreciate the Reviewer’s suggestion to include Latin American cohorts in this study. The TriNetX platform has both self-reported race and ethnicity demographic information. In Table 3 - Figure Supplement 5 and Table 4 - Figure Supplement 6 we include baseline demographic information for both race (Asian, Black or African American, Native Hawaiian or Other Pacific Islander, Other, White, and Unknown Race) and ethnicity (Not Hispanic or Latino, Unknown, and Hispanic or Latino). In this paper we focused our future health outcome sub-analysis on four self-reported race groups: Asian, Black or African American, Other (Native Hawaiian or Other Pacific Islander, Other, Unknown Race), and White. We agree that including Latin American cohorts in the analysis is essential to better understand the health disparities affecting this population. Future work to better define Latin American cohorts in EHR data would significantly aid our ability to investigate this further.

      (4) The authors didn't provide sufficient rationale for future health outcomes and this list didn't include diseases of the digestive system or disorders of thyroid glands, which can also cause abdominal pain.

      We appreciate the Reviewer comment and concern regarding additional rationale for future health outcomes. We originally chose to investigate general future health outcomes like disease of the digestive system, circulatory system, etc. These disease groups were selected based on being general and having high prevalence as future health outcomes for patients with PCOS and Pain.

      Our initial results highlight the prevalence of disorders of the digestive system (Figure 2). However, after considering the Reviewers comments and to further strengthen our analysis, we included the most prevalent digestive system disorder in our relative risk (RR) analysis. Gastro-esophageal reflux disease (GERD) was identified as the most prevalent future digestive condition for women with PCOS and Pain (13.5%). There was also a 10.5% prevalence in women with PCOS overall.

      We were not able to include the same analysis for thyroid dysfunctions as this condition is a part of our exclusion criterion. These updates have been incorporated into the revised manuscript to ensure clarity and completeness.

      Reviewer #2 (Public review):

      Summary:

      The study offers a thorough analysis of the prevalence of pain in women with polycystic ovary syndrome (PCOS) and its associations with health outcomes across various racial groups. Furthermore, the research investigates the prevalence of PCOS and pain among different racial demographics, as well as the increased risk of developing various conditions in comparison to individuals who have PCOS alone.

      Strengths:

      The study emphasizes pain as a significant comorbidity of PCOS, an area that is critically underexplored in existing literature. The findings regarding the increased prevalence of some of the diseases in the PCOS + pain group provide valuable direction for future research and clinical care. I believe physicians should incorporate pain score assessments into their clinical practice to improve patient's quality of life and raise awareness about pain management. If future research focuses on the mechanisms of pain, it would provide a better understanding of pain and allow for a focus on the underlying causes rather than just symptomatic management. The study also highlights the association between PCOS+pain and various comorbidities, such as obesity, hypertension, and type 2 diabetes, as well as conditions like infertility and ovarian cysts, offering a holistic view of the burden of PCOS.

      We sincerely appreciate the Reviewer’s insightful comments. We hope that our findings will encourage further research on the occurrence of pain in women with PCOS and that others will replicate our results to strengthen the evidence in this area. As noted in our introduction, there are currently no standardized abdominal pain score assessments specifically for women with PCOS. We hope that the findings from this study will contribute to efforts toward developing a standardized pain assessment for the PCOS community. In the meantime, further research across more diverse populations will be essential to build a more comprehensive understanding of this issue.

      Weaknesses:

      Due to the nature of the retrospective study, some data may not be readily available in the system. Instead of simply categorizing participants based on whether they experience pain, it would be more useful to employ a pain scale or questionnaire to better understand the severity and type of patients' pain. This approach would allow for a more thorough analysis of pain improvement following treatment with the three widely used medications for PCOS. Additionally, it would be beneficial for the authors to specify subtypes of the disease rather than generalizing conditions, such as mentioning specific digestive system disorders or mental health disorders. The lack of detailed analysis of specific disorders limits the depth of the findings. This may cause authors to make incorrect conclusions.

      We appreciate the Reviewer for highlighting the importance of categorizing pain levels experienced by women with PCOS.  However, there is currently no standardized pain assessment for abdominal pain, and therefore more research is required before such a classification can be made. Additionally, the electronic health record data we leveraged via the TriNextX platform does not include any pain scale data from unstructured notes. Despite these limitations, this study is an important step toward recognizing abdominal and pelvic pain in women with PCOS. Our findings indicate that women with PCOS report abdominal pain independent of digestive conditions such as irritable bowel syndrome— a condition often associated with pain in this population.

      We would like to thank the Reviewer for their thoughtful comment with respect to subtyping future health outcomes. To get at the most impactful future health outcomes affecting women with PCOS and Pain, we have included the top 5 most prevalent health outcomes associated with PCOS and Pain. Specifically, we included analysis for anxiety disorder, depressive episodes, essential hypertension, Gastro-esophageal reflux disease (GERD), and acute pharyngitis. We observed that 17.1%, 11.5%, 10.5%, 10.0% of patients with PCOS and 20.1%, 13.7%, 13.5%, 13.3% of patients with PCOS and Pain were at risk of developing anxiety, depression, acute pharyngitis, and GERD respectively. For our revision, we have included these 5 conditions in our PCOS, PCOS and Pain and self-reported race-stratified future health outcome relative risk (RR) analyses. The revised manuscript, figures, and tables all reflect these changes.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I highly recommend checking all papers and supplements for misprints. There are a lot of missing spaces in the Introduction.

      We would like to thank the Reviewer for bringing this to our attention. We have carefully reviewed the manuscript and all supplementary materials and corrected formatting issues, including missing spaces and typographical errors throughout the Introduction and the rest of the document.

      (2) Supplementary Table 3: numbers from the first line in "%No PCOS" should be in "No PCOS"?

      We thank the Reviewer for bringing this error to our attention. We have identified the source of the problem and values have been added to the appropriate column.

      (3) Why for the matching authors use the categorical data for overweight/obesity and not the entire values? There are different stages of obesity that can be predominant in different cohorts and contribute to the results.

      We would like to thank the Reviewer for their insightful question. While TriNetX does have some BMI values for patient participants, this data is not included for all patients. For example, only 29-30% of women in the PCOS control and case cohorts have BMI recorded. Therefore, we focused on ICD codes for obesity instead to include as much data as possible.

      (4) What criteria were being used to determine hyperlipidemia and obesity? Were these criteria equal for all patients, or did they depend on ethnicity?

      We would like to apologize to the Reviewer for any confusion. The criteria to determine hyperlipidemia and obesity are ICD-10-CM codes as recorded in the TriNetX platform. The ICD-10-CM codes for obesity are E65-E68 and the ICD-10-CM code for hyperlipidemia is E78.5. Please also see the Methods section of this manuscript where all the ICD-10-CM codes are described.

      (5) The section material and methods should provide information regarding quality assurance checks and any steps to eliminate data suspected to be unreliable or invalid, to process missing data, consisting of data or claim duplicates. If quality assurance of data hadn't been conducted, it should have been noticed in the study limitations.

      We thank the Reviewer for this suggestion. We have revised the Methods section to explicitly describe the data quality assurance procedures inherent to the TriNetX platform. Specifically, we clarified that TriNetX applies standardized data mapping to controlled clinical terminologies (ICD, CPT, RxNorm), performs automated quality checks and excludes records that do not meet platform-defined standards.

      (6) It's not clear why the authors didn't include in the analysis the information regarding taking painkillers or anti-inflammatory drugs by patients. Maybe there is no such data in EHR. However, if the patient has some chronic inflammatory or autoimmune disease, she should be prescribed medication. I recommend specifying this issue in the section Material and Methods and/or study limitations.

      We would like to thank the Reviewer for this important suggestion. We have now clarified this point in the limitations section of the discussion. Specifically, we added text explaining that over-the-counter analgesics and anti-inflammatory medications are not reliably captured by EHR or within the TriNetX platform and therefore could not be evaluated in our analysis.

      (7) The authors should provide the Table or complete Supplementary Tables 2 and 3 with the parameters of patients used for matching.

      We apologize to the Reviewer for any confusion. The parameters used for propensity score matching are described fully in the Methods section of the paper. Table 2 – Figure Supplement 5 and Table 3 – Figure supplement 6 display baseline characteristics for patients before and after the 1:1 propensity score matching using these parameters. We have now also added the propensity score matching parameters to the table descriptions to provide fluidity and further clarification.

      (8) The authors found out that women with PCOS and pain have higher RR for ovary cysts and liver diseases compared to women with PCOS who have higher RR for infertility, obesity, and T2D. Discussion includes thoughts regarding a higher risk of ovary cysts and liver disease in women with PCOS and pain, but there is not any suggestion as to why women with PCOS and without pain have a higher risk of infertility, obesity, and T2D. If there is no data explaining this phenomenon, I recommend noting the need for additional research.

      We would like to thank the Revier for this helpful feedback. The Discussion section now includes deeper insights into the pathophysiology behind the two distinct PCOS phenotypes (PCOS overall vs. PCOS and Pain) and their differing risk profiles for future health outcomes.  Specifically, we note that while women with PCOS overall may be more metabolically driven (higher risk of infertility, obesity, and T2D), women with PCOS and Pain show a higher risk of ovarian cysts and liver disease. We clarify that these findings are observational and hypothesis-generating and emphasize the need for future longitudinal and mechanistic studies.

      (9) The authors suggested that systematic contraceptives, metformin, or spironolactone reduce pain in PCOS women. The reduction is significant, but the number of patients with beneficial effects is low (2.5-7.5%). Is it enough to recommend prescribing this medication not only for PCOS treatment but against pain?

      We thank the Reviewer for this important comment. We agree that although the reduction in pain diagnoses following treatment with COCPs, metformin, or spironolactone was statistically significant, the absolute proportion of patients experiencing benefit was modest. Our intention was not to recommend prescribing these medications solely for pain management, but rather to highlight that standard PCOS therapies may have additional benefits in reducing pain symptoms. We have clarified this point in the Discussion to emphasize that these findings are observational and hypothesis-generating, and that prospective studies are needed before these medications can be considered specifically for pain management in PCOS.

      Reviewer #2 (Recommendations for the authors):

      (1) Including a subtype analysis of specific diseases on digestive, respiratory, and mental health diseases rather than generalizing the system will enhance the content.

      We would like to thank the Reviewer for this helpful suggestion. In the revised manuscript, instead of the generalized disease systems we previously reported on, we have included analysis for the top 5 most prevalent conditions. Specifically, we included analysis for anxiety disorder, depressive episodes, essential hypertension, Gastro-esophageal reflux disease (GERD), and acute pharyngitis. We observed that 17.1%, 11.5%, 10.5%, 10.0% of patients with PCOS and 20.1%, 13.7%, 13.5%, 13.3% of patients with PCOS and Pain were at risk of developing anxiety, depression, acute pharyngitis, and GERD respectively.

      (2) Including the prevalence of dysmenorrhea among healthy populations would allow readers to better compare its impact on the lives of individuals with PCOS.

      We would like to apologize to the Reviewer for any confusion. The prevalence of dysmenorrhea for cases and control cohorts can be found in Table 2 – Figure Supplement 5 and Table 3 – Figure Supplement 6 before and after propensity score matching.

      (3) Introducing an analysis of age subgroups will provide readers with a clearer understanding of the prevalence of pain and specific diseases across different age groups.

      We would like to thank the Reviewer for this helpful suggestion. For this revision, we did a sub-analysis to explore the prevalence of PCOS and PCOS and Pain stratified by 10-year age groups. A barplot of these results can be found in Figure 4 - Figure Supplement 7.

      Thank you again to the Reviewers for the positive and constructive feedback for this manuscript. We have made the appropriate edits and changes to the final revisions of the manuscript.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The authors aim to demonstrate that PGLYRP1 plays a dual role in host responses to B. pertussis infection. PGLYRP1 signaling is known to activate bactericidal responses due to recognition of peptidoglycan. Through NOD1 activation and TREM-1 engagement, it appears PGLYRP1 also has immunomodulator activities. The authors present mouse knockout studies and gene expression data to illustrate the role of PGLYRP1 in relation to B. pertussis peptidoglycan. Mice lacking PGLYRP1 had slightly lower pathology scores. When TCT peptidoglycan was removed from the bacteria, surprisingly IL23A, IL6, IL1B, and other pro-inflammatory genes encoding cytokines increased. The relationship to TCT and PGLYRP1 suggests the pathogen uses this strategy to decrease immune activation. The authors went on to show the relationship between PGLRP1 and TREM-1 as mediated by PGN using various versions of peptidoglycan. The study presents multiple angles of data to back up its findings and demonstrates an interesting strategy used by B. pertussis to downregulate innate responses to its presence during infection.

      Strengths:

      Use of knockout mice of the key factor being considered, paired with isogenic B.

      pertussis strains, to reveal the mechanism of immune modulation to benefit the bacteria. The authors used in vivo gene expression paired with in vivo assays to establish each aspect of the mechanism.

      Weaknesses:

      The main focus was on innate responses, and some analysis of antigen-specific antibody responses could improve the impact of the findings.

      The authors thank the reviewer for their careful reading of the manuscript. We agree that understanding the impact of peptidoglycan recognition in adaptive immunity, including antibody responses, would be beneficial. This is particularly apparent due to the pressing need for novel vaccination strategies for pertussis. To this end, we have modified the discussion section to highlight this and are embarking on detailed studies of the adaptive response generated with B. pertussis strains releasing alternative peptidoglycan structures.

      Reviewer #1 (Recommendations for the authors):

      (1) This reviewer is of the opinion that describing the PGLYRP1 as a "bactericidal protein" seems misleading. "To determine whether PGLYRP1 has bactericidal activity against B. pertussis, we performed in vitro and ex vivo killing assays." Bactericidal activity was measured in normal or knockout neutrophils, but this seems to say the PGLYRP1 itself is an antimicrobial peptide. It clearly plays a role in the response,e but it is a regulator and not a killing agent.

      We agree that ‘bactericidal’ is not the most accurate description and have revised the manuscript accordingly to be more accurate throughout results section 1.

      (2) PGN can induce IgM production. Antibody production of any type was absent from this study. Would IgA/IgM/IgG levels to B. pertussis or its TCT change due to PGLYRP1? To this reviewer, it would be good to use the serum and perform some ELISA analysis. It is also likely that T cell responses could be impaired, but that may be out of the scope of this manuscript, but could be acceptable to consider for future studies.

      The authors thank the reviewers for this suggestion. We have added text to the discussion section to highlight the importance and potential of this suggestion.

      (3) Please include sources of mice (vendors) and strain numbers for transparency.

      The authors have added the relevant detail to the methods section to address this valid concern.

      (4) Were female or male mice or both used?

      For PGLYRP1 vs BALB/c comparisons both male and female mice were used. These are presented as combined data. No discernible differences were noted between male and female mice following infection. For single cell RNA sequencing studies only female mice were used, to be consistent with the published pertussis mouse model and avoid sex-based complications in analysis. We have clarified these details in the text.

      (5) It appears B. pertussis was cultured in SSM or BG. What condition was used for the bacteria used for the mouse challenge? SSM or BG?

      For mouse studies, bacteria were grown on BG agar supplemented with 10% defibrinated sheep blood for 48 hours and inoculum prepared by suspending in PBS in accordance with our established protocols. For in vitro studies liquid cultures were grown to mid-log in SSM. This has now been clarified in the methods section

      (6) Are the raw RNAseq and scRNAseq reads deposited in SRA?

      Raw data has now been deposited in the Gene Expression Omnibus (GEO) under number GSE324217

      (7) Is the scRNAseq data from one mouse or a pooled set of mice? If pooled, were the individual mice barcoded?

      scRNAseq data was obtained from barcoded individual samples and replicates were pooled and integrated during analysis, but the individual mouse each cell came from is still noted in the downstream analysis. This is now clarified in methods.

      (8) Why were some studies done by aerosol and others were done by intranasal delivery?

      The authors thank the reviewer for careful reading of the manuscript which erroneously listed aerosol infections. All infections in these studies were intranasal. This has now been rectified in the text.

      Reviewer #2 (Public review):

      Since its original discovery, the mechanistic basis for TCT-mediated pathogenesis of Bordetella pertussis has been a moving target and difficult to uncouple from confounding variables. The current study provides some exciting data that suggest PGLYRP-1 modulates host responses upon 'activation' by TCT. While there are some strengths associated with the unbiased approaches and collective data to support the claims associated with TCT and PGLYRP-1's function in this system, caution should be used when interpreting and extrapolating some of the information provided. For instance, the amount and purity of TCT used in the studies are unclear, and the in vitro activity of PGLYRP1 on B. pertussis is questionable. Different mouse backgrounds are used for various assays throughout, and it is known that the PRRs vary in these systems, so the confounding variables are difficult to uncouple. Additional concerns include the types of statistical tests being performed to support some of the claims and the relevance of using whole, intact PG sacculi from other species for comparative studies with a fragment of released PG (i.e., TCT).

      We thank the reviewer for their insightful suggestions to improve the standard of our manuscript and for highlighting several important considerations regarding our interpretation of TCT mediated host responses. We have addressed the points made in the revised manuscript. In particular, we have amended the Methods section to include a description of the purification and quantification of tracheal cytotoxin. These additions clarify the dosing of TCT used throughout the manuscript. We have revised the Results and Discussion sections to avoid overstating the bactericidal activity of PGLYRP1 against B. pertussis and to more carefully describe in vitro observations. Our revised interpretation emphasizes the role of PGLYRP1 in modulating host immune responses. Additionally, we have clarified experimental design and strain usage descriptions in the Methods section. The reviewer provided valuable and insightful comments on the solubility and structure of muropeptides studies. In response, we have revised the Results and Discussion sections to acknowledge these differences and the limitations they pose. Further, we have removed conclusions regarding the specific role of the 1,6anhydro bond. The statistical analyses have been reviewed and validated as well as clarified throughout the manuscript and Methods and figure legends updated.

      We appreciate the reviewer’s comments and believe the revisions have improved the clarity and rigor of the manuscript while maintaining the central conclusions about how peptidoglycan recognition influences host inflammatory responses during B. pertussis infection.

      Reviewer #2 (Recommendations for the authors):

      Major Points:

      (1) The concentration, purity, etc. of TCT seems like it is entirely unknown. Only a couple of experiments actually state the amount used, and it's unclear how the author determined the concentration because this is not trivial. Given the long-standing concerns with purity and co-purifying contaminants, this issue is paramount and needs to be properly addressed.

      TCT was purified by HPLC in the Goldman lab (UNC). Concentration was determined by comparing the peak area of each preparation to a purified TCT standard quantified by amino acid analysis. We have added these details to the Methods and now report concentrations throughout the manuscript.

      (2) Related to the effects of bacterial PG, studies performed are comparing TCT (a muropeptide) to commercially acquired, insoluble PG sacculi from B. subtilis and S. aureus. One cannot make these comparisons. There are flaws in terms of solubility (one goes into solution, the other does not), the amount used, the molar concentrations, etc. The authors also state that these are non-1,6 anhydro PG samples. That is not true. They contain plenty of 1,6 anhydroMurNAc, the moiety just exists in a different form. Finally, B. subtilis PG is not just mDAP, it's amidated, which is known to have effects on host response(s).

      We thank the reviewer for this important critique. We agree that differences in solubility and structural composition between TCT and PG sacculi limit direct comparisons. We have revised the Results and Discussion to remove statements implying direct equivalence and instead frame these experiments as highlighting how structural and physical properties of PGN fragments influence PGLYRP1-mediated activation of TREM-1. We have also removed statements regarding the 1,6-anhydro bond which were not adequately supported.

      (3) The claim that PGLYRP-1 is bactericidal in vitro is not supported by the data. Figure 1G shows that 24 hours after incubation, there is no difference. The comparison is being made to BSA, which is much higher (possibly because they're catabolizing it?) and thus entirely inappropriate. All other data in Figure 1 suggest no effect in vitro. In fact, it's this reviewer's position that none of the studies in Figures 1G, H, and I are convincing and should be entirely excluded.

      The authors agree that language describing the bactericidal assays is not optimal and have made revisions. The text in this results section has been modified to more carefully describe bacterial killing assays and accurately describe the effects the data suggest, primarily removing claims of bactericidal effects. BSA was chosen as a control protein (concentration matched with PGLYRP1), based on published controls for PGLYRP bactericidal assays (Lu et al 2006, JBC) similar results were obtained with PBS (volume matched with PGLYRP1). Descriptions of Fig1G,H,I have been updated. Data in 1H demonstrates that TCT release does not protect against effects of PGLYRP1, despite free PGN inhibiting PGLYRP1 bactericidal activity in published literature, while 1I suggests that extracellular polysaccharides contribute to protection against PGLYRP1 activity, preventing a more bactericidal phenotype which were not observed in the earlier assays when B. pertussis retained its capacity to produce bps polysaccharide.

      (4) Histology studies are unclear, and the data presented do not support the claims. Not only are the methods and results text describing the analysis contradictory, but nowhere are the actual statistical tests supporting the claims that they are different provided. This might be an oversight, but based on the variation, I would be surprised if they were statistically significantly different if proper tests are being used.

      Significance for pathology scores were initially determined using 2-way ANOVA as we had 4 groups (WT&KO at 4&7DPI) providing p-values of 0.01 for WT vs KO at 7DPI and 0.003 at 4DPI. Following reviewers’ suggestions, we have reanalyzed these data using a Mann Whitney U test, which is more appropriate for comparisons between two groups. This analysis yielded p-values of 0.013 (4DPI) and 0.00316 (7DPI) respectively confirming that the observed differences remain statistically significant. Statistical methods are now described in the methods and figure legends.

      (5) The NOD reporter studies are not well controlled and should include a) mouse vs human for both NOD1 and NOD2; b) defined details in terms of how spent culture media was treated, amount of material normalized, etc., c) concentrations of all materials used.

      We appreciate the reviewer’s comments regarding the NOD reporter assays. In response: (a) We have clarified and articulated the murine/human NOD reporter assays and included both human and mouse NOD1, along with controls. (b) We have supplemented descriptions of how conditioned (spent) culture media were collected, processed, and normalized in the ‘Bacterial strains and infections’ and ‘Reporter Cell Assays’ methods sections; (c) and the final concentrations of all agonists and test materials used in the reporter assays are now specified in the Methods and corresponding figure legends. Together, these additions address the requested controls and clarify the experimental conditions

      (6) The scRNA-seq studies are provocative and informative, but the data shown are selectively included for the purposes of the paper. This is justified in terms of 'telling a story', but it's a disservice to the community not to include all the raw data attained. These should be deposited in an open-source system.

      The complete dataset has now been deposited in GEO (GSE324217) enabling full access for the community. The analyses presented in the manuscript focus on the datasets most relevant to the central conclusions.

      Minor points:

      (1) The authors refer to arthropod PGRPs but call them PGLYRPs. It is best to stick with the established nomenclature and use the proper names to distinguish each. There are a few sentences in the abstract that don't make sense as they're written.

      The authors thank the reviewer for their careful reading of the manuscript and have altered the manuscript to use PGRP for arthropod peptidoglycan recognition proteins.

      (2) The reciprocal result of bacterial burden at different time points in the context of PGLYRP-1 production in mice could be simply explained - it is bactericidal early, and the accumulation of dead/dying bacteria releases large pieces of PG that are not released during growth (anhydro) but rather lysis. It is the latter that causes the inverse relationship later.

      The authors believe this is an interesting and plausible explanation for differences in responses at different stages of disease. Further, we believe that elucidating the mechanism by which ‘large pieces of PG not released during growth” are recognized differently than PG from lysed bacteria is worthwhile. We speculate that the release of TCT could be a mechanism by which B. pertussis takes advantage of host differences in PG recognition. We thank the reviewers for this thought and have included this possible interpretation in the text.

      (3) The results section references Figure 1G while discussing results presented in Figure 1H.

      This has now been corrected.

      Reviewer #3 (Public review):

      Summary:

      This study evaluates the contributions of the mammalian PG-binding protein PGLYRP1 to Bordetella infection. The authors find potential roles for PGLYRP1 in both bacterial killing (canonical) and regulation of inflammation (non-canonical). While these are interesting findings and the idea that PG fragment release has differential impacts on infection depending on fragment structure, the study is limited by the lack of connection between the in vivo and in vitro experiments, and determining the precise mechanism of how PGLYRP1 regulates host responses and bacterial fitness during infection requires further study.

      Strengths:

      (1) The combination of scRNAseq with in vitro and in vivo assays provides complementary views of PGLYRP1 function during infection.

      (2) The use of TCT-deficient B. pertussis provides a useful control and perturbation in the in vitro assays.

      Weaknesses:

      (1) The study does not ultimately resolve the initial early versus late phenotype divergence. While the in vitro assays suggest explanations for their in vivo observations, further mechanistic links are lacking and necessary for the author's conclusions throughout. To state one example, what is the early and late infection phenotype of TCT- Bp in mice lacking PGLYRP1? RNAseq data are reported from these mice, but there are no burden or pathology studies. Furthermore, what are the neutrophil phenotypes (NOD-1/TREM-1 activation) in vivo? And are they dependent on PGLYRP1 and/or TCT?

      (2) It is unclear whether or how the NOD1 and TREM-1 pathways interact.

      (3) Many of the study's conclusions rely on the use of HEK293 reporter lines in the absence of bacterial infection, which may not be physiologically representative.

      (4) The methods lack detail overall, and the experimental procedures should be described more concretely, especially for the scRNAseq datasets.

      We thank the reviewer for their comprehensive and fair assessment of our study and for highlighting both its strengths and areas where clarification could improve the manuscript. As noted in the review the possibility that peptidoglycan fragment structure impacts disease pathogenesis is interesting and the role of PGLYRP1 in regulating host and bacterial fitness during infection requires further study.

      We have addressed the points made by the reviewer in the revised manuscript. We edited the Methods section to provide additional experimental detail, particularly for the scRNA-seq analyses and reporter assays. We also clarified the experimental design and interpretation of the in vitro studies to avoid overstating mechanistic conclusions.

      Studies with TREM-1 and NOD are attempting to assess multiple aspects of PGN/PGLYRP mediated enhancement of inflammatory responses via NFkB/MAPKs. No attempts have been made to assess synergistic, overlapping or compensatory effects between these systems. Other work from our group highlights the role of peptidoglycan in driving inflammatory responses via NOD receptors (doi: https://doi.org/10.1101/2025.08.08.669383) and TREM-1 (doi: 10.1128/IAI.00126-21). Work in this paper assesses the contribution of these pathways to the observed immune modulation noted by PGLYRP1.

      We have clarified figure legends and analyses, including interpretation of neutrophil transcriptional programs identified in scRNAseq datasets and comparisons to known neutrophil phenotypes.

      We appreciate the reviewers feedback and the opportunity to improve the clarity of our manuscript and optimize the conclusions and central findings.

      Reviewer #3 (Recommendations for the authors):

      (1) Please clarify in Figure 1C what the axis means, since the text refers to both uninfected and infected cells. What data allow the conclusion that PGLYRP1 expression "expanded" to other cell subsets?

      We thank the reviewers for catching this oversight. We were relying on data which we had not best represented in Figure 1C, so we updated this figure and corresponding text so that this violin plot demonstrates increased PGLYRP1 expression levels and an increasing or expanding number of cell types following infection. This is now also reflected in the text. Expression of PGLYRP1 is apparent in more cell types and to a greater extent following infection (red) with B. pertussis compared to PBS challenge (black). Expression represents normalized and transformed unique molecular identifier counts per gene per cell.

      (2) Please revise the Figure 1 legend to match the Figure panels, and mention the time point of the mPGLYRP1 killing assay in 1H/I. Were these assays performed at 6 or 24 hours? This could affect the interpretation of the data.

      This has been revised to reflect timing of data.

      (3) The text at the end of the first Results section is overstated, as the data in Figure 1 do not relate to immune-mediated clearance apart from expression levels.

      This text has been revised and reference to immune mediated clearance removed

      (4) More detail is needed in the explanation of Figures 3E-G. Do the neutrophil subsets correspond to known subsets from the literature?

      When we overlaid established neutrophil signatures from the literature onto our dataset the NOD2+ neutrophils most closely resembled inflammatory or activated neutrophil programs described previously (Xie et al. 2020 Nat. Immuno., Veglia et al. 2021 J. Exp. Med)- specifically, high il1a, Ccl3 and Ptgs2 expression. In contrast, NOD1+ neutrophils showed greater overlap with resolving or regulatory neutrophil states- including genes associated with lipid mediator metabolism and NFkB dampening. Importantly, the clustering itself was not driven by NOD1 or NOD2 expression alone. NOD expression segregated within transcriptionally distinct neutrophil programs that are consistent with previously described inflammatory versus regulatory subsets. We included descriptions of these inflammatory neutrophils and related them to previously identified neutrophil populations, supporting our findings and improving the representation and articulation of the single cell neutrophil data analysis. We deeply thank the reviewers for their help in improving this section.

      (5) The Methods section describes qPCR, but this is not presented in the Results.

      This has now been removed. We thank the reviewer for their careful and complete review of the manuscript.

    1. Author response:

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

      eLife Assessment

      This multi-omics study provides a comprehensive characterization of the context-dependent roles of the JAK-STAT pathway (JSP) across different cellular compartments within the breast cancer microenvironment. The authors present convincing evidence that high JSP activity paradoxically drives anti-tumor cytotoxicity in T cells but promotes malignancy and immunosuppression in tumor epithelial cells, leading to the fundamental discovery that broad JAK-STAT inhibition could be therapeutically counterproductive. Ultimately, the identification of the immune-related JSP score and the STAT4 axis as predictive biomarkers for anti-PD-1 immunotherapy response, particularly in triple-negative breast cancer, offers critical insights for precise patient stratification and targeted therapeutic interventions.

      We greatly appreciate the editor’s insightful and comprehensive summary of our study.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In their manuscript, Zhou and colleagues present a detailed look at how the JSP functions differently in the various cells of a breast tumor. The authors have effectively shown that the JSP acts as a double-edged sword, as it helps T cells fight cancer but also allows tumor cells to grow and avoid ferroptosis. These findings are important because they identify a useful biomarker to predict how TNBC patients might respond to PD-1 inhibitors.

      We highly appreciate Reviewer #1’s generous comments and thorough understanding of our study.

      Strengths:

      This work is important because it provides a clear explanation for the conflicting roles of the JSP in the tumor environment. The evidence is solid, as it combines data from thousands of patients with single-cell analysis and lab experiments to confirm the role of STAT4 in cancer progression and immunity.

      Weaknesses:

      However, there are areas for improvement in the scope of the review, the depth of analysis, and the potential for broader clinical implications. The authors are encouraged to address these issues to enhance the scientific and clinical impact of the study.

      We greatly appreciate the positive recognition and insightful comments from the reviewer. We are grateful that you acknowledge our solid evidence and the significance of clarifying the dual roles of JSP and STAT4. We will fully address your suggestions to expand the research scope, deepen the analysis, and strengthen the clinical implications in the revised manuscript.

      Major Issues:

      (1) The authors demonstrate that STAT4 upregulates SLC47A1, but this is currently supported only by expression correlation and western blot data. To confirm a direct link, the authors are encouraged to perform ChIP-qPCR or luciferase reporter assays to show that STAT4 binds directly to the SLC47A1 promoter.

      We highly appreciate this insightful and important comment. Due to time constraints, the first author has left the laboratory for clinical practice, and this manuscript is critical for fulfilling his degree requirements at Sichuan University. We are making every effort to supplement additional mechanistic experiments where feasible. In the meantime, we have performed protein–nucleic acid docking analysis between STAT4 protein and the SLC47A1 promoter region, and the corresponding results have been added to the supplementary figures.

      (2) The conclusion that the MIF-CD74 axis drives immunosuppression is based on computational inference. To support this, the authors could consider mining publicly available breast cancer spatial transcriptomics data to show the co-localization of MIF and CD74. Alternatively, performing simple dual-color immunofluorescence staining on a few clinical sections would effectively demonstrate the physical proximity of these cells.

      We sincerely appreciate your careful review and valuable suggestions. We fully agree that the conclusion regarding the MIF-CD74 axis driving immunosuppression requires further spatial evidence. Although we plan to collect additional clinical specimens for direct co-localization validation, the related ethical approval is still ongoing and cannot be completed in a short time. Therefore, we have supplemented analyses on publicly available breast cancer spatial transcriptomics datasets, which now provide solid bioinformatic evidence to support the spatial co-localization and interaction of the MIF-CD74 axis in the tumor microenvironment in the revised manuscript.

      (3) TNBC is highly heterogeneous and includes subtypes like mesenchymal and immunomodulatory groups. The authors should analyze whether the JSP score or STAT4 levels vary significantly between these subtypes, as this could further refine the selection of patients for JAK1 inhibitors.

      Thank you for this insightful suggestion. We have supplemented the expression levels of JSP score and STAT4 in two independent TNBC cohorts to explore their heterogeneity across the four TNBC subtypes (Fig. S5B-C).

      (4) While the JSP score works well in the current datasets, the authors should consider validating its predictive accuracy in additional independent immunotherapy cohorts, such as the TONIC trial, to ensure the biomarker is robust across different treatment settings.

      We sincerely appreciate this valuable suggestion regarding the validation of the JSP score in independent cohorts. To address your concern about the robustness of our biomarker across different treatment settings, we would like to provide the following clarification and updates:

      Status of TONIC-trial Data Access:

      We fully recognize the significance of validating the JSP score in the TONIC-trial (Nat Med 2019; https://www.nature.com/articles/s41591-019-0432-4), a seminal study exploring immune induction strategies for PD-1 blockade in metastatic TNBC. We have made persistent efforts to obtain these data. However, our previous application to the Data Access Committee (DAC) of the European Genome-phenome Archive (EGA, Study ID: EGAS00001003535) was declined. The official reason provided was a restriction on data sharing imposed by the US Department of Justice, related to Executive Order 14117, which prohibits the transfer of bulk sensitive personal data to certain countries.

      Compensatory Validation in Available Anti-PD-1 cohorts:

      Despite the limitation on the TONIC-trial data, we have rigorously evaluated the predictive accuracy of the JSP score in two additional, independent, and publicly available anti-PD-1 treated breast cancer cohorts to thoroughly demonstrate its generalizability (Fig. S5A):

      GSE194040 (I-SPY2-990, Pembrolizumab, anti-PD-1): A cohort investigating anti-PD-1 therapy in metastatic breast cancer.

      GSE173839 (I-SPY2 trial, Durvalumab, anti-PD-L1): A cohort evaluating neoadjuvant anti-PD-L1 therapy in TNBC.

      We believe these additional validations adequately address your comment.

      Minor Issue:

      The manuscript mentions a U-shaped trajectory of JSP activity during tumor transition. A more detailed biological explanation of why the pathway activity initially drops and then rises would add depth to the discussion.

      We greatly appreciate this constructive comment. The JAK–STAT pathway (JSP) is essential for maintaining normal epithelial growth; its expression is higher in normal epithelium than in tumor tissues and increases during normal epithelial differentiation. In datasets containing both normal and tumor cell populations, JSP activity naturally declines during the transition from normal epithelium to early tumor lesions. In the subsequent tumor differentiation stage, JSP activity gradually rises, which may be driven by intrinsic tumor heterogeneity and pathway-dependency among different subtypes. This dynamic trend is consistent with JSP pathway activity score, which is independent of pseudotime cell trajectory analysis. We have added this explanation in the first paragraph of the Discussion.

      Reviewer #2 (Public review):

      Summary:

      The JAK-STAT pathway (JSP) exhibits cell-type-specific functional heterogeneity in breast cancer. This study investigates the JSP in breast cancer and its response to anti-PD‑1 immunotherapy. JSP displays distinct cell‑type heterogeneity: it promotes malignant phenotypes and immunosuppression in tumor cells, while enhancing cytotoxicity and reducing exhaustion in T cells. Elevated JSP expression correlates with improved immunotherapy responses, especially in triple‑negative breast cancer. These findings highlight the paradoxical roles of JSP, indicating that broad inhibition may compromise anti‑tumor immunity.

      Strengths:

      The major strengths of this study include the comprehensive characterization of JSP heterogeneity across epithelial, tumor, and T cells in breast cancer. The identification of JSP and STAT4 as predictive biomarkers for immunotherapy response, particularly in triple-negative breast cancer, provides clinically relevant insights for patient stratification.

      Weaknesses:

      The findings rely heavily on public dataset analyses.

      We sincerely appreciate the reviewer’s insightful recognition and comprehensive summary of our study, as well as the positive comments on our strengths.

      We fully agree that the current findings are mainly based on multi‑omics analyses of public datasets. In response to this comment, we have supplemented additional validation using independent cohorts (e.g., FUSCC‑TNBC and METABRIC) to reinforce the reproducibility of the cell‑type-specific heterogeneity of the JAK–STAT pathway and the predictive value of JSP/STAT4 for immunotherapy response in TNBC.

      Moreover, we have clearly discussed this limitation in the Discussion section and explicitly proposed further prospective experimental validation and clinical sample verification in our future work.

      We have carefully revised the manuscript in full accordance with all of your valuable suggestions to further improve the quality and rigor of our work.

      Reviewer #3 (Public review):

      Summary:

      This multi-omics study by Zhou et al elucidates the context-dependent roles of the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway (JSP) across different cellular compartments in the breast cancer tumor microenvironment. While bulk JSP activity is associated with a favorable prognosis, single-cell analysis reveals a paradoxical landscape: high JSP in T cells drives anti-tumor cytotoxicity and reduces exhaustion, whereas high activity in tumor epithelial cells promotes malignancy and immunosuppression via the MIF-CD74 signaling axis. The JSP score (immune-related) serves as a robust predictive biomarker for response to anti-PD-1 immunotherapy, particularly in triple-negative breast cancer (TNBC). Furthermore, the study identifies the STAT4/SLC47A1 axis as a critical mechanism through which tumor cells resist ferroptosis, facilitating disease progression. These findings suggest that broad JAK-STAT inhibition may be counterproductive in cancer therapeutics; instead, therapeutic success depends on precise modulation and carefully timed interventions to preserve its T-cell-associated functions. This study may inspire future studies to explore specific factors that selectively modulate JAK-STAT activity in immune cells to achieve favorable therapeutic outcomes.

      Strengths:

      Significant therapeutic implications.

      Weaknesses:

      Limited molecular mechanisms.

      We sincerely appreciate the reviewer’s highly positive recognition and insightful summary of our work. Fully addressing your comment regarding limited molecular mechanisms, we have comprehensively supplemented and enriched the mechanistic elaborations in the revised manuscript—including detailed explanations of the dual cell-type-specific roles of the JSP pathway, the downstream MIF-CD74 axis, and the STAT4/SLC47A1-mediated ferroptosis resistance mechanism. All related revisions have been carefully incorporated into the text to strengthen the molecular depth and robustness of our findings.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) The Graphic Abstract in the current version fails to provide brief information about the submission.

      We appreciate your comment on the Graphic Abstract. We have redrawn a new, concise Graphic Abstract that clearly summarizes the key findings, workflow, and core message of our submission. The updated version now provides brief but complete information about the study.

      (2) Information regarding the epidemiology of breast cancer and TNBC is recommended to be included in the Introduction section.

      In response to your comment, we have supplemented up-to-date epidemiological data for both breast cancer and triple-negative breast cancer (TNBC) in the revised Introduction section.

      (3) Attention should be paid to the superscript, particularly for CD8+.

      We have revised the plus sign in CD4/8+ to the standard superscript format (CD8⁺) throughout the entire manuscript.

      (4) Typos are present, such as the error in "2.1" (please verify and correct accordingly).

      We have carefully checked and revised the entire manuscript, especially the section 2.1 Bioinformatical profiling. All typos, grammatical errors, and formatting inconsistencies pointed out in your comment have been fully corrected throughout the text.

      (5) Relevant information about MCF-10A cells in the cell culture protocol is missing.

      We sincerely apologize for the omission of MCF-10A cell culture details. We have supplemented the complete cell culture protocol for MCF-10A cells in 2.2.1 Cell culture.

      (6) For the Western blot experiments, information about the dilution ratios (of primary/secondary antibodies) is required.

      We have supplemented the detailed dilution ratios for all primary and secondary antibodies used in the Western blot experiments.

      (7) The Ethics Approval Number must be provided.

      We have supplemented the official ethics approval number for animal experiments in Section 2.2.6.

      (8) For the IHC staining experiments, information about the dilution ratios (of antibodies) is required.

      We have supplemented the detailed antibody dilution ratios for all primary antibodies used in the IHC staining experiments in Section 2.2.7 Immunohistochemistry (IHC).

      (9) Up-to-date citations are necessary, especially those published in 2026.

      We have thoroughly updated the reference list according to your suggestion in epidemiology of breast cancer.

      (10) Proofreading the language is recommended in order to enhance the fluency and readability of the manuscript.

      We have carefully polished the full manuscript with the help of a native English speaker to improve linguistic fluency, readability, and academic expression. All revisions have been completed strictly following your suggestions, and we deeply appreciate your efforts to help optimize this work.

      Reviewer #3 (Recommendations for the authors):

      Major points for the authors:

      (1) Please provide an overview figure of the datasets and approaches used in this study, as Figure 1.

      We sincerely appreciate your valuable suggestion. We have supplemented an overview figure (designated as Figure 1A) that systematically summarizes all datasets and experimental approaches used in this study, including the detailed workflow of bioinformatic profiling, pseudotime analysis, and functional validation.

      (2) The authors need to improve the organization of figure panels, as they appear cluttered in some regions, which impedes understanding of the figures.

      We sincerely appreciate your constructive comment. To address the cluttered figure panels that impeded understanding, we have redrawn Figures 2, 3, 5, and 6, and fine-tuned the image size, layout, and spacing of the panels.

      (3) The experimental section utilizes female mice for the MDA-MB-231 xenograft models. Given that a central finding of the paper is the pathway's role in T-cell-mediated anti-tumor immunity, the authors should discuss how the absence of a functional T-cell compartment in nude mice affects the interpretation of tumor growth data, or, ideally, provide data from immunocompetent syngeneic models.

      We thank the reviewer’s valuable comment. The MDA-MB-231 xenograft model in nude mice only supports our conclusion that STAT4 promotes tumor growth, given the deficient T-cell immune compartment in this model.

      We are currently constructing an orthotopic breast cancer model with stable STAT4 overexpression in 4T1 cells using immunocompetent mice, which possesses a complete immune microenvironment to further validate our immune-related findings. In addition, we plan to establish conditional STAT4 overexpression via the Cre/LoxP system in the MMTV-PyMT transgenic breast cancer mouse model. However, these elaborate in vivo validations cannot be completed within a short time frame due to experimental duration and technical limitations.

      This manuscript is critically important for the first author to complete their doctoral degree at Sichuan University. We sincerely appreciate the reviewer’s understanding and generous support for accepting our current data and future follow-up validation plans.

      (4) While the study links STAT4 to SLC47A1 upregulation, adding direct mechanistic evidence - such as ChIP-seq or luciferase reporter assays - would confirm that STAT4 directly binds the SLC47A1 promoter rather than acting through intermediary signaling.

      We highly appreciate this insightful and important comment. Due to time constraints, the first author has left the laboratory for clinical practice, and this manuscript is critical for fulfilling his degree requirements at Sichuan University. We are making every effort to supplement additional mechanistic experiments where feasible. In the meantime, we have performed protein–nucleic acid docking analysis between STAT4 protein and the SLC47A1 promoter region, and the corresponding results have been added to the supplementary figures.

      (5) Are there any potential upstream selective regulators of STAT4 in immune cells?

      IL‑12 acts as the upstream activator of STAT4 in immune cells. This cytokine binds to IL12R‑β1/β2, triggering Tyk2/Jak2 signaling to induce STAT4 phosphorylation, dimerization and nuclear translocation, thereby upregulating IFN‑γ transcription and enhancing T cell‑ and NK cell‑mediated antitumor immunity. We have added these details in the Discussion.

      (6) Recent studies have identified CD74+ lipid-associated macrophages (LA-MAMs) as a conserved niche in multi-organ metastasis of breast cancer. Linking the tumor-derived MIF-CD74 axis results to this broader metastatic framework could emphasize the clinical relevance of the findings.

      Recent study defines a conserved MIF-CD74 LA-MAM axis driving T-cell exhaustion and multi-organ metastasis in breast cancer, predicting poor patient survival. Our work further reveals that tumor-intrinsic JAK-STAT signaling reinforces this immunosuppressive cascade, while T-cell STAT4 activation reverses immune suppression. Combining MIF-CD74 blockade with precise STAT4-targeted strategies may synergize to remodel the metastatic niche and enhance immunotherapy efficacy in TNBC. We have supplemented the relevant mechanistic details and literature discussion in the revised Discussion section.

      Minor points for the authors:

      (1) The use of "spokesperson" to describe STAT4's role as a representative of the JAK-STAT pathway is somewhat informal for a scientific manuscript. Adopting more standard academic phrasing, such as "primary mediator" or "key transcriptional orchestrator," would enhance the professional tone.

      Thank you for your valuable comment. We have revised the manuscript accordingly by replacing the informal term "spokesperson" with the standard academic phrase "key transcriptional orchestrator".

      (2) The JSP score achieved a predictive AUC of 0.70-0.76. The authors could improve the work by testing whether combining the JSP score with existing clinical biomarkers, such as PD-L1 IHC or Tumor Mutational Burden (TMB), significantly enhances predictive accuracy.

      We have made every effort to collect publicly available breast cancer immunotherapy datasets for further validation. Unfortunately, none of these datasets provided immunohistochemistry (IHC) data for PD-L1/PD-1 expression. To address your valuable suggestion, we instead integrated mRNA expression levels of PD-L1/PD-1 with the JSP score to predict immunotherapy response.

      In cohorts GSE194040 and GSE173839 (Fig. S5A), this combined model exhibited improved predictive performance with an AUC exceeding 0.8, which is superior to using the JSP score alone. The corresponding results have been added and presented in the supplementary figures.

      (3) There is a potential contradiction in which bulk JSP scores correlate with better survival, whereas tumor-intrinsic JSP scores correlate with poor survival. A clearer discussion or a specific figure reconciling how the dominant immune signal overrides the pro-tumor signal in bulk analysis would be beneficial.

      In survival profiling, higher T-cells- and normal epithelial-specific JSP scores correlate with favorable patient survival, whereas elevated tumor-intrinsic JSP scores are associated with poor prognosis. This can be attributed to the predominant expression of JSP in T cells, which enhances T cell mediated anti-tumor immunity and counterbalances its pro tumor effects within cancer cells. We have added detailed clarification of this dual regulatory mechanism in the Discussion section.

      (4) The authors cite recent publications regarding the benefits of late-stage or intermittent JAK inhibition. Providing a more detailed proposed dosing schedule or "therapeutic window" based on their differentiation data could offer more actionable insights for clinical trial design.

      Based on the above clinical evidence and our findings, administering JAK–STAT inhibitors before or concurrently with immunotherapy may impair T‑cell cytotoxicity and disrupt normal epithelial differentiation in breast cancer patients. Instead, sequential delivery of JAK inhibition following immunotherapy represents a promising immune‑sensitizing strategy, particularly for the TNBC subtype. We have added corresponding descriptions in the third paragraph of the discussion section.

      (5) The authors note that they are unable to refine the analysis for TNBC subtypes, such as mesenchymal-like (MES), due to data limitations. If possible, using the METABRIC cohort (which was already accessed) to perform a secondary validation of JSP activity across these specific molecular subtypes would add significant depth.

      We appreciate this constructive suggestion. To address the subtype heterogeneity of JSP activity in TNBC, we have collected two TNBC datasets (FUSCC-TNBC and 2024_Nat.Comm.) and conducted further validation and analysis across different TNBC molecular subtypes in Fig. S5B-C.

      (6) The discussion evaluates both broad JAK inhibitors (Ruxolitinib) and STAT3-selective inhibitors (TTI-101). Explicitly comparing the potential biological impact of selective STAT3 inhibition versus selective STAT4 activation could clarify the most promising therapeutic direction.

      We greatly appreciate this valuable suggestion. We have supplemented the Discussion (in the penultimate paragraph) by proposing a translational strategy utilizing the specific cytokine IL‑12 to activate STAT4 for immune sensitization, while explicitly comparing the distinct biological effects and therapeutic directions between selective STAT3 inhibition and targeted STAT4 activation.

      In summary, we sincerely thank the editors and reviewers for their constructive comments and valuable suggestions. We have carefully addressed all the comments and revised the manuscript accordingly.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      A summary of what the authors were trying to achieve:

      (1) Identify probiotic candidates based on the phylogenetic proximity and their presence in the lower respiratory tract based on phylogenetic analysis and on meta-analysis of 16S rRNA sequencing of mouse lung samples.

      (2) Predefine probiotic candidates with overlapping and competing metabolic profiles based on a simple and easy-to-applicable score, taking carbon source use into consideration.

      (3) Confirm the functionality of these candidate probiotics in vitro and define their mechanism of action (niche exclusion by either metabolic competition or active antibacterial strategies).

      (4) Confirm the probiotic action in vivo.

      Strengths:

      The authors attempt to go the whole 9 yards from rational choice of phylogenetic close lower respiratory tract probiotics, over in silico modelling of niche index based on use of similar carbon sources with in vitro confirmation, to in vivo competition experiments in mice.

      Weaknesses:

      (1) The use of a carbon source is defined as growth to OD600 two SD above the blank level. While allowing a clear cutoff, this procedure does not take into account larger differences in the preferences of carbon sources between the pathogen and the probiotic candidate. If the pathogen is much better at taking up and processing a carbon source, the competition by the probiotic might be biologically irrelevant.

      While the definition of carbon utilization in this work is a commonly used definition, we agree that there are numerous ways that one could define carbon utilization. We also agree that it is possible that inclusion of additional features of carbon consumption such as the order of prioritization of carbon sources by CP could improve the model. Our data in Figure 3H and 3I do suggest that certain carbon sources may be disproportionately important for predicting antagonistic phenotypes. However, given that the objective of this work was to develop a simple model to aid in the design of probiotic communities, we feel that the current definition of carbon utilization allows maximum accessibility and is suitable for our needs. Work is currently underway to identify additional features, such as carbon source processing efficiency, that may improve the model’s utility.

      (2) The authors do not take into account the growth of candidate probiotics in the presence of Bt. In monoculture, three of the four most potent candidate probiotics grow to comparable levels as Bt in LSM.

      Yes, our model only accounts for a one way interaction (effect of pathogen on CP). This is for two reasons (1) We are only interested in characterizing and modeling the antagonistic potential of the CP on the pathogen as this antagonism, we propose, is what gives a CP therapeutic potential (2) The degree to which co-culture with Bt impacts CP activity will be captured by the performed competition experiments and therefore any inhibition of the CP by Bt will be accounted for.

      While further investigation of the effect of Bt on the growth of the CP may not be necessary to achieve our objective, we agree that ecologically it would be interesting to understand this dynamic better. To explore this, we conducted co-culturing studies between each CP and Bt or media-only control and measured the amount of CP after 24 hours of co-culture. From the data it appears that only a small number of organisms (CP4, CP7 and CP19) are significantly inhibited by the pathogen at the 1:1 ratio tested. This result is perhaps unsurprising as these CPs have the highest niche index and therefore have a greater metabolic overlap with the pathogen.

      These data have been incorporated into Figure S1B and additional text has been added to line 157 and the methods at line 712.

      (3) Niche exclusion in vivo is not shown. Mortality of hosts after infection with Bt is not a measure for competition of CP with the pathogen. Only Bt titers would prove a competitive effect. For CP17, less than half of the mice were actually colonized, but still, there is 100% protection. Activation of the host immune system would explain this and has to be excluded as an alternative reason for improved host survival.

      We have revised the manuscript to address these issues as follows:

      (1) We include Bt titer data as suggested, displayed in a new figure (Figure 5F). The results indicate that CP8 fails to reduce Bt titers as compared to the no-CP control, whereas the other CPs tested (CP13, CP17, CP19, CP20, and CP26) do reduce Bt titers to statistically significant degrees (p-value < 0.05 by ANOVA/Tukey). These results support the idea that the CPs competitively exclude Bt in vivo (as they do in vitro), with the notable exception of CP8 (which competitively excludes in vitro but not in vivo, consistent with the mortality results). Further, additional spearman correlation analysis was performed to understand the relationship between the Niche Index value for a given CP and pathogen instantiation when pre-treatment with a given CP is performed. We found that there was a strong relationship between NI<sub>CP</sub> and pathogen load (r = -0.84, P<0.0001, 95% CI [-0.90 to -0.76], N = 77) such that prophylactic treatment with a CP with a high Niche Index value strongly correlated with lower pathogen load following Bt challenge. Text describing these findings has been added at line 471.

      (2) We include survival studies of mice prophylactically treated with non-viable CPs, displayed in a new figure (Figure S7). Viability is required for niche exclusion, so protection conferred by non-viable CPs must be due to other effects such as elicited immune responses. We found that non-viable CPs provide some protection when administered at 3 days prior to Bt challenge, though not to the same degree as viable CPs. Together, our data suggest that with the day 3 dosing schedule there are alternative mechanisms of protection (potentially including immune priming) that our current model does not capture. These results are described in further detail at line 460.

      Appraisal:

      (1) Based on phylogenetic comparison and published resources on lower respiratory tract colonizing bacteria, the authors find a reasonably good number of candidate probiotics that grow in LSM and successfully compete with the pathogenic target bacterium Bt in vitro.

      (2) In vivo, only host survival was tested, and a direct competition of CP with Bt by testing for Bt titers was not shown.

      Impact:

      Niche exclusion based on competition for environmentally provided metabolites is not a new concept and was experimentally tested, e.g. in the intestine. The authors show here that this concept could be translated into the resource-poor environment of the respiratory tract. It remains to be tested if the LSM growth-based competition data in vitro can be translated into niche exclusion in vivo.

      Reviewer #2 (Public review):

      Summary:

      This study aims to establish a rational framework for designing bacterial probiotics against respiratory infections. The central hypothesis is that in vitro antagonism, particularly through metabolic niche overlap with a pathogen, predicts in vivo efficacy.

      Strengths:

      (1) Systematic pipeline: The study integrates bacterial isolation, in vitro characterization, model development, and in vivo validation into a cohesive workflow.

      (2) Quantitative model: The introduction of the Niche Index (NI) and Niche Index Fraction (NIF) provides a novel, quantitative tool for predicting probiotic efficacy based on ecological principles.

      (3) Mechanistic insight: The work dissects different modes of action, clearly demonstrating that inhibition can be driven by specialized metabolite production (CP8) or carbon resource competition (e.g., CP7), with lactate utilization identified as a key factor.

      Weaknesses:

      (1) Limited model generalizability: The predictive power of the NI model is not universal. It fails to account for the in vivo inefficacy of CP8 (a metabolite-dependent inhibitor) and cannot explain the short-term protection conferred by some non-inhibitory CPs in vivo, suggesting unmodeled mechanisms like immune priming are at play.

      The NI model is not able to identify antagonism of metabolite-dependent inhibitors as their inhibitory activity is unrelated to the variables for which the model accounts. Based on the NI model, CP8 is predicted to have the least metabolic overlap with the pathogen which may explain its in vivo inefficacy. We do agree that short-term protection is only moderately related to NI (r = 0.48, P<0.0001, 95% CI [0.33 to 0.62], N = 115) and may represent an unmodeled alternative mechanism of protection as discussed at line 445, 466 and 523. We have added additional data in Figure S6 and corresponding text at line 444 which gives additional information about CP8 colonization in the context of infection.

      (2) Preliminary nature of key findings: The emphasis on lactate consumption as a critical predictor, while interesting, is not sufficiently explored to establish its general importance beyond the specific strains and conditions tested.

      Indeed, our model and assertions about critical predictors of antagonism only extend to the specific strains and conditions tested. While we cannot assert that lactate consumption is a critical predictor of antagonism universally, several other studies have indicated the importance of lactate in infection at other body sites [53-57].

      To further characterize the role of lactate utilization in the respiratory context, we performed an ex vivo experiment to measure lactate concentrations in respiratory tissue with or without treatment with a key isolate - CP19. After 24 hours of incubation, we found that lactate levels were significantly reduced in the CP19-containing homogenate compared to the PBS-only control (Figure S8A). Additionally, the pathogen was unable to grow in the CP19 conditioned homogenate but was able to grow in the untreated homogenate (Figure S8B). This indicates that CP19 can deplete the total lactate in lung tissue, and that this conditioning can inhibit pathogen growth in the lung tissue. These results are reported in a new supplementary figure (Figure S8) and summarized in corresponding text (line 485), with a description of the experimental procedure in the Methods section (line 924). While this does not prove our theory about the importance of lactate utilization universally, we believe that our work contributes to the growing body of evidence around lactate and its role in infection. Work is ongoing to expand the number of strains screened and determine the generalizability of particular carbon sources and their role in interbacterial antagonism.

      Appraisal:

      The authors successfully achieve their aim of establishing a rational probiotic-design pipeline. The data robustly support the conclusion that metabolic niche overlap predicts efficacy for many strains, while also clearly delineating the model's limitations, as acknowledged by the authors.

      Impact:

      This work provides a valuable methodological framework for hypothesis-driven probiotic discovery. The quantitative Niche Index offers immediate utility to the field and, with further refinement, has the potential to become a fundamental tool for developing respiratory therapeutics.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Suggestions for improved or additional experiments, data or analyses.

      (1) CP titers at the end of the coculture experiment are missing in LSM.

      To quantify pathogen abundance after co-culture, cultures were plated on carbenicillin-100 to select for only colonies of the pathogen. As a result, no data about CP abundances were collected in the original experiments. However, we agree that ecologically it would be interesting to understand this dynamic better. We have added additional data about the impact of the pathogen on CP in co-culture to Figure S1B.

      (2) Bt titers in mice are essential to claim niche exclusion happens in vivo, and immune-mediated effects have to be excluded.

      Please see response to question 3 of the public review.

      (3) The definition of the use of carbon sources should be refined. Qualitative differences between the pathogen and the CP with regard to the usage of a given carbon source might have a substantial impact on the actual competitive effect.

      The definition of carbon utilization is stated at line 811. While we agree that there may be other carbon-consumption related variables (rate of growth on a particular carbon source, amount of biomass generation on that carbon source etc) that could be used in the model, for the purposes of this study a binary (can versus cannot grow on the carbon source) was sufficient. Work is currently ongoing to determine if metrics of growth on carbon sources such as those listed would improve the predictive capability of the model.

      Reviewer #2 (Recommendations for the authors):

      (1) Experimental & Analytical Suggestions:

      (a) To further validate the role of lactate, consider measuring lactate concentration in the airways of mice colonized by key CPs (e.g., CP7, CP19) versus controls. This would directly test if in vivo protection correlates with local lactate depletion.

      Unfortunately due to the funding for this project ending, we weren’t able to perform additional animal experiments. However, we were still able to test lactate utilization by CP19 in the respiratory context via an ex vivo experiment. We inoculated mouse lung homogenates with 10<sup>6</sup> CFU of CP19, or PBS as a negative control, and co-incubated for 24 hours. After 24 hours, we measured lactate levels and found that they were significantly reduced in the CP19-containing homogenate compared to the PBS-only control (A). Additionally, we measured the growth of the pathogen in CP19 conditioned (+CP19) and untreated (-CP19) homogenates and found that the pathogen was unable to grow in the CP19 conditioned tissues (B). This indicates that CP19 can deplete the total lactate in lung tissue, and that this conditioning can inhibit pathogen growth in the lung tissue. These results are reported in a new supplementary figure (Figure S8) and summarized in corresponding text (line 485), with a description of the experimental procedure in the Methods section (line 924).

      (b) The finding that CP8 provides no in vivo protection despite in vitro efficacy warrants further investigation. We suggest quantifying CP8 and Bt loads in co-colonized mice to determine if the probiotic fails to persist during infection or if the pathogen evades inhibition.

      Please see updated Figure S6 and accompanying text at line 444.

      (2) Quantitative Analysis:

      Please consider adding a brief justification in the manuscript explaining why the specific Niche Index formula (based on electron equivalents of shared carbon sources) was selected over alternative ecological metrics for quantifying niche overlap.

      Text was added starting at line 264 explaining our reasoning for choosing this model.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study presents a potentially important integrative model linking spontaneous retinal waves, apoptosis, microglial activity, and vascular development during postnatal retinal maturation. Its significance lies in proposing a mechanistic framework that could reshape understanding of how neural activity and tissue remodeling are coordinated in the developing central nervous system. The evidence is strengthened by the use of multiple complementary techniques, including Ca++ imaging, high-throughput electrophysiology, transcriptomics, histology, and pharmacology.

      Strengths:

      (1) Multimodal Validation: The authors correlate large-scale functional imaging (calcium imaging and MEA) with high-resolution structural and molecular data (scRNA-seq and IHC), providing strong topographical evidence for the "centrifugal expansion" pattern.

      (2) The primary significance lies in identifying apoptotic Retinal Ganglion Cells (RGCs) as the physiological "pacemakers" for stage II retinal waves. By linking programmed cell death directly to neural activity and subsequent angiogenesis, the authors propose a self-regulating developmental loop.

      We thank the reviewer for their nice summary and for highlighting the strengths of this work.

      Weaknesses:

      (1) While the PANX1 pharmacological data provide compelling functional support, extending these conclusions to the broader CNS may be premature. Additional direct mechanistic validation would further strengthen the claim of causality.

      We agree with the reviewer that the conclusions would be greatly solidified with more direct mechanistic validation. However, we are unable to conduct more experimentation as the grant is finished and the Sernagor lab is in the process of being shutdown, after the unexpected passing of the PI.

      In order to make clearer that this mechanism was found in retinal tissue, not CNS, we have moved any mention of the implications of our work to a broader CNS mechanism to the discussion section. We will add text into the discussion highlighting the need for more mechanistic investigation to uncover the full extent of the developmental processes described herein.

      (2) While the manuscript beautifully illustrates the co-occurrence of events during retinal development, strengthening the distinction between correlation and direct causation would enhance the impact of the findings.

      We have been clear to only present our findings as correlational as we were unable to fully explore the causational nature within the mechanisms presented. In the discussion, we have used published evidence and experimental papers to bolster our understanding of the causal aspects of this research. We will also include sections of text to address what experimentation is required to examine the causal interactions more directly.

      Reviewer #2 (Public review):

      Summary:

      Savage et al. investigate the synchronization of retinal Ca2+ waves with developmental cell death, microglia activation, and vascular outgrowth. These developmental processes occur through a mechanism where apoptotic cells release ATP through Panx-1 channels to stimulate both Ca2+ retinal waves and microglia activation. Using scRNAseq, the authors classify autofluorescence cell clusters (ACCs) at the leading edge of vasculature outgrowth as Hmox-1+ microglia. From here, they show microglia engulfment of apoptotic RGCs, and the potential release of ATP may contribute to Ca2+ wave generation. The authors demonstrate these mechanisms through the use of two pharmacological agents to either block the ATP release from Panx-1 or block receptor binding to ATP. Furthermore, while previous studies have described the site of initiation of retinal Ca2+ waves as random, this study shows that the initiation of Ca2+ waves is biased to the leading edge of vascular growth in the developing retina. To do this, the authors use a combination of wide-field Ca2+ imaging and multi-electrode arrays to pinpoint the sites of Ca2+ wave initiation in the developing retina.

      Strengths:

      The authors use several techniques to interrogate these mechanisms, including single-cell RNAseq, wide-field Ca2+ imaging, and multi-electrode arrays. With these experiments, this manuscript proposes several novel ideas, such as ATP as the Ca2+ wave-initiating cue, and the localization of the Ca2+ wave initiation to the leading edge of vascular growth.

      We thank the reviewer for their nice summary and for highlighting the strengths of this work.

      Weaknesses:

      The main weakness of the manuscript is the overreliance on only two pharmacological agents to test the central hypotheses. These conclusions would be strengthened if, in addition to their pharmacological manipulations, they used genetic knockout models to perturb programmed cell death or ATP release (i.e., BAX-KO, Panx-1 KO).

      We thank the reviewer for their insightful suggestions for further experimentation to bolster the research. Initially, we utilised pharmacological interventions as they provided acute and quick answering of the research question. At the outset of the research, we were not certain that purinergic release through PANX-1 channels was the mediator for the developmental mechanisms described. We tested a wide variety of specific agonists and blockers before seeing any profound effects on wave generation. These agonists and antagonists have been used before and are proven to deliver reliable results. In addition, since the ACCs had never been reported before we were unsure if a knockout animal would display the same anatomical phenotype. Furthermore, it is known that knockout mouse lines, especially connexin and hemichannel pores, do not lose function but rather have other isoforms or compensation mechanisms which can substitute the original function. For the retina, for example, it was shown that Cx36 can functionally replace Cx45 after Cx45 KO (Frank et al, 2010).

      We agree that while direct mechanistic validation would significantly reinforce the arguments, we are limited in conducting further experiments since the grant has been completed and the Sernagor lab is in the process of shutting down following her passing.

      In order to address the omission of mechanistic validation in the paper we will add text into the discussion highlighting the need deeper investigation in the causality of the developmental processes described herein.

      M. Frank et al., Neuronal connexin-36 can functionally replace connexin-45 in mouse retina but not in the developing heart, J. Cell Sci. 123, 3605 (2010).

    1. Author response:

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

      eLife Assessment

      This important study deepens our understanding of how populations of a given species may diverge in their molecular and physiological patterns as a result of adaptation to different thermal regimes. By approaching this question from multiple directions, the authors provide solid evidence for adaptive changes in three strains of the diamondback moth after only three years of experimental evolution, and support the causal involvement of the PxSODC gene in thermal adaptation to both cold and hot temperatures. This work would benefit from more sophisticated phylogenetic analyses, better statistical support, and a more detailed discussion of the differences in the three strains at the pathway level.

      We sincerely thank the editors for this positive and constructive assessment. In the revised manuscript, we have addressed the highlighted points by: (1) re-inferring the phylogenetic tree of the PxSODC gene using a model-based Maximum Likelihood method (IQ-TREE) to ensure a robust evolutionary analysis; (2) substantially expanding the description of our statistical methods across all data types to ensure reproducibility and clarify multiple-testing corrections; and (3) adding a more detailed discussion of the pathway-level differences between the hot and cold strains, particularly integrating how their distinct transcriptomic responses align with their shared metabolic adjustments and phenotypic traits.

      Reviewer #1 (Public review):

      (1) The authors identify pathways that are enriched in different strain comparisons (Figure 3E), but do not provide a detailed interpretation of these results. It would be great if the authors could explain in more detail how the physiological processes of a cold-adapted strain of this species may differ from those of a warmer-adapted strain.

      We agree. We have addressed this by directly integrating our pathway enrichment results (Figure 3E) with the observed life-history phenotypes (concurrently addressing Reviewer 2's Comment 36a). We expanded the Discussion to explain that while both strains share convergent adjustments in core pathways (e.g., lipid metabolism for energy reallocation), their specific physiological strategies differ. The cold-adapted strain relies on broader transcriptional reprogramming to maintain homeostasis and support extended longevity/cold hardiness, whereas the hot-adapted strain utilizes broader metabolic rewiring to actively fuel its accelerated development and higher fecundity.

      (2) The authors reconstruct a phylogenetic tree of the PxSODC gene using the neighbor-joining algorithm. The limitations of this algorithm have been known for many years now, especially for sequences separated by long evolutionary distances. According to Wang et al. (2016), the last common ancestor of the species shown in Figure S4C occurred 392-350 million years ago. Given this, I would strongly recommend that the authors infer a phylogenetic tree using model-based methods, such as those implemented in RAxML-NG or IQ-TREE. Also, in the absence of a valid outgroup sequence, I would show the gene tree as unrooted or rooted based on the corresponding species tree.

      Agree. We have re-inferred the phylogenetic tree of the PxSODC gene using the model-based Maximum Likelihood (ML) method implemented in IQ-TREE. As recommended, in the absence of a valid outgroup sequence, the revised tree is now presented as unrooted. Supplemental Figure S4C (Figure 5-figure supplement 1C) and the corresponding text in the manuscript have been updated.

      (3) There is a key piece of the puzzle that is currently missing: the structural mechanism behind the mutational effects described in this study (e.g., Figure 5). The authors could leverage AlphaFold to generate structural models of different mutants and conduct molecular dynamics simulations to examine their conformational dynamics.

      We thank the reviewer for this excellent suggestion. We generated AlphaFold structural models of the wild-type (WT) and mutant (MU) PxSODC proteins and conducted 100 ns molecular dynamics (MD) simulations using GROMACS 2022.3 at three physiologically relevant temperatures: 15°C (cold stress), 26°C (favorable baseline), and 32°C (heat stress). Using 26°C as the physiological baseline, three key structural parameters support enhanced thermostability of the mutant protein (Figure 5–figure supplement 3). First, RMSD analysis revealed that under heat stress (32°C), the WT underwent severe conformational drift (RMSD increased from the 26°C baseline of 1.62 to 2.49, an increase of 0.87), while MU remained remarkably stable (from 1.59 to 1.66, an increase of only 0.07). Second, MU possessed a significantly more compact structure, with lower SASA values at 15°C (118.39 vs. 127.29 nm²) and 26°C (113.82 vs. 125.61 nm²), indicating optimized hydrophobic core packing. Third, the intramolecular hydrogen bond network of MU demonstrated dual stress resistance: under cold stress, MU actively increased hydrogen bonds from its baseline (113→119), whereas WT lost bonds (117→112); under heat stress, MU fully maintained its bond count (113→113). These results provide a direct structural mechanism for the enhanced catalytic efficiency of the mutant SOD at lower expression levels.

      Reviewer #1 (Recommendations for the authors):

      (4) The experimental evolution component of this study is described in the text as lasting for three years. It would help if the number of generations per strain were also reported.

      We have added the number of generations per strain. Over the three-year period, the hot strain completed ~75 generations and the cold strain ~15 generations. The ancestral strain was continuously maintained at 26°C throughout this period. The revised text has been updated in both the Introduction and Materials and Methods.

      (5) In Figure 3B: There is a typo in the word “Statistics”.

      Corrected. The typo in “Statistics” in Figure 3B has been fixed.

      (6) In Figure 3D: “CS” appears twice.

      Corrected. The duplicated “CS” label in Figure 3D has been replaced with the correct label.

      (7) Figure 4: This is not accessible to colorblind readers, who will clearly not be able to tell each color apart. As a non-colorblind person, I, too, have trouble figuring out which color label in panel B corresponds to which color in panel A. For example, I do not know off the top of my head how 'blue' differs from 'midnightblue', 'royalblue', or 'skyblue'. I recommend that the authors replace colors with identifiers, such as 'g1' for group 1 and so on.

      We appreciate this suggestion. We have replaced all color-based module labels with alphanumeric identifiers (M1, M2, M3, etc.) and added a corresponding legend. The main text and supplementary materials have been updated accordingly.

      (8) Lines 246-247: "Its secondary structure mainly consisted of strands, helices and coils." This sentence is redundant. These three are the only possible secondary structural elements, according to most bioinformatics tools such as PSIPRED, which the authors used. This sentence would be more useful if the authors could report the percentage breakdown of each secondary structural element.

      We have removed the redundant sentence and updated the text to report the specific percentage breakdown of the secondary structural elements based on our PSIPRED predictions (approximately 55.24% random coils, 16.19% alpha helices, and 28.57% extended strands). The revised text has been updated in the Results section.

      (9) Lines 260-261: "This suggests that the PxSODC gene can alter its expression pattern and function in response to environmental change...". I find this sentence a bit imprecise. Would it not be more precise to mention that the expression of this gene is regulated by temperature triggers?

      We agree that the original phrasing was imprecise. We have revised the sentence in the manuscript to state: “This suggests that the expression of the PxSODC gene is regulated by temperature triggers, and its altered function contributes to temperature-adaptive evolution in P. xylostella.”

      (10) The data points in Figures S1 and S7 are very small and hard to tell apart without zooming in a lot. Perhaps the authors could change the orientation of those pages to landscape and increase the size of the figures.

      Done. We have changed the orientation of Supplemental Figures S1 (Figure 1-figure supplement 1) and S7 (Figure 5-figure supplement 4) to landscape and increased the size of the figures and individual data points to improve visibility.

      (11) In Figure S2, the panel labeled as 'C' should be 'B' (based on the caption) and vice versa.

      Corrected. The panel labels ‘B’ and ‘C’ in Supplemental Figure S2 (Figure 2-figure supplement 1) have been swapped. The Supplementary Materials have been updated accordingly.

      Reviewer #2 (Public review):

      (1) The paper in its current form is hard to digest and would benefit from improved clarification of the storyline, as well as a tighter integration between the phenotypic, omics, and functional validation data. Currently, it is not always clear what the relevance is of all the reported results, nor why certain decisions were made, or how all the different methods the authors used fit together. For example, the authors functionally validated a second gene, PxDnmt1, but it is unclear why this particular gene was chosen, nor how it relates to their selection regimes when looking at the results obtained with the phenotyping and omics data collection. Seeing how much work the authors did, this makes the paper overwhelming and difficult to read.

      We sincerely appreciate this constructive feedback. In the revised manuscript, we have made significant structural revisions to improve the storyline and logical flow. We have streamlined the Results section (moving extensive descriptive data like life table curves and detailed metabolomics of mutant strains to the Appendix 1-3) to focus on the key findings. Furthermore, we have clarified the logical transitions between experiments. For instance, regarding the choice to validate PxDnmt1, we now explicitly explain in the Results that our untargeted metabolomic analysis of the PxSODC mutant strains revealed consistent alterations in 5-hydroxymethyluracil (involved in DNA demethylation) and 5'-deoxyadenosine (a precursor to the primary methyl donor S-adenosylmethionine) across all developmental stages. This specific metabolic signature provided a strong, data-driven hypothesis linking PxSODC function to epigenetic regulation via DNA methylation, prompting us to functionally validate PxDnmt1. By explicitly stating these rationales, the narrative is now much clearer and cohesive.

      (2) The authors at times stretch their results too far, as the ecological relevance of their study design and results is not clear, limiting the generalizability and value of the results for understanding species' adaptive potential under climate change. For example, the selection regimes used present the minimum and maximum known temperatures at which the species can survive and develop, but it is unclear how the temperatures relate to the natural environment of the source population, to what extent wild populations might experience these temperatures, and whether they would experience them at the extended duration used (12h at max/min temperature). Moreover, I wonder whether the comparisons made would identify the genes that matter under natural conditions, as unevolved populations were kept under constant conditions compared to 12h:12h temperature regimes for the evolved populations, and the metabolic and transcriptomic profiling was done under a constant favorable 26°C rather than under thermal stress in a, as far as I can tell, randomly chosen life stage (larval stage).

      We appreciate the reviewer raising these important points regarding ecological relevance and experimental design. In the revised manuscript, we have added context and acknowledged these limitations in the Methods and Discussion sections. First, regarding ecological relevance: The source population is from Fuzhou, a subtropical region where summer high temperatures frequently exceed 32°C and winter lows can drop below 10°C, making our selection temperatures ecologically relevant extremes for this population. The 12h:12h cycling temperatures were designed to simulate severe but natural diurnal fluctuations.

      Second, regarding constant control vs. cycling regimes: The constant 26°C represents the established optimal developmental temperature and standard laboratory condition for P. xylostella. We acknowledge that comparing cycling selection regimes against a constant control might conflate adaptation to absolute temperature extremes with adaptation to thermal fluctuation itself. We have added this as a caveat in the Discussion. Third, regarding omics profiling conditions: The transcriptomic and metabolomic profiling was conducted under common garden conditions (26°C) specifically to identify constitutive, genetically fixed adaptations resulting from evolutionary selection, rather than immediate physiological plasticity under stress. We have clarified these rationales in the text.

      (3) The paper in its current form does not adequately describe the statistical analyses underlying the results, nor do the authors share their code, making it very hard to judge whether the analyses used are appropriate and the results trustworthy. I have concerns about the inappropriate use of t-tests, the lack of correcting for confounding variables, and the need for multiple testing corrections.

      We sincerely appreciate this concern. In the revised manuscript, we have made substantial improvements to the description of statistical analyses throughout the Methods section:

      (1) Statistical methods for each data type are now described separately and in detail, specifying the tests used, the number and type of comparisons, and sample sizes.

      (2) For metabolomic data, we have clarified that FDR correction was applied alongside multi-criteria thresholds (|log<sub>2</sub>Fold Change| ≥ 1, VIP ≥ 1, FDR < 0.05). For transcriptomic data, FDR correction (Benjamini and Hochberg, 1995) was applied via DESeq2.

      (3) For WGCNA, we have specified the total number of correlation tests (29 modules × 30 metabolites = 870) and the stringent dual threshold (|r| > 0.8, P < 0.05) used to control for false positives, following standard practice.

      (4) For life table parameters, the paired bootstrap method with 100,000 replications was used for all pairwise comparisons among strains.

      (5) For all other experimental data (qRT-PCR, SOD activity, O<sub>2</sub><sup>-</sup> levels, survival rates, supercooling/freezing points, etc.), we have specified that t-tests were used only for two-group comparisons, while one-way ANOVA with Tukey's or Tamhane's T2 test was used for three or more groups, with non-parametric alternatives applied when normality assumptions were not met.

      (6) The raw data have been deposited in public repositories (see Data availability), and all statistical procedures are now described in sufficient detail to enable independent reproduction of the results.

      Reviewer #2 (Recommendations for the authors):

      Title

      (4) I don't feel the title adequately captures the work, I would instead of 'adaptive evolution' use 'experimental evolution' and I would not use the word 'underpins' but instead 'indicates', as it is not clear from your work whether the adaptations to the lab conditions you used would be ecologically relevant nor whether they are involved in thermal adaptation in wild populations.

      Accepted. The title has been revised to: “Experimental evolution to thermal stress indicates climate resilience in a cosmopolitan arthropod.”

      Abstract

      (5a) Please add the phenotype results to the abstract.

      We have added key phenotype results to the abstract. The revised text now reads: “The hot strain showed accelerated development, higher fecundity, and increased survival under extreme heat, while the cold strain exhibited lower supercooling and freezing points, indicating enhanced cold hardiness.”

      (6b) The Abstract doesn't really detail the answer to your research question yet: so what insights into the genetic mechanisms underlying thermal adaptation did you gain that are novel?

      We agree. We have revised the Abstract to explicitly highlight the novel genetic and molecular mechanisms we discovered. Specifically, we now detail that thermal adaptation is driven by a coordinated mutational, metabolic, and epigenetic (1) an energy-efficient genetic mechanism where non-synonymous mutations in PxSODC enhance superoxide scavenging efficiency, enabling effective oxidative stress management at lower gene expression levels; (2) convergent metabolic adjustments, notably a reduction in lipid metabolism to conserve energy; and (3) epigenetic regulation of thermal tolerance via DNA methylation. The revised text has been updated in the Abstract accordingly.

      (7c) Line 3: replace 'ectotherms' with 'arthropods' to match the title?

      Done. “Terrestrial ectotherms” has been replaced with “terrestrial arthropods” in the abstract.

      (8d) Line 9: replace 'demographic' with 'life history'?

      Done. “Demographic” has been replaced with “life history” in the abstract.

      Introduction

      (9a) The storyline is a bit unclear. Do you want to focus on the increased threat from insect pests under climate change or on the threat of climate change on insect persistence? Please pick one and adapt your storyline accordingly. I would suggest focusing on the first and talking more about the range extension of pest species under climate change (which would also require adaptation to cold extremes).

      We agree and have refocused the Introduction on the increased threat from insect pests under climate change, emphasizing that range expansion into new regions requires adaptation to both heat and cold extremes. Both the first and second paragraphs have been revised accordingly.

      (10b) Line 31-33: What do you mean by 'shows a positive relationship between the thermal tolerance range and the level of climatic variability'? Are they able to tolerate a larger range of temperatures?

      This sentence has been revised as part of the restructured Introduction, which now focuses on the range expansion of pest species under climate change. The revised text reads: “Such range expansion requires adaptation not only to warmer conditions in existing habitats but also to cold extremes encountered during colonization of higher latitudes or elevations (Harvey et al., 2020).”

      (11c) Line 33-35: Is this information relevant here?

      Agreed. This sentence has been removed as part of the restructured Introduction, which now focuses on the threat of pest range expansion under climate change.

      (12d) Line 55-56: What exactly do we not know yet about the mechanisms that enable thermal adaptation that you aim to fill in this paper? Please rephrase your knowledge gap to be more concrete (e.g., "but we do not yet know how...").

      We have rephrased the knowledge gap to be more concrete and aligned with the revised storyline. The revised text now reads: “...we do not yet know how long-term thermal selection drives coordinated changes across gene function, metabolic networks, and life history traits to enable thermal adaptation and range expansion in pest species.”

      (13e) Line 57: Also, here, the storyline is unclear. Why did you use the diamondback moth as your model species? You provide many different reasons, but it would help if you emphasized one reason that is in line with whichever storyline you want to focus on: is it because it is an insect pest that can tolerate a wide range of temperatures?

      We have streamlined this paragraph to focus on the primary rationale: P. xylostella is a globally distributed pest that thrives across a wide range of thermal environments, making it an ideal model for studying the genetic mechanisms of thermal adaptation. Supporting details on genomic resources are retained briefly as they enable the multi-omics approach used in this study.

      (14f) Line 65: Demonstrated how? Please give a short summary of the evidence for their genetic capacity to tolerate future climates.

      We have added a brief summary of the evidence. Specifically, genome-wide SNP analysis of field populations from 114 locations across diverse biogeographical zones revealed climate-adaptive genetic variability, indicating that P. xylostella can tolerate projected future climates in most regions (Chen et al., 2021).

      (15g) Line 72: What does 'Age-stage' mean? Should it read 'Aged-staged'?

      “Age-stage, two-sex life table” is an established demographic method developed by Chi (1988) that simultaneously accounts for both age and developmental stage in both sexes. This is a standard term in the field (Chi et al., 2020), so we have retained the original wording but added a brief clarification upon first use.

      (16h) Line 78-80: This needs a bit more explanation. Why does an increased ability to scavenge superoxide anions affect adaptability under extreme temperature environments?

      We have added a brief explanation. Extreme temperatures induce oxidative stress by elevating intracellular reactive oxygen species (ROS), including superoxide anions, which can damage cellular structures. Enhanced scavenging capacity thus helps maintain cellular homeostasis under thermal stress.

      (i) Line 82-86: Please be more precise. What novel insights did you gain about the genetic mechanisms underlying thermal adaptation?

      We have revised this sentence to more precisely summarize the novel insights, encompassing both the multi-omics findings and the functional validation of PxSODC.

      Results

      (18a) The results section is very long and presents an overload of information at the moment, overwhelming the reader. Consider moving some sections to the Supplements (for example, a large part of the phenotypic data that cannot be linked to the omics data and the metabolic profiling of the mutant strains) or leave them out of the paper altogether.

      We agree that the Results section was too dense. We have streamlined it by moving the following content to the Supplementary Materials:

      (1) Detailed age-stage survival and fecundity curve data for the ancestral, hot and cold strains (Supplementary Text S1).

      (2) Detailed life table analysis of the PxSODC mutant strains (Supplementary Text S2).

      (3) Detailed untargeted metabolomic profiling of the SODC-MU mutant strains across developmental stages (Supplementary Text S3).

      The main text now retains only the key life history comparisons, extreme temperature tolerance results, omics-based evidence linking transcriptomics and metabolomics, functional validation of PxSODC, and the DNA methylation findings, with brief summaries and cross-references to the Supplements for supporting details.

      (19b) Please also provide the effect sizes for the different effects you report, for example, how many degrees difference was there between ancestral and cold strains in the supercooling/freezing points, and what was the variation?

      We have added specific effect sizes (mean ± SEM and between-group differences) for all key comparisons throughout the Results section, including preadult duration, stage-specific survival rates under extreme heat, supercooling/freezing points, and SODC-MU mutant strain comparisons. For example, the supercooling points of CS pupae (-23.99 ± 0.18°C) were 0.90°C lower than AS (-23.09 ± 0.26°C), and the freezing points were 2.66°C lower (-14.24 ± 0.61°C vs. -11.58 ± 0.52°C). Please refer to the revised manuscript for all updated values.

      (20c) Line 93-94: "Intrinsic and finite rate of increase" of what?

      Clarified. These are population growth parameters. The revised text now specifies “intrinsic rate of increase (r) and finite rate of increase (λ) of the population.”

      (21d) Line 98-99: Please start the paragraph with this summary of the results and then further detail them.

      We have restructured this paragraph by moving the summary sentence to the beginning, followed by the supporting details.

      (22e) Line 100-109: Why did you look at daily survival and fecundity rates? Please add why this is relevant.

      As part of the overall streamlining of the Results section, this paragraph on detailed age-stage survival and fecundity curves has been moved to Supplementary Text S1. A brief justification for their relevance has been added there, noting that these curves capture stage-specific variation in survival and fecundity that summary life table parameters alone may obscure.

      (23f) Line 106: What do HS, AS, and CS stand for? And please provide the statistics for comparison of daily survival rates between the strains.

      We have defined the abbreviations (HS = hot strain, AS = ancestral strain, CS = cold strain) at their first appearance in the Results section. This paragraph on daily survival and fecundity has been moved to Supplementary Text S1, where the abbreviations are also defined. The survival rates reported are the maximum daily survival rates derived from the age-stage specific survival rate curves (s<sub>xj</sub>), and the statistical comparisons among strains are presented in Supplemental Table S1.

      (24g) Line 144-146: Why are these differential metabolites likely to play a crucial role?

      We agree this statement was speculative. It has been removed from the revised manuscript.

      (25h) Line 159-161: Why is a reduction of lipid metabolites evidence for adaptive evolution?

      We have revised this sentence to clarify the reasoning. The reduction in lipid metabolites in both independently evolved hot and cold strains suggests a convergent metabolic response, indicating that lipid metabolism adjustment is a shared adaptive strategy rather than a random change.

      (26i) Line 184-185: It is difficult to judge from Figure 3E the extent of overlap in KEGG pathways between the hot and cold strains. Can you adjust the figure to emphasize that overlap more?

      Agree. To intuitively emphasize the extent of overlap in KEGG pathways between the hot and cold strains, we have completely redesigned Figure 3E. Instead of presenting two separate panels with unaligned vertical axes, we have consolidated the data into a single back-to-back (mirrored) bar chart with a shared central y-axis.

      (27j) Line 211: Not only the red module, but also the blue and green module correlates with many of the shared differential metabolites.

      We agree. We have revised the text to acknowledge that the blue and green modules also showed strong correlations with shared differential metabolites, while noting that the red module had the highest number of significantly correlated metabolites and was therefore selected for further analysis.

      (28k) Line 215: I would rephrase this as genes being interesting candidates for being involved in thermal adaptation or 'seem to be important for the adaptation of...', as you don't know from these results whether these genes play a critical regulatory role.

      Agreed. We have toned down the language to reflect the correlative nature of these results.

      (29l) Line 233: Do you mean that you further analyzed 15 genes of the 79 identified candidate genes in the previous paragraph?

      Yes, exactly. From the 79 candidate genes, we selected 15 that were both annotated in the genome and had high expression levels (FPKM > 10) for further analysis. We have clarified this in the revised manuscript.

      (30m) Line 238: What does SOD stand for?

      We have spelled out the abbreviation upon first use in this section.

      (31n) Line 254-255: Please provide the stats for this result.

      We have added the specific allele frequencies for each strain. The Leu194-Met194 mutation frequency was determined by direct sequencing of 10 individuals per strain, and the frequencies are now reported in the revised text.

      (32o) Line 303-304: How did you test for enhanced stability to temperature fluctuations? And enhanced compared to what?

      This observation was based on the survival rate data in Figure 5C, where mutant pupae at 43°C showed no significant difference from the ancestral strain, whereas other life stages (eggs, larvae, adults) at 42°C showed significantly reduced survival in the mutant strains. We have revised the text to clarify the comparison.

      (33p) Line 324-326: Why do decreased expression levels demonstrate increased O₂⁻ scavenging capacity? And why is that beneficial for adaptation to thermal stress? Please explain.

      We have revised this sentence to clarify the logic. The non-synonymous mutations in the hot and cold strains likely alter the protein conformation of SOD enzymes, increasing their catalytic efficiency per molecule. This allows effective O<sub>2</sub><sup>-</sup> scavenging at lower expression levels, which is energetically favorable under thermal stress where energy conservation is critical for survival.

      (34q) Line 404-406: I'm confused. Is there a direct link between the gene you knocked out here and the results you presented up until now? How do the reduced levels of 5-methylcytosine relate to the metabolite results you present at the beginning of the paragraph, other than that both could be involved in DNA methylation?

      We have revised this paragraph to clarify the logical chain. Among the three metabolites consistently altered across all developmental stages in the SODC-MU strains, 5-hydroxymethyluracil is involved in dynamic DNA demethylation and 5'-deoxyadenosine is a precursor to S-adenosylmethionine (the methyl donor for DNA methylation). This suggested a link between PxSODC deletion and DNA methylation. To test this, we examined PxDnmt1 expression and activity in the thermally adapted strains and found both were significantly reduced. We then used RNAi to silence PxDnmt1 and confirmed that reduced DNA methylation (lower 5-mC levels) directly impaired thermal tolerance. Thus the connection is: PxSODC deletion → altered methylation-related metabolites → reduced DNA methyltransferase activity → decreased thermal tolerance.

      (35r) Line 410: Saying that your knockdown of a gene that did not directly pop up in any of your other analyses confirms that DNA methyltransferase is associated with the response to thermal selection is a stretch. Please rephrase.

      We agree this was overstated. We have toned down the language to reflect that the RNAi results provide preliminary evidence for a potential role of DNA methylation in thermal tolerance, rather than confirmation.

      Discussion

      (36a) The phenotype data are currently not discussed at all. Please add it to the discussion and try to integrate it more with the omics data you collected.

      We agree. To provide a cohesive narrative and avoid redundancy, we have addressed this comment in conjunction with our pathway interpretation (please see our response to Reviewer 1, Comment 1). In the revised Discussion, we explicitly integrated our specific phenotypic findings (e.g., accelerated development, increased fecundity, and heat survival in the hot strain; prolonged lifespan and lowered supercooling points in the cold strain) with the distinct transcriptomic and metabolomic profiles. This integration demonstrates how molecular and metabolic rewiring directly underpins the divergent life-history traits without engaging in unwarranted speculation.

      (37b) Line 433-434: I don't think this adequately represents the relevance of your particular study. I would suggest changing it to be more in line with the storyline of understanding the capacity for global dispersal in insect pests under climate change.

      We agree. We have revised this sentence to align with the storyline of pest range expansion under climate change.

      (38c) Line 476: This is a very odd statement; don't all species' genomes have genes encoding proteins involved in thermal adaptation? The reference also doesn't seem to be appropriate. I would suggest deleting this sentence.

      Agreed. This sentence has been removed.

      (39d) Line 483: Please write out SOD the first time you use it in a new section.

      Done. SOD has been spelled out at its first use in the Discussion.

      (40e) Line 544-548: This is a bit too specific to be the last sentence of the discussion. Try to formulate it more broadly in terms of what future research should focus on in general, not just your specific research.

      We agree. We have broadened the final sentence to address future research directions more generally.

      Figures

      (41a) Figure 1A: I don't think t-tests are appropriate here since you are not simply comparing two treatments, but testing for the effects of 5-6 different temperatures. And how did you correct for replicate populations in your analysis?

      Clarified. In Figure 1A, our comparisons are independent pairwise tests between exactly two strains (HS vs. AS) at each specific temperature and time point, making t-tests statistically appropriate. We were not testing for a continuous effect across temperatures. Regarding replicate populations, the individuals used in these assays were drawn from across the six replicate populations per treatment, with each biological replicate (n = 6, with 20 individuals per replicate) comprising individuals pooled from across the replicate populations to account for inter-population variation. We have clarified this in the revised figure legend.

      (42b) Figure 1B, Figure 5D, Figure 7: bar graphs are used for count data, so do the data represent the number of individuals with a certain trait value? If they are instead showing the mean of the population/treatment group, please use mean points ± standard errors instead.

      Accepted. The data in these figures represent continuous physiological traits (e.g., supercooling/freezing points) showing the mean of the populations, rather than count data. To align with current data visualization standards for continuous variables and to provide full transparency of the underlying data distribution, we have replaced the bar graphs in Figures 1B, 5D, and 7 with scatter plots. These revised figures now display the mean ± SEM overlaid with all individual biological replicate data points.

      (43c) Figure 3B: There is a typo in the graph, it reads 'Stattistics' instead of 'Statistics'.

      Corrected. The typo ‘Stattistics’ in Figure 3B has been fixed.

      (44d) Figure 3C: I don't understand what the colors of the graph mean here. Is it the average differential expression of each replicate compared to the ancestral?

      Clarified. We have updated the figure legend to explain that the colors represent the Pearson correlation coefficient (r) between pairs of biological replicates, indicating the degree of transcriptomic similarity among samples.

      Methods

      (45a) Please start each new methods paragraph with the purpose of the method/analysis, for example, "To investigate XX, we used method X to measure X". It is at the moment hard to understand why certain things were done.

      We agree. We have revised each Methods paragraph to begin with a clear statement of purpose, so that the rationale for each analysis is immediately apparent. All changes are shown in the revised manuscript.

      (46b) Line 575-578: Why were the selection regimes with cycling temperatures and the control with constant?

      The cycling temperatures in the hot (32°C/27°C) and cold (15°C/10°C) regimes were designed to simulate diurnal temperature fluctuations (12h light/12h dark) that more closely reflect natural thermal environments. The control was maintained at a constant 26°C, which is the established optimal developmental temperature for P. xylostella (Liu et al., 2002) and represents the standard laboratory rearing condition. We acknowledge this asymmetry and have added a justification in the revised manuscript.

      (47c) Line 581: How many generations was the ancestral population kept in the lab before the start of the selection experiment? And for how many generations were the populations selected?

      The ancestral population was maintained in the laboratory for approximately ~170 generations (from July 2012 to the start of the selection experiment) before the thermal selection began. The hot strain was selected for ~75 generations and the cold strain for ~15 generations over the three-year experiment. We have added this information to the revised manuscript.

      (48d) Line 585-586: I don't understand what you mean by randomly selecting six replicate populations per treatment for downstream experiments when you only had six replicate populations per treatment to begin with (as detailed in Line 574)?

      We apologize for the confusion. All six replicate populations per treatment were used for downstream experiments. We have corrected this sentence to remove the misleading “randomly selected” wording.

      (49e) Line 590: Were these 90 eggs also randomly selected, like for the individual life tables? And were these kept at the baseline temperature conditions?

      Yes, the 90 eggs were randomly selected and maintained under the baseline favorable temperature (26°C). We have clarified this in the revised manuscript.

      (50f) Line 606: Which life history and population fitness parameters were calculated?

      We have specified all parameters calculated in the revised manuscript.

      (51g) Line 609: Link to software doesn't work.

      We have updated the software link to the current working URL.

      (52h) Line 611: Please spell out what 'BT' stands for.

      Done. “BT” has been spelled out as “bootstrap” upon first use.

      (53i) Line 612-613: How many tests did you do? Did you correct for multiple testing? Using what method?

      The paired bootstrap method implemented in TWOSEX-MSChart inherently accounts for multiple pairwise comparisons through 100,000 bootstrap replications. We have clarified the scope of comparisons in the revised manuscript.

      (54j) Line 620-621: What does biological replicate mean here? Individual eggs / larvae / pupae / adults, or were all or some life stages pooled? Also, you now only detailed which samples were collected for metabolomic profiling, were the same samples used for transcriptomic profiling, or a subset?

      Each biological replicate consisted of pooled individuals at the same developmental stage. The same sample collection strategy was used for both metabolomic and transcriptomic profiling, but from independent biological replicates (six for metabolomics, three for transcriptomics). We have clarified this in the revised manuscript.

      (55k) Line 637: Also here, how many tests did you do? Were p-values corrected for multiple testing? Using what method?

      Differential metabolites were identified through pairwise comparisons using Student's t-test with FDR correction for multiple testing. A multi-criteria threshold of |log<sub>2</sub>Fold Change| ≥ 1, VIP ≥ 1, and FDR < 0.05 was applied. This approach was used for all metabolomic comparisons, including HS vs. AS, CS vs. AS, and SODC-MU vs. AS. We have clarified this in the revised manuscript.

      (56l) Line 662: And here: how many tests did you do? Did you correct for multiple testing? Using what method?

      In the WGCNA analysis, Pearson correlations were calculated between each module eigengene and each of the 30 common differential metabolites, resulting in a total of 29 × 30 = 870 correlation tests. Following standard WGCNA practice, rather than applying FDR correction, we used a stringent dual threshold of |correlation coefficient| > 0.8 and P < 0.05 to identify significant module-metabolite associations, which effectively controls for false positives (Langfelder and Horvath, 2008). We have clarified this in the revised manuscript.

      (57m) Line 663: How did you select these modules? The ones that significantly correlated with differential metabolites? Why did you not use the phenotype data here?

      Modules were selected based on significant correlations (|correlation coefficient| > 0.8, P < 0.05) with differential metabolites shared between the hot and cold strains. We chose metabolites rather than phenotype data as the trait input for WGCNA because metabolites serve as intermediate molecular phenotypes that bridge gene expression and organismal phenotypes, providing a more direct link to the underlying regulatory mechanisms. This approach allowed us to identify gene modules most closely associated with the metabolic changes driven by thermal adaptation, which could then be connected to the observed life history and fitness divergence.

      (58n) Line 666: move RNA extraction details to before RNAseq methods description.

      Done. The “RNA extraction and cDNA synthesis” section has been relocated to before the “Transcriptomic profiling” section for better logical flow.

      (59o) Line 836: This paragraph describing the statistics is very short, and it is unclear to what data the described analyses apply. As the different types of data are very different, I expect the analyses to differ as well. Please describe the statistical analyses for each data type in more detail, specifying what tests you used, which, and how many comparisons were performed.

      We agree. The statistical methods for life table analysis, metabolomics, and transcriptomics have been detailed in their respective method sections. We have expanded the Data analysis section to specify the statistical tests for the remaining experimental data.

      (60p) Line 837: Please include your SPSS scripts to ensure the reproducibility of your results.

      The statistical analyses in SPSS were performed using the graphical user interface. As all statistical tests, parameters, and comparison groups have been described in detail in the revised Methods section, and the raw data have been deposited in public repositories (see Data availability), we believe the analyses are fully reproducible. We are happy to provide additional details if needed.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This research sheds light on the nuanced role of ABHD6 in the regulation of AMPARs, highlighting its interaction with TARP γ-2 as a critical factor in modulating receptor-gating kinetics. It is crucial to understand that while ABHD6 alone does not alter AMPAR kinetics, its presence alongside TARP γ-2 leads to accelerated deactivation and desensitization of AMPARs, impacting synaptic transmission dynamics.

      Strengths:

      Important findings in the research include:

      ABHD6 does not affect the gating kinetics of GluA1 and GluA2(Q) homomeric receptors independently.

      In the presence of TARP γ-2, ABHD6 accelerates deactivation and desensitization of these receptors, regardless of their splicing or editing isoforms.

      The effect is consistent for both homomeric GluA1 and GluA2(Q) receptors and heteromeric GluA1i/GluA2(R)i-G receptors.

      The recovery from desensitization of GluA1 with the flip splicing isoform is slowed by ABHD6 in the presence of TARP γ-2.

      We are grateful for the reviewer's positive comments. It is really exciting to have one’s comments like “This research sheds light on the nuanced role of ABHD6 in the regulation of AMPARs”.

      Weaknesses:

      However, the study focuses on specific receptor subunits and isoforms, which may not fully represent the diversity of AMPAR compositions found in vivo (e.g. though the authors have claimed that TARP γ-2 failed to increase GluA3-induced currents significantly, the effect on GluA4 or the explanation was missing). Further research is needed to explore the implications of these findings in more complex neuronal environments.

      Thank the reviewer for raising this point. To investigate whether ABHD6 is involved in the kinetic regulation of neurons, we recorded glutamate-induced currents at –70 mV using ABHD6 knockout neurons. We found that ABHD6 knockout neurons exhibited significantly slower deactivation and desensitization kinetics (Fig. 6, Table. EV7.1, EV7.2). Regarding the diversity of AMPAR subunit compositions, we obtained consistent results for GluA4, which is expressed at higher levels in the cerebellum and brainstem (Fig. 7, EV7, Table EV8.1, EV8.2). Specifically, we observed that ABHD6 accelerates the deactivation and desensitization of homomeric GluA4–TARP γ-2 complexes.

      Reviewer #2 (Public Review):

      Summary:

      Cong et al. investigated the regulatory effects of ABHD6 on AMPARs. The authors performed adequate electrophysiology recordings to show the exact pattern of this regulation and covered major critical points.

      Strengths:

      The authors have performed high-quality ephys recordings and examined all potential regulatory aspects of ABHD6 on AMPARs. This is important to understand the AMPAR functions.

      We greatly appreciate the reviewer’s positive comment on our manuscript and recognition of our quality ephys recordings.

      Weaknesses:

      (1) The authors discussed CNIH-2 extensively from line 92-110 in the introduction, however, they did not perform related experiments. I suggest they move this part to the discussion where they also discussed the roles of CNIH.

      We thank the reviewer for the suggestions. Accordingly, we have moved the discussion of CNIH‑2 to the Discussion section (lines 355–372) of the revised manuscript: “Other key modulators include cornichon family AMPA receptor auxiliary proteins (CNIH-2/3) and GSG1L, which generally slow receptor kinetics in heterologous expression systems (Kato et al., 2010; Schwenk et al., 2012), although their effects in neurons can be context-dependent (Gu et al., 2016; Mao et al., 2017). Additional diversity arises from synapse-enriched proteins such as SynDIG4 and CKAMP44, which exert complex and sometimes opposing effects on different kinetic parameters (Matt et al., 2018; Khodosevich et al., 2014). This diversity comes from the known co-assembly of AMPA receptor subunits (the pore-forming GluA subunit) with three classes of auxiliary proteins—collectively comprising 21 components, most of which are secretory or transmembrane proteins. Importantly, multiple auxiliary subunits (e.g., TARP γ-8 and CNIH-2) can co-assemble within a single AMPAR complex, and their combined presence modulates functional outcomes in ways not predicted by individual subunits alone, underscoring a combinatorial regulatory logic (Shi et al., 2010; Yu et al., 2021; Herring et al., 2013). Given that native synaptic AMPARs predominantly exist as GluA2-containing hetero-oligomers (e.g., GluA1/2, GluA2/3), although homo-oligomers have also structurally validated, understanding how novel auxiliary proteins such as ABHD6 integrate into this complex framework becomes paramount (Lu et al., 2009; Wenthold et al., 1996; Zhao et al., 2016; Malinow and Malenka, 2002).”

      (2) The authors need to report the "n" for all the experiments they have presented in this manuscript. How many cells were recorded in each condition? How many batches? This information has to be in all of the figure legends, but it is missing except Fig. 4.

      We appreciate the reviewer for pointing out these weaknesses, we added the cell number and corresponding batches in every figure and table in the revised manuscript.

      (3) One question is what the physiological meanings of this regulatory effect are. The authors may consider adding some discussions.

      We thank the reviewer for the suggestions. In the revised manuscript, we have included a discussion on the physiological implications of this regulatory effect in lines 386–412, as follows: “Although there is no direct evidence indicating that ABHD6 and TARP γ-2 bind to each other, both are known to associate with AMPA receptors, suggesting the possibility of indirect or regulatory interactions. For example, their relationship could be transient, condition-dependent, or mediated through mechanisms such as conformational changes or steric hindrance (Gill et al., 2011b; Sumioka, 2013; Wei et al., 2017). Studies have reported that scaffold proteins participate in the binding, anchoring, maintenance, and removal of AMPA receptors, either through direct interaction with receptors or through indirect binding via auxiliary subunits (Danielson et al., 2014). Additionally, we extended the same experimental approach to AMPA receptors containing the GluA1 flip subtype together with TARP γ-8. Our results demonstrate that this ABHD6-dependent regulatory mechanism also applies to other TARP family members, including TARP γ-8 (Figure 7, EV7, Table. EV9.1, EV9.2). Our findings indicate that ABHD6 plays a critical negative regulatory role on AMPA receptor function. It suppresses synaptic current amplitude and accelerates the deactivation and desensitization kinetics in a TARP γ-2-dependent manner. By shortening synaptic response duration and reducing total charge transfer, ABHD6 may thereby restrain neuronal excitability and narrow the temporal window for synaptic integration. Loss of ABHD6 function—as observed in our knockout neurons, which exhibit slowed kinetics—could promote excitatory hyperactivity. Thus, as a key “molecular brake” on synaptic excitability, dysregulation of ABHD6 may directly contribute to the pathogenesis of neurological disorders. Insufficient braking function may lead to excessive synaptic transmission, strongly correlating with hyperexcitability conditions such as epilepsy. Conversely, overly potent braking might result in synaptic dysfunction, potentially contributing to early synaptic impairment in cognitive disorders like Alzheimer’s disease. Overall, our research highlights ABHD6 as a promising target for novel therapeutic strategies in neurological disorders and provides a solid theoretical foundation for further investigation in this field.”

      (4) About statistics. The authors need to add more details and make sure their statistics sound. For example, they also need to check the equality of variances. In their Table EVs, where the P values are reported, the authors need to report which statistics they have used, one-way ANOVA, K-W test, or others, and the exact post-hoc test type for each comparison. For one-way ANOVA, report the F values simultaneously with the P values in all figure legends.

      We appreciate your thoughtful advice. Accordingly, we have added the description of statistical strategy in the revised manuscript in line 530-536: “Data were first assessed for normality using the D’Agostino–Pearson test (n<50) or the Kolmogorov-Smirnov test (n>50), and for equality of variances using the Brown-Forsythe ANOVA test. Depending on the outcome of these tests, data were analyzed by parametric (one-way ANOVA) or non-parametric methods (Kruskal-Wallis test) followed by Tukey's Honest Significant Difference (HSD) test as a post hoc analysis to determine specific differences among groups. Correlation was evaluated with Pearson correlation analysis. Values of P < 0.05 were considered statistically significant.”

      (5) Fig. 3J, the authors need to correct the label of the Y axis. It is shifted

      Thank the reviewer for raising this point, we have corrected the label of the Y axis of Fig. 3J in the revised manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      The manuscript is well-structured and the findings are presented clearly. While the study addresses multiple isoforms, a more detailed explanation of the isoform-specific effects observed, e.g. the unique behavior of the GluA2(Q)i-G isoform in terms of deactivation, would be beneficial.

      We appreciate the reviewer for pointing out these weaknesses. In response, we have added a discussion in the revised manuscript in line 330-345 that addresses RNA editing as a key regulatory mechanism of AMPAR function beyond subunit composition and splicing variants: “Beyond subunit composition and splicing variants, the function of AMPARs is also finely regulated by RNA editing. Q/R editing enables the conversion of neutral to positively charged residues in the ion-selective filter of the channel, causing impermeability to divalent cations such as Ca<sup>2+</sup>. This not only alters channel conductance and current but also contributes to neuronal dysfunction and excitotoxicity (Kawahara et al., 2004; Kwak and Kawahara, 2004). R/G editing markedly influences receptor desensitization and recovery kinetics, and may modulate interactions with auxiliary proteins, thereby playing a critical role in synaptic plasticity and development (Stern-Bach et al., 1998; Coombs et al., 2012; Wright and Vissel, 2012). The conversion from R to G weakens inter-dimer interactions within the binding domains, leading to structurally more flexible receptors (Lomeli et al., 1994). Furthermore, R/G editing exhibits strong developmental regulation and varies across brain regions and cell types (Geiger et al., 1995). Therefore, in this study, we systematically examined the effect of ABHD6 on different flip/flop splice variants and R/G editing subtypes. Our results demonstrate that ABHD6 also suppresses currents in HEK 293T cells expressing flop splice variants and R/G-edited receptors.”

      The authors should consider discussing potential mechanisms underlying the interaction between ABHD6 and TARP γ-2 in greater depth. This could include hypotheses on how ABHD6 might be influencing TARP γ-2's modulation of AMPARs if applicable (though the authors have mentioned either the potential binding domain of ABHD6 to AMPARs or TARP γ-2 to AMPARs, the proposed direct interaction between ABHD6 and TARP γ-2 is unknown). It's also unclear whether the effect of ABHD6 is specific to TARP γ-2 or is general to other TARP family members.

      We appreciate your suggestion and use affinity chromatography to examine the interaction between ABHD6 and TARP γ-2. Our investigation revealed no direct evidence of a physical binding between the two proteins. Accordingly, we have supplemented the discussion in the revised manuscript (lines 386–393) as follows: “Although there is no direct evidence indicating that ABHD6 and TARP γ-2 bind to each other, both are known to associate with AMPA receptors, suggesting the possibility of indirect or regulatory interactions. For example, their relationship could be transient, condition-dependent, or mediated through mechanisms such as conformational changes or steric hindrance (Gill et al., 2011b; Sumioka, 2013; Wei et al., 2017). Studies have reported that scaffold proteins participate in the binding, anchoring, maintenance, and removal of AMPA receptors, either through direct interaction with receptors or through indirect binding via auxiliary subunits (Danielson et al., 2014).”

      Expanding the discussion to include the potential physiological and pathophysiological implications of ABHD6's modulatory effects on AMPAR kinetics would provide a broader context for the findings.

      We thank the reviewer for the suggestions, in the revised manuscript we discussed the physiological meanings of this regulatory effect in line 386-412: “Although there is no direct evidence indicating that ABHD6 and TARP γ-2 bind to each other, both are known to associate with AMPA receptors, suggesting the possibility of indirect or regulatory interactions. For example, their relationship could be transient, condition-dependent, or mediated through mechanisms such as conformational changes or steric hindrance (Gill et al., 2011b; Sumioka, 2013; Wei et al., 2017). Studies have reported that scaffold proteins participate in the binding, anchoring, maintenance, and removal of AMPA receptors, either through direct interaction with receptors or through indirect binding via auxiliary subunits (Danielson et al., 2014). Additionally, we extended the same experimental approach to AMPA receptors containing the GluA1 flip subtype together with TARP γ-8. Our results demonstrate that this ABHD6-dependent regulatory mechanism also applies to other TARP family members, including TARP γ-8 (Figure 7, EV7, Table. EV9.1, EV9.2). Our findings indicate that ABHD6 plays a critical negative regulatory role on AMPA receptor function. It suppresses synaptic current amplitude and accelerates the deactivation and desensitization kinetics in a TARP γ-2-dependent manner. By shortening synaptic response duration and reducing total charge transfer, ABHD6 may thereby restrain neuronal excitability and narrow the temporal window for synaptic integration. Loss of ABHD6 function—as observed in our knockout neurons, which exhibit slowed kinetics—could promote excitatory hyperactivity. Thus, as a key “molecular brake” on synaptic excitability, dysregulation of ABHD6 may directly contribute to the pathogenesis of neurological disorders. Insufficient braking function may lead to excessive synaptic transmission, strongly correlating with hyperexcitability conditions such as epilepsy. Conversely, overly potent braking might result in synaptic dysfunction, potentially contributing to early synaptic impairment in cognitive disorders like Alzheimer’s disease. Overall, our research highlights ABHD6 as a promising target for novel therapeutic strategies in neurological disorders and provides a solid theoretical foundation for further investigation in this field.”.

      Some typos:

      p7L144, might miss a word 'of' after 'properties';

      Thanks for your careful advice, we have corrected “the channel properties TARP γ-2-containing AMPA receptors” to “the channel properties of TARP γ-2-containing AMPA receptors” in the revised manuscript.

      p9L178, remove '.';

      Thanks for your careful advice, we have corrected the subheading “ABHD6 accelerated the deactivation of homomeric AMPAR-TARP γ-2 complexes.” to “ABHD6 accelerated the deactivation of homomeric AMPAR-TARP γ-2 complexes” in the revised manuscript.

      p9L195, might be 'deact' instead of 'deac';

      Thanks for your careful advice, we have corrected “τ<sub>w, deac</sub>” to “τ <sub>w, deact</sub> " in the revised manuscript.

      p12L276, might be a missing 'ABDH6' after 'whether'.

      Thanks for your advice, we have added “ABHD6” after “whether” in the revised manuscript.

      Reviewer #2 (Recommendations For The Authors):

      (1) Line, 366, grammar mistake. The author used the expression "In this study, we systematically studies", which should be “study" instead of :”studies"

      Thanks for your advice, we have corrected “studies” to “study” in the revised manuscript.

      (2) Line 370, the author used the expression "However, previous studies also found poorly expressed but significant population of GluA1 homomeric receptors in the hippocampus". It looks like "poorly expressed" is somewhat contradictory to "significant". I suggest the authors revise this sentence.

      Thanks for your advice, we have deleted the statement in the revised manuscript.

      (3) Line 407-409. The authors stated, "The flip and flop isoforms were cloned into an IRES-GFP expression vector using polymerase chain reaction (PCR). ...editing variants were generated using PCR". It is impossible to use PCR only to finish all cloning, especially with IRES-GFP. This must be done via restriction enzyme, or Gibson assembly, or another method. The author probably PCRed the isoforms and then put them into the vectors using other methods. The authors need to revise their statement and make it complete and clear.

      We thank the reviewer for their suggestion. In response, we have added a description of the expression vector construction to the revised manuscript in line 431-437: “The flip and flop isoforms were cloned into an IRES-GFP expression vector using polymerase chain reaction (PCR). Q/R and R/G editing variants were generated by PCR-based cloning and FastCloning. GluA1 and TARP γ-2 were subcloned using EcoRI and SalI sites (Milstein et al., 2007), GluA2 and GluA3 were inserted with XhoI and SalI, and GluA4 was inserted with EcoRI and BamHI. All constructs were verified by restriction mapping and sequencing of PCR-amplified regions.”

      (4) It would help if the authors could show some WB blots or PCR results or other evidence that their transfection was successful, in particular with these many plasmid combinations.

      We thank the reviewer for raising this point. In response, we have included additional experiments in the revised manuscript in line 138-142: “Immunofluorescence assays and Western blot analysis were performed on cells co-transfected with GluA1, TARP γ-2, and ABHD6. These experiments were conducted to verify co-transfection efficiency and corresponding protein expression. Immunofluorescence results confirmed a high degree of co‑localization among GluA1, TARP γ-2, and ABHD6 (Fig. EV1).”

    1. Author response:

      eLife Assessment

      This is an important study that establishes a zebrafish model of PIK3CA-related overgrowth syndrome. The imaging characterization of the mesodermal, particularly vascular, lesions of the model is compelling. The scRNA-Seq analysis is convincing, revealing key perturbations in the PIK3CA-mutation model, although deeper investigation of the exact mechanism leading to the lesions, as well as validation at different time points, could further strengthen the findings. This work will be of interest to medical biologists working on PROS, and potentially to a broader audience interested in non-cell-autonomous signaling of PIK3CA and its implications in other diseases.

      We are delighted that the Editors and Reviewers consider the work of value and that it is interesting to a broad audience. We also appreciate and take on board the areas that the reviewers identify for improvement, and their suggestions on how this could be achieved.

      There are two major pieces of work suggested by the reviewers which we plan to carry out for this manuscript. The first of these is an additional scRNA-seq experiment at a later developmental stage when vascular malformations are established. Through comparison between pik3caPROS, pik3caWT and no-pik3ca injected controls, this would help answer if the global lineage and transcriptional dysregulation observed at 19 hpf persists over time, and if the largely inert ‘C0’ cluster of PROS mScarlet<sup>+</sup> cells changes during development (Reviewer 2 comment 3).

      Secondly, we are already optimising rescue experiments with the specific Pik3ca inhibitor alpelisib, which is currently used as a therapy for PROS. Some troubleshooting has been required for the best delivery method and concentration for this to rescue vascular malformations in embryos, and to cause measurable decreases in PI3K signalling at the protein level through Akt and S6 pathways.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Brunsdon et al. present a zebrafish model of mosaic PIK3CA activation to investigate mechanisms underlying PIK3CA-related overgrowth spectrum (PROS), with a particular focus on non-cell-autonomous mechanisms of tissue overgrowth. The study is timely and addresses an important gap in the understanding of how mosaic activation of PI3K signaling leads to tissue-specific developmental abnormalities.

      Using a Tol2-based mosaic expression system combined with single-cell transcriptomics, the authors provide evidence suggesting that mutant PIK3CA-expressing cells influence surrounding wild-type tissues through indirect signaling mechanisms, contributing to vascular malformations and tissue overgrowth.

      Overall, the work presents an interesting and potentially impactful model for studying mosaic PIK3CA-driven overgrowth and non-cell-autonomous signaling mechanisms. However, several aspects require clarification, additional controls, and improved presentation to strengthen the mechanistic conclusions and overall impact of the study.

      We thank Reviewer 1 for their support of our work, and constructive and helpful comments. 

      Strengths:

      This study addresses an important and timely question by investigating the mechanisms underlying mosaic PIK3CA activation in the context of PROS, a condition for which developmental mechanisms remain poorly understood. The use of a mosaic zebrafish model is particularly appropriate, as it closely reflects the mosaic nature of PIK3CA mutations observed in patients and allows the investigation of non-cell-autonomous effects.

      Another major strength of the study is the integration of single-cell transcriptomics, which provides valuable insight into potential signaling pathways involved in indirect tissue overgrowth and offers a rich dataset for hypothesis generation. The authors also propose an interesting conceptual framework in which PI3K-activated cells influence surrounding tissues through paracrine signaling, which could have broader implications beyond PROS and contribute to understanding mosaic developmental disorders more generally.

      Finally, the work has potential translational relevance, as identifying mechanisms driving mosaic PI3K activation and non-cell-autonomous signaling could inform future therapeutic strategies for PROS and related conditions.

      Weaknesses:

      Despite these strengths, several aspects of the study require clarification and additional experimentation.

      Major comments:

      (1) The Tol2-based system results in mosaic overexpression of mutant PIK3CA in the presence of endogenous wild-type PIK3CA, making it difficult to determine how co-expression of WT and mutant proteins influences the observed phenotypes. While mosaic expression is relevant to PROS, a complementary approach in which endogenous PIK3CA is knocked out prior to introducing mutant variants would allow clearer interpretation of mutant-specific effects.

      PROS/CLOVES patients co-express endogenous wild-type and mutant PIK3CA in affected cells, which in turn constitute only a small proportion of cells in affected tissues (Madsen et al. 2018). As our intent was strictly to model human PROS/CLOVES (an aim informed by support from and close collaboration with the CLOVES Syndrome Community, a key patient advocacy group), we designed our model to reflect this as closely as possible. It is not clear to us what translational end would be served by expressing mutants in a null background, interesting though this may be. Given our transgenic strategy, we did experiment with overexpressing wildtype pik3ca as a control for some experiments to test whether overexpression of pik3ca itself drives overgrowth phenotypes, without the presence of hotspot PROS mutations (Figure 3D, Supplementary Figure 1A). We found that ubiquitous or mesodermal overexpression of pik3caWT did not cause vascular malformations or cause the ectopic fli1:eGFP endothelial cell phenotype observed when overexpressing pik3caPROS variants. While not precisely addressing the reviewer’s comment, this adds to evidence that increased expression of wildtype pik3ca does not confound the observed gain of function phenotype in the PROS model. 

      (2) The authors do not clearly describe the validation of editing or integration efficiency. It would be important for the authors to clarify whether sequencing was performed to confirm integration, to quantify the proportion of mosaic expression, and to measure transgene expression levels. These controls would strengthen confidence in the model and interpretation of the results.

      We used secondary transgenesis markers, such as the cardiac reporter cmlc2:GFP, as a visual readout of integration efficiency and confirmation of integration – for example, embryos with >50% of GFP<sup>+</sup> heart cells indicates that Tol2 transgenesis has occurred efficiently and so these would be included in an experiment, whereas the presence of only 1 or 2 green cardiac cells would suggest the levels of transgene in the embryo would be negligible and so this would be excluded from the experiment. Independently of this reporter, we showed an upregulation of pik3ca transcript in PROS mosaics compared to control by scRNA-seq (Figure 4D, Supplementary Figure 4A) confirming the transgene produces a measurable upregulation of pik3ca. 

      We agree that it would be optimal to quantify the transgene expression and copy number for each individual embryo. However, for experiments where phenotypes are scored, hundreds of embryos are injected each time. Therefore, although it would be valuable to quantify the transgene expression and transgene copy number in terms of finding its correlation to phenotype severity, it is not feasible to do this at this scale. In the future, we would like to refine our model to include more sophisticated inducible transgenic models, with stable integration sites to control for integration site/copy number variation. However, for this manuscript, the priority as set out by our charity funders was to generate and characterise a pik3caPROS model that could rapidly test different patient hotspot alleles as well as tissue-specific promoter drivers. Thus, we chose this simpler model for now, but we would be very interested in continuing this work with a more refined model for one or two mutations (See Reviewer comment 1). 

      This heterogeneity in transgene dosage and expression levels will inevitably have introduced ‘noise’ into our data. We can account for this somewhat by large numbers of embryos injected per experiment and reproducibility across populations of zebrafish between experiments. We also note that this strategy reflects the heterogeneity in human PROS, with disease mosaicism, presentation, and severity being highly variable from person to person. Therefore, we don’t necessarily see this as a drawback for our current approach. 

      (3) The manuscript would benefit from rescue experiments to strengthen causal conclusions. It remains unclear whether the phenotypes induced by PIK3CA PROS variants can be rescued, either through expression of wild-type PIK3CA, pharmacological inhibition of PI3K signaling, or assessment of developmental reversibility. Such experiments would strengthen the link between PI3K activation and the observed phenotypes.

      We agree this is an exciting direction and a great next step for this research to take. This work is currently ongoing, using the specific Pik3ca inhibitor alpelisib, and optimizing treatment conditions to ensure our experimental readouts are meaningful. Through phenotype scoring we do see a significant rescue in the severity of vascular malformations in PROS mosaic embryos. However, we didn’t feel this work was ready for the initial submission because (1) the concentrations we must add to the zebrafish medium by immersion are far higher than the doses needed for inhibition of PI3K signalling in human cell lines and (2) we do not see an obvious decrease in pAkt or pS6 levels by western blot analyses of embryos at alpelisib doses of up to 100 μM, for either short or long term exposure. This drug is poorly soluble in water, and so we are also experimenting with introducing it to embryos intravenously. 

      (4) The authors propose candidate signaling molecules mediating non-cell-autonomous effects downstream of PI3K hyperactivation; however, these conclusions remain speculative, as no functional validation is provided. Testing selected candidate mediators identified in the RNA-seq dataset would significantly strengthen the mechanistic conclusions.

      We thank the reviewer for this suggestion, and it is indeed a long-term aim of our work to find better treatments for PROS by combining inhibition of PI3K signalling with other candidate mediators to treat overgrowth. Our scRNA-seq experiments suggest that Notch, Wnt and Ephrin signalling pathway components may contribute to disease, and so a lot of potential for treatment strategies. After we have optimised treatment with alpelisib to rescue our disease phenotype in line with current mammalian models (see response to Comment 3 above), then we will start to look at other candidate mediators alone or in conjunction with alpelisib. However, given the challenges we are facing with the alpelisib treatment, we may need to develop this work in a subsequent study. 

      Reviewer #2 (Public review):

      In this manuscript, Brunsdon et al. aim to study PIK3CA-related overgrowth spectrum (PROS) by establishing a mosaic zebrafish model with overexpression of pik3ca carrying hotspot mutations, coupled with an mScarlet+ reporter. Using fluorescence microscopy, the authors demonstrated that overexpression of pik3ca with a number of hotspot mutations led to mesodermal and particularly vascular malformations in the zebrafish model. Interestingly, they found a paucity of mScarlet+ mutant cells in the vascular lesions, consistent with the finding of low PIK3CA mutation burden in PROS tissue. Such data suggest a non-cell-autonomous effect of PIK3CA mutation. Following this logic, the authors performed single-cell RNASequencing on zebrafish overexpressing WT pik3ca and mutant pik3ca at 19 hpf, and demonstrated widespread transcriptomic perturbations across multiple lineages, including lineage frequencies, key cell pathways, and cell-cell interactions. Importantly, they demonstrate that mScarlet+ cells carrying mutant pik3ca cluster separately from other cell types, do not demonstrate clear lineage identity, and have a general downregulation in signaling components.

      Overall, the conclusions in the manuscript are well-supported by the presented data. The imaging studies are particularly convincing. The transcriptomic analysis generated a list of potential pathways to further investigate and potentially target with future therapeutic interventions. Importantly, this study provides a valuable in vivo model of PROS that: 1) recapitulates key features of PROS (e.g., multiple mesodermal defects, paucity of mutation burden in lesions suggesting non-cell-autonomous interactions); 2) is scalable; and 3) offers direct visualization of lesion development, compatible with time-course live imaging. This model will be valuable to further understand PROS and potentially study other diseases where the PIK3CA pathway is altered (e.g., certain cancers).

      We thank Reviewer 2 for their careful reading and support of our manuscript, and their helpful suggestions. 

      The following are not necessarily weaknesses of the data, but rather suggestions where the manuscript could be further strengthened:

      (1) The model recapitulates the variability of mesodermal lesions in PROS. It would be valuable to utilize this model to further study factors that are associated with the development of more severe lesions (e.g., by comparing samples with more severe lesions to those unaffected despite carrying the mutations, Figure 1F).

      This is a very interesting question, and something that we have wondered ourselves. The clinical observation that PROS mutations cause pathology in mesodermal-derived tissues suggests that there is a lineage permissivity of PROS mutations. We plan to perform additional scRNA-seq experiments on later stage embryos (aligned with Figure 1) and hope to incorporate comparison of embryos with more severe lesions to those unaffected despite carrying pik3caPROS mutations. 

      (2) ScRNA-seq analysis could be enriched with a comparison between cells overexpressing mutant pik3ca vs. those overexpressing WT pik3ca.

      The scRNA-seq experiment presented in this paper was limited by funding constraints at the time, and so we focussed on choosing samples that were likely to yield the most meaningful data. Ideally, we would have included a WT overexpression control in addition to an injected no-pik3ca control, however as we did not observe any phenotypes associated with mosaic pik3caWT transgenic embryos (Supplementary Figure 1A, Figure 3D), we chose to not include this condition. We are grateful for subsequent funding that will allow us to perform a scRNAseq experiment at a later timepoint, detailed below, where we plan to include this control.

      (3) In the scRNA-Seq analysis, it is curious that the C0 cluster, enriched with mScarlet+ cells, is found to have downregulated signaling interactions (Fig. 5C), yet exerts a widespread noncell-autonomous effect. Meanwhile, there is also a noticeable loss of certain lineages (e.g., notochord, Figure 4E) and related cell-cell interactions (e.g., notochord-related interaction, Figure 5A). A deeper exploration of the basis of the non-cell-autonomous effect would be valuable.

      Thank you for this important comment. We agree that this finding is very interesting and warrants further investigation, although a definitive answer may be too difficult for this current revision. Using conventional differential expression analyses on our scRNA-seq data (such as was used in Figure 4), we could not find significant upregulation of many genes and pathways, and CellChat and NICHES analyses did suggest that signalling between C0 and other clusters was weak. Nevertheless, using the Decoupler package, we did find significant upregulation of some footprint signatures enriched in mScarlet<sup>+</sup> vs - cells in PROS mosaics (Supplementary Figure 4B) including PI3K and EGFR (as one would expect), but also apoptosis and UV response suggesting that overexpression of pik3caPROS may cause cellular stress. Using NICHES, we also found Myc, Notch, Wnt and Ephrin ligand-receptor pairs to be upregulated in PROS mosaic C0 sending and receiving interactions compared to controls, which would be candidates for validating in subsequent studies (Supplementary Figure 4C). We will be interested to determine if C0 like cells are present in older embryos in our scRNA-seq analysis, and if they have similar signalling activity.

      (4) The scRNA-Seq analysis was performed at one time point (19 hpf). Additional analysis (not necessarily by scRNA-Seq) at other time points to study whether findings at 19 hpf are persistent throughout development or undergo dynamic changes (e.g., cell fate/state of mSc+ mutant cells) would be helpful.

      We agree that the inclusion of a later timepoint in our scRNA-seq experiment would be valuable in answering a lot of our questions about the fate of C0 cells and the persistence of the transcriptional dysregulation, including non-cell autonomous interactions that we see at 19 hpf. As mentioned above, we were constrained by time and funding for the original experiment but are now in a position to add to this work and address this point.

      (5) The scRNA-Seq analysis provides a valuable list of perturbed interactions that could be targeted by future therapeutic approaches. Validation of the scRNA-Seq findings with proteinlevel analysis, and studying the effect of targeting some of the pathways on the disease phenotype, would offer valuable data for the community.

      Thank you for this comment. We agree that this an essential next step to take and is also a priority for our patient advocates. As mentioned above (Reviewer 1, point 4), we would like to be confident that alpelisib is on-target in our system first, and then we very much want to identify new therapeutic venues to explore in this pre-clinical space.

      Reviewer #3 (Public review):

      Summary:

      The study "PIK3CA-related overgrowth spectrum (PROS) zebrafish models reveal panlineage developmental dysregulation" presents important findings that extend significantly beyond a single subfield, bridging developmental biology, vascular medicine, and cancerrelated PI3K signalling. By developing mosaic zebrafish models of PROS and combining live imaging with single-cell transcriptomics, the authors provide compelling evidence for a noncell-autonomous mechanism of tissue overgrowth, a conceptual shift with meaningful therapeutic implications.

      We thank Reviewer 3 for their time and thoughtful comments considering our work.

      Strengths:

      The evidence is overall convincing, with methodology appropriate and well-validated relative to the current state of the art; the integration of multiple approaches (in vivo modelling, scRNAseq, ligand-receptor inference) strengthens the central claims. However, some aspects of the proposed non-cell-autonomous signalling mechanisms remain partly correlative, and direct functional validation of the rewired ligand-receptor interactions would further consolidate the conclusions.

      Weaknesses:

      The transgenic overexpression approach chosen by the authors represents a well-established and effective strategy for generating mosaic models in zebrafish. However, this approach introduces notable limitations: the lack of control over transgene dosage and unknown integration sites may generate non-physiological effects, potentially confounding the interpretation of key findings.

      Thank you for this important comment. We agree that there are limitations in our current model, and we are working to refine it such that we have temporal as well as spatial control over the expression of pik3caPROS. 

      Our funding for the start of this study came from the CLOVES Syndrome community charity, and in collaboration with them, we decided that for this work, our priority was to understand more about the disease mechanisms at disease onset, and also to be able to test multiple pik3ca hotspot mutations that affect patients. One question for families is if the pik3ca hotspot mutations contribute differently to patient overgrowths. Our data here suggests that all mutations are able to promote overgrowth equally, and that differences between disease presentation in patients likely reflects the timing and cellular origins of the mutation. 

      As a side note, together with CLOVES Syndrome community, we also felt that we wanted to test actual patient mutations, rather than artificial hyperactivated variants of Pik3ca such as the widely used p110a* allele (Hu et al. 1995; Venot et al. 2018), which can inform important mechanisms about pathway dysregulation, but less about actual patient-specific disease mutations.

      The authors are certainly aware that alternative approaches (though technically more demanding) could be considered in future studies to further strengthen the model. For instance, a CRISPR/Cas9-mediated knock-in of the pik3ca-PROS allele at the endogenous locus (retaining upstream native regulatory elements with only a minimal promoter in the construct, co-expressed with a fluorescent reporter via P2A) could allow even more physiological, lineage-restricted expression while enabling direct visualisation of mutant cells. Mesodermal specificity could potentially be further refined by driving mosaic Cas9 expression under a pan-mesodermal tbx promoter, restricting editing to the relevant lineage while simultaneously marking mutant cells fluorescently, thus even more closely mimicking the postzygotic mutational events characteristic of PROS. As a complementary strategy, blastula transplantation experiments using pik3ca-PROS donor cells (ideally co-expressing a distinct fluorescent marker such as mCherry) into fli1:GFP transgenic hosts could provide a powerful and technically consolidated approach to directly visualise and quantify non-cell-autonomous effects on host vasculature, with precise control over mutant cell burden. This combinatorial framework, separating donor mutant cells from host tissue in a two-colour imaging setup, could be particularly compelling for validating the ligand-receptor rewiring predicted by single-cell transcriptomics in future investigations.

      These reflections are offered in the spirit of prospective methodological development and do not diminish the value of the current work, which opens a valuable new avenue for therapeutic investigation, suggesting that targeting indirect overgrowth-propagating signals, alongside PI3K inhibition, deserves serious consideration.

      Thank you for these excellent suggestions and feedback. We are keen to try to generate fish that more closely align with what is happening in patients. Two challenges we have faced include: 

      (1) In our hands, the pik3ca promoter itself is not strong enough to drive fluorophore expression to an extent that we can observe fluorescent PROS cells in zebrafish. As a control, after we saw no fluorescence attempting to knock-in fluorophores at the 5’ end of endogenous pik3ca, we tried making a transgenic using various lengths of pik3ca promoter regions driving GFP expression. Despite having stable integration of the transgene shown by a secondary transgene reporter inherited through to F1 generation, we could not visualise GFP/mNeonGreen expression at any stage of development.

      (2) A drawback of the IRES approach we used here is that the fluorophore expression levels will be lower than using a short cleavable peptide sequence such as P2A. Unfortunately, the critical kinase region (and location of the orthologous hotspot codon 1048) is located only a few amino acids from the stop codon, and we found that the function of Pik3ca was likely impeded by the addition of several extra amino acids after the P2A cleaves itself.

      Despite these challenges, we hope to be able to generate models in future with more precise control over mutant cell burden. 

      References

      Hu Q, Klippel A, Muslin AJ, Fantl WJ, Williams LT. 1995. Ras-dependent induction of cellular responses by constitutively active phosphatidylinositol-3 kinase. Science 268: 100102.

      Madsen RR, Vanhaesebroeck B, Semple RK. 2018. Cancer-Associated PIK3CA Mutations in Overgrowth Disorders. in Trends in Molecular Medicine, pp. 856-870. Elsevier Ltd.

      Venot Q, Blanc T, Rabia SH, Berteloot L, Ladraa S, Duong JP, Blanc E, Johnson SC, Hoguin C, Boccara O et al. 2018. Targeted therapy in patients with PIK3CA-related overgrowth syndrome. Nature 558: 540-546.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Javid and colleagues worked to understand the molecular mechanisms involved in mistranslation in mycobacteria. They had previously discovered that mistranslation is an important mechanism underlying antibiotic tolerance in mycobacteria. Using a clever genetic screen they identify that deletion of gidB, a 16S ribosomal RNA methyltransferase, leads to lowered mistranslation (i.e. higher translational fidelity), but only in genetic backgrounds or environmental conditions that increase mistranslation rates.

      Strengths:

      The strengths of this manuscript are the clever genetic screen, the powerful mistranslation assays, and the clear writing and figures explaining a complex biological problem. Their identification of gidB as a factor important for mistranslation deepens our knowledge about this interesting phenomenon.

      We thank the Reviewer for their summary of our work and the strength of coupling specific mistranslation assays with the genetic screen approach.

      Weaknesses:

      The structural work at the end feels like both an afterthought in terms of the science and the writing. I would suggest re-writing that section to be clearer about what the figure says and does not say. For example, the caption of Figure 6 appears to be more informative than the text and refers to concepts not present in the main text. In general, I found this section to be the most difficult to understand.

      We have revised this section, including re-analysis of the structural data and completely new figures, as well as revised comments placing the findings in the context with the other data. See Revised Figs. 6.

      Reviewer #2 (Public review):

      Summary:

      Protein synthesis - translation - involves repeated recognition and incorporation of amino-acyl-tRNAs by the ribosome. This process is a trade-off between the rate and accuracy of selection (for review see (Johansson et al, 2008; Wohlgemuth et al, 2011)). The ribosome does not just maximise the rate or the accuracy, it balances the two. Therefore, it is possible to select mutants that translate faster than the wt (but are sloppy) or that are very accurate (more than the wt) but translate slower. Slow translation is detrimental as it limits the rate of protein synthesis (and, therefore, growth) and hyper-accurate mutants accumulate mis-translated proteins, which is detrimental for the cell.

      Bi and colleagues employ genetics, MIC measurements, reporter assays, and structural biology to characterise the role of GidB rRNA methylase in translational accuracy in Mycobacterium smegmatis.

      Strengths:

      The genetics and phenotypic assays are convincing and establish the biological role of the methylase. The authors use a powerful set of complementary assays that convincingly demonstrate that the loss of GidB results in mistranslation.

      We thank the Reviewer for their recognition of the strengths of our work, including the combination of genetic screens and specific assays to demonstrate the contribution of GidB in specific translational fidelity in mycobacteria.

      Weaknesses:

      (1) It would be essential to provide information regarding the growth rate and, ideally, translation rates in the gidB KO and the isogenic WT. As translation balances accuracy and speed, only characterising the speed is not sufficient to understand the phenomenon.

      We have now performed these assays (New Fig. S6). (1) The growth rate of gidB1-KO is the same as the respective background (WT or HWS19) strain with functional GidB. (2). We have performed a measure of translational efficiency as a surrogate for speed (see PMID 32723820), New Fig. S7. As can be seen, deletion of GidB does not affect translation of Nluc luciferase, in both WT and HWS19 backgrounds, suggesting that discrimination of mischarged tRNAs (even in a context in which that is the dominant form of translational error), is not rate-limiting, and that this form of accuracy is distinct to ribosomal mRNA decoding. This is further corroborated by a new preprint from our group (https://www.biorxiv.org/content/10.1101/2024.10.20.619312v2) that a novel small molecule that also increases specific translational fidelity does not affect translational efficiency, suggesting that this is a conserved phenomenon in mycobacterial translation.

      (2) Cryo-EM analysis of vacant 70S ribosomes is not sufficient for understanding the mechanisms underlying the accuracy defects in the gidB KO. One should assemble and solve structurally near-cognate and non-cognate complexes. I believe the authors are over-interpreting the scant structural data they have. Furthermore, current representation makes it impossible to assess the resolution of the structure, especially in the areas of interest.

      While we agree with the Reviewer that structures of translating ribosomes will be most informative in elucidating the molecular mechanism(s) by which methylation (or not) by GidB contributes to mistranslation, those experiments are ongoing and beyond the scope of the current study. Unlike E. coli ribosomes, for which there are a plethora of structures for mutants available, there are very structures of mycobacterial ribosomes beyond wild-type apo ribosomes. Therefore, we feel that the structures of apo mycobacterial ribosomes +/- GidB-mediated methylation are still of value, and a necessary “first step” for the mechanistic work alluded to above. Secondly, the apo ribosome structures still hint at potential mechanisms by which mistranslation and 16S rRNA methylation may impact on each other – as in the comments to R#1 above, we have revised the text to increase clarity and coherence of this section.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      In this manuscript, the authors investigate the relationship between genetic codes and their robustness to single-point mutations. They construct ten alternative genetic codes by reassigning nine codons to Leu, Ser, or Ala, and assess mutational robustness using three reporter proteins subjected to error-prone PCR. This represents an interesting experimental approach to addressing the hypothesis that the standard genetic code is optimized for mutational robustness.

      We sincerely thank the reviewer for the positive evaluation of our experimental approach. We are encouraged that the reviewer recognizes the value of constructing multiple non-standard genetic codes in vitro and using them to experimentally examine the relationship between genetic code arrangement and mutational robustness. In the revised manuscript, we have further clarified the scope of our experimental system and the interpretation of the results, particularly emphasizing that our conclusions concern the mutational robustness of individual reporter protein activity measured in an in vitro translation system.

      Major comment:

      While I find the experimental design valuable, I am not fully convinced by the authors' conclusion that "alterations of the genetic code within the ranges explored in this study have no significant effect on mutational robustness". The current analysis is based on the functional output of three individual reporter proteins. Given that cellular systems involve far more complex interactions, it would be more appropriate to limit this conclusion to mutational robustness at the level of individual protein activity, rather than making broader generalizations.

      We thank the reviewer for this important comment. We agree that our original wording was broader than what can be directly supported by the present experiments. Because our analysis is based on the functional outputs of three individual reporter proteins translated in a reconstituted in vitro system, the results do not directly address mutational robustness at the level of the cellular system, protein interaction networks, or organismal fitness.

      Accordingly, we have revised the manuscript to limit our conclusion to the mutational robustness of individual reporter protein activity. In the revised Abstract, Results, and Discussion, we now state that within the experimentally tested range of non-standard genetic codes, we did not detect a dependence of the mutation-induced decrease in reporter protein activity on mutational cost. We have also added a statement in the Discussion noting that cellular systems involve many additional layers, including protein–protein interactions, metabolic networks, quality-control systems, and growth selection, and that whether genetic code arrangement affects robustness at these higher biological levels remains an important question for future work.

      Specifically, we have added this explanation and the new experiment to the revised manuscript as follows.

      Abstract

      “This result provides direct experimental evidence that mutational robustness does not significantly change in individual reporter protein activity when the genetic code is altered within the range of mutational cost tested in this study…”

      Introduction

      “Random mutations decreased reporter protein function at similar levels across all genetic codes examined, implying that alterations of the genetic code within the ranges explored in this study have no significant effect on mutational robustness of individual protein activity.”

      Result

      “Taken together, these results indicate that mutational robustness of individual reporter protein function did not substantially differ among the genetic codes…”

      Discussion

      “…suggesting that mutational robustness of protein activity remained largely unchanged within at least the ranges of mutational cost tested in this study. It should be noted that this conclusion is limited to the activity of individual reporter proteins translated in a reconstituted in vitro system. Therefore, whether similar trends would be observed at the level of cellular fitness or long-term evolution remains an open question.”

      Specific comments

      (1) tRNA modification and expression efficiency (Page 5, line 131)

      The authors attribute the observed inefficiency to the lack of chemical modifications in the tRNAs used. However, gene expression efficiency can also be strongly influenced by DNA sequence design. To better support this claim, it would be helpful to compare luciferase activity when expressed using native E. coli tRNAs. This comparison could clarify whether the observed effects are due to tRNA modification status or other sequence-dependent factors.

      We thank the reviewer for this important suggestion. We agree that the translation efficiency of NanoLuc templates with 21-, 32-, and 46-codons may be affected not only by the chemical modification of tRNAs but also by sequence-dependent factors, such as codon context and mRNA structure.

      To examine this possibility, we performed an additional comparison using native E. coli tRNAs in the tfPURE system. When the NanoLuc templates encoded with 21, 32, or 46 codons were translated using native E. coli tRNAs, the observed luminescence values were 1.2 × 10<sup>10</sup>, 0.78 × 10<sup>10</sup>, and 0.60 × 10<sup>10</sup>, respectively. Thus, the 46-codon NanoLuc template showed lower activity than the 21- and 32-codon templates even with native tRNAs, indicating that sequence-dependent effects indeed contribute to translation efficiency.

      However, the difference among these templates with native E. coli tRNAs was within approximately two-fold. This effect was much smaller than the marked decrease observed when the 46-codon template was translated using the in vitro prepared 46 tRNAs SGC system. Therefore, while sequence-dependent effects cannot be excluded, the inefficient translation in the reconstructed 46 tRNAs SGC is likely to be mainly attributable to the limited functionality of unmodified tRNAs decoding NNA codons.

      We have revised the manuscript to clarify this interpretation and have added the new comparison using native E. coli tRNAs.

      “We also examined whether the lower translation efficiency of the 46-codon NanoLuc template could be explained by sequence-dependent effects, such as codon context or mRNA structure. When the 21-, 32-, and 46-codon NanoLuc templates were translated using native E. coli tRNAs in the tfPURE system (Figure 1–figure supplement 2), the 46-codon template showed lower activity than the 21- and 32-codon templates; however, this difference was within approximately two-fold. Accordingly, we decided to use only the 32 codons used in near-SGC (i.e., excluding NNA codons) in the subsequent construction of non-standard genetic codes.”

      (2) Discrepancy between expression level and activity (Figure S7 vs Figure S8).

      Although GAL expression levels appear similar across different genetic codes (Figure S7), their activities differ substantially (Figure S8), even in the low-mutation library. This discrepancy warrants further investigation. Possible explanations include differences in protein folding efficiency or translational error rates, as mentioned by the authors in the main text.

      To address this, the authors could analyze the protein products using mass spectrometry. If this is not feasible due to low expression levels, alternative approaches such as SDS-PAGE (e.g., with radiolabeling or Western blotting) would still provide valuable information. Additionally, comparing activity after in vitro refolding could help distinguish between folding defects and sequence-level errors. While I understand that the primary aim of this study is to compare mutational robustness across genetic codes, discussing these observations would significantly enhance the mechanistic insight of the work.

      We agree that the discrepancy between similar GAL expression levels and different GAL activities across genetic codes is important for interpreting the results.

      In our experiment, GAL protein amounts were quantified using a C-terminal HiBiT tag. Because the HiBiT tag was fused to the C-terminus of GAL, this assay indicates that the amount of C-terminally completed GAL products did not differ substantially among genetic codes. However, we agree that this assay does not evaluate the sequence fidelity, amino acid misincorporation patterns, or folding state of the translated products. Therefore, the observed differences in GAL activity despite similar HiBiT signals may reflect genetic code-dependent differences in translational error rates, amino acid misincorporation, protein folding efficiency, or other effects on the fraction of catalytically active protein.

      We have revised the Discussion to explicitly describe this interpretation and to clarify that detailed mechanistic dissection of these baseline activity differences, for example by mass spectrometry, SDS-PAGE/Western blotting, or refolding analysis, is an important future direction but beyond the scope of the present study. We also clarified that the main analysis in this study uses the ratio of activity from the high-mutation library to that from the corresponding low-mutation library within each genetic code.

      We have added this explanation to the revised manuscript as follows.

      “Although protein amounts quantified by the HiBiT tag were comparable among genetic codes, GAL activities differed substantially. This indicates that the activity differences among genetic codes were not primarily attributable to differences in the amount of C-terminally completed translation products. The HiBiT assay does not provide information on the fraction of catalytically active protein, including sequence fidelity or folding state, and therefore cannot distinguish among these possibilities. Detailed characterization of translated products by mass spectrometry would provide further mechanistic insight into how individual non-SGCs affect protein quality. However, the primary objective of the present study was to compare mutation-dependent activity loss across genetic codes. Therefore, we evaluated this effect by normalizing the activity of the high-mutation library to that of the corresponding low-mutation library within each genetic code.”

      (3) Protein expression analysis for additional reporters.

      Since protein expression levels are critical for interpreting reporter activity, similar analyses should also be performed for luciferase (Luc) and mSG in both high- and low-mutation libraries. This would ensure that differences in activity are not confounded by variations in protein abundance.

      We agree that protein abundance is an important factor for interpreting reporter activity. In this study, we performed HiBiT-based protein quantification for GAL because GAL showed the largest variation in absolute activity among genetic codes, even in the low-mutation library. This analysis showed that the amount of C-terminally completed GAL products was broadly comparable among genetic codes and between low- and high-mutation libraries, indicating that the observed GAL activity differences were not primarily attributable to differences in total protein abundance.

      For all three reporters, our main analysis was based on the ratio of activity from the high-mutation library to that from the corresponding low-mutation library within each genetic code. This normalization was intended to evaluate mutation-dependent activity loss while reducing the influence of code-specific baseline differences in expression level or protein quality. We believe that the data are sufficient to evaluate the effect of mutations on protein activities. Nevertheless, we agree that protein quantification for Luc and mSG would provide useful information regarding variation in the baseline levels of reporter activity, and this is an important direction for future work.

      Reviewer #2 (Public review):

      Summary:

      The study addresses the long-standing question in molecular biology and genetics: why has nature selected the current genetic code (SGC, or standard genetic code)? The authors have tested 'error minimization theory', one of the prevailing hypotheses to explain this. Their approach is to create a minimum genetic code (MGC) and its variants (3^9 theoretical possible codes). Using three parameters to quantify the effect of mutations (Polarity, volume, and hydropathy), they computationally test the cost of these genetic codes (3^9) by simulations. Finally, they test this cost experimentally using an in vitro translation system with 10 select genetic code variants with a range of costs (low to high). They use three randomly mutated reporter genes for this purpose - beta-galactosidase, luciferase, and mSG. They find no correlation between the cost of the genetic code and the reporters' output. Based on these observations, they suggest that error-minimization theory may not explain the current egocentric code.

      The question they are asking is very exciting, and their approach is solid. The authors are very careful in their analyses and conclusions.

      We sincerely thank the reviewer for the positive assessment of our study and for the helpful suggestions. We are encouraged that the reviewer found the question exciting and the approach solid. In the revised manuscript, we have clarified the rationale for using the MGC/near-SGC framework, added further analyses and explanations of the mutational cost calculations, and revised the wording of our conclusions to more explicitly define the scope and limitations of the present experimental system.

      (1) The rationale for using MGC instead of SGC: It is unclear why the authors rely on the MGC for this analysis when the central question concerns the SGC. If the goal is to evaluate whether the SGC minimizes mutational cost, a more direct approach would be to generate alternative variants of the SGC itself and compare their mutational cost distributions. At present, it is difficult to assess whether conclusions drawn from this comparison are fully relevant to the stated biological question.

      We thank the reviewer for this important comment. We agree that directly constructing alternative variants of the SGC by changing amino acid assignment from SGC would be the most straightforward approach to testing whether the SGC minimizes mutational cost. However, this approach is currently not feasible in our reconstituted translation system for two reasons.

      First, our attempt to construct a 46-tRNA SGC-like system revealed that translation using the 46-codon NanoLuc template was approximately 100-fold less efficient than translation using the MGC or near-SGC (Fig. 1). This low activity likely reflects inefficient decoding of NNA codons by in vitro-prepared tRNAs, which lack native post-transcriptional modifications. Because this system did not provide sufficient translational activity for systematic reporter assays, we restricted subsequent experiments to the 32-codon near-SGC framework, excluding NNA codons. We now describe this technical limitation more explicitly in the revised manuscript.

      Second, the MGC framework provides vacant codons that can be reassigned by adding anticodon-variant tRNAs. This feature is essential for constructing multiple genetic code variants in parallel under controlled in vitro conditions. We, therefore, constructed the near-SGC-based non-SGC by adding each tRNA variant to the MGC as an experimentally tractable model system to verify whether differences in genetic code arrangement affect mutation-induced decreases in reporter protein activity.

      We have added this explanation to the revised manuscript as follows.

      “We first established a minimal genetic code, composed of 21 tRNAs with vacant codons, which allows multiple alternative codon assignments to be introduced under otherwise comparable translation conditions.”

      Despite this technical limitation, we believe that the central conclusion of this study—that mutational robustness in individual reporter protein activity does not change significantly when the genetic code is altered within the range of mutational costs tested here—remains well-supported by the present results.

      (2) The mutational cost analysis appears biologically oversimplified because all amino acid substitutions are treated equivalently. The analysis assumes that all mutations contribute equally to fitness consequences, which does not reflect biological reality. In natural proteins, the impact of an amino acid substitution depends strongly on its structural and functional context. For example, substitutions affecting catalytic residues, ligand-binding interfaces, phosphorylation sites, or other regulatory motifs can severely impair protein function even when associated changes in polarity, hydropathy, or volume are minimal. Conversely, substitutions in structurally permissive or functionally dispensable regions may have little or no measurable effect despite larger physicochemical differences. Therefore, changes in polarity, hydropathy, and volume alone do not necessarily predict functional consequences.

      We agree that the mutational cost used in this study is a simplified measure and does not capture the full biological complexity of amino acid substitutions. As the reviewer pointed out, the functional consequence of a substitution depends strongly on its structural and functional context, including whether the affected residue is involved in catalysis, ligand binding, protein–protein interactions, regulatory motifs, folding, or structurally permissive regions.

      In this study, we used physicochemical-property-based mutational costs because this type of definition has been widely used in classical formulations of the error minimization theory. Our aim was therefore not to construct a comprehensive predictor of protein fitness effects, but to experimentally test whether the conventional theoretical cost metrics used to discuss genetic code optimality are reflected in the average mutation-induced decrease in reporter protein activity. We have now clarified this rationale in the revised manuscript.

      “It should be noted that this conclusion is limited to the activity of individual reporter proteins translated in a reconstituted in vitro system. Therefore, whether similar trends would be observed at the level of cellular fitness or long-term evolution remains an open question.”

      (3) It is not clear why they increased the concentration of the two tRNAs in near-SGC. Have they maintained the same tRNA concentrations in experiments explained in Fig 5 for all 10 genetic codes tested?

      We apologize that the rationale for increasing the concentrations of tRNA<sup>Val</sup><sub>CAC</sub> and tRNA<sup>Arg</sup><sub>CCU</sub> was not sufficiently clear in the original manuscript. As we wrote in the previous manuscript, “To improve translation efficiency with near-SGC, we focused on two tRNA concentrations (tRNA<sup>Val</sup><sub>CAC</sub> and tRNA<sup>Arg</sup><sub>CCU</sub>), which were suggested to have low activities in a previous study (Iwane et al., 2016),” we tested whether increasing their concentrations would improve translation efficiency. As shown in Figure 1–figure supplement 1, NanoLuc activity increased as the concentrations of these two tRNAs were raised and used at 100 ng/µL for tRNA<sup>Val</sup><sub>CAC</sub> and tRNA<sup>Arg</sup><sub>CCU</sub> in the optimized near-SGC, referred to as near-SGC (RV), and in all subsequent experiments. Additional anticodon-variant tRNAs required for each non-SGC were used at optimized concentrations determined from Figure 2–figure supplement 1. For each genetic code, the same tRNA composition and concentrations were used for the low- and high-mutation libraries (See Supplementary Table S7). To clarify this point, we added the sentence, “The increased concentrations of these two tRNAs were used in all the subsequent experiments,” in the corresponding part.

      Reviewer #3 (Public review):

      In this manuscript, Miyachi and Ichihashi investigate whether the arrangement of the genetic code affects mutational robustness. Using an in vitro minimal genetic code with vacant codons, they constructed 10 non-standard genetic codes by reassigning Ala, Ser, and Leu, generating codes with replacement costs that were generally higher than those of the standard genetic code across several amino acid property measures. They then tested how random mutations affected the activity of reporter proteins translated under these altered codes. Although error minimization theory predicts that higher-cost codes should make mutations more harmful, the authors report that protein function declined to a similar extent across all codes examined, suggesting that mutational robustness remains largely unchanged within the range of genetic code alterations tested here.

      Strengths:

      This is an interesting study that investigates one of the most fundamental and intriguing questions in molecular evolution: the emergence of the genetic code, which is nearly universal across nature. The in vitro approach is a powerful aspect of the work and provides an opportunity to examine this phenomenon experimentally at a depth that has previously been inaccessible.

      Weaknesses:

      However, the authors' use of random mutation libraries has certain limitations that prevent the study from realizing its full potential to uncover the mechanisms governing the molecular evolution of the genetic code.

      We sincerely thank the reviewer for the positive evaluation of our study and for recognizing the strength of the in vitro approach. We are encouraged that the reviewer considers this system a powerful way to experimentally address the emergence of the genetic code.

      We also appreciate the reviewer’s constructive comments regarding the limitations of random mutation libraries. We agree that pooled random libraries do not allow us to assign functional effects to individual mutations or to fully uncover the molecular mechanisms underlying mutational robustness. In the revised manuscript, we therefore clarify that our conclusions concern the library-averaged effects of random mutations on individual reporter protein activity, rather than the effects of specific mutations or cellular-level fitness. To address this limitation, we have added explanations of the scope and limitations of the present approach.

      (1) Statistical analyses are missing for several of the manuscript's main claims. This issue applies throughout the paper, including, but not limited to, Figures 1D, 2B, 4B-D, and 5B.

      We thank the reviewer for this important comment. We agree that statistical analyses are necessary to support the major claims of the manuscript. We have therefore added statistical analyses appropriate for the purpose and experimental design of each figure.

      For Fig. 1D, we performed one-way ANOVA followed by Tukey’s post hoc test on NanoLuc activity to compare translation efficiencies among the MGC, near-SGC, near-SGC (RV), and SGC conditions. This analysis showed a significant overall difference among conditions (one-way ANOVA, p < 0.0001). Tukey’s post hoc test showed that near-SGC was significantly lower than MGC, that near-SGC (RV) significantly improved near-SGC translation, and that near-SGC (RV) was not significantly different from MGC. In contrast, the 46-tRNA SGC remained significantly less efficient than near-SGC (RV). We have summarized the major comparisons in Supplementary Table S8.

      For Fig. 2B, we compared NanoLuc activity between the 21-code control and the corresponding 21+1-code condition for each codon reassignment using Welch’s t-test on luminescence. This analysis was added to statistically support whether each anticodon-variant tRNA increased NanoLuc translation from the corresponding reassigned template. The statistical results are summarized in Supplementary Table S9.

      For Fig. 4B–D, we converted mutation rates per base to estimated numbers of mutations per gene and performed Spearman’s rank correlation analysis to evaluate whether reporter activity decreased monotonically with increasing mutational load. This analysis showed strong negative monotonic trends between mutation rate (estimated mutation number) and reporter activity for all three reporters (ρ = −0.90 to −1.00), supporting that the random mutation libraries reduced protein activity in a mutation-load-dependent manner.

      For Fig. 5B, replicate-level data were available for GAL, and we therefore performed two-way ANOVA using genetic code and mutation level as factors. This analysis detected significant main effects of genetic code and mutation level, indicating that GAL activity differed among genetic codes and decreased in the high-mutation library. However, no significant interaction between genetic code and mutation level was detected, indicating that the magnitude of mutation-induced activity reduction was not strongly code-dependent under the conditions examined.

      Finally, because the central claim of Fig. 5C, 5E, and 5G is that mutational cost does not systematically predict mutation-induced activity loss, we performed Spearman’s rank correlation analysis between each mutational cost metric and the high-/low-mutation activity ratio. No significant correlations were detected for any reporter or cost metric (Spearman’s ρ = −0.23 to 0.25), supporting the conclusion that mutational cost did not show a detectable monotonic relationship with mutation-induced activity loss within the tested range.

      We have added these statistical analyses to the revised manuscript. The following sentences were added to the figure legends:

      Fig. 1

      “Statistical comparisons in (D) were performed using one-way ANOVA followed by Tukey’s post hoc test on NanoLuc activity; major comparisons are summarized in Table S8.”

      Fig. 2

      “For each template, NanoLuc activity in the 21-code and corresponding 21+1-code conditions was compared using Welch’s t-test on luminescence. Statistical results are summarized in Table S9.”

      Fig. 4

      “Spearman’s rank correlation coefficients were ρ = −0.90 for GAL, ρ = −1.00 for Luc, and ρ = −1.00 for mSG”

      Fig. 5

      “For GAL activity in (B), two-way ANOVA was performed using genetic code and mutation level as factors. Significant main effects of genetic code and mutation level were detected (both p < 0.0001), whereas their interaction was not significant. For (C), (E), and (G), Spearman’s rank correlation analysis was performed between each mutational cost metric and the high-/low-mutation activity ratio. Statistical details are summarized in Table S10.”

      (2) In Figure 2A, the authors modify the NanoLuc gene by reassigning Ala, Leu, or Ser to new codons and elegantly show that the in vitro availability of the corresponding tRNAs is important for protein function. However, the functional importance of the specific modified positions within NanoLuc is not clear. As a result, it is difficult to determine what the expected consequences of these codon changes should be, which in turn limits the interpretation of the observed changes in protein activity. To improve the interpretability of this experiment, the authors should report exactly how many codons were modified in each variant and, ideally, examine the effect of progressively increasing the number of reassigned codons.

      We agree that the exact positions and numbers of codon replacements should be clearly reported. In the revised manuscript, we have added a list of the modified amino acid positions. In brief, two Ala codons, three Ser codons, or four Leu codons were replaced with the target vacant codon; the modified positions were Ala16 and Ala120, Ser31, Ser49, and Ser150, and Leu32, Leu67, Leu144, and Leu170, respectively.

      We also agree that progressively increasing the number of reassigned codons would provide additional mechanistic insight. However, the purpose of Fig. 2 was to test whether each vacant codon could be decoded by the corresponding anticodon-variant tRNA to produce functional NanoLuc, rather than to analyze the positional contribution of each replacement. We previously performed such progressive codon replacement analysis for one reassigned codon, ACG, in a related study (Miyachi et al., 2025), and the results supported the same qualitative interpretation. Although we did not repeat this progressive analysis for all codons in the present study, we expect that the qualitative interpretation of Fig. 2 would not be substantially changed.

      We have revised the figure text to clarify the scope of the experiment and added the detailed codon replacement information.

      “(A) Schematic illustration of reassignment experiments. Translation with the original MGC and NanoLuc template is shown at the top for comparison. An example of Ala reassignment to the UUG codon is shown at the bottom. In this example, three Ala codons in the NanoLuc sequence were replaced with one type of vacant codon (e.g., UUG), generating a 21 + 1 (UUG-Ala) codon set. Similar reassignment experiments were performed for three amino acids (Ala, Ser, and Leu) and nine vacant codons. Specifically, two Ala codons (Ala16 and Ala120), three Ser codons (Ser31, Ser49, and Ser150), or four Leu codons (Leu32, Leu67, Leu144, and Leu170) were replaced.”

      (3) The calculations presented in Figure 3 raise an interesting conceptual question: why does the near-standard genetic code not exhibit the lowest cost? One possible explanation is that the standard genetic code evolved under multiple competing constraints and is therefore not expected to be optimal for any single cost metric, while still achieving strong overall performance. In this context, it would be informative if the authors combined the three cost measures into a single integrated index and examined whether the near-SGC performs more favorably when all three dimensions are considered together. Such an analysis could add important depth to the study.

      We agree that the near-SGC is not necessarily expected to minimize each individual cost metric, because the standard genetic code may reflect multiple competing physicochemical, translational, biosynthetic, and evolutionary constraints rather than optimization of a single property.

      To address this point, we added an integrated cost analysis combining the three physicochemical cost metrics, Cost<sub>PR</sub>, Cost<sub>MV</sub>, and Cost<sub>HI</sub>. Because these three metrics have different numerical scales, we normalized each metric before integration. We used two types of integrated indices.

      First, for each metric m 𝛜 {PR, MV, HI}, we calculated a min–max normalized cost,

      Where G denotes the set of 19,683 candidate non-SGCs generated by assigning Ala, Ser, or Leu to the nine vacant codon boxes. We then defined the integrated min–max cost as

      Second, we calculated a z-score-normalized cost for each metric,

      Where µ<sub>m,G</sub> and 𝜎<sub>m,G</sub> are the mean and standard deviation of Cost<sub>m<sub>norm</sub></sub> across the candidate non-SGCs. The integrated z-score cost was then defined as

      Using both integrated indices, the near-SGC ranked first when compared with all 19,683 candidate non-SGCs; in other words, no candidate non-SGC showed a lower integrated cost than the near-SGC. The integrated min–max cost of the near-SGC was 0.01525, whereas the lowest value among candidate non-SGCs was 0.12301. Similarly, the integrated z-score cost of the near-SGC was −2.47947, whereas the lowest candidate value was −1.90838.

      We have added this integrated cost analysis as Supplementary Figure 5–figure supplement 7. We have also revised the Discussion to note that the near-SGC does not necessarily minimize every individual physicochemical cost, but performs most favorably when PR, MV, and HI are considered comprehensively. This result is consistent with the idea that the standard genetic code may represent a compromise among multiple constraints rather than optimization of a single physicochemical property.

      “We consider that the cost ranges examined in this study represent substantial fractions, especially for MV and HI. Although the near-SGC did not necessarily exhibit the lowest cost for each individual physicochemical metric, this does not mean that it is unfavorable in the multidimensional cost space. Because the SGC may reflect a balance among multiple physicochemical constraints rather than optimization of a single property, we also calculated integrated cost indices by combining Cost_PR, Cost_MV, and Cost_HI after min–max normalization or z-score normalization. In both integrated indices, the near-SGC showed the lowest overall cost when compared with all 19,683 candidate non-SGCs (Figure 5–figure supplement 7), indicating that no candidate non-SGC exhibited a lower combined cost than the near-SGC when the three physicochemical properties were considered comprehensively.”

      (4) It is difficult to assess the consequences of the random mutations presented in Figure 4 on reporter gene function based solely on the reported "error rate/base" parameter. In particular, the x-axis in Figure 4B should be converted into the estimated number of mutations per gene. This would make the results more intuitive and would allow the reader to better evaluate the expected degree of disruption to protein function.

      We agree that the mutation rate per base alone does not provide an intuitive sense of the expected mutational burden for each reporter gene. We therefore added a second x-axis to Fig. 4B–D showing the estimated number of mutations per gene. This value was calculated by multiplying the mutation rate per base by the coding sequence length of each reporter gene.

      We retained the original mutation rate per base axis to preserve the direct link to the sequencing-based mutation rate measurement, while adding the estimated mutations per gene axis to improve interpretability. We have revised the figure and figure 4 legend accordingly.

      “The lower x-axis indicates the estimated number of mutations per gene, calculated by multiplying the mutation rate per base by the coding sequence length of each reporter gene.”

      (5) A central limitation of the random mutagenesis libraries used in Figure 5, which also underlie one of the manuscript's main claims, is that the exact mutations and their distribution across the reporter genes are not reported. In addition, protein activity is measured only at the level of the entire library, without directly linking individual mutations to their functional consequences. This substantially limits mechanistic interpretation. In my view, this issue can only be addressed convincingly if the authors test a set of defined variants carrying specific mutations and directly evaluate their functional effects.

      (6) Related to the previous point, in Figures 5C, 5E, and 5G, the authors present the ratio between low-mutation-rate and high-mutation-rate libraries. However, because each library contains a different collection of mutations, it is unclear what can be inferred from these comparisons. To overcome this limitation, the authors should assess the effects of altered genetic codes on specific, defined mutations rather than on heterogeneous mutation pools alone.

      (7) Along the same lines, in Figures 5C, 5E, and 5G, it is unclear why the effects of random mutations would be expected to correlate with the three calculated cost metrics, given that the positions, identities, and functional relevance of the mutations within the genes are not known. Without this information, the biological meaning of these correlations remains difficult to evaluate.

      We agree that using pooled random mutation libraries does not allow us to directly link individual mutations to their functional consequences. We also agree that testing defined variants carrying specific mutations would provide a more direct and mechanistic understanding of how each genetic code affects the functional impact of particular amino acid substitutions. However, the purpose of the present study was different from such a defined-variant analysis. Our aim was to experimentally test whether the conventional mutational cost metrics used in error minimization theory predict the average effect of random mutational loads on protein activity. Because these theoretical costs are themselves defined as average expected physicochemical effects over many possible single-nucleotide substitutions, we reasoned that pooled random mutation libraries provide an appropriate first experimental framework to evaluate whether such average-cost metrics are reflected in the average functional output of translated proteins.

      We agree that low- and high-mutation libraries do not contain identical sets of mutations. Therefore, the high-/low-mutation activity ratio should not be interpreted as the effect of the same individual variants before and after additional mutations. Rather, it represents the relative reduction in average activity caused by increasing the mutational burden in a heterogeneous mutation pool under each genetic code. We have revised the text to clarify this interpretation.

      We also agree that the positions, identities, and functional relevance of individual mutations are not resolved in this pooled assay. This limitation prevents us from assigning mechanistic effects to specific substitutions. At the same time, using a small set of defined variants would introduce its own selection bias, because the conclusions could strongly depend on which mutations and which protein positions were chosen. Therefore, we consider the random-library approach to be a useful first step for testing library-averaged effects, whereas systematically defined variant analysis or genotype-resolved activity assays will be necessary to reveal mutation-specific mechanisms in future studies.

      In response to the reviewer’s concern, we have revised the Discussion to explicitly limit our conclusion to library-averaged effects on individual reporter protein activity. We now state that this approach does not identify the functional effects of individual mutations and that future studies using defined variants or high-throughput genotype–phenotype mapping will be required to determine how specific substitutions contribute to genetic code-dependent mutational robustness.

      Result

      “To estimate the average activity reduction associated with increased mutational burden under each genetic code, we calculated the ratio of activity obtained from the high-mutation library to that from the corresponding low-mutation library and plotted this ratio against each of the three mutational costs (Fig. 5C).”

      Discussion

      “A further limitation of this study is that the reporter activities were measured at the level of pooled random mutation libraries. Therefore, the high-/low-mutation activity ratio used in this study should be interpreted as the relative reduction in average activity caused by increasing the mutational burden in a heterogeneous mutation pool, rather than as the effect of identical variants before and after additional mutations. This library-averaged approach was chosen because the mutational costs considered here are also defined as average expected physicochemical effects over many possible single-nucleotide substitutions. In addition, because the non-SGCs constructed in this study were generated by reassigning only Ala, Ser, and Leu, the detectable effects may depend on how frequently mutations involving these amino acids occur in each reporter gene and whether the affected positions are functionally important. If genetic code dependent effects are restricted to a small subset of deleterious variants, such effects may be masked in pooled activity measurements. Future studies using defined variants or high-throughput genotype–phenotype mapping assays will be required to determine the mutation-specific and position-specific mechanisms underlying genetic code dependent effects on protein function (Rozhoňová et al., 2024).”

      (8) For each mutagenesis library, the number of variants, the average number of mutations per variant, and the distribution of mutation positions should be reported clearly and transparently. These details are important for evaluating the strength of the conclusions.

      We agree that a more transparent characterization of the random mutagenesis libraries is necessary for evaluating the strength and limitations of our conclusions.

      In the revised manuscript, we have added the estimated number of mutations per gene to the Results section. This value was calculated by multiplying the mutation rate per base by the coding sequence length of each reporter gene. For the high-mutation libraries used in Fig. 5, the estimated numbers of mutations per gene were approximately 8.0 for GAL, 4.5 for Luc, and 3.3 for mSG. We also added position-wise mutation profiles along each reporter gene (Figure 4–figure supplement 2), in addition to the heatmap shown in the original manuscript. These analyses clarify the mutational burden of each library and show that mutations were broadly distributed across the analyzed regions (approximately 300 nt in the middle of each gene) of the reporter genes.

      Regarding the number of variants, the translation reactions were performed using 5 nM DNA template in a 5 µL reaction, corresponding to approximately 1.5 × 10<sup>10</sup> DNA molecules. However, this value represents the total number of DNA molecules introduced into the reaction and does not directly indicate the number of unique full-length sequence variants, because multiple molecules can share the same genotype, and our sequencing analysis was designed to quantify mutation frequencies and positional distributions rather than to reconstruct full-length genotypes of individual library members. Therefore, we do not infer the exact number of unique variants in each library. Instead, we report the average mutation burden and position-wise non-reference rate distributions.

      We have revised the Results and added Supplementary Figure 4–figure supplement 2 accordingly.

      “For this experiment, two random mutation libraries were used: a low-mutation library prepared using the high-fidelity polymerase and a high-mutation library prepared using Taq DNA polymerase at a Mn<sup>2+</sup> concentration that yields mutation rates of 0.002 – 0.005 per base (0.0026 for GAL, 0.0027 for Luc, and 0.0048 for mSG, corresponding to approximately 8.0, 4.5, and 3.3 mutations per gene). We also plotted position-wise non-reference rates along the analyzed regions of each reporter gene, confirming that mutations were broadly distributed across the amplicons (Figure 4–figure supplement 2).”

      (9) Because only three amino acids were manipulated in the non-standard genetic codes, it remains unclear whether these particular amino acids occupy positions in the reporter proteins that are especially important for function and therefore likely to generate strong phenotypic effects. More broadly, it is not clear whether the assay is sufficiently sensitive to detect the effects of only a subset of deleterious variants within a pooled library. This point should be addressed more explicitly.

      We agree that this is an important limitation of the present study. Because our non-SGCs were constructed by reassigning only Ala, Ser, and Leu, the mutation-dependent effects that can differ among genetic codes are limited to mutations involving these reassigned codons or amino acid substitutions affected by these assignments. Therefore, the sensitivity of the assay depends on how frequently such substitutions occur in the reporter genes and whether the affected Ala, Ser, and Leu-related positions are functionally important.

      We have revised the Discussion to address this point more explicitly. In the revised manuscript, we now state that the absence of a detectable cost-dependent effect may reflect not only the limited cost range examined, but also the limited set of reassigned amino acids, the position-dependent importance of Ala/Ser/Leu residues in the reporter proteins, and the sensitivity limit of pooled activity measurements. We further note that future studies using genotype-resolved activity assays (defined variants) will be required to determine whether specific amino acid substitutions or specific protein positions exhibit stronger genetic code-dependent effects.

      “A further limitation of this study is that the reporter activities were measured at the level of pooled random mutation libraries. Therefore, the high-/low-mutation activity ratio used in this study should be interpreted as the relative reduction in average activity caused by increasing the mutational burden in a heterogeneous mutation pool, rather than as the effect of identical variants before and after additional mutations. This library-averaged approach was chosen because the mutational costs considered here are also defined as average expected physicochemical effects over many possible single-nucleotide substitutions. In addition, because the non-SGCs constructed in this study were generated by reassigning only Ala, Ser, and Leu, the detectable effects may depend on how frequently mutations involving these amino acids occur in each reporter gene and whether the affected positions are functionally important. If genetic code-dependent effects are restricted to a small subset of deleterious variants, such effects may be masked in pooled activity measurements. Future studies using defined variants or high-throughput genotype–phenotype mapping assays will be required to determine the mutation-specific and position-specific mechanisms underlying genetic code-dependent effects on protein function (Rozhoňová et al., 2024).”

      Recommendations for the authors:

      Reviewing Editor Comments:

      While we suggest that you address all the technical points raised by the reviewers, you may specifically want to limit the conclusion of the study to mutational robustness at the level of individual protein activity, rather than making broader generalizations. Also, the statistical analysis needs to be strengthened, as indicated in the reviews.

      We thank the Reviewing Editor for these important suggestions. We agree that the conclusion of the original manuscript was broader than what can be directly supported by the present experiments. In the revised manuscript, we have therefore limited our conclusion to mutational robustness at the level of individual reporter protein activity measured in a reconstituted in vitro translation system. We now explicitly state that our results do not directly address robustness at the level of cellular fitness, protein interaction networks, or long-term evolution.

      We have also strengthened the statistical analyses throughout the manuscript. Specifically, we added one-way ANOVA followed by Tukey’s post hoc test for Fig. 1D, Welch’s t-tests for Fig. 2B, Spearman’s rank correlation analyses for Fig. 4B–D and Fig. 5C/E/G, and two-way ANOVA for GAL activity in Fig. 5B. These analyses have been incorporated into the revised Results, figure legends, and supplementary information.

      Reviewer #2 (Recommendations for the authors):

      (1) Discuss other alternative hypotheses if the error minimization theory is unlikely.

      We thank the reviewer for this helpful suggestion. We think that the absence of a detectable relationship between mutational cost and reporter protein activity in our assay should not be interpreted as excluding all possible roles of error minimization in the evolution of the genetic code. Our results specifically address one aspect of the error minimization theory: whether physicochemical-property-based mutational cost predicts the average effect of random point mutations on individual reporter protein activity within the experimentally accessible range of non-SGCs tested here.

      In the revised Discussion, we have clarified that the organization of the SGC may have been shaped by multiple factors, including robustness to translational errors, historical constraints associated with genetic code expansion, biosynthetic or coevolutionary processes, stereochemical interactions, and the evolvability of proteins. Our results suggest that the contribution of mutational robustness at the level of individual protein activity may be limited within the range examined here, but they do not exclude the possibility that the SGC provides advantages under other forms of error, at the level of translation fidelity, cellular fitness, or long-term evolution.

      We have added a short discussion to clarify this point without expanding the scope of the manuscript beyond the present experimental results.

      “It should be noted that this conclusion is limited to the activity of individual reporter proteins translated in a reconstituted in vitro system. Therefore, whether similar trends would be observed at the level of cellular fitness or long-term evolution remains an open question. Moreover, our results do not exclude other possible roles of SGC organization. The SGC may have been shaped by multiple factors, including robustness to translational errors, historical constraints during genetic code expansion, biosynthetic or coevolutionary relationships among amino acids, stereochemical interactions, and effects on protein evolvability (Katoh and Suga, 2023; Koonin and Novozhilov, 2017, 2009; Novozhilov et al., 2007; Wong, 2005).”

      (2) A brief description of the PURE translation system can be provided for people from outside the field.

      We have added a brief description of the PURE system in the Introduction to make the experimental platform more accessible to readers outside the field. Specifically, we now explain that the PURE system is a reconstituted cell-free translation system composed of purified translation factors, ribosomes, aminoacyl-tRNA synthetases, tRNAs, amino acids, and energy-regeneration components. We also clarify that, in this study, we used a tRNA-free version of the PURE system, in which defined synthetic tRNA sets were supplied externally to reconstruct each genetic code.

      Introduction

      “A representative platform for such reconstitution is the PURE system (Shimizu et al., 2001), a reconstituted cell-free translation system composed of purified translation components, including ribosomes, translation factors, aaRSs, amino acids, and energy-regeneration components. In particular, a tRNA-free PURE system (Miyachi et al., 2022), in which endogenous tRNA activity is minimized and defined tRNA sets are supplied externally, enables genetic codes to be reconstructed by controlling the supplied tRNAs.”

      (3) Figure 5D and F - Technical replicates are provided only for GAL. A similar approach should be taken for LUC and mSG.

      We agree that replicate-level measurements for Luc and mSG would further improve reliability. However, repeating the full translation experiments for these reporters was not feasible in the current revision, as each experiment requires large amounts of freshly prepared tRNA-free PURE system and multiple defined tRNA mixtures for every genetic code variant tested. Given these material and technical constraints, we were unable to perform additional biological replicates within the scope of this revision. We would like to emphasize, however, that the GAL replicates shown in Fig. 5D and F are fully consistent across independent experiments, providing direct evidence for the reproducibility of the assay itself. Furthermore, the key metric in our analysis, the activity ratio between high- and low-mutation groups within each genetic code, is an internally normalized measure that is inherently less sensitive to between-experiment variability than absolute activity values. The correlation analyses further showed no significant relationship between mutational cost and this ratio across all three reporters, and this conclusion is consistent regardless of which reporter is examined. Together, we believe these results provide a robust basis for the conclusions drawn, even in the absence of full replication for Luc and mSG.

      (4) Provide statistical analysis wherever it is relevant (e.g, to support a lack of correlation).

      We have strengthened the statistical analyses throughout the revised manuscript. In particular, to support the lack of detectable correlation between mutational cost and mutation-induced activity loss, we performed Spearman’s rank correlation analyses between each mutational cost metric and the high-/low-mutation activity ratio for all three reporters. No significant correlations were detected for any reporter or cost metric. In addition, we added statistical analyses for other relevant figures, including one-way ANOVA followed by Tukey’s post hoc test for Fig. 1D, Welch’s t-tests for Fig. 2B, Spearman’s rank correlation analyses for Fig. 4B–D, and two-way ANOVA for GAL activity in Fig. 5B.

      Reviewer #3 (Recommendations for the authors):

      (1) In line 122, the phrase "as evenly as possible" is ambiguous and should be explained more precisely.

      We thank the reviewer for pointing this out. We have revised the phrase “as evenly as possible” to describe the codon design more precisely. Specifically, we now state that the NanoLuc coding sequences were designed so that the codons available in each genetic code were used with minimal differences in codon counts, while preserving the amino acid sequence of NanoLuc.

      “For near-SGC and SGC, the NanoLuc coding sequences were designed so that the codons available in each genetic code were used with minimal differences in codon counts, while preserving the amino acid sequence (Fig. 1B, 32 codons and 46 codons).”

      (2) For Figure 1D, a Western blot or another protein gel-based assay would be helpful to exclude the possibility that the observed differences arise from variation in translation efficiency rather than differences in protein activity.

      We agree that a protein gel-based assay such as Western blotting would in principle allow us to distinguish differences in translated protein amount from differences in specific activity, and we understand why such data would be informative. However, we would like to clarify that the primary purpose of Fig. 1D was to evaluate the overall functional translation output of each reconstructed genetic code, rather than to determine the mechanistic basis of any observed differences. In this context, NanoLuc luminescence serves as an integrated readout of the entire translation process, encompassing both translational efficiency and protein folding/activity. Crucially, regardless of whether the observed differences in NanoLuc luminescence reflect lower protein yield, reduced specific activity, or a combination of both, the conclusion of Fig. 1D remains the same. Although we did not perform Western blotting in this study, we believe that such an analysis would not change this interpretation and that the current data are sufficient to support this conclusion.

      (3) The number 3^9 is not immediately intuitive. It would be helpful if the authors also stated that this corresponds to approximately 20,000 possible non-standard genetic codes.

      We have revised the text to state both the exact number and the approximate value: 3<sup>9</sup> = 19,683, approximately 20,000 possible non-standard genetic codes.

      (4) The rationale for using the three cost parameters (PR, MV, and HI) should be explained in greater detail. Because these parameters are central to the manuscript, a citation alone is not sufficient. A concise explanation of their biological relevance would improve the clarity and accessibility of the study.

      We agree that the biological relevance of the three cost parameters should be explained more clearly. In the revised manuscript, we have added a concise explanation of why polar requirement (PR), molecular volume (MV), and hydropathy index (HI) were used.

      These parameters were selected because they have been widely used in theoretical studies of genetic code optimality and represent distinct physicochemical aspects of amino acid substitutions. PR reflects polarity-related interactions and has been a classical metric in error minimization analyses of the genetic code. MV represents side-chain size and steric volume, which could influence packing and structural stability in proteins. HI reflects hydrophobicity, which is closely related to protein folding and hydrophobic core formation. We have also clarified that these metrics are simplified descriptors and do not capture residue-specific structural or functional context, which we now discuss as a limitation of the study.

      “PR reflects polarity-related interactions of amino acids and has been used as a classical measure of amino acid similarity in error minimization analyses. MV represents side-chain size and steric volume, which could affect protein packing and structural stability, whereas HI reflects hydrophobicity, which could be closely related to protein folding or hydrophobic core formation.”

      (5) In Figure 3, the experimental framework would be easier to follow if the authors included a schematic and data for one representative non-SGC, explicitly illustrating how it differs from the near-SGC with respect to each of the three cost measures.

      We agree that showing one representative non-SGC would make the experimental framework and cost calculation more intuitive.

      In the revised manuscript, we added a new panel to Fig. 3 comparing the near-SGC with a representative non-SGC. We selected the PR<sub>max</sub> code as the representative example because it clearly illustrates how reassignment of vacant codon boxes can increase one mutational cost metric relative to the near-SGC. In this panel, we first show the codon assignment schemes of the near-SGC and PR<sub>max</sub> code in the same genetic-code format used in Fig. 1. We then show the corresponding heatmap representations for the three physicochemical properties used in the cost calculation: polar requirement, molecular volume, and hydropathy index. The Cost<sub>PR</sub>, Cost<sub>MV</sub>, and Cost<sub>HI</sub> values are shown for each code.

      This new panel illustrates how changes in codon assignment are translated into different physicochemical cost landscapes and clarifies how the representative non-SGC differs from the near-SGC with respect to each of the three cost measures.

      “To make the design of non-SGCs more explicit, we show one representative non-SGC together with the near-SGC in Fig. 3B. This comparison illustrates how assignment of Ala, Ser, or Leu to the vacant codon boxes changes the three mutational cost metrics, Cost<sub>PR</sub>, Cost<sub>MV</sub>, and Cost<sub>HI</sub>.”

      (6) In line 329, the phrase "similar pattern" is ambiguous and should be explained more explicitly.

      We have revised the ambiguous phrase “similar pattern” to describe the observation more explicitly. Specifically, we now state that the relative differences in GAL activity among genetic codes observed in the low-mutation library were broadly retained in the high-mutation library, although overall activity decreased.

      “For the high-mutation library, GAL activity decreased overall, while the relative differences in activity among genetic codes observed in the low-mutation library were broadly retained.”

      (7) Figure S7 appears to be an important control for the experiments shown in Figure 5, and I recommend moving it to the main figures.

      We thank the reviewer for this helpful suggestion. We agree that the HiBiT-based quantification of GAL protein amount is an important control for interpreting the GAL activity measurements in Fig. 5, and we appreciate the recommendation to increase its visibility. This analysis shows that the amount of C-terminally completed GAL products was broadly comparable among genetic codes, indicating that the large differences in GAL activity were not primarily attributable to differences in total translated protein amount.

      After careful consideration, we have opted to retain this analysis in the supplementary figures because the main focus of Fig. 5 is the relationship between mutational cost and mutation-induced activity loss, quantified by the high-/low-mutation activity ratio. The HiBiT experiment addresses a related but distinct question: whether differences in absolute GAL activity among genetic codes can be explained by differences in protein abundance, and we felt that including it in the main figures might shift the emphasis away from the central message of Fig. 5. Nevertheless, we have added a clear reference to Figure 4–figure supplement 1 in the main text and the figure legend to ensure that readers are directed to this control when interpreting Fig. 5.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In their article, Guo and coworkers investigate the Ca²⁺ signaling responses induced by Enteropathogenic Escherichia coli (EPEC) in epithelial cells and how these responses regulate NF-κB activation. The authors show that EPEC induces rapid, spatially coordinated Ca²⁺ transients mediated by extracellular ATP released through the type III secretion system (T3SS). Using high-speed Ca²⁺ imaging and stochastic modeling, they propose that low ATP levels trigger "Coordinated Ca²⁺ Responses from IP₃R Clusters" (CCRICs) via fast Ca²⁺ diffusion and Ca²⁺-induced Ca²⁺ release. These responses may dampen TNF-α-induced NF-κB activation through Ca²⁺-dependent modulation of O-GlcNAcylation of p65. The interdisciplinary work suggests a new perspective on calcium-mediated immune response by combining quantitative imaging, bacterial genetics, and computational modeling.

      Strengths:

      The study provides a new concept for host responses to bacterial infections and introduces the concept of Coordinated Ca²⁺ Responses from IP₃R Clusters (CCRICs) as synchronized, whole-cell-scale Ca²⁺ transients with the fast kinetics typical of local events. This is elegantly done by an interdisciplinary approach using quantitative measurements and mechanistic modelling.

      Weaknesses:

      (1) The effect of coordination by fast diffusion for small eATP concentrations is explained by the resulting low Ca2+ concentration that is not as strongly affected by calcium buffers compared to higher concentrations. While I agree with this statement on the relative level, CICR is based on the resulting absolute concentration at neighboring IP3Rs (to activate them). Thus, I do not fully agree with the explanation, or at least would expect to use the modelling approach to demonstrate this effect. Simulations for different activation and buffer concentrations could strengthen this point and exclude potential inhibition of channels at higher stimulation levels.

      We fully agree that CICR is determined by the local Ca<sup>2+</sup> concentration at each IP<sub>3</sub>R cluster, not by a global cytosolic average. In our stochastic model, IP<sub>3</sub> R clusters are represented as phenomenological entities at discrete spatial sites. Each cluster senses the local Ca<sup>2+</sup> concentration at its position, and its stochastic gating depends only on this local [Ca<sup>2+</sup>] and on [IP3]. Buffers are not included explicitly. Instead, we use an effective Ca2+ diffusion coefficient Deff, which accounts for the effect of endogenous Ca<sup>2+</sup> buffers. To reproduce the coordinated low-amplitude Ca<sup>2+</sup> responses observed experimentally, we found that we had to use Deff = 100 µm<sup>2</sup>/s. In the supplementary analysis, we show that an effective diffusion coefficient of this order is indeed plausible for a realistic mixture of mobile and immobile Ca<sup>2+</sup> buffers (Supplementary Note 2. Figure 1).

      In the revised manuscript, we now provide a supplementary analysis (Supplementary Note 2) to justify this choice. Using an equation to compute the effective diffusion coefficient considering a plausible mixture of mobile and immobile buffers and an explicit reaction–diffusion model, we show that:

      - The effective diffusion coefficient of Ca<sup>2+</sup> becomes Ca<sup>2+</sup> dependent, and

      - There exists a regime in which low-amplitude Ca<sup>2+</sup> elevations are characterized by an effective diffusion coefficient of Deff = 100 µm<sup>2</sup>/s and a larger spatial extent than higher-amplitude transients (Supplementary Note 2. Figure 1).

      Thus, the value of Deff used in the cluster model is quantitatively consistent with classical buffering theory and with plausible cytosolic buffer mixtures. This provides a mechanistic basis for the observation that small-amplitude, short-lived events can nevertheless produce coordinated signals with large spatial extent and, occasionally, almost immediate activation of IP<sub>3</sub>R clusters at distant locations in both simulations and experiments.

      In this respect, I would also include the details of the modelling, such as implementation environment, parameters, and benchmarking. The description in the Supplementary Methods is very similar to the description in the main text. In terms of reproducibility, it would be important to at least provide simulation parameters, and providing the code would align with the emerging standards for reproducible science.

      We apologize for the lack of details of the modelling in the previous submission. In this revised version, we are providing with a full description of the model in the Supplementary Information, Note1.

      To address the reviewer’s request for simulations at different activation levels, we now show an additional simulation in which [IP<sub>3</sub>] is higher (0.1 µM, constant in time and space) and Deff is set to 40 µm<sup>2</sup>/s (Supplementary Note 3). This lower effective diffusion coefficient is consistent with the stronger buffering and reduced Ca<sup>2+</sup> mobility expected for higher-amplitude signals. In this case, the same phenomenological cluster model generates a global Ca<sup>2+</sup> response with larger amplitude and longer duration, rather than a loss of activity due to excessive inhibition ((Supplementary Note 3, Figure 1, left panel). The Supplementary Note 3. Figure 1, right panel shows the 2D cell geometry, where dots indicate the random positions of IP<sub>3</sub>R clusters whose behavior is described by our phenomenological cluster model.

      (2) Quantitative characterization of CCRICs:

      The paper would benefit from a clearer definition of the term CCRICs and quantitative descriptors like duration, amplitude distribution, frequency, and spatial extent (also in relation to the comment on the EGTA measurements below). Furthermore, it remains unclear to me whether CCRICs represent a population of rapidly propagating micro-waves or truly simultaneous events. Maybe kymographs or wave-front propagation analyses (at least from simulations if experimental resolution is too bad) would strengthen this point.

      We agree and completed the description of the CCRICs by adding:

      In the Results section, p. 8, l. 27:

      “…with a duration of 2.1 ± 1.0 sec (mean ± SEM) (N = 4, 128 responses)”. p. 9, l. 13:

      “In rare instances (less than 3%), typical local “Puff” responses elicited by these ATP concentrations could also be detected often occurring at the cell periphery (Figs. 4B, red region and 4C, red arrow; Fig. S6D, blue trace) (N > 20, cells > 500). As expected from the small concentrations of Ca<sup>2+</sup> released at puff sites, no increase in cytosolic Ca<sup>2+</sup> was detected in a distal cell region (Fig. S6D, top), indicating that isotropic Ca<sup>2+</sup> diffusion from a puff release site cannot account for Ca<sup>2+</sup> increase over large cell area. Puffs could also be detected concomitantly with CCRICs in different ROIs of the same cell (Fig. S6D, bottom). In contrast to puffs, CCRICs often showed responses of comparable amplitude in distal regions over the whole cell (Figs. 4C and S6A, B), suggesting the contribution from IP<sub>3</sub>R cluster activation by Ca<sup>2+</sup>-Induced Ca<sup>2+</sup> Release (CICR). Within a given cell, the vast majority of CCRICs appeared quasi-synchronized at the fatest acquisition rate of 22 ms / frame that we could achieve. However, in few instances a delay could be detected in the elicitation of a peak in distant region of a cell (Fig. S6C). These observations suggest that the quasi-synchronization of CCRICs result from the fast diffusion of Ca<sup>2+</sup> leading to the activation of IP<sub>3</sub>R clusters over large cell area, which may be delayed in a some instances. Scrutinizing of CCRICs showed that while their profiles were comparable, the amplitude of these responses varied in different regions of the cell, with often a single 1 µm<sup>2</sup> region, likely corresponding the initial firing cluster, showing a prominent amplitude and other regions with smaller amplitude for a given response (Figs. 4B and 4C). For example, in Fig. 4C, the highest amplitude is observed in the red region for peaks 1 and 3, whereas it is observed and in the purple region for peak 2. Thus, for a given CCRIC, the respective contribution of local IP<sub>3</sub>R cluster activation and isotropic diffusion of Ca<sup>2+</sup>from other release sites in Ca<sup>2+</sup> increase may vary in different regions of the cell”.

      In the Discussion section, 2nd sentence p. 12:

      “CCRICs showed rapid kinetics with an average duration of ca 2.1 seconds and amplitude corresponding to an increase in Ca<sup>2+</sup> cytosolic concentration of a few hundreds nM, seemingly smaller than that of puffs (Fig. S6D), often occurring repeatedly with a frequency of up to 12 CCRICs / min over the whole cell.”

      We have tried to clarify the notion of coordination versus synchronization of CCRICs by showing the delay observed in some instances in the elicitation of CCRICs at distal regions of the cell, now illustrated shown in Fig S6C.

      (3) Specificity of pharmacological tools:

      Suramin and U73122 are known to have off-target effects. Control experiments using alternative P2 receptor antagonists like PPADS or inactive U73343 analogs would strengthen the causal link.

      As suggested by the referee, we have performed complementary experiments showing the inhibitory effects of PPADS and absence of effects of U73343 on EPEC-induced Ca2+ responses including CCRICs now shown in the amended Fig. S2.

      Reviewer #2 (Public review):

      Summary:

      The authors of this study are trying to resolve how cellular infection by enteropathogenic E. coli (EPEC) subverts cellular signaling pathways to promote infection and dampen immune responses. Specifically, alteration in calcium dynamics has been evidenced in the prior literature as a potential initiator of these adaptations, and this study provides ideas and mechanistic detail as to how cellular calcium dynamics may be subverted by pathogens.

      Strengths:

      The clear strengths of this paper relate to the new ideas inherent in the proposed hypothesis and their support from the experimental approaches used. Overall, the proposed work provides new ideas in this area, which will benefit from further investigation. Certainly, this is an interesting and challenging paradigm to pick apart mechanistically, and is important for improving treatments from intestinal infections.

      Weaknesses:

      Additional insight is needed in three specific areas to convincingly support the conclusions drawn by the authors. These three areas are: first, a better description of the infection-associated calcium signals. Second, a mechanistic definition of the relevant purinoceptors versus other pathways to increase cellular calcium. Third, an effort to show that the proposed pathways have relevance in a polarized epithelial cell.

      (1) first, a better description of the infection-associated calcium signals.

      We agree and have added a more detailed description of the CCRICs in the results and discussion section, as detailed in response to referee 1, Weakness 2 by adding:

      In the Results section, p. 8, l. 27:

      “…with a duration of 2.1 ± 1.0 sec (mean ± SEM) (N = 4, 128 responses)”. p. 9, l. 13:

      “In rare instances (less than 3%), typical local “Puff” responses elicited by these ATP concentrations could also be detected often occurring at the cell periphery (Figs. 4B, red region and 4C, red arrow; Fig. S6D, blue trace) (N > 20, cells > 500). As expected from the small concentrations of Ca<sup>2+</sup> released at puff sites, no increase in cytosolic Ca<sup>2+</sup> was detected in a distal cell region (Fig. S6D, top), indicating that isotropic Ca<sup>2+</sup> diffusion from a puff release site cannot account for Ca<sup>2+</sup> increase over large cell area. Puffs could also be detected concomitantly with CCRICs in different ROIs of the same cell (Fig. S6D, bottom). In contrast to puffs, CCRICs often showed responses of comparable amplitude in distal regions over the whole cell (Figs. 4C and S6A, B), suggesting the contribution from IP<sub>3</sub>R cluster activation by Ca<sup>2+</sup>-Induced Ca<sup>2+</sup> Release (CICR). Within a given cell, the vast majority of CCRICs appeared quasi-synchronized at the fatest acquisition rate of 22 ms / frame that we could achieve. However, in few instances a delay could be detected in the elicitation of a peak in distant region of a cell (Fig. S6C). These observations suggest that the quasi-synchronization of CCRICs result from the fast diffusion of Ca<sup>2+</sup> leading to the activation of IP<sub>3</sub>R clusters over large cell area, which may be delayed in a some instances. Scrutinizing of CCRICs showed that while their profiles were comparable, the amplitude of these responses varied in different regions of the cell, with often a single 1 µm<sup>2</sup> region, likely corresponding the initial firing cluster, showing a prominent amplitude and other regions with smaller amplitude for a given response (Figs. 4B and 4C). For example, in Fig. 4C, the highest amplitude is observed in the red region for peaks 1 and 3, whereas it is observed and in the purple region for peak 2. Thus, for a given CCRIC, the respective contribution of local IP<sub>3</sub>R cluster activation and isotropic diffusion of Ca<sup>2+</sup> from other release sites in Ca<sup>2+</sup> increase may vary in different regions of the cell” In the Discussion section, 2nd sentence p. 12:

      “CCRICs showed rapid kinetics with an average duration of ca 2.1 seconds and amplitude corresponding to an increase in Ca<sup>2+</sup> cytosolic concentration of a few hundreds nM, seemingly smaller than that of puffs (Fig. S6D), often occurring repeatedly with a frequency of up to 12 CCRICs / min over the whole cell.”

      We have tried to clarify the notion of coordination versus synchronization of CCRICs by showing the delay observed in some instances in the elicitation of CCRICs at distal regions of the cell, now illustrated shown in Fig S6C.

      CRICCs are observed over the whole cell or very large cell area. We agree that this point as well as comparison with previously described puffs needed clarification. We have added the following sentences in the discussion and inserted the seminal Thomas et al. 1999 citation in the references, p. 13, l. 18:

      “Consistently, while CRICCs were detected in the vast majority of cells at these very low agonist concentrations, in rare instances, local “puff-like” responses were also detected at the cell periphery. These observations are in contrast to previously described Ca<sup>2+</sup> puffs preceding global responses reported to occur preferentially in perinuclear area (Thomas et aL., 1999). These earlier studies, however, involved higher agonist concentrations (1-5 µM ATP) expected to lead to the release of higher IP<sub>3</sub> concentrations, which may preferentially stimulate larger IP<sub>3</sub>R clusters at the perinuclear region because of the higher density of IP<sub>3</sub> Rs. In addition, larger IP<sub>3</sub> clusters may release higher amounts of Ca<sup>2+</sup> for which, as opposed to CCRICs, diffusion would be restrained by Ca<sup>2+</sup> buffers thereby favoring the spatial confinement of the response. “

      (2) Second, a mechanistic definition of the relevant purinoceptors versus other pathways to increase cellular calcium

      We do not believe that CCRICs are specific to EPEC, since they are also elicited by low agonist concentrations. The discrete action of Type III translocons leading to the release of small amounts of extracellular ATP at the onset of EPEC prompted us to perform fast Ca<sup>2+</sup> imaging at low agonists concentrations (150 nM ATP, 100 nM histamine now shown in Fig. S4), which to our knowledge, differ from higher agonist concentrations used in all previous studies describing puffs. Our modelling studies support the notion that CCRICs correspond to generic Ca<sup>2+</sup> release-dependent responses triggered by low levels of IP3.

      We now show inhibition of CCRICs by PPADS, another purinergic receptor antagonist, and extracellular ATP depletion by addition of hexokinase in the extracellular medium in Figs. S4 and S7.

      Knocking down ATP receptors represents a challenging task since HeLa cells were shown to express transcripts for most of the described 8 P2Xs and 7 P2Ys purinergic receptors (10.1016/j.bbamem.2009.03.006). Mostly, we do not believe that CCRICs are triggered by a specific ATP receptor and do not expect to see inhibition of CCRICs in single knock-down experiments. Our experimental and modelling studies suggest that CCRICs are not specific to EPEC nor to a particular ATP receptor, but instead correspond instead to generic Ca<sup>2+</sup> elicited at low agonist concentrations such as ATP or histamine.

      Zhong et al., 2020 indeed previously showed a role for Ca<sup>2+</sup> influx mediated by the TRPV2 receptor in EPEC-mediated cell death. However, this influx occurred following 8 hours of cell infection with EPEC. We do not detect significant cell death or Ca<sup>2+</sup> influx at the onset of infection corresponding to the 12 hours infection kinetics that we used. Our experiments indicate that CCRICs do not involve Ca<sup>2+</sup> influx.

      (3) Third, an effort to show that the proposed pathways have relevance in a polarized epithelial cell.

      We agree and have performed complementary experiments showing induction of CCRICs by EPEC and eATP in polarized intestinal epithelial cells, now shown in Figure S8.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Statistical treatment and data presentation:

      Some figure legends lack clarity on replicates (n = cells vs N = independent experiments). Timecourse quantifications of p-IκB and p-p65 should include normalized fold-change plots with clear statistical tests.

      To clarify, we replaced “n” by “cells”. The number of determinations and independent experiments (N) has been added in the legends to all relevant Figures and Supplementary Figures.

      As requested, we now show the p-IκB and p-p65 plots as plots normalized to basal p-IκB and p-p65 levels. We mentioned in legend to Fig. 6 that we used an ANCOVA test showing significance of the effects of eATP on TNF-∝-induced IκB- and p65 phosphorylation.

      (2) Clarification on the temperature used in imaging (why measured at 35{degree sign} C)?

      We have added the following clarification in the Materials and Methods section p. 14, l. 21:

      “Imaging was then carried out at 35°C to allow for bacterial type III secretion, …”

      (3) Figure 4A:

      The image shows a lower image acquisition interval than every 2s that is stated in the caption.

      We apologize for the mistake. The legend to Fig. 4A now reads:

      “Image acquisition every 52 ms (A)…”

      (4) Figure 4B:

      The color of ROIs could be more intense for better identification.

      We have replaced the colors of blue and green ROIs, by light cyan and purple ROIs

      (5) Figure 4c:

      I don't understand the meaning of the dashed lines described by "The dashed red and green lines point at the aggregation of responses throughout the cell" in the caption or in the text.

      We apologize for the lack of clarity and have re-written the corresponding text p. 9, l.25 as follows:

      “Scrutinization of CCRICs showed that while their profiles were comparable, the amplitude of these responses varied in different regions of the cell, with often a ca 3 µm<sup>2</sup> single region, likely corresponding to a source point release, showing a prominent amplitude and other regions with smaller amplitude for a given response (Figs. 4B and 4C). For example, in Fig. 4C, the highest amplitude is observed in the red region for peaks 1 and 3, whereas it is observed and in the purple region for peak 2. Thus, for a given CCRIC, the respective contribution of local IP3R cluster activation and isotropic diffusion of Ca<sup>2+</sup> from other release sites in Ca<sup>2+</sup> increase may vary in different regions of the cell.”

      (6) Figure S4A:

      The responses for EGTA are not really pointed out. Are the traces meant to show events?

      We have added arrowheads in traces corresponding to ATP + EGTA-AM treatment pointing at “flattened Ca<sup>2+</sup> responses”. The Legend to Fig. S4A now includes the sentence: “ATP + EGTA-AM treatment led to an inhibition of Ca<sup>2+</sup> responses, associated with small variations in the Ca<sup>2+</sup> baseline, that were arbitrarily scored as flattened Ca<sup>2+</sup> pseudo-responses (ATP+EGTA-AM, red arrows).”

      (7) Figure S5:

      Could not identify the purple arrow for the less mobile cluster.

      We agree that the former Figure lacked clarity and have remade Figure S5, now Figure S6, with higher magnification of panels with fast acquisition. The previously purple arrows pointing at larger and less mobile clusters are now shown in black in these enlarged panels. The legend has been changed accordingly.

      (8) There are some typos and suboptimal formulations throughout the manuscript, such as:

      P8: "minute amount" could be changed to low, minor or similar.

      “minute” amounts of eATP was replaced by “low amounts of eATP”.

      P8: put a "%" to the numbers 61.2 {plus minus} 5.8.

      “%” was added.

      P16: "manuscript".

      Thank you.

      Reviewer #2 (Recommendations for the authors):

      Suggestions relate to the following three topics.

      First, a better description of the infection-associated calcium signals. The authors emphasize throughout the paper that their imaging data challenge established concepts in the calcium signaling field (discussion). I do not see the calcium imaging data explained either with data or textually with sufficient clarity to evaluate this assertion. A start would be a clear description of the characteristics of the EPEC-evoked calcium signals relative to other local and global domains of calcium signaling previously described in HeLa cells. Prior work has shown that PI-coupled agonists evoke local calcium signals that are perinuclear in HeLa cells (PMID: 10660296), but the relationship of EPEC-evoked transients to these previously defined responses is not clear.

      We agree and have added a more detailed description of the CCRICs in the results and discussion section, as detailed in response to referee 1, Weakness 2.

      Most importantly, it is ambiguous where in the HeLa cell recordings are made. Are these recordings close to the plasma membrane and/or deeper within the cell? The only spatial information is provided in Figure 3A, and these responses are not well described in the text or presented in a way that comparisons can be made to responses from a PI-coupled agonist.

      CRICCs are observed over the whole cell or very large cell area. We agree that this point as well as comparison with previously described puffs needed clarification. We have added the following sentences in the discussion and inserted the seminal Thomas et al. 1999 citation in the references, p. 13, l. 18:

      “Consistently, while CRICCs were detected in the vast majority of cells at these very low agonist concentrations, in rare instances, local “puff-like” responses were also detected at the cell periphery. These observations are in contrast to previously described Ca<sup>2+</sup> puffs preceding global responses reported to occur preferentially in perinuclear area (Thomas et aL., 1999). These earlier studies, however, involved higher agonist concentrations (1-5 µM ATP) expected to lead to the release of higher IP<sub>3</sub> concentrations, which may preferentially stimulate larger IP<sub>3</sub>R clusters at the perinuclear region because of the higher density of IP<sub>3</sub>Rs. In addition, larger IP<sub>3</sub> clusters may release higher amounts of Ca<sup>2+</sup> for which, as opposed to CCRICs, diffusion would be restrained by Ca<sup>2+</sup> buffers thereby favoring the spatial confinement of the response. “

      If I understand the described responses correctly, could not these rapid local responses result from a change in cellular calcium buffering capacity consequent to infection? Are the authors proposing that these responses occur in other cells also, or represent a pathogen-specific signaling mode?

      We do not believe that CCRICs are specific to EPEC, since they are also elicited by low agonist concentrations. The discrete action of Type III translocons leading to the release of small amounts of extracellular ATP at the onset of EPEC prompted us to perform fast Ca<sup>2+</sup> imaging at low agonists concentrations (150 nM ATP, 100 nM histamine now shown in Fig. S4), which to our knowledge, differ from higher agonist concentrations used in all previous studies describing puffs. Our modelling studies support the notion that CCRICs correspond to generic Ca<sup>2+</sup> release-dependent responses triggered by low levels of IP3.

      Second, evidence supporting a mechanistic role of ATP comes from prior literature, together with the authors' presented data showing the effects of PLC (to inhibit IP3), pharmacological inhibition (suramin, a non-selective purinoceptor blocker), and the effects of T3SS-deficient mutants (to prevent ATP release). However, there are missing steps here to mechanistically identify how ATP is working. First, does degradation of extracellular ATP (e.g., apyrase) block these responses? Second, given HeLa cells are easily amenable to knockdown approaches, does knockdown of particular ATP receptors, or TRPV2 as suggested in the prior literature, impact the calcium signal dynamics?

      We now show inhibition of CCRICs by PPADS, another purinergic receptor antagonist, and extracellular ATP depletion by addition of hexokinase in the extracellular medium in Figs. S4 and S7.

      Knocking down ATP receptors represents a challenging task since HeLa cells were shown to express transcripts for most of the described 8 P2Xs and 7 P2Ys purinergic receptors (10.1016/j.bbamem.2009.03.006). Mostly, we do not believe that CCRICs are triggered by a specific ATP receptor and do not expect to see inhibition of CCRICs in single knock-down experiments. Our experimental and modelling studies suggest that CCRICs are not specific to EPEC nor to a particular ATP receptor, but instead correspond instead to generic Ca<sup>2+</sup> elicited at low agonist concentrations such as ATP or histamine.

      Zhong et al., 2020 indeed previously showed a role for Ca<sup>2+</sup> influx mediated by the TRPV2 receptor in EPEC-mediated cell death. However, this influx occurred following 8 hours of cell infection with EPEC.

      We do not detect significant cell death or Ca<sup>2+</sup> influx at the onset of infection corresponding to the 12 hours infection kinetics that we used. Our experiments indicate that CCRICs do not involve Ca<sup>2+</sup> influx.

      Third, while the use of HeLa cells provides advantages for imaging and mechanistic assays, the effort to replicate findings in an intestinal cell line would heighten relevance, given the likely importance of cell type and cell polarity on the pathogen-evoked responses.

      We agree and have performed complementary experiments showing induction of CCRICs by EPEC and eATP in polarized intestinal epithelial cells, now shown in Figure S8.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors present a compelling case for the necessity of age-specific templates in functional hyperalignment. Given that the brain undergoes substantial developmental, structural, and functional changes across the lifespan, a 'one-size-fits-all' canonical template is often insufficient. This study effectively demonstrates that incorporating age-congruent features significantly enhances the performance and sensitivity of hyperalignment models. By validating these findings across two independent datasets (Cam-CAN and DLBS), the paper provides robust evidence that accounting for age-related functional organization is a critical prerequisite for accurate functional alignment in lifespan research.

      Strengths:

      (1) The authors used three metrics to evaluate performance. Across all metrics, they found that age-congruent templates outperformed age-incongruent templates, suggesting that age-specific templates can improve alignment.

      (2) These findings highlight the superiority of age-congruent templates for hyperalignment. This work underscores the importance of age-matching in cross-subject functional mapping and represents a vital step forward for the methodology.

      We thank the reviewer for the summary and the positive evaluation of our manuscript.

      Weaknesses:

      (1) Participant Demographics and Group Separation:

      The study defines the 'older' cohort as 65-90 years and the 'younger' cohort as 18-45 years. While this 20-year gap (ages 46-64) effectively maximizes the contrast between groups, the results in Figure 4a suggest that the predicted individualized connectomes follow a continuous distribution. Given this continuity, could the authors provide the average median trends for Figures 2a and 2b to illustrate how the model behaves across the missing age range?

      Thanks for raising this important point. We had calculated the results for the middle-aged cohort template and have included them in the Supplementary Figures 4 & 5. Similar to Figure 2a, 2b, 3a and 3b, we directly compare the intersubject correlation and prediction performance of the middle-aged participants when aligned to their congruent middle-aged template versus an incongruent template. We observed consistent results across validation analyses (ISC and prediction) and groups (young vs. middle-aged, middle-age vs. old). Consistent with our main findings, the middle-aged cohort exhibits significantly higher intersubject correlation and prediction performance when using the age-congruent middle-age template. These results confirm that the age-related shifts in functional brain organization captured by the hyperalignment templates follow a continuous trajectory across the lifespan.

      (2) Request for Implementation:

      I have been unable to locate the source code associated with this publication. Could the authors please provide a link to the repository or clarify if the implementation is available for reproduction?

      We have made our scripts public in GitHub and here’s the link: https://github.com/yuqi98/Aging_templates_scripts

      (3) Analysis of Prediction Performance and Distribution:

      While Figures 3b and 5b clearly demonstrate that the congruent template improves correlation, Figure 4a shows a distinct shift in the scatter distribution. Could the authors provide a detailed explanation of the prediction performance metrics used? Specifically, I would like to understand how the underlying method accounts for the distribution differences observed when applying the congruent template.

      Our prediction performance metric is the average Pearson correlation. We calculated the correlation between the model-predicted data (the individualized connectome in Figure 3 and the movie response in Figure 5) and the participant's actual measured data for each cortical vertex and averaged the correlations across vertices. A higher correlation indicates that the group template, when combined with the participant’s individualized transformation matrix, more accurately reconstructs the individualized functional connectome and responses to stimuli.

      The distinct upward shift in prediction performance when using a congruent template occurs because brain functional organization shows age-specific features. A congruent template captures these age-specific connectivity and response features. Importantly, the template creation algorithm aims to reflect the central tendency of the training data, including representational/connectivity geometry and functional topographies. Therefore, the observed differences in templates reflect differences in functional organization across age groups. As a result, when projecting the common template back into an individual’s native cortical space using the transformation matrix derived from independent data, the congruent template provides a richer, more accurate basis for reconstructing the individualized connectome and movie-watching responses.

      Reviewer #2 (Public review):

      Summary:

      In this study, Zhang and colleagues examine the role of participant selection in creating and using functional templates to improve analyses using hyperalignment. Hyperalignment aligns participants' functional MRI data to a shared functional template, analogous to the anatomical templates used to bring anatomical MRI data into a shared space (e.g., MNI152). The question of appropriate template creation is especially pressing for population-level analyses, where a large number of demographic groups (e.g., different age ranges, clinical statuses) may be included in the same analysis. These different demographic groups may have differences in their functional organization that complicate the creation of a single study-specific functional template.

      To provide an initial investigation of the potential effect of demographic-specific templates, the authors use the publicly available Cam-CAN dataset, which contains participants from 18 to 87 years of age. They define a young adult (< 45 years of age) and an older adult group (> 65 years of age) from this dataset with approximately the same number of participants. They investigate whether "age-congruent" templates (i.e. defined in the same age group they are used) improve three analyses where hyperalignment has been previously shown to boost performance: inter-subject correlation, predicting individual connectomes, and predicting individual functional responses. Using the Cam-CAN-derived older adult template, they then replicate the ISC analyses using the publicly available Dallas Lifespan Brain Study (DLBS).

      Overall, the presented results are highly suggestive that age-congruent templates consistently improve performance, though the absolute effects are small.

      Strengths:

      The use of a separate validation sample, reusing the same template calculated with Cam-CAN, highlights the potential of developing independent templates for individual demographic groups and then distributing these for wider use, analogous to the MNI templates that are widely used throughout the field of neuroimaging. This suggests that the potential impact of this framework is significant.

      We thank the reviewer for the summary and the positive evaluation of our manuscript.

      Weaknesses:

      While the authors appropriately highlight the potential applications of this result (e.g., to different clinical statuses), it is not apparent how to appropriately extend this methodology to many common experimental paradigms. For example, in case-control studies (where researchers are interested in comparing clinical and non-clinical participants) the use of two different functional templates may complicate rather than ease analyses. Providing this as a potential limitation of the current template construction method, or providing recommendations to researchers interested in comparing across groups, would help to increase the impact of this work.

      We appreciate the reviewer raising this important practical consideration. We have added additional explanation to the Discussion section to provide clear recommendations for researchers applying this methodology, which we summarize below:

      When the goal of a case-control study is to directly compare functional organization or brain responses between clinical and non-clinical participants, it is essential that all individuals are hyperaligned to the same common template. For these analyses, researchers should either construct a joint template containing a balanced, representative sample from both groups, or align all participants to a normative control template. This ensures that the resulting data share a single coordinate system, allowing for valid statistical comparisons between groups.

      However, disease-specific or age-specific templates are highly advantageous when the research objective is to maximize decoding accuracy or predictive performance within a specific population. In real world clinical or lifespan research, if the goal is to build a reliable diagnostic biomarker for disease progression or map individualized connectomes for a specific patient's cohort, researchers should use a template congruent with that specific group. The congruent template will preserve the group-specific representational geometry, providing a better individual-level prediction than a general cortical template.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      In general, there appears to be significantly more spread in the values for older adults (e.g., Figure 4b). It would be useful to know whether subdividing this group improves its relative performance; however, this will likely require additional investigation into the number of participants needed to establish a minimal template.

      We thank the reviewer for this constructive comment. We agree that older adults exhibit greater inter-individual variability in functional organization, which likely drives the larger spread observed in Figure 4b. We also appreciate the suggestion to subdivide this group to see if narrower age bins improve relative performance.

      We have constructed templates using narrower, 10-year age intervals and evaluated their performance. Because model performance increases with the amount of training data, we use a fixed number of training participants for each age group (two thirds of the people from the group with the minimal number of people) to build the templates to make a fair comparison. We have added the results in the Supplementary Figure 6. The results show a continuous gradient of age-related divergence. When predicting data for the 80–90 cohort, the 20–30 template performs the worst and the performance steadily improves as the template age gets closer to the target demographic. This systematic gradient further supports our main finding: the penalty for using an incongruent template increases with the discrepancy between the template age and participant age.

      Interestingly, we noticed that at the extreme ends of the age range (20–30 and 80–90), the strictly congruent template was slightly outperformed by the immediately adjacent age bin (i.e., the 30–40 template for young participants, and the 70–80 template for the oldest participants). Because we strictly matched the number of training subjects across all bins, this slight dip is likely driven by differences in raw data quality. It is common for fMRI data from the extreme ends of the lifespan to have slightly lower signal-to-noise ratios or higher head motion compared to the intermediate 30–40 or 70–80 cohorts. This suggests that while age congruency is a key driver of hyperalignment success, the intrinsic data quality of the cohort used to build the template also plays a practical role in its overall performance.

      This brings up the reviewer’s second point regarding the number of participants needed to establish a minimal template. Subdividing the age groups reduces the sample size available to construct each template. Previous research has demonstrated that while a hyperalignment template derived from a relatively small number of participants can achieve acceptable performance, increasing the amount of data and the number of subjects in the template space consistently and robustly improves alignment quality (See Supplementary Figure 7 in Feilong et al., 2023). Ultimately, our long-term goal is to build highly robust, standardized templates for fine-grained age cohorts across the entire lifespan. We are preparing to collect large-scale datasets from age 20 to 100 to build age-specific templates and provide them as open resources. This will allow future researchers to directly align their data to an age-appropriate template without needing to construct one from their own limited samples.

      Reference

      Feilong, M., Nastase, S. A., Jiahui, G., Halchenko, Y. O., Gobbini, M. I., & Haxby, J. V. (2023). The individualized neural tuning model: Precise and generalizable cartography of functional architecture in individual brains. Imaging Neuroscience, 1, 1–34. https://doi.org/10.1162/imag_a_00032

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      This manuscript presents a tunable Bessel-beam two-photon fluorescence microscopy (tBessel-TPFM) platform that enables high-speed volumetric imaging with stable axial focus. The work is technically strong and broadly significant, as it substantially improves the flexibility and practicality of Bessel-beam-based two-photon microscopy. The demonstrations are generally strong and bridge a wide range of neuroimaging applications, namely vascular dynamics, neurovascular coupling, optogenetic perturbation, and microglial responses. These convincingly show that the approach enables biological measurements that are difficult or impractical with existing methods.

      The evidence supporting the technical and biological claims is generally strong. The optical design is carefully motivated, clearly described, and validated through a combination of simulations and experimental characterization. The biological applications are diverse and well chosen to highlight the strengths of the proposed method, and the data are of high quality, with appropriate controls and comparative measurements where relevant.

      Strengths:

      (1) The optical innovation addresses a well-recognized limitation of existing Bessel-TPFM implementations, namely axial focus drift during tuning, and does so using a relatively simple, light-efficient, and cost-effective design.

      (2) The manuscript provides convincing experimental evidence for this being a versatile platform to map flow dynamics across diverse vessel sizes and orientations in both healthy and pathological states.

      (3) Biological demonstrations are comprehensive and span multiple domains such as hemodynamics, neurovascular coupling, and neuroimmune responses.

      (4) Quantitative analyses of blood flow across vessel sizes and orientations, including kilohertz line scanning, are particularly compelling and clearly beyond the reach of standard Gaussian TPFM.

      (5) Particular advantages are that higher blood slow speeds become measurable up to 23mm/sec (20x more than conventional frame scanning), and that simultaneous (Bessel-)imaging and (Gaussian-)perturbation are possible because of the stable axial focus.

      We thank the reviewer for this thoughtful and encouraging evaluation of our work. We are particularly grateful for the recognition of both the technical rigor and the broad applicability of the tBessel-TPFM platform, as well as the assessment that our approach enables biological measurements that are difficult or impractical with existing methods. We appreciate the reviewer’s detailed summary of the strengths of the manuscript, including the identification of axial focus drift as a major limitation in prior Bessel-TPFM implementations, and the value of our center-stable, light-efficient, and accessible solution. We thank the reviewer for the encouraging comment that our biological demonstrations to be compelling and well supported by quantitative analysis.

      Weaknesses:

      (1) At present, the paper does not properly position the new Bessel-beam method against previous work, and fails to compare it to alternative fast volumetric imaging methods without Bessel beams.

      We thank the reviewer for this important point. We agree that a more explicit comparison with existing fast volumetric imaging methods helps clarify the unique advantages of our system. Alternative fast volumetric imaging methods without Bessel beams include remote focusing (Sofroniew et al., 2016), acousto-optic deflectors (AOD) (Villette et al., 2019), piezoelectric objective stages (Göbel and Helmchen, 2007), tunable acoustic gradient lenses (TAG lens) (Huang et al., 2019), electrically tunable lenses (ETLs) (Grewe et al., 2011; Yang et al., 2018), and light beads microscopy (Demas et al., 2021). These methods have each enabled important forms of rapid volumetric imaging, but they differ in their speed, resolution, axial range, and optical complexity. For example, remote focusing can provide rapid axial refocusing while preserving high-resolution imaging but has limited defocus range and requires a carefully aligned relay system and aberration control to maintain image quality. AOD-based approaches enable fast random-access sampling, but introduce optical and calibration complexity associated with dispersion, and suffer light loss with limited diffractive efficiency. Piezoelectric objective scanning is comparatively simple and broadly accessible, but its mechanical inertia limits volume rate and can introduce artifacts during rapid or large axial motion. TAG lenses and ETLs provide compact non-mechanical axial scanning, but pose challenges on aberration control and synchronization. Light-beads microscopy achieves high volumetric throughput by near-simultaneously sampling multiple axial positions, but faces intrinsic compromise among axial coverage, number of sampling planes, and lateral sampling density, which limit lateral resolution when imaging over large depth ranges.        

      Previous Bessel-beam TPFM approaches address some of these limitations by converting volumetric imaging into two-dimensional scanning with an axially extended focus. However, many existing implementations either rely on a fixed Bessel beam profile, which limits the ability to adapt spatial resolution and axial coverage to different biological applications, or use spatial light modulators, which provide tunability but introduce higher cost, increased optical complexity, reduced light efficiency, and sequential rather than simultaneous multi-wavelength operation. Other axicon or lens based tunable Bessel approaches have also been reported, but these designs generally introduce axial displacement of the Bessel focus during tuning.

      In contrast, our tBessel-TPFM design provides full tunability comparable with SLM based methods, maintaining a stable axial beam center, at the same time low cost, easy to implement, intrinsically high light efficiency and support simultaneous multi-color imaging. Therefore, tBessel-TPFM provides a unique solution for applications where axial projection is acceptable and where high-speed volumetric monitoring, tunable axial coverage, motion robustness, optical simplicity, and compatibility with simultaneous perturbation are valuable.

      (2) The cost-effectiveness of the proposed method is not well described or supported by evidence; it would be useful to include more detail or remove this claim.

      We thank the reviewer for requesting clarification and supporting evidence regarding the cost-effectiveness of our method. We now provide a detailed cost breakdown of the tBessel module. Briefly, the module consists of three axicons, three lenses, and one iris that together enable independent control of the NA and ΔNA of the generated Bessel beam. Based on the specified components, the three axicons (AX252B and AX255B, Thorlabs) cost $635 each, the three lenses (AC254-125-B×2 and AC254-150-B, Thorlabs) cost $110 each, and the iris (SM2D25D, Thorlabs) costs $105, resulting in a total system cost of approximately $2,340. For comparison, spatial light modulator (SLM)-based implementations that offer comparable tunability typically require an SLM module costing on the order of $20,000 USD, in addition to more complex optical alignment and reduced optical efficiency.

      (3) Some biological conclusions, e.g., regarding novel features of microglial dynamics (i.e., the observed two-wave responses and coordinated extension-retraction), are based on relatively limited sample size and would benefit from clearer discussion of variability across animals and fields of view.

      We thank the reviewer for this important comment regarding the limited sample size of the microglial dynamics study. We agree that a more comprehensive assessment across animals would be required to establish the generality of these biological findings. In the current study, our intent is not to draw broad biological conclusions, but rather to report observations enabled by the tBessel-TPFM platform. As noted in the manuscript, we have deliberately used descriptive language (e.g., “two distinct waves of process extension were observed” “process dynamics revealed…” and “advancing processes displayed…”) to avoid over claim of the biological findings beyond the data presented.

      (4) The use of neural network-based denoising for microglial imaging is reasonable but introduces potential concerns about trustworthiness; additional clarification of validation or failure modes would strengthen confidence in these results.

      We thank the reviewer for raising this important point regarding the reliability of neural network-based denoising. We agree that additional validation and discussion of potential failure modes are essential to build confidence in these results. To assess the fidelity of the CARE-denoised data, we performed several additional analyses (Author response image 1). First, we compared normalized raw and denoised images averaged over 10 frames. The difference between the two images was spatially uniform and primarily reflected residual noise present in the raw data, rather than structured discrepancies (Author response image 1a). As expected, brighter features like microglial somata exhibited smaller differences due to their intrinsically higher signal-to-noise ratio, whereas weaker processes showed larger noise-related differences. Second, we extended this comparison across the full time-lapse sequence by applying consistent color mapping to both raw and denoised videos and computing frame-by-frame difference maps. These analyses show that the observed differences are consistent with noise suppression, without introducing coherent structural features or altering the apparent microglial dynamics (Author response image 1b).

      Author response image 1.

      Validation of CARE-based denoising for microglial imaging. (a) Comparison of 10-frame averaged normalized raw (left), CARE-denoised (middle), and their pixel-wise difference (right) images. The second row shows a zoomed-in view of the boxed region. (b) Color-coded time-lapse projections over a 10-minutes imaging session for the raw (left) and CARE-denoised (middle) data, along with their pixel-wise difference (right).

      To conclude, most of the authors' claims are well supported by the data. The central conclusion, namely that tBessel-TPFM provides tunable volumetric imaging enabling experiments not feasible with existing two-photon approaches, is justified. Some biological interpretations would benefit from a more cautious framing, but they do not undermine the main technical and methodological contributions of the study. This is a strong and technically rigorous manuscript that makes a substantial methodological advance with clear relevance to neuroscience and intravital imaging. Minor clarifications and a slightly more measured discussion of certain biological findings are recommended.

      We thank the reviewer for this thoughtful and encouraging summary of our work. We greatly appreciate the recognition that tBessel-TPFM provides a meaningful methodological advance and enables volumetric imaging experiments that are difficult or impractical with existing two-photon approaches.

      Reviewer #2 (Public review):

      The authors describe a tunable Bessel beam two-photon microscope (tBessel-TPFM) designed to overcome a common limitation of Bessel-based volumetric imaging: axial shifts of the effective focus during Bessel beam parameter tuning. Their optical design allows independent control of axial beam length and resolution while keeping the axial center fixed. This is extensively validated through simulations and experiments.<br /> Strengths:

      A major strength of the work is the breadth of validation combined with the level of technical detail provided. The authors carefully characterize the optical performance of the system and clearly explain the design choices and underlying derivations, which will make it easier for others to understand and implement. The authors demonstrate the utility of the method across several in vivo applications, including neurovascular imaging, blood flow measurements, optogenetic stimulation, and microglial dynamics.

      We thank the reviewer for their thoughtful and encouraging comments. We greatly appreciate the recognition of the technical rigor, breadth of validation, and clarity of explanation presented in our work.

      Weaknesses:

      In the in vivo demonstrations, the authors employ different Bessel beam configurations across experiments, but the beam parameters are not dynamically tuned during live imaging. A video example showing continuous or interactive tuning of the Bessel beam within a single in vivo imaging sequence would further highlight the practical advantages of this platform and strengthen the case for its potential applications.

      We thank the reviewer for their suggestion. While we agree that continuous or interactive tuning of the Bessel beam during imaging would further highlight the practical flexibility of the platform, and changing the Bessel beam parameters during imaging session is feasible in our tBessel-TPFM implementation, for the in vivo applications presented in this manuscript, dynamic tuning during the actual recording is generally not required. In practice, the Bessel beam parameters are selected before data acquisition based on the biological target, desired axial coverage, spatial resolution, and acceptable level of projection overlap.

      In addition, while excitation powers are reported, the manuscript does not place these values in the broader context of known photodamage thresholds for two-photon microscopy, which would be helpful to the readers.

      We thank the reviewer for bringing up this important point. It is known that multiphoton imaging relies on relatively high illumination power, which causes brain heating and thus photodamage. Previous studies have reported that continuous illumination with a 920-nm laser beam at 0.8 NA over 1000s results in a peak temperature increase of ~1.73 °C/100 mW in the brain, with power above 300 mW observed to cause cellular damage. Power levels below 250 mW were considered to be safe for long-term imaging. (Podgorski and Ranganathan, 2016) In our experiments, the measured post-objective powers range from 20 mW to 149 mW, which are well below the established safe threshold.

      Denoising/image restoration are applied in one of the in vivo examples, but it is unclear why this step was used specifically for this dataset and whether it was necessary to achieve adequate SNR or primarily included as an additional demonstration.

      We thank the reviewer for requesting clarification on the usage of the CARE denoising model. The CARE-based denoising was applied only in Figure 5, the microglial imaging example, and was primarily included as an additional demonstration of how neural network–based image restoration can be used to enhance low-SNR volumetric datasets acquired with tBessel-TPFM. All other images and analyses in the manuscript were performed on raw data without any denoising. To assess the reliability of the CARE denoising method, we further compared raw and denoised data using 10-frame averages and color-mapped the full 10-minute time-lapse video, both showed minimal differences (Response Fig 1). These analyses confirm that the CARE denoising model did not introduce structural artifacts or affect the biological dynamics observations in our dataset.

      Reviewer #3 (Public review):

      The manuscript presents an elegant and cost-effective approach for generating a tunable Bessel beam on a conventional two-photon microscope. The authors assemble a compact optical module comprising three axicons and a series of lenses that permits rapid adjustment of both lateral resolution and axial extent without modifying the focal plane. This flexibility enables the system to be readily adapted to a variety of biological preparations. As a proof of concept, the authors employ the device to record blood flow velocities in cortical microcapillaries, arterioles, and venules, thereby directly visualizing vasodilatation and vasoconstriction dynamics and permitting quantitative analysis of neurovascular coupling across cortical layers in awake mice.

      The authors demonstrate that the tunability of the Bessel beam can be exploited to match the numerical aperture to the vessel type: a high NA configuration, albeit slower scan, is optimal for resolving flow in capillaries, whereas a low NA setting provides faster acquisition suitable for arterioles and venules. By implementing a one-dimensional line scan with the Bessel beam, they achieve an imaging speed that is twentyfold faster than conventional frame-by-frame scanning, which proves sufficient to capture hemodynamic transients before and after an induced ischemic stroke.

      In addition to pure observation, the authors integrate a co-propagating Gaussian line to the system, allowing simultaneous imaging and photostimulation within the same focal plane. This capability addresses a common limitation of other Bessel beam implementations, in which the observation and perturbation planes often become misaligned when the Bessel beam is altered. The manuscript also emphasizes the advantage of Bessel beam excitation for calcium imaging after a perturbation, because it captures neuronal activity in planes both above and below the nominal focal plane, signals that would be missed with a standard Gaussian focus. Finally, the authors apply the technique to investigate the neuroimmune response following targeted microglial ablation; they report that adjacent microglia extend processes toward the injury site while retracting processes in the opposite direction.

      Overall, the work offers a technically straightforward yet powerful extension to existing two-photon platforms, providing high-speed, volumetric imaging and stimulation capabilities that are well-suited to a broad range of neurovascular and neuroimmune studies. The experimental validation is quite thorough, and the presented data convincingly illustrates the benefits of the approach.

      Strengths:

      The authors present a truly clever and inexpensive optical module that can be integrated into almost any two-photon microscope, providing a tunable Bessel beam with a minimal modification of the existing system. The experimental data and accompanying quantitative analysis convincingly demonstrate that the system can reveal physiological events, such as capillary flow, calcium transients across multiple axial planes, and microglial process dynamics, that are difficult or impossible to capture with a conventional Gaussian beam. The breadth of experiments chosen for the manuscript illustrates the practical utility of the device and supports the authors' conclusions that it extends the functional repertoire of standard two-photon microscopy.

      We sincerely thank the reviewer for the thoughtful and encouraging feedback. We're glad that the technical design and broad applicability of the tBessel module came through clearly, and we appreciate the recognition of its ease of integration and ability to capture dynamic physiological processes.

      Weaknesses:

      The manuscript would benefit from a more detailed contextualisation of the claimed speed advantage. Although the authors mention other techniques in the introduction, they do not provide any direct comparison with other state-of-the-art high-speed two-photon approaches such as light beads microscopy (Demas et al., Nat. Methods 2021), temporal multiplexing schemes (Weisenburger et al., Cell 2019), or random access microscopy (Villette et al., Cell 2019). A brief comparison of imaging speed, spatial resolution, and instrumental complexity would enable readers to assess the relative merits of the present method.

      We thank the reviewer for this important suggestion. We agree that a more explicit comparison with other high-speed two-photon imaging methods helps clarify the speed advantages of our system. Several existing approaches, including light-beads microscopy (LBM), temporal multiplexing, and AOD-based random-access microscopy, have demonstrated impressive high-speed volumetric imaging capabilities. Light-beads microscopy (Demas et al., 2021) reported imaging over a large volume of 5.4 × 6 × 0.5 mm<sup>3</sup> at 2 Hz. However, this large-volume acquisition used 5-μm lateral pixel sampling, corresponding to an effective lateral resolution of approximately 10 μm. In a more comparable mesoscopic volume, LBM imaged 0.6 × 0.6 × 0.5 mm<sup>3</sup> at 9.6 Hz with 1-μm lateral pixel sampling. In addition, the LBM module uses off-axis reflective concave mirrors, which require careful alignment, and the axial sampling range is not readily tunable. Temporal multiplexing approaches (Weisenburger et al., 2019), reported imaging over approximately 1 × 1 × 0.6 mm<sup>3</sup> at 17 Hz. However, this volume rate was achieved with relatively coarse spatial resolution of approximately 5 μm, together with a more complex optical design involving multiplexed excitation, detection, and synchronization. AOD-based random-access microscopy (Nadella et al., 2016; Villette et al., 2019) provides very fast point or region sampling, and reported 250 × 250 μm<sup>2</sup> imaging with 512 × 512 pixels and a 50-ns pixel dwell time, corresponding to ~0.5-μm pixel sampling and ~76 frames/s for two-dimensional imaging. However, volumetric imaging requires additional axial sampling, which lowers the effective 3D acquisition rate. In addition, AOD-based systems rely on diffractive beam steering, which introduces light loss due to finite diffraction efficiency and increases optical and calibration complexity. In comparison, tBessel-TPFM imaged a 0.4 × 0.4 × 0.12 mm<sup>3</sup> volume at 58 Hz with 0.2-μm lateral pixel sampling. Our largest demonstrated imaging volume reached 2.5 × 2.5 × 0.45 mm<sup>3</sup> while maintaining diffraction-limited lateral resolution. Therefore, compared with these high-speed volumetric approaches, tBessel-TPFM provides a distinct balance of volume rate and spatial sampling, and easier implementation simplicity.

      A second limitation that warrants discussion is the inherent trade off between volumetric coverage and image specificity. Because the Bessel beam excites fluorescence throughout an extended axial range, the detector inevitably integrates signal from a three dimensional volume into a two dimensional image. In densely labelled tissue, this can lead to significant signal crosstalk, reducing contrast and complicating quantitative interpretation. A brief analysis of how labeling density affects the fidelity of flow or calcium measurements, or suggestions for mitigating crosstalk (e.g., computational deconvolution, adaptive excitation shaping, or combinatorial sparse labeling), would broaden the applicability of the technique.

      We thank the reviewer for highlighting this important trade-off between volumetric coverage and image specificity in Bessel beam imaging. As Bessel beams project fluorescence from multiple features along the z-axis onto the same x–y plane, longer beams expand depth coverage at the same acquisition speed but can confound signals from axially spaced structures (Line 119-121 in manuscript). For densely labeled samples, the probability of having structures overlap in their x-y locations is high, and thus a shorter beam should be used. In sparsely labeled samples, structures have a lower probability of overlapping, and thus longer foci can be used (Line 166-168 in manuscript). Additionally, at the same NA, longer Bessel beam have more energy in the side rings surrounding the central peak, which may lead to higher background signal (Line 121-123 in manuscript) (Lu et al., 2017). These reasons necessitate to have not only NA tuning, but also independent length tuning (ΔNA tuning) to optimize imaging Bessel length to provide a balance between structural overlap that obscures signal localization, and the volumetric speedup, in any given sample based on labeling density and imaging goals, which are realized in our tBessel design.

      Reference:

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      Göbel, W., Helmchen, F., 2007. In Vivo Calcium Imaging of Neural Network Function. Physiology 22, 358–365. https://doi.org/10.1152/physiol.00032.2007

      Grewe, B.F., Voigt, F.F., van ’t Hoff, M., Helmchen, F., 2011. Fast two-layer two-photon imaging of neuronal cell populations using an electrically tunable lens. Biomed Opt Express 2, 2035–2046. https://doi.org/10.1364/BOE.2.002035

      Huang, C., Tai, C.-Y., Yang, K.-P., Chang, W.-K., Hsu, K.-J., Hsiao, C.-C., Wu, S.-C., Lin, Y.-Y., Chiang, A.-S., Chu, S.-W., 2019. All-Optical Volumetric Physiology for Connectomics in Dense Neuronal Structures. iScience 22, 133–146. https://doi.org/10.1016/j.isci.2019.11.011

      Lu, R., Sun, W., Liang, Y., Kerlin, A., Bierfeld, J., Seelig, J.D., Wilson, D.E., Scholl, B., Mohar, B., Tanimoto, M., Koyama, M., Fitzpatrick, D., Orger, M.B., Ji, N., 2017. Video-rate volumetric functional imaging of the brain at synaptic resolution. Nat Neurosci 20, 620–628. https://doi.org/10.1038/nn.4516

      Nadella, K.M.N.S., Roš, H., Baragli, C., Griffiths, V.A., Konstantinou, G., Koimtzis, T., Evans, G.J., Kirkby, P.A., Silver, R.A., 2016. Random-access scanning microscopy for 3D imaging in awake behaving animals. Nat Methods 13, 1001–1004. https://doi.org/10.1038/nmeth.4033

      Podgorski, K., Ranganathan, G., 2016. Brain heating induced by near-infrared lasers during multiphoton microscopy. Journal of Neurophysiology 116, 1012–1023. https://doi.org/10.1152/jn.00275.2016

      Sofroniew, N.J., Flickinger, D., King, J., Svoboda, K., 2016. A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging [WWW Document]. eLife. https://doi.org/10.7554/eLife.14472

      Villette, V., Chavarha, M., Dimov, I.K., Bradley, J., Pradhan, L., Mathieu, B., Evans, S.W., Chamberland, S., Shi, D., Yang, R., Kim, B.B., Ayon, A., Jalil, A., St-Pierre, F., Schnitzer, M.J., Bi, G., Toth, K., Ding, J., Dieudonné, S., Lin, M.Z., 2019. Ultrafast Two-Photon Imaging of a High-Gain Voltage Indicator in Awake Behaving Mice. Cell 179, 1590-1608.e23. https://doi.org/10.1016/j.cell.2019.11.004

      Weisenburger, S., Tejera, F., Demas, J., Chen, B., Manley, J., Sparks, F.T., Traub, F.M., Daigle, T., Zeng, H., Losonczy, A., Vaziri, A., 2019. Volumetric Ca2+ Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy. Cell 177, 1050-1066.e14. https://doi.org/10.1016/j.cell.2019.03.011

      Yang, W., Carrillo-Reid, L., Bando, Y., Peterka, D.S., Yuste, R., 2018. Simultaneous two-photon imaging and two-photon optogenetics of cortical circuits in three dimensions. eLife 7, e32671. https://doi.org/10.7554/eLife.32671

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #2 (Public review):

      Summary:

      The authors pair analysis of replication timing and allele-specific expression in clonal populations of primary human cells. They combine these data with previously published data on clones from transformed human cell lines. They identify a number of genomic regions that display asynchronous replication timing in at least one clone and correlate these regions with allele-specific expression of genes within them. They also observe that several interesting gene sets, including genes that are associated with human diseases, map to asynchronously replicating regions. This is a good experimental approach that builds on already published data demonstrating the connection between allelic imbalance and replication timing.

      - This is a research topic that touches on a few sub-fields of biology, and thus to make the paper more approachable we would recommend a careful edit of the text for clarity and precision of language.

      We thank the reviewers for their thoughtful and constructive comments, which substantially improved our manuscript. In response, we have revised the text and figures throughout to address the points raised.

      - Authors point out that this is a decades-old field; we would suggest to use terminology established within the field is possible. Allelic imbalance has been referred to as AI, MAE (monoallelic expression), RMAE (random monoallelic expression) etc. The paper whose mouse data the authors make use of uses Asynchronous Stochastic Replication Timing (ASRT) instead of VERT to refer to the same phenomenon.

      While we agree that allelic expression imbalance has been described by different investigators using many different phrases, we believe that MAE, RMAE and AI do not represent accurate descriptions of the phenomenon. We point out that “Allelic Expression Imbalance” has been used to describe this variable allelic expression by other investigators >120 times in the Pubmed database.  In our study [and our previous study; Nat Commun. 2022; 13(1):6301] we used clonal analysis of allele-specific expression and found that while some clones display equivalent levels of expression between alleles of a given gene (i.e. bi-allelic expression) other clones express only one allele (i.e. mono-allelic expression), and yet other clones have undetectable expression (i.e. silent on both alleles). This pattern of allele-restricted expression indicates that each allele independently adopts either an expressed or silent state. Importantly, because these expression states are mitotically stable, allele-autonomous, and independent of parental origin, we refer to the choice of the expressed allele as stochastic. Given this variability, we believe that the phrase “Allelic Expression Imbalance” (AEI) represents a more accurate descriptor for this phenomenon.

      In addition, the replication asynchrony that exists at these loci is not consistent with purely ASynchronous Replication Timing (ASRT) between alleles. We found that each allele can independently adopt either earlier or later replication timing in different clones. This variability results in some clones exhibiting pronounced asynchrony between alleles, while in others, the two alleles replicate synchronously, with both adopting either the earlier or later timing state. As reported in our previous study (Nat. Commun. 2022; 13:6301), this behavior reflects a stochastic and allele-autonomous process, leading us to describe these loci as exhibiting Variable Epigenetic Replication Timing (VERT), which we believe is a more accurate descriptor of this phenomenon.

      - Methods do not provide fully sufficient detail to fully evaluate or reproduce these experiments.

      We now provide a more detailed description of how VERT regions were identified, annotated, and quantified, including thresholds for allelic imbalance, replication timing variability, and sampling depth. We also justify the ≥80% AEI cutoff, which is based on recently published studies showing that modest allelic biases can have biological and clinical significance (Nature 2025; 637, 1186-1197). We also refer the readers to our recent description of these methods (Nat. Commun. 2022; 13:6301).

      - It is helpful to show representative loci as the authors do in Fig 1F and G and Fig 2 but these panels are very densely rendered and thus difficult to process visually - even the cartoon version (1D) is thick with overlapping lines. The point that allelic imbalance is enriched in VERTs would be enhanced if the authors could present the allelic ratio for all genes found in all VERTs, demonstrating how replication timing on either chromosome affects the allelic ratio.

      The stochastic nature of the allelic expression and replication timing observed at I/SCs is best visualized with each allele and each transcription unit displayed from multiple clones in the same panel. One of the goals of these figure panels is to emphasize that each I/SC has multiple transcription units that acquire expressed or silent states independently in each clone.  Therefore, the expressed or silent status of one allele of a transcription unit does not predict expression status of the same or opposite allele of any other transcription unit within the same VERT region. In addition, the Early/Late pattern of replication timing that we detect is not correlated with which allele is transcriptionally active (see below). In these figure panels, we display each clone using different colors, each allele as solid or dotted lines, and each transcription unit based on chromosome position. While this arrangement makes for busy images, we believe that this format captures the full breadth of the variability in expression and replication timing that occurs at I/SCs.

      Regardless, because each transcription unit is independent, we now provide the expression ratios for all transcripts that are generated from the VERT regions for the coding and non-coding transcription units in Figures 1, 2, and 6; shown in Supplemental Table 9. This analysis indicated that 4,017 informative reads were derived from the earlier replicating allele and 3,161 informative reads were derived from the later replicating allele, generating an allelic ratio of 1.3 (early/late) and a binomial P value of 1.0.

      In addition, a similar analysis of imprinted loci revealed that even at genomic regions with parent-of-origin–specific expression, the replication timing of each allele does not align with transcriptional activity, i.e. both early- and late-replicating alleles can be transcriptionally active, depending on the gene. This observation is consistent with the complex organization of many imprinted domains, where genes on opposite alleles exhibit reciprocal expression patterns. To illustrate this point, we now include Supplemental Figure 1 demonstrating that imprinted loci harbor genes expressed from both the earlier- and later-replicating alleles. In addition, quantification of the total number of informative transcripts at the DLK1/MEG8 imprinted locus (Supplemental Figure 1a-1c) indicates that the ratio of transcripts derived from the early versus late replicating alleles is equivalent (i.e. an allelic expression ratio of 1.0; See Supplemental Table 9).

      - The authors make the important point that VERTs are unlikely to be shared among different cell types and tissues (Fig 1i), but then find an enrichment for neuronal and immune genes in VERT regions identified in ACPs. It follows that these same genes are unlikely to be in such regions in the tissues where they are relevant. Some of the GO terms presented are too broad to suggest any biological significance to the result, even if there is statistical significance (for example, the top term for LCL clones 'Cytoplasm' is associated with 12,000 genes, and the second term for mouse clones 'Membrane' is associated with 10,000). It would be helpful to focus on GO terms lower in the GO hierarchy.

      We now include our complete Gene Ontology analysis, with more specific biological categories, in Supplemental Table 5.

      - Figure 3 highlights the association of related gene clusters with VERTs but the VERTs are assigned based on variable replication timing in just 1 or 2 clones. This is an interesting observation, but to make the point that "VERT regions frequently coincide with gene clusters in the human genome" there needs to be a systematic assessment of replication timing at all gene clusters across all clones, and a statistical test for significance.

      Our intent in Figure 3 was not to suggest that all gene clusters are subject to VERT and AEI, but rather to highlight that several well-characterized multigene families that are known to exhibit AEI, such as olfactory receptor, protocadherin, and HLA gene clusters, coincide with VERT regions at their genomic locations. These examples serve as representative illustrations demonstrating that I/SC-associated regulation occurs at established AEI loci organized in gene clusters.

      To clarify this point, we have revised the text to explicitly state that Figure 3 presents illustrative examples of known AEI-associated gene clusters overlapping with VERT regions, rather than a comprehensive or statistically exhaustive analysis of all gene clusters across the genome.

      - It is an interesting hypothesis that VERTs are conserved between species at syntenic loci. If such regions are really conserved, one would expect that replication timing at these sites would be consistently asynchronous. However the data presented shows that in human clones these VERTs can be specific to an individual donor (as in 5A) or an individual clone (as in 5H).

      As discussed in our Limitations Section, our analysis was restricted to a limited number of cell types, individuals, and clones, which may not capture the full diversity of I/SC usage across tissues and populations. While our dataset was sufficient to identify robust patterns of AEI and VERT, it likely represents only a subset of the broader landscape of I/SC regulation in both humans and mice. We anticipate that future studies incorporating a wider range of tissues, individuals, and clones will uncover an even greater degree of conservation and diversity in I/SC usage across genomes.

      - The finding that VERTs coincide with neurodevelopmental disease genes in immune and cartilage cells is at odds with the previous statements and data about the tissue specificity of VERTs. In order to support the claim that neurodevelopmental disease associated genes reside in asynchronously replicating regions, and are thus more prone to allelic imbalance, it would be helpful if the authors demonstrated this phenomenon in neuronal cells.

      We make two points that address this critique: First, many of the neurodevelopmental disease genes associated with VERT regions are not exclusively expressed in neuronal cells and have previously been shown to exhibit AEI in non-neuronal contexts. For example, Gimelbrant and Chess (Science, 2007; 318:1136–1140) demonstrated AEI of the Parkinson disease genes SNCA and LRRK2 in lymphoblastoid cell lines (LCLs), and in our previous study, that also used LCL cells, we detected AEI of DNAJC6, which is another Parkinson disease gene (Nat. Commun. 2022; 13:6301). In the present study, using cartilage progenitor cells, we identified VERT and AEI of several epilepsy-associated genes, including SCN1A, SCN2A (Fig. 6b), GABRA1(Fig. 6e), and SAMD12 (Fig. 6j), as well as a gene implicated in autism and neurodevelopmental disorders, SEMA5A (Fig. 5c), indicating that expression of these genes is not exclusive to neuronal cell types.

      Second, independent studies from the Dr. E. Heard laboratory have provided further evidence that AEI occurs in neuronal lineages. Using mouse neural progenitor cells (NPCs), they identified genes subject to AEI (Dev. Cell, 2014; 28:366–380) and they later evaluated AEI of syntenic human neurodevelopmental disease genes, including Snca, App, Eya4, and Grik2 (Nat. Commun. 2021; 12:5330). In our data, we find that these mouse genes are located within VERT regions. In addition, and consistent with our use of AEI, they used the phrase “Allelic Expression Imbalance” to describe the epigenetic expression biases at these genes.

      Together, these findings reinforce that AEI, and by extension I/SC regulation, is not restricted to specific cell types, but rather represents a generalizable mechanism of stochastic epigenetic regulation that includes genes relevant to neuro development and disease.

      - The authors consistently lean on sparse samples (i.e. a single clone) within a modestly sized dataset (4 clones from 2 donors each) to propose a new model for haploinsufficiency in human disease. It may well be but the consistent focus on limited elements in the data and perhaps an overreach in the interpretation makes it difficult to appreciate the very good experiments presented.

      We agree that our analysis was conducted on a modest number of cell types, individuals, and clones, which we explicitly acknowledge as a limitation of the present study. However, several key points support the robustness and broader relevance of our conclusions:

      i) Clonal Design and Replication: The strength of our approach lies in its clonal resolution. Each clone represents a single-cell–derived population expanded to over a million cells, enabling direct detection of stable, mitotically heritable allele-specific epigenetic states that would not be apparent in population-averaged data. Importantly, many of the VERT regions we identified are shared between independent clones from different donors and across distinct cell types (ACP and LCL), demonstrating reproducibility and biological consistency.

      ii) Cross-Species Validation: We further identified syntenic VERT regions in mouse pre-B cell clones, including at loci known to exhibit AEI in prior studies, providing independent validation and evolutionary conservation of the phenomenon.

      iii) Integration with Published Evidence: Our findings extend prior observations of AEI and VERT (e.g. Gimelbrant et al. Science 2007; Heskett et al. Nat. Commun. 2022) and are fully consistent with known stochastic allelic expression imbalance of autosomal genes.

      iv) We also draw parallels with the absence of cellular selection mechanisms that dictate dominant inheritance patterns for loss of function alleles for X linked disease genes (reviewed in: J Clin Invest, 2008, 20-23; and Nat Rev Genet. 2025, 26, 571–580). Our proposed model linking I/SC regulation to haploinsufficiency is therefore a synthesis of our results with an extensive body of published data, not an inference drawn from isolated observations.

      v) Scope and Framing: We have revised the manuscript to clarify that our proposed model represents a mechanistic framework, not a definitive or exclusive explanation, for how stochastic allelic regulation could contribute to dosage-sensitive disease phenotypes. We also explicitly discuss the need for larger datasets and additional tissues to refine and test this model.

      - This section refers to the revised version of the paper. We would like to thank the authors for the changes and explanations offered. Although we don't fully agree with a few answers offered, overall the answers and changes in the manuscript have significantly improved the work presented. As such it should be of interest to many readers.

      We thank the reviewers for their thoughtful evaluation and constructive feedback. We appreciate their recognition that the revisions have strengthened the manuscript and are pleased that they find the work to be of broad interest.

    1. Author response:

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

      Joint Public Review

      This manuscript puts forward the provocative idea that a posttranslational feedback loop regulates daily and ultradian rhythms in neuronal excitability. The authors used in vivo long-term tip recordings of the long trichoid sensilla of male hawkmoths to analyze spontaneous spiking activity indicative of the ORNs' endogenous membrane potential oscillations. This firing pattern was disrupted by pharmacological blockade of the Orco receptor. They then use these recordings together with computational modeling to predict that Orco receptor neuron (ORN) activity is required for circadian, not ultradian, firing patterns. Orco did not show a circadian expression pattern in a qPCR experiment, and its conductance was proposed to be regulated by cyclic nucleotide levels. This evidence led the authors to conclude that a post-translational feedback loop (PTFL) clockwork, associated with the ORN plasma membrane, allows for temporal control of pheromone detection via the generation of multi-scale endogenous membrane potential oscillations. The findings will interest researchers in neurophysiology, circadian rhythms, and sensory biology. However, the manuscript has limited experimental evidence to support its central hypothesis and is undermined by several questionable assumptions that underlie their data analysis and model builds, as well as insufficient biological data, including critical controls to validate and/or fully justify the model the authors are proposing.

      We thank the reviewers for their thorough and thoughtful comments and believe that the manuscript is much stronger now after the revision which incorporates the requested changes. We added results of new experiments and additional analyses. Although these new insights did not change the previous conclusions, we significantly reworked the Discussion and added further references to clarify the conclusions we want to make.

      Please note that we used ORN as acronym for “olfactory receptor neuron” throughout the manuscript. ORNs contain odorant receptors (ORs), and in insects these ORs associate with the olfactory receptor co-receptor (Orco) to be trafficked to the membrane of the cilium of the ORN, where they can be contacted by pheromones and odorants. In Manduca sexta, evidence is accumulating for G-protein coupled metabotropic pheromone transduction and not for OR-Orco dependent ionotropic transduction, as shown for Drosophila melanogaster. In both insect species, besides its chaperone function, Orco can form leaky cation channels, which can regulate the spontaneous spiking activity of ORNs. In this study, we explored this role of Orco.

      Strengths:

      The study is notable for its combination of long-term in vivo tip recordings with computational modeling, which is technically challenging and adds weight to the authors' claims. The link between Orco, cyclic nucleotides, and circadian regulation is potentially important for sensory neuroscience, and the modeling framework itself - a stochastic Hodgkin-Huxley formulation that explicitly incorporates channel noise - is a solid and forward-looking contribution. Together, these elements make the study conceptually bold and of clear interest to circadian and olfactory biologists.

      Major weaknesses:

      At the same time, several limitations temper the conclusions. The pharmacological evidence relies on a single antagonist and concentration, without key controls. The circadian analysis is based on relatively small numbers of neurons, with rhythms detected only in subsets, and the alignment procedure used in constant darkness raises concerns of bias. The molecular evidence is sparse, with only three qPCR timepoints, and the model, while creative, rests on assumptions that are not yet fully supported by in vivo data.

      Please see our responses to the detailed comments.

      Detailed comments are provided below:

      (1) The role for Orco proposed in the authors' model largely stems from the effects seen following the administration of (a single dose) of the Orco antagonist, OLC15. However, this hypothesis is undercut by the lack of adequate pharmacological controls, including a basic multipoint OLC15 dose-response series in addition to the administration of blockers for the other channels that are embedded in their model, but which were ruled out as being involved in the modulation of biological rhythms. In addition, these studies would (ideally) also benefit from the inclusion of the same concentration (series) of an inactive OLC15 analog to better control for off-target effects.

      The Orco agonist VUAA1 (Jones et al., 2011) binds directly to Orco and increases the channel open time probability. In M. sexta hawkmoths, we have already published that VUAA 1 increases the low spontaneous activity of ORNs in a dose-dependent fashion (Nolte et al., 2013). Chen and Luetje (2012) systematically varied the chemical structure of VUAA1 to identify new Orco ligands and discovered 22 Orco ligand candidates (OLCs) that either activated or inhibited Orco. In their heterologous expression system, Orco was most sensitive to inhibition by OLC15. Based on these results, we published a dose-response curve of OLC15 inhibition (1-100 µM) using in vivo tip recordings of pheromone-sensitive long trichoid sensilla of M. sexta (Nolte et al., 2016). There, we also demonstrated that OLC15 dose-dependently antagonizes the VUAA1-dependent activation of Orco.

      Furthermore, we tested other published Orco antagonists, which were characterized in heterologous assays, in primary cell cultures of hawkmoth ORNs, as well as in in vivo assays in intact hawkmoths. We focused on amiloride-derived antagonists, because we previously identified an amiloride-sensitive cation channel in hawkmoth ORNs. We found that, in contrast to OLC15, the amilorides HMA and MIA were not Orco-specific antagonists but instead affected different ion channel targets depending on the time of day (Nolte et al., 2016). Based on those experiments and the dose-response curves we determined that the Orco agonist VUAA1 (Jones et al., 2011) and the Orco antagonist OLC15 (Chen and Luetje, 2012) worked best in hawkmoth ORNs to target Orco pharmacologically. Due to those results and other comparative tests with other published Orco antagonists we settled since then in all further experiments on a dose of 50 µM OLC15 as most adequate to antagonize Orco functions in Manudca. In the current study, we focus on Orco without excluding the possibility that other ion channels in the ORNs contribute to the control of membrane potential rhythms.

      We have clarified the Methods section accordingly.

      (2) The expression pattern of Orco was assessed using qPCR at only three timepoints. Rhythmic transcripts can easily be missed with such sparse sampling (Hughes et al., 2017). A minimum of six evenly spaced timepoints across a 24-hour cycle would be required to confidently rule out circadian transcriptional regulation. In addition, the use of the timeless mRNA control from another study is not acceptable. Furthermore, qPCR analysis measures transcript abundance, not transcription, as the authors repeatedly state. Transcriptional studies would require nuclear run-off or, more recently, can be done with snRNAseq analysis. Taken together, these concerns undermine the authors' desire to rule out TTFL-based control that directly led them to implicate a PTTF-based model.

      We agree with the referees that more time points and a direct comparison between timeless and Orco mRNA levels should be included in this manuscript. We included these additional qPCR experiments and edited the manuscript to make clear that we measure transcript abundance, but we will not perform snRNAseq analysis due to time- and financial constraints.

      (3) The modelling presented is based on Orco as a ZT-dependent conductance tied to the cAMP oscillations that were reported by this group in the cockroach and from the presence and functionality in Manduca of homomeric Orco complexes that are devoid of tuning ORs. While these complexes have been generated in cell culture and other heterologous expression systems, as well as presumably exist in vivo in the Drosophila empty neuron and other tuning OR mutants, there is no evidence that these complexes exist in wild-type Manduca ORNs. While this doesn't necessarily undermine every aspect of their models, the authors should note the presence of Orco/OR complexes rather than Orco homomeric complexes.

      Our ELISAs found circadian oscillations in cAMP levels not only in antennae of the Madeira cockroach (Schendzielorz et al., 2014, 2012), but also in hawkmoth antennae (Schendzielorz et al., 2015). For clarification, we added the 2015 citation to the Modeling chapter in the Methods section.

      We agree with the referees that we cannot distinguish between Orco homo- and heteromers in the different compartments of our hawkmoth ORNs but we know that both are expressed in the pheromone-sensitive ORNs. Thus, as the referee suggests, we added text regarding the presence and localization of OR-Orco heteromers. Consistent data collected across different experiments (heterologous expression systems, primary cell cultures of hawkmoth ORNs, in vivo/in situ studies) support that Orco homomers are present in hawkmoth ORNs. In addition to co-expression of MsexOrco and MsexSNMP-1 with either MsexOr-1 or MsexOr-4 in a heterologous expression system, MsexOrco expression alone was already sufficient to increase intracellular Ca<sup>2+</sup> levels spontaneously as a result of its property as leaky, non-specific cation channel, and in response to VUAA1 application (Nolte et al., 2013). Both in developing hawkmoth pupae and differentiating primary cell cultures of hawkmoth ORNs, Orco expression started during a developmental time window where ORNs did not yet express pheromone receptors but where Orco affected spontaneous activity and intracellular Ca<sup>2+</sup> levels dependent on VUAA1 (Nolte et al., 2016). In vitro patch clamp studies of differentiating cultured hawkmoth ORNs during this time window of pupal development characterized ion channels/currents with properties of Orco as a leaky, non-specific cation channel/current that depends on protein kinase C and cyclic nucleotides (Dolzer et al., 2021, 2008; Krannich and Stengl, 2008; Stengl, 1993). Thus, Orco homomers are present in developing hawkmoth ORNs during a time window where ORNs already express spontaneous activity but they do not heteromerize with pheromone receptors. However, we do not know whether and in what ratio homo- and heteromers of Orco and ORs are present in the respective sensillum compartments of adult hawkmoths because all OR-specific antibodies tested did not work in immunocytochemical studies of hawkmoth antennae (Nolte et al., 2013; Stengl, 1994; Stengl and Hildebrand, 1990). Our hypothesis of differential distribution of Orco homomers in the some and dendrite compartment, and OR-Orco heteromers in the cilia is based on differential immunocytochemical localization of Drosophila ORs mainly in the cilia compartment (Benton et al., 2006).

      We clarified our manuscript accordingly.

      (4) Some aspects of the authors' models, most notably the decision to phase align/optimize their DD and OLC15 recordings, are likely to bias their interpretations.

      It is consensus that insects display daily and circadian rhythms in pheromone-dependent mating, odor-gated feeding, and egg-laying behavior that phase-locks to environmental rhythms, corresponding with daily/circadian rhythms of sensory neuron physiology (e.g., Merlin et al., 2007; Rymer et al., 2007; Schendzielorz et al., 2015, 2012). However, circadian rhythms can be easily masked by stress, like the disturbances during an experimentally very challenging long-term recording experiment over several days. In addition, we observed over the years in our animal raising facility that in 17:7 light-dark cycles the originally nocturnal hawkmoths M. sexta distribute their activity patterns over the course of the day, finding nocturnal as well as diurnal hawkmoths. Thus, light-dark cycles were not enough to ensure phase-synchronized behavioral rhythms, and it is very likely that the nocturnal hawkmoths, next to stress signals, rely heavily on pheromone/odor dependent synchronization as also found in other moth species (Ghosh et al., 2024). Because we focus on spontaneous activity and not on pheromone-dependent physiology in this study, we used isolated males that were never exposed to the female pheromones, taking phase dispersal into account. Therefore, it became necessary in free-running conditions to first determine the respective behavioral rhythm for each animal, and then to phase-align their activity patterns to allow for statistical analysis. Otherwise, circadian differences would average out in a phase-dispersed free-running population. As requested by the referees in point (7), we added RAIN to test for rhythmicity in each of our recordings and revised the manuscript accordingly.

      Furthermore, in preliminary experiments we briefly exposed hawkmoths to pheromone the night before the start of the experiment. However, we failed to obtain phase-synchronized spiking rhythms. Most likely, a circadian pattern of pheromone exposure would have been necessary as zeitgeber, which could not be used here due to long-term pheromone-dependent effects in spiking activity. These results are added as supplementary figure to Fig 3.

      (5) The tip recordings from long trichoid sensilla are critical aspects of this study. These recordings were carried out on upper sensillar tips located on the distal-most second annulus. Since there are approximately 80 annuli on the Manduca antennae, it is unclear whether the recordings are representative of the antennal response.

      We think the reviewers might have misinterpreted our description of the recording site. In the Methods, we state that we clip off the 20 most distal annuli (leaving a stump of about 60 annuli) and insert the reference electrode into the flagellum up to the second annulus from the cut end, i.e., the recording sites are located at 2/3 – 3/4 of the antenna length as seen from the head of the animal. We clarified this in the Methods section.

      In addition, our lab did show with antibody stainings against Orco that apparently all ORNs that innervate long and short trichoid sensilla along the whole flagellum express the same staining pattern (Nolte et al., 2016). Lee and Strausfeld (1990) mapped all types of antennal sensilla, and together with pheromone-dependent tip-recordings of Kaissling et al. (1989) it was shown that most of the male antennal sensilla are pheromone-sensitive long trichoid sensilla, with one of the two innervating ORNs always responding to bombykal, ensuring high sensitivity to pheromone detection. Furthermore, our patch clamp recordings of primary cell cultures of whole male antennae found largely overlapping ion channel populations across ORNs (review: (Stengl, 2010)). This would indicate that all ORNs, whether they express ORs sensitive to pheromone or general odorants, could potentially share the same Orco-dependent spontaneous activity rhythms. Furthermore, in our lab, different experimenters from different years that recorded from long trichoid sensilla on different annuli did not detect obvious differences in neither the spontaneous activity nor the pheromone responses (c.f., Dolzer et al., 2003; Gawalek and Stengl, 2018; Schneider et al., 2025). Thus, it is very likely that we are reporting a general encoding mechanism that is not locally restricted along the antennal flagellum and is very likely shared by all types of OR-Orco expressing ORNs.

      (6.1) The authors do not provide any data in support of their cAMP/cGMP-based Orco gating…

      There are publications supporting cyclic nucleotide gating of Orco in Drosophila, but only after previous phosphorylation via protein kinase C (PKC; review: (Wicher and Miazzi, 2021)). Since Orco is very conserved among insect species, it is likely that PKC- and cGMP/cAMP-dependent regulations are present for Orco in other insect species. To test this, we are currently characterizing second messenger-dependence of spontaneous spiking activity, which is the focus of a follow-up manuscript. Nevertheless, to provide more evidence for our hypothesis of the current manuscript, we added a new set of tip-recording experiments that demonstrate cAMP-dependent gating of Orco. Because of the addition of this figure, we merged figures 8-10 into Figure 8 and added the cAMP data as Figure 9.

      (6.2) … and the PTTF model proposed is somewhat disappointing.

      For a detailed introduction of our PTFL membrane clock hypothesis please see our opinion paper that we refer to in the manuscript (Stengl and Schneider, 2024). We added clarification of how Orco activation can influence cAMP levels. A more elaborate PTFL clock model including many more of the identified ion channels in hawkmoth ORNs is the focus of another manuscript to come.

      (6.3) The model seems to be influenced by their long-held proposal that insect olfactory signaling has a critical metabotropic component involving cyclic nucleotides, PKC, etc, a view that may be influenced by the use of Orco homomeric complexes generated in HEK cells.

      Indeed, we propose a metabotropic pheromone-transduction cascade, which in moths and cockroaches is based on G-protein-mediated activation of phospholipase C but not on adenylyl cyclase activation. Our hypothesis is not influenced by HEK cell heterologous expression studies of Orco but is supported by our own work comparing in vivo tip recordings of intact hawkmoths with patch clamp experiments on hawkmoth primary cell cultures of olfactory receptor neurons, which are able to respond to their species-specific pheromones in vitro (Schneider et al., 2025; Stengl, 2010; Stengl and Funk, 2013; Wicher and Miazzi, 2021). In addition, a multitude of publications by other laboratories with in vivo and in vitro studies using physiological, genetic, and immunocytochemical assays all support a metabotropic signal transduction cascade in insect olfaction (Stengl, 2010; Stengl and Funk, 2013; Takagi et al., 2025; Wicher and Miazzi, 2021). In contrast, the hypothesis suggesting a solely ionotropic pheromone- and general odor-dependent transduction cascade for all insect species is based on very sparse experimental evidence, based primarily on heterologous expression studies such as HEK cells that lack the insect’s WT molecular surroundings, and thus, cannot predict OR-Orco function in vivo. Furthermore, the ionotropic hypothesis is heavily based upon the argument that an inverse 7TM receptor cannot couple to G-proteins, which lacks careful backup via biochemical and structural studies. In addition, the ionotropic hypothesis lacks support via carefully performed physiological in vivo studies in different insect species that paid attention to analysis of the distinct kinetic components of ORN´s odor/pheromone responses and that employ physiological concentrations and durations of odor/pheromone stimuli (please see our most recent publication by Schneider et al. (2025)). We added references to the possible odor transduction mechanisms to the introduction.

      (6.4) Nevertheless, structural studies on Orco do not support a cyclic nucleotide binding site, although PKC-based phosphorylation has been implicated in the fine-tuning/adaptation of olfactory signaling.

      While structural studies did not find evidence for conserved known cyclic nucleotide binding sites on Orco, this does not exclude the presence of indirect cAMP effects via e.g., Orco subunits complexing with other molecules under direct cAMP control, such as other ion channel subunits. Furthermore, it does not exclude so far unknown binding sites, or via sites that fold out only after a specific sequence of previous phosphorylations of the many phosphorylation sites on Orco. Indeed, physiological studies in Drosophila presented evidence for cyclic nucleotide dependence of Orco after previous PKC-dependent phosphorylation (Getahun et al., 2013). Our ongoing in vivo experiments in hawkmoths further corroborate a zeitgeber time-dependent PKC- and cyclic nucleotide-dependent modulation of Orco. These detailed studies will be published in a follow-up publication. In the revised version of this manuscript, we added tip-recording experiments that indicate cAMP involvement in Orco gating (new Figure 9).

      (7) Because only 5/11 LD and 7/10 DD animals showed daily rhythms, with averages lacking clear daily modulation, the methods are not sufficiently reliable enough to reveal novel underlying mechanisms of circadian rhythm generation. The reported results are therefore not yet reliable or quantifiable. To quantify their results, the authors should apply tests for circadian rhythmicity using methods such as RAIN, JTK CYCLE, MetaCycle, or Echo. The use of FFT and Wavelet is applauded, but these methods do not have tests of significance for rhythms and can be biased when analyzing data in which there could only be 1-3 circadian cycles. Because the conclusions appear to be based on 11-12 neurons that were recorded for 2-4 days, the reader is concerned that the methods are not yet perfected to provide strong evidence for circadian regulation of spontaneous firing of ORNs. The average data (e.g., Figure 3Bii and 3Cii) highlight the apparent lack of daily rhythms. In summary, the results would be more compelling if more than 50% of the recordings had significant circadian amplitudes and with similar periods and phases.

      The long-term tip-recordings of intact hawkmoths are very challenging and take a very long time to accomplish, thus, we are very happy that we succeeded in obtaining so many of them (N=40). We are thankful to the reviewers’ suggestion to use RAIN since this analysis revealed circadian rhythms in 7 of 11 LD recordings, 8 of 12 DD recordings, and 2 of 12 OLC15 recordings. Please see also our response to (4) above, commenting the phase-dispersal of activity rhythms observed in our experiments, as well as in the behavior of hawkmoth males in the mating cage.

      (8) The statement that circadian patterns of ORN firing are lost with the Orco antagonist (OLC15) is not strongly supported. The manuscript should be revised to quantify how Orco changed circadian amplitude in the 12 recorded neurons. Measures of circadian amplitude can avoid confusing/vague statements like Line 394 “low and high frequency bands appeared to merge during the activity phase around ZT 0 in the animals that showed clear circadian rhythms (N = 5 of 11 in LD)”. The conclusion that Orco blocks circadian firing appears to be contradicted by Figure 6, which indicates that ~6 of these neurons had circadian periods detected by wavelet. The manuscript would be strengthened with details about the specificity and reproducibility of the Orco antagonist. The authors quantify the gradual decrease in firing with the slope of a linear fit to estimate how the “effectiveness [of OLC15] increased over time.” They conclude that the drug “obliterated circadian rhythms and attenuated the spontaneous activity in several, but not all experiments (N = 8 of 12).” The report would be greatly strengthened with corroborating data from additional Orco antagonists and additional doses of OLC15 (the authors use only 50 uM OLC15).

      According to the valuable suggestions of the referees, we used RAIN to detect circadian rhythms in the spiking attributes in each individual animal. Since only 2 of 12 animals displayed a circadian rhythm in OLC15, statistical comparison of circadian amplitudes is not possible. We revised the results section accordingly and added to the figure legend to make it clearer that the heat maps in Fig 5 are representative from one animal each and not averages across animals.

      As the reviewer states correctly in (7), wavelet results of circadian rhythmicity must be interpreted carefully because of the low number of circadian cycles in ~3-4 day recordings. Since the heatmaps in Figure 5 visually revealed the presence of ultradian rhythms, the main focus of the wavelet analysis in Figure 6 is in the detection and quantification of ultradian periods up to 20 h.

      We revised the Methods section to include references to previous experiments that characterized the effect of different doses of OLC15 and other Orco antagonists and agonists in M. sexta antennae (Nolte et al., 2016). Please see also our response to (1).

      (9) The manuscript includes several statements that are more speculation than conclusion. For example, there is no evidence for tuning or plasticity in this report. Statements like the following should be removed or addressed with experiments that show changes in odor response specificity or sensitivity: "ORN signalosomes are highly plastic endogenous PTFL clocks comprising receptors for circadian and ultradian Zeitgebers that allow to tune into internal physiological and external environmental rhythms as basis for active sensing." (Discussion Line 622). The paper concludes that (line 380) "mean frequency of spontaneous spiking and the frequency of bursting expressed daily modulation, and are both most likely controlled via a circadian clock that targets the leak channel Orco." This is too bold given the available results.

      We revised the manuscript accordingly and clarified which statements are supported via published evidence and which are predictions based upon our novel hypothesis published in our opinion paper (Stengl and Schneider, 2024).

      (10.1) Because Orco conductance is modulated by cyclic nucleotides, it remains highly plausible that circadian regulation occurs upstream at the level of signaling pathways (e.g., calcium, calcium-binding proteins, GPCRs, cyclases, phosphodiesterases).

      We agree with the referees that it is very likely that there are multiple layers of interconnected feedback cycles that control Orco localization and activity. Our novel hypothesis suggests interlocked TTFL and PTFL control of physiological circadian rhythms, not strictly hierarchical TTFL control, which would require a daily turnover of membrane proteins and transcriptional control via the established TTFL clock in insect ORNs. We are currently searching for TTFL control at all levels of odor/pheromone transduction using ZT-dependent transcriptomics in combination with qPCR and single-nucleus transcriptomics, involving also all the molecules suggested by the referees. These studies are ongoing, are very time- and money-consuming, and are beyond the scope of this manuscript. However, we added a set of experiments to this manuscript in which we demonstrate that the effect of increased cAMP on the spontaneous spiking activity is mediated by Orco (new Figure 9).

      (10.2) The possibility that circadian oscillations of cyclic nucleotides are generated by the canonical TTFL mechanism has not been excluded. In fact, extensive work in Drosophila has demonstrated that the TTFL-based molecular clock proteins are required for circadian rhythms in olfaction.

      Our experiments that test circadian TTFL control at different levels of the cAMP transduction cascade in hawkmoth antennae are on the way and are part of another publication. In section 6.2 we already stated that our experiments do not exclude that Orco is under indirect control of the TTFL. We revised our discussion accordingly.

      The experiments published for TTFL dependent control of Drosophila olfaction that we are aware of (Krishnan et al., 1999; Tanoue et al., 2004) do not exclude interlinked PTFL and TTFL clocks. Krishnan et al. (1999) demonstrated that the TTFL clock in antennal olfactory receptor neurons correlates with circadian rhythms in odor responses measured in electroantennogram (EAG) recordings, not in single sensillum recordings as in our experiments. EAG recordings comprise not only voltage responses of the olfactory sensory neurons but also voltage changes generated in non-neuronal antennal cells such as trichogen and tormogen cells that built the transepithelial potential gradient via vATPases that generates the high K<sup>+</sup> concentration in the sensillum lymph (Jain et al., 2024; Klein, 1992; Thurm and Küppers, 1980). In addition, EAG recordings most likely contain responses of afferent neurons originating from somata in the brain that maintain central control of the antennae. Thus, EAG recordings are difficult to interpret.

      (11) A defining feature of circadian oscillators is the feedback mechanism that generates a time delay (e.g., PERIOD/TIMELESS repressing their own transcription). While the authors describe how cyclic nucleotides can regulate Orco conductance, they do not provide a convincing explanation of how Orco activity could, in turn, feed back into the proposed PTFL to sustain oscillations. For these reasons, the authors should consider:

      (a) Providing a broader discussion of non-TTFL models of circadian rhythms (e.g., redox cycles, post-translational modifications).

      We revised the discussion accordingly.

      (b) Reassessing Orco expression using a higher-resolution temporal sampling ({greater than or equal to}6 timepoints per 24 h).

      We added those experiments to the revised version of the manuscript (see our response to (2)).

      (c) Clarifying or revising the PTFL model to explicitly address how feedback would be achieved. Alternatively, the data may be more consistent with Orco conductance rhythms being regulated by post-translational mechanisms downstream of the canonical TTFL oscillator, as suggested by the Drosophila olfactory system literature.

      We added possible negative feedback elements to the Discussion to explain how our proposed PTFL could in principle work independent of TTFL clock.

      Minor weaknesses:

      (1) The authors should compare the firing patterns of ORN neurons to the bursts, clusters, and packets of retinal efferent spikes reported in Liu JS and Passaglia CL (2011; JBR). By comparing measures in moths to measures in Limulus, the authors might be able to address the question: Is the daily firing pattern of ORN neurons likely a conserved feature of circadian control of sensory sensitivity?

      We have revised the discussion accordingly.

      (2) The methods need further details. For example, it is unclear if or how single neuron activity was discriminated and whether the results were compromised by the relatively large environmental fluctuations in temperature (21-27oC), humidity (35-60%), or other cues known to modulate spontaneous firing.

      These large fluctuations stem from doing experiments at different seasons (higher temperature and humidity in the summer months, lower temperature and humidity in winter). Throughout each individual experiment, conditions were stable. We clarified the Methods section accordingly.

      Recommendations for the authors:

      The authors should post the code for their computational model to a repository like GitHub.

      The code for the computational model is now available at https://github.com/a-c-schneider/VijayanForlinoEtAl2025_Model.git

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    1. Author response:

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

      eLife Assessment

      This well-designed, valuable study uses isotope tracing to analyse how iron limitation alters TCA cycle metabolism in Mycobacterium tuberculosis, revealing potential antibiotic targets for non-replicating bacteria in the host. The findings provide insights into metabolic remodelling under iron-limited conditions. Whilst some of the evidence is solid, the data around the GABA shunt is incomplete, requiring genetic validation, as was done for the glyoxylate shunt. Questions remain about the underlying mechanisms and their specific role in M. tuberculosis pathogenesis.

      We thank the Editor and the reviewers for the positive evaluation of our work and for the constructive comments, which helped us improve the manuscript. We have carefully considered all the points raised and addressed them to the best of our ability. Regarding the GABA shunt, we acknowledge that genetic validation would significantly strengthen our conclusions; as this was not feasible within the revision timeframe, we have revised the relevant section by adopting more cautious language and have included genetic validation among the future perspectives. Additionally, we have expanded the discussion to address the relevance of our findings in the context of Mtb pathogenesis and host-pathogen interaction. A point-by-point response to each comment is provided below.

      We also made minor adjustments to the main text and figures:

      We removed “normalised” from the Y-axis of Figure 1 (the data are normalised and the procedure is described in the Materials and Methods).

      We rearranged the order of a paragraph in the Introduction: the first paragraph “During infection pathogenic bacteria […] extensively investigated” has been moved down, (page 2, lines 8-12). -We edited two sentences in the Introduction (page 2, lines 4-7)

      Supplementary Information: we added the following sentence at page 4, lines 23-24: “The probability of the Figure 3 and 4–figure supplement 1E scenario should be equivalent to that of the Figure 3 and 4–figure supplement 1F scenario.”

      We made minor typing adjustments: page 3, lines 30 and 31; page 4, lines-11-12, lines 22-24; page 5, lines 23-24; page 7, line 6; page 12, lines 28 and 32.

      We added details to the Materials and Methods section at page 17, lines 1 and 19-21.

      Public Reviews:

      Reviewer #1 (Public review):

      M. tuberculosis exhibits metabolic flexibility, enabling it to adapt to various environmental stresses, including antibiotic treatment. In this manuscript, Serafini et al. investigate the metabolic remodeling of M. tuberculosis used to survive iron-limited conditions by employing LC-MS metabolomics and 13C isotope tracing experiments. The results demonstrate that metabolic activity in the oxidative branch of the TCA cycle slows down, while the reductive branch is reverted to facilitate the biosynthesis of malate, which is subsequently secreted.

      Overall, this study is experimentally well-designed, particularly the use of 13C isotope tracing to monitor TCA cycle remodeling under iron-limited conditions. The findings are valuable as they offer potential new targets for antibiotics aimed at non-replicating M. tuberculosis occurring in the hosts. However, despite these strengths, the reviewer has concerns regarding the mechanistic basis underlying the observed metabolic remodeling and its role in M. tuberculosis pathogenesis.

      We thank the reviewer for the positive evaluation of our work and for the constructive comments. Regarding the role of the observed metabolic remodelling in Mtb pathogenesis, we have expanded the discussion to address this aspect, contextualising our findings within the framework of Mtb infection and host-pathogen interaction (page 13, line 28-37; page 14, lines 1-23). Detailed responses to each specific comment are provided below.

      Major comments

      The authors argue that iron starvation is a physiologically relevant stressor encountered by M. tuberculosis post-infection. Using Erdman and H37Rv strains under DFO conditions, Erdman loses viability, whereas H37Rv maintains it. Nonetheless, both strains exhibit similar metabolic remodeling in the TCA cycle based upon metabolomics and isotope tracing data. The authors should clarify the specific metabolic adaptations in H37Rv that enable it to sustain viability under DFO conditions.

      We thank the reviewer for this observation. Following additional experiments performed in response to subsequent comments, we re-analysed the secreted metabolite data and monitored ATP, NADH, and NAD<sup>+</sup> levels over 17 days in both the Erdman and H37Rv strains. The results were concordant between the two strains, supporting the hypothesis that the decrease in CFU/mL over time does not reflect a loss of viability, but rather entry into a non-culturable state or, alternatively, an increased tendency to aggregate in liquid culture. Comments have been added at page 3, lines 16-24 and page 5, lines 30-36

      A mechanistic explanation of how Mtb sustains viability under iron starvation is provided at page 13, lines 2837.

      The authors report no significant changes in NAD/NADH and ATP levels in H37Rv and Erdman exposed to DFO conditions. They observe TCA cycle remodeling, particularly the reversal of the reaction between OAA and MAL, catalysed by malate dehydrogenase, an enzyme that uses NAD+ and NADH as cofactors. The directionality of this reaction likely depends on the relative levels of NAD+ and NADH. Additionally, other dehydrogenases, such as pyruvate DH and aKG DH, also require NAD+/NADH cofactors.

      We thank the reviewer for this important observation. We agree that the directionality of the malate dehydrogenase reaction, as well as the activity of other NAD<sup>+</sup>/NADH-dependent dehydrogenases, is likely influenced by the redox state of the cell. We therefore measured the NADH/NAD<sup>+</sup> ratio over 17 days in both strains under DFO conditions. We also note that the Y-axis title in Figure 1 was incorrectly reported and has been corrected accordingly. Results and interpretation of these new data are provided at:

      page 3 lines 16-21

      page 11 lines 16-36

      page 12 lines 1-9

      page 13 lines 3-5

      In Figure 1I, NAD+ and NADH levels are monitored only at day 3 post-exposure to DFO conditions. Since Erdman loses viability after 2-3 weeks, the authors should include measurements of NAD+, NADH, and ATP levels at weekly intervals up to 3 weeks.

      We thank the reviewer for this suggestion. As recommended, we extended the monitoring of NAD<sup>+</sup>, NADH, and ATP levels over 17 days in both strains. Results and interpretation have been discussed together and are reported in the manuscript. Please refer to the response above for the relevant page and line references.

      Furthermore, glycine levels - which are linked to NAD+ recycling via the conversion of glyoxylate - should be measured under both HI and DFO conditions as an indirect indicator of the NAD+/NADH ratio.

      We thank the reviewer for this comment. However, we believe that glycine levels cannot be considered a reliable indirect indicator of the NAD<sup>+</sup>/NADH ratio, as glycine is involved in multiple metabolic pathways. It can originate from serine, threonine, glyoxylate, or protein degradation, and can be incorporated into proteins, degraded to CO<sub>2</sub> and NH<sub>4</sub><sup>+</sup>, converted to glyoxylate, or transformed into other amino acids. Due to its metabolic versatility, therefore, glycine levels lack the specificity required to reliably reflect the cellular NAD<sup>+</sup>/NADH ratio. In addition, we could not find a single study that claim that glycine levels can be used as indicators of NAD<sup>+</sup>/NADH ratio.

      Nevertheless, this comment prompted us to examine glycine levels and isotopologue distribution under iron deprivation. Glycine levels showed no consistent trend under DFO conditions, remaining unchanged or increasing in both the Erdman and H37Rv backgrounds.

      Importantly, the isotopologue distribution analysis led us to conclude that glyoxylate is not a key precursor of glycine under iron starvation. This new analysis is described at page 10 (lines 1-20), and a new supplementary figure has been added, Figure 3 and 4 – figure supplement 3.

      In Figure 2A, it is unclear why a 100-fold accumulation of aKG does not correspond proportionally to the accumulation of (iso)citrate.

      We thank the reviewer for this observation. We agree that this point required clarification and have added a comment addressing this apparent discrepancy in the main text at page 4, lines 12–17.

      The authors state that fumarate, aKG, (iso)citrate, malate, and pyruvate are secreted under DFO conditions. While the secretion of aKG and pyruvate makes sense, given their marked intracellular accumulation, it is puzzling why (iso)citrate, malate, and fumarate are secreted even though there are no changes in their intracellular abundance.

      To rule out the possibility that these metabolites are released due to bacterial lysis rather than active secretion, the authors should analyze the 13C-labeled fractions of these metabolites in the culture filtrate using the M. tuberculosis culture in media containing 13C glycerol.

      We thank the reviewer for this important observation.

      Regarding the possibility of cell lysis, although it cannot be completely ruled out, several observations indicate that the increase in extracellular malate was not due to lysis. If substantial cell lysis had occurred, we would expect a general increase in all extracellular metabolites. However, the extracellular fumarate and succinate levels remained unchanged in both strains under DFO (similarly to the control conditions, HI and LI). Glutamate was detected in the culture filtrate, but its abundance increased only under HI conditions, not under DFO, in either H37Rv or Erdman. The lack of increase in extracellular glutamate, fumarate and succinate, therefore suggests that, even if some cell lysis occurred, it was minimal and did not significantly affect our observations.

      Regarding the 13C-fractions, we note that it is unclear how should the labelling profile would differ if extracellular metabolite derived from cell lysis. Nevertheless, as suggested by the reviewer, we compared the labelled fractions of extracellular isocitrate, malate, fumarate and glutamate. The comparison revealed variations consistent with two blocks in the carbon flow occurring at the levels of pyruvate and alpha-ketoglutarate, resulting in a slowdown in the downstream flux.

      A description of these new considerations has been added at page 5 (lines 27-36) including the Figure 2 – figure supplement 2 and a new section of SI-Appendix. Therefore, we are confident that the selective appearance of some but not all metabolites in culture filtrates is consistent with secretion but not cell lysis.

      To validate the role of the PCK-mediated reductive TCA cycle in malate biosynthesis and secretion under DFO conditions, the authors should generate a malate dehydrogenase (MDH) knockdown strain, considering that MDH is essential, and examine the 13C labeling patterns and NAD/NADH under DFO conditions.

      The authors also observe decreased GABA abundance and overall 13C labeling in DFO conditions, suggesting that the GABA shunt is the primary route for succinate biosynthesis under DFO conditions. Thus, it is strongly recommended that the authors perform a 13C glutamate tracing experiment to directly track labeling in aKG and GABA shunt metabolites, providing more definitive evidence for the involvement of the GABA shunt.

      We thank the reviewer for these valuable suggestions. We fully agree that both experiments would significantly strengthen the conclusions of our work.

      Regarding the MDH knockdown strain, we acknowledge that this experiment would provide direct validation of the PCK/PCA-mediated reductive TCA cycle in malate biosynthesis. However, generating a knockdown strain in Mtb is a technically demanding and time-consuming process, requiring several months even under optimal conditions, which makes it unfeasible within the revision timeframe. We have therefore incorporated this experiment as a future perspective in the conclusions, highlighting its importance for further validating the proposed model.

      Regarding the GABA shunt, we took the reviewer's comment as an opportunity to critically re-evaluate the strength of our data. As a result, we have revised the manuscript by merging the GABA shunt discussion with the glyoxylate shunt section, while adopting more cautious language in the concluding statement to reflect its hypothetical nature. The related figures have been moved to the Supplementary Materials. These aspects have been included among the future perspectives in the conclusions. Page 11, lines 10-13; page 14, lines 3-7.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated the effect of prolonged iron limitation (which does stop growth but does not lead to cell death), altering central metabolism in M. tuberculosis. The major tool they used is metabolomics combined with stable isotope tracing. They show that the Krebs cycle is still active, despite the fact that it is dependent on some iron-dependent enzymes. They show that carbon flux through the oxidative branch of the Krebs cycle is stalled, resulting in the accumulation of metabolites, such as malate and alphaketoglutarate, that are partially secreted. Apparently, the carbon flux from glycolysis is partially diverted to the reductive branch of the Krebs cycle. This is not achieved by using the glyoxylate shunt but probably through the GABA shunt. This unprecedented split of the Krebs cycle and malate secretion allows a continuous flow of carbon through the core of carbon metabolism, overcoming the metabolic stalling triggered by iron starvation.

      Strengths:

      Novel insight into the central metabolism of a major pathogen and its adaptation to iron starvation. Carefully conducted experimentation. The paper ends with a clear and helpful model.

      Weaknesses:

      The authors show some surprising and important findings, but they would need a little more effort to really substantiate these. Especially the role of the GABA shunt should be genetically tested, as they did for ICL and the glyoxylate shunt.

      We thank the reviewer for the positive evaluation of our work. We agree that genetic validation of the GABA shunt would significantly strengthen our conclusions. However, generating the required mutant strains in Mtb is a technically demanding and time-consuming process that is unfeasible within the revision timeframe. In light of this, we have revised the manuscript by merging the GABA shunt discussion with the glyoxylate shunt section. This reorganization contextualizes the GABA shunt within a broader discussion, while adopting more cautious language in the concluding statement to reflect its hypothetical nature. Future genetic validation, including the generation of appropriate mutant strains, has been included among the future perspectives in the conclusions.

      Page 11, lines 10-13; page 14, lines 3-7.

      Also, dataset 1 is not very convincing, it is only based on transcriptomics and shown with up or down; this is not a strong base for major conclusions. As a minimum, one would want actual differences, preferably on the protein level, where it really counts.

      We thank the reviewer for this comment. We would like to clarify that Dataset S1 compiles transcriptomic and proteomic data from previously published studies, which represent the rational basis of our investigation. These data are consistently cited throughout the manuscript. The dataset was included solely as a convenience tool for the reader, to provide easy access to the relevant published information. To avoid any misunderstanding regarding its scope, we have renamed the file to 'Dataset S1 - Publicly available transcriptomic datasets referenced in this study'. Our conclusions derive from the integration of these published data with the novel biochemical and metabolomic evidence generated in this study. Further, to assist the reading, we added a clarifying description at top of “DE” column.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Clarify the definitions of "growth defect" and "growth arrest" under LI and DFO conditions, respectively.

      (2) In Figure 2A, specify the unit of the y-axis. Is it on a log scale?

      (3) Raw data of metabolomics and 13C isotope tracing experiments should be either deposited in public websites or provided as a separate file.

      We thank the reviewer for these comments.

      Regarding the definition of 'growth defect' and 'growth arrest': we replaced 'defect' with 'slowdown' to better reflect the observed phenotype under LI conditions.

      Regarding Figure 2A: we have specified the unit of the Y-axis and clarified whether the scale is logarithmic in the figure legend. We have done that for all the figures containing charts with Y/X axis in logarithmic scale. We added secondary tick marks in the charts of Figure 5G.

      Regarding raw data availability: the metabolomics data have been deposited in the Zenodo database. The reference number has been added to the manuscript."

      Reviewer #2 (Recommendations for the authors):

      It is mentioned that measurement of the activity of these two enzymes in cell-free extracts revealed the presence of PCA activity in the DFO condition (Figure 5E), but not of MEZ activity (data not shown). Activity measurements are a great added value, but then activities should be shown, also for MEZ.

      We thank the reviewer for this suggestion. We agree that showing enzyme activity data adds value to the manuscript. As recommended, activity measurements have been included in the supplementary materials (Figure 5 – figure supplement 1).

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper provides a novel method to improve the accuracy of predictions of the impact of ITN strategies, by using sub-national estimates of the duration of ITN access and use over time from cross-sectional survey data and annual country ITNs received.

      Strengths:

      The approach is novel, makes use of available data, and has considered all of the relevant components of ITN distributions.

      Weaknesses:

      (W1.1) The main message of the paper was not very clear, and did not seem to fit the title. The title focuses on sub-national tailoring of ITN, but the abstract did not feature results directly about SNT. It was not very clear what the main result of the paper was - there are several ITN observations in the results and discussion. Most did not seem to be directly about SNT, but rather sub-national differences in use and access were accounted for in the analyses. It was not clear if the same conclusions would be reached without accounting for sub-national differences, but the estimates and predictions could be expected to be more accurate.

      Thank-you for highlighting this. We agree the title could be improved to better reflect the main messages of the paper and have now updated it to “Heterogeneity of use, access and retention of insecticide-treated nets: implications for subnational tailoring to maximise malaria control”. All parameters are estimated at a subnational level; this is not always the case a national level. We therefore do not have national-level models without subnational differences that our results could be compared to.

      (W1.2) Some of the results seemed to me to be apparent even without a modelling exercise (eg high coverage could not be maintained between campaigns, use would be higher with 2-yearly distributions rather than 3-yearly) or were not in themselves new insights (eg estimates of the duration of use). It would be helpful to clearly state what the novel results are in the abstract, the first paragraph of the discussion and the conclusions, and to make sure that the title is consistent.

      It is our understanding assessments on ITN coverage are often made from infrequent surveys, for example from MIS. These are typically conducted six months postcampaign and may miss notable reductions in use and access beyond this. Comparisons on ITN use and access are also frequently made directly between DHS surveys, which can be misleading in isolation if the time between campaigns and surveys is not considered. We have tried to highlight this more clearly in relation to Burkina Faso with the following text:

      “The observed decrease in use and access across many regions in Burkina Faso may therefore be a by-product of DHS surveys being conducted at progressively later dates relative to the most recent campaign; this does not necessarily indicate an underlying trend in decreasing use or access over longer timescales.”

      We do believe modelling exercises, such as the methodology presented here, can help generate improved estimates of ITN use and access over time than estimates from surveys alone, which can be biased by the relative timings of campaigns. It is also our understanding previous studies have generated national estimates of ITN retention. We are not aware of any previous studies that have estimated the duration ITNs continue to be used for, which is arguably of greater epidemiological importance than retention time. To best knowledge, these have also not been estimated at subnational scales previously.

      We acknowledge the novelty of some results were not clearly presented previously and are grateful to the reviewer for highlighting this. We have now highlighted some of the novel findings more clearly in the abstract, with the following text:

      “However, subnational variation in ITN retention and the duration that ITNs remain in use have not previously been quantified.”

      “Our results highlight that although transmission intensity remains an important factor for subnational tailoring of malaria control interventions, other factors, such as ITN use given access, meaningfully influence optimal deployment strategies.”.

      We have also highlighted the novelty and relevance of our findings more clearly in the first paragraph discussion, with the following text:

      “Funding constraints have also increased the need for consideration of subnational tailoring, with many recommendations being made on the basis of transmission intensity in the World Health Organisation (2025) Subnational Tailoring Reference Manual. However, a key uncertainty in assessing the potential impact of different ITN interventions has been how long nets remain in use rather than how long they are retained, and how this varies between regions. Here, to our best knowledge, we present the first estimates of subnational variation in ITN retention and the duration that ITNs remain in use, and also quantify for the first time how ITN use, access and retention vary between subnational regions across multiple African countries. Our work supports the change in guidance to optimal coverage as it highlights ITN interventions have notable differences in impact between settings, and that distributing fewer but more effective ITNs, particularly pyrethroid-chlorphenapyr products, is likely to be more impactful than maximising long-term coverage through increased campaign frequencies with pyrethroid-only ITNs. Our work also broadly supports World Health Organisation (2025) recommendations for subnational tailoring, particularly the consideration of deprioritisation of ITN distribution in very low transmission settings. However, our results provide new indications that deprioritisation of areas with higher ITN use given access may lead to greater resurgences in cases, highlighting that subnational tailoring decisions could be optimised further by considering additional factors to transmission intensity alone.”

      The novelty and relevance of our results are also now highlighted in the following text, which has been incorporated into the concluding paragraph:

      “In conclusion, the work indicates that universal coverage targets of 80% are unlikely to be consistently met due to waning overall ITN use in the intervening years between triennial mass campaigns. Improved coverage can be achieved through more frequent biennial distributions, though this is unlikely to be feasible at scale given the current funding landscape. Indeed, when resources are constrained, deprioritisation of ITN mass campaigns in certain settings is being increasingly considered through subnational tailoring of malaria control interventions. Our work highlights that the relationship between transmission intensity (whether measured in terms of prevalence or clinical cases) and intervention impact is non-linear, and notable resurgences in cases may follow when campaigns are deprioritised in all but very low transmission settings. This broadly supports WHO subnational tailoring guidance, which suggests consideration of deprioritising distribution of ITNs in regions with PfPR<sub>2-10</sub> < 1% (World Health Organization, 2025). However, while the World Health Organization (2025) Subnational Tailoring Reference Manual proposes that the withdrawal of ITNs in favour of indoor residual spraying should be considered in areas with low ITN use, here we estimate that ITN use alone appears to be a notably poorer predictor of the impact of ceasing mass campaigns than use given access. Our findings suggest that regions with higher use given access may experience disproportionately greater resurgences in cases following deprioritisation. This implies that regions with low use given access may warrant consideration for cessation of ITN distribution, rather than decisions being based solely on low overall ITN use irrespective of whether communities have sufficient ITN access. However, subnational differences in ITN use, access and retention are key knowledge gaps in many settings, and when estimated from infrequent surveys they are highly sensitive to bias arising from the timing of surveys relative to when campaigns were conducted. To our knowledge, this study is the first to estimate subnational variation in ITN retention and the first to estimate the duration that ITNs remain in use, which is of greater epidemiological relevance than retention time. It also provides a novel framework to correct for biases in estimates of ITN use and access arising from when campaigns were conducted. Although campaigns have historically aided increasing ITN use and access over time, we estimate the mean duration of ITN use is consistently shorter than mean retention times in all regions. This raises questions about whether punctuated distribution of ITNs through campaigns is the optimal mechanism for maximising their effectiveness and cost-effectiveness. Maximising the cost-effectiveness of interventions has become increasingly pertinent in the current funding context, and consideration of alternative distribution strategies, such as increased distribution through continuous distribution channels, including school- or community-based distribution, may be warranted. Frameworks such as the one presented here, which take into account the potential for impact from different net types and the high variability of ITN duration and use, could support NMP decision making on how best to maximise impact from available funds. Whilst such frameworks may be a useful tool, local knowledge of factors impacting ITN access and use as well as operational decision making will be paramount for NMP-led tailoring of subnational strategies.”

      (W1.3) On L236, the link to SNT is stated: "the models indicate trends that can support subnational tailoring of ITNs". They could indeed, but SNT itself is not done in this paper. It seems to be about improving sub-national predictions of the impact of single ITN strategies, by taking into account sub-national variation in access and use duration. This is useful, and the model developed has novel aspects.

      Thank-you for highlighting this. We hope our updated title and response to W1.12 below help address this. Where relevant we have also framed our findings in relation to the World Health Organization’s Subnational tailoring of malaria strategies and interventions: refence manual which was published following our original submission; examples of this are highlighted in our response above to W1.2.

      (W1.4) Individual countries may have records on when nets were distributed to the regions rather than needing to use the annual country number of nets together with the DHS data. It could be helpful to say what the analysis steps would be in that case.

      We have now added the following text of appendix 3.2 to clarify how the methodology could be adapted:

      “In contexts where national malaria programmes or other stakeholders have knowledge of the timings of mass campaigns (i.e. when there is no uncertainty in ɸ<sub>ij</sub>), the methodology can be adapted by deterministically evaluating the time since the last campaign (equation S18) for each time point.”

      (W1.5) There were several assumptions that needed to be made in building the model. There is some validation of the timing of the distributions (L633 "verified where possible through discussion with interested parties nationally and internationally") and the fit of estimated access and use to survey data, and agreement between predictions of prevalence and MAP estimates. It would be helpful to say which assumptions are important for the results (and would be key knowledge gaps) and which would not make a difference. It might be possible to validate the net timing model using a country where net distributions are known reasonably well.

      Thank-you for raising this. We acknowledge that to investigate which assumptions are less likely to make a meaningful difference, we would ideally have conducted a full sensitivity analysis on these. This however would be challenging, since many of these are structural assumptions rather than numerical ones (for example, the assumption of an exponential decay in use and access) which would require the entire methodology to be adapted to conduct a sensitivity analysis. We did validate our estimated campaign timings against some known subnational campaign timings for Senegal. However, we could not source data on when all campaigns were conducted for all regions of Senegal to the nearest month to be able to conduct validation against this. We were also not able to source other use and access data from separate data sources to the DHS to be able to validate our discrete-time models of historical use and access. PfPR2-10 estimates are however fitted to equivalent MAP estimates. These were validated against DHS estimates of PfPR6-59mo, which were not used at any stage to fit our models. We have made slight changes to the original wording in relation to this at the end of appendix 5.2.

      (W1.6) What was assumed about what happens to old nets after a mass campaign was not clear. This assumption is likely to affect the predictions of access for the biennial distributions.

      To generate our initial estimates of the mean duration of use and retention time with our hierarchical model, we assume nets are only distributed to individuals who do not already have ITNs (appendix 2). This initial step is necessary for our methodology, but is relaxed later under our discrete-time model where we assume ITNs are distributed at random such that individuals with an ITN are equally likely to receive a new ITN (and replace their existing one) following a mass campaign (appendix 4). Much of the aforementioned sections has been rewritten and we hope this is now clearer.

      (W1.7) L312 and elsewhere: That use given access declines with net age is plausible. However, I wondered if this could be partly a consequence of the assumptions in the model (eg the two exponential decays for access and use, the possible assumption that new nets displace the current ones when there is a mass campaign).

      Declining use given access as nets age is not affected by model assumptions. Due to being fitted independently of each other, there are no constraints that would prevent a faster decay in access than use. Had the data supported this, this would have led to use given access increasing over time since the last campaign. The data did not support this. Further clarification that use and access are fitted independently of each other is has now been provided in the following text:

      “All subsequent analyses described are conducted independently for use and access”

      (W1.8) The Methods section on Estimating historical use and access seemed to be aimed at readers familiar with formulae, but I think it could lose other interested readers. It could be useful to explain a little more about what is happening at each step and also why.

      Thank-you for highlighting this. We have re-written this section in the main manuscript, now named ‘Historical use, access and retention times’, where we now only highlight key equations and provide a high-level overview of the methodological steps. We have sought to provide clearer explanations here behind the rationale for each step to ensure maximum accessibility for interested readers. The original wording was used as a basis for the newly provided series of appendices which provide further technical detail; this wording has also been heavily re-drafted to improve clarity of each step.

      (W1.9) The model was fitted to MAP estimates of PfPR2-10, which themselves come from a model. It may be that there is different uncertainty in the MAP estimates for different regions. I couldn't see this on the graph, but maybe the uncertainty is small. Was this taken into account in the fitting?

      We only used median MAP estimates of PfPR2-10 to calibrate the baseline EIR for each region in our model. We have clarified our rationale in appendix 5.2:

      “Since the relationship between baseline EIR and PfPR2-10 here is specific to malaria simulation, MAP uncertainty estimates were not propagated through to our estimates in baseline EIR since these would not faithfully represent its true uncertainty.”

      (W1.10) Was uncertainty from each estimated component integrated into the other components?

      Thank-you for highlighting this as this indicates we had failed to clearly indicate this. To confirm, we propagate uncertainty in each component through to our estimates of cases averted. New text has been provided to clarify this in the following text:

      “Region-specific uncertainty in ITN efficacy, use, retention, and the relative contributions of continuous and campaign channels is therefore propagated through to our estimates of cases averted.”

      Further details are also provided in the preceding text of the same paragraph. The central 95% credible intervals of cases averted shown in figures 5.C and 6 and associated figure supplements are reflective of this uncertainty.

      (W1.11) Eyeballing Figure 2 (Burkina Faso), there is a general pattern of decline in all the regions, some differences between the regions and some differences in how well the model fits between the regions. If possible, it could be helpful to say how much better the fit was when using regionspecific compared to countrywide parameter values for access and use, and how different the results would be.

      In the “Universal coverage: was it achievable under triennial mass campaigns” results section, we have now provided further emphasis that the observed decrease from DHS data may be driven by surveys being conducted progressively later in relation to the last campaign:

      “The observed decrease in use and access across many regions in Burkina Faso may therefore be a by-product of DHS surveys being conducted at progressively later dates relative to the most recent campaign; this does not necessarily indicate an underlying trend in decreasing use or access over longer timescales.”

      In the case of Burkina Faso (figure 2.A), aside from months when very small numbers of individuals were surveys where either 0% or 100% use or access was reported, no other data lie outside our 95% credible interval for any region.

      We are unable to generate comparisons with countrywide parameters as these are not generated when fitting our discrete-time model, even though they are a by-product of the initial hierarchical model used to generate initial estimates of region-specific ITN retention, which was a necessary methodological step. We hope the extensive revision of the text in the methods and appendices helps to improve the clarity on this. Where national estimates are provided, these are population-weighted means of the subnational median posterior estimates. New text is included in appendix 1 to clarify this:

      “National and continental values are reported as population-weighted summaries of the median subnational estimates generated from the discrete-time models”

      (W1.12) The question of moving from a campaign every three to every two years may not be the most pertinent question in the current funding landscape. I realise that a paper is in development for a long time, but it would be helpful to comment on what else the model could be used for when fewer rather than more nets are likely to be available.

      We acknowledge the funding landscape has changed substantially, but we still believe this work has important implications in the current context. We have emphasised this further in the following text:

      “If budget constraints necessitate the deprioritisation of campaigns, our results highlight that this should be avoided, if possible, in regions with moderate to high transmission intensity, particularly those with mean annual incidence exceeding 100– 150 clinical cases per 1,000 people. Shortening campaign intervals from three to two years in moderate- and high-transmission regions is projected to avert more cases than the additional cases that may arise from ceasing campaigns in some lower-transmission settings. Additionally, although pyrethroid–chlorfenapyr ITNs are more costly, the additional cases projected to be averted by them relative to pyrethroid-only and pyrethroid–PBO ITNs are substantial. In certain national contexts it may be more cost-effective for biennial pyrethroid-chlorfenapyr campaigns to be conducted in fewer subnational regions even under reduced budgets. However, more thorough economic analyses will be needed to understand this fully. Moreover, as ITNs remain one of the most cost-effective malaria control interventions, improving the impact of them could still be more cost-effective than the introduction of new untested interventions (Topazian et al., 2023; Schmit et al., 2024).”

      We have also related some of our findings to the WHO Subnational Tailoring Reference Manual (as highlighted in W1.2), which we hope better relates our findings to the current context.

      Reviewer #2 (Public review):

      Summary:

      The authors design a custom Bayesian model to estimate the probabilities of access, use and use given access of insecticide-treated nets in six African countries, providing sub-national estimates and inferring the average duration of ITN use and access. An individual-based model was employed to simulate malaria epidemics and estimate the effectiveness of different ITN distribution strategies. The study finds that the mean probability of use or access did not reach 80% (a universal coverage formely targeted by WHO) for any of the regions, even for biennial campaigns, demonstrates that switching from triennial to biennial distribution campaigns increases population use by 7.9%, and evaluates the impact of employing more efficient ITNs on P. falciparum prevalence.

      Strengths:

      The authors developed a data-driven model that accounts for data collection imperfections and sources of uncertainty while differentiating between ITN use and access. They developed a methodology to infer the timing of a mass campaign from publicly available data instead of assuming fixed dates. The probability of use given access allows for determining the regions where ITN distribution is least effective. This work can help better inform future interventions by identifying regions where increasing mass campaign frequency or employing better ITNs are most effective. Finally, in addition to insights on ITN access and use for the six countries analyzed, the paper contributes a methodological framework that can likely be extended to other countries.

      Weaknesses:

      Since the models employed are rather complex, the description of the methodology may be hard to follow for most readers. In addition, the models assume many hypotheses, including:

      (W2.1) Exponential decay of ITN use/access.

      We do acknowledge different modelling studies have typically assumed either an exponential decay or an “S-shaped” smooth-compact loss function, with many of these studies having been validated against cluster-randomised trial data for both functional forms. We believe the ITN age distribution data across the DHS surveys inspected provides reasonable evidence to support the use of an Exponential decay function here. We have now included a proof (appendix 2.1) demonstrating an exponentially distributed ITN age distribution will be yielded for an exponential decay function with the same rate parameter; this is true under periodic ITN distribution and becomes an approximation for a finite number of surveys. We now also included additional text (appendix 2.2) highlighting the empirical ITN age distributions appear to support our exponential decay assumption.

      (W2.2) The decay rates for the probability of the ITN repelling and killing a mosquito are the same.

      Although the same decay rate parameter (\gamma_N) is present in our expressions for the probability of repellency and mortality (equations (53) and (54)), the half-life of the latter is shorter, since repellency is assumed to decay towards a constant value. These structural forms are not unique to this paper but are shared among all malaria simulation-based studies with ITN interventions. This decay rate parameter has been estimated in previous studies (Sherrard-Smith et al., 2022; Churcher et al., 2024), and we carry through uncertainty estimates from those previous studies into the work presented here; additional text has been added to clarify this:

      “Uncertainty in ITN repellency and mortality parameters (equation (53) and (54)) is also propagated forward to this study by simulating random draws from previous posterior distributions (Sherrard-Smith et al., 2022; Churcher et al., 2024) across each distribution event and realisation.”

      (W2.3) Given a time instant, all individuals in the same administrative unit and have the same probability of using a net;

      Our discrete-time model estimates the proportion of the population with use and access at each time instant. We purposefully do not conflate this with the probability of use and access, which can vary between individuals within the same subnational unit of analysis (urban and rural regions of each administrative-one area). We are grateful this point has been raised as it indicates we had not communicated this sufficiently clearly before. We hope the extensive re-draft of the ‘Historical use, access and retention times’ methods section has helped address this, in particular in the following text preceeding equation (7):

      “We do not assume the probability of access is the same for all individuals in a region at a given point in time. Instead, we assume the probability any given individual has access to an ITN at time t<sub>j</sub> can be described by a Beta distribution”

      (W2.4) ITN use/access decay models do not depend on the distribution strategy (e.g. bienal vs trienal distribution).

      We may not have fully understood this point, but in terms of our historical models of use and access, assumptions are not imposed on the frequency of previous campaigns. Instead, historical campaign timings are estimated from data from DHS surveys and the AMP Net Mapping Project (now detailed in appendix 3.1); historical estimated intervals could be either two or three years (or indeed any interval) as informed by this data. In terms of the duration of use and retention time, these are estimates how long a net would continue to be used, or provide access, if an individual were not to replace it at earlier date; these estimates are therefore independent of campaign intervals, and we have now added addition text to provide additional clarity:

      “However, throughout this study, the durations of use and retention time are always estimates of how long an individual continues to use or have access to a net in the absence of future replacement; estimates of these are therefore reflective of behaviour or ITN durability and not distribution patterns themselves.”

      We do acknowledge under our approach, use immediately following a campaign is agnostic of campaign frequency; however, given an absence of data on how use changes following a switch from triennial to biennial campaigns, we believe this was a reasonably conservative assumption. Further confirmation is now provided in the following text, with additional preceding context:

      “Future campaigns, whether conducted every two or three years, are therefore assumed to achieve a consistent initial level of use.”

      (W2.5) The Bayesian model assumes some narrow prior distributions.

      Thank-you for highlighting this. We acknowledge the need for further justification for the choice of priors. We have provided this in depth for the hierarchical model of the mean duration of use and access (in appendix 2.2). Further justification for the choice of priors for the discrete-time model are also now provided in appendix 4.2).

      The impact of these hypotheses on the estimated parameters is not explored in the paper, and no sensitivity analyses are performed, although some limitations are discussed.

      We fully acknowledge we had not conducted sensitivity analyses for many of our assumptions, and we have now tried to provide better justification for our assumptions. The assumptions most likely to influence inference are structural components of the modelling framework rather than scalar parameters that can be varied independently in a conventional sensitivity analysis. Many of the assumptions highlighted above are structural, such as the assumption of an exponential decay (W2.1). In the case of our assumption of exponential decay, multiple elements of the methodology are restricted by this (for example, when correcting for biases that arise from nets being lost between campaigns and survey times when estimating the timing of campaigns in appendix 3.1). Investigating the sensitivity of this assumption over an assumed smooth compact function would require extensive adaptation of the methodology that would be beyond the scope of this paper. Some other assumptions, such the assumption of the same decay rate parameter for repellency and mortality (W2.2) have been estimated in the previous studies referenced and have been validated against cluster-randomised, controlled trials. We nevertheless recognise our justification of some assumptions could have been expanded upon previously, and we hope the changes highlighted above go towards addressing this.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (R1.1) I looked for the reference WHO 2024b for the recent optimal allocation guideline, but there were just three WHO 2024 references in the bibliography. In addition, what exactly the 80% rule applies to is not clear - this could be explained so it is clearer what result to compare to it (or explain that the rule itself is not clear).

      We have used the eLife LaTeX/BibTex template for citations throughout and acknowledge this doesn’t show letter suffixes in the reference list for multiple author-year entries. We unsure of how to address this given this is generated by the official template, though we note that when citations are clicked on in the document, the relevant citation is then shown at the top of the page on the web version.

      (R1.2) L24 'estimated', but this seems more like a prediction. The words 'estimated' and 'predicted' should be carefully used throughout when combining statistical and mechanistic modelling.

      This has now been changed.

      (R1.3) The point estimates should always have measures of uncertainty.

      The rationale for the omission of credible intervals for some point estimates has now been clarified in the manuscript (appendix 1). The following text has been added:

      “Additionally, in relation to uncertainty estimates, credible intervals are shown for all subnational quantities that are directly estimated in our models. National and continental values are reported as population-weighted summaries of the median subnational estimates generated from the discrete-time models (appendix 4) and therefore do not correspond to explicitly estimated model parameters, so credible intervals are not shown for these aggregated estimates.”

      (R1.4) It would be helpful to justify the choice of ADM1 as the geographical unit.

      We have clarified the rationale for this on the following text:

      “Here, (subnational) regions are defined as the first administrative unit below the country level and are further divided into rural and urban areas to align with DHS stratification”

      (R1.5) The terminology was slightly confusing: in some places, it sounded as if regions were the sub-national regions, in others as if they were different things (eg L74, L105). L45 'and' seems odd here.

      ‘Region’ is used interchangeably with ‘subnational region’ at points in the paper to aid the flow of the text. We hope the use of paratheses around (subnational) in the updated text quoted above (and on the following text) helps provide clarity:

      “here, the units of analysis are consistently referred to as (subnational) regions”

      (R1.6) Spurious accuracy in some estimates, e.g. L52.

      This was a result cited from Bertozzi-Villa et al. (2021) for which uncertainty estimates were not available. We hope the response to R1.3 above helps clarify the rationale for omitting credible intervals for some estimates generated here.

      (R1.7) L68 'lose' instead of 'loose'.

      Now corrected.

      (R1.8) L534. I suspect that the model was actually fitted in Stan via the R interface rstan.

      Language adjusted accordingly.

      (R1.9) L633 'through' rather than 'though'.

      This section has been heavily redrafted and we have checked for typos.

      Reviewer #2 (Recommendations for the authors):

      The paper is well-written and presents an important contribution to better aid interventions. The proposed models are reasonable, but because of their complexity, even readers who work with epidemic modelling might have issues understanding the methodology.

      We thank the reviewer for highlighting that the methodology may be difficult to follow. The methods section has now been substantially rewritten to provide a clearer conceptual description of the modelling framework, with detailed model specification and derivations moved to the appendices. We hope this restructuring will allow readers to follow the modelling approach at a high level in the main text with technical details contained in the appendices.

      To improve the clarity of the methods section, I suggest:

      (R2.1) Include a list of symbols with the meaning of each variable defined in the text.

      Definitions for symbols are now also shown in appendix 1 – tables 1-5.

      (R2.2) Include a centralized full description of each model, clearly stating the priors and likelihood (similarly to a Stan code).

      There are two models that are fitted with Stan (the hierarchical retention model and discrete-time use/access model). To improve clarity for the hierarchical model, priors are now presented in a single block (equations 11 – 17) in appendix 2.2, with the likelihood (equation 18). For the discrete-time model, we have split the presentation of the priors (equations 37 – 42) and the likelihood expressions (equations 43 – 45) into different subsections (respectively appendices 4.2 and 4.3).

      (R2.3) If needed, include additional data preprocessing in the form of an algorithm.

      Although we have not included an algorithm outlining the preprocessing steps, we have ensured sufficient detail has been provided to facilitate replicability. For example, in appendix 1, we now outline how use and access are inferred from DHS data:

      “ITN use is inferred from DHS data (ICF, 2025) on whether individuals slept under an ITN the previous night, while all individuals who used an ITN are assumed to have access; when fewer than two individuals used an ITN, the ITN is assumed to be able to provide access at random to up to two individuals in a household.”

      (R2.4) Mention the main hypotheses and limitations of the model in the main text.

      We have ensured key assumptions of the model are stated in the re-written ‘Historical use, access and retention times’ methods subsection; for example, in the following text:

      “Due to the sparsity and irregularity of DHS and MIS surveys, we were unable to investigate seasonal fluctuations in either access or use; we therefore assume that nets provide access or are used continuously over some period of time.”

      (R2.5) Including a flowchart or diagram that provides an overview of the proposed framework could be helpful.

      We have now included a flowchart of methodological steps in appendix 1 – figure 1.

      (R2.6) Line 89: Define NMP before presenting the acronym.

      We have ensured this is defined in the first instance on line 39.

      (R2.7) Equation (1): Explain why you chose the Exponential distribution (e.g. constant hazard), as this is one of the main hypotheses of the model.

      As highlighted in our response to W2.1, we have now included justification of this assumption in the final paragraph of appendix 2.2.

      (R2.8) Equation (2): Although Equation (2) passes a clear message of how alpha_i^x is distributed, I wonder if it is mathematically correct to express the limit this way, since the argument of the limit is a random variable. Maybe the limit should be applied to gamma_i^x instead.

      Thank-you for highlighting this. We acknowledge the limit behaviour was expressed in a short-hand manner that is not strictly mathematically correct. Indeed, the limit should be applied to the decay rate parameter gamma (now shown in equation 10). In appendix 2.1, we have now provided a proof demonstrating the rate parameter of the pooled ITN age distribution should tend to the same decay rate as the assumed exponential loss function.

      (R2.9) I think the difference between pho_i^x (Equation (1)) and alpha_i^x (Equation (2)) is not very clear in the text.

      In the context of access, rho_{i(l)} and alpha_{i(l)} are respectively the duration an ITN l is retained for and its age at the time of a survey. We hope the redrafted appendices make this clearer, in addition to the inclusion of the new parameter tables in appendix 1.

      (R2.10) Line 479: Typo (and or).

      Updated wording is now contained in appendix 2.

      (R2.11) Line 711: Typo (The limit is equal to infinity).

      This has now been corrected.

      (R2.12) Equation (15): I could not understand this equation. What is rho(s) and rho(s \in I), where I is one of the intervals mentioned in this equation?

      Rho(tau_ik) was introduced as simplified notation for the probability density of the timing of campaign k in region i (tau_ik) but we acknowledge this was not explained clearly. We also acknowledge this equation presented a lot of concepts at once. The equation attempted to describe the probability density of the last campaign in region i relative to time t_j, denoted phi_ij. We no longer make use of this previously notation (rho) for the probability density. This equation has been updated to equation (30), with incremental explanation of its construction now provided on lines in appendix 3.2.

      (R2.13) Line 642: What is t?

      The use of $t_j \ni t$ was previously used to indicate that the discrete time point t_j lies within continuous time t. We acknowledge this was a non-standard use of notation and was not clearly explained. This section (now in appendix 4) has been rewritten without this notation. The use of t and t_j to denote continuous time and discrete time points respectively is now defined in the core notation table (appendix 1 – table 1).

      (R2.14) The proposed model has narrow hyperhyperpriors because of convergence issues. Are the estimated parameters sensitive to the choice of hyperhyperpriors?

      We acknowledge limited justification was previously provided for the choice of hyperhyperpriors. We have now provided additional justification within appendix 2.2.

      (R2.15) Since the proposed Bayesian models are relatively complex, it might be useful to provide convergence diagnostic plots in the supplement.

      Convergence diagnostics were inspected using the ShinyStan packagxe. Chains showed satisfactory convergence based on standard diagnostics. We have not included diagnostic plots due to the large number of parameters in the fitted models. Under the hierarchical model (appendix 2) for ITN use, 146 region-specific parameters (one for each region), 12 country-level hyperparameters (two for each country), and four hyperhyperparameters were estimated. Under the discrete-time model (appendix 4), a further 876 parameters (six for each region) were estimated. In total, 1,038 parameters were fitted for the ITN use models. The same number of parameters were estimated for the ITN access models, giving a total of 2,076 estimated parameters.

    1. Author response:

      We thank you and the three reviewers for their careful examination and critical assessment of our work.

      All acknowledge the significance of revealing the widespread occurrence of programmed DNA elimination (PDE) in nematodes, a phenomenon long considered a parasitic specificity. The reviewers, particularly Reviewer #2 and the Editors, have raised important concerns regarding confirming PDE with more sensitive methods, in particular using genomic data to characterize breaksite motifs across the phylogeny and to better understand the amount and nature of eliminated sequences across species. While we fully agree that such confirmation would ideally complement our discovery, this approach extends beyond the scope of the current manuscript. Our primary aim was to inform the scientific community of the widespread occurrence of PDE in the short term.

      In the longer term, an ambitious collaborative effort is currently underway to produce high-quality genome assemblies of several 100s of nematode species (ENA: PRJEB36817) , covering the diversity of Rhabditina and beyond. These will enable precisely characterising PDE, ultimately addressing these concerns. However, given the scale of this project, aiming at telomere-to-telomere assemblies - which can be particularly challenging for species that perform PDE - it will take considerable time. We believe the community should be informed of the widespread nature of PDE now, rather than waiting for this genomic data.

      Nevertheless, we would like to emphasize that PDE has already been confirmed using genomics in the three clades where we have identified it cytologically: through our own work in Mesorhabditis (1) and Letcher et al., in prep, and also in Caenorhabditis (2) and Oscheius (3, 4). We will state this explicitly in our revision.

      For these reasons, and to avoid overstepping extensive genomic studies that are underway, we will maintain our focus on the cytological description in this manuscript.

      In addition to the above-mentioned concern, we will also address the other points:

      Reviewer #1:

      “Although most PDE claims are supported by solid evidence, some of the existing data do not describe the depth of characterization, e.g., how many replicates were conducted for each species? How reproducible are the claimed PDEs between embryos in terms of timing and cell identities destined for PDE? Is it possible to validate a subset of PDE with independent evidence, especially for those with marginal PDE? This is important because some dying embryos may fail to maintain their chromosome integrity and release some of the broken DNA, some others may suffer from noise such as intracellular parasites, for example, microsporidia, or even highly condensed mitochondrial DNA.

      we will provide the missing information concerning number of observed embryos (using DNA stainings or DNA-FISH), and better explain and illustrate the reason why the observed fragments cannot be attributed to intracellular parasites, or to the consequence of dying embryos.

      Reviewer #3:

      Some clarifications are necessary to make the figures more reader-friendly.

      This will be improved, thank you for pointing this out

      Important references to ciliates are missing.

      Thank you for pointing this out. We will improve the comparisons that can be made with the mechanism of PDE found in ciliates.

      References

      (1) C. Rey, C. Launay, E. Wenger, M. Delattre, Programmed DNA elimination in Mesorhabditis nematodes. Curr Biol 33, 3711-3721.e5 (2023).

      (2) L. Stevens, S. Sun, N. Haruta, L. Xiao, N. Uwatoko, M. Kieninger, K. Sato, A. Yoshida, D. Absolon, J. Collins, A. Sugimoto, T. Kikuchi, M. Blaxter, Programmed DNA elimination was present in the last common ancestor of Caenorhabditis nematodes. bioRxiv [Preprint] (2025). https://doi.org/10.1101/2025.10.23.681605.

      (3) T. C. Dockendorff, B. Estrem, J. Reed, J. R. Simmons, S. B. Zadegan, M. V. Zagoskin, V. Terta, E. Villalobos, E. M. Seaberry, J. Wang, The nematode Oscheius tipulae as a genetic model for programmed DNA elimination. Curr Biol 32, 5083-5098.e6 (2022).

      (4) P. M. Gonzalez de la Rosa, M. Thomson, U. Trivedi, A. Tracey, S. Tandonnet, M. Blaxter, A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. G3 (Bethesda) 11, jkaa020 (2021).

    1. Author response:

      Reviewer 1:

      Clarification of sample sizes, assay structure, and experimental design.

      Reviewer 1 noted that the number of animals tested across strains, assays, sexes, parent sets, conditioned and unconditioned groups, and longitudinal conditions is difficult to track through the manuscript. Given the extent of the experimental and data processing procedures such as filtering for inactive or injured flies, we agree that a summary table and/or a visual schematic of the full experimental setup would be helpful.

      Importantly, the vast majority of individuals was used for the main experiment where we conditioned the flies to avoid the green arm, and where the colors of the arms were fixed throughout the assat. A smaller number of flies were tested in the validation experiments (such as different types of conditioning). In each experiment, 64 flies were always set up per genotype and their behaviour was measured in parallel. Usually, around ~60 flies passed the filtering step before analysis (filtering due to inactivity or injured flies). Among those 60-ish flies per genotype the distribution of flies of different sex or flies raised in different replicate vials was balanced. Different individual flies were tested across different assays, except in the multiday experiment, where each individual was tested across four different assays.

      We will add a supplementary summary that includes how many flies were tested across assays, how individuals, males, females, replicates and genotype were distributed across batches (and in the multiday experiments how they were distributed across experiments), and how many flies were filtered out from the final analysis. 

      Clearer presentation of the statistical argument that learning amplifies individuality.

      Reviewer 1 also noted that the presentation of the statistical analyses, particularly in Figure 2, was difficult to follow (e.g. what is residual individuality, how is it tracked over time, and why not replace it with something simpler like variance?).

      Our experimental design combines multiple, replicated environments and genotypes. For example, genetically identical flies from genotype A, are raised under identical developmental environments that are replicated two times in two vials. The same is true for genotype B. Individuals from both genotypes are then tested under different conditions, i.e. control and conditioned. 

      As we saw, combinations of these factors can change both the means and variance of distributions of individual behaviours in both genotype- or environment-specific manner. Normally, variance would be a good estimate for expressed individuality within a genotype, and comparison of variances would be a good estimate of change in individuality due to some factor (genotype, replicate, or type of conditioning).

      However, we saw that the resulting shape of the data in these experiments, (the shape of the distributions) was incompatible with the classical definition of extent of individuality measured by variance. While it would be more intuitive to track variance over time, we found that this measure obfuscates some obvious changes in the normal shape of the distributions of individual behaviours, as can be visually observed for example between conditioned and control experiments. This is why we moved to develop the measure of residual individuality. Residual individuality aims to measure exactly this dimension of individuality that is missed by measures of variance. We will add a schematic presentation of residual individuality in Figure 2 to explain more explicitly and visually what is being measured here, and what residual individuality represents. This should shed more light on how these analyses support the conclusion that learning increases behavioural variability among individuals in both Figure 2 and Figure 3. The schematic should provide more intuition on how to interpret the data to those unfamiliar with some of the statistics. Besides the schematics, we will also add more intuitive visualizations of the behaviour data in the supplementary, including representations of how within-strain distributions of behaviour change before and during learning or in control condition for all strains, so that the reader may inspect them in more detail.

      Improved explanation of Figure 3 and the link between statistical outputs and behavioural measurements.

      Reviewer 1 also noted that the analyses in Figure 3 are difficult to interpret without relying heavily on the Results text. Hopefully the added schematic in Figure 2 that explains what Divergence represents should address this note and make the interpretation of Figure 3 easier. Indeed, upon reflection, we agree that the label “Divergence” is quite vague. The “Divergence” in fact shows again residual individuality, and how it changes with every made decision in the case where we compare distributions of flies that start at green versus the blue arm. We further subset the distributions by clustering flies that share the same individual initial color bias or similar learning score and measure residual individuality for them as well. Here, value 0 means the two distributions have the same shape, and higher values mean the shapes are more different. We will rename Divergence to “Residual individuality Start” to make it clear that this is conceptually the same type of measurement, and revise the figure legends accordingly so that they match the new schematic in Figure 2. This should hopefully clarify what the figures show. We will also add a schematic to depict how change in the shape of the distribution with each decision can affect residual individuality.

      Reviewer 2:

      Clarification of the term “deterministic” when referring to genetic sources of variation.

      Reviewer 2 noted that describing genotype as a deterministic source of variation could be confusing, since gene expression and downstream cellular phenotypes are themselves noisy and stochastic. Indeed, gene expression as a phenotype is noisy, but also at the core it is a result of G x E (albeit the environment at the molecular scale). What we meant to emphasize here is that an individual’s genotype can be considered a fixed variable that determines phenotype expression across environments. The environment also determines the phenotype, again, in concert with genotype, but it will always vary over time. We agree with the reviewer that the wording should be made stricter to avoid confusion.

      We changed this sentence from “In every individual, behaviour is shaped by deterministic, genetic factors and by environmental events throughout lifetime, which may be stochastic and can occur at the molecular, cellular, organismal and even population scales.” to “In every individual, behaviour is shaped by fixed genetic factors and by variable environmental events throughout lifetime, which may be stochastic and can occur at the molecular, cellular, organismal and even population scales.” 

      Longitudinal analysis and neural sources of learning variability.

      Reviewer 2 suggested that additional longitudinal analysis could further strengthen the evidence for individuality, and that identifying neural sources of learning variability would be an interesting future direction. We appreciate these suggestions and very much agree with them. But as it was pointed out by the reviewer, this was beyond the scope of this study. Nonetheless, it may be good to note that we have in fact already started this (ongoing and quite extensive) experimental endeavour to identify neural sources of individuality, which we hope will be soon available as a follow-up study.

      Within the current study we were able to track behaviour longitudinally within a 20-minute experiment, and in one case over multiple days, though for only a smaller subset of flies. Broader conclusions on how behaviour would change over longer timeframes (except those already included in the manuscript) could not be made with the current dataset. We have added a figure in the supplement where the reader can visually explore the temporal changes to the distributions of behaviour. More extensive study to see how individuality evolves over longer time frames is indeed planned for the future.

      We thank the reviewers again for their thoughtful and constructive comments. We believe that addressing these points improved the manuscript.

    1. Author response:

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

      eLife Assessment

      This manuscript presents a useful computational framework for systematically characterising how heterogeneity in initial conditions or biophysical parameters shapes the dynamic behaviour of protein signalling networks, with potential relevance to understanding adaptive drug resistance. While the approach represents a significant methodological contribution, the extent to which its conclusions are biologically informative remains debated, as the model is not qualitatively or quantitatively validated against experimental data. As a result, the strength of evidence supporting the mechanistic claims is viewed as incomplete.

      We thank the editors and reviewers for their further assessment of the manuscript. The revised public review raises several issues that overlap with points addressed in our previous response, particularly around the intended scope of MDN modelling, the interpretation of parameter sampling, and the qualitative nature of the experimental comparison. In this final revision, we have made targeted clarifications in the main text, Methods, figure legends, and Supplementary Information to make these points more explicit for readers. We emphasise that the present work is intended as a theoretical and exploratory framework for mapping the qualitative dynamic behaviours accessible to a fixed network topology, rather than as a quantitatively calibrated model of a specific tumour or cell line.

      Joint Public Review:

      In this manuscript, the authors proposed an approach to systematically characterise how heterogeneity in a protein signalling network affects its emergent dynamics, with particular emphasis on drug-response signalling dynamics in cancer treatments. They named this approach Meta Dynamic Network (MDN) modelling, as it aims to consider the potential dynamic responses globally, varying both initial conditions (i.e., expression levels) and biophysical parameters (i.e., protein interaction parameters). By characterising the "meta" response of the network, the authors propose that the method can provide insights not only into the possible dynamic behaviours of the system of interest but also into the likelihood and frequency of observing these dynamic behaviours in the natural system.

      The authors study the Early Cell Cycle (ECC) network as a proof of concept, focusing on pathways involving PI3K, EGFR, and CDK4/6 with the aim of identifying mechanisms that may underlie resistance to CDK4/6 inhibition in cancer. The biochemical reaction model comprises 50 state variables and 94 kinetic parameters, implemented in SBML and simulated in Matlab. A central component of the study is the generation of large ensembles of model instances, including 100,000 randomly sampled parameter sets intended to represent intra-tumour heterogeneity. On the basis of these simulations, the authors conclude that heterogeneity in kinetic rate parameters plays a stronger role in driving adaptive resistance than variation in baseline protein expression levels, and that resistance emerges as a network-level property rather than from individual components alone. The revised manuscript provides additional clarification regarding aspects of the simulation and filtering procedures and frames the comparison with experimental data as qualitative. Nonetheless, the study is best interpreted as a theoretical and exploratory analysis of the model's behaviour under heterogeneous conditions. Consequently, questions remain regarding the biological grounding of the sampled parameter regimes and the extent to which the reported frequencies of resistance-associated behaviours can be directly interpreted in physiological terms.

      While the authors propose a potentially useful computational framework to explore how heterogeneity shapes dynamic responses to drug perturbation, a number of important conceptual and methodological concerns remain to be addressed:

      (1) The sampling of kinetic parameters constitutes the backbone of the manuscript, yet important concerns remain regarding its biological grounding and transparency. Although the revised version provides additional clarification on the exploration of "model instances", it is still not sufficiently clear how parameter values and initial conditions are generated, nor how the chosen ranges relate to biological measurements. The kinetic rates are sampled over broad intervals without explicit justification in terms of experimentally measured bounds or inferred distributions. As a consequence, it remains uncertain whether the ensemble of simulated behaviours reflects physiologically plausible cellular regimes or primarily the properties of the assumed parameter space. In this context, the large-scale sampling (100,000 parameter sets) resembles a Monte Carlo exploration of the model rather than a biologically calibrated representation of tumour heterogeneity.

      Parameters were sampled from a uniform distribution spanning values 10-5 to 104. Conserved totals were sampled from the range 100 to 104. Each of these is roughly in line with measured spans of orders of magnitude for parameter values and protein expression (REF). Again, we would like to point out that we intentionally kept our ranges broad, and sampled from uniform distributions, to assess upper bounds of heterogeneity, not biologically informed heterogeneity. We also comment on the likely effects of expanding these ranges in our response to (26) in our original rebuttal.

      Main text has been updated to include this information. LINES: 175-179

      Furthermore, the adequacy of the sampling strategy in such a high-dimensional space (94 free parameters) remains open to question. In the absence of biologically informed constraints, the combinatorial space of possible parameter configurations is vast, and it is unclear to what extent the sampled ensembles can be considered representative. This issue is particularly relevant because the manuscript interprets the frequency of resistance-associated behaviours as indicative of their likelihood.

      This was addressed extensively in our original rebuttal, response to point (3). A new section was added to the supplementary text, along with new figures demonstrating the validity of the claims.

      The validation presented in Figure 7 does not fully resolve these concerns. The comparison with experimental data is qualitative, and the simulations are performed in arbitrary time units, which complicates direct interpretation alongside time-resolved experimental measurements. Moreover, certain qualitative discrepancies between simulated and experimental trends (e.g., persistent versus decreasing CDK4/6 activity) are not thoroughly discussed. As this figure represents the primary empirical reference point in the manuscript, the extent to which the model captures experimentally observed dynamics remains uncertain.

      This was addressed in the original rebuttal, response to point (12). The actual time units are arbitrary in the sense that they are determined by the units of the parameters in our model. It is important to understand that the meta-dynamic analysis is not calibrated to data and so the meaning of time units is far less important than the distribution of behaviours. We have updated the figure to reflect the arbitrary units of time in our simulations.

      Finally, aspects of presentation continue to limit transparency. Parameter ranges are described at different points in the manuscript but are not consolidated clearly in the Methods, and the definition of initial conditions remains ambiguous - particularly whether these correspond to conserved quantities or to the dynamic variables used to initialise simulations. In addition, the exact number of model instances underlying specific analyses and figures is not always explicit. Greater clarity on these issues is essential for assessing reproducibility and for interpreting the quantitative claims of the study.

      (2) A central conclusion of the manuscript is that heterogeneity in protein-protein interaction kinetics is a stronger driver of adaptive resistance than heterogeneity in protein expression levels. To assess the latter, the authors fix a nominal set of kinetic parameters and generate 100,000 random initial concentrations for the 50 model species. However, according to the simulation protocol described in the manuscript, each trajectory includes three phases: (i) simulation under starvation conditions to equilibrium, (ii) mitogenic stimulation to a second ("fed") equilibrium, and (iii) application of drug treatment. The equilibrium concentrations reached in phases (i) and (ii) are determined by the kinetic parameters of the model and are independent of the initial concentrations, provided the system converges to a stable steady state. In dynamical systems terms, stable equilibria are defined by the parameter set and attract all initial conditions within their basin of attraction. Since the kinetic parameters are fixed in this experiment, the pre-treatment equilibrium that serves as the starting point for drug application should likewise be fixed. Under these conditions, it is therefore not unexpected that sampling a large number of initial concentrations has limited influence on the treated dynamics.

      This raises conceptual questions about the interpretation of the comparison between kinetic and expression heterogeneity. If the system converges to a unique stable steady state prior to treatment, then variability in initial concentrations does not propagate into variability in drug response, and the observed dominance of kinetic heterogeneity may partly reflect this structural property of the model rather than a biological principle. Clarification is needed regarding whether multiple steady states exist under the nominal parameter set, and if so, how basins of attraction are explored.

      More broadly, it remains unclear why initial protein concentrations can be sampled independently of the kinetic parameters. In biological systems, steady-state expression levels are typically determined by the underlying kinetic rates. A more consistent approach might require constraining initial concentrations to correspond to equilibrium states of the chosen parameter set, thereby introducing relationships between at least some of the 50 initial conditions and the 94 kinetic parameters. Finally, the manuscript employs a non-standard terminology regarding "initial conditions," which may further obscure interpretation of these results and would benefit from clarification.

      This was addressed in the original rebuttal, response to point (4). Text was modified to clarify what was meant by initial conditions to clarify that this meant the conserved total for the protein species. A supplementary figure (supp. fig. 4) was added to demonstrate that changes to the conserved totals of protein species does, in fact, shift the dynamics and steady state equilibria of protein species. Text was updated throughout the paper to ensure that our definition of ‘initial conditions’ was consistent throughout the text.

      (3) The technical implementation of the modelling and simulation framework remains difficult to evaluate due to insufficient methodological detail. Although the authors state that kinetic parameters are randomly sampled, the manuscript does not specify the distributions from which parameters are drawn, nor whether potential correlations between parameters are considered or explicitly ignored. Without this information, it is not possible to assess how implicit modelling assumptions shape the ensemble of simulated behaviours. Given that the conclusions rely on frequency-based interpretations across sampled parameter sets, greater transparency regarding the sampling procedure is essential.

      Updated the main text to clarify random sampling from a log transformed uniform distribution. LINES: 175-179

      A further concern relates to the parameter filtering step. The authors report that the "vast majority" of sampled parameter sets produced systems that were "too stiff," and that these were excluded on the grounds that stiff dynamics are not biologically plausible. However, the manuscript does not clearly define how stiffness is assessed, nor why stiffness is interpreted as biologically unrealistic rather than as a numerical property of the formulation. In standard practice, stiff systems are typically handled using appropriate implicit solvers rather than being discarded. Similarly, parameter sets that produce negative state values are excluded, yet such behaviour may arise from numerical artefacts rather than from intrinsic model inconsistency. The rationale for excluding these parameter sets, rather than adapting the numerical scheme, is not sufficiently justified.

      The reported rejection rate - approximately 90% of sampled parameter sets - is substantial and raises questions regarding the interplay between model structure, parameter ranges, and numerical methods. As currently described, the filtering step appears to select parameter sets based primarily on computational tractability rather than on experimentally motivated biological criteria. The manuscript would be strengthened by clarifying whether the retained parameter sets are representative of biologically meaningful regimes, and by distinguishing clearly between exclusions based on biological plausibility and those arising from numerical considerations.

      This was extensively addressed in the original rebuttal, response to points (6) and (7). Main text was updated to clarify that a solver specific for stiff systems was used. Furthermore, we addressed this issue but consequential analysis revealed that lack of drug response and not achieving steady state in the simulated time period now accounted for the majority of filtering. This had no effect on the distributions of behaviours identified in our analyses. Main text was updated to reflect these changes. Rejection rate was explicitly discussed in main text.

      Finally, important aspects of the simulation protocol require clarification. The model is simulated under "fasted" and "fed" conditions until equilibrium is reached, yet the criterion used to determine convergence is not specified. It would be important to describe how equilibrium is assessed (e.g., based on the norm of the time derivatives). Additionally, it remains unclear whether the mitogenic stimulus applied in the "fed" phase is assumed to be constant over time and, if so, how this assumption relates to biological experimental conditions. Greater detail on these implementation choices is necessary to ensure interpretability and reproducibility.

      This was addressed in the original rebuttal, response to point (8). Clarification about simulations were added to main text, including explicitly stating that mitogenic and drug inputs were continuous stepwise functions and how steady state equilibrium was defined/calculated.

      (4) The manuscript states that the modelling conclusions are strongly supported by existing literature; however, the validation presented does not fully substantiate this claim. As noted above, the comparison with CDK2 and CDK4/6 experimental data remains qualitative, and the use of arbitrary simulation time units complicates interpretation of temporal agreement. The extent to which the model quantitatively or mechanistically recapitulates experimentally observed dynamics therefore remains uncertain.

      This was addressed in the original rebuttal, response to points (13) and (14). Wording was changed to remove the suggestion of strong evidence and the tone was shifted to reflect reasonable qualitative support for our analysis, not strong evidence.

      The claim that the model reproduces known resistance mechanisms is also difficult to assess in light of Figure S10, where a large fraction of network nodes (~80%) appear implicated in resistance under some conditions. If most components of the network can, in at least some parameter regimes, be associated with resistance phenotypes, the resulting lack of selectivity weakens the strength of model-based validation. It becomes challenging to distinguish specific mechanistic insights from generic consequences of network connectivity.

      In addition, the Supplementary Information notes that certain components of the mitogenic and cell-cycle pathways were abstracted or excluded in order to maintain computational tractability. While such abstraction is understandable in a large ODE framework, it raises interpretative questions. Proteins identified as potential resistance drivers within the model may, in some cases, represent aggregated or simplified pathway effects. Clarifying in the main text how such abstractions may influence the attribution of resistance mechanisms would strengthen the biological interpretation of the results.

      This was addressed in the original rebuttal, response to points (15). The discussion was significantly revised to reflect our reasoning with respect to our conclusions. We completely understand that more work could be done to verify our claims, however, our intention is to demonstrate the generalised relationship between network heterogeneity and drug resistance, not to predict patient-specific resistance mechanisms.

      Drug inhibition is central to the manuscript's conclusions. The revised version clarifies that inhibition is implemented as a fixed fractional modification of specific kinetic rate laws. This abstraction is appropriate for exploring network-level responses, but it represents a stylised perturbation rather than a pharmacologically calibrated model of drug action. For full interpretability and reproducibility, the mathematical form of the modified rate laws, as well as the timing of inhibition relative to network equilibration, should be specified unambiguously. The biological implications of the findings depend critically on understanding this modelling choice.

      All equations were included in the supplementary model files, including typeset ODEs, as requested by the reviewers. R15 and R27 contain the relevant equations, which specify the exact implementation of the drug inhibition. Number of time units per simulation phase now included in main text. LINES: 166 – 168

      The one-at-a-time perturbation analysis presented in Figure 5 provides an interpretable ranking of first-order control points across the ensemble and offers mechanistic insight into primary sensitivities of the network. However, many targeted therapies act on multiple components, and resistance frequently arises through combinatorial mechanisms. The reported rankings should therefore be interpreted as identifying primary influences under isolated perturbations, rather than as a comprehensive account of multi-target drug behaviour.

      Overall, the manuscript succeeds in presenting a conceptual and exploratory framework for analysing how signalling network topology can shape the qualitative landscape of adaptive responses under heterogeneous kinetic conditions. Its principal contribution lies in establishing a systematic platform for large-scale in silico exploration. At the same time, the current limitations in biological calibration, parameter grounding, and validation constrain the extent to which the conclusions can be interpreted as predictive or quantitatively representative of specific tumour contexts. Addressing these issues would further strengthen the connection between the theoretical landscape described here and experimentally observed resistance dynamics.

      Joint Recommendations for the authors:

      (1) Supplementary Figure S4 is not sufficiently explained in its current form. The structure of the figure, the meaning of its colour coding, and the intended interpretation are not clearly described, making it difficult for readers to extract the key message without substantial inference. Given that the manuscript relies heavily on large-scale ensemble analyses, clear visual communication is essential. A more detailed legend, explicit definition of axes and colour scales, and improved visual labelling would substantially enhance clarity, accessibility, and reproducibility.

      Supp. Fig. 4 legend updated with additional detail. LINES: Supp. Text. 256 - 263

      (2) The approximately 90% rejection rate of sampled parameter sets should be reported explicitly in the main text of the manuscript rather than only in the Supplementary Information. Given the central role of large-scale parameter sampling in the study, this level of exclusion is a critical aspect of the modelling workflow and directly affects the interpretation of robustness and representativeness. Clear disclosure in the main text would allow readers to properly evaluate the effective size of the analysed ensemble and the implications of the filtering procedure for the generality of the conclusions.

      This was explicitly addressed in the original rebuttal.

      (3) The model would benefit from quantitative validation against experimental data. In Figure 7C, the authors note in the response letter that the simulations are performed in arbitrary time units. However, the figure itself labels the time axis in hours, which may lead readers to infer a direct quantitative correspondence between simulated and experimental time courses. If the simulations are not calibrated to real time, this labelling is potentially misleading and should be corrected. Either the model should be explicitly time-calibrated and quantitatively compared to experimental measurements, or the figure should clearly indicate that the time axis is dimensionless. Clarifying this point is essential to avoid overinterpretation of the agreement between model and data.

      Label updated.


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

      Joint Public Reviews:

      In this manuscript, the authors proposed an approach to systematically characterise how heterogeneity in a protein signalling network affects its emergent dynamics, with particular emphasis on drug-response signalling dynamics in cancer treatments. They named this approach Meta Dynamic Network (MDN) modelling, as it aims to consider the potential dynamic responses globally, varying both initial conditions (i.e., expression levels) and biophysical parameters (i.e., protein interaction parameters). By characterising the "meta" response of the network, the authors propose that the method can provide insights not only into the possible dynamic behaviours of the system of interest but also into the likelihood and frequency of observing these dynamic behaviours in the natural system.

      The authors studied the Early Cell Cycle (ECC) network as a proof of concept, specifically focusing on PI3K, EGFR, and CDK4/6, with particular interest in identifying the mechanisms that cancer could potentially exploit to display drug resistance. The biochemical reaction model consists of 50 equations (state variables) with 94 kinetic parameters, described using SBML and computed in Matlab. Based on the simulations, the authors concluded the following main points: a large number of network states can facilitate resistance, the individual biophysical parameters alone are insufficient to predict resistance, and adaptive resistance is an emergent property of the network. Finally, the authors attempt to validate the model's prediction that differential core sub-networks can drive drug resistance by comparing their observations with the knock-out information available in the literature. The authors identified subnetworks potentially responsible for drug resistance through the inhibition of individual pathways. Importantly, some concerns regarding the methodology are discussed below, putting in doubt the validity of the main claims of this work.

      While the authors proposed a potentially useful computational approach to better understand the effect of heterogeneity in a system's dynamic response to a drug treatment (i.e., a perturbation), there are important weaknesses in the manuscript in its current form:

      (1) It is unclear how the random parameter sets (i.e., model instances) and initial conditions are generated, and how this choice biases or limits the general conclusions for the case studied. Particularly, it is not evident how the kinetic rates are related to any biological data, nor if the parameter distributions used in this study have any biological relevance.<br /> (2) Related to this problem, it is not clear whether the considered 100,000 random parameter samples sufficiently explore parameter space due to the combinatorial explosion that arises from having 94 free parameters, nor 100,000 random initial conditions for a system with 50 species (variables).<br /> (3) Moreover, the authors filter out all the cases with stiff behaviour. This filtering step appears to select model parameters based on computational convenience, rather than biological plausibility.<br /> (4) Also, it is not clear how exactly the drug effect is incorporated into the model (e.g., molecular inhibition?), nor how it is evaluated in the dynamic simulations (e.g., at the beginning of the simulation?). Moreover, in a complex network, the results may differ depending on whether the inhibition is applied from the start or after the network has reached a stable state.<br /> (5) On the same line, the conclusions need to be discussed in the context of stability, particularly when evaluating the role of initial conditions. As stable steady states are determined by the model parameters, once again, the details of how the perturbation effect is evaluated on the simulation dynamics are critical to interpret the results.<br /> (6) The presented validation of the model results (Fig. 7) is only qualitative, and the interpretation is not carefully discussed in the manuscript, particularly considering the comparison between fold-change responses without specifying the baseline states.

      We thank the reviewers for their thoughtful and constructive comments. In response to their comments, we have undertaken a substantial revision to address all the comments, improve clarity, transparency, and robustness while preserving the paper’s core contribution: a principled, scalable framework (MDN) for mapping how molecular heterogeneity and network architecture shape adaptive drug-response dynamics. At a high level, we clarified the study design and analysis goals, tightened definitions, and added methodological detail where it most advances interpretability. Importantly, these updates leave the analytical pipelines and major conclusions unchanged.

      Conceptually, we now make explicit that our objective is coverage of the output space of qualitative dynamics supported by the network topology, not exhaustive enumeration of parameter space. To support this, we added a convergence analysis and clarified that “triplicates” refers to independent ensembles used to demonstrate reproducibility. We also refined how we describe and implement initial conditions (as conserved total abundances that encode expression heterogeneity) and reframed filtering as minimal numerical/feasibility checks, using rejection sampling to obtain the prespecified ensemble size. Solver choices and input modelling (constant step mitogen/drug) are now spelled out succinctly.

      We expanded the model specification and rationale (complete reaction list with rate laws and brief biological justifications in the Supplement) and unified terminology throughout. Figures and legends have been overhauled for readability and accuracy, with missing labels added and ordering corrected. For validation, we clarified the nature of the single-cell reporter readout, improved Figure 7’s presentation, and emphasised - consistent with our aims - that comparisons are qualitative.

      Finally, we have rewritten the Discussion to centre on interpretation, implications, and connect our findings to the literature. It now: (i) frames MDN as a systems-level framework that links molecular heterogeneity to qualitative signalling “meta-dynamics” and adaptive escape under constant drug pressure; (ii) highlights two key findings: an asymmetry in control (interaction kinetics exert stronger, more consistent influence than protein abundance) and a topology-driven convergence whereby a vast parameter space funnels into a finite set of recurrent behaviours; (iii) shows that resistance is a network-level property, with many possible routes but a small set of recurrent hubs/modules dominating; and (iv) provides a qualitative alignment with single-cell reporter data while clarifying the intent and limits of that comparison. Moreover, we now explicitly discuss limitations (rate-law simplifications, broad priors, determinism, and modular abstractions) and outline next steps for future research, including data-constrained priors and stochastic extensions.

      We believe these revisions materially strengthen the manuscript and fully address all the reviewers’ comments. A detailed, point-by-point response follows.

      Joint Recommendations for the Authors:

      (1) It is confusing exactly what are the different sets evaluated in each cases, e.g. "generated 100,000 model instances, each with the same set of ICs but a unique set of randomly generated parameter values" (lines 299-300), "generated 100,000 model instances (in triplicate), each with the same set of 'nominal' parameter values (see supplementary Table S1), and a unique set of ICs, and repeated the analysis as performed previously" (lines 366-368), "combined the 1000 IC sets with each parameter set to create 1000 model instances" (lines 382-383), "repeated for 1000 parameter sets, allowing us to observe how frequently IC variation induced adaptive resistance independent of the chosen parameter set" (lines 386-387). A small table or just a clearer explanation is needed.

      In response to these comments, we have revised the main text to clarify the process of model instance generation. Specifically, we have made changes at page 7: line 297 - page 8: line 302, page 8: lines 305 - 310, page 9: lines 372-378, and page 9: line 384 – page 10: line 399 in the revised main text.

      We have also added a new Figure (Figure S1) to the supplementary file to allow readers to visualise the model generation process for each relevant set of experiments. Supplementary figures are referenced in the main text where appropriate.

      (2) The authors mentioned performing each simulation in triplicate, which is puzzling as the model is based on deterministic ODEs with fixed parameters for each simulation. Under such conditions, one would anticipate identical results from multiple simulations with the same initial conditions and fixed parameters. Perhaps the authors expect the model to exhibit chaos or aim to assess the precision of the parameter estimates through triplicate simulations. Further clarification from the authors would be valuable to comprehend the rationale behind conducting triplicate simulations in a deterministic setting.

      We agree that repeating deterministic ODE simulations with identical inputs would be redundant. In our study, “triplicate” referred instead to generating three independent ensembles of 100,000 unique model instances each, where model parameters (or initial conditions) were randomly resampled. These ensembles were analysed separately to assess whether the inferred meta-dynamic distributions converged robustly. Indeed, the distributions from the three replicates were nearly indistinguishable, confirming that the results are reproducible and not artefacts of a particular random draw.

      We have revised the main text to clarify this distinction (page 8: lines 305 - 310) and added an extended explanation for meta-dynamic behaviour convergence in the new section Error Convergence in the supplementary text (page 6: lines 184 - 210).

      (3) While the lack of a connection between model parameters and biological data (mentioned in the public review) may not be a fatal flaw in the manuscript, the concern about the 100,000 random samples being insufficient to explore the parameter space is valid. In a thought experiment, considering the high and low rate for each parameter and the combinatorial explosion of possibilities (2^94), the number of simulations performed (100,000) represents only an extremely small fraction of the entire parameter space (~1/10^(23)). This limitation might not accurately capture the true heterogeneity present inside a solid tumour. One potential solution is to determine biological bounds on model parameters through data fitting, which can provide more meaningful constraints for the simulations. Alternatively, increasing the number of simulations and adopting more efficient sampling techniques can enhance the coverage of possible parameter sets.

      We thank the reviewer for this insightful comment. We agree that the 94-dimensional parameter space is vast, and that 100,000 simulations represent only a fraction of the total combinatorial possibilities. However, the objective of our study is not to exhaustively sample the entire parameter space, but rather to sufficiently sample the ‘output space’ - that is, the complete spectrum of qualitative dynamic behaviours the network topology can generate. The key question is whether 100,000 model instances are sufficient for the distribution of these output dynamics to converge.

      To formally address this, we have performed a convergence analysis, which is now detailed in the new supplementary section "Error Convergence" (Supplementary text page 6: lines 184 - 210) and illustrated in Supplementary Figure S12. This analysis demonstrates that the mean squared error (MSE) between dynamic distributions from N and 2N simulations exponentially decreases as N increases, and the distribution of protein dynamics changes negligibly well before reaching 100,000 instances. Furthermore, performing the entire analysis in triplicate with independent random seeds yielded nearly identical meta-dynamic maps (average standard deviation < 0.04%), giving us high confidence that we have robustly captured the network's behavioural repertoire.

      We believe this convergence occurs because the system is degenerate: many distinct parameter sets within the high-dimensional space map to the same qualitative outcome (e.g., 'rebound' or 'decreasing'). Our goal was to capture the set of possible outcomes, not every unique parameter combination that leads to them.

      Regarding the parameter range, we intentionally chose a broad, unbiased range (10<sup>-5</sup> to 10<sup4></sup>)as a proof-of-concept to delineate the theoretical upper limit of heterogeneity the network can support, thereby capturing even rare but potentially critical resistance dynamics. We agree with the reviewer that a future direction is to constrain these ranges using biological data. Such an approach would transition from defining what is possible (the focus of this manuscript) to predicting what is probable in a specific biological context. We have added this important point to the Discussion (page 16: lines 663-679) to highlight this avenue for future work.

      (4) One of the manuscript's main results indicates that protein interactions play a more significant role in driving adaptive resistance than protein expression. To explore the impact of protein expression, the authors fixed a nominal parameter set and generated 100,000 initial concentrations of the 50 proteins in the ODE model. However, the simulations' equilibrium concentrations in the "starvation" and "fed" phases, which form the initial condition for the treated phase, are uniquely determined by the nominal model's kinetic parameters and not the initial conditions, which remain identical for each simulation. From a dynamical systems perspective, stable steady states are determined by the model parameters and attract all initial conditions within their basin of attraction. As a result, a random sampling of the initial conditions has a limited impact on the model dynamics. The authors' conclusion that "the ability of expression to induce resistance also seems to be dependent on the master parameter set" can be explained by this dynamical systems perspective, where the resistance state corresponds to a stable steady state determined by the master parameter set. Considering this, the evidence presented in the manuscript may not fully support the authors' conclusion regarding the importance of protein expressions relative to protein dynamics. The discrepancy might be attributed to a possible misunderstanding of this point, and further clarification from the authors could be helpful.

      We thank the reviewer for the thoughtful perspective. We agree that, in a monostable system with fixed kinetic parameters and fixed conserved totals, varying only the initial split among moieties (e.g., X vs pX) will not change the final steady state; trajectories converge to the same attractor. In our analysis, however, “initial conditions” predominantly refer to total protein abundances (e.g., X_tot = X + pX + complexes), used as a proxy for expression heterogeneity. These totals are invariants on the simulated timescale (no synthesis/degradation in the pre-equilibration phases), and therefore alter the value of the steady state under a given parameter set. In other words, our IC sampling mostly varies conserved totals rather than merely redistributing a fixed total; hence the equilibrium reached after the starvation/fed pre-equilibrations depends on the sampled totals and the kinetics. This can be seen in the new Supplementary Figure S4, showing that changing the ICs does shift the eventual steady state even when kinetic parameters are fixed.

      We have revised the text to: (1) define ICs explicitly as total abundances for multi-state species, (2) distinguish “initial split” from “conserved totals,” and (3) clarify that expression effects are context-dependent rather than universally dominant (page 4: lines 139-141 and page 10: lines 413-416)

      (5) Additionally, it is important to note that the random sampling of 100,000 initial concentrations might not sufficiently explore the vast space of possible initial conditions. In the thought experiment mentioned earlier, where each protein can have high or low expression concentrations, there are approximately 2^(50) = ~10^(15) possible combinations of initial concentrations. Thus, the 100,000 random simulations only represent around ~1/10^(10) of the possible initial conditions in this simplistic scenario. Consequently, this limited sampling of initial conditions may not provide enough information to draw meaningful conclusions, even if the initial conditions were more directly linked to kinetic rates.

      Please see our response to Comment (3). Briefly, our ICs are continuous total abundances (conserved moieties), not binary high/low states; many IC configurations converge to the same qualitative attractors, so we estimate distributional properties rather than enumerate all combinations. Our convergence diagnostics (independent replicates and sample-size doubling) show that the meta-dynamic distributions stabilise well before N=100,000 (see Supplementary Figure S12). We have clarified this in the Supplementary Information (Error Convergence section) with the new convergence results.

      (6) The authors implement a parameter selection step in the manuscript, where they filter out parameter sets that lead to what they term non-biological simulations. However, the rationale for determining if a given parameter set results in a stiff system of ODEs remains unclear. The authors cite references [38,39] to support the claim that stiff equations are not biologically plausible. Still, upon review, it is evident that [38] does not include the term "stiff," and [39] discusses using implicit methods to simulate stiff ODE models without specifically commenting on the biological plausibility of stiff systems. The manuscript lacks direct evidence to justify the conclusion that filtering out parameter sets that result in stiff ODE systems is reasonable. Since the filtering step accounts for the majority of discarded parameter sets, a stronger foundation is required to support the statement that stiff equations are non-biological.

      We thank the reviewer for pointing out the issue in our original justification. The reviewer is correct: stiff systems are a common feature of biological models, and our claim that they are likely ‘biologically implausible’ was not well substantiated. The filtering of these model instances was, in fact, due to a computational limitation rather than a biological principle. The issue was that these parameter sets produced systems of ODEs that were so numerically stiff they were unsolvable within a reasonable timeframe by the SUNDIALS ODE solver suite, which is specifically designed for such systems.

      Following the reviewer's comment, we investigated the source of this prohibitive stiffness. We discovered it was not an intrinsic property of the parameter sets themselves, but rather an artifact of our simulation setup. The extreme stiffness occurred almost exclusively during the initial integration timesteps, caused by the large initial discrepancy between the concentrations of active and inactive protein forms. This large discrepancy created the conditions for overtly stiff solutions i.e. unsolvable with implemented ODE solve settings. To overcome this problem, we set a large maximum number of steps in the ODE solver for the first couple of time points, enabling the solver to overcome the excessively stiff portion of the solve. We found that the vast majority of the previously 'unsolvable' model instances could now be successfully simulated. Consequently, the number of parameter sets discarded due to solver failure is now negligible (< 1%), and this filtering step no longer accounts for the majority of discarded parameter sets. Most importantly, the distributions of dynamics were not significantly altered by this adaptation.

      We have revised the " Sampling and filtering of model instances (page 5: lines 174 – 189)" part in the Methods section to reflect this more accurate understanding. We have corrected our original claim regarding the biological plausibility of stiff systems and corrected our use of the references. Ref [38] was included to demonstrate that models of biological systems are stiff, which was a major conclusion of that paper, and [39] was originally included to demonstrate that solving ODEs is reliant on solvers that can integrate stiff systems. Upon review, ref [39] has been removed.

      Overall, this investigation has made our analysis more robust by allowing us to include a wider, more representative range of parameter sets, and has tangibly improved the quality of our study.

      (7) Additionally, it is important to consider the standard method for accounting for stiff systems, as presented in [39], which involves using implicit numerical methods for ODE simulation. The authors mention using numerical methods from the SUNDIALS suite, which includes implicit methods, but the specific numerical method used remains unclear. Furthermore, it would be valuable for the authors to disclose the number of parameter sets that were filtered to obtain the final set of 100,000 accepted parameter sets. This information would provide insights into the extent of filtering and the proportion of parameter sets that were excluded during the selection process.

      We apologise for the lack of specific detail and have now updated the text. To clarify, all ODE simulations were performed using the CVODE solver from the SUNDIALS suite. This solver employs an implicit, variable-order, variable-step Backward Differentiation Formula (BDF) method, which is robust and specifically designed for handling the stiff systems common in biological network modelling. We have now explicitly stated this in the "ODE model construction, modelling, and simulations (page 4: lines 162 – 164)" section of the Methods.

      Regarding the filtered parameters, we have included a revised and detailed discussion of this in the "Sampling and filtering of model instances (page 5: lines 174 – 189)" part in the Methods section (see our response to comment (6) above). Briefly, after applying the filters, ~40–45% of instances did not reach steady state within the simulation timeframe, and ~50–55% did not meet the minimum drug-response criterion. Approximately 10% satisfied all criteria and were retained for analysis. Importantly, we employed ‘rejection sampling’ and continued drawing until we had N = 100,000 accepted instances that satisfied all the criteria.

      (8) An important step in the simulation process described by the authors is the simulation of the "fasted" and "fed" states until an equilibrium is reached. However, it is not clear how the authors determine if the system has reached an equilibrium. It would be helpful if the authors could provide more information regarding the criteria used to assess equilibrium in the simulations. Regarding the "fed" state, it is not explicitly stated whether the mitogen stimulus is assumed to be constant throughout the "fed" experiment. Considering the dynamic nature of mitogen stimulation in biological systems, it would be beneficial if the authors could clarify this assumption and discuss its biological relevance.

      We apologise for the lack not specifying this in the original text. A simulation was considered to have reached equilibrium when the concentration of every protein species changed by < 1% over the final 100 time steps of the simulation phase. We have now added this criterion to the "Sampling and filtering of model instances (page 5: lines 177 – 179)" part of the Methods section.

      Regarding the second part of the comment, in our simulations, both the mitogenic and the drug inputs were modelled as constant, stepwise functions that, once turned on, remained at a fixed concentration for the remainder of the simulation. The biological rationale for this choice was to rigorously test for bona fide adaptive resistance. By maintaining a constant mitogenic and drug pressure, we can ensure that any observed recovery in the activity of downstream proteins is due to the internal rewiring and adaptation of the signalling network itself, rather than an artefact of the removal or decay of the external stimulus/drugs. We have now clarified this rationale in the "ODE model construction, modelling, and simulations (page 4: lines 168 – 171)" part of the Methods section.

      (9) The "Description of Model Scope and Construction" section in the Supplementary Information should include explicitly the model reactions and some discussion about their specific form (e.g., why is '(((kc2f1*pIR*PI3K) / (1 + (pS6K/Ki2))) + (kc2f2*pFGFR*PI3K))' representing the phosphorylation rate of PI3K, with pS6K in the denominator?).

      The reviewer is right to ask for model justification. We have expanded the Supplementary “Description of Model Scope and Construction” section (page 2: line 63 – page 5: line 185) to include a complete reaction list with rate laws and a brief rationale for each. We also explain the specific PI3K phosphorylation term: activation by pIR and pFGFR is attenuated by pS6K via a denominator, which captures the well-described S6K-mediated negative feedback that reduces activation (e.g., via IRS1 phosphorylation).

      (10) In line 349, the statement "Given that CDK46cycD is only strongly suppressed in just under 60% of the model instances (Figure 3C)" lacks clarity regarding where to look to interpret the 60% value. If this means that 4 out of the 7 model instances are resistant, and the other 2 proteins also have the same percentage of resistance, then there is no apparent reason to focus solely on CDK46cycD.

      The reviewer is correct; the figure reference was an error, which has been rectified in the main text (page 9: line 355). The actual figure reference was to Supplementary Figure 2A, which shows the heatmap of all the frequencies for each protein dynamics for all the active protein forms. CDK4/6cycD shows a sustained decreasing dynamic for 59.93% of model instances, which is where this number was derived. We have also now explicitly referenced this number in the supplementary Figure 2A legend.

      We focus on CDK4/6cycD because it is the direct pharmacological target of CDK4/6 inhibitors. Our point was to suggest that even when the target is suppressed in the majority of instances (~60%), this does not reliably propagate to uniform downstream inhibition across the network, thus highlighting emergent, network-driven adaptive responses.

      (11) We observed that in Fig. 5A, the authors show that multiple pathways are blocked. However, it is unclear whether they reduced the value of one parameter in the experiment or simulated multiple combinations of parameter inhibition. Considering the large number of parameters (94) in the model, if the authors simulated all possible combinations of parameter inhibition, the number of combinations would be significantly more than 94. An actual inhibitor typically has an inhibitory effect on multiple molecules. Therefore, it would be necessary to identify the parameters that lead to drug resistance when multiple molecules are inhibited. However, examining the inhibition patterns for all 94 parameters would be practically impossible. As a potential approach, we suggest using ensemble learning techniques, such as random forests, to handle this problem efficiently. With a dataset of binary outputs indicating the presence or absence of resistance for a sufficient number of inhibition patterns, ensemble learning can be applied to find the parameters that contribute to drug resistance. Popular feature selection algorithms like Boruta could be utilised to identify the most relevant parameters. The results obtained by ensemble learning are similar to the ranking in Fig. 5C, potentially providing a more robust validation of the authors' findings. By incorporating these additional analyses, the authors could strengthen the reliability and significance of their results related to parameter inhibition and drug resistance.

      We appreciate the suggestion and the opportunity to clarify. Figure 5A depicts multiple pathways were interrogated, but in the analysis, parameters were inhibited one at a time (OAT) - not in combination. We have revised the figure legend and added a section named “Protein knockdown perturbation analyses (page 6: lines 228 – 233)” in the Methods section to make this explicit. Moreover, some additional text in the main text has been slightly modified to make this clearer (page 11: lines 462-463, page 24: lines 856-857).

      We chose the OAT design intentionally to obtain causal, first-order attribution of control points across a broad parameter ensemble without confounding from simultaneous co-inhibition. This provides an interpretable ranking of primary drivers (Figure 5C) that is consistent with the paper’s mechanistic focus. We agree that a multi-target inhibition approach could be a useful next step; however, an exhaustive combinatorial screen is beyond the scope of this proof-of-concept. In such future studies, the ensemble learning, as suggested by the reviewer, could be layered onto our MDN framework to assess robustness of the ranking under co-inhibition.

      (12) In explaining the parameterization of the model, we find an implication of a quantitative model. However, upon examining the results in Fig. 7D, we observe that they are only qualitatively correct. When comparing Figs. 7A and 7C, we note that many model instances are immediately suppressed, and the time scale remains unknown. We believe it would be essential for the authors to explain how the model of this study maintains its quantitative nature despite the results in Fig. 7. If such an explanation cannot be provided, it raises concerns regarding the biological reliability of several findings within this study.

      While our framework is built on quantitative ODEs, the validation we present in Figure 7 is indeed qualitative. This is an intentional and key feature of our study's design. Our goal was not to build a calibrated, quantitative model of a specific cell line (e.g., MCF10A), but rather to establish a proof-of-concept theoretical framework that systematically explores the full spectrum of dynamic behaviours a given network topology can possibly generate. To achieve this, we intentionally sampled parameters from a very broad, unbiased range to delineate the theoretical upper limit of heterogeneity. This in silico population is therefore designed to be far more heterogeneous than any single isogenic cell line.

      The striking qualitative agreement seen between our meta-dynamic distributions and the single-cell data in Figure 7D is thus not a failure of quantitative prediction, but rather a strong validation of our core premise: that a significant degree of signalling heterogeneity exists in cell populations and that our framework can effectively capture its emergent properties.

      Regarding the specific comment on Figure 7C, we apologise for the lack of clarity. Nominally, we chose to simulate for 24 hours however, the x-axis in our simulations represents arbitrary time units, as the timescale is dependent on the meaning/units of the parameter values. The goal is to compare the qualitative shape of the response (e.g., rebound, sustained decrease), not the absolute time in hours. Moreover the rapid initial suppression seen in many of our model instances (Fig 7C) is a direct parallel to the rapid suppression seen in the experimental data (Fig 7A). This initial phase is followed by a wide variety of adaptive behaviours (or lack thereof) in both our simulations and the real cells, which is the key phenomenon we are studying.

      We have revised the text (page 14: lines 598-601) and Figure 7’s legend to state more explicitly that our validation is qualitative and to clarify the purpose of our broad, uncalibrated approach. We have also added a note in the Discussion (page 18: lines 744-747) that calibrating this framework with cell-line-specific data is a natural next step for generating quantitative, context-specific predictions.

      (13) Related to the previous point, the experimental data is presented as fold-change during CDK4/6 inhibition, and we notice that the initial fold-change at time 0 varies between 1 and 1.8. The difference in initial fold-change is unclear to us, as our understanding of fold-change typically corresponds to the change from baseline, typically represented by the protein concentration at time 0.

      Furthermore, while the experimental data exhibits uniformly decreasing CDK4/6 activity, a substantial number of simulations indicate constant CDK4/6cycD, showing a significant qualitative discrepancy between the simulations and experimental findings. This disparity makes it difficult for us to interpret the comparison between the two datasets effectively, given the complexities in comprehending the experimental fold-change figure.

      As Figure 7 serves as the primary validation of model simulations in the manuscript, we believe that the current presentation may not provide a compelling reason to believe that the model accurately captures experimental data. To enhance clarity and validation, we suggest overlaying the experimental data over the simulations or considering the median and 10/90% percentile of the experimental data, which may potentially offer improved readability and facilitate a more robust interpretation of the comparison.

      The experimental data from Yang et al. (ref 55, main text) measures kinase activity using a nucleus-to-cytoplasm translocation reporter system, wherein a bait protein is phosphorylated by the target kinase causing it to translocate from the nucleus to the cytoplasm. Hence, the y-axis represents the ratio of nuclear vs. cytoplasmic fluorescence, not a fold-change from a t=0 baseline. The variation in the starting value (between 1 and 1.8) reflects the inherent heterogeneity in the reporter's localization across individual cells even before the drug is added. We have updated the y-axis label and revised Fig. 7’s legend to state this explicitly.

      The most likely explanation for the discrepancy between experimental dynamics and our simulation dynamics is that the experimental data comes from an isogenic cell line that is largely sensitive to CDK4/6 inhibition. Our simulations are derived from a very wide parameter sweep, where the intent is to represent all possible cell states. It is quite striking that that there is such a high correlation between the experimental data and simulations, indicating that perhaps the heterogeneity of even isogenic cell lines is significantly greater than might be intuited; a point we now mention in the revised Discussion (page 17: lines 716-727).

      It is worth noting again, that our analysis is intentionally constructed to be as heterogeneous as possible, and is not trained on any biological data that might otherwise constrain the output-behaviour space. The isogenic cell line almost certainly represents a much more constrained output-behaviour space than our analysis.

      The y-axis label has also been updated accordingly. As mentioned in (12) this result is intended as a qualitative validation, showing that cell lines indeed have highly variable signalling dynamics. Given the range of parameters tested, we think it is surprising that the degree of agreement between the experiment and our analysis is as high as it is. Again, we believe this suggests that heterogeneity may be more prevalent than is intuited. We do not believe we have made any strong quantitative claims in the main text, and we certainly aim to work towards biological, quantitative validation in the future. Finally, we altered the wording of the results heading (page 14: line 562) to make it clear that we are only making qualitative claims and removed the claim that the evidence was strong.

      With these clarifications and corrections, we believe the validation is now much more compelling. The key point is not a perfect quantitative match, but the strong similarity in the distribution of heterogeneous behaviours.

      (14) The authors mention simulating treatment with 10nM of CDK4/6i or Ei, but specific details on how this treatment is included in the model simulations are not provided. This lack of information makes it challenging to fully evaluate the comparison between model simulations and experimental evidence in Figure 7. It would be highly appreciated if the authors could clarify how the treatment with CDK4/6i or Ei is incorporated into the simulations to facilitate a better understanding and interpretation of the results.

      To clarify, the effects of the inhibitors were incorporated directly into the kinetic rate laws of their respective target reactions.

      CDK4/6 inhibitor (CDK4/6i): This was modelled as an inhibitor of the formation of the active CDK4/6-cyclin D complex. We have now explicitly detailed this in the description for reaction R27 in the "Description of Model Scope and Construction" section of the Supplementary Information.

      Estrogen Receptor inhibitor (Ei): This was modelled as an inhibitor of the estrogen-dependent activation of the Estrogen Receptor. This is now explicitly detailed in the description for reaction R15 in the same supplementary section.

      It is however important to reiterate that our goal in Figure 7 is qualitative, shape-based comparison; therefore, we used a fixed fractional inhibition (reported in Methods) rather than a calibrated IC50/Hill model.

      (15) The authors state strong support for their modelling conclusions based on the literature. However, we still have concerns regarding the validation of the model against CDK2 or CDK4/6 data in Figure 7, as it appears less convincing to us. Furthermore, the authors list known resistance mechanisms that are replicated in their modelling. Nevertheless, we find the conclusion somewhat weakened by Figure S10, where approximately 80% of the nodes are implicated in some form of resistance pathway. This raises questions about the model's selectivity, as many proteins included in the model seem to drive resistance in some manner. In the Supplementary Information, the authors mention excluding or abstracting some protein species from the mitogenic and cell cycle pathways to manage computational resources effectively. This abstraction makes it difficult to determine if the proteins identified as potential drivers of resistance genuinely drive resistance or might represent abstractions of other potential drivers. To enhance the manuscript's clarity and address potential concerns about the model's selectivity and abstraction, we suggest providing more details and discussion in the main text.

      The reviewer's observation that a large number of nodes are implicated in resistance pathways in Figure S10 is correct. However, we argue this is not a weakness of the model's selectivity, but rather a key finding that reflects the biological reality of adaptive resistance. The literature is replete with a wide and growing number of distinct mechanisms of resistance even to a single class of drugs (1,2), which supports the idea that cancer can co-opt a wide variety of network nodes to survive.

      Figure S10 is not a binary map where every implicated node is equal, instead it is a likelihood map, where the colour and weight of the connections represent how often a particular interaction participates in driving resistance across the theoretical full range of possible network dynamics. The figure shows that while many nodes can contribute to resistance, they do so in a hub-like manner i.e. small subsets of nodes coordinate to drive resistance. This provides a rationalised, data-driven prioritisation of the most dominant and recurrent resistance strategies. We draw two important conclusions from this work 1) Resistance likely occurs due to resistance hubs, not individual proteins, and 2) that the frequency of a resistance hub in an MDN analysis is likely proportional to the frequency of that hub emerging as a resistance mechanism in a population of cells and patients.

      Regarding the issue of abstraction, the reviewer is correct that this is an inherent feature of any tractable systems model. In our case, several species in the mitogenic/cell-cycle pathways are module-level proxies to control model size. The highly implicated "hub" nodes in our model likely represent critical cellular processes that are themselves composed of several individual protein interactions.

      To address these concerns, we have significantly revised the Discussion (page 16: lines 681 – 694) to: (1) frame resistance as a network-level phenomenon; (2) show that our frequency-based ranking is selective, prioritising the most probable, recurrent mechanisms; and (3) clarify that - given model abstraction -our findings implicate critical processes (modules), not just single proteins, as the drivers.

      Overall, these changes do not alter our main conclusions: adaptive resistance is an emergent, network-level property; many routes exist, but a smaller set of nodes/modules consistently carry the largest influence across heterogeneous contexts.

      (16) We consider that the figures and legends, including the supplementary information, are inadequately explained. The information provided is insufficient for us to comprehend the figures fully, leading to the need for interpretation on our part as readers. This could potentially introduce biases when trying to understand the claims made by the authors. To improve our understanding, it would be essential for the authors to assign appropriate labels to the figures and provide comprehensive explanations in the legends. For example, in Fig 3, we suggest labelling the tree diagrams in panels A and B, as well as the colour bars. We also recommend applying the same approach to other figures, adding accurate axis labels and descriptions of colour gradients to enhance clarity.

      We thank the reviewer for this critical feedback. To address this comment, the figure legends have been revised where appropriate and greatly expanded to improve their comprehension. Moreover, we have added explicit labels to all previously unlabelled components, such as the cluster dendrograms and colour code bars in Figure 3A, B.

      (17) To enhance readability, we recommend interchanging the order of Figures 1 and 2 in the sequence they appear in the main text. Alternatively, the text can be adjusted to refer to the figures in the correct order. Additionally, attention should be given to the bottom of Fig 1, which appears to be cropped or cut off. Furthermore, the incorrect word spacing in some figure elements, such as Fig. 3A title, Fig. 5B title, and Fig. 6B y-label, should be corrected for improved visual presentation.

      Following the reviewer’s comment, the order of Figures 1 and 2 has been switched to reflect the order in which they are referred to in the main text. These Figures have been re-exported to fix unintentional word spacing errors.

      (18) We recommend that the language used to refer to the initial conditions in the manuscript is clarified and homogenised. Currently, the authors use different terms such as "basal expression," "protein expression," "state variable values," or "initial conditions" to refer to them. This variation in terminology can be confusing for readers. In particular, the use of "basal expression" is problematic, as it typically refers to the leaky value of a reaction in the absence of an inducer, making it another biophysical parameter of the system rather than an initial condition. To enhance clarity and consistency, we suggest the authors decide on a single term to refer to the initial conditions throughout the manuscript and provide a clear explanation of its meaning to avoid any confusion. This will help readers better understand the concept being discussed and prevent any potential misinterpretations.

      We thank the reviewer for this very helpful suggestion. To resolve this and improve clarity, we have homogenized the language throughout the manuscript. We now clarify the use the following 3 terms in their specific contexts:

      We use “protein abundances” exclusively for the conserved total abundances of multi-state species (e.g., Xtot = X + pX + complexes) that are sampled across instances to represent expression heterogeneity.

      We use ‘initial conditions’ to refer to initial values of the state variables in a model simulation. This term is related to protein abundance as the setting of initial conditions for conserved species sets the protein abundance. This is explicitly stated in the text (page 3: lines 87 - 91).

      We use “state variables” to refer to the time-dependent model species.

      We avoid the term “basal expression” in technical descriptions. Where a biology-facing phrase is helpful, we use “protein expression level”. This is used when referring to the biological concept that the initial conditions are intended to represent, i.e. the heterogeneity in protein amounts across a cell population.

      We have performed a thorough search-and-replace to ensure this new convention is applied consistently and have removed the potentially confusing term "basal expression" from the revised manuscript.

      (19) Why are saturable functions (e.g., Michaelis-Menten functions) ignored in the model? What are the potential consequences?

      The main objective of this work was to perform a large-scale, systematic exploration of a high-dimensional parameter space (94 parameters) to map the full repertoire of qualitative dynamic behaviours a network topology can support. Using saturable functions like Michaelis-Menten kinetics would have roughly doubled the number of parameters to be explored (from k to Vmax and Km for each enzymatic reaction), making a parameter sweep of this scale computationally intractable. We therefore prioritised the breadth of the parameter search over the depth of kinetic detail, which we believe is the appropriate choice for a proof-of-concept study focused on heterogeneity.

      This simplification has potential consequences. A major one is that our model cannot capture phenomena that arise specifically from enzyme saturation, such as zero-order kinetics or certain forms of ultrasensitivity (switch-like responses). However, we argue that this is an acceptable trade-off for two main reasons: (1) Our analysis is based on classifying broad, qualitative response shapes (increasing, decreasing, rebound, etc.). Mass-action kinetics are fully capable of generating this rich spectrum of behaviours; and (2) by varying the mass-action rate constants over nine orders of magnitude (from 10<sup>-5</sup> to 10<sup4></sup>), our parameter sweep effectively samples a vast range of reaction efficiencies. A very low rate-constant can approximate the behaviour of a saturated, low-efficiency enzyme, while a high rate-constant can approximate a highly efficient, non-saturated one. In this way, the broad sweep of the rate parameter partially reflects the effects that would be captured by varying Vmax and Km.

      For transparency, we have added a brief rationale to the “ODE model construction, modelling, and simulations” part of the Methods (revised main text, page 4: lines 153-155) and the "Description of Model Scope and Construction" section in the Supplementary file (Supplementary text page 2: lines 63-73).

      (20) Given the relevance of the concept of "heterogeneity" in this work, a short discussion about biochemical noise and its implications on the analysis (e.g., why it is not included, and if it will be a next step) would be appreciated.

      Our MDN modelling framework represents heterogeneity by creating an ensemble of deterministic models, where each model instance has a unique set of kinetic parameters and/or initial protein abundances. We propose that this is a powerful way to mechanistically represent the functional consequences of all sources of cellular variation. Over time, the effects of genetic mutations, epigenetic states, and even the time-averaged impact of intrinsic biochemical noise will manifest as changes in the effective interaction strengths and protein concentrations within a cell. Our large-scale parameter/IC sweep is designed to systematically explore the full range of dynamic behaviours that can emerge from this underlying biological variation. Therefore, our approach does not compete with stochastic modelling but is complementary to it. While stochastic simulations can capture the dynamic trajectories of single cells, our framework provides a panoramic view of the entire spectrum of possible stable phenotypes that can emerge at the population level. We agree that modelling intrinsic biochemical noise (stochasticity arising from finite copy numbers), e.g. using chemical Langevin or SSA, is a possible extension in future work but expected to be very computationally expensive. We have added a brief discussion on this as future direction in the revised Discussion.

      (21) We have noticed that the first four paragraphs of the Discussion section overlap with the Introduction, as they mainly reiterate the significance of the study itself rather than focusing on the specific results obtained. To avoid redundancy and provide a more cohesive and informative discussion, we recommend that the authors shift the focus of the Discussion section towards presenting potential interpretations, even if they are not definitive, of the results obtained. By doing so, the Discussion will serve as a valuable platform for deeper analysis and insightful observations, allowing readers to better comprehend the implications and significance of the research findings.

      We thank the reviewer for this structural feedback. Following the reviewer's feedback, we have significantly rewritten and restructured the Discussion section. The redundant introductory material has been removed.

      The rewritten Discussion centres on interpretation, implications, and connect our findings to the literature. It now: (i) frames MDN as a systems-level framework that links molecular heterogeneity to qualitative signalling “meta-dynamics” and adaptive escape under constant drug pressure; (ii) highlights two key findings: an asymmetry in control (interaction kinetics exert stronger, more consistent influence than protein abundance) and a topology-driven convergence whereby a vast parameter space funnels into a finite set of recurrent behaviours; (iii) shows that resistance is a network-level property, with many possible routes but a small set of recurrent hubs/modules dominating; and (iv) provides a qualitative alignment with single-cell reporter data while clarifying the intent and limits of that comparison. Moreover, we now explicitly discuss limitations (rate-law simplifications, broad priors, determinism, and modular abstractions) and outline next steps for future research, including data-constrained priors and stochastic extensions.

      We believe this substantial revision has transformed the Discussion into a much more insightful and valuable part of the manuscript that directly addresses the reviewer's concerns.

      (22) The supplemental text file containing the model equations can be a bit challenging to read and understand. It would be greatly beneficial if the authors could consider generating a file using a typesetting program.

      We have now included a typeset list of state variable equations and ODEs, along with the original model files.

      (23) The authors mentioned that some model parameterizations result in negative solutions, which is surprising. Access to the model equations would help understand why this happens and is crucial for researchers who may want to use this approach. Clarifying the model equations' presentation would enhance transparency and aid other researchers in applying this method for similar research questions.ach. Clarifying the model equations' presentation would enhance transparency and aid other researchers in applying this method for similar research questions.

      The reviewer is correct to be surprised by the mention of negative solutions, as negative concentrations are physically impossible. We clarify that these are not a result of any structural flaw in our model's equations but are a well-known, although rare, numerical artifact of floating-point arithmetic in computational solvers.

      Our model is constructed using standard mass-action and first-order kinetics, which structurally guarantee non-negativity. However, when a species' concentration approaches the limits of machine precision (i.e., becomes a very small number extremely close to zero), the ODE solver can, in rare instances, numerically undershoot zero, resulting in a small negative value. If this occurs, it can lead to instability in subsequent integration steps.

      This is not a biological phenomenon but a computational one. Therefore, the standard and appropriate procedure, which we follow, is to implement a filter that discards any simulation trajectory where such a numerical instability occurs.

      (24) The reference listed for the CDK4/6 and CDK2 measurements is Yang et al. [55] in the figure caption, but as Xe et al. in lines 559-561 of the manuscript.

      The text has been updated to match citation.

      (25) We suggest that the authors revise and cite a previous study conducted by Yamada et al. (Scientific Reports, 2018), which presents an approach to expressing cell heterogeneity as a probability distribution of model parameters.

      Following this suggestion, we have revised the Discussion (see response to comment (21)) to include and discuss Yamada et al. (Scientific Reports, 2018), which models cell heterogeneity as a probability distribution over parameter values.

      (26) In the manuscript, on line 677, the authors state, "This indicates that there is an upper limit to the degree to which parameter sets can influence the qualitative shape of a protein's dynamic within a given network topology." We wish to highlight that this finding may not be particularly surprising. Given that the parameters were randomly determined within a specific range, it is understandable that altering the number of parameter samples would not substantially impact the distribution of model instances.

      We thank the reviewer for this insightful comment, which allows us to clarify the significance of this finding. While it is true that any sampling from a fixed distribution will eventually converge statistically, our conclusion is not about statistics but about the intrinsic, constraining properties of the network's topology. The novelty is not that the distribution converges, but that it converges to a surprisingly limited and finite repertoire of qualitative dynamic behaviours. A complex, non-linear network with nearly 100 free parameters could theoretically generate an almost endless variety of complex dynamics. Our finding is that this specific biological topology acts as a powerful filter, robustly channelling the vast majority of the near-infinite parameter combinations into a small, recurring set of functional outputs (increasing, decreasing, rebound, etc.).

      The reason for this finite limit is mechanistic, as the reviewer's comment prompted us to investigate further. Our parameter sweep already covers an extremely wide, 9-order-of-magnitude range. As we pushed parameter values to even greater extremes in exploratory simulations, we found they do not generate novel, complex dynamic shapes. Instead, they tend to drive network nodes into saturated states- either permanently "on" (maximally activated) or permanently "off" (minimally activated). In both cases, the node becomes unresponsive to upstream perturbations.

      Therefore, further expanding the parameter range would be unlikely to uncover new behavioural categories; it would simply increase the proportion of model instances classified as "no-response." This demonstrates a fundamental principle: the network topology itself enforces an upper limit on its dynamic complexity. We think this inherent robustness is what allows for reliable cellular signalling in the face of constant biological variation. We believe this is a non-trivial finding, and we have revised the Discussion (page 16: lines 664 - 680) to state this conclusion and its implications more clearly.

    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 investigate the impact of rare and extreme events on rodents' decisionmaking under risk, in gain and loss contexts. They describe the behavior of 20 rats performing a four-armed bandit task, where probabilistic gains (sugar pellets) and losses (time-out punishments) can - in some arms - incorporate extremely large - but rare - outcomes. They report that most rats are sensitive to rare and extreme outcomes despite their infrequent occurrence, and that this sensitivity is primarily driven by extreme loss events which they try to avoid, rather than extreme gains that they seek to obtain.

      They finally propose a modification of standard reinforcement-learning, which features a specific sensitivity to rare and extreme outcomes and can account for the observed behavior.

      Strengths:

      The manuscript really taps into a surprisingly neglected but very relevant aspect of decision-making: the effect of rare and extreme events (REE). The authors have developed an experimental setup that seemingly allows investigation of this aspect, which is not trivial given the idiosyncratic properties of rare and extreme events.

      The parameters of the experimental setup seem also to be well thought off: basically, in the absence of REE, some options are objectively better than others (because, in expectation, they overall deliver more food, or minimize time-out punishments), but this ordering reverses if REE are taken into account. This allows for a clean test of the integration of REE in the rodent's decision-making model.

      The data is presented and analyzed in a very descriptive but exhaustive and transparent way, down to the description of individual rodent's behavior.

      Weaknesses:

      While the description and analyses of the behavioral patterns are rigorously done under the economic lens of risky decision-making, the authors' interpretation heavily relies on the assumption that rodents have built the correct model of the task during the training. Extensive details are provided about the training procedure, and the observed behavior at the end of the training, but it remains virtually impossible to disambiguate choices due to imperfect learning to choices made due to intrinsic preferences for risk or REE.

      As detailed in Material and Methods, the animals were progressively overtrained following standard behavioral procedures. During this process, they experienced all available options, including both positive and negative REE. We assume that repeated exposure to these REE supported learning, as would be expected for any event occurring throughout such an extended training phase. The rats ultimately displayed an asymmetric pattern of choices: they consistently avoided the Black Swan, indicating that they had learned its negative consequences, yet they did not systematically seek the Jackpot. If their behavior were driven solely by incomplete learning or by an inherent preference for risk or REE, we would expect to see the opposite pattern systematic Jackpot seeking or inconsistent avoidance of the Black Swan.

      By nature, gains (food pellets) and losses (time-out punishments) are somewhat incommensurable so the interpretation of the asymmetry due to outcome valence is also subject to interpretation. There might be some additional subtleties due e.g. satiety that could come from gaining REE (i.e. the delivery of 80 pellets from the Jackpot).

      As described in Material and Methods, we used mouse pellets (20 mg) instead of rat pellets (45 mg) to prevent satiety during Jackpot delivery (80 pellets). We also selected gains (sweet pellets) and losses (delays) that we have successfully used in previous rat decision-making paradigms, such as the rat gambling task (Adams et al., 2017; doi: 10.1523/ENEURO.0094-17) and the loss-chasing task (Breysse et al., 2021; doi: 10.1111/ejn.14895). Notably, if the Jackpot induced satiety, one would expect animals to stop seeking it yet this was not systematically observed. Nonetheless, we added a sentence to the Discussion on page 18 of the manuscript to acknowledge that we cannot fully exclude the possibility that satiety contributed to the lack of systematic Jackpot Seeking.

      In its current form, the paper is quite hard to digest. This is naturally the case with interdisciplinary work (here mixing economists and neurobiologists). But I am afraid that with the current frame, the paper is going to miss its target, in terms of audience.

      We have rewritten entirely and the english was corrected thanks to ChatGPT. We hope that the paper is now easier to digest.

      The proposed model seems somewhat disconnected from the behavioral patterns: while the model suggests an effect of REE at the decision stage (i.e. with specific decision weights for those rare events), this formalism seems at odds with the observation that REE (notably in the loss domain) has an impact of subsequent behavior - (Black Swans tend to reinforce Total Sensitivity to REE) which rather suggests an effect at the learning stage.

      We agree with the referee that this may appear surprising at first glance. However, we would first like to emphasize that the general model allows REE to influence learning—that is, to contribute to the updating of the Q-subvalues. Moreover, even when REE are incorporated only as decision weights, as is the case for most rats, this does not imply that REE are unimportant during learning. In fact, the model assumes that REE are learned once and for all when they first occur during a trial of the corresponding option. Unreported simulation exercises indicate that a more gradual learning of maximal and minimal values would likely yield similar results.

      Second, the Before/After analysis shows that the behavioral response to Black Swans is locally small in terms of both total and one-sided sensitivities. This suggests that such effects are likely too subtle to be captured by this class of models for most rats. We have added this clarification to the revised version (page 17).

      Discussion:

      This study convincingly demonstrates that REEs are processed rather uniquely, which makes sense given their evolutionary relevance. REE has indeed been somewhat neglected in previous research, and this study therefore opens an interesting new front on the fundamental aspects of decision under risk. The authors have devised an original theoretical and empirical framework that will be useful for the community, and the combination of economics analysis and rodent behavior constitutes a thoughtprovoking ground to think about the nature of risk preferences. The interpretation and mechanistic account of these aspects, as well as their generalizability outside the specific context of this study, remain to be strengthened.

      We have modified the discussion to further insist on the translational aspect of the study and its interest for various populations (page 22). We hope that the generalizability is now strengthened.

      Reviewer #2 (Public Review):

      Summary:

      This paper attempts to examine how rare, extreme events impact decision-making in rats. The paper used an extensive behavioural study with rats to evaluate how the probability and magnitude of outcomes impact preference. The paper, however, provides limited evidence for the conclusions because the design did not allow for the isolation of the rare, extreme events in choice. There are many confounding factors, including the outcome variance and presence of less-rare, and less-extreme outcomes in the same conditions.

      Strengths:

      (1) The major strength of the paper is the significant volume of behavioural data with a reasonable sample size of 20 rats.

      (2) The paper attempts to examine losses with rats (a notoriously tricky problem with non-human animals) by substituting time-outs as a proxy for losses. This allows for mixed gambles that have both gain and loss possible outcomes.

      (3) The paper integrates both a behavioural and a modelling approach to get at the factors that drive decision-making.

      (4) The paper takes seriously the question of what it means for an event to be rare, pushing to less frequent outcomes than usually used with non-human animals.

      Weaknesses:

      (1) The primary issue with this work is that the primary experimental manipulation fails to isolate the rare, extreme events in choice. As I understand the task, in all the conditions with a rare extreme event (e.g., 80 pellets with probability epsilon), there is also a less-rare, less-extreme event (e.g., 12 pellets with probability 5). In addition, the variance differs between the two conditions. So, any impact attributable to the rare, extreme event could be due to the less rare event or due difference in the variance. The design does not support the conclusions. Finally, by deliberately confounding rarity and extremity, the design does not allow for assessing the impact of either aspect.

      We agree with the referee that both the REE and the rare (≈10% frequency) but non-extreme outcomes are present in the relevant options. However, the rare but non-extreme reward is not large enough to make the convex option attractive and to shift choice away from the concave option. In other words, unlike REE, these outcomes do not reverse stochastic dominance in our design (as noted in Material and Methods). We have explored modified designs for human subjects in which the rare but non-extreme outcomes are removed. Preliminary results indicate that the behavioral phenotypes observed in rats also emerge in humans under these modified conditions, suggesting that REE are the primary drivers. We have added a statement to the Discussion (page 22) to clarify this point.

      We elaborate further in our response to point (3) below on why analyses based solely on variance are insufficient when dealing with REE. To clarify the role of rare and extreme outcomes in distinguishing convex from concave options, we provide two new columns to Table 2 in the Materials and Methods, in our reply to point (3).

      Finally, although a detailed analysis of rare but non-extreme outcomes lies outside the scope of this paper, the symmetric treatment of extreme and frequent outcomes can be addressed straightforwardly using strong First-Order Stochastic Dominance. Classical decision-theoretic approaches indeed satisfy this property.

      (2) The RL-modelling work also fails to show a specific impact of the rare extreme event. As best as I can understand Eq 2, the model provides a free parameter that adds a bonus to the value of either the two options with high-variance gains (A and V in the paper) or to the two options with high-variance losses (F and V in the paper). This parameter only depends on whether this option could have possibly yielded the rare, extreme outcome (i.e., based on the generative probability) and was not connected to its actual appearance. That makes it a free parameter that just bumps up (or down) the probability of selecting a pair of options. In the case of the "black swan" or high-variance loss conditions, this seems very much like a loss aversion parameter, but an additive one instead of a multiplicative one.

      We agree with the referee that the additional parameters, compared to more standard Q-learning models, specifically capture the fact that some options deliver REE while others do not. In our estimation procedure, these parameters become nonzero as soon as REE are observed for the first time for a given option. Therefore, the first step is to estimate a baseline nested model in which REEs contribute only at the learning stage (i.e., they affect the updating of Q-subvalues), while the additional parameters are constrained to zero. The next step is to compare alternative models against this baseline, allowing REEs to enter through the additional parameters. In this respect, our specification is parsimonious, especially given that very little is known about REEs in computational neuroscience. More structural modeling is certainly a promising direction for future research, and this paper constitutes a first step toward that goal.

      We provide the BIC, in addition to the AIC, to account for the presence of additional parameters in model selection and to ensure that the observed improvement in fit is not merely driven by their inclusion.

      Unlike most of the existing literature, our results extend the notion of loss aversion to extreme losses. The negative decision weight on options yielding the Black Swan can be interpreted as a differential treatment of negative REE, an issue we discuss extensively in the Discussion (page 20).

      (3) The paper presented the methods and results with lots of neologisms and fairly obscure jargon (e.g., fragility, total REE sensitivity). That made it very hard to decipher exactly what was done and what was found. For example, on p. 4, the use of concave and convex was very hard to decipher; the text even has to repeat itself 3 times (i.e., "to repeat" and "in other words") and is still not clear. It would be much clearer (and probably accurate) to say that the options varied along the variance dimension, separately for gains and losses. Option A was low-variance gains and losses. Option B was low-variance losses and high-variance gains. Option C was high-variance losses and low-variance gains, and Option D was high-variance losses and gains. That tells much more clearly what the animals experienced without the reader having to master a set of new terminologies around fragility and robustness, which brings a set of theoretical assumptions unnecessarily into the description of the experimental design. In terms of results, "Black Swan" avoidance is more simply known as risk aversion for losses.

      Because our experimental design focuses on REE, outcomes cannot be summarized only by their variance. This is well known from the large literature on so-called fat-tailed statistical distributions. Unlike the Normal distribution that is entirely characterized by its expected value and variance, fat-tailed distributions have nonzero kurtosis. This implies that a fat-tailed distribution (e.g. exponential) with the same expected value and variance as the Normal differs importantly by possessing extreme values that are much more likely in terms of frequency. To illustrate, if the distribution of pellets was assumed to be Normal with expected value set at 3.89 and variance set at 9.37 as for the convex option, the probability of getting 80 pellets would be about 2.10<sup>-16</sup>, practically zero. In contrast, this probability is smaller than, but close to 1% in our design.

      In Material and Methods, we clearly explain how our novel approach in terms of convexity relates to the moments of the reward distributions, including but not limited to the variance. To clarify further, we provide two new tables (Author response table 2 and Author response table 3) to be compared to Table 2 of the manuscript in which we report the first four moments (mean, standard deviation, skewness and kurtosis) of the full concave and convex gain distributions, reproduced for convenience

      Author response table 1.

      In Author response table 2 we report the first four moments when REE are truncated. Comparing convex and concave gains shows that the convex option has a smaller but still close mean compared to the concave option. In contrast, the former has larger variance, skewness and kurtosis compared to the latter. Therefore, interpreting choosing the convex option as reflecting “preference” for variance is at best incomplete.

      Author response table 2.

      First four moments of concave and convex gains when REE are removed

      Author response table 2 further shows that REE alone goes a long way towards explaining the differences between convex and concave options in terms of the first four moments: removing the rare and extreme value results in the concave option having now a larger mean, while the convex option still has larger variance, skewness, and kurtosis but by a smaller margin.

      In Author response table 3 we report the first four moments when both RE and REE are truncated, which shows that the convex and concave options differ only with respect to their mean (which is here also larger for concave).

      Author response table 3.

      First four moments of concave and convex gains when both RE and REE are removed

      In addition, our focus on REE implies that we go beyond mean-variance preferences that apply mostly to Gaussian distributions. It is not clear theoretically what type of utility functions would reflect preferences that combine a taste for variance, skewness and kurtosis, even though all those moments affect expected utility. See for example Phelps, C.E. “A user’s guide to economic utility functions”. J Risk Uncertain 69, 235–280 (2024) for a recent overview (on page 242, Phelps states that “In situations where risk is not normally distributed, it is ill-advised to ignore statistical parameters beyond variance, unless the deviations from normality are relatively small”).

      More importantly, our proposed measure of the convexity of the reward distributions, the Jensen gap, further reveals how even restricting the analysis to the first four moments is incomplete in the sense that it fails to characterize the difference between options: the fifth moment of the concave contributes more the Jensen gap than even kurtosis, while one needs to look at much higher moments to find significant contributions to the Jensen gap for the convex option. In that sense, there is no reason to restrict the analysis to variance, and even to skewness and kurtosis, to compare options, in general and in our particular setup as well. Note that introducing REE would result in convex distributions even in simplified designs, e.g. with 3-value support. Studying REE implies the need to look beyond variance, and our proposal is to use the Jensen gap as a measure of convexity. In the Material and Methods section of the paper, we did not develop an in depth analysis of Jensen gap so as to spare the reader confronted with an already rather technical paper.

      We thank the referee for raising the issue of whether variance is a simpler explanation of our results. To keep the main text as short as possible, we chose to refrain from adding technical complexity. We hope we made clear in our reply that the analysis cannot be restricted to variance when studying REE. We believe that Jensen gap is a useful notion in this regard. As our replies will be made publicly available, we chose not to integrate the above discussion in the main text.

      (4) Were the probabilities shuffled or truly random (seem to be fixed sequences, so neither)? What were the experienced probabilities? Given the fixed sequences, these experienced ("ex-post") probabilities, could differ tremendously from the scheduled ("ex ante") probabilities. It's quite possible that an animal never experienced the rare, extreme event for a specific option. It's even possible (if they only picked it on the 10th/60th choices by chance), that they only ever experienced that rare extreme event. This cannot be known given the information provided. The Supplemental info on p.55 only gives gross overall numbers but does not indicate what the rats experienced for each choice/option-which is what matters here. A simple table that indicates for each of the 4 options, how often they were selected, and how often the animals experienced each of the 6-8 possible outcome would make it much clearer how closely the experience matched the planned outcomes. In addition, by restricting the rare outcome to either the 10th or 60th activations in a session, these are not random. Did the animals learn this association?

      Probabilities are not random and a limited number of fixed sequences has been used, as stated in Material and Methods. We have chosen sequences that satisfy our assumptions about ex-post stochastic dominance reversal of convex over concave options when REE are added. We have added in Table S4 the choice frequencies for all four options. If the animals had learnt the 10th and 60th activation, they would exhibit a strategy in their choice that would tend to be more optimized than what is observed. For example, the options offering the possibility to obtain the Jackpot are not optimal in terms of gains for the frequent events, therefore the animals should tend to select these options only around the 10th and 60th choice. Most of their other choices should favor the options delivering the larger gains in the frequent domain. This is not what is observed. We have added this important point in the discussion (page 18).

      (5) The choice data are only presented in an overprocessed fashion with a sum and a difference (in both figures and tables). The basic datum (probability/frequency of selecting each of the 4 options) is not provided directly, even if it can theoretically be inferred from the sum and the difference. To understand what the rats actually do, we first need to see how often they select each option, without these transformations.

      As described in Material and Methods, the 4 options are combinations of 2 convex and concave sub-options for gains and losses, which is why our analysis of the behavioral data focuses on convexityrelated total and one-sided sensitivities to REE. The third dimension needed to fully characterize rats’ behavior is simply 1−ff<sub>FF</sub>, the fraction of non-Fragile choices. In addition, we also provide in Table S4 of the Supplementary Material an alternative interpretation in terms of Black Swan Avoidance and Jackpot Seeking. We have added in Table S4 the choice frequencies for all four options. Finally, all the raw data will be made available with open access and no access codes.

      (6) There is insufficient detail provided on the inferential statistical tests (e.g., no degrees of freedom or effect sizes), and only limited information on exactly what tests were run and how (bootstrapping, but little detail). Without code or data (only summary information is provided in the supplement), this is difficult to evaluate. In addition, the studies seem not to be pre-registered in any way, leaving many researchers with degrees of freedom. Were any alternative analysis pipelines attempted? Similarly, there were many sub-groupings of the animals, and then comparisons between them - were these post-hoc?

      We understand the concern of the referee for pre-registration of the referee, as an epistemic safeguard to make empirical claims more falsifiable, more transparent, and less dependent on post hoc rationalization. But the contemporary push for preregistration is often presented as an “epistemic improvement,” but in practice it functions largely as a norm of moral regulation, not a scientific necessity. The rhetoric is moralistic: preregistered research is “clean,” “transparent,” “credible,” while non-preregistered work is viewed with suspicion—even when the methodology is sound. This language is not epistemologically neutral; it enforces ought to be done, irrespective of the diversity of legitimate scientific practices.

      From a philosophy of science perspective, this is historically and conceptually problematic. Scientific progress has never followed a uniform, rule-based method. As e.g. Feyerabend has argued, major discoveries have emerged precisely because researchers were not bound by predetermined plans: they followed anomalies, improvised, reinterpreted data, and revised methods and hypotheses in light of new evidence — practices that a rigid preregistration ethos can suppress and that are not aligned with how genuine discovery often occurs.

      Even from a statistical standpoint, preregistration is far from a panacea. It reduces some degrees of freedom (mainly in confirmatory statistics), but it does not eliminate flexibility; researchers can still choose models, transformations, exclusion rules, stopping rules, etc. And more importantly: reducing flexibility is not inherently epistemically virtuous. Flexibility is often necessary to understand data properly—especially in new paradigms or first-of-their-kind experiments, which is the case for this study. Science needs exploration, opportunism, and theoretical plasticity. Preregistration is compatible with these only if it is treated as one optional tool among many—not as a universal evaluative standard.

      As the referee pointed out, this study “taps into a surprisingly neglected but very relevant aspect of decision-making.” Our work is therefore mainly exploratory: the experimental paradigm reveals new behavioral patterns in how rats cope with rare and extreme events, and much of our analysis is necessarily descriptive. We conduct formal inference only where it is methodologically appropriate — the short-term behavioral response to rare events (for which we now provide more details in the Material & methods section p.35) and the estimation of augmented Q-learning models, which follow a standard econometric approach (documented in the Material & Method section–see also our response to recommendation 4). These inferential results support the descriptive patterns that motivate this new line of research.

      (7) On p. 17, there is an attempt to look at the impact of a rare, extreme event by plotting a measure of preference for the 10 trials before/after the rare, extreme event. In the human literature, the main impact of experiencing a rare, extreme event is what is known as the wavy recency effect (See Plonsky et al. 2015 in Psych Review for example). What this means is that there tends to be some immediate negative recency (e.g., avoiding a rare gain) followed by positive recency (e.g., chasing the rare gain). Using a 10-trial window would thus obscure any impact of this rare, extreme event. An analysis that looks at a time course trial-by-trial could reveal any impact.

      We thank the referee for drawing our attention to the wavy recency effect documented in human experiments. We have added the corresponding reference in the Discussion (page 20). Regarding rats, the Before/After analysis reported in the paper suggests that there is no sizeable immediate recency effect for Jackpots. Even for Black Swans, the immediate recency effect we report remains modest when using a 10-trial window, and the analysis of the choice immediately following a REE does not show evidence of immediate negative recency. This casts doubt on the presence of such an effect in rats.

      (8) As I understood the method (p. 31), the assignment of options to physical locations was not random or counterbalanced, but deliberately biased to have one of the options in the preferred location. This would seem to create a bias towards a particular option and a bias away from the other options, which confounds the preference data in subsequent analyses.

      We agree that the design incorporated an intentional bias toward the anti-fragile option as a proof of concept. Nevertheless, Figure 8 demonstrates that animals substantially altered their choices between training and final testing, with a median change of approximately 35% across sessions. This indicates that behavior was driven by the structure of possible outcomes rather than by a stereotyped location-based preference.

      (9) Are delays really losses? This is a big assumption. Magnitude and delay are different aspects of experience, which are not necessarily commensurable and can be manipulated independently. And, for the model, how were these delays transformed into outcomes for the model? Eq 1 skips over that. Is there an assumption of linearity? In addition, I was not wholly clear if the delays meant fewer trials in a session or if the delays merely extended the session and meant longer delays until the next choice period.

      Consistent with established rodent decision-making paradigms (Adams et al., 2017 doi: 10.1523/ENEURO.0094-17; Breysse et al., 2021 doi: 10.1111/ejn.14895), we employed sweet pellets as gains and imposed delays as losses. Delays are operationalized as losses because they preclude the animal from engaging in reward-generating behavior; thus, increasing the delay duration proportionally increases the magnitude of the opportunity cost.

      (10) The paper does not sufficiently accurately represent the existing literature on human risky decision-making (with and without rare events). Here are a few examples of misrepresented and/or missing literature:

      Most studies on decision-making do not only rely on p > 10% (as per p. 2). Maybe that is true with animals, but not a fair statement generally. Some do, and some don't. There is substantial literature looking at rarer events in both descriptions (most famously with Kahneman & Tversky's work), but also in experience (which is alluded to in reference 19). That reference is not only about the situation when choices are not repeated (e.g. the sampling paradigm), but also partial feedback and full-feedback situations.

      We have corrected that statement in the main text (page 3) and we thank the referee for pointing this out.

      The literature on learning from rewarding experiences in humans is obliquely referenced but not really incorporated. In short, there are two main findings - firstly people underweight rare events in experience; second, people overweight extreme outcomes in experience (both contrary to description). Some related papers are cited, but their content is not used or incorporated into the logic of the manuscript.

      One recent study systematically examined rarity and extremity in human risky decision-making, which seems very relevant here: Mason et al. (2024). Rare and extreme outcomes in risky choice. Psychonomic Bulletin & Review, 31, 1301-1308.

      There is a fair bit of research on the human perception of the risk of rare events (including from experience) and important events like climate. One notable paper is Newell et al (2015) in Nature Climate Change.

      We agree with the referee that the related literature on REE in animal Decision Making is scant and that it is more developed in humans. We thank the referee for pointing at Mason et al. (2024), who clarify where the literature on humans stands and why combining rarity and extremity, as we also do, is important and highly relevant. We have added a new statement and references in the Introduction and Discussion (pages 3, 20, 22).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) As said above, I think the manuscript would really benefit from a rewriting, to replace some technical terms with more readable ones, and maybe rebalance the focus from the current focus on the framework (heavily loaded with economics concepts, which will be hard to digest for the eLife readership) to a higher weight on information that is critical to understand and interpret the behavior (e.g. information about training & training behavior, etc.).

      We have revised the entire manuscript to improve readability and have clarified in the main text: (1) why convexity of exposures to REE could, beyond variance, be useful for experiments in other settings that our own; (2) why the associated notion of antifragility may be applicable to other settings and therefore of broader interest; (3) what was done in the training sessions compared to the final sessions.

      (2) From Figure 8, it seems that rodent behavior is more clustered after the training (i.e. before the sessions) than after the sessions. Could that be a sign of imperfect learning?

      Figure 8 mostly suggests that there is some flexibility in the choices made and that the intended initial bias towards the antifragile choice in the design of the task could be over ridden by the rats.

      (3) The modelling section seems incomplete. I think the authors want to tease apart where REE enters the model and should propose an alternative where REE affects the learning rather than the decision.

      In fact, the general model allows REE to have an effect at the learning stage only (i.e. to contribute to the updating of the Q subvalues), when the specific decision weights attached to options delivering REE are both zero. However, our analysis shows that such a model is rejected by the behavioral data for all rats. We have clarified this point in the revised version.

      (4) Also, parameter and model recovery exercises seem mandatory (Wilson & Collins, 2019).

      We thank the referee for highlighting this valuable reference in computational modeling, particularly in the context of model identification and estimation in computational biology. In the present research, we adopted an econometric perspective on model identification—especially with regard to the integration of Q-values for gains and losses. The softmax choice function is formally equivalent to a multinomial logit model, and as is well known in econometrics, identification in such models presents non-trivial challenges. The standard approach in classical Q-learning is to multiply the Q-value by an inverse temperature parameter (also known as a precision parameter in random utility models). When extending the model to include separate Q-values for gains and losses, specifying the model in an identifiable way becomes more complex.

      To address this issue, we considered several alternative model specifications and conducted grid-based estimation of starting parameter values. This approach allowed us to examine the shape of the loglikelihood function and assess whether the parameters are globally identified, rather than only identifiable up to a linear combination. We found that the most parsimonious and empirically identified specification in our experimental paradigm is one in which Q-values for gains and losses are summed, each weighted by distinct decision weights (see our Equation 2 in the paper).

      The inclusion of decision weights for REE for each option (Equation 2) is then structurally equivalent to introducing constant terms in a logit model. The identification of these parameters follows standard econometric results on discrete choice models (e.g., Davidson & MacKinnon, 2003): since we model choices among four options, three free parameters can be estimated, leaving one degree of freedom in the specification. As mentioned in the "Modelling and Statistical Analysis" section, we further guarded against the presence of local maxima by applying a two-step estimation procedure, combining two optimization algorithms with multiple sets of starting values for the baseline model (i.e., the model without decision weights for REE). We also tested the addition of a global optimization method— simulated annealing—but found that it did not significantly improve upon our two-step procedure. This is not surprising, as our preliminary investigation of model identification, based on grid searches over starting parameter values, confirmed that all parameters were identified in our simple specification. Our intuition is that simulated annealing may yield different estimates than gradientbased methods primarily in cases where the model is not theoretically identified—suggesting that the need for such global optimization techniques can be indicative of underlying identification issues in Qlearning models.

      Regarding model comparison, we have used penalized information criteria to account for additional parameters. Although we do not report confusion or inversion matrices for our nested models, we verified that the estimated models replicate observed behaviors across all phenotypes, as shown in the main text (see bottom left panel of Figure 5 for the Total and One-Sided sensitivities). Most importantly, we conducted 100 additional simulations of 40 artificial sessions for each phenotype using the “winning” models and the median fitted parameters. These simulated rats—playing the task 100 times over 40 sessions—offer strong evidence that the selected models are valid: they quantitatively capture the behavior of all phenotypes in terms of our key metrics, Total and One-Sided sensitivities (see bottom right panel of Figure 5).

      Taken together, this methodical econometric approach to model specification and estimation gives us strong confidence in the identification and robustness of our model. Overall, while Wilson & Collins (2019) provide an interesting framework for model estimation in computational biology, we believe that a more formal theoretical analysis of model identification in Q-learning models would be a valuable addition to the field—though it lies beyond the scope of the present work. In our view, computational biologists should complement simulation-based validation and empirical fit with formal methods for assessing theoretical identifiability, particularly when estimating complex choice models.

      Davidson, R. and J.G. MacKinnon (2003) Econometric Theory and Methods. Oxford University Press (New York).

      Wilson, R. C., & Collins, A. G. (2019). Ten simple rules for the computational modeling of behavioral data. eLife, 8, e49547. https://doi.org/10.7554/eLife.49547

      Reviewer #2 (Recommendations For The Authors):

      (1) The paper confuses risk sensitivity and exploration in the opening lines. These are not the same.

      What we have in mind here is that uncertainty about outcomes is one of the main drivers of exploration, in the sense that there would be no need to explore in a counterfactual world with deterministic gains and losses. We have modified the opening lines of the paper to better reflect this dimension (page 2).

      (2) p. 9. "awfully long" is an unnecessary descriptor. Descriptions of methods should be more factual.

      The manuscript has been entirely rewritten.

      (3) p. 13. Most points lie on the left of the square (not right?).

      We thank the referee for pointing at this typo, that is now corrected in the text (page 8).

      (4) p. 13. Last line. "obviously" is patronizing to the readers.

      The manuscript has been entirely modified to address related points.

      (5) p. 23. The avoidance of black swans by not choosing that option sounds like a hot-stove effect (see Denrell & March, 2001). Is this evidenced here?

      To the best of our knowledge, the statement that “people tend to avoid activities they have had a negative experience of, resulting in a negativity bias” (from Jerker Denrell’s website) does not explicitly concern REE. Instead, it appears to refer broadly to reinforcement learning mechanisms driven by negative outcomes, irrespective of their magnitude or frequency. In our task, animals encounter both negative rare events (RE) and negative rare and extreme events (REE; Black Swans). Notably, the task design does not allow rats to completely avoid negative RE unless they cease performing the task altogether—a pattern typically seen in paradigms involving aversive stimuli such as electric foot shocks. The fact that all 20 rats maintained stable performance across the 41 sessions provides evidence against a pronounced hot-stove effect. This point has been incorporated into the revised discussion (page 20).

      (6) "menus" is an odd term. Better described as reward schedules?

      “Menu” has been replaced by “option” in the main text.

      (7) Why are they 20-minute sessions? I thought it was 120 trials per session? And 41 sessions? Or was this only in training?

      Each session ended after 20 minutes had elapsed, which led to approximately 120 trials (but not systematically). The choice of 20 minutes was made in order to limit the number of trials to prevent satiety. The total number of sessions ran with all 20 animals for the final testing was 41, an odd number but there was no justification to remove one session from the analysis. The training was much longer and is not included in the 41 sessions.

      (8) Really not clear why these Jensen inequalities were relevant or even calculated for these options? How is it relevant to what animals chose or experienced? They seem to be based on the generative probabilities for different options, which is not what happened in reality.

      We propose the Jensen gap as a general measure of convexity that relates to all moments of the probability distribution, as described in more detail in our answer to point (3) above. As such, we think it is a characterization of options with stochastic outcomes that could prove useful to other experimenters in alternative settings beyond our own.

      (9) Only some summary data in supplemental materials. No open data or code for recreating the experiment or analyzing the data.

      The data is available on Github (see page 38) and the code will be available upon request.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      I read this paper with great interest based on my experience in insect sciences. I have some minor comments (and recommendations) that I believe the authors should address.

      (1) The paper has an original biological question that is overly broad and mechanistically ambitious. The central biological question, namely how CLas infection enhances fecundity of Diaphorina citri via dopamine signaling, is clearly stated and well motivated by previous literature. However, my advice to the authors is that, while the general question is clear, the manuscript attempts to answer multiple mechanistic layers simultaneously. As a result, I feel that the biological narrative becomes diffuse, especially in later sections where DA, miRNA regulation, AKH signaling, and JH signaling are all proposed as parts of a single linear cascade. In summary, my key concern is that the paper often moves from correlation to causal hierarchy without fully disentangling whether these pathways act sequentially, in parallel, or redundantly. A more explicitly framed primary hypothesis (e.g., "DA-DcDop2 is necessary and sufficient for CLas-induced fecundity") may improve conceptual clarity.

      We sincerely thank the reviewer for these constructive comments and agreed that the initial version of our manuscript attempted to integrate multiple signaling layers, which may have blurred the logical distinction between sequential, parallel, or redundant pathways. To address this concern, we have restructured the narrative to center on a clearly defined hypothesis by changing “DA/DcDop2-miR-31a-AKH-JH signaling cascade” to “DA-DcDop2 signaling axis” in Abstract (Line 33) of the revised manuscript.

      (2) On the novelty of the data, I feel they are moderately novel, with substantial confirmatory components. If I am correct, the novel contributions include the identification of DcDop2 as the DA receptor responsive to CLas infection in D. citri, the discovery that miR-31a directly targets DcDop2, which is supported by luciferase assays and RIP, and thirdly, the integration of dopamine signaling into the already-described CLas-AKH-JH-fecundity framework. My advice to the authors is to focus more on the manuscript's novelty, which lies more in pathway integration than in discovering fundamentally new biological phenomena. This is appropriate for a mechanistic paper, but should be framed as an extension of existing models rather than a paradigm shift.

      We sincerely thank the reviewer for this thoughtful and highly constructive assessment. We greatly appreciate the clear articulation of what constitutes the novel contributions of our work, and we fully agree with the characterization that the primary novelty lies in pathway integration rather than the discovery of entirely unprecedented biological phenomena. We also accept the valuable advice that our manuscript should be framed as an extension of existing models rather than a paradigm shift. In response to this insightful comment, we have carefully revised the Results part in Line 275-278 of the revised manuscript.

      (3) On the conclusions, I recommend that the authors modify their statements a little. I feel that there are some overstated or insufficiently supported claims. For instance, the assertion that CLas "hijacks" the DA-DcDop2-miR-31a-AKH-JH cascade implies direct pathogen manipulation, but no CLas-derived effector or mechanism is identified. Also, that the model suggests a linear signaling hierarchy, but the data largely show correlation and partial dependency rather than strict epistasis. In third, the term "mutualistic interaction" may be too strong, as host fitness costs outside fecundity (e.g., longevity, immunity) are not evaluated. In conclusion, I confirm that the data support a functional association, but mechanistic causality and evolutionary interpretation are somewhat overstated.

      We sincerely thank the reviewer for these insightful comments and agreed that there are some overstated or insufficiently supported claims. In response to this insightful comment, we have changed "hijacks" to "regulates" (Line 32 and 124), and "mutualistic interaction" to “coevolution” (Line 2, 34, 127, 257, 763, 806, and 842) in our revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      Nian and colleagues comprehensively apply metabolomics, molecular, and genetic approaches to demonstrate that CLas hijacks the DA/DcDop2-miR-31a-AKH-JH signaling cascade to enhance lipid metabolism and fecundity in D. citri, while concurrently promoting its own replication.

      Strengths:

      These findings provide solid evidence of a mutualistic interaction between CLas proliferation and ovarian development in the insect host. This insight significantly advances our understanding of the molecular interplay between plant pathogens and vector insects, and offers novel targets and strategies for HLB field management.

      Weaknesses:

      While the article investigates the involvement of dopamine signaling and specific microRNAs in enhancing fecundity and pathogen proliferation, it still needs to provide a detailed mechanistic understanding of these interactions. The precise molecular pathways and feedback mechanisms by which CLas manipulates dopamine signaling in Diaphorina citri remain unclear.

      These comments are extremely helpful for revising and improving our manuscript.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) In Figures 1C and 1D, please maintain consistent gene nomenclature: change "henna" to "Henna", "TH" to "Th", and "DDC" to "Ddc".

      Thanks for your great suggestion. We have changed "henna" to "Henna", "TH" to "Th", and "DDC" to "Ddc" in Figure 1C and 1D of our revised manuscript.

      (2) In Figure 7, correct "Emergy metabolism" to "Energy metabolism".

      Thanks for your valuable suggestion. We have corrected "Emergy metabolism" to "Energy metabolism" in Figure 7 of our revised manuscript.

      (3) Please specify the number of biological replicates in the figure captions.

      Thanks for your perfect suggestion. We have specified the number of biological replicates in the figure captions of Figure 1 (Line 737-738), Figure 2 (Line 757-759), Figure 3 (Line 780-782), Figure 4 (Line 799-800), Figure 5 (Line 816-819), and Figure 6 (Line 833-836).

      (4) For Figure 2I, 3J, and 5H, clarify that CLas 16s rRNA was detected by FISH. The age of the dissected females should also be described in the captions.

      Thanks for your insightful suggestion. We have added the female age (at 7 DAE) in the captions for Figure 2I (Line 752), 3J (Line 773), and 5H (Line 813) of our revised manuscript.

      (5) A blot is shown in Figure 3B but not discussed in the text. Since the manuscript describes mRNA levels, please specify whether these blots are from Northern or Western blotting and provide relevant methodological details.

      Thanks for your great suggestion. The blot in Figure 3B is Western blot result. We have added the related descriptions in Result (Line 202), Materials and Methods (Line 521-536), and figure legend (Line 766) of our revised manuscript. 

      (6) In Figure 3G-3K, an "inhibitor" was used, but its name and functional role are not described. Please give more details.

      Thanks for your valuable suggestion. We have added the detail information for “Dop2 inhibitor” in the Figure 3G-3K legend (Line 772-776) of our revised manuscript.

      (7) In Lines 23-24 of the Abstract, consider revising "their neuroendocrine regulation remains unclear" to "their neuroendocrine regulation mechanisms remain unclear" for grammatical accuracy.

      Thanks for your perfect suggestion. We have revised "their neuroendocrine regulation remains unclear" to "their neuroendocrine regulation mechanisms remain unclear" for grammatical accuracy in Line 24 of our revised manuscript.

      (8) The last sentence of the Abstract is overly long. It is recommended to split it as follows: "These findings reveal a mutualistic interaction between CLas proliferation and ovarian development in the insect host. This discovery enhances our understanding of the molecular interplay between plant pathogens and vector insects and offers novel targets and strategies for HLB field management."

      Thanks for your excellent suggestion. We have splited the last sentence of the Abstract as follows: "These findings reveal a coevolution between CLas proliferation and ovarian development in the insect host. This discovery enhances our understanding of the molecular interplay between plant pathogens and vector insects and offers novel targets and strategies for HLB field management." in Line 34-37 of our revised manuscript.

      (9) In Line 139, remove the comma between "female" and "adult".

      Thanks for your great suggestion. We have removed the comma between "female" and "adult" in Line 139 of our revised manuscript.

      (10) In Line 149, replace "d" with day.

      Thanks for your perfect suggestion. We have replaced "d" with "day" in Line 149 of our revised manuscript.

      (11) The JH determination method references a previous study but lacks a detailed description of the extraction procedure. Please include this information in the methodology section.

      Thanks for your valuable suggestion. We have added the detailed description of the JH extraction procedure in Line 511-514 of our revised manuscript.

      (12) In Figure S2, since the panel shows interference efficiencies for four genes, "treated with dsDcAKHR" should be revised to "treated with dsRNA" for accuracy.

      Thanks for your insightful suggestion. We have revised "treated with dsDcAKHR" to "treated with dsRNA" for accuracy in the Figure S2 legend.

      (13) In line 354-355, change "DcVg1-like, DcVgA1-like and DcVgR" to "DcVg1-like, DcVgA1-like, and DcVgR".

      Thanks for your great suggestion. We have changed "DcVg1-like, DcVgA1-like and DcVgR" to "DcVg1-like, DcVgA1-like, and DcVgR" in Line 350 of our revised manuscript.

      (14) The study primarily investigates the role of agomir-31a. Would antagomir-31a promote ovarian development in CLas- females? In addition, did the authors perform a rescue experiment using antagomir-31a in CLas+ females after dsDcDop2 treatment?

      Thanks for your valuable suggestion. The proposed experiments will be instrumental in further elucidating the functional role of miR-31a and represent a key direction for our future research. We will carefully consider and incorporate these approaches in our subsequent study.

      (15) The method used to determine CLas-negative and CLas-positive individuals should be described in more detail in the Materials and Methods section.

      Thanks for your great suggestion. We have added more details about CLas detection in the Materials and Methods section (Line 378) of our revised manuscript.

    1. Author response:

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

      Reviewer #1:

      (1) The biological and/or mathematical meaning of the Soma and Neurite Density Imaging (SANDI) indices (apparent soma density, apparent soma size, extracellular water signal fraction, extracellular diffusivity, apparent neurite density, fractional anisotropy, and mean diffusivity) should be briefly introduced for those less familiar with this novel technique.

      Further explanations about the biological and mathematical meaning of the SANDI indices were added to the introduction on page 6.

      (2) The study implements a novel biophysical diffusion model that extends up-to-date methodologies and presents a significant potential for quantifying neurodegenerative processes of the grey matter of the human brain in vivo. The authors comment on the usefulness of this technique in other pathologies, but they exemplify it only with multiple sclerosis. Further development of this, building evidence, should be provided.

      Clinical applications of SANDI have primarily focused on MS. However, since preparation of the manuscript, one study has been published reporting reductions in apparent soma density and white and grey matter specific differences in apparent soma size in amyotrophic lateral sclerosis (ALS) (Zeng et al., Eur J Radiol 2025, 10.1016/j.ejrad.2025.111981). These findings accord with the loss of motor neurons and glial responses in ALS. We have added this study to the introduction of SANDI on page 7.

      (3) Why are the basal ganglia compared against thalami? The rationale of this decision is missing.

      The thalami were selected as control regions based on the established trajectory of neurodegeneration in HD, which begins with early loss of medium spiny neurons in the striatum and later extends to surrounding structures, including the putamen and thalamus. Given that most participants in our study were at early disease stages, we assumed the thalami would remain relatively unaffected in this sample. This explanation has been added to the introduction on page 7.

      (4) The use of bullet points is unusual for a scientific paper format.

      Bullet points have been removed throughout the manuscript.

      (5) The authors mention that they eroded the boundaries of the subcortical masks. Providing the details and parameters of this erosion would be beneficial.

      Details of the default parameters of the FSL erode function that was used have been added to the method section on page 13.

      (6) In the conclusion, the authors state that their results will bridge the gap between histopathological findings and in vivo imaging, but it would be helpful if they could briefly explain how they imagine such a bridge (e.g., which kind of comparisons or correlations) and whether there exists any literature in this regard so far.

      We have added the following brief explanation to the conclusion on page 26: “Although conventional MRI lacks the resolution to directly capture histopathology, advanced biophysical models such as SANDI may help bridge this gap by providing biologically interpretable parameters that reflect tissue composition and capture histopathological changes in vivo.”

      (7) The scale is missing in Figure 3.

      The scale has been added to Figure 3.

      (8) In general, the work would benefit from a better organization and potentially a smaller number of figures and tables.

      The manuscript has been re-edited to improve the readability and organization throughout and the number of figures and tables were reduced by moving some of them to the Supplementary Material (old Tables 2 and 5 are now Supplementary Tables 2 and 3, old Figure 3 is now Supplementary Figure 1).

      Reviewer #2:

      Certain aspects of the study would benefit from clarification:

      (1) Scanner and acquisition consistency: While HD data are from the WAND study, it is not clear whether controls were scanned on the same scanner or protocol. Given the use of model-derived metrics (especially SANDI), differences in scanner or acquisition could introduce confounds. From the text, the HD participants are explicitly said to come from the WAND study (a longitudinal HD cohort). On the other hand, while the HC participants are described as age-matched controls, the paper does not clearly state whether they were scanned in the same study (i.e., WAND), on the same scanner, or with the same acquisition protocol. This ambiguity is potentially problematic, especially since they use model-derived diffusion metrics that can be very sensitive to scanner hardware, gradient strengths, and protocol settings. If the WAND HD data were acquired on a specific scanner (e.g., 3T Connectom) and the HCs were not, then differences in SANDI/DTI metrics might reflect scanner bias, not disease pathology. This is particularly critical in SANDI, which is sensitive to high b-values and SNR. It would strengthen the manuscript to explicitly state whether the HD and control data were acquired using the same scanner model, sequence, and protocol, and ideally at the same site. If this were not the case, the authors should include this as a limitation and discuss any harmonization strategies applied (e.g., ComBat, covariate modeling, etc).

      For harmonization and comparison purposes, HD and control data were acquired using the same strong gradient (300mT/m) 3T Connectom MRI system at CUBRIC with the same acquisition protocols and sequences. It should also be noted that the Connectom scanner has not had any software upgrades that could introduce scanner biases in data acquired at different time points. This is now made explicit on page 8 by stating that all MRI data for all participants were acquired on the same MRI system using the same acquisition protocols, and on page 10 by stating that all HD and HC MRI data included in our analyses were acquired on the same 3T Siemens Connectom scanner at CUBRIC using the same acquisition protocols described in this section.

      Also, although it offers novel and biologically informative markers, widespread clinical translation still faces hurdles. For instance, the study used a 3T Connectom scanner (300mT/m gradients), which is not widely available. Reproduction of these results in standard 3T clinical scanners would be a great addition, in scenarios with lower resolution, less precise parameter recovery, and longer scans if SNR needs to be maintained.

      We agree that for clinical adoption it is important to demonstrate that HD-related SANDI differences can also be detected on clinical MRI systems and do not require ultra-strong gradient imaging. While we have not collected such data in people with HD, we have demonstrated the feasibility of modelling SANDI metrics from multi-shell diffusion-weighted imaging acquired on a clinical 3T MRI (maximum b-value of 6,000 s/mm<sup>2</sup>) in healthy adults and people with MS (Schiavi et al 2023, https://doi.org/10.1002/hbm.26416). Furthermore, Zeng et al 2025, reported significant differences in SANDI metrics acquired on a 3T MRI Prisma system between individuals with ALS and healthy controls (maximum b-value of 3,000 s/mm<sup>2</sup>).

      Two additional studies demonstrated that SANDI could be implemented and microstructural differences could be detected in MS using 3T scanners with standard gradient strength (Barakovic et al., 2024; Margoni et al., 2023). Collectively, these findings indicate that SANDI can be applied on clinical scanners, particularly as clinical systems move toward stronger gradient capabilities such as Siemens Magnetom Cima.X. These explanations can be found under the clinical implication section in the Discussion on page 25.

      (2) Limitations of HD-ISS staging resolution and group separation:

      The use of HD-ISS staging to anchor progression analyses is conceptually appropriate, but, in practice, the sample is quite limited.

      (a) Only 26-27 out of 56 gene-positive participants could be assigned HD-ISS stages, and none were classified into stages 0 or 4. This restricts the interpretation of progression to a narrow clinical window (mostly stages 1-3) and excludes over 50% of the cohort.

      (b) Furthermore, visual inspection of the scatter plots (e.g., Figures 3 and 4) reveals substantial overlap between stages 1 and 2, particularly in CAP100 and Q-Motor measures. This suggests that the separation between early disease stages may not be robust in this dataset, potentially due to limited power or phenotypic variability.

      (c) The above may lead to claims based on progression across HD-ISS stages to be overinterpreted or underpowered

      Despite this, the paper treats the staging as a reliable stratification for group comparisons. To improve clarity and transparency, I would recommend that the authors:

      (a) Acknowledge that over 50% of the HD cohort could not be classified.

      (b) Discuss whether those excluded differed from those included in key metrics.

      (c) Explicitly comment on the substantial overlap between stages 1 and 2, and limit claims about progression unless such separation is statistically supported.

      (d) Avoid overinterpreting staging-related effects without statistical support for group separability

      Re a-d) We have added to the study limitations on pages 23 ff that only 54% (30 out of 56) HD participants could be HD-ISS classified due to missing data, and provide an overview of demographic and clinical information for HD-ISS stages and unclassified individuals in Supplementary Table 1. We acknowledge that the combined groups (HD-ISS 0-1 versus HD-ISS 23) for exploratory group analyses did not represent discrete disease stages and that there was some overlap in imaging and behavioural features between them as illustrated in Figures 3, 4, and 7. We state explicitly that these exploratory findings should be interpreted with caution and require replication in larger, prospective cohorts before SANDI metrics can be considered as potential markers of disease progression.

      (3) Clarify regression strategy and interpretational limits of SANDI-derived regressors: While the hierarchical regression strategy is broadly appropriate, several aspects would benefit from clarification to improve both interpretability and robustness of the findings. For example:

      (a) Why were only a subset of SANDI parameters (fis and De) considered in the HC models (Figure 6), while additional metrics (fec and rs) were tested in HD models (Figures 7-8)? Including the same variables across groups could aid comparability?

      The same SANDI indices were included in regression models for HD and HC groups, Figure 7-8 report only significant predictors. This has been clarified in the figure legend and on pages 14 of the manuscript.

      (b) Were any checks for multicollinearity (e.g., variance inflation factors) conducted? Given known interdependencies among some SANDI parameters, I wonder whether some of the reported regression coefficients may be unstable or difficult to interpret.

      Cross-correlation matrices between all imaging metrics for HD, HC, and total samples have been included to Supplementary materials Figure 3.

      To improve transparency and interpretability, I suggest actions such as:

      (a) SANDI metrics included in the models differ between HC and HD groups, reducing comparability. Consider using consistent full models across ROIs for comparison purposes, even if some predictors are not significant.

      (b) Report the correlation structure between SANDI metrics within each group to assess multicollinearity (The potential impact of multicollinearity (e.g., between fis and rs) is not discussed)

      (c) Explicitly acknowledge the limitations imposed by parameter degeneracy in the SANDI model and clarify how the authors ensured the biological interpretability of regression outputs in this context - Beta coefficients could reflect model instability or parameter degeneracy rather than true biological effects.

      (a) The same SANDI metrics and age were included in the first regression models for HD and HC data. The first models only differed by the inclusion of TFC as estimate of disease burden for the HD data. HD and HC participants were not included in a single regression model, as our aim was not to perform formal between-group inference on regression coefficients. Instead, models were fitted separately to explore within-group associations and to descriptively compare patterns of relationships across groups. This approach avoids imposing identical model structures across groups that may differ in variance structure, disease burden, and biological coupling between SANDI metrics. We have clarified these points on page 13/14.

      (b) We agree that multicollinearity is an important consideration when interpreting regression coefficients derived from microstructural models. To address this, we examined pairwise Spearman correlations between all imaging (SANDI, DTI, volume) metrics (averaged across ROIs), shown in the revised Supplementary Figure 2. As can be seen in the healthy control data, SANDI indices of apparent soma and neurite fractions showed a strong inverse correlation (rho = -0.92) and did not correlate with soma radius (rho = 0.1). All SANDI indices correlated only weakly with FA and volume and moderately with MD. This correlation pattern suggests that apparent soma density and radius capture distinct information about grey matter microstructure that differs from neurite fraction and is not captured by FA or volume. We note in HD participants a negative correlation between soma radius and fraction, and stronger correlations between SANDI metrics and volume measures. We would argue that these reflect disease-related reorganization of micro- and macro-structural relationships rather than uniform collinearity across groups. This information has been added to the Methods, Results and Discussion sections on pages 13, 19, and 21, 23ff.

      (c) We agree that regression coefficients derived from interdependent microstructural parameters should be interpreted with caution, as they may reflect shared variance or partial parameter degeneracy rather than fully independent biological effects. For this reason, we do not interpret individual beta coefficients in isolation. Instead, our conclusions focus on the consistency and directionality of associations across regions and metrics, and on the overall feasibility and sensitivity of SANDI to detect biologically meaningful variation in HD. The observed correlation structure (Supplementary Figure 2) provides important context for these interpretations and supports a multivariate, pattern-based rather than univariate reading of the results. These points have been added to the Discussion on pages 23 ff. Please also refer to our response to point (5) below.

      (4) Preprocessing order:

      Gibbs ringing correction was applied after TOPUP and EDDY, which deviates from the commonly recommended order in diffusion MRI preprocessing. Since Gibbs artifacts are introduced by kspace truncation and affect the spatial domain, it is typically advised to perform Gibbs correction prior to geometric corrections like TOPUP and EDDY. This avoids potential blurring or propagation of ringing artifacts during resampling. Could the authors clarify the rationale for this ordering, and whether an early application of Gibbs correction was tested?

      We agree that the application of Gibbs ringing correction prior to TOPUP and EDDY correction deviates from the commonly recommended order in diffusion MRI preprocessing. However, as some of the data included in this paper were preprocessed before this consensus was agreed in the literature, we kept the preprocessing order consistent for all datasets for harmonization and comparison purposes. We have since changed the order for subsequent preprocessing of the HDDRUM data and have found comparable FA maps for data processed with Gibbs ringing correction before and after TOPUP and EDDY correction.

      (5) Expand on SANDI model assumptions:

      SANDI is presented as being used for the very first time in this problem. However, a vague explanation is given: "using all the default settings". Given the novelty of applying SANDI in a clinical HD context, the manuscript would benefit from a discussion of the model's key assumptions and limitations. For instance:

      (a) The potential degeneracy between fis and rs in the absence of protocol features (e.g., long Δ or high b) that can disambiguate them.

      (b) Whether a dot compartment was included, and the implications of excluding it for the interpretation of rs or fis.

      (c) The lack of exchange modeling or fixed stick diffusivity, and how these may bias compartment estimates (particularly in diseased or aging tissue).

      (d) Any steps taken to verify robustness or identifiability (e.g., simulations, synthetic fitting). These issues are not flaws in the method, but they do affect how confident we can be in interpreting fis/rs as markers of neuron loss or glial hypertrophy, especially given the subtle group differences and the potential for biological heterogeneity in HD. Even a brief acknowledgment would strengthen the manuscript and provide useful context to readers less familiar with multicompartment modeling.

      We thank the reviewer for this constructive suggestion and fully agree that, because this is the first application of SANDI in our clinical HD cohort, the manuscript should more explicitly describe the model assumptions, potential identifiability limitations under our protocol, and the implications for biological interpretation.

      We have revised the Methods (pages 11-12) and Discussion (page 24) to (i) specify the exact SANDI implementation used (the SANDI MATLAB toolbox, available at: https://github.com/palombom/SANDI-Matlab-Toolbox-Latest-Release), (ii) describe which components are included in the default formulation and the key modelling assumptions, and (iii) add a dedicated “Limitations and interpretability” paragraph addressing points (a–d) below. We also avoid the previous shorthand “default settings” and provide a clear description of the fitting setup.

      “The SANDI model [Palombo M. et al, NeuroImage 2020] assumes three compartments, namely intra-neurite signal modelled as diffusion inside impermeable randomly oriented sticks, intra-soma signal modelled as restricted diffusion inside spheres, and extra-cellular signal modelled as Gaussian isotropic diffusion. The direction-averaged (or spherical mean) normalized diffusion signal has thus the following expression:

      S(b) = f<sub>is</sub>A<sub>sphere</sub> (b, r<sub>s</sub>, D<sub>is</sub>) + f<sub>in</sub>A<sub>stick</sub> (b, D<sub>in</sub>) + f<sub>ec</sub>A <sub>ball</sub> (b, D<sub>e</sub>)

      where f<sub>in</sub> + f<sub>is</sub>+ f<sub>ec</sub> = 1; A<sub>stick</sub> and A<sub>sphere</sub> are the normalized, directionally-averaged (or spherical mean) signals for restricted diffusion within neurites and soma, respectively and A<sub>ball</sub> is the normalized, directionally-averaged (or spherical mean) signal of the extra-cellular space. The specific expressions are given in [Palombo M. et al. NeuroImage 2020]. The parameters estimated from the direction-averaged (or spherical mean) data are D<sub>in</sub>, proxy of the intra-neurite effective axial diffusivity; D<sub>e</sub>, proxy of the extracellular effective mean diffusivity; r<sub>s</sub, a proxy of apparent soma radius as well as the signal fractions subject to the constraint f<sub>in</sub> + f<sub>is</sub> + f<sub>ec</sub> = 1, proxy respectively of the relaxation-weighted neurite, soma and extracellular volume fractions. The bulk diffusivity inside the sphere D<sub>is</sub> is fixed to 3 μm<sup>2</sup>/ms. The parameters were fitted using a Random Forest regression algorithm (TreeBagger Matlab®) with 200 trees, trained on simulated data, using the code publicly available at https://github.com/palombom/SANDI-Matlab-Toolbox-Latest-Release. The training data consisted of simulated signals for 10<sup>5</sup> parameter combinations, uniformly sampled: f<sub>in</sub> and f<sub>is</sub> ∈ [0, 1], D<sub>in</sub> ∈ [0.5, 3] μm<sup>2</sup>/ms, D<sub>e</sub> ∈ [0.5, 3] μm<sup>2</sup>/ms and r<sub>s</sub> ∈ [1, 12.5] μm. Rician noise with a distribution of standard deviations randomly sampled from the voxels within the brain mask of the noise map obtained using MPPCA denoising was added to account for realistic SNR levels and rectified noise floor. The loss function of the training was the mean squared error between predicted parameters and ground truth values. Model fitting provided maps of f<sub>in</sub>, f<sub>is</sub>, f<sub>e</sub>, D<sub>in</sub>, D<sub>e</sub> and r<sub>s</sub>.”

      (a) Potential degeneracy between f<sub>is</sub>and r<sub>s</sub>. We agree that partial coupling (or degeneracy) between the soma fraction f<sub>is</sub> and soma radius r<sub>s</sub> is possible when the acquisition does not provide strong sensitivity to restricted sphere size (e.g., in the low b-values regime). Our protocol benefits from high b-values (up to 6000 s/mm<sup>2</sup>) enabled by the Connectom gradient system, which increases sensitivity to signal attenuation from restricted compartments and reduce the f<sub>is</sub>-r<sub>s</sub> coupling/degeneracy. However, we acknowledge that the specific choice of fixed diffusion timing (in our case δ=7 ms, Δ=24 ms) can further modulate the f<sub>is</sub>-r<sub>s</sub> coupling/degeneracy in a protocol-dependent way. To reflect this appropriately, we now explicitly state that r<sub>s</sub> should be interpreted as an “apparent soma radius” under our protocol, and that our inferences focus on relative group differences and spatial patterns rather than absolute histological soma radii.

      We have now added a paragraph in the limitations section acknowledging this point.

      (b) Dot compartment. We did not include an explicit “dot” (immobile) compartment, because there is no evidence that in human in vivo this is required (see for example very low and negligible contribution provided in Tax C. et al. NeuroImage 2020: https://www.sciencedirect.com/science/article/pii/S1053811920300215). Accordingly, our fits did not include a dot term, and we now state this explicitly in the Methods. However, we would like to clarify that our fitting method (described in details at https://github.com/palombom/SANDI-Matlab-Toolbox-Latest-Release) includes accurately the impact of Rician noise and thus it account for the corresponding rectified noise-floor that very often, in high b-values applications, is mistakenly associated with a “dot” compartment. Therefore, there is no expected bias on the estimated f<sub>is</sub> and r<sub>s</sub> due to not including a “dot” compartment.

      (c) Exchange modelling and fixed stick diffusivity. We agree that SANDI, as implemented here, does not explicitly model inter-compartment exchange during the diffusion encoding and uses simplified representations of neurites (sticks), but the intra-stick diffusivity, D<sub>in</sub>, was not fixed but rather fitted. In diseased or aging tissue, deviations from these assumptions (e.g., altered membrane permeability) may bias compartment estimates. This has been investigated in dept in Schiavi S. et al. HBM 2023 (https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.26416), so we refer the redear to that. We have added an explicit limitation statement noting that HD-related microstructural changes (e.g., changes to membrane permeability) could affect model parameter fidelity, and thus f<sub>is</sub>and r<sub>s</sub> should be treated as MRI-derived effective indices rather than direct quantitative measures of neuron loss or glial hypertrophy. Importantly, our analysis compares groups under an identical acquisition and fitting pipeline, so grouplevel contrasts remain informative even if absolute parameter values are biased.

      (d) Robustness / identifiability checks. We agree that reporting robustness strengthens confidence, particularly given subtle effects and biological heterogeneity. The SANDI Matlab Toolbox we used extensively investigates model parameters robustness and identifiability using numerical simulations and synthetic signals accounting for the specific experimental protocol and noise distribution. An example of the results supporting the robustness / identifiability is reported in the Author response images. These results show that accuracy and precision of all SANDI model parameters, except D<sub>in</sub>, is very high (>~80%, Author response image 1)

      Author response image 1.

      Analysis of the accuracy and precision of SANDI model parameters estimation. We simulated 10<sup>4</sup> synthetic diffusion signals using the SANDI model with random combinations of five parameters: f<sub>neurite</sub>(f<sub>in</sub>), f<sub>soma</sub>(f<sub>is</sub>), D<sub>in</sub>, R<sub>soma</sub>(r<sub>s</sub>), and D<sub>e</sub>. Parameters were sampled uniformly from: f<sub>neurite</sub>, f<sub>soma</sub> ∈ [0,1]; D<sub>in</sub>, D<sub>e</sub> 𝛜[0.5,3.0] µm<sup>2</sup>/𝑚𝑠; 𝑅<sub>soma</sub> 𝛜[1,12] µm. Rician noise with experimentally estimated variance was added, and the SANDI model was then fit to the noisy signals. For each parameter, we report the relative percentage error between estimated and ground-truth values as a function of the parameter value (normalized to [0,1]), together with goodness-of-fit (R<sup>2</sup>).

      and sensitivity to changes as small as 5% in each of the model parameters is correctly captured (Author response image 2A), with small to negligible degeneracy (except, once again, for D<sub>in</sub>), even in presence of exchange (Author response image 2B).

      Author response image 2.

      Sensitivity to 5% parameter modulations. The matrices show how a controlled perturbation in one parameter propagates into the estimated values of all model parameters. Each row corresponds to a 5% increase in the parameter on the y-axis; the resulting percentage change observed in each estimated parameter is reported along the x-axis. An ideal estimator would yield a purely diagonal matrix, with 5% on the diagonal and 0% elsewhere (no cross-talk). In (A), we used the same synthetic SANDI signals as in Figure 1. In (B), we additionally generated 10<sup>4</sup> synthetic signals incorporating neurite–extra-cellular exchange using the NEXI model [https://doi.org/10.1016/j.neuroimage.2022.119277] and an exchange time representative of human cortex (𝜏<sub>ex</sub> ≈ 30 ms) [https://doi.org/10.1162/imag_a_00104].

      We have therefore revised the manuscript language to be more precise and appropriately cautious, describing f<sub>is</sub> and r<sub>s</sub> as apparent compartment indices and explicitly discussing potential confounds (e.g., parameter coupling, and unmodelled exchange), while clarifying the value of SANDI for detecting reproducible group-level microstructural differences in HD.

      (6) Clarify "not-classified" group in figures:

      It is not clear to me what the "not-classified" groups shown in Figures 3-4 represent, what criteria determined their inclusion, and whether their inclusion affects the comparability or interpretability of staging-based analyses

      We have added to the legends of Figures 3 and 4 that not-classified refers to HD participants who could not be HD-ISS classified due to missing clinical data or their CAG repeat falling within the 36-40 range. As correlation analyses were conducted across the whole HD sample though, these datapoints were included in the scatterplot.

      (7) Figure labeling:

      There appears to be a mismatch between figure numbering and captions around Figures 3-4. Please ensure alignment.

      Mismatch between figure numbering and captions has been corrected.

      Minor suggestions:

      (1) Figures 1-2:

      (a) Label axis values meaningfully, e.g., negative vs. positive instead of 0 vs 1.

      (b) Add units to MD axes (e.g., ×10⁻⁴ mm²/s).

      (c) Figure 6 colors: Consider improving the color distinction between "Age" and "fis" predictors, which are currently hard to differentiate.

      The suggested adjustments have been made to Figures 1, 2, 5 and 6 and Figure 2 legend.

      (c) Discuss why apparent soma size decreases in some ROIs (e.g., pallidum), if unexpected.

      We offer the following speculation about the reduced soma size in the pallidum (pages 20/21): Changes in apparent soma size may reflect alterations in neural and glial cell proportions and/or morphology, including astrocyte and microglia swelling in response to neurodegeneration and soma shrinkage preceding neuronal cell death. Thus, increased apparent soma size in the striatum may indicate HD-related reorganisation of cell types driven by MSN loss and reactive glial cell swelling, whereas smaller soma size in the pallidum may result from infiltration of smaller glia cells prior to secondary neuronal loss following striatal MSN degeneration.

      Reviewer #3:

      (1) An important question is whether the SANDI measures, which require an expensive scanner and elaborate processing, are better biomarkers than the more traditional DTI measures. Can the authors compare the effect size of FA/MD with SANDI measures? In some of the plots and tables, FA/MD seem to have comparable, if not higher, correlations with QMotor or CAP scores. On the same vein, it is unclear whether DTI measures were included in hierarchical stepwise regression. I wonder if the stepwise models may have picked up FA/MD instead of SANDI measures if they are given a chance. Overall, I hope the authors can discuss their findings also in this light of cost vs. benefit of adopting SANDI in future studies, which is an important topic for clinical trials.

      Effect sizes (ES) of group differences in all microstructural indices can be found in Table 4. ES of DTI and SANDI indices in the caudate and putamen were broadly comparable with a trend for MD showing larger ES (FA: r<sub>rb</sub> = 0.38 -0.55, MD: r<sub>rb</sub> = 0.51 -0.61, f<sub>is</sub>: r<sub>rb</sub> = 0.32 -0.45, r<sub>s</sub>: r<sub>rb</sub> = 0.45 0.53).

      This information is now reported in the result section on pages 15/16 and is being discussed in light of cost versus benefit considerations on pages 21 and 25.

      (2) Similar to the above point, it is very important to consider how strong the biomarking signal is from SANDI measures compared to the good old striatal volume. Some plots seem to indicate that volumes still have the highest correlation with QMotor and the highest effect size in group comparisons. It would be helpful for the community to know where the new SANDI measures stand compared to the most typically used volumes in terms of effect size.

      Effect sizes (ES) of group differences in volumes can be found in Table 2. ES in caudate and putamen volumes ranged between r<sub>rb</sub> = 0.49 -0.55 and were comparable to the ES of apparent soma size r<sub>rb</sub> = 0.45 -0.53 but slightly larger than ES of soma density r<sub>rb</sub> = 0.32 -0.45.

      This information is now reported in the result section on page 15/16 and is being discussed on pages 21 and 25.

      (3) The diffusion measures are inevitably correlated to some degree. Please provide a correlation matrix in the supplementary material, including all DWI measures, to enable readers to better understand how similar SANDI measures are to each other or vs. other DTI measures. Perhaps adding volumes to this correlation matrix may also be a good future reference.

      We have added cross-correlation matrices between all imaging measures (SANDI, DTI, Volumes) for the total sample as well as for HC and HD participants separately to the Supplementary material (Figure 3), providing an overview of the shared variance within SANDI parameters and between SANDI and DTI and volume metrics for each group.

      (4) ISS stages:

      (a) The online ISS calculator requires cut-offs derived from the longitudinal Freesurfer pipeline, while the authors do not have longitudinal data. Thus, the ISS classification might be inaccurate to some degree if the authors used the FS cross-sectional pipeline. Please review this issue and see if updated cut-offs should be used to classify participants.

      We acknowledge that our HD-ISS classifications may have been biased due to the use of crosssectional rather than longitudinal FreeSurfer v6 volumes (page 23).

      (b) Were there really no participants with ISS 0 among the 56 HD individuals? Please clarify in the manuscript.

      We classified four individuals as ISS 0 based on their caudate and/or putamen z-scored volumes falling below 2SD of the healthy control mean. These analyses are described on pages 14-15 and were based on the cross-sectional data of this study.

      (5) A note on terminology that might be confusing to some readers. According to the creators of ISS, the ISS stages are created for research only; they are not used or applied in the clinic. On the other hand, the terms "premanifest" and "manifest" have a clinical meaning, typically based on the diagnostic confidence level. The assignment of ISS0-1 to premanifest and ISS2-3 to manifest may create some non-trivial confusion, if not opposition, in some segments of the HD community. The authors can keep their current terminology, but will need to at least clarify to the reader that this assignment is speculative, does not fully match the clinically-based categories, and should not be confused with similarly named groups in the previous literature.

      To avoid confusion about terminology, we have removed the labels “premanifest” versus “manifest” throughout the manuscript. We refer to HD-ISS 0-1 and HD-ISS 2-3 when referring to the exploratory comparisons between HD-ISS stages.

      (6) The population in the study seems to be obtained from different other studies or research projects, and there are missing scores for several participants due to the retrospective nature of sample gathering for the analyses. Please state clearly that this study was done with retrospective data to properly justify why there are missing data. Also, and this is important, please clarify for the reader whether there was any temporal bias in the acquisition of data of a certain group (HD) vs. another (HC). It is important to rule out that there were no scanner changes or upgrades that may confound the reported group differences.

      We can confirm there were no Connectom scanner changes or upgrades that may have confounded the reported group differences. This was added to the image acquisition section on page 10. We have added to the participant section on page 9 that data were retrospectively pooled from separate studies and explain this was the reason why HD-ISS classification was only available for a subset of participants.

      (7) Several of the significant results with SANDI scores seem to be driven by a subgroup of HD individuals that are more clearly different than the healthy control distribution. Not sure if this may help, but one idea the authors can consider is to check if HD individuals that deviate more than 2 SDs from the healthy control distribution of SANDI scores have also worse QMotor, worse atrophy, or higher CAP scores than those HD individuals that are practically within the 2SD boundary distribution of HDs. This is another way of showing that the new measures have potential for application in individualized medicine (the MRI Z score of a patient as a proxy of the clinical deterioration). It is not a request to authors but just a suggestion for their consideration.

      The data points in the scatterplots of Figures 3, 4, and 7 have now been color-coded according to HD-ISS stage, showing a stage-related worsening of microstructural and volumetric imaging markers and Q-Motor performance.

      (8) The variance explained in hierarchical regression is obtained by fitting models within the sample, and can be subject to overfitting. In the absence of a more robust cross-validated R2, the authors may want to at least briefly inform the reader that the current approach can be subject to overfitting and does not represent a true out-of-sample R2.

      We have added this point to the study limitations in the Discussion section on page 23.

      (9) There are two Figure 3 labels, and all figures thereafter do not match the manuscript.

      The Figure numbering has been corrected.

      (10) In (the currently labelled) Figure 8, there seem to be fewer than 56 data points in the scatterplots. Is there a reason why not all 56 HD individuals do not have the CAP100 score available? CAP needs only CAG and age, which all HD gene carriers should have, to be included in the study.

      Inclusion criteria for individuals with HD for the HD-DRUM project were a positive genetic test for the presence of the mutant huntingtin allele (CAG length ≥ 36 repeats) and/or a clinical diagnosis of HD. Thus, for a small number of participants CAG was not available for the calculation of CAP100 score.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      The current claims should be better supported by more evidence.

      R1-1: In the first experiment, have the statistics undergone multiple comparison corrections (e.g., Line 441-442)? Given the small sample size, incorporating additional statistical tests (such as the Bayes Factor) could strengthen the analysis.

      We confirm that corrections for multiple comparisons are now applied where appropriate, particularly in the group-level ANOVA analyses.

      “Post-hoc tests using Holm-Bonferroni correction show that V1 neuronal populations receiving inputs from the central visual field (0.5-4.5°) showed greater contrast sensitivity to high spatial frequency as compared to low spatial frequency stimuli (steeper slope for the 3cpd versus 0.3cpd condition: 0.5-2.5º: t(6) = 4.35, p<sub>bonf</sub> = 0.0149; 2.5-4.5º: t(6) = 3.471, p<sub>bonf</sub> = 0.0266). Conversely, peripheral eccentricities in V1 (above 9.5°) showed higher contrast sensitivity to low as compared to high spatial frequency stimuli (steeper slope for 0.3cpd versus 3cpd condition: 9.5-15º: 𝑡(6) = −4.591, p<sub>bonf</sub> = 0.0149; 15-20º: t(6) = −6.615, p<sub>bonf</sub> = 0.0029). Between 4.5° and 9.5°, V1 contrast sensitivity was similar for both spatial frequencies (t(6) = −0.226, p<sub>bonf</sub> = 0.8286). Crucially, these effects remained when using retinotopic estimates based on structural scans derived from the Benson retinotopic atlas instead of the pRF-mapping measures (0.5-2.5º: 𝑡(6) = 5.768, p<sub>bonf</sub> = 0.0059 ; 2.5-4.5º: t(6) = 2.531, p<sub>bonf</sub> = 0.0892 ; 4.5-9.5º: 𝑡(6) = −0.293, p<sub>bonf</sub> = 0.7792; 9.5-15º: t(6) = −3.274, p<sub>bonf</sub> = 0.0509; 15-20º: t(6) = −3.528, p<sub>bonf</sub> = 0.0496; see Figure A2 and Table A3 in Appendix section).”

      “Post-hoc pairwise comparisons using Holm-Bonferroni corrections revealed that, as predicted, the cortical contrast response function had a higher slope – indicating better V1 sensitivity – along the horizontal versus vertical quadrants (Horizontal-Vertical Anisotropy – HVA: 𝑡(6) = 5.908, p<sub>bonf</sub> = 0.0031) and along the lower versus upper quadrant (Vertical Meridian Anisotropy – VMA: 𝑡(6) = 4.106, p<sub>bonf</sub> = 0.0126). Conversely, no difference in cortical contrast sensitivity was found between V1 neuronal populations encoding the left and right quadrants of the visual field (Left-Right Horizontal Meridian Anisotropy – LRHMA: t(6) = 0.7197, p<sub>bonf</sub> = 0.4988).”

      “We found that the horizontal-vertical anisotropy effect was recovered (HVA: t(6) = 3.584, p<sub>bonf</sub> = 0.0347), but that the vertical meridian anisotropy effect was not (VMA: t(6) = 0.744, p<sub>bonf</sub> = 0.9697) with this approach.”

      R1-2a: The authors claim that "structure-based atlases can replace the need for pRF mapping in cases where it might otherwise be difficult or impossible to collect pRF data." This claim needs further scrutiny. Currently, only one simulated condition of visual field loss was examined in one subject.

      AR-R1-2a: We agree that further work is needed to fully establish the utility of structure-based atlases. As a first step, we have followed the reviewer’s suggestion and collected an additional dataset from one of the seven participants, in whom we simulated another condition of visual field loss – specifically, loss of the upper right quadrant. This participant is the same individual already presented in the manuscript (C5), but with a different simulated vision loss condition.

      This new condition has been introduced in the Methods, Results and Discussion section, and a new Figure 10 alongside Figure 9 which showed the 3º-8º scotoma. With relevant changes as follows:

      “We also demonstrate the clinical relevance of this approach by recovering simulated scotomas (i.e., a ring of visual field loss around fixation and the loss of an entire visual field quadrant), as well as visual field loss in a patient with a neurodegenerative disorder causing large areas of visual field loss.”

      “Additionally, one participant (C5) repeated the task under two simulated vision loss conditions (ring or quadrant loss), and two others (C5, C6) completed it with different levels of eye movement.”

      “Simulated vision loss

      One healthy control participant (C5) also performed a version of the task designed to simulate two forms of visual input loss (i.e., artificial scotoma). These simulations were implemented by: (a) masking a region of the visual field with a grey, annular ring, covering 3º-8º eccentricity, and (b) masking the upper right visual quadrant using a grey quarter-sector overlay. The stimuli and contrast levels used in this task were identical to those described in the original task.”

      “A test-case of simulated loss of visual inputs

      In the previous sections, we showed that the slope of a square root function provides a reliable measure of contrast sensitivity in the brain of healthy controls. But can this brain-level model also quantify loss of visual inputs? To test this, we first simulated an artificial scotoma in one normal sighted participant, by (a) masking a region of the visual field with a grey, annular ring, covering 3°-8° eccentricity (Figure 9A), and (b) masking the upper-right visual quadrant using a grey quarter-sector overlay (Figure 10A). We expect smaller slope values in V1 neuronal populations that would under normal circumstances encode that part of the visual space.

      As expected, we observed reduced responses in V1 locations corresponding to the artificial scotoma (Figures 9 and 10), with increased responses along the edges of the mask for the ring scotoma condition (Figure 9B). This artificial loss of visual input was also clearly present in the cortical contrast sensitivity estimate, with significantly reduced slope steepness in V1 between 3-8° for the ring scotoma condition (Figure 9C&D) and in the upper-right quadrant for the quarter-sector scotoma condition (Figure 10B&C). Additionally, we could recover this scotoma using the calibrated Benson template, although less accurately (Figures 9E and 10D). These results show that this measure of V1 contrast sensitivity is sensitive enough to detect loss of visual inputs in the brain at an individual level, when a complete local loss of sight is simulated, and that this approach does not crucially rely on pRF mapping data from the individual. This supports the utility of our approach in recovering patterns of vision loss and recovery at a cortical level.”

      “Mapping Simulated and Pathology-Driven Vision Loss

      Our method successfully identified both simulated retinal loss in a healthy volunteer and real visual field loss in a patient with Leber Hereditary Optic Neuropathy (LHON). The signal drop observed in response to masking portions of the visual field in the healthy control was both large and significant at the individual level, as demonstrated by non-overlapping 95% confidence intervals (Figures 9B-C and 10B). This provides proof-of-concept evidence that our approach can detect signal changes in individual patients, which is a critical requirement for clinical translation.

      Unlike previous fMRI studies that used high-contrast stimuli (Farahbakhsh et al., 2022; Pawloff et al., 2023; Ritter et al., 2019), which may not accurately represent partial vision loss due to potential saturation effects and the stimulation of less sensitive retinal cells, our use of multiple contrast levels offers a more nuanced assessment of cortical contrast sensitivity.

      Combined with the large-field set-up allowing stimulation up to 20° eccentricity, this approach may be particularly well-suited for evaluating treatment efficacy in cases of widespread and variable vision loss.

      Future work will focus on further validating reconstruction accuracy under controlled conditions, including simulated scotomas of varying severity and location, expanding testing to larger patient cohorts, and establishing a normative dataset to contextualize patient data.

      R1-2b: Also, in Figure 7, contrast sensitivity in the periphery differs between pRF mapping and the Benson atlas. How do the authors explain this discrepancy?

      AR-R1-2b: The discrepancy in periphery between pRF mapping and Benson atlas is caused by various factors. These include (a) individual differences in the retinotopy/structure relationship that are not captured in the template, (b) the fact that the Benson atlas at larger eccentricities was obtained with hemifield stimulation, and (c) a larger impact of any inaccuracies at larger eccentricities because of cortical magnification. As a result, peripheral vertices are more likely to be mis-assigned by the template than central ones. Note that this adds distortion in cortical visual field maps which will be consistent across timepoints (rather than noise). Critically, a reduction in accuracy does not preclude utility if meaningful differences in spatial patterns in cortical sensitivity can still be recovered, as is the case in our data. We cover this in the discussion.

      “Particularly at large eccentricities however, we initially observed inaccuracies between the template and individual retinotopy eccentricity estimates which led to substantial distortions in cortical visual field maps due to cortical magnification (see Figure A4 in Appendix section). To address this, we adjusted the Benson eccentricity estimates to align with the cortical magnification scaling function (Horton & Hoyt, 1991).”

      “Beyond ROI considerations, we still observed differences in cortical sensitivity between pRF mapping and the adjusted Benson atlas - particularly in the periphery. Several factors likely contribute to this. First, individual differences in the relationship between cortical structure and retinotopy are not fully captured by the template. Second, the Benson atlas has never been fit with empirical data more eccentric than approximately 20°, which naturally limits its precision in the far periphery. Third, because of cortical magnification, any small inaccuracy at larger eccentricities has a disproportionately large effect, making peripheral vertices more susceptible to mis-assignment than central ones. These influences introduce systematic distortions in cortical visual field maps rather than random noise and thus remain consistent across time points - an important point when assessing longitudinal changes (e.g., ageing or gene-therapy interventions). Importantly, the spatial gradients in cortical contrast sensitivity were preserved across both the pRF and Benson atlas approaches, indicating that minor ROI differences do not affect our conclusions. Together, these findings show that the Benson Atlas remains a useful alternative when pRF mapping is not feasible.

      R1-3: Overall, the writing could be significantly improved.

      AR-R1-3: We have made edits throughout the manuscript and hope this has improved the writing.

      Reviewer #1 (Recommendations for the authors):

      R1-Recommendation 1a: The writing can be significantly improved for clarity.

      The introduction section is not well-organized, and the motivation for developing the current method (Paragraphs 2-3) is vague and lacks adequate documentation.

      Several references are missing (e.g., Lines 90-92) or incorrectly placed (e.g., Lines 108-109).

      AR-R1-Recommendation 1a: We have revised the Introduction to clarify the motivation for developing the current method and to correct missing or misplaced references.

      “Still, testing visual function across the visual field remains limited in clinical and therapeutic contexts, especially in patients with drastic central vision loss. In this study, we aimed to address this gap by introducing a novel fMRI-based approach to measure visual field sensitivity across a wide expanse of the visual field (40º diameter).”

      “Beyond visual acuity, functional impairment across the wider visual field can be measured using a range of visual field tests, from the finger counting visual confrontation field test to more complicated and/or computerized tests (e.g., standard automatic perimetry, kinetic perimetry, microperimetry; Rai et al., 2024). Computerized tests typically involve measuring sensitivity to the luminance contrast of a target relative to a background at different visual field locations while the participant’s gaze is fixed on a central point. In some cases (e.g., microperimetry), sensitivity measurements are paired with fundus imaging, offering greater precision in linking visual field functions to specific retinal locations (Rai et al., 2024). As a result, visual field assessments can reveal functionally relevant deficits – including localized sensitivity loss and scotomas – that are not captured by foveal acuity alone, and are therefore potentially valuable for tracking disease progression and therapeutic efficacy.

      Despite their clinical relevance, visual field testing comes with challenges and limitations, and as a result, the inclusion of visual field measures in sight-rescuing therapy trials is limited. Firstly, it requires prolonged fixation and sustained visual attention. This can be very challenging for patients with severe vision loss, who often struggle to fixate, and strain to detect even high intensity stimuli. This can lead to long and unpleasant testing sessions with unreliable results. Secondly, as perception of light stimuli is inherently subjective (Rai et al., 2024) and effortful, patients may vary in their criteria for visual recognition, and in their ability to report visual signals that are weakened or distorted by disease. Together, these constraints reduce the feasibility, robustness, and interpretability of conventional visual field testing in clinical trials, underscoring the need for alternative or complementary approaches that can assess functional vision while placing fewer demands on subjective reporting.”

      “Functional MRI (fMRI) has recently been proposed as a promising alternative to measure visual field loss, as it requires no overt task, and instead measures visual sensitivity directly from brain responses (Farahbakhsh et al., 2022; Prabhakaran et al., 2021; Ritter et al., 2019). Population receptive field (pRF) mapping fMRI can measure which parts of the cortex respond to which parts of the visual scene (Dumoulin & Wandell, 2008).”

      “Finally, most studies use a single maximum contrast stimulus to assess visual function (Broderick et al., 2022; Farahbakhsh et al., 2022; Liu et al., 2006; O’Connell et al., 2016; Ritter et al., 2019).”

      R1-Recommendation 1b: The strengths of the current method and its applicable scenarios are unclear. For example, in Lines 39-40: "We developed an fMRIbased approach to measure contrast sensitivity across the visual field without the need for precise fixation." To what extent can fixation be imprecise? Could this protocol be applied to patients with strabismus, who have biased fixation?

      AR-R1-Recommendation 1b: We agree with the reviewer that the tolerance to fixation challenges is key here and so we collected additional data to respond to your points regarding the effects of eye movement on the cortical contrast sensitivity maps.

      In terms of biased fixation, the approach should be very robust to this, as this would just reduce the cortical visual field covered on one side and extend it on the other.

      We collected new data to test the tolerance to fixation instability across a wide range of eye movement, including severe nystagmus-level movement. Despite large eye movements, the cortical contrast-sensitivity pattern remained largely consistent, though extreme movements reduced slope estimates and flattened the cortical sensitivity pattern for 3cpd, indicating reduced measurement sensitivity for extreme eye movement to high spatial frequency gratings.

      These additions have been incorporated into the Abstract, Methods, Results, and Discussion sections as follows:

      Abstract

      “To assess the method’s tolerance to fixation variability, we further investigated how different levels of eye movement affect cortical sensitivity patterns in two participants. We found that cortical sensitivity patterns were largely preserved across eye movement, particularly at low spatial frequencies. This suggests that our approach can accommodate several degrees of fixation instability, making it suitable for populations with unstable or biased fixation for whom visual field maps are harder to acquire behaviorally (e.g., patients with dense central scotoma or strabismus).”

      Methods

      “Additionally, one participant (C5) repeated the task under two simulated vision loss conditions (ring or quadrant loss), and two others (C5, C6) completed it with different levels of eye movement.”

      Results

      “Effect of eye movement

      Participants C5 and C6 also performed a version of the task designed to test the effect of eye movements. In this version, saccades were elicited by randomly and rapidly shifting the fixation dot away from central fixation (C5: 2º and 5º from fixation and random motion; C6: up to 2º from fixation). Participant C5 was tested using 0.3 and 3cpd gratings at four contrast levels (7.5, 42.2, 60, 100%), while participant C6 was tested only under the low spatial frequency condition (0.3cpd).

      Fixation stability was assessed for each fMRI run using the bivariate contour ellipse area (BCEA), which estimates the area (in degrees<sup>2</sup> or arcmin<sup>2</sup>) of an ellipse that contains approximately 95% of fixation points. BCEA was calculated using the formula: , as described by Morales et al. (2016). In this expression, σ<sub>h</sub> and σ<sub>v</sub> represent the standard deviations of eye position in the horizontal and vertical directions, respectively, while p corresponds to the Pearson correlation coefficient between horizontal and vertical eye positions. The constant k determines the size of the ellipse based on the desired probability area, defined by the relationship P =1 – e<sup>-k</sup>, with P set to 0.95 in this study. A smaller BCEA indicates greater fixation stability.

      “Effect of eye movements on V1 cortical sensitivity

      So far, we have demonstrated that our measure of cortical sensitivity can reliably recover known gradients in sensitivity across eccentricities and visual quadrants. We also showed that this measure was consistent across visits and sessions, suggesting its potential utility for monitoring changes over time. However, all prior tasks were conducted under conditions of central fixation, with participants instructed to maintain gaze on a central dot. A key motivation for this approach was its theoretical robustness to fixation instability. We therefore also aimed to investigate how varying degrees of eye movement might influence cortical sensitivity across the visual field.

      To address this, two participants (C5 and C6) completed a modified version of the contrast sensitivity task in which they made eye movements either by following a dot moving randomly at a radius of 2º or 5º around fixation, or by self-initiated very large eye movements. Eye movements across these or by self-initiated very large eye movements. Eye movements across these conditions (Figure 7, bottom row; Figure 8, bottom row), were quantified using BCEA (C5 – Central fixation: mean±SD = 0.57±0.11 deg<sup>2</sup>, 2º eye motion: 2.69±0.48 deg<sup>2</sup>, 5º eye motion: 20.3±1.32 deg<sup>2</sup>, random eye motion: 133.7±23.36 deg<sup>2</sup>; C6 – Central fixation: 0.96±0.56 deg<sup>2</sup>, 2º eye motion: 1.28±0.15 deg<sup>2</sup>). For reference, in severe (idiopathic) nystagmus, the eye movement variability along the vertical and horizontal planes is on average 1.08 deg and 1.60 deg, respectively (Tailor et al., 2021). Assuming a moderate correlation between axes (p = 0.3), the average fixation stability would equate to a BCEA of ~21.46 deg<sup>2</sup> (i.e., ~5º eye motion condition in our data).

      Despite these very large levels of eye movements, we observed that the overall cortical contrast sensitivity spatial pattern across eccentricity remained remarkably consistent (Figure 7, top and middle rows; Figure 8, top row). However, at the most extreme movements, contrast sensitivity estimates (slope values) were lower; and while the overall cortical visual field map structure was still clearly present for low spatial frequencies, it appeared more flattened for 3cpd, suggesting reduced sensitivity of our measure for large eye movement and high spatial frequency stimuli.”

      Discussion

      “Crucially, one advantage of cortical visual field mapping is that the maps are inherently centered on the foveal confluence, providing a stable reference point for comparing responses across eccentricities. When combined with large-field, spatially homogeneous stimuli, this anchoring means that our approach should remain robust to moderate fixation variability and still quantify sensitivity changes across the visual field – provided that fixation instability does not exceed the stimulus extent (40º diameter).

      When measuring the impact of eye movements, we found that spatial sensitivity patterns were largely preserved, even for extreme eye movements (emulating severe nystagmus). However, under the most extreme conditions, sensitivity estimates (i.e., slope values) were reduced, especially for high spatial frequency (SF) stimuli. This likely reflects image blurring from large rapid eye movements, which degrades high-SF inputs and shifts activation toward neurons tuned to lower SFs. This aligns with evidence that nystagmus and large saccades impair perception of fine detail and grating stimuli due to retinal image slip (Abadi & Bjerre, 2002; Dickinson & Abadi, 1985; Hertle et al., 2017; Randall et al., 2020). While classic findings report suppression of low-SF signals during saccades (Burr et al., 1994; Ross et al., 2001), our results suggest that high SF sensitivity may be more vulnerable to large eye movements when participants are presented with 2Hz phase-flickering gratings. Further validation in clinical groups with naturally-occurring fixation instability would further strengthen these conclusions.”

      R1-Recommendation 1c: There are also some confusing descriptions, such as Lines 130-132.

      AR-R1-Recommendation 1c: We have also clarified ambiguous descriptions of the Benson atlas templates.

      “We therefore also evaluated the approach using the structure-based atlas of retinotopic values developed by Benson et al. (Benson et al., 2014; Benson & Winawer, 2018). This atlas predicts retinotopic organization by aligning individual cortical anatomy (e.g., surface curvature) to a group-average template that incorporates an algebraic model of retinotopy (Benson et al., 2014). Once the subject’s brain is aligned to this structural atlas, retinotopic maps defined by the model – i.e., polar angle and eccentricity maps – are projected onto the individual’s cortex. This allows estimation of visual field maps without requiring functional imaging, and provides a non-invasive, anatomy-driven approximation of visual field representations.”

      R1-Recommendation 1d: Line 361: "Assessing the brain's ability to discriminate shapes"-is the author referring to the functional relevance of contrast tuning assessment here? Since the task or stimuli are not related to shapes, this description is unclear.

      AR-R1-Recommendation 1d: We have revised the reference to “discriminating shapes” to more accurately reflect the functional relevance of contrast sensitivity mapping.

      “To measure visual field function, we developed a new measure of cortical contrast sensitivity, assessing the brain’s ability to discriminate gratings of varying spatial frequencies based on luminance variations.”

      R1-Recommendation 2a: Simulated visual loss experiment: only one condition of visual field loss was examined in a single subject. I encourage the authors to include additional subjects to meet statistical test criteria at group level. Simulated scotomas in more visual quadrants, including both central and peripheral areas, should be examined, as asymmetries may exist.

      AR-R1-Recommendation 2a: We agree that it is important to verify that the approach can also capture other types of scotomas. We have therefore now incorporated another simulated condition of visual field loss, namely loss of the upper right quadrant.

      Regarding adding more participants: The drop in signal is clearly large and significant at the individual level (error bars corresponding to 95% confidence interval do not overlap; Figures 9B-C & 10B). The ability to detect signal change at the individual level is what we need for clinical application, and here we are showing proof-of-concept of its feasibility with our approach. However, we do appreciate that it might be valuable to test cortical visual field loss reconstruction accuracy with simulated scotomas of varying levels of vision loss in variable locations. We now highlight this as a future direction.

      Please refer to our response to R1-2a, where we also detail the corresponding changes made in the manuscript.

      R1-Recommendation 2b: Additionally, why do the results from pRF mapping and the corrected Benson atlas differ, particularly in the far periphery?

      AR-R1-Recommendation 2b: Please refer to our response to R1-2b, where we also detail the corresponding changes made in the manuscript.

      R1-Recommendation 3: To validate the recovery of visual field loss in the case study, it would be necessary to include fundus imaging to characterize the structural loss and correlate it with the behavioral and fMRI results.

      AR-R1-Recommendation 3: We included Compass perimetry data for the LHON patient, which is fundus-tracked perimetry and uses fundus imaging to keep the visual stimulation fixed to retinal locations.

      In the context of LHON, the fundus image is not expected to provide more information than perimetry. This is because the visual deficit in LHON arises from optic nerve dysfunction, and retinal abnormalities are typically minimal. Aside from the characteristic pallor of the optic disc, the fundus appearance is usually normal in appearance.

      For illustration, Author response image 1 shows the Compass-acquired fundus image from the LHON patient included in this study. For comparison, we also show a normal fundus image from a 25-year-old male volunteer, reproduced from Häggström, Mikael (2014). "Medical gallery of Mikael Häggström 2014". WikiJournal of Medicine 1 (2). DOI:10.15347/wjm/2014.008. ISSN 2002-4436. Public Domain.

      Author response image 1.

      We do, however, recognize the importance of linking functional changes to structural alterations (e.g., retinal thickness measured with OCT), and we now highlight this as a key future direction in the discussion. This will be a central focus of a planned follow-up study involving a larger patient cohort.

      “Next steps in this work will therefore involve testing larger patient cohorts with diverse forms of vision loss, validating the approach for tracking pathology over time, and investigating how cortex-based visual field measures relate to and complement other visual field and retinal integrity indices including Compass measures and OCT-derived retinal layer thickness.”

      “Additionally, linking brain-based variations in function across the visual field to behavioral performance (e.g., perimetry, microperimetry) and retinal structure (fundus imaging, retinal thickness from Optical Coherence Tomography), could help bridge the gap between neural measures and functional outcomes. Such integration would provide deeper insights into developmental, learning, and vision loss mechanisms.”

      R1-Recommendation 4a: Why is a 0.5 mm smoothing applied to the contrast task data?

      AR-R1-Recommendation 4a: We have now clarified in the Methods section. This 0.5 mm FWHM smoothing kernel was applied to the contrast sensitivity task data to meet the minimum requirements of the GLM module in SPM.

      “To accurately capture neural activity across various eccentricities and polar angle locations, minimal smoothing (0.5mm FWHM Gaussian blur) was applied to the contrast sensitivity task data using FSL’s 3dmerge program. This was done to meet the minimum requirements of the GLM module in SPM.”

      R1-Recommendation 4b: Is this the first time the cortical magnification calibration has been applied to the Benson atlas? I recommend including a figure to describe this method.

      AR-R1-Recommendationn 4b: This is indeed the first time this correction has been applied to the Benson atlas. We have now added a figure (Figure 3) to illustrate the eccentricity adjustment procedure applied to the Benson atlas.

      R1-Recommendation 5: In Figure 5, the test-retest reliability can be reported by including r-values.

      AR-R1-Recommendation 5: We have now included Spearman correlation 𝜌-coefficients for test-retest and between-condition comparisons in Figure 6 (previously Figure 5).

      R1-Recommendation 6: Inconsistency in the reporting format of statistical values: e.g., the degrees of freedom are presented with, or without parentheses.

      AR-R1-Recommendation 6: Thank you for pointing this out. We have reviewed and standardized the reporting format of all statistical values throughout the manuscript to ensure consistency. Degrees of freedom are now all presented with parentheses, in details:

      “Using ANOVA, we found the expected interaction between spatial frequency and eccentricity (F(1.96,11.79) = 28.66, p < 0.001; Figure 4) as well as a main effect of eccentricity (F(2.33,13.99) = 12.67, p < 0.001).”

      “We found a main effect of visual field quadrant location on V1 sensitivity (F(2.46,14.76) = 20.71, p < 0.001).”

      “Moreover, there was no interaction between spatial frequency and (F(2.16,12.99) = 1.34, p = 0.298), visual field quadrant positions suggesting V1 visual field anisotropies are relatively constant across spatial frequencies.”

      Reviewer #2 (Public reviews):

      R2-1a: Questionable sensitivity to differences in patients. The variability in heat maps across healthy control participants is somewhat surprising. Do differences between individuals represent actual visual sensitivity differences, or are they an artifact of the measurement technique, e.g., due to signal-to-noise differences introduced by local variations in brain anatomy? Will the substantial variance across controls allow for a sufficiently stable baseline to detect meaningful differences in individual patients?

      AR-R2-1a: We agree the variability across healthy controls is surprising. It is unclear whether this reflects true individual differences in visual sensitivity or arises from factors like local signal-to-noise introduced by local variations in brain anatomy. It will be really interesting to investigate this further by examining structural variations across the visual field and comparing them with behavioral measures.

      As for establishing a stable baseline for patient comparisons, this is inherently an empirical question and depends on the degree of vision loss. LHON patients typically show dense central scotomas (up to 15º) in the chronic phase, making them well suited for detecting sensitivity differences – e.g., between central versus peripheral locations. Detecting subtler changes – in the acute phase or other conditions – may be more challenging. We agree with the reviewer that a normative range will be essential for contextualizing patient data, which we now mention in the Discussion, and we aim to develop in the future based on the present data.

      “Future work will focus on further validating reconstruction accuracy under controlled conditions, including simulated scotomas of varying severity and location, expanding testing to larger patient cohorts, and establishing a normative dataset to contextualize patient data.”

      R2-1b: Also, as the authors rightly point out, Benson atlas does not model differences along meridians, so upper/lower field differences might not be detectable.

      AR-R2-1b: We acknowledge the limitations of the Benson atlas, particularly its inability to model meridional asymmetries (e.g., upper vs. lower visual field). Still, our goal is to provide a method for tracking visual cortex changes over time. By consistently projecting longitudinal functional data onto the same structural image fitted with the Benson atlas, we maintain a stable anatomical reference, which supports reliable comparisons across timepoints – even with limited spatial accuracy. Future improvements could include shearing corrections, Bayesian updating, or alternative models such as DeepRetinotopy developed by Ribeiro et al.

      “Further enhancing the alignment between retinotopic template atlases and individual retinotopic tuning could improve this approach further, for example, by integrating them with functional measures using Bayesian methods (Benson & Winawer, 2018). In parallel, geometric deep learning frameworks such as DeepRetinotopy (Ribeiro et al., 2021) could also offer anatomy-driven predictions from structural MRI, and combining these strategies may yield more accurate and generalizable retinotopic reconstructions.”

      R2-2: Effects of unstable fixation/eye movements not explicitly tested: The methods state, 'In all tasks, participants were asked to report when the color of a central fixation dot changed', suggesting participants maintained fairly good fixation. Most of the results seem to pertain to measurements where central fixation is required. How does unstable fixation affect measurements?

      AR-R2-2: This is an important point. We have now extensively and systematically investigated the impact of eye movements on the cortical contrast sensitivity maps and updated the Abstract, Methods, Results, and Discussion sections (see R1-1b).

      R2-3: Potential for clinical translation. Although it is a sensitive measure, functional MRI is costly, is not available in all clinical settings, requires significant post-processing analyses, and may be contraindicated in some individuals due to safety (e.g., metallic implants) or other concerns (e.g., claustrophobia). These could present significant barriers to widespread clinical translation if this were the ultimate goal of the study.

      AR-R2-3: We agree that fMRI, while sensitive, has practical limitations for broad clinical adoption due to cost, accessibility, and contraindications. However, it remains a valuable tool in targeted contexts, where sensitive detection of visual field loss has large utility – for example for evaluating treatment effects in clinical trials. This application has been demonstrated in recent studies (Farahbakhsh et al., 2022; Maimon-Mor et al., 2025; Haal et al., 2016; Ritter et al., 2019).

      R2-4: Limited range of spatial frequencies. The spatial frequencies tested were still quite low (0.3 and 3cpd) compared to measures such as visual acuity. Extending the measurements to higher spatial frequencies could allow better characterization of central vision, although necessarily for peripheral vision.

      AR-R2-4: We agree that extending to higher spatial frequencies could improve central vision characterization and note this can be readily incorporated into future studies using the current framework. However, LHON patient’s acuity tends to be very low, and we found that 5cpd did not allow us to measure any cortical contrast sensitivity in a prior pilot. So, to characterize the visual field in LHON with fMRI, we therefore aimed to balance central and peripheral coverage: 0.3 cpd ensured broad detectability, while 3 cpd offered a middle ground to assess central vision without exceeding acuity of this population. Additional approaches, such as neural contrast sensitivity functions (e.g., Roelofzen et al., 2025) may also offer complementary insights such as acuity, and contrast sensitivity across the full spatial frequency range (area under the curve).

      Reviewer #2 (Recommendations for the authors):

      R2-Recommendation 1: It appears that the reliability measures, comparing differences in Spearman correlations between and within sessions, were not tested statistically, but evaluated qualitatively. What was the justification for this? The results only state Spearman values, but the discussion claims that the differences between the two comparisons were significant.

      AR-R2-Recommendation 1: The differences in Spearman correlations between and within sessions were tested statistically, and the omission of p-values was an oversight. We have now revised the Results section results from the paired one-tail t-test as follows:

      “We collected test-retest reliability measures from 4 out of 7 participants (Figures 6A-B) and benchmarked them against the correlations between the 0.3cpd condition and 3cpd spatial frequency condition, collected in the same session (Figure 6C). If measures are reliable, correlations should be higher for repeated measures with the same spatial frequency stimulus, collected on different days. We tested this prediction using a one-tailed paired t-test.”

      “This difference was statistically significant (t(3) = 2.62, p < 0.0395).”

      R2-Recommendation 2a: The variability of heat maps (visual field sensitivities) between healthy controls should also be discussed. What are potential explanations for this variability?

      AR-R2-Recommendation 2: We have expanded the Discussion section to address the variability observed in cortical sensitivity maps across healthy controls.

      “We also observed intriguing variability in cortical visual field maps across healthy controls, and this variability was consistent across measures. This may reflect genuine individual differences in visual sensitivity that are relevant for behavioral performance. Alternatively, it could arise from factors such as local signal-to-noise differences driven by anatomical variability. However, the fact that maps derived from different spatial stimulus conditions showed markedly different patterns argues against a purely anatomical explanation and suggests that at least part of the variability is functional. Despite this inter-subject variability, variations in cortical contrast sensitivity across eccentricities and visual field quadrants were significant at the individual level indicating high sensitivity.”

      R2-Recommendationn 2b: There should also be more discussion about any potential effects of eye movements/unstable fixation in order to address the suitability of the methods for these clinical populations.

      AR-R2-Recommendation 2b: Please refer to our response to R2-2, where we also detail the corresponding changes made in the manuscript.

      Reviewer #3 (Public review):

      R3-1: The authors should more strongly emphasize their findings on the organization of contrast sensitivity, particularly in light of the stimulation extent provided by the wide-field setup.

      AR-R3-1: Thank you for this important point – we have now emphasized more clearly in the manuscript that our method extends the measurement of contrast sensitivity to 20º eccentricity, which represents a significant advancement over previous studies.

      “These results demonstrate that our approach can detect subtle changes in visual sensitivity across eccentricities at the individual participant level. The ability to reveal these gradients was made possible by the large peripheral coverage provided by our large-field stimulation set-up (see Figure A1 in Appendix section), which enabled a more complete characterization of V1 sensitivity across the visual field. Importantly, the same effects were preserved when using retinotopic estimates derived from structure-based atlases, demonstrating that atlas-based methods can be used as alternative to pRF mapping in cases where it might otherwise be difficult or impossible to directly collect pRF measures. Together, these highlight both the validity of our approach and its potential to broaden the scope of visual neuroscience.”

      “Crucially, the ability to visualize these sensitivity gradients was made possible by the large peripheral coverage provided by our large-field stimulation set-up. Such coverage is particularly important for clinical applications, as it enables the detection of visual field losses beyond the macula (i.e., beyond 10º eccentricity) and the evaluation of residual peripheral vision in patients with macular-restricted damage. In doing so, this work provides a useful tool for advancing both basic visual neuroscience and translational research in clinical populations.”

      R3-2: Certain methodological aspects require further clarification, particularly regarding the correction of eccentricity values from the Benson atlas. It's not clear which V1 masks are used for the specific analysis which could have a substantial impact on the reported differences between the two approaches of pRF mapping and atlas-based pRF parameters.

      AR-R3-2: The correction of eccentricity values was performed using the V1 label provided by the Benson atlas. We have now explicitly stated this in the Methods section:

      “We collected data from 7 healthy controls (mean±SD: 29.6±4.7yo; 1M). All controls either had normal or corrected to normal vision, with no other ocular pathologies, and were recruited from the local staff and student pool at the University College of London. Each control completed both the population receptive field (pRF) mapping and the fMRI contrast sensitivity task. To assess measurement repeatability, four participants (C2, C4, C5, C6) performed the contrast sensitivity task twice. Additionally, one participant (C5) repeated the task under two simulated vision loss conditions (ring or quadrant loss), and two others (C5, C6) completed it with different levels of eye movement.”

      “Four participants (C2, C4, C5, C6) were invited for a second session in which they repeated the task to assess the reliability of the measures.”

      R3-4: The conclusion that high-contrast patterns as in pRF mapping are not optimal to test for subtle but potentially clinically relevant changes in the visual field coverage is very valid. The suggested use of contrast sensitivity can therefore be a potentially well-suited parameter for estimating visual field losses. The presented work is an interesting starting point and the proposed method of using contrast sensitivity as a measure for partial vision loss should further be explored.

      AR-R3-4: Thank you for the positive evaluation of our work.

      Reviewer #3 (Recommendations for the authors):

      R3-Recommendation 1: The shown organization of contrast sensitivities is consistent with previous studies; however, it extends the measurements to up to 20º eccentricity, which is, to my knowledge, much more than previously reported. The authors should therefore emphasize this more strongly.

      AR-R3-Recommendation 1: Please refer to our response to R3-1, where we also detail the corresponding changes made in the manuscript.

      R3-Recommendation 2: In the Methods section, it is not entirely clear why the eccentricity values originating from the Benson atlas need to be corrected using Horton & Hoyt cortical magnification. Do the authors consider these cortical magnification measurements as ground truth? Is the correction only applied to higher eccentricity values that are not mapped by the Benson atlas?

      AR-R3-Recommendation 2: The Benson et al. (2014) atlas predicts both polar angle and eccentricity from cortical anatomy (curvature, thickness) using a template pRF dataset and a mathematical retinotopic model. However, it does not incorporate a smooth parametric cortical magnification function such as Horton & Hoyt. Because the atlas is fit to an average map across subjects, and because the FreeSurfer alignment used to apply the template cannot incorporate functional information, the atlas cannot capture individual variability in eccentricity or cortical magnification. In practice, we therefore treat the Benson atlas as providing the correct topological layout of eccentricity, but not necessarily the correct eccentricity values for a given individual. Moreover, the data used to generate the Benson atlas have mainly been restricted to the central visual field (roughly 8º-12º) and the Benson atlas themselves has never been fit with data more eccentric than 20º. Consequently, peripheral eccentricity values are more model-driven and less constrained by ground-truth data.

      To improve the correspondence between the atlas and expected cortical representations, we applied Horton & Hoyt cortical magnification function to all eccentricities in the V1 Benson mask (from the foveal confluence to the periphery, up to 90º). We assume that the Horton & Hoyt model, adapted from physiology data, provides an accurate model of group level cortical magnification (Benson et al., 2021) – even though it does not capture individual differences. This means it offers the best approximation of ground-truth in the absence of individual pRF data, which is often not feasible to collect in patients with unstable fixation. We have now added a figure that showcases the method and shows how this correction affects the distribution of eccentricity values in the Benson atlas.

      R3-Recommendation 3: For the analysis using the atlas-based retinotopy, it is not entirely clear whether the authors also use the provided V1 masks. In other words, differences between the original pRF-based and atlas-based analyses could originate from different borders of V1 rather than from the atlas-based pRF parameters. The authors could try using the same mask for both analyses, either the manually delineated one or the atlas-based one.

      AR-R3-Recommendation 3: This is a well-noted point that is important to clarify. We used a manually delineated V1 mask for the own pRF map data and the Benson mask for the adjusted Benson atlas-based analysis – both restricted to the screen size. The difference in included vertices could have indeed introduced some additional error beyond the atlas/pRF mapping itself. We have opted not to correct this in this version of the manuscript because (1) the error introduced is likely small (as we inspected that the alignment of V1 ROI delineations with the Benson ROIs are good, so effects are likely not too major - although using identical masks may slightly improve the mapping further in particular the very center and outer-periphery), and (2) our ROI selection for each respective approach is in line with typical procedures used in reality. Critically, the spatial gradients in cortical contrast sensitivity are preserved across the pRF and Benson atlas approach with the different ROIs, so we believe that improvements would not alter our conclusions that Benson offers a useful alternative when pRF mapping is not possible - however, we now highlight this important difference across the two approaches in the paper.

      “With this structure-based atlas, we successfully replicated key variations in visual field function (across eccentricity and polar quadrants), although sensitivity to more subtle differences (e.g., upper versus lower quadrant anisotropy) was reduced. This reduction may partly stem from differences in ROI definitions: a manually delineated V1 mask was used for the pRF-based data, while the Benson atlas mask was used for the adjusted Benson atlas analysis. Such differences could introduce minor error beyond the atlas/pRF mapping itself due to differences in the vertices included by each mask.”

      “Importantly, the spatial gradients in cortical contrast sensitivity were preserved across both the pRF and Benson atlas approaches, indicating that minor ROI differences do not affect our conclusions. Together, these findings show that the Benson atlas remains a useful alternative when pRF mapping is not feasible.”

      R3-Recommendation 4: The patient was measured monocularly. Given the widefield stimulation setup and the fact that the blind spot is located at about 15º eccentricity, do the authors expect to measure this blind spot with the given setup?

      Does this have an influence in binocular measurements?

      AR-R3-Recommendation 4: This is an interesting point. In theory, our wide-field setup could allow for the detection of the blind spot, as located around 12-15º eccentricity. However, in our LHON patient, the visual field defect typically extends to or beyond the blind spot, making it difficult to isolate its boundary, as shown in Figure 11 (previously Figure 7). Additionally, under binocular viewing, the brain integrates inputs from both eyes to create a unified percept, which may obscure blind spots unless specific paradigms are used (e.g., binocular rivalry or dichoptic tasks). Whilst this is outside the scope of this work, our setup could be adapted to map out the blind spot or explore phenomena like binocular rivalry more directly in future research.

      R3-Recommendation 5: How stable is the presented wide-field stimulation setup? In other words, does the eye tracker still capture the eye reliably after small head movements?

      AR-R3-Recommendation 5: While small head movements can occur, these were minimized by the use of padding cushions and monitored throughout the session, and the eye tracker maintained reliable tracking throughout the sessions.

      R3-Recommendation 6: Are the shown sine-wave gratings always oriented the same? We would expect orientation tuning curves in the early visual cortex; how could this influence the results?

      AR-R3-Recommendation 6: For six of the seven control participants (C1-C6), the sinewave gratings were presented with a fixed horizontal orientation. In an updated version of the task – used for participant C7, cases of simulated eye movements, cases of artificial scotoma, and the patient – the orientation of the gratings was varied every 5 seconds among four angles (−45º, 0º, 45º, 90º) during each 15-second stimulus block.

      We acknowledge that orientation tuning in the early visual cortex could influence responses, since V1 neurons are selective for specific stimulus orientations and respond most strongly to their preferred orientation. However, we replicated the same overall pattern of results in groups tested with a single orientation and with multiple orientations. Importantly, some participants completed both versions of the task, and the contrast sensitivity patterns remained consistent across conditions. This suggests that the results we report are robust across different orientation-tuned populations for the purposes of this study. A more fine-grained investigation of orientation effects would nevertheless be an interesting direction for future work.

      “For six control participants (C1–C6), gratings were initially presented with a fixed horizontal orientation. In an updated version of the task – used for C7, cases of simulated eye movement, cases of artificial scotoma, and the LHON patient – the orientation varied every 5 s among four angles (−45º, 0º, 45º, 90º). Contrast sensitivity patterns were consistent across single and multiple-orientation conditions, including in participants who completed both versions, indicating robustness across orientation-tuned populations.”

      R3-Recommendation 7: Are pRF centers also fitted outside the stimulated 20º radius? If yes, were they masked for the analysis?

      AR-R3-Recommendation 7: During pRF model fitting, pRF centers were allowed to extend beyond the stimulated visual field, up to approximately 1.5 times the maximum stimulus eccentricity (~30°), to improve model stability near stimulus boundaries. Eccentricity was sampled on a logarithmically spaced grid defined as 2<sup>*</sup>, with 𝑥 ranging from -5 to 0.6 in steps of 0.2, and then scaled by the maximum stimulus eccentricity (20°) to express pRF centers in degrees of visual angle. This spacing approach provided finer sampling near the fovea and progressively coarser sampling at larger eccentricities, consistent with cortical magnification principles. For all subsequent analyses of cortical contrast sensitivity, pRF centers located outside the stimulated 20° eccentricity were explicitly excluded. Likewise, although the Benson atlas provides eccentricity estimates extending well beyond the stimulated range (up to ~90°), only pRF centers within 20° were included to ensure consistency across pRF based and atlas-based analyses.

      “During pRF model fitting, pRF centers were allowed to extend beyond the stimulated visual field to improve model stability near stimulus boundaries – up to approximately 1.5 times the maximum stimulus eccentricity (~30°). Eccentricity was sampled on a logarithmically spaced grid defined as 2*, with x ranging from −5 to 0.6 in steps of 0.2, and then scaled by the maximum stimulus eccentricity (20°) to express pRF centers in degrees of visual angle. This sampling scheme provided finer resolution near the fovea and progressively coarser sampling at larger eccentricities, consistent with cortical magnification principles.”

      “For all subsequent analyses of cortical contrast sensitivity, pRF centers outside the stimulated 20° eccentricity were excluded. Similarly, although the Benson atlas provides eccentricity estimates extending far beyond the stimulated range (up to ~90°), only values within 20° were retained to maintain consistency across pRF-based and atlas-based analyses.”

      R3-Recommendation 8: L212: Could the authors please clarify what "scaled across eccentricity to account for cortical magnification" means for the given stimulus?

      AR-R3-Recommendation 8: The pRF stimulus was scaled across eccentricity using a logarithmic transformation of retinal radius to approximate cortical magnification. Radial checker boundaries were defined in log eccentricity space (log(r)), resulting in an exponential increase in checker size with eccentricity (scaling factor = 3.2; ~1.37× increase per radial step). As a result, the spatial frequency content of the stimulus decreases with eccentricity (i.e., checker size increases), compensating for known changes in V1 spatial frequency preference across the visual field. This eccentricity dependent scaling inherently relies on precise fixation to stimulate the intended retinal locations, which can be difficult for patients with central vision loss and therefore motivates the use of Benson templates.

      “This scaling was implemented by applying a logarithmic transformation of retinal radius, such that radial checker boundaries were defined in log eccentricity space (log(r)), where r denotes to eccentricity relative to the fixation target). This produced an exponential increase in checker size with eccentricity (scaling factor = 3.2; ~1.37 times increase per radial step), resulting in lower spatial frequency content at larger eccentricities – consistent with known variations in V1 spatial frequency tuning. Because this eccentricity dependent scaling assumes precise fixation, it can be challenging for individuals with central vision loss, further motivating the use of Benson atlas templates in such populations.”

      R3-Recommendation 9: L213: Three runs were measured per session, were they averaged before analysis or analyzed independently? If analyzed independently, how were the individual results handled?

      AR-R3-Recommendation 9: As described in the Methods, data from all three runs were first aligned to an alignment scan that had been co-registered to the MPRAGE image – typically the scan with the fewest outlier voxels, or alternatively, a single-band reference scan in cases of misregistration. The runs were then analyzed as separate regressors in a single design matrix in SPM to account for run-specific variation - following standard recommendations for this software (Author response image 2 shows the SPM design matrix for the GLM). We did not average the runs beforehand due to differences in the order of stimulus presentation across runs. Instead, the GLM modeled each run’s specific presentation sequence to estimate condition-specific beta values, capturing the average contribution of each spatial frequency and contrast level to the BOLD response.

      Author response image 2.

      R3-Recommendation 10: L289: Did the authors check for very small pRF sizes, as SamSrf is prone to fitting many small sizes?

      AR-R3-Recommendation 10: We did not apply an explicit filter to remove very small pRF sizes; we excluded only pRFs with σ > 6.

      R3-Recommendation 11: L384: p is missing before the value.

      AR-R3-Recommendation 11: Thank you for catching this oversight. We have now added the missing p-value in the revised manuscript.

      “Post-hoc tests using Holm-Bonferroni correction show that V1 neuronal populations receiving inputs from the central visual field (0.5-4.5°) showed greater contrast sensitivity to high spatial frequency as compared to low spatial frequency stimuli (steeper slope for the 3cpd versus 0.3cpd condition: 0.5-2.5º: t(6) = 4.35, p<sub>bonf</sub> = 0.0149; 2.5-4.5º: 𝑡(6) = 3.471, p<sub>bonf</sub> = 0.0266).”

      R3-Recommendation 12: I have a very subjective comment regarding the figures. I do not really like the use of the hot colormap in this setting, as I feel it is hard to interpret high and low values.

      AR-R3-Recommendation 12: We appreciate the suggestion, but we have had many heated discussions amongst the authors about this and have moved back forth several times before settling. Hopefully the reviewer will be happy for us to stick with the author’s eventually agreed-on subjective preference although we acknowledge that it is by no means a perfect color scheme.

      R3-Recommendation 13: L474: Suddenly, a second session appears in the Results section; please report this in Methods.

      AR-R3-Recommendation 13: Please refer to our response to R3-3, where we also detail the corresponding changes made in the manuscript.

      R3-Recommendation 14: Figure 5C: are the reported results from the first session of the same subjects?

      AR-R3-Recommendation 14: That is correct. The results shown in Figure 6C (previously 5C) reflect correlations between slope estimates obtained from the 0.3 and 3cpd conditions within the same session for each subject. We have updated the panel title to “C. 0.3cpd vs 3cpd (within session)” to clarify this point.

      R3-Recommendation 15: For the classic pRF mapping (Figure 6D), the artificial scotoma shows lower contrast sensitivity within the scotoma and increased values outside its borders. In contrast, using the retinotopic template (Figure 6E), the area of increased sensitivity is shifted inside the scotoma. Can the authors please comment on this discrepancy?

      Is this shift due to systematic differences between the eccentricity values estimated during the pRF run and those derived from the template?

      If such a shift exists, is it induced by the eccentricity correction step performed?

      AR-R3-Recommendation 15: The shift inside the scotoma observed in the atlas-based analysis (Figure 9E; previously Figure 6E) compared to the pRF-based analysis (Figure 9D; previously Figure 6D) likely reflects residual inaccuracies in eccentricity estimates from the adjusted Benson atlas. While the Horton & Hoyt correction improves the alignment of eccentricity values, it does not ensure perfect matching with the pRF data. Without the Horton & Hoyt correction, the misalignment and shift of activity in the scotoma region are even more pronounced (see below).

      We have added a sentence to the Methods section to justify the applied correction. Furthermore, to illustrate the impact of misalignment and its correction on cortical sensitivity maps, we have included an additional figure in the Appendix section showcasing the effect of applying the correction to improve mapping of the artificial scotoma.

      “We initially observed inaccuracies between the template and individual retinotopy eccentricity estimates which led to substantial distortions in cortical visual field maps due to cortical magnification – especially in peripheral locations (see Figure A4 in Appendix section).”

      R3-Recommendation 16: L532: The age and mutation type of the patient are already reported in the Methods. In general, many Methods and Discussion statements are embedded within the Results section.

      AR-R3-Recommendation 16: We are aware that it is a stylistic choice to remind of method in the results and foreshadow discussion. We chose this approach to support the interpretability of the results for less specialist readers.

      R3-Recommendation 17: L636: Did the authors consider other options for estimating pRF parameters based on anatomical features, like Ribeiro et al. (2021;https://github.com/felenitaribeiro/deepRetinotopy_TheToolbox).

      AR-R3-Recommendation 17: We agree that alternative approaches to estimating pRF parameters based on anatomical features, such as the DeepRetinotopy method proposed by Ribeiro et al. (2021), are promising and worth exploring. In this study, we used the Benson atlas as a starting point, along with an adjustment of eccentricity estimates based on cortical magnification. Future work could compare the performance of different retinotopic template fitting approaches, including deep learning-based methods, to further improve anatomical alignment and functional predictions.

      “Further enhancing the alignment between retinotopic template atlases and individual retinotopic tuning could improve this approach further, for example, by integrating them with functional measures using Bayesian methods (Benson & Winawer, 2018). In parallel, geometric deep learning frameworks such as DeepRetinotopy (Ribeiro et al., 2021) could also offer anatomy-driven predictions from structural MRI, and combining these strategies may yield more accurate and generalizable retinotopic reconstructions.”

      R3-Recommendation 18: Figure A4: This figure brings up a very important point, namely, whether small eye movements reduce the accuracy of pRF and contrast sensitivity estimates. However, these experiments and results are not reported in the manuscript. I would prefer the authors to add all necessary Methods and Results, or at least not leave this Figure unexplained.

      AR-R3-Recommendation 18: We thank the reviewer for highlighting the importance of this figure. To address this point, we collected additional data and have revised the manuscript to include a dedicated section on the effects of eye movements, with corresponding updates in the Abstract, Methods, Results, and Discussion.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) First, a central claim is that arousal modulates functional connectivity in a hemispherically asymmetric and community-specific manner. Although structured asymmetries are demonstrated at the group level, it remains unclear whether these effects reflect a stable neurobiological principle or arise from high-dimensional, connection-wise analyses that are sensitive to sampling variability. Given the interpretive weight placed on hemispheric lateralization, stronger evidence of robustness and individual-level consistency would be necessary to support this conclusion.

      We appreciate your critical comments on the robustness of our lateralization findings. We fully agree with you that it is essential to demonstrate that the observed hemispheric asymmetries reflect a stable neurobiological principle rather than an artifact of sampling variability or high-dimensional noise. To address this concern, we performed two rigorous validation analyses using 500-iteration resampling schemes, consisting of a split-half reliability test and a participant-level consistency assessment.

      First, to ensure our findings do not depend on specific sample compositions, we conducted a split-half reliability test where the dataset was randomly partitioned into two independent subgroups over 500 iterations. As shown in Figure S1A, the community labels maintained high spatial consistency across iterations (as evidenced by the confusion matrix and Dice coefficient distributions), and our original findings—including network-pair community architecture (Fig. S2A), regional affiliation patterns (Fig. S3A-B), and arousal–tvFC coupling lateralization (Fig. S4A-B)—were consistently situated at the center of the iteration distributions.

      Second, to account for potential within-participant dependencies in the HCP 7T dataset, we performed a participant-level resampling analysis (N = 139). By randomly selecting a different session for each participant across 500 iterations, we confirmed that the community architecture and hemispheric biases remain robust even under this strict control (Figure S1A, S2B, S3C-D and S4C-D). Collectively, these additional analyses provide strong evidence that the hemispheric lateralization we reported is not a byproduct of sampling bias, but instead represents a stable organizational principle of the arousal-modulated connectome.

      (2) Second, all analyses are based on ultra-high-field imaging. The manuscript does not address whether the reported arousal-related patterns, including the community structure and hemispheric asymmetries, are expected to be reproducible at standard field strengths. It therefore remains unclear whether the findings depend critically on the use of high-field data or whether they would generalize to more widely available datasets, limiting the broader applicability of the results.

      We appreciate your constructive comments on the generalizability of our findings across different field strengths.

      As you noted, our primary motivation for employing 7T ultra-high-field imaging was to leverage its superior signal-to-noise ratio (SNR) and significantly enhanced BOLD sensitivity. These technical advantages were instrumental in capturing the subtle, moment-to-moment coupling between spontaneous pupillary fluctuations and tvFC—signals that might be close to the detection threshold in standard field strength environments.

      However, we fully recognize your point that 3T remains the standard in most clinical and research settings. In the revised manuscript, we have added a dedicated discussion to address this (page 21, lines 447-456):

      “Fifth, the findings reported here were derived exclusively from ultra-high-field (7T) imaging data. The superior BOLD sensitivity of 7T fMRI was instrumental in resolving the fine-scale community architecture of arousal–tvFC coupling, which involves subtle signals that may be challenging to detect at lower field strengths. Given that 3T remains the most common parameter for neuroimaging research and clinical applications, future investigations are needed to determine the extent to which these organizational principles generalize to standard field strength data. Validating these motifs in large-scale 3T datasets will be essential to establish their broader applicability across different imaging environments.”

      (3) Third, arousal-connectivity coupling is assessed using zero-lag correlations between pupil diameter and time-resolved connectivity estimates. Physiological and hemodynamic considerations suggest that pupil-linked arousal and blood-based imaging signals may exhibit systematic temporal delays. The absence of analyses examining sensitivity to such delays raises the possibility that the reported coupling patterns depend on a specific temporal alignment assumption.

      Given the inherent delay of the hemodynamic response function (HRF) and the complex temporal relationship between pupillary dynamics and neural activity, we conducted an additional lagged cross-correlation analysis to test the sensitivity of our findings. Following established frameworks for linking BOLD signals with pupillometry (Yellin et al., 2015; Gonzalez-Castillo et al., 2022; Lloyd et al., 2023), we systematically shifted the pupil time series relative to the fMRI data by -3 TR to +3 TR (-3s to +3s) and evaluated the consistency of the community architecture across these different lags using Dice coefficients.

      As shown in Figure S5, these results demonstrate that the community organization remain stable across the tested range of physiological delays. This stability indicates that the arousal-modulated communities we reported are not specific to the zero-lag assumption but instead persist throughout the physiologically plausible lag window. Consequently, our findings reflect a robust neurobiological phenomenon rather than an artifact of a specific temporal alignment.

      (4) Fourth, the estimation of time-resolved connectivity relies on a single choice of sliding-window length. The manuscript does not examine whether the reported patterns are stable across different window sizes. Given ongoing concerns about parameter dependence in time-resolved connectivity analyses, sensitivity analyses would be important to establish that the findings are not artifacts of a particular analytical choice.

      To ensure that our findings are not artifacts of a specific analytical choice, we performed an exhaustive sensitivity analysis by repeating our entire pipeline across a wide range of window lengths (30s, 35s, 60s, and 90s) and step sizes (1s, 5s, and 10s). We then employed Dice coefficients to quantify the topological similarity between these alternative configurations and our original parameters (30s window, 5s step).

      As shown in Figure S5, our results demonstrate high topological consistency, with Dice coefficients for community structures remaining consistently above 0.8 across all tested parameter combinations. These findings provide strong evidence that the arousal-modulated organizational principles we reported are inherent to the data rather than being driven by specific analytical choices in the sliding-window setup.

      (5) Finally, the identification of seven connectivity communities is a central result, yet the justification for this choice relies primarily on a single clustering quality measure. In practice, evaluation of clustering solutions typically draws on multiple complementary criteria, including measures of compactness and separation, approaches for selecting the number of clusters, and assessments of stability under resampling. Without such complementary evaluations, it is difficult to determine whether the reported community structure reflects a stable organizational feature or sensitivity to specific methodological decisions.

      We agree that relying on a single measure can be limiting, and in the revised manuscript, we have implemented a comprehensive multi-criteria evaluation to justify our selection of K=7. To ensure the robustness of the community partition, we expanded our analysis to include several complementary indices, such as the Davies-Bouldin Index, Calinski-Harabasz Score, and Silhouette Coefficient, alongside the original Within-Cluster Sum of Squares (WCSS), as detailed in Figure S7A.

      To further minimize subjective bias in "elbow" detection, we utilized the L-method (Salvador & Chan, 2004), which identifies the optimal K by minimizing the combined root-mean-square error (RMSE) of two linear regression segments. As illustrated in Figure S7B, the RMSE was minimized at K=7, providing a robust mathematical basis for our partition. Furthermore, we systematically visualized the community maps across a range of granularities from K=5 to 9 (Figure S7C). This stability analysis demonstrates that the fundamental topological features and the resulting hemispheric asymmetries are not transient artifacts of a specific K but are consistently preserved as the clustering granularity increases. These additional evaluations demonstrate that the seven-community structure reflects a stable organizational feature of arousal-modulated connectivity

      Reviewer #2 (Public review):

      (1) Arousal effects on BOLD signals and on pupil size can have different delays, so it would be valuable to test lagged relationships (for example, shifting the pupil series forward and backward) to show that the main community structure and lateralization results are not sensitive to an arbitrary temporal alignment.

      We agree with you that accounting for the varying delays between BOLD signals and pupillary dynamics is essential for ensuring the robustness of our results. We conducted a comprehensive lagged cross-correlation analysis to address it. Following established frameworks for linking BOLD signals with pupillometry (Yellin et al., 2015; Gonzalez-Castillo et al., 2022; Lloyd et al., 2023), we systematically shifted the pupil time series relative to the fMRI data by -3 TR to +3 TR (-3s to +3s) and evaluated the consistency of the community architecture across these lags using Dice coefficients.

      As shown in Figure S5C, these results demonstrate that the core community organization remain stable across the tested range of physiological delays. This stability confirms that our findings are not sensitive to an arbitrary temporal alignment but instead reflect a robust neurobiological phenomenon that persists throughout the physiologically plausible lag window.

      (2) Pupil diameter covaries with blinks, eye closure, and other factors that can covary with head motion and physiological noise. The Methods include substantial quality control and denoising, including motion regression and scrubbing, plus exclusions for eye closure.

      We appreciate your attention to these potential confounding factors. While we implemented rigorous preprocessing including regressing out confounds on fMRI images, we agree that physiological noise and motion may influenced pupil signals.

      To address this, we conducted an additional control analysis where we included head motion (framewise displacement, FD) and the global signal (defined as the mean signal across all gray matter voxels) as covariates when calculating the arousal–tvFC coupling. We then re-evaluated the similarity between the resulting community architecture and our original findings. As shown in Figure S4, the community structure remained stable after controlling for these variables.

      Regarding eye closure, we intentionally did not regress this out, as extensive literature demonstrates that eye closure is itself a reliable physiological proxy for arousal levels (Sommer & Golz, 2010; Chang et al., 2016; Gonzalez-Castillo et al., 2022); regressing it out would likely remove the very arousal-related coupling effects we aim to investigate.

      (3) The dataset is described in terms of runs retained (for example, 485 resting runs), and runs are treated as observations in clustering after z-scoring across runs. If multiple runs come from the same individuals, the manuscript would benefit from explicitly showing that results replicate at the participant level (for example, community structure stability within participant across runs, and participant-level summary statistics used for inference), rather than relying primarily on pooled run-level patterns.

      We fully agree with you that it is essential to demonstrate that the observed hemispheric asymmetries reflect a stable neurobiological principle rather than an artifact of sampling variability or high-dimensional noise. To address this concern, we performed two rigorous validation analyses using 500-iteration resampling schemes, consisting of a split-half reliability test and a participant-level consistency assessment.

      First, to ensure our findings do not depend on specific sample compositions, we conducted a split-half reliability test where the dataset was randomly partitioned into two independent subgroups over 500 iterations. As shown in Figure S1A, the community labels maintained high spatial consistency across iterations (as evidenced by the confusion matrix and Dice coefficient distributions), and our original findings—including network-pair community architecture (Fig. S2A), regional affiliation patterns (Fig. S3A-B), and arousal–tvFC coupling lateralization (Fig. S4A-B)—were consistently situated at the center of the iteration distributions.

      Second, to account for potential within-participant dependencies in the HCP 7T dataset, we performed a participant-level resampling analysis (N = 139). By randomly selecting a different session for each participant across 500 iterations, we confirmed that the community architecture and hemispheric biases remain robust even under this strict control (Figure S1A, S2B, S3C-D and S4C-D). Collectively, these additional analyses provide strong evidence that the hemispheric lateralization we reported is not a byproduct of sampling bias, but instead represents a stable organizational principle of the arousal-modulated connectome.

      (4) Time-resolved connectivity is estimated using a 30-second sliding window and 5 second step. It is reasonable to wonder whether the same conclusions hold with alternative estimators that do not rely on fixed windows. The Discussion acknowledges this limitation, but adding a small robustness analysis would make the paper more definitive.

      To ensure that our findings are not artifacts of a specific analytical choice, we performed an exhaustive sensitivity analysis by repeating our entire pipeline across a wide range of window lengths (30s, 35s, 60s, and 90s) and step sizes (1s, 5s, and 10s). We then employed Dice coefficients to quantify the topological similarity between these alternative configurations and our original parameters (30s window, 5s step).

      As shown in Figure S3, our results demonstrate high topological consistency, with Dice coefficients for community structures remaining consistently above 0.8 across all tested parameter combinations. Furthermore, the core hemispheric asymmetry patterns were robustly preserved regardless of the specific windowing configuration used. These results provide strong evidence that the arousal-modulated organizational principles we reported are inherent to the data and are stable across a broad range of temporal scales.

      Reviewer #3 (Public review):

      (1) A major limitation of the study is the limited discussion of subcortical regions, which play a central role in arousal regulation according to extensive prior literature. Although the current analyses focus primarily on cortical organization, the authors should include a brief discussion of how their findings relate to subcortical arousal systems.

      We completely agree that subcortical structures are pivotal drivers of arousal regulation. While our study primarily utilized a symmetric cortical atlas to ensure a mathematically rigorous assessment of hemispheric lateralization, we recognize that the exclusion of subcortical regions limits the functional interpretation of the observed patterns.

      In the revised manuscript, we have added a dedicated discussion part (page 20, lines 412-428) to address this point:

      “First, to ensure a mathematically rigorous assessment of hemispheric asymmetry, our analysis was restricted to a symmetric cortical parcellation. Consequently, while we demonstrate that arousal-modulated connectivity follows a structured macroscopic architecture, we did not explicitly analyze the subcortical nuclei hypothesized to drive these patterns. We hypothesize that the presence of these low-dimensional cortical communities reflects coordinated motifs rather than a homogeneous gain modulation, potentially mirroring the differentiated projection patterns of subcortical neuromodulatory systems. For instance, the locus coeruleus–noradrenergic pathway (Chandler et al., 2014; Schwarz & Luo, 2015) and thalamus (Hwang et al., 2017; Shine, 2019; Müller et al., 2020; Shine et al., 2023) possess extensive yet non-uniform projections that may anchor the community-specific and hemispherically asymmetric patterns observed here. “

      (2) While sliding window methods can capture temporal changes in functional organization, they have limitations in characterizing moment-to-moment neural fluctuations. In particular, results can be highly sensitive to window length and step size. The manuscript would benefit from (a) a clearer discussion of these methodological limitations, (b) justification for the chosen window length and step size, and (c) a sensitivity analysis demonstrating whether the main findings are robust across different parameter choices.

      To ensure that our findings are not artifacts of a specific analytical choice, we performed an exhaustive sensitivity analysis by repeating our entire pipeline across a wide range of window lengths (30s, 35s, 60s, and 90s) and step sizes (1s, 5s, and 10s). We then employed Dice coefficients to quantify the topological similarity between these alternative configurations and our original parameters (30s window, 5s step).

      As shown in Figure S5, our results demonstrate high topological consistency, with Dice coefficients for community structures remaining consistently above 0.8 across all tested parameter combinations. Furthermore, the core hemispheric asymmetry patterns were robustly preserved regardless of the specific windowing configuration used. These results provide strong evidence that the arousal-modulated organizational principles we reported are inherent to the data and are stable across a broad range of temporal scales.

      (2) The authors use k-means clustering to identify groups of brain regions and refer to these groupings as "communities." However, in general, community detection typically refers to graph-based algorithms that identify modules based on connectivity structure (e.g., modularity maximization). The clusters derived from k-means in feature space are not necessarily equivalent to graph-theoretic communities. The authors should explicitly clarify this distinction and adjust terminology accordingly to avoid conceptual ambiguity.

      We agree that the term "community detection" is often specifically associated with graph-based algorithms, such as modularity maximization, which define modules based on topological connectivity. In contrast, our implementation of k-means identifies groupings based on the similarity of arousal–FC coupling patterns within a high-dimensional feature space.

      To avoid any conceptual ambiguity or potential confusion, we have explicitly clarified this distinction in the Methods (pages 24-25, lines 533-542) section of the revised manuscript:

      “We employed the k-means clustering algorithm (Euclidean distance) to explore a range of cluster solutions from K = 2 to 15. To ensure the stability of the results and avoid local optima, each K was repeated 250 times with random initializations. The optimal number of clusters was determined by evaluating clustering quality and reproducibility (e.g., maximizing silhouette stability). It is important to clarify that "communities" in this context refer to clusters of edges that exhibit similar arousal-modulation motifs within a high-dimensional feature space, rather than topological modules typically derived from graph-theoretic algorithms like modularity maximization. This procedure consistently identified seven distinct communities, each representing a robust, arousal-sensitive connectivity motif that characterizes the large-scale organization of brain-pupil coupling.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) To strengthen confidence in the reported hemispheric effects, the authors should provide additional robustness analyses, such as subject-level consistency of lateralization measures, split-half or resampling reliability, and sensitivity to alternative preprocessing or analysis choices. Reporting the distribution of lateralization effects across individuals would help clarify whether the observed asymmetries reflect stable features or group-level averages driven by a subset of connections or participants.

      We agree that establishing the individual-level stability of lateralization is essential. We have now provided extensive validation, including split-half reliability tests and participant-level consistency analyses (500 iterations). These results confirm that the reported asymmetries are robust and consistent across the sample. Please refer to Reviewer #1 Weakness2 for the full analysis and associated figures (Figure. S1-S4).

      (2) The authors should examine whether arousal-connectivity coupling patterns are robust to plausible temporal delays between pupil diameter and BOLD signals. Lagged or time-shifted analyses would help establish that the findings do not depend on a specific zero-lag assumption.

      We agree that validating the coupling between pupil dynamics and the time varying FC is essential. To address this, we conducted a lag sensitivity analysis by shifting the pupil-derived arousal signal within a physiologically plausible range (-3 to +3 TR). The community architecture remains highly consistent across these temporal offsets, showing high spatial correlation and Dice coefficients with our original findings. This stability confirms that the identified organizational motifs are robust and not dependent on a specific zero-lag assumption. For the full details of this validation and the associated figures, please refer to Reviewer #1 Weakness3 and Figure S5 in the Supplementary Material.

      (3) Given reliance on a single sliding-window length, the authors should assess how key results vary across different window sizes. Demonstrating stability of the community structure and lateralization patterns across parameter choices would strengthen the methodological foundation of the study.

      We have conducted an exhaustive sensitivity analysis across various window lengths (30s, 35s, 60s, 90s) and step sizes (1s, 5s, 10s). The high Dice coefficients (>0.8) confirm that our findings are not dependent on specific windowing choices. Please refer to Reviewer #1 Weakness3 and Figure S5 for the full results.

      (4) The justification for the chosen number of connectivity communities would benefit from additional clustering evaluations. Complementary criteria such as measures of compactness and separation, model selection approaches for determining the number of clusters, and stability or reproducibility under resampling would help establish whether the reported community structure is robust rather than method-dependent.

      To strengthen the mathematical basis for our partition, we have implemented a multi-metric evaluation and the L-method for objective K selection. These metrics consistently support the seven-community structure. Please refer to our response to Reviewer #1 Weakness5 and Figure S7 for the comprehensive evaluation.

      (5) The manuscript would benefit from a clearer discussion of why ultra-high-field imaging was required for the present analyses and whether similar results are expected at standard field strengths. If feasible, validation using lower-field data or reference to existing datasets would substantially enhance generalizability.

      We have expanded our discussion to clarify that 7T was instrumental for capturing the subtle, high-frequency arousal-tvFC coupling due to its superior SNR. We also explicitly discuss the potential and limitations of generalizing these findings to 3T datasets. Please refer to our response to Reviewer #1 Weakness2 for the full discussion (page 21, lines 447-456).

      (6) The authors should more explicitly report exclusion related to pupil measurements and discuss how missing or noisy pupillometry may affect the applicability of the approach in other datasets or experimental settings.

      We agree that transparency in data screening is essential for the reproducibility of our method. In the revised manuscript, we have clarified our quality control pipeline in the quality control section in Methods (page 23, lines 502-510):

      “The final analyzed sample for the resting-state consisted of N = 139 healthy participants (mean age = 29.1±3.5 years, 77 female). Runs were excluded if (a) more than 20% of frames exceeded motion thresholds, (b) eye tracking did not cover the full fMRI time series, or (c) more than 90% of samples were classified as eye closure. After applying these criteria, 485 of the initial 723 scans were retained for analysis. The same quality-control pipeline was applied to the movie-watching dataset, yielding 513 usable scans out of the original 725. Detailed information on data retention and run distribution per participant is summarized in Figure S9.”

      Furthermore, we have added a discussion regarding how noisy or missing pupillary signals might affect the generalizability of our approach (pages 20-21, lines 437-447):

      “Fourth, the generalizability of our approach to external cohorts warrants caution regarding pupillary data integrity. In contexts where high-fidelity eye-tracking is technically demanding—such as in clinical settings involving patients with restricted compliance or in naturalistic fMRI studies—the prevalence of blink artifacts and signal dropouts may bias the estimation of arousal-modulated states. Excessive reliance on data interpolation in such cases could artificially smooth temporal fluctuations, leading to an overestimation of community stability. Future applications should therefore prioritize high-frequency sampling and potentially incorporate multi-modal physiological features (e.g., respiratory or cardiac signals) to cross-validate arousal dynamics when pupillary data is suboptimal (Meissner et al., 2023; Bolt et al., 2025; Weijs et al., 2025).”

      (7) The authors should ensure that all data and analysis code necessary to reproduce the results are made publicly available in accordance with eLife policies, including clear documentation of preprocessing steps, parameter choices, and clustering procedures.

      All analysis code and the necessary processed data required to reproduce our findings have been made publicly available through https://github.com/kongxy6478/Arousal-modulates-functional-connectivity. This repository includes documented pipelines for pupillometry cleaning and fMRI denoising, alongside the core Python scripts used for sliding-window connectivity calculation, k-means clustering, and hemispheric lateralization analysis.

      Reviewer #2 (Recommendations for the authors):

      (1) Add a lag sensitivity analysis between pupil-derived arousal and time-resolved connectivity, and report whether the seven community structure and key lateralization findings are stable across a plausible lag range.

      We agree that validating the coupling between pupil dynamics and the time varying FC is essential. To address this, we conducted a lag sensitivity analysis by shifting the pupil-derived arousal signal within a physiologically plausible range (-3 to +3 TR). The community architecture remains highly consistent across these temporal offsets, showing high spatial correlation and Dice coefficients with our original findings. This stability confirms that the identified organizational motifs are robust and not dependent on a specific zero-lag assumption. For the full details of this validation and the associated figures, please refer to Reviewer #1 Weakness3 and Figure S5 in the Supplementary Material.

      (2) Quantify and report the extent to which residual head motion, blink rate, eye closure segments, and global signal changes explain arousal connectivity coupling, for example, via partial correlation or regression controls, and show that key effects persist.

      We agree that it is essential to demonstrate that the observed arousal-connectivity coupling is not driven by non-specific physiological or motion-related artifacts. As requested, we have quantified the influence of head motion (FD) and global signal on our primary results. By implementing partial correlation analyses, we confirmed that the identified arousal-modulated community structures persist even after strictly controlling for these variables. These results indicate that the arousal-tvFC coupling we report reflects a specific neuro-arousal process rather than a byproduct of motion or systemic physiological fluctuations. For the detailed quantitative results and control analysis figures, please refer to our response to Reviewer #2 Weakness3 and Figure S6 in the Supplementary Material.

      (3) Add participant-level validation: demonstrate that community profiles and lateralization signatures are consistent within participants across runs, and consider participant-level statistical summaries rather than treating all runs as independent observations.

      We agree that demonstrating participant-level consistency is vital. In response, we performed two rigorous 500-iteration resampling schemes: a split-half reliability test and a participant-level consistency assessment (N = 139). These analyses, which involved randomly partitioning the sample and selecting single sessions per participant, confirm that our community architecture and hemispheric biases are remarkably stable and not driven by sampling variability or high-dimensional noise. For a comprehensive description of these validations and the associated statistical distributions, please refer to our detailed response to Reviewer #2 Weakness3 and Figures S1–S4.

      (4) Provide an alternative dynamic connectivity estimator robustness check, or at a minimum, vary the window length and step size to show stability of the primary conclusions.

      We have conducted an exhaustive sensitivity analysis across various window lengths (30s, 35s, 60s, 90s) and step sizes (1s, 5s, 10s). The high Dice coefficients (>0.8) confirm that our findings are not dependent on specific windowing choices. Please refer to Reviewer #1 Weakness3 and Figure S5 for the full results.

      (5) Consider validating the seven community solutions with at least one additional unsupervised approach, and report agreement with the main k-means solution.

      We agree that validating the clustering scheme is essential. To this end, we implemented a multi-criteria evaluation (including Davies-Bouldin and Silhouette indices) and utilized the L-method (Salvador & Chan, 2004) to mathematically confirm K=7 as the optimal granularity (Figure S7A–B). Furthermore, we verified that the core topological features and hemispheric asymmetries remain robustly consistent across a range of granularities from K=5 to 9 (Figure S7C). These analyses demonstrate that our findings are not dependent on a specific K or subjective bias. For the full quantitative evaluation and stability maps, please refer to our response to Reviewer #2 Weakness5 and Figure S7.

      (6) State explicitly, early in Results, what the main inferential unit is (run or participant) for each key analysis, and clarify how repeated runs per participant are handled.

      We agree that defining the inferential unit is critical for methodological clarity. In the revised manuscript, we have explicitly stated at the beginning of the Results section (page 5, lines 113-116):

      “While our primary inferential analyses were conducted at the run level to leverage the high-density sampling of the HCP 7T dataset, we further validated the robustness of these findings using participant-level statistical summaries and resampling to account for within-participant dependencies (see Figure. S1-S2 in Supplementary Materia).”

      Specifically, all key findings—including community architecture and hemispheric asymmetries—were validated using participant-level statistics and resampling schemes (N = 139) to ensure that the results are not biased by within-participant dependencies.

      (7) When introducing the integration and segregation indices, add a brief intuitive explanation of what a positive or negative value means in plain language before the equations.

      We thank the reviewer for this suggestion to improve the accessibility of our methods. We have added brief, intuitive explanations for both indices in the Methods section (pages 26-27, lines 569-582):

      “The integration index provides a measure of the overall hemispheric dominance of arousal-modulated connections. A positive value indicates that arousal-related edges are preferentially concentrated in the left hemisphere (including its internal and outgoing connections) compared to the right.” and “The segregation index assesses whether arousal preferentially modulates local, intra-hemispheric communication versus long-range, inter-hemispheric communication. A positive value reflects a "segregated" left-hemisphere bias, where arousal strengthens within-hemisphere connections more than it strengthens across-hemisphere communication for that same hemisphere. “

      (8) In the Discussion, separate claims into "what we show" versus "what we hypothesize," especially when connecting findings to neuromodulatory pathways.

      In the revised manuscript, we have carefully separated our direct empirical findings from our mechanistic hypotheses. we have utilized more cautious and speculative language (e.g., "suggesting a potential role of," "may be mediated by," and "we hypothesize that”) (page 17, lines 352-358):

      “Specifically, we show the presence of low-dimensional, reproducible communities suggests that arousal modulates the connectome through coordinated motifs rather than homogeneous gain modulation. We hypothesize that this structured macroscopic architecture reflects the differentiated projection patterns of subcortical neuromodulatory systems, such as the locus coeruleus–noradrenergic pathway (Aston-Jones & Cohen, 2005; Jordan, 2024) and thalamus (Magnin et al., 2010; Lewis et al., 2015; Liu et al., 2018)”

      (9) Provide a clear participant-level summary (number of participants contributing to the retained runs, demographics if available, and distribution of runs per participant), alongside the reported run counts retained after quality control.

      We agree that clear reporting of participant-level data is essential. In the revised Methods section, we have added a detailed summary of participant demographics (age and sex) and clarified the sample composition (page 23, lines 502-503):

      “The final analyzed sample for the resting-state consisted of N = 139 healthy participants (mean age = 29.1±3.5 years, 77 female).”

      Furthermore, to provide a transparent view of the data retained after quality control, we have included Figure S9 to illustrate the distribution of valid runs per participant. This visualization confirms the amount of data contributing to our group-level inferences and accounts for exclusions due to motion or pupillary signal quality.

      (10) Report the robustness of results to reasonable changes in pupil preprocessing choices (for example, smoothing parameters or interpolation rules), since pupil diameter is the key arousal index.

      We agree that the robustness of pupil-derived arousal estimates is fundamental to our findings. To address this, we conducted an extensive validation analysis by comparing our original pupil preprocessing pipeline against 18 alternative combinations of parameters. These variations included different smoothing window sizes (100 ms, 200 ms, and 500 ms), interpolation methods (linear vs. cubic spline), and blink buffer durations (25 ms, 50 ms, and 100 ms). As shown in Figure S8, the pupil diameter time courses derived from these diverse pipelines remained highly correlated with our original estimates (all above 0.65). This demonstrates that our arousal-modulated connectivity results are remarkably robust to reasonable changes in pupil preprocessing choices.

      Reviewer #3 (Recommendations for the authors):

      I have two additional minor comments:

      (1) Given the overall goal of this study to identify large-scale brain communities or clusters underlying arousal, the results may be sensitive to the choice of cortical parcellation. The authors should consider:

      (a) including analyses using additional parcellation schemes, or

      (b) discussing how the current findings might depend on the chosen parcellation and the implications for robustness and generalizability.

      We have addressed this by adding a dedicated point in the Discussion (page 21, lines 456-465):

      “Sixth, our findings were derived using a single high-resolution cortical parcellation. While the specific choice of atlas can influence fine-grained regional connectivity, it is important to note that our primary conclusions—such as hemispheric asymmetries and community-level preferences—were identified and interpreted at the macroscopic network and system level. By aggregating signals across broad functional systems, this approach likely mitigates the dependency on precise regional boundary definitions. Nevertheless, future studies employing alternative parcellation schemes would be valuable to further confirm that these organizational principles are not specific to the current atlas but represent a generalizable feature of the arousal-modulated connectome.”

      (2) Some key details, such as the number of participants included in the study, as well as basic demographic information, are not reported.

      We apologize for this omission. In the revised Methods section, we have now included a detailed summary of the participant demographics, including the final sample size (N = 139), age, and sex distribution (page 23, lines 502-503):

      “The final analyzed sample for the resting-state consisted of N = 139 healthy participants (mean age = 29.1±3.5 years, 77 female)”

      Furthermore, to ensure full transparency regarding data retention, we have added a new figure (Figure S9) illustrating the distribution of valid fMRI runs per participant following our quality-control procedures. We believe these additions provide a clear and complete overview of the study sample.

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    1. Author response:

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

      Reviewer #1 (Public review):

      (1) Figure 1A and B: Although a trend is evident, it does not appear that the absolute number of cNK cells at day 14 is significantly changed from day 6.5?

      We thank the reviewer for this careful observation. We had not originally performed a statistical comparison between the number of cNK cells present at gds 6.5 and 14.5. We have now conducted the appropriate statistical analysis for this dataset and found that the absolute number of cNK cells at day 14.5 is in fact significantly different from day 6.5 (p = 0.0005; unpaired t test, Mann-Whitney correction). The figure and corresponding legend have been updated to reflect this analysis. Please see Figure 1B:

      “Statistics were calculated using unpaired t tests with the Mann-Whitney correction. Error bars indicate SEM; *** p < 0.001.”

      (2) Figure 2E: The authors state, "This reduction of uterine trNK cells was accompanied by a concomitant increase in the absolute number and frequency of CD49b+Eomes+ cNK cells within the pregnant uterus of TGF-βRIINcr1Δ dams (Figure 2 D, E). The number of cNK cells appears relatively low (visually ~1,000-1,300), and although the difference is statistically significant, its physiological relevance is unclear. More importantly, this modest increase does not correlate with the marked decrease in trNK and ILC1 populations, as cNK cells do not appear to accumulate. In my opinion, the conclusion "Collectively, these findings indicate that a TGF-β-driven differentiation pathway directs the conversion of peripheral cNK cells into uterine trNK cells during murine pregnancy" should be slightly toned down.

      We thank both reviewers for this suggestion. Regarding the absence of cNK cell accumulation in the absence of TGF-β signaling, we suggest that this may be related to the normal passage of cNK cells circulating in the placenta, i.e., these cells may not have acquired signals to remain in the uterus and are simply continuing to pass through and not accumulating. Nonetheless, we have rephrased our wording in to address this concern as follows:

      “This reduction of uterine trNK cells was accompanied by a small increase in the absolute number and frequency of CD49b<sup>+</sup> Eomes<sup>+</sup> cNK cells within the pregnant uterus of TGF-βRII<sup>Ncr1∆</sup> dams (Figure 2 D, E). Collectively, these findings suggest that a TGF-β–driven differentiation pathway directs the conversion of peripheral cNK cells into uterine trNK cells during murine pregnancy.”

      “The absence of cNK cell accumulation in the gravid uterus in the setting of impaired TGF-β signaling suggests a defect in tissue retention rather than recruitment. In the absence of TGF-β–mediated cues, circulating cNK cells that enter the uterine vasculature may fail to acquire the molecular programs required for residency and instead continue to transit through the tissue. This is consistent with a model in which TGF-β signaling promotes not only phenotypic conversion but also the acquisition of retention signals necessary for persistence within the uterine microenvironment, reinforcing that acquisition of tissue-residency in the gravid uterus is an actively instructed process [29,32].”

      (3) Figures 2-4: It is unclear whether the littermate controls are floxed mice or floxhet-Ncr1iCre mice? This distinction is important, as Ncr1iCre expression itself could potentially lead to a phenotype.

      To address these concerns, we characterized the uterine innate lymphoid cell compartment in the pregnant uterus of Ncr1<sup>icre</sup> dams at gestational day 6.5. We did not observe a difference in the absolute number and frequency of trNK cells, cNK cells, and ILC1s in the gravid uterus of Ncr1<sup>icre</sup> dams compared to wildtype CD45.1 C57BL/6 mice. Additionally, the number of implantation sites and resorption rates in Ncr1<sup>icre</sup> dams was comparable to wildtype CD45.1 C57BL/6 mice. Together these data indicate that Ncr1<sup>icre</sup> expression itself does not influence the phenotype we report in TGF-βRII<sup>Ncr1∆</sup> dams. These additional findings have been included in Supplementary Figure 1 and in the text as follows:

      “To ensure we exclude a confounding effect of Ncr1<sup>iCre</sup> expression, we profiled the uterine innate lymphoid compartment in pregnant Ncr1<sup>iCre</sup> dams at gestational day 6.5. No differences were observed in the absolute number of trNK cells, cNK cells, or ILC1s relative to wildtype controls (Figure S1 A-D), and implantation site number and resorption rates were likewise unchanged (Figure S1 E-F). These data indicate that Ncr1<sup>iCre</sup> expression alone does not perturb uterine ILC composition or early pregnancy outcomes.”

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 1C &D: The adoptive transfer experiment is convincing. As a minor point, why is the gate setting for Eomes different between panels 1C and 1D?

      To clarify the phenotype of the adoptively transferred cNK cells, we included two additional gates depicting the expression of CD49a and CD49b in unlabeled (non-vascular) trNK cells and cNK cells in the pregnant uterus Please see the revised Figure 1C and revised figure legend:

      “(C) Concatenated flow plots of implantation sites showing that adoptively transferred cNK cells in pregnant uterus of wildtype dams upregulate CD49a and down regulate CD49b by gd 10.5, acquiring a CD49a<sup>+</sup> CD49b<sup>-</sup> Eomes<sup>+</sup> phenotype characteristic of uterine trNK cells (C57BL/6 dams n=4). Here, 2.5x10<sup>6</sup> CD45.2<sup>+</sup> CD3<sup>-</sup> CD19<sup>-</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> CD49b<sup>+</sup> splenic cNK cells were adoptively transferred into pregnant C57BL/6-CD45.1 dams at gd 0.5, and the receptor profile of these cells was subsequently assessed at gd 10.5. Gating strategy: Live, Single Cells; CD3<sup>-</sup> CD19<sup>-</sup> CD45.1<sup>-</sup> CD45.2–PE-Cy7<sup>-</sup> CD45.2–PE<sup>+</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> cells.”

      (2) Figure 3: Has the pup ratio male/female changed?

      We did not observe a statistically significant difference in the female-to-male pup ratio between groups.

      Reviewer #2 (Public review):

      (1) The authors suggest cNK extravasation and local differentiation into iv- trNK. Can it be estimated how much this process contributes to the trNK pool vs. a potential local proliferation of already existing trNK? How do absolute numbers of CD49a+ Eomes+ trNK change during pregnancies? (In Figure 1A, the cell numbers of CD49a+ Eomes+ trNK seem to go down dramatically between gd 6.5 and 14.5). The plot in 1B could also include absolute numbers of ILC1s and trNKs. Would recruited cNK cells compensate for a potential loss of CD49a+ Eomes+ trNK?

      Our prior work as well as others have tracked the changes in uterine trNK cells, cNK cells, and ILC1s over the course of murine pregnancy. Consistent with these studies, the absolute number of uterine CD49a<sup>+</sup> Eomes<sup>+</sup> trNK cells peaks during early pregnancy (roughly between gds 5.5 7.5) and subsequently declines until term. The decrease in uterine trNK cells between gd 6.5 and gd 14.5 observed in Figure 1A is therefore consistent with the known physiological contraction of the decidual NK compartment as pregnancy progresses. Thus, it is unlikely that cNK cells recruited within the uterine tissue compensate for the loss of CD49a<sup>+</sup> Eomes<sup>+</sup> trNK cells observed. To address the reviewer’s request, we have now included the absolute number of uterine trNK cells and ILC1s in Figure 1–please see updated Figure 1C and D and corresponding figure legend (provided below). With respect to the relative contribution of cNK cells extravasation vs local proliferation of trNK cells, our data do not allow us to quantitatively distinguish between these mechanisms. Moreover, previous studies have demonstrated that uterine trNK cells express Ki67, suggesting that they exhibit proliferative activity during this period. Thus, we hypothesize that both local proliferation of existing trNK cells and recruitment of circulating cNK cells contribute to the population of uterine trNK cells during early pregnancy.

      “(C) Concatenated flow plots of implantation sites showing that adoptively transferred cNK cells in pregnant uterus of wildtype dams upregulate CD49a and down regulate CD49b by gd 10.5, acquiring a CD49a<sup>+</sup> CD49b<sup>-</sup> Eomes<sup>+</sup> phenotype characteristic of uterine trNK cells (C57BL/6 dams n=4). Here, 2.5x10<sup>6</sup> CD45.2<sup>+</sup> CD3<sup>-</sup> CD19<sup>-</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> CD49b<sup>+</sup> splenic cNK cells were adoptively transferred into pregnant C57BL/6-CD45.1 dams at gd 0.5, and the receptor profile of these cells was subsequently assessed at gd 10.5. Gating strategy: Live, Single Cells; CD3<sup>-</sup> CD19<sup>-</sup> CD45.1<sup>-</sup> CD45.2–PE-Cy7<sup>-</sup> CD45.2–PE<sup>+</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> cells. (D) Proportion of uterine ILC subsets derived from adoptively transferred splenic cNK cells in the pregnant uterus of wildtype dams. Statistics were calculated using unpaired t tests with the Mann-Whitney correction. Error bars indicate SEM; ***p < 0.001.”

      Barahona, J.D., Yang, L. and Yokoyama, W.M., 2025. Eomesodermin defines uterine NK cells crucial for pregnancy success in mice. The Journal of Immunology, 214(10), pp.2549-2556.

      Filipovic, I., Chiossone, L., Vacca, P., Hamilton, R.S., Ingegnere, T., Doisne, J.M., Hawkes, D.A., Mingari, M.C., Sharkey, A.M., Moretta, L. and Colucci, F., 2018. Molecular definition of group 1 innate lymphoid cells in the mouse uterus. Nature Communications, 9(1), p.4492.

      (2) Figure 1C: 2.5 Mio cNK cells have been transferred, but only very few cells can be detected within the uterus (concatenated FACS plot shown). What may represent the limit to generate uterine trNK out of cNK? Is the niche supporting cNK-trNK differentiation limited? Is it only a specific subset of (splenic) cNK capable of differentiating into trNK? Is gd 0.5 the optimal timepoint for the transfer? Is there continuous recruitment of cNK into the uterus and differentiation into trNK, or is it enhanced at specific timepoints of pregnancy? Could there be local proliferation of cNK-derived trNK? This could be studied by proliferation dye dilution of WT cNK cells in this transfer-setup.

      We recognize that transferring cNK cells at gestational day 0.5–prior to placental formation–may partially account for the low uterine reconstitution observed. At this time point, the local signals necessary for efficient recruitment and retention of cNK cells in the uterus may not yet be fully established, potentially resulting in preferential homing to peripheral tissues such as the spleen and liver. Consistent with this possibility, we do observe a robust population of adoptively transferred cNK cells in the spleen and liver of our pregnant dams. We decided to transfer cNK cells at gestational day 0.5 to ensure that the cells were present at throughout most of early pregnancy, particularly during implantation and the initial stages of decidualization. We also did not transfer cells before mating to minimize the number of mice that did not get pregnant. Additionally, performing the transfer at this early time point minimized repeated manipulation of pregnant dams, as procedural stress itself has been shown to affect physiological processes of gestation and could thereby confound the pregnancy outcomes we were assessing. Furthermore, Filipovic et al. 2018 previously showed that both trNK cells and cNK cells in the pregnant uterus expressed Ki67 at gestational 9.5, suggesting that there could be local proliferation of cNK-derived trNK cells in the gravid uterus that could limit the migration of circulating cNK cells into this microenvironment. We have discussed in more depth in our discussion section as follows:

      “Interestingly, the inability to fully reconstitute the uterine trNK cell compartment following adoptive transfer suggests that only a subset of circulating cNK cells may be capable of differentiating into trNK cells during pregnancy, or alternatively that trNK cells already present in the virgin uterus may undergo in situ proliferation in the gravid uterus. Previous studies from our lab as well as others show that trNK cells within the pregnant murine uterus express marked levels of Ki67, supporting a model in which local proliferation of uterine trNK cells is a major contributor to the uterine trNK cell pool during pregnancy [7,32]. Prior studies have also described hematopoietic precursors within endometrial and decidual tissues that generate uterine trNK cells, suggesting that the compartment may be also sustained by local precursor differentiation [33-35]. Together, these findings suggest that uterine trNK cell ontogeny may be more complex than a single-source model and raise the possibility that distinct developmental pathways may operate at different stages of reproductive life. Therefore, defining the relative contribution and developmental timing of hematogenous versus locally maintained sources in vivo could provide relevant insights into the developmental trajectories and transcriptional programs that underlie decidual NK cell heterogeneity.”

      Zhai, Q.Y., Wang, J.J., Tian, Y., Liu, X. and Song, Z., 2020. Review of psychological stress on oocyte and early embryonic development in female mice. Reproductive Biology and Endocrinology, 18(1), p.101.

      Wiebold, J.L., Stanfield, P.H., Becker, W.C. and Hillers, J.K., 1986. The effect of restraint stress in early pregnancy in mice. Reproduction, 78(1), pp.185-192.

      Sánchez-Rubio, M., Abarzúa-Catalán, L., Del Valle, A., Méndez-Ruette, M., Salazar, N., Sigala, J., Sandoval, S., Godoy, M.I., Luarte, A., Monteiro, L.J. and Romero, R., 2024. Maternal stress during pregnancy alters circulating small extracellular vesicles and enhances their targeting to the placenta and fetus. Biological Research, 57(1), p.70.

      Filipovic, I., Chiossone, L., Vacca, P., Hamilton, R.S., Ingegnere, T., Doisne, J.M., Hawkes, D.A., Mingari, M.C., Sharkey, A.M., Moretta, L. and Colucci, F., 2018. Molecular definition of group 1 innate lymphoid cells in the mouse uterus. Nature Communications, 9(1), p.4492.

      (3) The authors should consider inducible Tgfbr2 deletion (e.g. with Tamoxifen-inducible Cre) to enable development of the uterine NK compartment in virgin mice and only ablate trNK differentiation during pregnancy. This could help to estimate the turnover of cNK into trNK, or to understand if constant cNK recruitment is required to form the uterine trNK compartment during pregnancy.

      Thank you for this suggestion. We did initially consider incorporating a mouse model with a tamoxifen-inducible deletion of the TGF-βRII to examine the differentiation of peripheral cNK cells into uterine trNK cells more precisely. However, the administration of tamoxifen during murine pregnancy has well-established deleterious effects on implantation, fetal viability, and placentation, which would confound our interpretations of any adverse pregnancy outcome observed in our studies. Because our goal was to assess NK cell-specific contributions to murine gestation without introducing additional pregnancy-related perturbations, we elected to use an Ncr1<sup>iCre</sup> – based mouse model in our studies.

      Ved, N., Curran, A., Ashcroft, F.M. and Sparrow, D.B., 2019. Tamoxifen administration in pregnant mice can be deleterious to both mother and embryo. Laboratory animals, 53(6), pp.630-633.

      Sun, M.R., Steward, A.C., Sweet, E.A., Martin, A.A. and Lipinski, R.J., 2021. Developmental malformations resulting from high-dose maternal tamoxifen exposure in the mouse. PLoS One, 16(8), p.e0256299.

      Ilchuk, L.A., Stavskaya, N.I., Varlamova, E.A., Khamidullina, A.I., Tatarskiy, V.V., Mogila, V.A., Kolbutova, K.B., Bogdan, S.A., Sheremetov, A.M., Baulin, A.N. and Filatova, I.A., 2022. Limitations of tamoxifen application for in vivo genome editing using Cre/ERT2 system. International Journal of Molecular Sciences, 23(22), p.14077.

      (4) Did the authors consider transfer of Tgfbr2-floxed Ncr1-Cre cNK in the same setup as in Fig. 1C? This experiment could confirm the requirement of Tgfbr-dependent signaling for cNK to trNK conversion during pregnancy versus effects of Tgfb signals on trNK numbers in the uterus at steady state (before pregnancy).

      We thank the reviewer for this mechanistically insightful suggestion. We did consider performing reciprocal transfer experiments using TGF-βRII<sup>fl/fl</sup> Ncr1<sup>icre</sup> cNK cells in the same adoptive transfer system as in Figure 1C. Our current adoptive transfer experiments already directly address this question. Transfer of congenically labeled wild-type splenic cNK cells into TGF-βRII<sup>Ncr1Δ</sup> dams at gestational day 0.5 resulted in partial reconstitution of the uterine trNK compartment and, importantly, this was sufficient to rescue the adverse pregnancy outcomes observed at midgestation. These findings indicate that TGF-β–competent cNK cells can differentiate and function appropriately within the pregnant uterine environment, supporting a requirement for TGF-β–dependent signaling in cNK-to-trNK conversion during pregnancy. Because restoration of TGF-β–sufficient cNK cells rescues these pregnancy outcomes, we believe this experiment functionally demonstrates the importance of TGF-β signaling in this process and therefore did not pursue reciprocal transfer of TGF-βRII–deficient cNK cells.

      “Partial reconstitution of uterine trNK cells restores midgestational pregnancy outcomes in TGF-βRII<sup>Ncr1∆</sup> dams

      To determine whether restoring uterine trNK cells could rescue the midgestational pregnancy defects observed in TGF-βRII<sup>Ncr1∆</sup> dams, we adoptively transferred wildtype, congenically labeled splenic cNK cells into pregnant TGF-βRII<sup>Ncr1∆</sup> dams at gd 0.5. By gd 10.5, donor cNK cells were detected in the pregnant uterus, where a subset upregulated CD49a and downregulated CD49b, consistent with acquisition of a uterine trNK cell phenotype (Figure 5 A). However, adoptively transferred splenic cNK cells only partially reconstituted the uterine trNK cell population in the gravid uterus of TGF-βRII<sup>Ncr1∆</sup> dams, as evidenced by reduced absolute number and frequency of donor-derived trNK cells in reconstituted TGF-βRII<sup>Ncr1∆</sup> dams (Figure 5 A-C). Notably, this partial reconstitution was sufficient to rescue the gestational defects caused by impaired TGF-β–mediated uterine trNK cell differentiation. Reconstituted TGF- βRII<sup>Ncr1∆</sup> dams exhibited implantation site numbers and fetal resorption rates at gd 10.5 comparable to those observed in littermate controls (Figure 5 D, E). Together, these findings suggest that even partial restoration of the uterine trNK cell in pregnant TGF-βRII<sup>Ncr1∆</sup> dams is sufficient to restore pregnancy outcomes at midgestation, supporting a central role for uterine trNK cells as the principal NK cell subset required for successful murine pregnancy.”

      (5) Figures 2D/E: The authors should state that ILC1s are reduced in the virgin uterus of female Tgfbr2-floxed or Tgfb1-floxed Ncr1-Cre mice and cite the relevant work (the Ref #29 discussed in this context did not show that?). It would be helpful to include an analysis of all three uterine ILC subsets in steady state. This could help to answer the question if the cNK cell changes are pregnancy-specific or a general phenomenon in Tgfbr2-floxed Ncr1-Cre mice.

      We thank the reviewer for this important comment and for noting the miscitation. We regret the error and have corrected the reference in the revised manuscript to cite the appropriate study demonstrating reduced ILC1s in the virgin uterus of Tgfb1<sup>fl/fl</sup> Ncr1<sup>iCre</sup> mice {Sparano, C. et al. 2024. Autocrine TGF-β1 drives tissue-specific differentiation and function of resident NK cells. Journal of Experimental Medicine, 222(3), p.e20240930}. Please see Line 148. Importantly, the steady-state ILC compartment in virgin Tgfb1<sup>fl/fl</sup> Ncr1<sup>iCre</sup> mice has already been carefully characterized in the previously published work, including analysis of all three uterine ILC subsets. Because the steady-state uterine ILC landscape in this mouse model has already been established by Sparano, C. et al. 2024, our study focuses specifically on the pregnancy-associated changes in the uterine ILC landscape occurring in the absence of TGF-β signaling in Ncr1-expressing cells and their subsequent effects on gestational outcomes. In the absence of TGF-β signaling there appears to be a higher frequency of cNK cells in both the virgin uterus and pregnant uterus, suggesting that this is more of a general phenomenon.

      “However, in the pregnant uterus, CD49a<sup>+</sup> Eomes<sup>-</sup> ILC1s were markedly reduced in implantation sites of TGF-βRII<sup>Ncr1∆</sup> dams, paralleling the reduction of ILC1s previously reported in the virgin uterus of TGF-βRII<sup>Ncr1∆</sup> female mice [26].”

      (6) Figure 2E: Please phrase more carefully about the "concomitant increase" of cNKs, since this increase is much less pronounced compared to the very strong reduction (absence) of trNKs in Tgfbr2-floxed Ncr1-Cre mice. Do the authors suggest that cNKs are halted at this stage and cannot differentiate into trNK, based on these data?

      We thank both reviewers for this suggestion, and we have rephrased our wording to address this concern as follows:

      “This reduction of uterine trNK cells was accompanied by a small increase in the absolute number and frequency of CD49b<sup>+</sup> Eomes<sup>+</sup> cNK cells within the pregnant uterus of TGF-βRII<sup>Ncr1∆</sup> dams (Figure 2 D, E). Collectively, these findings suggest that a TGF-β–driven differentiation pathway directs the conversion of peripheral cNK cells into uterine trNK cells during murine pregnancy.”

      Please also see our response to Reviewer #1, Comment #2.

      (7) Can the reduced litter size and the abnormal spiral artery formation be rescued by transfer of WT cNK into Tgfbr2-floxed Ncr1-Cre mice?

      We thank the reviewers for this interesting question. In subsequent experiments, we transferred congenically labeled, splenic cNK cells from wildtype female mice into TGF-βRII<sup>Ncr1∆</sup> dams at gestational day 0.5. We only observed partial reconstitution of uterine trNK cell population; however, the number of viable implantation sites and resorption rates in reconstituted TGF-βRII<sup>Ncr1∆</sup> dams were comparable to the number of viable implantation sites and resorption rates in HBSS-treated littermate controls at gestational day 10.5. Given that partial reconstitution of the uterine trNK cell compartment in reconstituted TGF-βRII<sup>Ncr1∆</sup> dams was sufficient to rescue the defects in implantation site number and fetal resorption rates observed at midgestation, we hypothesize that this level of restoration may permit patrial but functionally sufficient spiral artery remodeling to reestablish maternal-fetal blood flow adequate to support fetal viability, although spiral artery remodeling was not directly assessed in this transfer study.

      “Partial reconstitution of uterine trNK cells restores midgestational pregnancy outcomes in TGF-βRII<sup>Ncr1∆</sup> dams

      To determine whether restoring uterine trNK cells could rescue the midgestational pregnancy defects observed in TGF-βRII<sup>cr1∆</sup> dams, we adoptively transferred wildtype, congenically labeled splenic cNK cells into pregnant TGF-βRII<sup>Ncr1∆</sup> dams at gd 0.5. By gd 10.5, donor cNK cells were detected in the pregnant uterus, where a subset upregulated CD49a and downregulated CD49b, consistent with acquisition of a uterine trNK cell phenotype (Figure 5 A). However, adoptively transferred splenic cNK cells only partially reconstituted the uterine trNK cell population in the gravid uterus of TGF-βRII<sup>Ncr1∆</sup> dams, as evidenced by reduced absolute number and frequency of donor-derived trNK cells in reconstituted TGF-βRII<sup>Ncr1∆</sup> dams (Figure 5 A-C). Notably, this partial reconstitution was sufficient to rescue the gestational defects caused by impaired TGF-β–mediated uterine trNK cell differentiation. Reconstituted TGF-βRII<sup>Ncr1∆</sup> dams exhibited implantation site numbers and fetal resorption rates at gd 10.5 comparable to those observed in littermate controls (Figure 5 D, E). Together, these findings suggest that even partial restoration of the uterine trNK cell in pregnant TGF-βRII<sup>Ncr1∆</sup> dams is sufficient to restore pregnancy outcomes at midgestation, supporting a central role for uterine trNK cells as the principal NK cell subset required for successful murine pregnancy.”

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1C: The shown gate seems to "cut" into the CD49b staining; staining for all transferred cells should be shown; have cNK cells been stained in parallel with the same panel to provide a positive and compensation control?

      To clarify the phenotype of the adoptively transferred cNK cells, we included two additional gates depicting the expression of CD49a and CD49b in unlabeled (non-vascular) trNK cells and cNK cells in the pregnant uterus Please see the revised Figure 1C.

      “(C) Concatenated flow plots of implantation sites showing that adoptively transferred cNK cells in pregnant uterus of wildtype dams upregulate CD49a and down regulate CD49b by gd 10.5, acquiring a CD49a<sup>+</sup> CD49b<sup>-</sup> Eomes<sup>+</sup> phenotype characteristic of uterine trNK cells (C57BL/6 dams n=4). Here, 2.5x10<sup>6</sup> CD45.2<sup>+</sup> CD3<sup>-</sup> CD19<sup>-</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> CD49b<sup>+</sup> splenic cNK cells were adoptively transferred into pregnant C57BL/6-CD45.1 dams at gd 0.5, and the receptor profile of these cells was subsequently assessed at gd 10.5. Gating strategy: Live, Single Cells; CD3<sup>-</sup> CD19<sup>-</sup> CD45.1<sup>-</sup> CD45.2–PE-Cy7<sup>-</sup> CD45.2–PE<sup>+</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> cells.”

      (2) Figure 2A: The authors could include an isotype control or a staining in a genetic knockout as a control staining.

      Thank you for this suggestion. As suggested, we included staining in a genetic TGF-βRII<sup>Ncr1∆</sup> knockout as additional control staining. Please see the revised Figure 2A.

      “Representative histograms depicting TGF-β Receptor II expression on splenic NK cells from virgin TGF-βRII<sup>Ncr1∆</sup> and wildtype mice as well as splenic and uterine NK cell subsets from pregnant wildtype mice at gd 10.5 (virgin TGF-βRII<sup>Ncr1∆</sup> mice, n=2; virgin mice: C57BL/6, n=5; gd 10.5: C57BL/6 dams, n=8, implantation sites n=8). MFI, median fluorescent intensity. Gating strategy: Live, Single Cells; CD3<sup>-</sup> CD19<sup>-</sup> CD45.1<sup>-</sup> CD45.2<sup>+</sup> NK1.1<sup>+</sup> NKp46<sup>+</sup> cells.”

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors generated mouse and zebrafish models for DeSanto-Shinawi Syndrome, caused by loss-of-function variants in the WAC gene. Using these vertebrate systems, they demonstrate conserved craniofacial and social-behavioral phenotypes that parallel human clinical features, along with deficits in GABAergic markers. They observe increased seizure susceptibility and male-biased brain volumetric changes in Wac mutant mice. Together, these findings begin to define the biological consequences of Wac haploinsufficiency and provide valuable resources for future mechanistic studies.

      Strengths:

      WAC is a high-confidence neurodevelopmental disorder gene and one of the genes identified by large-scale exome sequencing efforts, including the Satterstrom et al. (2020) autism spectrum disorder cohort. This study establishes the first vertebrate Wac models, addressing a major gap in the understanding of DeSanto-Shinawi Syndrome, and provides a framework for studying other syndromic forms of autism. The models generated will be impactful and useful to the community to study and understand DeSanto-Shinawi Syndrome.

      The cross-species analysis is important and well executed, and reveals both conserved and divergent phenotypes. The behavioral and anatomical assays are rigorously executed and well-controlled, and the inclusion of RNA-sequencing analyses adds valuable insights into the mechanisms underlying brain function in Wac mutants. Notably, the RNA-seq data reveal upregulation of several clustered protocadherins, genes central to neuronal identity and cell-cell interactions, which are known to be regulated by dynamic developmental regulation of chromatin architecture. This observation provides an intriguing hint that could link Wac function to higher-order chromatin organization and neuronal connectivity.

      Weaknesses:

      The evidence is solid, but the study remains incomplete in its mechanistic depth and molecular interpretation. The authors compellingly describe behavioral, anatomical, and transcriptomic phenotypes associated with WAC loss, yet do not explore how WAC mechanistically regulates chromatin or transcription. Given prior evidence that WAC interacts with the RNF20/40 ubiquitin ligase complex and promotes histone H2B ubiquitination and transcriptional elongation, the paper would benefit from a discussion of these functions as a potential link between Wac haploinsufficiency and the observed changes in neuronal gene expression. Similarly, the authors mention WAC's WW and coiled-coil domains but do not consider how these domains could mediate nuclear interactions or recruitment of transcriptional cofactors that shape gene regulation and chromatin organization in neurons.

      We agree that many mechanisms underlying how both animal model phenotypes and human symptoms that are caused by the Wac gene still need to be worked out. Due to the need to generate a great deal of data to first describe these models in this manuscript this will be expanded upon later. In lieu of this, we plan to follow up with mechanistic papers later to fully address the gap that remains. We have now added a paragraph in the discussion to bring up these important points regarding the roles of Wac during transcription and how its protein domains might be involved in these processes.

      The transcriptomic analysis is rich but largely descriptive. Although the upregulation of clustered protocadherins is particularly intriguing, these findings are not validated or localized to specific neuronal populations. The study would be strengthened by independently validating the most significant RNA-seq changes, such as protocadherin gamma genes, using in situ hybridization methods to confirm the spatial and cellular specificity of expression changes.

      We have greatly expanded the analyses of the bulk RNA-seq data, including a more rigorous look into the differences in gene expression between sexes, which has additionally revealed males to be more impacted by Wac loss of function. We have also added new western blot data for pan protocadherin alpha, which is now validated to be upregulated in the cortex (new Figure 7I and 7J). We are holding back any additional data from this report as we have single nucleus RNA-seq data that will be reported on in follow-up papers with targeted conditional deletion models.

      Finally, while the behavioral and MRI results add valuable breadth, their interpretation would be improved by clearer reporting of sample sizes, statistical corrections, and effect sizes to support claims of sex-specific and regional brain volume differences.

      Some additional details have been added to the methods section. In addition, we have now provided sample sizes assessed in each figure legend.

      Reviewer #2 (Public review):

      The authors describe the first deep neurological characterization of WAC mutation in two vertebrate species (zebrafish and mouse). They examine these at various levels, guided by the work in humans that has associated a heterozygous WAC mutation with DeSantos Shinawi Syndrome (DESSH). Therefore, they investigate the animals for a variety of phenotypes, following a template for what is seen when characterizing a new mouse/fish model of a developmental disability gene. Investigations include analysis of skull and jaw for abnormalities(both species), MRI of brain structure(in mice), electrophysiology(mice), assessment of signaling pathways (by Western blot, in mice), cell counts (both, more in mice), transcriptomics (mice), and behavior (both).

      Generally, this describes an important first characterization of the consequences of the mutation. Most of the studies appear well-conducted and reasonably powered, thus solid or convincing. However, there are a few places where the data presentation could be improved for clarity, and a few concerns about some choices in analytical approach for a couple of the experiments, where improved statistical approaches could improve their sensitivity and/or better rule out false positives, and thus the support of some of these claims is currently incomplete. There is also some lack of clarity about the rationale for some decisions regarding the fish genetics. Nonetheless, this is an important and useful first characterization of many phenotypes of these lines. Such experiments form a baseline for future mechanistic studies in the same lines and a platform to test approaches to reverse phenotypes.

      Individual claims and their strength & weaknesses:

      (1) The authors developed mouse and zebrafish models of WAC deletion

      They used the existing KOMP floxed WAC line to generate a null allele. For the mouse, there is a Western showing that it is indeed null for the protein. The fish data is less robustly validated - they don't confirm the allele in null at the protein or RNA level, and fish have two paralogs (waca and wacb), and this paper only characterizes one of these. So this evidence is less clear. The evaluated mice are heterozygous (Het), similar to patients, while the fish appear to be evaluated as homozygous mutants.

      We agree with the reviewer’s comments on zebrafish genetics. Since antibodies against zebrafish Wac proteins are not available, we could not examine protein levels in zebrafish. We predicted frameshift mutations due to DNA analyses in waca and wacb KO zebrafish. We made waca KO, wacb KO, and waca/wacb double KO zebrafish. waca/wacb double KO zebrafish showed a lethal phenotype, similar to homozygous mice mutants. Since wacb KO zebrafish did not show any detectable phenotype we do not report those here. However, we now show examples of the wacb and dKO zebrafish in Figure S1. Since waca KO zebrafish showed craniofacial and behavioral phenotypes that are comparable to mice Het and human patients, they are focused on in this report.

      (2) The authors show that both species show altered craniofacial features

      These data appear well powered, and the findings are robust.

      We appreciate this confirmation.

      (3) Each model altered GABAergic neurons

      In mice, the authors stained with PV antibodies and saw a decrease in cells positive for this staining. A second marker, Lhx6, does not show a difference, suggesting this might be a change in PV expression rather than cell number. They could maybe look into the literature to see if this loss of just the protein also occurs in other models. Overall, the sample size here is a bit smaller than other parts of the paper (n=3), and the methods on the cell counts were less clear, so it is not as clear that this finding is as robust. The authors counted several other broad classes of cells, and those appear normal. Interestingly, there might also be some TBR1 mislocalization in layer 6 that might be significant with added power.

      Thank you for these suggestions. Yes, other models also show this lack of PV expression even when MGE-lineage interneurons are present at normal levels. We mention in the discussion a previous study on the ASD gene CTNNAP2 that showed this. We also agree that there is a trend going on in the Tbr1 population. We assessed another WT and Het pair for Tbr1 laminar distribution and were able to determine that these changes held up and are now significantly different; the person counting these numbers was blind to the genotypes. Finally, we added more details to the methods to describe how the counting was performed.

      The fish data is based on an in situ hybridization for GAD. The measure shown is the width of the positive area in the forebrain. This measure is not one I have seen much before, and has potential to be driven by something unrelated to GABA (e.g., if the whole forebrain were simply a bit smaller). So this analysis could use a couple of other approaches (density of signal?) and/or a control probe for some other brain gene showing the measure is normal, and thus it is not just a size issue.

      To compare altered GABAergic neurons in mice and zebrafish, we tried to isolate zebrafish PV genes and examined their expression by whole-mount in situ hybridization, now included Figure S3 but found no differences. However, we could not find any zebrafish PV gene useful for GABAergic neurons. We chose to examine gad1b expression in the positive area of the forebrain in WT and waca KO zebrafish and then found differences in the brain area with gad1b expression. Since WT and waca KO brain sizes are generally the same we believe this measurement is reasonable to make this conclusion and have added text to the results section to justify.

      (4) Mice were more susceptible to the seizure-inducing agent PTZ

      These data appear well powered, and the findings are robust. The authors also did a fair amount of useful electrophysiology that was all normal, but appeared to be well executed.

      Thank you, we appreciate this confirmation.

      (5) Mice had changes in brain volume that interact with sex

      The authors conducted an MRI on a good number of mice and reported a slight increase in global volume just in males. Sample size is fair, but the statistical approach here may be better if it puts males and females in the same model (to boost power and explicitly test for sex by genotype interaction that they report), and there is some chance that the brain region level differences that they report could include some false positives. They tested many regions, and it is not clear whether or not they corrected for the number of tests. Often, an FDR correction would be used in such imaging studies. It may be that only the most robust regional findings will survive those corrections. It is interesting data either way, but the analysis could be improved.

      Given the 80 regions (bilaterally) that we used and the number of mice, i.e. 6-7, we are underpowered to robustly undertake FDR types of corrections. In the data presented we used t-tests between sex and regions to illuminate putative regional changes. However, we did revisit our MRI data and found three data sets where the results were not normally distributed. We thus changed our statistical test to Mann Whitney for male retrosplenial cortex, male parietal cortex and female corpus callosum, which are now reflected in the figures and differential statistics noted in figure legends.

      (6) Several behaviors are altered in the mice as well

      These studies were fairly well-powered (n=15,16), and they found several positive and negative results, including alterations in memory and sociability in both species. There is a minor statistical flaw in the three-chamber analysis (they don't actually compare the Hets directly to the wildtypes in their statistical testing - a common mistake in neuroscience that should be addressed. But the data look like they will probably still be significant when correctly analyzed. In the supplement, the authors could do a bit more with the data they have to look at hyperactivity (i.e., show total motion in open field, not just time in center vs. periphery), and adding sex to their model might improve sensitivity for genotype effects.

      Thank you for these suggestions. We have done several things to address this behavioral paradigm. First, we added more n’s and also switched from comparing the mouse vs. object to just comparing genotypes as a variable. In addition, we switched to quantifying a discrimination index, described in Phiilips et al., 2019 PMID: 31112129 for our measurement. These new data are shown in Figure 3A. Open field total distance traveled has now been added to Figure S2A. For all other measurements, we did first assess for sex differences but found none and thus compiled both sexes for the graphs.

      (7) Some biochemical signaling pathways are altered in the brain

      These are n=4 immunoblots, and show altered phospho ERK, but no changes in other signaling events predicted from prior WAC literature like H2B ubiquitination. They appear well done, and the authors share the full blots in the supplement.

      Thank you, we appreciate this confirmation. Since Wac is an adaptor protein we needed to test these reported molecular changes in neurons that were previously only reported in cell lines and drosophila. We were not surprised that some of these previously reported changes would not be the same in brain cells. However, it is possible that these changes might arise in more discrete brain regions or at different times during development, which will be tested in our future conditional knockout models.

      (8) WAC deletion also alters gene expression in the brain

      These studies were well-powered for RNAseq, with 10 and 14 samples, using neonates (P2), just the forebrain. The sequencing quality metrics all looked good, and the approach to analysis was okay. It would be stronger to again include sex in the model, rather than separate by sex. There were some typos in this part of the paper that made part of the conclusions unclear, but the RNAseq nicely confirmed the mutation of the mice, and discovered many differentially expressed genes, consistent with the role of this gene as a regulator of transcription. The presentation could be expanded to make more use of the data. Overall, though, this is a useful first characterization of the transcriptome in the line.

      Thank you for the suggestions. We have greatly expanded our assessments of the RNA-seq data. Upon analyzation of the data we found many differences between males and females and now show combined and sex-separated data. Our new data isolate several more extreme and some unique changes in males that are better shown as stand alone figure panels. In addition to these edits, we have also reworked all the text in this section of the results for better reading.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The cause and timing of lethality in the homozygous Wac knockout should be reported or discussed. Investigating Wac homozygous knockout embryos, if viable at early stages, could provide valuable insight into the developmental origins of the neuroanatomical and behavioral phenotypes described in the heterozygous animals. Even a brief histological or transcriptomic characterization of embryonic brains would strengthen the mechanistic understanding of Wac function during neurodevelopment.

      We agree and have collected embryos as early as embryonic day 12.5 from multiple litters but never detected a knockout. We have added this text to the animal methods sections to let readers understand effort had been done to determine when death occurs. While we don’t currently explore this further in mice we now include zebrafish waca; wacb double knockouts. Notably, while we were able to generate a few of these mutants, most died. However, some zebrafish were aged long enough to observe lethal deficits in heart formation and swim bladder development, suggesting that early loss of Wac could impact these critical organs that leads to death.

      (2) A better description of the data reported in Supplementary Tables 3 through 5 is needed. Supplementary Table 3 does not report any statistically significantly differentially expressed genes in the FDR column, and Supplementary Table 5 reports only two, and the reader should understand what the columns are indicating.

      We have now added figure legend text to the supplementary file to explain each Table mentioned here.

      Reviewer #2 (Recommendations for the authors):

      (1) Page 3, last paragraph. The description of wacb is confusing. I recommend that the authors provide the unshown data they mention and also further explanation of the breeding scheme and result. Indeed, if wacb is homozygous lethal, does that make it more like the mouse WAC gene, and thus potentially the more relevant paralogue to study? Are both waca and wacb expressed in the same tissues? How does that compare to mouse and human WAC expression? Such figures about gene expression (even when adapted with permission from public resources like Allen brain atlas or GTEX) are common in this sort of paper, as they can be helpful to understand when and where the gene is thought to act. For waca vs. wacb, they may help determine which gene is more relevant to the brain (for example, if only one is expressed in the brain).

      First, this is a great question and we have now added whole mount in situ for the waca and wacb genes as Figure S1. These data show low to no wacb expression in brain regions while waca is highly expressed there. Since the waca mutants showed phenotypes relevant to DESSH but wacb mutants did not, this correlates with observed expression patterns without fully excluding wacb from any role. Thus, we also made waca/wacb double KO zebrafish that showed a lethal phenotype, similar to homozygous mice mutants. Only a few waca; wacb double knockouts survived a little through development and are now shown in Figure S1. Since wacb KO zebrafish did not show any detectable phenotype on their own, we did not include the data since there are already several figures/tables in this manuscript. However, the waca KO zebrafish did show phenotypes similar to humans with DESSH and are the ones we focused on.

      (2) Why did the authors cross the mice into the outbred CD1 background? Usually, most labs keep the lines on an inbred background. Was there a particular rationale here? I am not saying that they could not outcross them. It is just a bit puzzling why. Perhaps a sentence of explanation in the methods section would be warranted.

      This is a great question and we have now added text to the animal methods section. Many labs that study development, especially on genes critical for survival/life like the Wac gene, use a more robust strain like CD-1. By doing this, we have a better chance of evaluating mutants at more mature ages and getting enough progeny to do more reproducible studies.

      (3) A typical first experiment in a new knockout (fish or mouse) is to establish that the deletion does indeed result in a loss of RNA and protein. In the absence of this, the rest of the paper cannot be as confidently interpreted.

      We did this for the mouse model and found reduced protein expression in the constitutive Het, however this datum is part of the western blots in figure 5. We now mention this in the early results section that protein levels were reduced in the Hets but maintain that the presentation of the western blot is better suited in Fig. 5 to compare to the other western blots. For zebrafish this was attempted but was more difficult. Available antibodies don’t work in zebrafish. RNA expression was attempted in both models and due to Wac being a critical gene for life, there are checks in place to upregulate faulty and normal RNA in the waca model. We screened for frameshift mutations in multiple KO lines and confirmed it by genomic DNA sequencing. In making many KOs and large-scale mutagenesis in zebrafish, we usually depend on phenotype-genotype segregation in Mendelian inheritance for many generations.

      (4) Are these new lines indeed knockouts? I did find a WAC western as part of a later figure for the mouse. The authors may want to mention that earlier, or present at least that data right away. What about in the fish? Is there a way to confirm at the RNA or protein level that it is indeed a null allele?

      Yes, as mentioned in the above response we have now mentioned our Wac western blot results early when introducing the mouse mutants and the issues with doing this in fish are presented above as well.

      (5) Why are fish used that are KO while mice are Hets? Are WAC homozygous mice not viable? This should be mentioned. Regardless, the rationale for examining heterozygous mice and homozygous mutant fish should be provided. Each kind of experiment is useful, but they are interpreted in different ways. Hets will genocopy the patients, who are generally hets, while KOs are often useful for a study of the essential roles of the genes, even if they are not really modeling the patient gene dose.

      Wac homozygous mice in our hands are embryonic lethal, now mentioned in the animal methods section, but we found early on that the Hets mimic several human DESSH patients. In zebrafish it is more complicated. We analyzed waca and wacb hets in zebrafish but found no phenotypes. This could be in part due to some complementation between the waca and wacb genes. It is also possible that a full waca KO could resemble a human DESSH individual since wacb may complement somewhat, even though deleting wacb entirely does not have a measurable phenotype. We have added more text to the discussion to explore these complexities. We also made waca/wacb double KO (dKO) zebrafish but they showed lethal phenotype, similar to homozygous mice mutants and suggesting some complementation by the wacb gene even though alone it did not exhibit phenotypes.

      (6) Figure 3A: It does not appear that the authors are directly statistically comparing the two groups (genotypes) that they are drawing conclusions about. This is an unfortunately common mistake in the neuroscience literature across papers. There is a nice older review about it here. https://pubmed.ncbi.nlm.nih.gov/21878926/. To draw conclusions about the differences between the mouse genotypes, they need to compare the two genotypes directly with a statistical test. See Nygard et al for a recommended approach, like comparing social preference indexes

      (https://onlinelibrary.wiley.com/doi/abs/10.1002/aur.2154).

      Thank you for this information. Previous reviewers at a different journal asked for this particular evaluation. We have now made changes to address the assessment, and graphs now reflect comparisons of genotypes instead of a single genotype between time with a mouse or object. We have also moved to using a social discrimination index to compare the genotypes, similar to the study mentioned.

      (7) MRI - it is a bit weird to separate the male and female brains just for the MRI. Was there a premise from human data to do so? If not, the authors should probably pool them. If they are concerned there are sex effects (or, more likely, a sex by genotype interaction) I recommend that they use a two-factor ANOVA and simply put both sex and genotype into the model. This will also have the advantage of increasing their statistical power for genotype effects a bit. If their current results are robust, they will still show up as a significant sex x genotype interaction.

      All data in the manuscript initially compared the sexes to each other. We have now added this text to the animal section of the methods: For MRI, some zebrafish behaviors and now the RNA-seq data, sex was a difference and due to this observation, sex was (or now is) presented independently for these measurements. We now state that if no sex differences were observed the data were pooled.

      (8) Also, did the authors correct for multiple testing in the MRI analysis? Since they are testing many regions, there is a risk of false positives if they do not. This could be confounded further by their splitting the data by sex, thus doubling the number of tests.

      As noted above we did not do multiple corrections given the large number of regions and low number of replicates.

      (9) How many images per animal were analyzed for the cell counts? This detail is absent from the methods and would help with evaluating the robustness of these findings. What other approaches were used to make sure the counting was unbiased?

      We analyzed 3-4 images per animal for counts and counted hundreds of cells per image. In addition, the person counting was blinded to avoid any bias. These details have now been updated in the methods.

      (10) As with the MRI, for the DEG analysis, I recommend the authors simply put sex and genotype into the same model as two factors (with an interaction), to increase their sensitivity to genotype effects, as well as be able to report on robust genotype x sex differences, if there are any. They may also consider testing the model with and without excluding the three outlier animals on their PCA. It may be that the noise of those outliers is detracting from their sensitivity for DEGs somewhat.

      We greatly expanded our analyses and found more robust and unique changes in males that are now added to Figure 7 and supplemental files. After considering the data, decided to highlight the sex differences separately.

      (11) A few more relatively simple things could readily be done with the RNAseq data to add some depth and interpretation. For example, do the hits here overlap other published IDD/autism DEG lists from mouse knockouts studies of genes like FoxP2, Chd8, Dnmt3a, Myt1l, Tcf4, etc? Do autism genes show up in the lists of hits here? And if so, more than expected by chance? Can they provide some visualization of their GO results in the main figure?

      When we looked into the sex differences more we found that only the males showed significant upregulation of other autism risk genes increase that was previously unappreciated when the sexes were assessed together. Yes, several autism genes do show up but is heavily biased to males. Our main Figure 7 and new supplemental files show new GO term analyses and provide additional data looking not only autism but other factors.

      (12) It appears the IMPC has phenotyped this mouse somewhat, including craniofacial abnormalities. They also report on some blood cell differences. Anyway, if no one has written about that data yet (as it was generated in the context of a big consortium effort), their guidelines may allow you to include some of their data as Supplementary Figures here with proper attribution. It might help to at least summarize useful findings from there in your discussion.

      Due to the large number of figures/tables already in this report we don’t think this will be helpful. However, we do refer readers to the consortium in the animal methods section so they can explore data already generated by the IMPC.

      (13) Minor/Typos:

      (a) Figure 2K: I am confused by the description of three genotypes in the legend, but only two in the panel?

      Corrected.

      (b) I found it a little distracting that some results figures were embedded in the introduction.

      We have moved the figures further in the manuscript to start in the results section.

      (c) I don't understand this sentence: "Due to reduced sample size, sex-stratified DE was performed without model corrections at FDR < 0.1, 7 and found genes significantly upregulated and downregulated, respectively;" The sample size here seemed robust, so I am not sure what they were referring to? Are there missing numbers form this sentence? What is the 7? I think there are enough typos here that I am not sure how to evaluate this claim. Thus, the writing and clarity of this part could be improved.

      This section had several typos that have now been corrected.

      (d) "Marwan Shinawi, (unpublished results)" is a bit atypical of a citation. Are these results being reported with his permission? If so, then it should say 'personal communication' (if the journal permits this - some do not). If not, they should not report someone else's unpublished results without their explicit permission. It might upset some people to have their results presented this way.

      We have changed unpublished results to personal communication. Marwin Shinawi is an author on this manuscript and has approved of everything we have reported.

      (e) In all figures, consider shape or color coding for sex, even when pooling the data (e.g, the data points in the behavior figures).

      This is a good idea but since we found no difference when analyzing the data we don’t see how this extra work will make a difference. Since we now mention that sex differences were only presented as separate graphs when observed in the methods we think this should be acceptable.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The behaviour of cells expressing constitutively active HRas is examined in mosaic monolayers, both in MCF10a breast epithelial and Beas2b bronchial epithelial cell lines, mimicking the potential initial phase of development of carcinoma. Single HRas-positive cells are excluded from MCF10a but not Beas2b monolayers. Most interestingly, however, when in groups, these cells are not excluded, but rather sharply segregated within a MCF10a monolayer. In contrast, they freely mix with wt Beas2b cells. Biophysical analysis identifies high tension at heterotypic interfaces between HRas and wild-type cells as the likely reason for segregation of MCF10a cells. The hypothesis is supported experimentally, as myosin inhibition abolishes segregation. The probable reason for lack of segregation in the bronchial epithelium is to be found in the different intrinsic properties of these cells, which form a looser tissue with lower basal actomyosin activity. The behaviour of single cells and groups is recapitulated in a vortex model based on the principle of differential interfacial tension, under the condition of high heterotypic interfacial tension.

      Strengths:

      Despite being long recognized as a crucial event during cancer development, segregation of oncogenic cells has been a largely understudied question. This nice work addresses the mechanics of this phenomenon through a straightforward experimental design, applying the biophysical analytical approaches established in the field of morphogenesis. Comparison between two cell types provides some preliminary clues on the diversity of effects in various cancers.

      Weaknesses:

      Although not calling into question the main message of this study, there are a few issues that one may want to address:

      (1) One may be careful in interpreting the comparison between MCF10a and Beas2b cells as used in this study. The conditions may not necessarily be representative of the actual properties of breast and bronchial epithelia. How much of the epithelial organization is reconstituted under these experimental conditions remains to be established. This is particularly obvious for bronchial cells, which would need quite specific culture conditions to build a proper bronchial layer. In this study, they seemed to be on the verge of a mesenchymal phenotype (large gaps, huge protrusions, cells growing on top of each other, as mentioned in the manuscript).

      As an alternative to Beas2b, comparison of MCF10a with another cell line capable of more robust in vitro epithelial organization, but ideally with different adhesive and/or tensile properties, would be highly interesting, as it may narrow down the parameters involved in segregation of oncogenic cells.

      (2) While the seminal description of tissue properties based on interfacial tensions (Brodland 2002) is clearly key to interpreting these data, the actual "Differential Interfacial Tension Hypothesis" poses that segregation results from global differences, i.e., juxtaposition of two tissues displaying different intrinsic tensions. On the contrary, the results of the present work support a different scenario, where what counts is the actual difference in tension ALONG the tissue boundary, in other words, that segregation is driven by high HETEROTYPIC interfacial tension. This is an important distinction that should be clarified.

      (3) Related: The fact that actomyosin accumulates at the heterotypic interface is key here. It would be quite informative to better document the pattern of this accumulation, which is not clear enough from the images of the current manuscript: Are we talking about the actual interface between mutant and wt cells (membrane/cortex of heterotypic contacts)? Or is it more globally overactivated in the whole cell layer along the border? Some better images and some quantification would help.

      (4) In the case of Beas2b cells, mutant cells show higher actin than wt cells, while actin is, on the contrary, lower in mutant MCF10a cells (Figure 2b). Has this been taken into account in the model? It may be in line with the idea that HRas may have a different action on the two cell types, a possibility that would certainly be worth considering and discussing.

      Comments on revisions:

      There is still one last point that should be made even clearer:

      The system is being modelled based on the principle of INTERFACIAL TENSION, a description pioneered by the works of Steinberg and of Harris, and nicely conceptualized by Brodland (2002). Now the observed behaviour is a perfect case of sorting based on higher interfacial tension AT the boundary between cell types (with nice additional documentation of local actin and myosin enrichment in the revised manuscript). What needs to be made crystal clear it that this is NOT equivalent to the model of DITH ("DIFFERENTIAL INTERFACIAL TENSION HYPOTHESIS)" (Brodland 2002, Krieg et al 2008). It is important to stop using DITH in this context, as it leads to confusion and misinterpretations. Indeed, DITH predicts cell/tissue sorting based on differences in interfacial tension WITHIN the two cell types. While DITH accounts for relative POSITIONING (one tissue engulfing the other), it is now established that this is not the motor for cell sorting and tissue segregation, the key parameter is being heterotypic tension at the heterotypic interface. I thus invite the authors to avoid the terms "differential"/DITH, and rather use either "interfacial tension", or specifically to "HIGH HETEROTYPIC INTERFACIAL TENSION".

      Related: the authors correctly cite Canty et al NatComm2017 when discussing this phenomenon. I suggest to add an additional key supporting reference "D.M. Sussman, J.M. Schwarz, M.C. Marchetti, M.L. Manning, Soft yet sharp interfaces in a vertex model of confluent tissue, Phys. Rev. Letters 120 (2018) 058001". One may also include another pioneer work in Drosophila is "M. Aliee, J.C. Roper, K.P. Landsberg, C. Pentzold, T.J. Widmann, F. Julicher, C. Dahmann, Physical mechanisms shaping the Drosophila dorsoventral compartment boundary, Curr. Biol. 22 (2012) 967-976."

      We thank the reviewer for this important clarification. We fully agree that the mechanism underlying the observed segregation in our system is best described in terms of elevated heterotypic interfacial tension, rather than the classical Differential Interfacial Tension Hypothesis (DITH). As the reviewer correctly points out, DITH in its original formulation refers to differences in intrinsic interfacial tensions within each cell population, which primarily governs relative positioning (e.g., tissue engulfment), rather than the local sorting dynamics we observe here.

      In contrast, our experimental and modeling results support a scenario in which segregation is driven by increased tension specifically at heterotypic interfaces between HRasV12 and wild-type cells. We agree that continued use of the term “Differential interfacial tension” in this context may lead to conceptual ambiguity.

      Accordingly, we have revised the manuscript throughout to replace references to “differential interfacial tension” with more precise terminology, namely “interfacial tension” or “heterotypic interfacial tension”, wherever appropriate. We have also updated the Discussion to explicitly clarify this distinction and its implications for interpreting our results.

      We thank the reviewer for suggesting additional relevant literature which have now included.

      Reviewer #2 (Public review):

      Summary:

      The authors investigate the behavior of oncogenic cells in mammary and bronchial epithelia. They observe that individual oncogenic cells are preferentially excluded from the mammary epithelium, but they remain integrated in the bronchial epithelium. They also observe that clusters of oncogenic cells form a compact cluster in mammary epithelium, but they disperse in the bronchial epithelium. The authors demonstrate experimentally and in the vertex model simulations that the difference in observed behavior is due to the differential tension between the mutant and wild-type cells due to a differential expression of actin and myosin.

      Strengths:

      Very detailed analysis of experiments to systematically characterize and quantify differences between mammary and bronchial epithelia

      Detailed comparison between the experiments and vertex model simulations to identify the differential cell line tension between the oncogenic and wild-type cells as one of the key parameters that are responsible for the different behavior of oncogenic cells in mammary and bronchial epithelia

      Weaknesses:

      It is unclear what is the mechanistic origin of the shape-tension coupling, which is used in the vertex model, and how important that coupling is for the presented results. Authors claim that the shape-tension coupling is due to the anisotropic distribution of stress fibers when cells are under external stress. It is unclear why the stress fibers should affect an effective line tension on the cell boundaries and why the stress fibers should be sensitive to the magnitude of the internal isotropic cell pressure. In experiments, it makes sense that stress fibers form when cells are stretched. Similar stress fibers form when cytoskeleton or polymer networks are stretched. It is unclear why the stress fibers should be sensitive to the magnitude of internal isotropic cell pressure. If all the surrounding cells have the same internal pressure, then the cell would not be significantly deformed due to that pressure and stress fibers would not form. Authors should better justify the use of the shape-tension coupling in the model, since most of the observed behavior is already captured by the differential tension even if there is no shape-tension coupling.

      We thank the reviewer for this comment. We agree that we did not provide a mechanistic origin for the shape-tension coupling. In our model, stress fiber formation, along with actin ring formation, indicated that cells at the interface were elongated. Hence, we hypothesised that an interfacial force could induce nematic alignment at the interface. However, such an activity would only be feasible if the interface interaction were sufficiently high. Thus, the isotropic pressure at the heterotypic interface served as a proxy for cell-cell interactions in our model. However, inspired by recent work [1], we have tested whether activation of cells at the interface by shear stress would produce similar results. Exploring this aspect will require additional simulations.

      (1) Pérez-Verdugo, F., Maniou, E., Galea, G. L., & Banerjee, S. (2026). Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis. Current Biology.

      The observed difference of shape indices between the interfacial and bulk cells in simulations in the absence of differential line tension is concerning. This suggests that either there are not enough statistics from the simulations or that something is wrong with the simulations. For all presented simulation results, the authors should repeat multiple simulations and then present both averages and standard deviations. This way it would be easier to determine whether the observed differences in simulations are statistically significant.

      The observed differences in shape indices between interfacial and bulk cells in simulations in the zero-line-tension case (Lambda=0) remain non-zero at the zero-stress threshold because the interface cells are still subject to the shape-dependent contribution gamma_ij, since the current model treats gamma_ij as independent of Lambda. We are exploring the possible relationship between Lambda and gamma_ij, and we will update this in the next version of the manuscript.

      Recommendations for the authors:

      The editor recommends considering the new comment made by reviewer #1 in his/her report:

      "There is still one last point that should be made even more clear:

      The system is being modelled based on the principle of INTERFACIAL TENSION, a description pioneered by the works of Steinberg and of Harris, and nicely conceptualized by Brodland (2002). Now the observed behaviour is a perfect case of sorting based on higher interfacial tension AT the boundary between cell types (with nice additional documentation of local actin and myosin enrichment in the revised manuscript). What needs to be made crystal clear it that this is NOT equivalent to the model of DITH ("DIFFERENTIAL INTERFACIAL TENSION HYPOTHESIS)" (Brodland 2002, Krieg et al 2008). It is important to stop using DITH in this context, as it leads to confusion and misinterpretations. Indeed, DITH predicts cell/tissue sorting based on differences in interfacial tension WITHIN the two cell types. While DITH accounts for relative POSITIONING (one tissue engulfing the other), it is now established that this is not the motor for cell sorting and tissue segregation, the key parameter is being heterotypic tension at the heterotypic interface. I thus invite the authors to avoid the terms "differential"/DITH, and rather use either "interfacial tension", or specifically to "HIGH HETEROTYPIC INTERFACIAL TENSION".

      Related: the authors correctly cite Canty et al NatComm2017 when discussing this phenomenon. I suggest to add an additional key supporting reference "D.M. Sussman, J.M. Schwarz, M.C. Marchetti, M.L. Manning, Soft yet sharp interfaces in a vertex model of confluent tissue, Phys. Rev. Letters 120 (2018) 058001". One may also include another pioneer work in Drosophila is "M. Aliee, J.C. Roper, K.P. Landsberg, C. Pentzold, T.J. Widmann, F. Julicher, C. Dahmann, Physical mechanisms shaping the Drosophila dorsoventral compartment boundary, Curr. Biol. 22 (2012) 967-976."

      Please see response to Reviewer 1

      Reviewer #2 (Recommendations for the authors):

      The authors have improved the manuscript and addressed some of my concerns. However, some of the questions were not adequately addressed.

      (1) I appreciate additional justification regarding the need for the shape-tension coupling in the vertex model. However, the authors have not answered my question regarding why the shape-tension coupling model should be sensitive to the magnitude of the internal isotropic cell pressure. In experiments, it makes sense that stress fibers form when cells are stretched, but it is unclear why the stress fibers should be sensitive to the magnitude of internal isotropic cell pressure. If all the surrounding cells have the same internal pressure, then the cell would not be significantly deformed due to that pressure, and stress fibers would not form.

      We thank the reviewer for pointing this out. We agree that we did not provide a mechanistic origin for the shape-tension coupling. In our model, stress fiber formation, along with actin ring formation, indicated that cells at the interface were elongated. Hence, we hypothesized that an interfacial force could induce nematic alignment at the interface. However, such an activity would only be feasible if the interface interaction were sufficiently high. Thus, the isotropic pressure at the heterotypic interface served as a proxy for cell-cell interactions in our model.

      However, inspired by recent work [1], we have tested whether activation of cells at the interface by shear stress would produce similar results. Exploring this aspect will require additional simulations.

      (1) Pérez-Verdugo, F., Maniou, E., Galea, G. L., & Banerjee, S. (2026). Mechanosensitive feedback organizes cell shape and motion during hindbrain neuropore morphogenesis. Current Biology.

      (2) I appreciate that the authors provided additional statistics related to simulations. I am still very concerned about the observed difference in the shape indices between the cells at the interface and the bulk, when the interfacial line tension is exactly zero (Lambda=0). In that case, the cells at the interface and at the boundary are identical, and there should be no difference in the shape indices. Are cells at the interface for the zero-line tension case (Lambda=0) still subject to the shape dependent contribution gamma_ij? If that contribution is still included for the cells at the interface, then this could explain why cells at the interface are still different from cells in the bulk even when Lambda=0.

      The observed differences in shape indices between interfacial and bulk cells in simulations in the zero-line-tension case (Lambda=0) remain non-zero at the zero-stress threshold because the interface cells are still subject to the shape-dependent contribution gamma_ij, since the current model treats gamma_ij as independent of Lambda. We are exploring the possible relationship between Lambda and gamma_ij, and we will update this in the next version of the manuscript.

      (3) Authors included several additional supplemental figures (Figs. S4, S5, S6, S7) , but they are not discussed in the manuscript text. These new supplemental figures were only discussed in the rebuttal letter. These figures should also be discussed in the manuscript text.

      We have cited the new supplementary figures in the main text.

      (4) Authors have answered in the rebuttal letter what experimental data was used in Fig. 4c. This information also needs to be provided in the manuscript text.

      We have added this information in the caption of Figure 4

      (5) Supplementary Figure 3 is missing. That figure got moved to the appendix.

      This has been rectified in the Supplementary file and the citations have been updated accordingly in the main text.

      (6) At the end of section 4 in the main text, the authors introduced a new sentence regarding simulations of the vertex model with interfacial tension and mechanochemical feedback. The details of that model are described in the appendix, but it would be helpful to add a sentence or two already in the main text describing what is the mechanism of the mechanochemcial feedback.

      We have added a line describing the mechanism of mechanochemical feedback.

      (7) In the definition of the eccentricity, 'a' should be the minor axis and 'b' the major axis, i.e., 'a' and 'b' should be swapped.

      We have corrected this.

      (8) There is a typo at the end of the vertex model description in the methods section. "The details of the shape-tension coupling is described in the interface." The word interface should be an appendix.

      We have fixed the typo.

      (9) In the appendix section describing the shape-tension coupling, the authors should explain how the cell's director n is defined.

      We have added a line in the appendix section describing shape-tension coupling explaining how the cell’s director n is defined.

      (10) In Appendix Fig. 1, the two angles are defined as theta and theta' but the figure caption is defining angles theta_1 and theta_2. These angles need to be consistent.

      This has been fixed.

    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 reveal that the availability of extracellular asparagine (Asn) represents a metabolic vulnerability for the activation and differentiation of naive CD4+ T cells. To deplete extracellular Asn, they employed two orthogonal approaches: activating naive CD4+ T cells in either PEGylated asparaginase (PEG-AsnASE)-treated medium or custom-formulated RPMI medium specifically lacking Asn. Importantly, they demonstrate that depletion not only impaired metabolic reprogramming associated with CD4+ T cell activation but also reduced CD4+ helper T cell lineage-specific cytokine production, thereby ameliorating the severity of experimental autoimmune encephalomyelitis.

      Strengths:

      The experiments presented here are comprehensive and well-designed, providing compelling evidence for the conclusions. The conclusions will be important to the field.

      We thank the reviewer for their assessment of our work and enthusiasm towards our findings.

      Weaknesses:

      (1) EAE is the prototypic T cell-mediated autoimmune disease model, and both Th1 and Th17 cells are implicated in its pathogenesis. In contrast, Th2 and Treg cells and their associated cytokines (such as IL-4 and IL-10) have been shown to play a role in the resolution of EAE, and potentially in the modulation of disease progression. Thus, it will be important to determine whether Asn depletion affects the differentiation of naive CD4+ T cells into corresponding subsets under Th2 and Treg polarization conditions, as well as the expression of lineage-specific transcription factors and cytokine production.

      We appreciate that the reviewer recognizes the functional relevance of our findings showing that Asn is important for proper Th17 differentiation and promotion of EAE (Figure 5 E-J, Figure 6). Given that multiple CD4+ T cell subsets play a role in both the initiation and resolution of EAE, we agree that it would be valuable to further support these findings with complementary Th2 and Treg differentiation experiments.

      To address this, we examined the effects of asparagine depletion during in vitro iTreg and TH2 differentiation. We found that the frequencies of FOXP3+ iTreg and GATA3+ Th2 cells were reduced when cultures were grown in asparagine-deficient media. These results have been added to Supplementary Figure 5.

      (2) EAE is characterized by inflammation and demyelination in the central nervous system (CNS), leading to neurological deficits. Myelin destruction is directly correlated with the severity of the disease. For Figure 6, did the authors perform spinal cord histological analysis by hematoxylin and eosin (H&E) or Luxol fast blue (LFB) staining? This is important to rigorously examine pathological EAE symptoms.

      We agree with the reviewer that histopathology including H&E and/or LFB staining is a useful indicator of EAE disease severity. However, we are no longer able to obtain PEGAsnASE (Oncaspar) to perform these studies.

      Reviewer #2 (Public review):

      While the importance of asparagine in the differentiation and activation of CD8+ T cells has been previously reported, its role in CD4+ T cells remained unclear. Using culture media containing specific amino acids, the authors demonstrated that extracellular asparagine promotes CD4+ T cell proliferation. Consistent with this, depletion of extracellular asparagine using PEG-AsnASE suppressed CD4+ T cell activation. Proteomic analysis focusing on asparagine content revealed that, during the early phase of T cell activation, most asparagine incorporated into proteins is derived from extracellular sources. The authors further confirmed the importance of extracellular asparagine in vivo, demonstrating improved EAE pathology.

      While the data are well organized and convincing, the mechanism by which asparagine deficiency leads to altered T cell differentiation remains unclear. It is also necessary to investigate the transporters involved in asparagine uptake. In particular, elucidating whether different T cell subsets utilize the same or distinct transport mechanisms would provide important insight into the immunoregulatory role of asparagine.

      (1) The finding that asparagine supplementation promotes T cell proliferation under various amino acid conditions is highly significant. However, the concentration at which this effect occurs remains unclear. A titration analysis would be necessary to determine the dosedependency of asparagine.

      Our studies indicate that the concentration of asparagine present in conventional RPMI lymphocyte media is sufficient to support CD4+ T cell activation and proliferation in vitro (Figure 1, Supplementary Figure 1 & Figure 2). This concentration was consistently used throughout our studies. In line with the reviewer’s comments, however, we have not yet determined the dose dependency of Asn during CD4+ T cell activation.

      To address this, we performed a titration experiment in which asparagine was supplemented at varying concentrations in DMEM and Asn-deficient RPMI. Activation markers were measured 24 hours after TCR stimulation under these culture conditions. We found that the critical asparagine concentration lies between 37.8 and 3.78 uM. This concentration range is consistent with the physiological concentration of asparagine in murine plasma, which is approximately 50 uM (PMID: 24842860; PMID: 23853755). These data have been added to Supplementary Figure 1.

      (2) The effects of asparagine deficiency occur during the early phase of T cell activation. Thus, it is likely that the transporters responsible for asparagine uptake are either rapidly induced upon activation or already expressed in the resting state. Since this is central to the focus of the manuscript, it is interesting to identify the transporter responsible for asparagine uptake during early T cell activation. A recent paper (DOI: 10.1126/sciadv.ads350) reported that macrophages utilize Slc6a14 to use extracellular asparagine. Is this also true for CD4+ T cells?

      While a comprehensive characterization of the amino acid transporter network is certainly of interest, it is beyond the scope of the present study. As the reviewer notes, others have explored asparagine transport in lymphocytes. For example, Wu et al. (PMID: 33420490) determined that the asparagine transporter, Slc1a5, is significantly upregulated in CD8+ T cells upon activation, based on qRT-PCR measurements comparing mRNA from naïve and activated CD8+ T cell. They further validated the functional role of Asn transporters in CD8+ T cells by measuring N15-labeled asparagine uptake in the presence of siRNAs targeting the asparagine transporters Slc1a5 or Slc38a2 and found that inhibition of either transporter significantly reduced intracellular N15-Asn accumulation.

      To gain additional insight into Asn transporters in distinct CD4+ T cell subsets, we reanalyzed a published RNA-seq dataset (Thakore et al., 2024; PMID: 39009838). We quantified the expression of transporters Slc1a5, Slc38a2, and Slc6a14 in naïve and activated CD4+ T cells polarized under Th1, npTh17, or pTh17 conditions at various time points. We observed that Slc1a5 expression increased upon activation in all subsets. Similarly, Slc38a2 expression increased during early activation stage, but subsequently returned to basal levels similar to naïve cells. In contrast, Slc6a14 showed relatively low basal expression in naïve cells compared to the other transporters investigated, and its expression decreased over the differentiation period in all CD4+ T cell subsets examined. These results indicate that Asn transporters Slc1a5 and Slc38a2 are expressed in CD4+ T cells during early activation and differentiation. These data have been included in Supplementary Figure 3.

      (3) Given that depletion of extracellular asparagine impairs differentiation of Th1 and Th17 cells, it is possible that TCR signaling is compromised under these conditions. This point should be investigated by targeting downstream signaling molecules such as Lck, ZAP70, or mTOR. Also, does it affect the protein stability of master transcription factors such as Tbet and RORgt?

      We agree with the reviewer that asparagine deprivation could impact several aspects of T cell function. In our study, we demonstrate that asparagine is crucial for CD4+ T cell protein synthesis and the expression of activation markers (Figure 1B-K, Figure 2K-L, and Figure 3AC). We also highlight its importance in promoting CD4+ T cell subset differentiation and lineage-defining cytokine production (Figure 5B-J). Other studies have reported a role for asparagine in early activation marker expression in CD8+ T cells and in enhancing LCK function (PMID: 33822775; PMID: 33420490). Given its proposed function as a promoter of LCK signaling function in CD8+ T cells, it will be important to determine if a similar mechanism operates during CD4+ T cell activation in future studies.

      We appreciate the reviewer’s inquiry regarding the stability of critical transcription factors defining Th1 and Th17 subsets. We have examined the expression of the transcription factors RORγT and Tbet in Th17 and Th1 polarized cells and observed reduced expression in the absence of asparagine. We have included these findings in Supplementary Figure 5.

      (4) Is extracellular asparagine also important for the differentiation of helper T cell subsets other than Th1 and Th17, such as Th2, Th9, and iTreg?

      Please see our response to Reviewer 1 regarding iTreg and TH2. Investigation of Th9 cells is beyond the scope of the present study.

      (5) Asparagine taken up from outside the cell has been shown to be used for de novo protein synthesis (Figure 3E), but are there any proteins that are particularly susceptible to asparagine deficiency? This can be verified by performing proteome analysis, and the effects on Th1/17 subset differentiation mentioned above should also be examined.

      The investigation of specific proteins that exhibit asparagine dependency would indeed be interesting. Given our results showing that global protein synthesis is blunted with asparagine deprivation (Figure 3A-C), it would be particularly compelling to identify proteins with a specific requirement for asparagine. However, this level of analysis is beyond the scope of our study.

      (6) While the importance of extracellular asparagine is emphasized, Asns expression is markedly induced during early T cell activation. Nevertheless, the majority of asparagine incorporated into proteins appears to be derived from extracellular sources. Does genetic deletion of Asns have any impact on early CD4+ T cell activation? The authors indicated that newly synthesized Asns have little impact on CD8+ T cells in the Discussion section, but is this also true for CD4+ T cells? This could be verified through experiments using CRISPR-mediated Asns gene targeting or pharmacological inhibition.

      We appreciate the reviewer’s consideration of the contribution of endogenous asparagine to CD4 +T cell function. However, genetic perturbation of Asns is beyond the scope of our study, which is specifically focused on defining the requirements for extracellular asparagine and its role in CD4+ T cell activation.

    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 set out to define how arginine availability regulates lipid metabolism and to explore the implications of this relationship in pancreatic ductal adenocarcinoma (PDAC), a tumor type known to exist in an arginine-poor microenvironment. Using a combination of rigorous genetic and metabolomic approaches, they uncover a previously underappreciated role for arginine in maintaining lipid homeostasis. Importantly, they demonstrate that arginine deprivation sensitizes PDAC cells to ferroptosis through lipidome perturbations, which can be exploited therapeutically via co-treatment with aESA and ferroptosis inducers (FINs). These findings have meaningful implications for the field. They not only shed light on the metabolic vulnerabilities created by nutrient restriction in PDAC, but also suggest a practical avenue for combination therapies that exploit ferroptosis sensitivity. This is particularly relevant in the context of pancreatic cancer, which is notoriously resistant to conventional treatments. The methods employed are broadly applicable to other nutrient-stress contexts and may inspire similar investigations in other solid tumor types.

      Strengths:

      One of the major strengths of the study is the use of complementary and well-controlled approaches-including metabolomic profiling, genetic perturbations, and in vivo models-to support the central hypothesis. The experiments are thoughtfully designed and clearly presented, and the conclusions are, for the most part, well supported by the data. The findings provide mechanistic insight into nutrient-lipid crosstalk and identify a potential therapeutic strategy for targeting arginine-deprived tumors.

      We thank the reviewer for their positive assessment of our manuscript.

      Weaknesses:

      A key weakness of the study lies in the mechanistic connection between arginine levels and SREBP1 activation. While the authors show that arginine restriction leads to reduced SREBP1 expression, the magnitude of this effect appears modest relative to the substantial changes observed in the lipidome. The study would benefit from a deeper analysis of SREBP1 regulation-particularly whether nuclear translocation or activation is affected. This could be addressed by examining the nuclear pool of SREBP1, using either subcellular fractionation or improved immunofluorescence imaging in both cell lines and tissue samples.

      We thank the reviewer for this comment and in our revised manuscript have undertaken several new studies to assess how the nuclear pool of SREBP1 is regulated by arginine starvation. We further identified one mechanism by which arginine starvation suppresses SREBP1 protein levels, namely GCN activation. We believe these additional studies strengthen the manuscript and appreciate the reviewer suggesting these studies.

      Another area where additional context would strengthen the manuscript is in the transcriptomic profiling of PDAC cells cultured in a tumor interstitial fluid mimic (TIFM). While the study emphasizes lipid-related pathways, highlighting the most significantly upregulated and downregulated pathways in Figure 1B would give readers a broader perspective on how arginine restriction reprograms the PDAC transcriptome. For instance, because polyamines are downstream of arginine and are known to influence lipid metabolism, it would be worth discussing whether these metabolites contribute to the phenotypes observed. Similarly, an evaluation of whether Dgat1/2 expression is altered could help delineate the full scope of lipid metabolic rewiring.

      We thank the reviewer for suggesting this change to our manuscript and we now provide much more extensive analysis of our transcriptomic analyses in Figure 1 – Figure supplement 1, which we think will make our manuscript more useful to readers.

      Finally, it is worth noting that the KPC mouse model used in this study is based on conditional deletion of p53, which leads to faster-growing tumors and a distinct tumor microenvironment compared to models harboring the p53^R172H point mutation. Including a brief discussion of this distinction would help readers contextualize the translational relevance of the findings.

      We have revised the manuscript to include a discussion of this point.

      Reviewer #2 (Public review):

      This study by Jonker et al. examines how the metabolic adaptations to the microenvironment by pancreatic ductal adenocarcinomas (PDAC) present vulnerabilities that could be used for therapeutic purposes. The evidence supporting the claims of the authors is mostly solid, and the multiplicity of models used, as well as the combination of in vitro and in vivo work, are appreciated, but some conclusions would benefit from additional substantiation. This work would be of interest to biologists working on the impact of microenvironment and metabolism in cancer, and especially those investigating pancreatic cancer.

      We thank the reviewer for their positive assessment of our manuscript.

      In this study, the authors use mostly "doublings per day" as an indicator of cell death, notably for Figures 4 to 6. However, proliferative arrest (or a decrease in the proliferative rate) is not necessarily synonymous with cell death. It might be nice to complement these experiments with a true measure of cell death (e.g., PI uptake).

      We thank the reviewer for this important comment and have performed extensive additional experiments to measure cell death directly via viability markers in addition to our indirect measurements of cell number at the start and end of experiments. We believe these additions strengthen our claims that PUFAs cause arginine starved PDAC cells to undergo ferroptotic cell death.

      The composition of Tumor Interstitial Fluid Medium (TIFM) was published previously, but nonetheless a reminder of the composition of this medium in a Supplemental file of this study might be helpful. In particular, at the start of the Results section, the nature of serum/lipids in the different media should be specifically noted, especially given that the subsequent focus of the work is on lipids/SREBP. It is known that differences in the extracellular availability of lipids can profoundly alter de novo lipid biosynthesis pathways.

      We thank the reviewer for this comment. We have edited the text to provide additional context on the composition of TIFM, especially lipid availability. We further have provided a supplemental file with the composition of TIFM. We hope this will make the manuscript more useful and readily interpretable for readers.

      Reviewer #3 (Public review):

      This important study investigates the impact of nutrient stress in the tumor microenvironment (TME), focusing on lipid metabolism in pancreatic ductal adenocarcinoma (PDAC).

      Understanding TME composition is crucial, as it highlights cancer vulnerabilities independent of intracellular mutations, particularly because PDAC tumors are often exposed to limited nutrient availability due to reduced perfusion.

      By utilizing a medium that mimics the nutrient conditions of PDAC tumors, the authors convincingly show that TME nutrient stress suppresses SREBP1, leading to reduced lipid synthesis, with low arginine levels identified as a key driver of this suppression. Importantly, mice with arginine-starved pancreatic tumors respond to a polyunsaturated fatty acid-rich diet. This discovery uncovers a synthetic lethal interaction in the tumor microenvironment that could be leveraged through dietary interventions.

      The conclusions of this paper are mostly well supported by data; however, below are some aspects that could be further clarified.

      We thank the reviewer for their positive assessment of our manuscript.

      This study uses PDAC cells from the LSL-Kras G12D/+ ; Trp53 ; Pdx-1-Cre PDAC model. The authors convincingly demonstrate that the cell-extrinsic stimuli of low arginine availability suppress lipid synthesis and thus exert a dominant effect over the cell-intrinsic oncogenic Ras mutation, which is known to enhance fatty acid synthesis. Could the effect of low arginine on lipid synthesis be specific for certain mutations in PDAC? It would be interesting to investigate or discuss whether different mutations show the same SREBP1 reduction caused by low arginine levels, and whether these low SREBP1 levels can be ameliorated by arginine re-supplementation. Here, Jonker et al. show that human PDAC cells cultured in TIFM have reduced SREBP1 levels (Figure 1 - Figure supplement 1C). It would be further supportive of their conclusions if the authors could show that arginine re-supplementation is sufficient to restore SREBP1 levels in human PDAC cells.

      We thank the reviewer for this comment. In response, we have now shown that arginine supplementation increases SREBP1 levels and fatty acid synthesis in human PDAC cells (Figure 2 – Figure supplement 2). Further, we have also updated the manuscript to discuss that using the LSL-Kras G12D/+; Trp53; Pdx-1-Cre PDAC model limits our ability to assess how genetic differences influence the response to arginine starvation. We additionally discuss the genetic diversity of the human PDAC cell lines used in these studies, which do include different oncogenic mutations. We believe that these results provide some data that the findings we have made regarding arginine deprivation and SREBP in our genetically defined murine PDAC cell line are applicable to human PDAC cells with more diverse oncogenic lesions.

      The authors demonstrate that mPDAC cells cultured in RPMI and subsequently implanted into an orthotopic mouse model exhibit reduced expression of SREBP target genes when compared to in vitro cultured mPDAC-RPMI cells. This finding is in line with the observation that culturing PDAC cells in TIFM downregulates SREBP target genes compared to PDAC cells cultured in RPMI. However, caution is needed when directly comparing mPDAC-RPMI cultured cells to those in the orthotopic model, as the latter may include non-tumor cells and additional factors that could confound the results. The authors should explicitly acknowledge this limitation in their study.

      We thank the reviewer for this important caveat and we have revised to text to address this point. Importantly, we note that for all comparisons between in vitro and in vivo cultures, we carefully sort malignant cancer cells from orthotopic tumors prior to analysis. We believe this approach mitigates the impact of stromal contamination on our analyses.

      The in vivo evidence demonstrating that PUFA-rich tung oil reduces tumor size is compelling. However, the specific in vitro findings regarding its impact on doubling rates per day, particularly in the context of arginine-dependent PUFA supplementation, require further explanation. To enhance the robustness of their data and conclusions, the authors could consider conducting additional cell viability and proliferation assays. Moreover, it would be valuable to assess whether the observed effects on doubling rates per day remain significant after normalizing the data to the initial doubling time prior to PUFA supplementation. This is in particular important regarding the statement that "Addition of arginine significantly decreases sensitivity to a-ESA" as these cells already start with a higher doubling rate prior to a-ESA treatment.

      We thank the reviewer for this important comment and have performed additional experiments to measure cell death directly via viability markers in addition to our indirect measurements of cell number at the start and end of experiments. Furthermore, to address the issue of different rates of cell growth in cultures affecting the response to perturbations, we also used growth rate corrected metrics (PMID: 27135972) to ensure that affects of perturbations on cell growth and viability are not confounded by the baseline proliferative kinetics of the cells under various media conditions. We believe these additions strengthen our claims that arginine starvation sensitizes PDAC cells to PUFAs.

      Overall, this paper presents a compelling study that significantly enhances our understanding of the PDAC tumor microenvironment and its complex interactions with the tumor lipid metabolism.

      We again thank the reviewer for their positive assessment of our manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In this study, the authors employ rigorous genetic and biochemical (metabolomic) approaches to uncover a previously unappreciated role for arginine in regulating lipid homeostasis. They further demonstrate the relevance of this pathway in pancreatic tumors, a solid tumor type often characterized by limited access to extracellular arginine. The authors present compelling evidence that arginine deprivation creates a metabolic liability, rendering tumors more susceptible to lipidome perturbations. This vulnerability can be therapeutically exploited through co-treatment with aESA and FIN to induce ferroptosis. Overall, the conclusions are convincing, the manuscript is well-written, and the figures are clearly presented.

      We again thank the reviewer for their positive assessment of our manuscript.

      The key weakness of the study lies in the mechanistic link between arginine levels and SREBP1 expression. While the data support the authors' argument, the observed changes in SREBP1 expression following arginine restriction appear modest relative to the more pronounced changes in the lipidome. To strengthen this connection, the authors may consider performing cellular fractionation to focus their analysis on the nuclear (active) pool of SREBP1. Improved immunofluorescence imaging and quantification of nuclear SREBP1 levels in tissues would also provide additional support for their model.

      We thank the reviewers for this helpful comment. To strengthen this study, we both examined the nuclear levels of SREBP1 in TIFM cultured cells and worked to identify the mechanistic link connecting arginine levels of SREBP1 expression.

      First, we found that arginine starvation does not lead to nuclear exclusion of SREBP1. We believe this finding strengthens our conclusion that arginine starvation regulates SREBP1 at the level of protein expression. We do agree with the reviewer that the change in SREBP1 protein level is modest, but we do show the effects of arginine on PDAC cell lipid metabolism are SREBP1 dependent (Figure 3O-P, Figure 5F, Figure 5 – Figure supplement 2D). Thus, we interpret these data that even the relatively modest change in SREBP1 protein levels are sufficient to cause large changes in the output of this transcription factor and the cellular lipidome.

      Second, we determined if the arginine-responsive GCN2 signaling pathway, which is known to regulate SREBP1, could contribute to the suppression of SREBP1 observed in PDAC cells. We found that GCN2 signaling is activated in PDAC cells in TIFM culture by arginine starvation and is active in animal tumors. We further found that activation of GCN2 is in part responsible for suppression of SREBP1, which is consistent with prior literature describing a role for GCN2 activation in suppressing SREBP1 translation (PMID: 17276353). Thus, while other mechanisms are at play in transducing arginine starvation to reduced SREBP1 protein levels, we have identified one mechanism (activation of GCN2) by which arginine starvation suppresses SREBP1, leading to the lipidomic changes we observed upon starvation of this amino acid.

      In addition, it would be helpful for the authors to highlight the most significantly upregulated and downregulated pathways in Figure 1B to give a more comprehensive view of transcriptomic changes in PDAC cells cultured under TIFM conditions. For example, since polyamines are downstream of arginine and known to regulate lipid metabolism, could some of the observed effects be attributed to changes in polyamine levels? Similarly, do arginine levels affect the expression of Dgat1 or Dgat2?

      We have added an additional Figure supplement to Figure 1 that include a comprehensive list of up- and downregulated gene sets in PDAC cells cultured in TIFM via GSEA analysis. We also added additional KEGG metabolic pathway analysis via GATOM (PMID: 35639928). We hope these additions will be useful for readers and point their attention to other metabolic pathways that are significantly altered by nutrient stress, such as the TCA cycle and oxidative phosphorylation, beyond those related to lipid metabolism that we investigated here.

      From this analysis, we did not specifically note strong changes in the expression of polyamine metabolic enzymes or DGATs.

      Finally, the KPC model used in this study involves conditional deletion of p53, which is known to produce tumors with a faster progression and a distinct tumor microenvironment compared to the more commonly used p53^R172H knock-in model. Including this point in the discussion would help contextualize the findings.

      We thank the reviewers for mentioning this limitation of our study. In the results section of the test, we now included a discussion of the limitations of the mouse model used in the discussion of the work. We also highlight in the text now that in addition to our studies using the murine p53 deletion model that our studies make use of human PDAC lines that contain p53 mutations. We believe that these results provide some data that the findings we have made regarding arginine deprivation and SREBP in our genetically defined murine PDAC cell line are applicable to human PDAC cells with more diverse oncogenic lesions.

      Minor comments to improve clarity:

      (1) In Figure 3C, it would be helpful to annotate the PE-linked TG for clarity.

      We do not understand exactly what PE-linked TGs refers to. We note in Fig. 3C that ether-linked triglycerides are labeled in orange and annotated as O-TG and vinyl ether-linked triglycerides are labeled in grey and annotated as P-TG.

      (2) Is Figure 3P mislabeled? Both conditions are labeled as +Arg / -lipid.

      We thank the reviewers for pointing out this mistake in the figure and have updated it to correctly label these samples as sgSREBP1 and sgNTG transduced PDAC cell lines.

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1B: Misspelling in Y axis "Normalized enrichment score".

      We thank the authors for catching this mistake and have corrected this error.

      (2) Figure 1B: Could the authors elaborate on why they decided to focus specifically on these three hits, which are not the most downregulated genes (the "top hits") appearing in the GSEA?

      We chose to focus on lipid metabolism as multiple transcriptomic analysis tools, namely GSEA and GATOM, which specifically focuses on enrichment in KEGG annotated metabolic pathways, highlighted lipid synthesis as being the most transcriptionally regulated metabolic pathway in TIFM. To make this apparent to readers, we added an additional Figure supplement to Figure 1 that includes a comprehensive list of up- and downregulated gene sets in PDAC cells cultured in TIFM from GSEA and GATOM analysis. We hope these additions will make the logic for our focus on lipid synthesis clear and will be useful for readers in highlighting other metabolic pathways that are significantly altered by nutrient stress, such as the TCA cycle and oxidative phosphorylation.

      (3) Figure 1: It might improve the clarity of the text if the three pairs of murine cell lines (mPDAC1, mPDAC2, mPDAC3) were introduced in a bit more detail in the main text and not just in the figure legend.

      We have added more detail describing the three mouse cell lines used in the main text.

      (4) Figure 1E: The authors may wish to comment on why they chose to perform transcriptomic analyses with the mPDAC3 derived models, and not mPDAC1 or mPDAC2, given that mPDAC3 appears to exhibit the most distinct phenotype of the three, according to the results presented in Figure 1 J-L.

      The transcriptional analysis described in Fig. 1E was performed on a previously acquired dataset using mPDAC3 cell lines (PMID: 37254839), which is why this line was used. We have revised the text to make it clear that this transcriptional analysis uses pre-existing data from a previous publication.

      (5) Figure 1L: The authors may wish to clarify why they only show relative palmitate to assess global fatty acid biosynthesis in these cell lines. There is a decrease in labeled palmitate of mPDAC3 cells cultured in TIFM in comparison to the cells cultured in RPMI media, showing a decrease in the lipid biosynthesis of these cells in these conditions. However, there also seems to be lower palmitate levels in the TIFM-cultured mPDAC3 cells specifically, in comparison to their mPDAC1 and mPDAC2 counterparts. Why is that? Could the authors comment on this result?

      We thank the reviewers for this helpful observation. In Figure 1L (now Figure 1N), we wanted to show how culture conditions (RPMI/TIFM) affected both the total amount of palmitate in PDAC cells but also the fraction that is labeled (i.e. arising from de novo synthesis). We think this provides more information for readers by allowing them to assess both changes in pool size of palmitate and changes in the fraction of palmitate that is synthesized. We like this presentation as it shows clearly that while total palmitate levels behave differently across cell lines (with TIFM culture reducing levels in mPDAC1-2 but increasing levels in mPDAC3) the amount of palmitate that is synthesized de novo is decreased in all three cell lines when cultured in TIFM. To highlight this, we also present the fraction of palmitate that is labeled in Fig. 1O.

      We are unsure why TIFM culture reduces total palmitate levels in some PDAC cell lines, while others are able to maintain total palmitate pools. We assume that TIFM cultures increase lipid uptake to compensate for lack of synthesis, and potentially differences in lipid scavenging capacity between the lines could explain this difference. We are currently working on experiments to test these hypotheses and will present the results in a future study.

      (6) Figure 2 - Figure Supplement 1A: It would be informative and appreciated to know which nutrients are actually represented and correspond to certain points on the graph, in particular for the ones that are the most differentially present in the two different media.

      We have now updated this graph to highlight key metabolites that are most differentially abundant between the two media. We also now provide as a Supplementary file the composition of TIFM, which provides readers with all the information needed to understand which metabolites are differentially abundant in TIFM and any media they wish to compare.

      (7) Figure 2 - Related to Figure supplement 1D: It would be useful to know how or why arginine was selected for further investigation from the subset of amino acids. The authors could elaborate on this, by showing or highlighting the data that drew attention to this amino acid initially.

      We thank the reviewers for this note. We have tried to make Figure 2 – Figure supplement 1 more clear as to how arginine was selected for further investigation. We have updated the figure to improve clarity for the comparisons of different media that enabled us to identify differences in amino acids between RPMI and TIFM as driving the difference in lipid metabolism. We have also highlighted in Figure 2 – Figure supplement 1A that arginine is the most differentially abundant amino acid and editing the text to explain the logic that this high degree of differential abundance is why we focused on arginine amongst all the amino acids as a likely candidate for regulation of SREBP1.

      (8) The legends for Figures 2G and 2H could be improved, i.e., making clearer that 2H shows incorporation in the circulating fatty acids, unlike 2G.

      We have updated the figure with improved labeling as the reviewer suggested to denote which panels correspond to which sample type.

      (9) Figure 3E and 3G: The heatmaps displayed here show that the addition of arginine to TIFM culture medium restores fatty acid synthesis; however, it appears that the nature of the lipids synthesized in this condition may differ from the ones synthesized in RPMI cultured conditions.

      We have added additional text highlighting that arginine supplementation to TIFM and RPMI culture led to induction of different SREBP1-target genes, but that both lead to activation of fatty acid synthesis and desaturation genes, which contributes to the focus of our study on de novo synthesis of saturated and monounsaturated fatty acids in the study.

      (10) Figure 3O: The SREBP1 immunoblot still seems to show some residual bands for the cells transduced with SREBP1 targeting sgRNAs, therefore, the authors may want to be more nuanced and present this model as a KD, instead of a KO, as mentioned in the text?

      We agree with the reviewer’s suggestion, and we have changed the text to describe these as knockdowns rather than full knockouts.

      (11) Figure 3P: Is it possible that there is an error in the legend of the figure (Lipids + for the first bar and - for the second one?). The figure could also be improved by a legend that explains what the different colored bars represent.

      We thank the reviewers for pointing out this mistake in the figure and have updated it to correctly label these samples as sgSREBP1 and sgNTG transduced PDAC cell lines.

      (12) Figure 4: The authors are stating in Figure 4 - Figure supplement 1A-F, that argininerestricted mPDAC cells are not sensitized to xCT or GPX4 inhibitors that trigger ferroptosis and that therefore SREBP1 suppression by arginine restriction in the TME does not sensitize PDAC cells to ferroptosis inducers. However, this does not appear to be so clear with the data shown. This might be due to the limitations associated with the population doubling measurements instead of the lethality measures noted above. Likewise, later it is proposed that arginine restriction sensitizes both mPDAC cells and human PDAC cells to α-ESA induced ferroptosis. These results would benefit from a direct measure of cell death. Related to the above point, it would be useful to better understand why cells cultured in arginine-deprived TIFM do not appear to be sensitized to ferroptosis inducers, but these same cells die from ferroptosis when treated with α-ESA. It would be useful to present some thoughts.

      We thank the reviewers for bringing up this important point. To the reviewers first point, we repeated xCT and GPX4 inhibitor treatment experiments to include both growth corrected (PMID: 27135972) proliferation assays and Sytox-based viability assays. In both cases, we did not find consistent sensitization to xCT or GPX4 inhibitors across multiple PDAC lines when cultured in TIFM. In contrast, we found consistent sensitization to PUFA treatment across multiple murine and human PDAC cell lines cultured in TIFM. Together, this analysis suggests that arginine starvation specifically sensitizes PDAC cells to PUFAs, but not other ferroptosis inducers.

      We agree with the reviewer that this is an interesting and unexpected observation. We do not have a mechanistic understanding as to why this is the case. However, we believe this is quite interesting and suggests that PUFAs maybe a better method of inducing ferroptosis in certain conditions than other ferroptosis inducing approaches. We have added text to the discussion to highlight this interesting and unexplained observation.

      (13) Figure 6: The authors mention that α-ESA is used here at sublethal doses, which do not affect viability or proliferation, but this is not shown in either the main or supplementary data. These data should be provided somewhere. It might also be nice to mention in the main text (not just in the legend) the dose of α-ESA used for the combination treatments.

      We thank the reviewers for this helpful suggestion. To illustrate that α-ESA is used at a sublethal dose, we altered each panel to be on a linear rather than logarithmic x-axis, therefore including the DMSO control arm for each ferroptosis inducer in combination with α-ESA. We hope this now clearly illustrates that this dose α-ESA is not perturbing cell growth or viability in these assays.

      (14) Figure 6B: Fer-1 treatment does not seem to rescue the phenotype very clearly. This could again be because cell death is being conflated (to degree) with effects on proliferation, and Fer-1 is not expected to affect cell proliferation. Again, measuring cell death directly would be better than measuring population doublings.

      We thank the reviewers for this helpful comment. To address this concern, we have added Sytox-based viability assays to figure 6. These assays indicate that Fer-1 treatment rescues the viability of PDAC cells treated with ferroptosis inducers, α-ESA, or the two in combination.

      Reviewer #3 (Recommendations for the authors):

      General notes:

      (1) It would be easier for the reader if one condition were consistently placed in the same position throughout the graphs. For example, RPMI results should always appear first and TIFM second. Currently, this is inconsistent throughout the manuscript (e.g., Figure 1 - Figure Supplement 1: RPMI is first and TIFM second; Figure 2 - Figure Supplement 1: TIFM is first and RPMI second).

      We thank the reviewers for this note. We have updated the figures to remain consistent in their ordering throughout the manuscript.

      (2) Please briefly explain the differences between PDAC1-3 and clarify why most follow-up experiments were conducted using PDAC1. Presumably, this was because PDAC1 showed the most robust effect on fatty acid synthesis.

      We have added additional text in the results section of the manuscript describing the different murine PDAC lines used in this study. We performed most studies with mPDAC1 as this line has robust differences in fatty acid synthesis between culture conditions. However, murine PDAC lines recapitulate the transcriptional subtype diversity of PDAC (PMID: 29364867), so we critically repeat key experiments in multiple mPDAC lines to determine if a given finding is translatable to other PDAC subtypes.

      (3) Are only SREBP1 protein levels affected or are SREBP1 RNA levels also decreased in low arginine TME?

      We appreciate this important comment. We have added SREBP1 RNA levels to Figure 1 to show that RNA levels do not differ between conditions, whereas protein levels of SREBP1 change significantly.

      (4) What was the rationale for investigating lipid metabolism even though it was not the top changed metabolic gene signature? It would be interesting to briefly discuss which pathways were the most enriched.

      We chose to focus on lipid metabolism as multiple transcriptomic analysis tools, namely GSEA and GATOM, which specifically focuses on enrichment in KEGG annotated metabolic pathways, highlighted lipid synthesis as being the most transcriptionally regulated metabolic pathway in TIFM. To make this apparent to readers, we added an additional Figure supplement to Figure 1 that includes a comprehensive list of up- and downregulated gene sets in PDAC cells cultured in TIFM from GSEA and GATOM analysis. We hope these additions will make the logic for our focus on lipid synthesis clear and will be useful for readers in highlighting other metabolic pathways that are significantly altered by nutrient stress, such as the TCA cycle and oxidative phosphorylation.

      Further comments:

      (1) Figure 1 Supplement 1A: It is not clear which SREBP target genes are significant. Please indicate this more clearly.

      The analysis in this section was done on expression level of all the indicated genes between groups (tumor/normal) rather testing for significance of individual genes between the two groups. We have updated both the text and the figure legend to clarify this as the statistical analysis that was performed.

      (2) Figure 1J and 2C: The Western blot loading control (Actin) does not appear equal across all samples. It would be helpful to include a quantification normalized to the Actin loading control.

      We have included quantification of each western blot to help interpret these immunoblots.

      (3) Supplementary Figure 2: How often has this experiment been performed? The TIFM results appear to consistently show the same values. If this is the case, it needs to be labeled appropriately.

      Thank you for pointing out that how we presented the data was confusing as to how the experiment described was performed. Initially, we performed multiple separate experiments to identify arginine starvation as the TIFM-driver of SREBP1 suppression. To compare across all the separate media conditions, we performed one experiment with all the relevant media conditions together, which is the experiment that is described in the manuscript. Thus, there was one set of control TIFM/RPMI conditions to which we compared all of the different media conditions. As we initially presented the data, it appeared as if we had performed multiple experiments in which the TIFM/RPMI controls had exactly the same behavior, which is not the case. We have updated the data presentation in this figure to make it clear that this was the experimental design for the data presented.

      (4) Figure 3P: Please add a legend for this panel.

      We thank the reviewers for point out this mistake in the figure and have updated it to correctly label these samples as sgSREBP1 and sgNTG transduced PDAC cell lines.

      (5) Figure 4 - Figure Supplement 1: Please review the legend carefully. The legend currently includes only circles, but some of the graphs (A and F) display squares.

      Thank you for catching this mistake. We have updated the panels and legends for this figure so they are concordant.

      (6) Figure 4D: The effect of a-ESA treatment on the doubling delta of arginine-treated versus non-treated TIFM cells looks similar. It looks like the difference is because cells treated with arginine start at higher doubling values from the beginning. I would suggest looking at the delta and subsequently tone down the statement: "Addition of arginine significantly decreases sensitivity to a-ESA."

      Thank you for this helpful comment. To avoid any confounding effects of differences in basal growth rate between mPDAC cells grown in different media, we have converted all of our data to GR values as described in (PMID: 27135972) which enables us to take into account the basal growth rates of cultures when calculating the effects of treatments/perturbations on culture growth and viability. We hope this addition makes the effect that arginine has on α-ESA sensitivity clear beyond the impact that arginine has on basal growth rate.

      In addition, we also measured the viability of α-ESA treated mPDAC cells with and without supplemental arginine (current Fig. 5E) by Sytox-exclusion assay. We believe this new data supports the claim that arginine makes PDAC cells resistant to the addition of exogenous PUFAs.

    1. Author response:

      We appreciate the constructive feedback from the reviewers and are currently working diligently to address all concerns raised in both the public reviews and the recommendations for the authors. Below, we outline the revisions planned for the revised manuscript.

      (1) We acknowledge the limitations of the current modeling framework regarding spatial integration, and we agree that the present model does not account for the short lifetime of the dot stimuli.

      For spatial integration, our current data suggest a relatively narrow, center-weighted integration function in zebrafish, compared to a broader integration function in medaka. While incorporating such spatial weighting into the model would improve its completeness, we do not expect it to substantially alter our current interpretation of the underlying mechanisms.

      Regarding the responses to short-lifetime dot stimuli, we hypothesize that medaka may possess local retinal receptive units that function as low-pass filters, as illustrated schematically in Figure 3e. At present, however, we believe that explicitly modeling this component would remain largely uninformative and would not substantially increase the explanatory power of the model.

      In the revised manuscript, we will discuss these limitations and the possible neural implementations more explicitly in the Discussion section.

      (2) We appreciate the reviewer’s comments regarding the clarity of data presentation and statistical descriptions.

      In the revised manuscript, we will improve the clarity of the figures and legends and provide more explicit explanations of the statistical analyses and summary metrics used throughout the study. We will also revise several sections of the text to improve the framing and interpretation of the results.

    1. Author response:

      We thank the editors and reviewers for their constructive feedback on our manuscript. We accept the reviewers' recommendations and will implement them fully in our revised manuscript and include all of the suggested literature references. Below, we highlight several key points raised during the evaluation and outline exactly how we will address them. We will also explicitly address every other point and minor recommendation raised by the reviewers in our final, comprehensive point-by-point response.

      Population-level quantification and statistical thresholds: The reviewers noted that our manuscript relied on single-neuron examples without fully demonstrating how widespread these patterns are across the recorded population. To address this, we will add population-level quantification across the recorded units using standard False Discovery Rate (FDR) corrections for multiple comparisons. We will include summary tables in the text and add statistical threshold lines to the distribution figures to report the proportion of significant neurons per region.

      Identifying amodal neurons: Reviewers raised concerns that our classification of amodal language neurons required a more direct test. We will provide additional measures of modality and, in particular, we will implement a cross-modal generalization analysis where our encoding models are trained on one modality (e.g., listening) and evaluated on the other (e.g., reading). This additional procedure will classify neurons as amodal if their cross-modal predictive performance exceeds a baseline null model.

      Isolating linguistic features from sensory confounds: A point was raised regarding whether some neurons were tracking low-level sensory properties (like sound amplitude or visual text size) rather than language features. We will address this by running encoding analyses that include additional basic acoustic envelopes and visual baseline properties as control variables. This will allow us to evaluate the unique variance explained by linguistic features after accounting for these low-level sensory baselines.

      Evaluating the "Compositional Code" in the Fusiform Gyrus: Reviewers pointed out that our claim regarding a "compositional code" (neurons tracking a combination of letter identity and position) was supported primarily by individual examples. To provide population-level context, we will perform a model comparison across our fusiform gyrus neurons. We will compare a baseline letter-only model against a model that includes letter-by-position interactions to report how many neurons statistically support this compositional structure.

      TRF Feature and procedure explanation: Reviewers requested clarification on the construction of our TRF features. We will update the Methods section to explicitly detail how the features were constructed for both modalities. We will also include a feature correlation matrix in the Supplementary Materials. Furthermore, in order to contrast low-level possible confounds and high-level linguistic features, we will also conduct a control analysis tracking, e.g., specific affixes across different structural roles – for example, comparing how neurons respond to the phoneme /-s/ when it functions as a plural number marker versus when it appears as part of a lexical item (e.g., pass) or a third-person verb agreement. We will conduct such analyses in addition to fitting the main TRF models with these additional confounds included, ensuring a clear dissociation between high and low-level features.

    1. Author response:

      Reviewer #1 (Public Review): 

      The medial reticular formation (MRF) in the brainstem has long been implicated in the regulation of locomotion. One common - albeit very simple - model often presents the MRF as a major relay station receiving inputs from MLR circuits, among other brain regions, that together convey locomotor signals through efferent projections targeting the caudal brainstem and the spinal cord. Yet, the MRF is a particularly large brain area whose cellular complexity is far from understood. How molecularly distinct MRF ensembles contribute to the regulation of locomotor behaviors is largely unknown. Here, the authors apply focal activation of either glutamatergic, GABAergic, or serotonergic neurons throughout the MRF using a chemogenetic gain-of-function approach to uncover the putative modulatory properties of these neuronal ensembles during walking. Using kinematic analysis of mice limbs during self-paced over-ground walkway locomotion, the authors find that activation of GABAergic MRF neurons can selectively slow down walking, whereas activation of glutamatergic neurons can induce a specific "shuffle" limb trajectory, altogether revealing that distinct MRF populations may retain the capability to engage divergent walking signatures, whose behavioral relevance are not yet clear. In contrast, the activation of serotonergic neurons did not affect walking signatures as described for the other two subgroups but led to an increase of locomotor speed. Interestingly, MRF neurons in each regional activation "hotspots" appear to target different domains in the lumbar spinal cord, suggesting that distinct circuit mechanisms are at play for the slowmo vs shuffle effects. 

      Major points: 

      (1) While the experiments are carefully done and the results are well analyzed and clearly presented in a series of beautiful figures, several aspects of the methodology remain very confusing. 

      A) In particular, the initial choice for the injection coordinates is not justified and the authors don't leverage the mapping of spinal projection neurons to drive their chemogenetic screen. 

      Thank you for pointing this out. To clarify this, we now start the results with an extra paragraph and accompanying figures (Figure 2 and its supplementary figures) in which we define the region of interest (ROI) within the mRF. The ROI is based upon the distribution of reticulospinal neurons in the brainstem mRF that connect directly with the lumbosacral enlargement (whether or not this ROI projects to other CNS sites), which contains the main networks important for hindlimb control during locomotion, including walking gait. Reticulospinal neurons in the mRF in the caudal pons and medulla oblongata form longitudinal columns that together occupy up to more than half of the entire brainstem. While the morphology of the medulla and caudal pons varies little from level to level, in contrast to rapid changes at the midbrain level, this doesn’t necessarily mean that the neuronal populations, even within neurotransmitter classes, are homogeneous in connectivity and function. We have now clearly denoted the rostrocaudally extensive field with its dorsoventral and mediolateral dimensions that comprises the anatomical region of interest in the new figure. While this dataset is rather basic, it allows us to directly refer back to it and clarify additional queries that came up related to the anatomy (i.e. that the hotspots for slomo- and shuffle-like gaits only cover a small portion of the reticulospinal field).

      We then included detailed anatomical mapping of the spinal projections for the identified hotspots for changes in walking quality (phenomenology), the central theme of the study, and immediately adjacent regions to highlight contrasting location-connectivity-functional properties between these adjacent sites. To better incorporate these mapping results we now present it directly following the walking function based transfection site mapping, but before delving into the details of the walking gait phenotypes. We did not systematically include mapping results from all sites in the mRF ROI into this manuscript as this was beyond the scope of this already very large functional-anatomical study. 

      B) Similarly, the authors group very different injection schemes (unilateral or bilateral targeting of MRF neurons), that should be analyzed separately. 

      We now clarify early in the results section how uni- and bilateral groups were composed and what the rationale was for this. As pilot data suggested that the slomo gait style was only seen following bilateral activation in VGaT-cre mice, but not in all bilateral cases, we designed the VGaT cohort to contain mainly bilateral injections, spread across the mRF region of interest, with a smaller group of unilateral injections to verify the pilot data. 

      For the shuffle gait style, pilot data suggested that both uni- and bilateral activation of VGluT2 neurons could elicit this style, but only in a subset of uni- and bilateral cases. Therefore we mainly included unilateral injections in this group with a smaller bilateral cohort for verification.  This approach served the main goal of the study, which was to map the walking style changes to subregions in the mRF.

      However, laterality is indeed very important when it comes to locomotor control. The effects of laterality on the walking gait styles generated from the hotspots were included in supplemental figures and accompanying Tables. We have now better highlighted these in the body of the text and we have added analyses of the motor tests for uni- or bilateral groups. 

      Furthermore, it should be noted that the uni- and bilateral groups are heterogeneous when it comes to rostrocaudal and dorsoventral placement within the mRF ROI. As such, we were not able to rigorously compare uni- versus bilateral activation effects while at the same time separating cases out by dorsoventral and rostrocaudal location (which would be needed to do justice to the functional anatomical organization of the mRF) as we do not have sufficient power in each of the subgroups (i.e. 3 rostrocaudal levels, with each a dorsal, intermediate and ventral region to target, which each would have to be injected unilaterally and bilaterally). This was beyond the scope of this already very large study. Further studies designed to balance ipsi- and contralateral groups will be necessary to map out the hotspots for mobility phenotypes that may be driven by the mRF beyond the slomo- and shuffle-hotspots or to systematically study the impact of laterality on mobility from the mRF.  

      To summarize, analyses of uni- vs bilateral stimulation demonstrate that bilateral inhibition within the slomo hotspot is necessary to create the slomo walking phenotype, and that unilateral inhibition within the shuffle hotspot is sufficient to create the shuffle walking phenotype (with bilateral stimulation not enhancing the phenotype further). Unilateral activation of the slomo hotspot did not induce asymmetries in gait or a reduction in motor performance, whereas unilateral activation of the shuffle hotspot induced an asymmetry in swing time but not stride length, with laterality affecting horizontal ladder but not other motor tests. Mice with transfection sites within the mRF region of interest but outside of the slomo and shuffle hotspots did not display these walking phenotypes but did display slowed walking without qualitative changes. The connectivity to spinal and other supraspinal substrates differed between these sites, providing clues for the substrates that mediate these differential functions.

      C) The choice of Z score cutoff that dictates the in-depth analysis of the chemogenetic phenotypes appears arbitrary and is not grounded in a set of objective criteria. 

      We are sorry that the Z score cutoff appeared arbitrary as that was not our intention. 

      The values to separate mice with and without a significant change were simply set at 2 standard deviations from the population mean in the control mice (i.e. Z=2). Two standard deviations from the population mean is widely used in all types of statistical analyses. We have now included the rationale for the cutoff of Z=2 in the text. Where group size allowed, to increase contrast between positive and negative groups in terms of gait characteristics, other behavioral assays and mapping, we used data from Z scores >3 (or < -3), but can assure that all moderately positive data (i.e. from mice with gait style Z scores between 2 and 3, and between -3 and -2) was reported as well in the statistical tables or supplementary figures. We have now included the links to theses supplementary tables and figures in the text, rather than only in the figure legends.

      The Z scores for the different gait styles indeed appear to map to discrete sites, but the Z score cutoff was not informed by these sites or by anatomical data. Similarly, Z scores for changes in tonic muscle activity elicited by activation of inhibitory neurons also mapped to a hotspot in the same rostrocaudal column as the slomo gait style, but further caudally. This further demonstrates the strength of function-based mapping. 

      (2) One issue that arise from the work presented here is that we don't know if these MRF neurons are active during locomotion in normal, unperturbed conditions. Knowing the recruitment profile of these MRF neurons would clarify whether the chemogenetic activation boosts the firing of neurons that are already active during walking, or activate neurons that are otherwise silent. Disentangling between these possibilities may have a profound impact on the overall interpretation of the results. 

      We agree that this knowledge would improve our ability to interpret and apply the findings of the current study. It is indeed important to learn when these mRF sites are being recruited, whether part of normal modulatory strategies in order to navigate through a complex environment or as part of specialized behavioral modules or both.  Another question is how loss of function in these sites impacts behavior and function. This concept has been added to the discussion and these questions can now be pursued in future experiments. 

      (3) The results should be discussed in the broader context of historic stimulation experiments, notably in cats and other species, as well as more recent circuit mapping approaches in rodents. For instance, the notion that focal stimulation of distinct area within the MRF can elicit or modify the pattern of locomotion is not really new, so is the notion that some of these modulations are phase-specific and can influence the duration of single muscle activation during stance or swing phases. This last point has for instance already been assessed through individual muscle recordings paired with MRF stimulation in cats. Perhaps better introducing these key studies and a thorough discussion of what the results presented in this manuscript bring in terms of novelty will help readers ground this work into a more comprehensive and larger body of work. 

      There is indeed a rich series of meticulous work done in cats, which included effects from stimulation of inhibitory and excitatory neurons on limb EMG, and rodent work focusing on excitatory mRF neurons. These studies show that distinct neurons or sites within the mRF drive distinct changes in motor readouts, albeit not described in terms of modulation of walking gait as we do here in terms of gait signatures. Despite this solid body of prior work, the notion of phase specificity and separate modulation of swing versus stance phase metrics has been underappreciated and therefore deserves to be emphasized. We have expanded the discussion to better highlight prior work and the interpretation of phase specificity has been enriched.  

      Reviewer #2 (Public Review): 

      This paper is an interesting conceptual work where certain hotspot areas were found to induce unique gait patterns. These patterns differed from a classic change in speed or gait pattern from a walk to a gallop. From this, a hypothesis was formed that these areas could be important for possible alternative walking patterns seen, for example, during pathologies such as Parkinson's disease or perhaps related to stalking behaviors. 

      While I liked the work and found it interesting, it remains descriptive in that the actual behaviors observed can't be causally related to a particular behavior such as stalking or shuffling. If the necessity or sufficiency of this region was related to a specific hunting behavior, for example, its interest to the field would be greater. 

      Nevertheless, this paper does contribute to growing evidence that specific behaviors can be triggered by specific neuronal populations within the brainstem. 

      We thank the reviewer for their thoughtful comments. We agree that more studies are necessary to understand how the slomo and shuffle hotspots serve behavioral repertoires (such as stalking or other internally driven activities) and adaptations (such as object avoidance or more subtle adjustments to terrain or internal cues). The experimental details of the present study leave ample leads for the research community to pursue these new directions.

  2. May 2026
    1. Author response:

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

      Reviewer #1.

      We appreciate the constructive comments, which greatly improved this manuscript.

      Reviewer #2.

      We appreciate Reviewer #2's thorough analysis of our manuscript. However, we are concerned that the reviewer criticized a conclusion different from the one we claim in the manuscript. Although Reviewer #2's public comment stated, "Such an approach is insufficient to unequivocally support the central claim that DNA methylation increases accessibility of H2A.Z-containing nucleosomes", we did not draw such a bold conclusion. In the Abstract, we cautiously described that the impact of DNA methylation we observed was subtle and based on satellite II-derived DNA sequences. We made a nuanced proposal regarding this observation, stating, "Altogether, we propose that SRCAP drives the biased association of H2A.Z to unmethylated DNA, while additional mechanisms, potentially taking advantage of the subtle DNA methylation-induced physical effects, further assist the exclusion of H2A.Z from methylated DNA". We believe our analysis will contribute valuable insights into the mechanistic basis behind the antagonism between DNA methylation and H2A.Z.

      Reviewer #3.

      We appreciate the constructive comments, which greatly improved this manuscript.


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

      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 DNAmethylation 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 ATPdependent 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.

      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/s41576-02400759-1).

      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.

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      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors designed two sets of experiments to explore the molecular mechanisms underlying the mutually exclusive distribution of H2A.Z and DNA methylation previously reported by several groups.

      First, they examined how DNA methylation affects the physical stability of H2A.Z-containing nucleosomes. Although their results point to subtle differences between nucleosomes assembled on methylated versus unmethylated DNA, the authors did not extend their analyses to directly test the stability of these H2A.Z-containing nucleosomes under more challenging conditions. Prior studies have demonstrated that certain nucleosomes, such as those containing H3.3-H2A.Z or H2A.Z-H3K56Q, exhibit specific instability, but such instability is only revealed under challenging conditions, for example, altered salt concentrations or the presence of additional factors like FACT (PMID: 17575053; PMID: 19633671; PMID: 19639024; PMID: 41303375). In light of this literature, the observable structural features noted here for nucleosomes containing H2A.Z and methylated DNA are suggestive of increased instability, yet the authors did not employ comparable approaches to rigorously test whether such instability might explain the absence of H2A.Z from methylated genomic regions.

      As a result, at this stage of analysis, the idea that nucleosomes containing both H2A.Z and methylated DNA are intrinsically unstable, and that this instability accounts for the depletion of H2A.Z from methylated regions, remains unsubstantiated.

      We thank the reviewer's constructive criticisms. Through our response to these points, we were able to significantly improve our manuscript, including major rewriting of the Abstract and Discussion as well as incorporation of new data.

      We agree that combinations with other histone variants, modifications, and mutations could further affect our observed impact of DNA methylation on H2A.Z-nucleosome stability. What we observed based on satellite II-derived DNA was that DNA methylation made H2A.Znucleosomes (with H3.2) more open, although the effect of DNA methylation is relatively small (as compared to the general impact of H2A.Z incorporation). We readily admit that such a subtle physical effect is unlikely to be the main driver of the antagonistic distribution of H2A.Z and DNA methylation, though small physical changes have been known to influence larger biological functions, and sought to describe additional regulatory factors that could play major roles.

      We also agree that H3.3 is of major interest when discussing H2A.Z. In our Xenopus egg extract experiments using DNA beads, the primary H3 variant deposited is H3.3 as no DNA replication occurs on the beads to allow for H3.1/.2 replication-coupled deposition. From those experiments, we demonstrated that preferential loading of H2A.Z can be primarily explained by SRCAP. In other words, in the absence of SRCAP, loading/retention of H2A.Z on H3.3nucleosomes was not noticeably affected by DNA methylation, indicating that DNA methylation’s physical effects on H2A.Z nucleosomes plays little, if any, role in the preferential accumulation of H2A.Z on unmethylated DNA at least in the context of synthetic DNA beads incubated in

      Xenopus egg extract lacking active transcription. Our sequencing data hints at the interesting possibility that transcription, along with other factors missing in egg extract, may be involved in further pruning H2A.Z from methylated DNA which conceivably could take advantage of subtle physical alterations. However, we agree we lack firm supporting evidence for such a mechanism which led us to forgo including that in our final model figure and we instead only report on our observations with discussions on potential biological implications and limitations. Of note, it has been reported that the H2A.Z nucleosome is more accessible than the H2A nucleosome, while inclusion of H3.3 does not further enhance accessibility of the H2A.Z nucleosome (PMID 38920622). We have now noted these points in the Discussion of our revised manuscript.

      We appreciate and agree with this reviewer’s point that nucleosome instability sometimes requires challenging conditions to be fully revealed. However, in our system, use of H2A.Z was the challenge provided as we find in our hands that H2A.Z by itself substantially destabilizes histone-DNA contacts compared to canonical H2A. And it is only with this already destabilized nucleosome that we see further enhancement of accessibility/openness in the presence of DNA methylation. This is similar to findings by [PMID: 23260052] that reported that only an intrinsically destabilized sub-population of canonical H2A nucleosomes on 601 DNA experienced detectable physical changes in the presence of DNA methylation.

      In response to this reviewer's comment, we edited the Abstract and Discussion to clearly note the subtly of the impact of DNA methylation on H2A.Z nucleosome structure, and that the potential functional significance remains an open question.

      Second, the authors investigated whether SRCAP-C contributes to preferential H2A.Z incorporation into unmethylated DNA. The absence of H2A.Z from methylated regions does not necessarily imply that it cannot be incorporated there; it may instead reflect the chromatin environment associated with DNA methylation, which could disfavor SRCAP-C activity, whereas open chromatin environments strongly promote SRCAP-dependent H2A.Z deposition.

      This reviewer suggested an alternative model where SRCAP prefers to act on open chromatin and that the apparent preferential H2A.Z deposition to unmethylated DNA is due solely to the increased accessibility associated with unmethylated DNA. Following such a model, one would predict that SRCAP-C's preference to unmethylated DNA would be eliminated on nucleosome-free DNA in Xenopus egg extracts. To test this alternative model, we repeated the SRCAP-C binding experiment in egg extracts depleted of the HIRA complex, the H3.3-H4 chaperone responsible for de novo nucleosome assembly on exogenously added DNA in egg extracts. Contrary to this prediction, both SRCAP and ZNHIT1 still display preferential binding to unmethylated DNA substrates in HIRA-depleted extracts in which nucleosome assembly is suppressed (newly added Suppl Fig 16). The results argue that discrimination of SRCAP-C from methylated DNA is not due to a potential effect of chromatin compaction by DNA methylation. Furthermore, our new result is in line with an idea that SRCAP employs 1D diffusion on the linker DNA before engaging the H2A nucleosome (PMID 39131301), implying that discrimination of SRCAP-C from methylated linker DNA contributes to this process. This is now illustrated in the new model Figure 6.

      Please note we also indicate in both our model and in text that there exists an additional methylation-insensitive mechanism that drives H2A.Z deposition on methylated DNA, leading to a substantial amount of colocalized H2A.Z and DNA methylation. Why two different deposition pathways for H2A.Z differing in their methylation sensitivities must exist is an interesting topic for future work and has not been described prior to our report.

      This interpretation is consistent with the authors' own comparative mapping of H2A.Z and DNA methylation in sperm pronuclei incubated in egg extract versus a transcriptionally active Xenopus fibroblast line. They observed that about 40% of H2A.Z-associated genomic DNA is methylated in sperm pronuclei, but only 3% in fibroblasts. As they note, the major difference between these systems is the presence of transcription in fibroblasts, a process known to drive H2A.Z eviction/recycling, and which is absent in the egg-extract system. Thus, no specific inhibition of SRCAP-C by methylated DNA needs to be invoked: H2A.Z deposition on both methylated and unmethylated accessible regions, followed by preferential eviction from methylated sites in active nuclei, could fully account for the observed patterns.

      As the reviewer correctly notes here, we proposed that transcription is likely to play an important role in pruning H2A.Z from methylated DNA. Our observations and proposed mechanism do not argue against the possible existence of a DNA methylation-insensitive, transcription-dependent mechanism that promotes dissociation of H2A.Z from methylated DNA, which we believe likely would be correlated to gene body methylation. In fact, we did propose in our Discussion that such a transcription-mediated mechanism may conceivably take advantage of the subtly destabilized DNA wrapping of H2A.Z nucleosomes on methylated DNA to further selectively prune H2A.Z at colocalized regions. However, such a mechanism would be an additional component to what we have already described and does not explain the observed preferential recruitment of SRCAP-C to unmethylated DNA in Xenopus egg extracts in the absence of active transcription.

      In this respect, studies from the Felsenfeld laboratory showing that double-variant nucleosomes are highly unstable under physiological ionic conditions are particularly relevant (PMID: 19633671; PMID: 19639024). They demonstrated that such unstable nucleosomes are only evident under low ionic strength extraction conditions, emphasizing that the apparent absence of H2A.Z may reflect facilitated removal rather than failure of assembly.

      The authors may also have been influenced by the study of Berta et al. (cited in the manuscript), which examined uterine leiomyomas harboring somatic or germline mutations in SRCAP-C subunits. In those tumors, the normal association of H2A.Z with accessible, active chromatin, and its exclusion from methylated regions, was lost. However, this observation does not demonstrate that SRCAP-C actively prevents H2A.Z incorporation into methylated DNA. Instead, it may simply reflect that in the absence of SRCAP-C, a default, less efficient deposition pathway operates regardless of whether the chromatin environment is normally permissive or restrictive for SRCAP-dependent activity.

      Even if one accepts the more straightforward interpretation proposed by the present authors, that SRCAP-C is actively inhibited by methylated DNA, as suggested by their pull-down experiments from Xenopus egg extracts using unmethylated and methylated DNA, the hypothesis lacks mechanistic support.

      Considering this reviewers' criticism, we have expanded our discussion to indicate a possibility that SRCAP-C may have an alternative mechanism to find open chromatin independent of DNA methylation status. However, our data show that SRCAP-C preferentially binds to unmethylated DNA in a manner independent of transcription or other epigenetic status in Xenopus egg extracts, and that SRCAP-C carries the major mechanism that explains preferential deposition of H2A.Z to unmethylated DNA. Therefore, we believe that our study for the first time offers a mechanistic explanation of how H2A.Z discrimination from methylated DNA is accomplished through SRCAP-dependent H2A.Z deposition.

      The following points summarize the issues discussed above:

      (1) The authors did not sufficiently test the hypothesis that H2A.Z-methylated DNA nucleosomes are inherently unstable and could explain the exclusion of H2A.Z from methylated genomic regions.

      We stand by our conclusion that DNA methylation has an intrinsic capacity to make the H2A.Z nucleosome more open and accessible, even though the effect is subtle. We did not argue that this subtle effect can fully explain the exclusion of H2A.Z from methylated genomic regions. Rather, our Xenopus egg extract experiment suggested that in the transcriptionally inactive egg extract setting, such a mechanism plays little or no role and it is SRCAP-C instead that is the major driver. Whether this physical mechanism also contributes to their exclusion in cells with active transcription remains a future subject of study.

      (2) The proposed active role of SRCAP-C in preventing H2A.Z assembly on methylated DNA is supported only by limited experimental data and lacks a mechanistic explanation. In particular, this hypothesis does not account for the significant H2A.Z assembly observed on methylated DNA regions in sperm nuclei after incubation in egg extract.

      We respectfully disagree with this summary assessment. Our conclusions are well aligned with the substantial H2A.Z association with methylated DNA in sperm pronuclei assembled in Xenopus egg extracts seen. We demonstrated that:

      (1) In transcriptionally-silent Xenopus egg extracts using synthetic DNA beads, DNAbinding of SRCAP-C is inhibited by DNA methylation.

      (2) In this set up, H2A.Z is preferentially, if not exclusively, loaded to unmethylated DNA over methylated DNA.

      (3) Depletion of SRCAP-C almost completely eliminated preferential association of H2A.Z to unmethylated DNA, while leaving some DNA methylation-insensitive H2A.Z loading.

      (4) These data indicate the presence of a SRCAP-C-dependent, DNA methylationsensitive mechanism as well as a SRCAP-C-independent, DNA-methylation-insensitive mechanism to load H2A.Z to chromatin. This conclusion matches well with our genomic analysis showing that H2A.Z is preferentially but not exclusively loaded to hypomethylated genomic segments to sperm pronuclei in Xenopus egg extracts.

      (5) As we clearly discussed, this SRCAP-C-dependent mechanism by itself is insufficient to explain the much clearer exclusion of H2A.Z in somatic cells. We discussed the possibility that transcription contributes to further pruning of H2A.Z from methylated DNA.

      To deliver this overall message with nuances that we noted above, we have heavily revised the Abstract, the model Figure 6, and Discussion. Thanks to the criticisms raised by this reviewer, we believe that our revised manuscript has been significantly improved.

      Reviewer #2 (Recommendations for the authors):

      (1) 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.

      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, considering the cost and effort for this additional cryo-EM analysis.

      (2) 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. 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 that the effect of DNA methylation on intrinsic H2A.Z nucleosome stability is relatively subtle. We will accordingly revise the Abstract, the model Figure 6, and Discussion to make this point clearer.

      (3) The cryo-EM structures of methylated and unmethylated 601L H2A.Z nucleosomes show no detectable differences. As presented, this negative result adds little value and should be removed.

      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, however, we believe that 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.

      (4) 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).

      (5) 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).

      (6) 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.ZDNA methylation relationships across promoters, 5′UTRs, exons, gene bodies, enhancers, etc., as described in Supplementary Figure 10A.

      We appreciate recognition of the importance of our finding by this reviewer. 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 methylationinsensitive H2A.Z deposition mechanism also exists. We realized that this interesting point was not clearly highlighted in Abstract, so we will revise it accordingly.

      (7) 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. The authors need to discuss this in more detail.

      As depicted in Figure 6 and described in the Discussion, we 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. In the revised manuscript, we heavily edited the Discussion to better clarify these points.

      (8) 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.

      In response to this, quantification of the SRCAP depletion is now included as Supplementary Figure 13A and B. Since our anti-ZNHIT1 antibodies reproducibly detected ZNHIT1 on DNA beads isolated from egg extracts, we have conducted additional verification of the SRCAP depletion by probing for SRCAP and ZNHIT1 on DNA beads, confirming that these proteins were depleted on DNA beads upon immunodepletion with anti-SRCAP antibodies (Author response image 1). To further validate this conclusion, we added data showing that the effect of SRCAP depletion on methylation-sensitive H2A.Z deposition was reproduced through use of a different commercially available antibody raised against human SRCAP (newly added Suppl Fig 14).

      Author response image 1.

      Verification of SRCAP depletion using DNA beads. DNA beads were incubated in interphase-cycled Xenopus egg extract that had been depleted with either our custom SRCAP antibody or an IgG negative control. SRCAP and ZNHIT1 association was then assessed via Western Blot.

      (9) 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.

      Thank you very much for raising this interesting point. We were 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 (shown in the revised Supplementary Figure 15). 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. However, we have now added descriptions to note that TIP60-C is a likely candidate to execute the SRCAPindependent and methylation-insensitive mechanism of H2A.Z loading in Xenopus egg extracts. In the model figure, we initially did not include Tip60-C, but we now infer TIP60-C is a likely candidate in the revised model (Figure 6) to facilitate the future research in the field.

      (10) 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). These references should be considered.

      We appreciate that the reviewer points out this important issue. Although we had described that controversy exists regarding how H2A.Z and DNA methylation contributes to nucleosome stability, it was not clearly explained. We understand that this confusion was in part due to the term “nucleosome stability”, which is broad and encompasses many physical aspects. As noted in a prior response, we now better specify our use of the term within the manuscript, emphasizing the nucleosome openness and accessibility, particularly at the nucleosome core particle entry/exit sites. As noted by published studies (PMID 38920622), the impact on nucleosome stability may differ between the internal and external segments of nucleosomal DNA. 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 at DNA ends 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. This may be caused by usage of different assays (for example, nucleosome assembly during salt dialysis or salt sensitivity vs openness/accessibility of preassembled nucleosome). In the Discussion of the revised manuscript, we now explain these factors, with the hope that our study will help clarify some of the field’s controversies.

      Reviewer #3 (Recommendations for the authors):

      (1) Since the cryo-EM structure determined by single-particle analysis represents only one major population, it would be important to determine the dyad axis position by complementary biochemical assays, such as MNase-seq or chemical digestion by the Fenton reaction (PMID: 22929776).

      We would like to thank the reviewer for bringing up this important issue. We agree that the high-resolution structure represents only a subpopulation in which we specifically selected for the most stably wrapped nucleosomes in each sample. This issue is why we then supplemented our high-resolution structure with our in-silico classification analysis to survey the overall structure distribution of the full nucleosome particle population. The classification input contains all nucleosome-like particles picked from both unmethylated and methylated sample micrographs mixed together, ensuring that all particles are taken into consideration and that both samples have been analyzed in an identical manner. From our sorting analysis, we find an increased population of open and shifted nucleosome structures present in our methylated DNA sample, indicating destabilization of DNA-histone wrapping with DNA methylation. This is corroborated by the lower local resolution seen on the DNA backbone of our high-resolution H2A.Z on methylated DNA structure, despite it having a higher global resolution compared to its unmethylated counterpart. This suggested to us that DNA positioning along the nucleosome is overall weaker under the presence of DNA methylation.

      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 realized that we did not explain how we decided to place the HinfI site in the context of our solved cryo-EM structure. In the revised Figure 3B, we now illustrate that the HinfI site is located at a segment where H2A/H2A.Z directly contacts the DNA and explained that this segment belongs to the region that exhibited clear methylation-induced flexibility in our cryo-EM structures. Thus, our structure helped us design this experiment.

      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, as subtle technical errors in the MNase concentration can have significant effects. 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.

      (2) I assume that the authors confirmed complete DNA methylation by restricted enzyme digestion. It would be helpful to include this validation in supplementary figures.

      We would like to thank the reviewer for pointing out that this critical verification was missing from our initial manuscript. DNA methylation of Sat2R-P and Sat2R was verified via BstBI digestion (Suppl Fig 1B and 7D, respectively); 601L verified with HpaII digestion (Suppl Fig 6B); and 19x601 DNA verified via BstUI digestion (Suppl Fig 11A). All data has been added to the specified figures. Unfortunately, the 16xHSat2 DNA substrate we used in our assays does not contain appropriate cut-sites for methylation-sensitive restriction enzymes. Due to that, we always prepared the 16xHSat2 DNA in parallel with the 19x601 substrate under identical conditions then use digestion of the 19x601 substrate to verify quality of methylation for each batch. To more directly verify methylation of 16xHSat2 DNA, we used Xenopus laevis ZHX2 and ZHX3, which we recently identified as proteins that selectively associate with methylated DNA in Xenopus egg extracts. Although identification and characterization of Xenopus ZHX2/3 will be described elsewhere, previous published proteomic studies have also identified mammalian ZHXs as proteins that enrich on methylated DNA (PMID 21029866, 23434322). By incubating DNA beads in Xenopus egg extract and probing for endogenous ZHX2/3 (our antibody recognizes both ZHX2 and ZHX3), we verified that ZHXs selectively binds to methylated 16xHSat2 but not unmethylated DNA (Author response image 2). Although this does not necessarily verify that all CpGs in 16xHSat2 were methylated, we observed comparable methylation-induced inhibition of SRCAP binding between 16x601 and 16HSat2, supporting our conclusion.

      Author response image 2.

      Verification of 16xHSat2 methylation status via ZHX2/3 protein binding. 16xHSat2 DNA beads were incubated in Xenopus egg extract and endogenous ZHX2/3 protein binding assessed via Western Blot with a custom generated antibody that recognizes both ZHX2 and ZHX3.

      (3) Figure 1A: The dyad position is difficult to identify. Please indicate it clearly using a distinct color (not green).

      We now directly indicate each sequence midpoint with a black triangle and also changed the font of DNA sequences to further clarify that the dyad resides at the palindromic center.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript presents an extensive body of work and an outstanding contribution to our understanding of the IFN type I and III system in chickens. The research started with the innovative approach of generating KO chickens that lack the receptor for IFNα/β (IFNAR1) or IFN-λ (IFNLR1). The successful deletion and functional loss of these receptors was clearly and comprehensively demonstrated in comparison to the WT. Moreover, the homozygous KO lines (IFNAR1-/- or IFNLR1-/-) were found to have similar body weights, and normal egg production and fertility compared to their WT counterparts. These lines are a major contribution to the toolbox for the study of avian/chicken immunology.

      The significance of this contribution is further demonstrated by the use of these lines by the authors to gain insight into the roles of IFN type I and IFN-type III in chickens, by conducting in ovo and in vivo studies examining basic aspects of immune system development and function, as well as the responses to viral challenges conducted in ovo and in vivo.

      Based on solid, state-of the-art methods and convincing evidence from studies comparing various immune system related functions in the IFNAR1-/- or IFNLR1-/- lines to the WT, revealed that the deletion of IFNAR1 and/or IFNLR1 resulted in:

      (1) impaired IFN signaling and induction of anti-viral state;

      (2) modulation of immune cell profiles in the peripheral blood circulation and spleen;

      (3) modulation of the cecum microbiome;

      (4) reduced concentrations of IgM and IgY in the blood plasma before and following immunization with model antigen KLH, whereby also line differences in the time-course of the antibody production were observed;

      (5) decrease in MHCII+ macrophages and B cells in the spleen of IFNAR1 KO chickens, although the MHCII-expression per cell was not affected in this line; and

      (6) reduction in the response of αβ1 TCR+ T cells of IFNAR1 KO chickens as suggested by clonal repertoire analyses.

      These studies were then followed by examination of the role of type I and type III IFN in virus infection, using different avian influenza A virus strains as well as an avian gamma corona virus (IBV) in in ovo challenge experiments. These studies revealed: viral titers that reflect virus-species and strain-specific IFN responses; no differences in the secretion of IFN-α/β in both KO compared to the WT lines; a predominant role of type I IFN in inducing the interferon-stimulated gene (ISG) Mx; and that an excessive and unbalanced type I IFN response can harm host fitness (survival rate, length of survival) and contribute to immunopathology.

      Based on guidance from the in ovo studies, comprehensive in vivo studies were conducted on host-pathogen interactions in hens from the three lines (WT, IFNAR1 KO, or IFNLR1 KO). These studies revealed the early appearance of symptoms and poor survival of hens from the IFNR1 KO line challenged with H3N1 avian influenza A virus; efficient H#N1 virus replication in IFNAR1 KO hens, increased plasma concentrations of IFNα/β and mRNA expression of IFN-λ in spleens of the IFNAR1 KO hens; a pro-inflammatory role of IFN-λ in the oviduct of hens infected with H3N1 virus; increased proinflammatory cytokine expression in spleens of IFNAR1 KO hens, and Impairment of negative feedback mechanisms regulating IFN-α/β secretion in IFNAR1-KO hens and a significant decrease in this group's antiviral state; additionally it was demonstrated that IFN-α/β can compensate IFN-λ to induce an adequate antiviral state in the spleen during H3N1 infection, but IFN-λ cannot compensate for IFN-α/β signaling in the spleen.

      Strengths:

      (1) Both the methods and results from the comprehensive, well-designed, and well-executed experiments are considered excellent. The results are well and correctly described in the result narrative and well presented in both the manuscript and supplement Tables and Figures. Excellent discussion/interpretation of results.

      (2) The successful generation of the type I and type III IFN KO lines offers unprecedented insight and opens multiple new venues for exploring the IFN system in chickens. The new knowledge reported here is direct evidence of the high impact of this model system on effectively addressing a critical knowledge gap in avian immunology.

      (3) The thoughtful selection of highly relevant viruses to poultry and human health for the in ovo and in vivo challenge studies to examine and assess host-pathogen interactions in the IFNR KO and WT lines.

      (4) Making use of the unique opportunities in the chicken model to examine and evaluate the host's IFN system responses to various viral challenges in ovo, before conducting challenge studies in hens.

      (5) The new knowledge gained from the IFNAR1 and IFNLR1 KO lines will find much-needed application in developing more effective strategies to prevent health challenges like avian influenza and its devastating effects on poultry, humans, and other mammals.

      (6) The excellent cooperation and contributions of the co-authors and institutions.

      Weaknesses:

      No weaknesses were identified by this reviewer.

      We thank Reviewer #1 for the very positive and thoughtful evaluation of our manuscript. We appreciate the recognition of the effort involved in generating and characterizing the IFNAR1<sup>-/-</sup> and IFNLR1<sup>-/-</sup> chicken lines and for highlighting their significance as valuable tools for advancing avian immunology.

      We are grateful for the reviewer’s clear summary of our findings and for acknowledging the quality of the experimental design, data presentation, and interpretation. The encouraging feedback affirms the broader impact of our study and its contribution to understanding type I and type III interferon biology and antiviral defense mechanisms in chickens.

      We have carefully considered all reviewer comments and revised the manuscript accordingly to further clarify methodological details and improve the presentation of our results.

      Reviewer #1 (Recommendations for the authors):

      Minor suggestions/corrections:

      (1) Line 192, 193, 196 - the superscript "+" sign appears to be underlined.

      We corrected the formatting of all superscript "+" symbols (L 192-196).

      (2) L195: ...in the spleen "of both IIFNR KO lines" (or some clarification of what you are comparing).

      The sentence was revised to read “in the spleen of both IFNR knockout lines” for clarity (L 195).

      (3) L198: replace "highlighting" with "and".

      “Highlighting” was replaced with “and” as suggested (L 198).

      (4) L231 and 235: change "monocytes" to "macrophages" as this description appears to refer to spleen cells. Also, make this change in Figure 3b and in the Figure 3 caption (e.g. monocytes/macrophages).

      “Monocytes” was replaced with “macrophages” to accurately describe spleen cells. The same correction was made in Figure 3b and the Figure 3 caption as well as in the supplementary Figure 4 (L 229-234).

      (5) L257: indicate this significant difference in Figure 5b.

      The significant difference has now been clearly indicated in Figure 5b.

      (6) L420, 421: change "monocytes" to "macrophages" as this discussion appears to refer to the spleen.

      “Monocytes” was replaced with “macrophages” to reflect the correct cell type discussed in the spleen context (L 226-227).

      (7) L564-565: has the anti-human MX antibody been shown to cross-react with chicken Mx?

      We thank the reviewer for this valuable comment. Yes, the cross-reactivity of the anti-human MxA monoclonal antibody (clone M143, mouse IgGκ; Merck, Germany) with chicken Mx protein has been previously demonstrated. This antibody has been used successfully to detect chicken Mx in several published studies, including Schusser et al., Journal of Virology (2011). Accordingly, supporting references have been added to the revised manuscript (L584-586).

      (8) L608: how were PBMC and splenocytes (mononuclear spleen cells?) isolated -Line 647 on page 14 mentions their isolation using Histopaque-1077 density gradient centrifugation

      We thank the reviewer for this helpful comment. A detailed description of the isolation procedure for PBMCs and mononuclear spleen cells has now been added to the Materials and Methods section under the new subsection titled “Isolation of peripheral blood and splenic mononuclear cells” In this section, we specify that both PBMCs and splenic mononuclear cells were isolated using Histopaque®-1077 density gradient centrifugation as described on page (14), lines (668-676)

      Reviewer #2 (Public review):

      Summary:

      This study attempts to dissect the contributions of type I and type III IFNs to the antiviral response in chickens. The first part of the study characterises the generation of IFNAR and IFNLR KO chicken strains and describes basic differences. Four different viruses are then tested in chicken embryos, while the subsequent analysis of the antiviral response in vivo is performed with one influenza H3N1 strain.

      Strengths:

      Having these two KO chicken strains as a tool is a great achievement. The initial analysis is solid. Clear effect of IFNAR deficiency in in vivo infection, less so for IFNLR deficiency.

      Weaknesses:

      (1) The antibody induction by KLH immunisation: No data indicated whether or not this vaccination induces IFN responses in wt mice, so the effects observed may be due to steady-state differences or to differential effects of IFN induced during the vaccination phase. No pre-immune results are shown. The differences are relatively small and often found at only one plasma dilution - the whole of Figure 4 could be condensed into one or two panels by proper calculation of Ab titers - would these titres be significantly different? This, as all of the other in vivo experiments, has not been repeated, if I understand the methods section correctly.

      We thank the reviewer for the valuable comments and helpful suggestions.

      Regarding interferon induction by KLH immunisation, we agree that KLH is not known to strongly induce type I or type III interferon responses. Importantly, the goal of this experiment was not to quantify IFN induction per se, but to assess how the absence of IFN receptors affects adaptive antibody responses under standard immunisation conditions. KLH is a highly immunogenic, copper‑containing extracellular oxygen‑carrier protein derived from the marine gastropod Megathura crenulata and is widely used as a T cell–dependent model antigen to study B‑cell activation, antibody production, and class switching in vivo (Harris & Markl, Micron 1999, doi: 10.1016/s0968-4328(99)00036-0; Schusser et al., 2016, doi: 10.1002/eji.201546171). Because chickens are extremely unlikely to encounter KLH under natural conditions, KLH behaves as a neo‑antigen, and anti‑KLH antibodies can be considered to arise from de novo adaptive responses rather than pre‑existing antigen experience. Owing to its structural complexity and unusual glycosylation, KLH provides broad antigenic stimulation and engages adaptive immune mechanisms largely independently of pathogen‑specific innate pattern recognition, while still supporting robust T helper cell responses (Swaminathan et al., 2014, doi: 10.1111/bcp.12422; Geyer et al., 2004, doi: 10.1016/j.micron.2003.10.033). This makes KLH particularly suitable for dissecting intrinsic differences in adaptive immune responses between genotypes.

      We have now included pre-immune plasma controls (Figure 4 c, d), demonstrating that baseline antibody levels did not differ statistically between groups and were negligible prior to immunisation.

      As for the use of different plasma dilutions, this was necessary to ensure that all samples were measured within the linear detection range of our in-house ELISA. For example, after the primary immunisation, IgY concentrations were relatively low (e.g., day 5 post-immunisation), and plasma samples had to be diluted only 1:100 to detect measurable differences between groups. In contrast, after the booster immunisation, IgY concentrations increased substantially, and lower dilutions such as 1:100 led to signal saturation. Therefore, higher dilutions (up to 1:1600) were required to keep the values within the measurable range.

      Following the reviewer’s recommendation, we have now unified the presentation of results by showing data at a single representative dilution for each isotype: 1:100 for IgM (Figure 4C) and 1:1600 for IgY (Figure 4D). These dilutions fall within the linear part of the standard curve to distinguish between groups. We also calculated endpoint antibody titers, which confirmed that the observed differences remain statistically significant (p < 0.05).

      Regarding experimental replication, the study design already incorporated sufficient biological replication and longitudinal sampling to ensure robustness of the findings. Each experimental group consisted of ten animals, including three animals that served as negative controls. In addition, animals were sampled at multiple time points following immunisation, allowing the dynamics of the antibody response to be monitored over time. This longitudinal design provides repeated biological measurements within the same experimental cohort and allows confirmation of consistent response patterns across time points. All ELISA measurements were performed in technical triplicates. Together, the combination of adequate group size, appropriate controls, repeated sampling over time, and technical replication provides sufficient statistical power and internal validation of the observed effects. Furthermore, all animal experiments were conducted under strict approval of the Government of Upper Bavaria and in accordance with German animal welfare regulations, which limit unnecessary repetition of in vivo experiments beyond the approved experimental design.

      (2) The basic conundrum here and in later figures is never addressed by the authors: Situations where IFN type 1 and 3 signalling deficiency each have an independent effect (i.e., Figure 4d) suggest that they act by separate, unrelated mechanisms. However, all the literature about these IFN families suggests that they show almost identical signalling and gene induction downstream of their respective receptors. How can the same signalling, clearly active here downstream of the receptors for IFN type 1 or type 3, be non-redundant, i.e., why does the unaffected IFN family not stand in? This is a major difference from the mouse studies, which showed a rather subtle phenotype when only one of the two IFN systems was missing, but a massive reduction in virus control in double KO mice (the correct primary paper should be quoted here, not only the review by McNab). Reasons could be a direct effect of IFNab on B cells and an indirect effect of IFNL through non-B cells, timing issues, and many other scenarios can be envisaged. The authors do not address this question, which limits the depth of analysis.<br />

      We thank the reviewer for this insightful comment. Indeed, this represents one of the most interesting and novel findings of our study. Unlike in mice, where both type I and type III interferon systems need to be disrupted to observe clear susceptibility to influenza infection, in our chicken model the loss of IFNAR1 alone was sufficient to render the animals highly susceptible. This highlights a key difference between mammalian and avian interferon biology and supports the main goal of our work, to investigate the specific biological activities of avian interferons rather than directly transferring conclusions from mammalian systems.

      In relation to Figure 4d (anti-KLH IgY), we observed that both IFNAR1<sup>-/-</sup> and IFNLR1<sup>-/-</sup> animals reduced IgY levels compared to wild type at day 3 after the booster immunisation. However, by day 5 post-booster, IgY levels in IFNLR1<sup>-/-</sup> animals had returned to wild-type levels, while IFNAR1-/- animals still showed significantly lower IgY. This indicates that type III IFN contributes to the early phase of the IgY response but that its absence can later be compensated by type I IFN signalling. In contrast, loss of type I IFN cannot be compensated by type III IFN, suggesting that type I IFN plays a more dominant or sustained role in antibody induction.

      Although type I and type III IFNs share overlapping signaling pathways and induce similar sets of ISGs, their effects are not entirely redundant in chickens. A likely explanation is the difference in receptor distribution: IFNAR1 is broadly expressed across most cell types, while IFNLR1 expression is mainly confined to epithelial cells (Reuter et al. 2014, doi: 10.1128/jvi.02764-13; Santhakumar et al., 2017, doi: 10.3389/fimmu.2017.00049). This systemic versus localized receptor pattern likely determines the range of responsive cells and may account for the differential outcomes observed when either receptor is absent.

      Taken together, our findings indicate that while type I and type III IFNs share overlapping signaling mechanisms, they maintain distinct biological functions in chickens, consistent with their differing receptor expression and cellular responsiveness. This contrasts with mammalian models, where redundancy between these systems is more apparent and only double knockouts show strong phenotypes especially during influenza infection (Mordstein et al., 2008, doi: 10.1371/journal.ppat.1000151; Mordstein et al., 2010, doi: 10.1128/jvi.00272-10). We have now cited this primary study instead of the McNab review and expanded the Discussion to reflect this interpretation (Page 10, Line 463-467).

      (3) In the one in vivo experiment performed with chickens, only one virus was tested; more influenza strains should be included, as well as non-influenza viruses.

      We thank the reviewer for this valuable suggestion. The main objective of the present study was to generate and characterize novel chicken models lacking type I and type III interferon receptors in order to investigate their physiological relevance and to obtain the first insights into their roles during viral infection with more emphasis on avian influenza. As part of this manuscript, we performed detailed in ovo experiments using both influenza and non-influenza viruses (Figure 6). These included three influenza strains: H1N1, a mammalian-adapted strain; H3N1, a low pathogenic avian strain showing features of high pathogenicity; and H9N2, a low pathogenic avian strain, as well as a non-influenza virus, the infectious bronchitis virus (IBV). The in ovo analyses revealed clear strain-dependent modulation of interferon responses, and have provided a comprehensive overview of virus-specific interferon activity in chickens. The subsequent in vivo experiment was therefore designed as a proof of concept using the most suitable viral strain to robustly challenge the immune system and to identify the distinct functions of chicken interferons.

      (4) The basic conundrum of point 2 applies equally to Figure 6a; both KOs have a phenotype. Again in 6d, both IFNs appear to be separately required for Mx induction. An explanation is needed.

      We thank the reviewer for raising this important point. We have revised the Discussion (page 10, lines 442-454) and provided supporting references to clarify how the composition of the chorioallantoic membrane (CAM) and virus tropism together determine the apparent requirement for type I and type III interferons. The CAM contains both epithelial and mesodermal–vascular layers, which support complementary interferon functions: type I IFN acts mainly in systemic and vascular compartments, while type III IFN provides localized protection at the epithelial surface. Consequently, viruses that replicate in both compartments (e.g., WSN33, H3N1) require both IFN pathways for maximal Mx induction (Figures 6a, 6d), whereas viruses with a predominant or prolonged epithelial phase (e.g., H9N2, IBV) at the time point analyzed are effectively controlled by type I IFN signaling alone.

      These differences likely reflect virus-specific factors, including cell tropism, replication kinetics, and the spatial–temporal dynamics of receptor expression and signaling. Notably, our measurement of Mx expression at 24 hours post infection (hpi) may represent a phase when type I IFN signaling is dominant and can compensate for the absence of type III IFN. It remains possible that IFN-λ plays a more critical, non-redundant role at earlier stages post infection, when rapid antiviral protection is first required at the epithelial surface. Thus, the apparent redundancy observed at 24 hpi likely reflects temporal compensation and crosstalk between the IFN pathways rather than a lack of biological relevance for type III IFN.

      (5) Line 308, where are the viral titers you refer to in the text? The statement that the results demonstrate that excessive IFNab has a negative impact is overstretched, as no IFN measurements of the infected embryos are shown here.

      We thank the reviewer for this comment and would like to clarify that measurements of type I IFN (IFN-α/β) concentrations were indeed performed. The data are presented in Figure 6b and cited in the Results section (“Knockout of IFNAR1 and IFNLR1 did not affect IFN-α/β secretion in ovo”). To avoid misunderstanding, the Results section has been revised to explicitly reference the IFN-α/β measurements supporting this conclusion (line 302-309).

      These data indicate that all genotypes produced comparable IFN-α/β levels upon viral infection, with the IBV infection inducing approximately tenfold higher IFN-α/β secretion than the influenza strains tested (Figure 6b). The interpretation that an excessive type I IFN response can negatively affect host fitness is based on the combination of quantified IFN-α/β data (Figure 6b) and survival probability results (Supplementary Figure 10), where embryos exhibiting the highest IFN-α/β levels (embryos of all genotypes infected with IBV and embryos infected with IFNLR1<sup>-/-</sup> H9N2) showed the poorest survival despite moderate or low viral titers.

      (6) The in vivo infection is the most interesting experiment, and the key outcome here is that IFN type 1 is crucial for anti-H3N1 protection in chickens, while type 3 is less impactful. However, this experiment suffers from the different time points when chickens were culled, so many parameters are impossible to compare (e.g., weight loss, histopathology, IFN measurements, and more). Many of these phenomena are highly dynamic in acute virus infections, so disparate time points do not allow a meaningful comparison between different genotypes. What are the stats in 7b? Is the median rather than the mean indicated by the line? Otherwise, the lines appear in surprising places. SD must be shown, and I find it difficult to believe that there is a significant difference in weight, for e.g., IFNAR KO, unless maybe with a paired t test. What is the statistical test?

      We thank the reviewer for these thoughtful comments and agree that disease progression and sampling time can influence comparisons in acute infection studies. Hens were euthanized upon reaching predefined humane endpoint scores in full compliance with the Bavarian animal welfare regulations. Because the infection produced markedly different clinical kinetics among genotypes, all data were interpreted with reference to matched disease stages rather than absolute days post-infection.

      For matched comparisons: Viral titers in the trachea and cloaca, as well as plasma IFN-α/β concentrations, were compared between day 2 in IFNAR1<sup>-/-</sup> hens and day 3 in WT and IFNLR1<sup>-/-</sup> hens, which represent equivalent clinical stages before the sharp viral rise seen later in WT and IFNLR1<sup>-/-</sup> birds. At these comparable stages, viral titers were still low and IFN-α/β concentrations remained significantly lower in WT and IFNLR1<sup>-/-</sup> than in IFNAR1<sup>-/-</sup> hens (Figure 7c, d, f), indicating that uncontrolled viral replication and IFN-α/β secretion in the absence of type I signaling occur earlier and more intensely.

      For Figure 7b: Because chickens reached humane endpoints at different days post infection (2 dpi for IFNAR1<sup>-/-</sup> and 5–7 dpi for WT and IFNLR1<sup>-/-</sup>), statistical comparisons were performed within each genotype using paired t-tests and all data were shown together as mean ± SD.

      We acknowledge that unequal survival times limit direct temporal comparison. However, the consistent pattern across all parameters including early severe disease, high viral load, and excessive IFN-α/β secretion in IFNAR1<sup>-/-</sup> hens versus delayed onset in WT and IFNLR1<sup>-/-</sup>, supports the conclusion that type I IFN signaling is essential for early viral restriction and host survival, while type III IFN contributes mainly to localized inflammatory responses. The experiment cannot be repeated under the current animal welfare authorization.

      (7) Figures 7e,f: these comparisons are very difficult to interpret as the virus loads at these time points already differ significantly, so any difference could be secondary to virus load differences.

      We thank the reviewer for this valuable comment. We agree that viral load can influence interferon induction; however, our comparisons in Figures 7e and 7f were designed to reflect equivalent stages of disease progression rather than identical time points post-infection. For IFN-λ mRNA expression (Fig. 7e), spleens from IFNAR1<sup>-/-</sup> hens were sampled on day 2 post-infection, when viral titers were maximal, and compared to WT and IFNLR1<sup>-/-</sup> hens sampled on day 5 post-infection, at which point viral titers reached comparable levels. Thus, this comparison represents the phase of peak infection and systemic immune activation across all genotypes rather than an absolute temporal comparison.

      Similarly, for IFN-α/β concentrations (Fig. 7f), two levels of comparison were made: between IFNAR1<sup>-/-</sup> hens at day 2 post-infection (high viral titer) and WT and IFNLR1<sup>-/-</sup> hens at day 3 (low viral titer), and between WT and IFNLR1<sup>-/-</sup> hens at day 5 post-infection (high viral titer). In both cases, IFN-α/β levels remained disproportionately elevated in IFNAR1<sup>-/-</sup> hens, indicating that the excessive type I IFN response is primarily due to the loss of receptor-mediated feedback regulation rather than viral load alone.

      We have clarified this rationale in the legend of figure 7 and in the results (Line 338-345). We believe these results are valuable as they provide important insight into the temporal dynamics and regulatory interplay between type I and type III interferons during avian influenza infection.

      Reviewer #2 (Recommendations for the authors):

      Experiments need to be repeated. Comparisons in infection experiments must be done on the same day. More viruses need to be tested.

      We thank the reviewer for these constructive recommendations. All infection experiments were conducted under approved animal welfare regulations, which limited the number of replicates and prevented repeating in vivo challenges beyond the authorized design, in line with the 3R principles, particularly Reduction, to avoid unnecessary animal use. To ensure comparability, samples were analyzed at matched disease stages rather than identical time points, as clarified in the revised figure legends (figure 7) and Results (Line 338-345). The study already includes multiple influenza and non-influenza viruses (H1N1, H3N1, H9N2, and IBV) tested in ovo to capture virus-specific interferon responses, while the in vivo H3N1 infection served as a proof-of-concept to dissect genotype-specific immune dynamics.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Ducrocq et al. present research exploring the genetic link between simple multicellular group formation (ace2Δ/ace2Δ) and its interaction with cell-cycle progression mutants (e.g., cln3Δ/cln3Δ), demonstrating that this combination can provide fitness benefits during fluctuating resource conditions, resulting in a rapid increase in the fraction of multicellular cell-cycle mutants over unicellular yeast without selection for multicellular size. Because both the multicellular phenotype and the regulatory link enabling faster escape from the stationary phase are controlled by the Ace2 transcription factor, this work demonstrates that multicellularity can arise as a side-effect of a completely independent fitness advantage unrelated to the benefits of group formation itself. As a "passenger phenotype," multicellularity could thus emerge for other selective reasons, potentially facilitating a later transition to more entrenched multicellularity if novel conditions arise where group formation becomes directly beneficial.

      Strengths:

      This work is novel and exciting for research exploring the very first steps of the transition from unicellularity to simple multicellularity. This is particularly significant because the formation of multicellular groups is almost always assumed to come at a cell-level fitness cost due to reduced reproductive fitness compared to remaining unicellular. This cell-level fitness cost generally needs to be outweighed by the benefits of multicellular group formation (e.g., large size escaping predation) for the multicellular phenotype to be stable, which is true for a large number of cases studied in the literature, where the multicellular phenotype can only evolve over unicellular competitors under strong selection for multicellular groups. However, this study presents an interesting case of a genetic and environmental condition under which individual cells (forming simple multicellular clusters) can actually have higher reproductive fitness than unicellular yeast. This demonstrates that the assumed cost at the single-cell level does not always apply. In summary, this work represents a unique example contrary to common assumptions regarding the costs of multicellular phenotypes, showing that simple multicellular phenotypes can evolve and remain stable without requiring strong selection for multicellular size or other benefits of group formation.

      The claims and interpretation of the results align well with the data presented. This is due to the careful and straightforward experimental design testing predictions with a clear, stepwise methodology, ruling out alternative explanations and providing support for the proposed link between the mutations (ace2, cln3, and others), their impact on faster exit from quiescence, and thus earlier entry into reproduction in fresh media, resulting in higher fitness in the snowflake yeast phenotype compared to unicellular yeast.

      Weaknesses:

      The authors show that the same multicellular phenotype with higher cell-level fitness due to faster exit from the stationary phase can also be observed with alleles found at other loci in non-laboratory yeast strains, implying that the results are likely not specific to a peculiar case genetically engineered in laboratory strains, but that similar phenotypes may be present in nature. However, this remains to be explored further by examining the natural ecology of commercially available or wild yeast isolates and their genomes. This is by no means a weakness of this study and, therefore, not necessarily something the current work can improve. It does mean, however, that the relevance of these findings for early multicellularity in yeast, and even more so for nascent multicellularity in distinct taxa, remains to be explored in the future. Until then, it is difficult to make strong claims about how applicable these results would be for non-laboratory yeast and other taxa. Regardless, this work does its part by representing a very exciting finding.

      Reviewer #2 (Public review):

      Summary:

      Here, the authors attempt to demonstrate that a simple model of multicellularity - snowflake yeast - exhibits key ecologically relevant changes in the regulation of the cell cycle. By examining the effects of the ace2 mutation in environments where multicellularity is not directly selected for or against, and combining it with mutations in key cell cycle regulators, they hope to show that mutations driving simple multicellularity can be selectively favored due to their effects on the release from quiescence rather than their effects on multicellularity itself.

      Strengths:

      The experiments performed are extensive and thorough. The yeast genotypes examined are judiciously chosen, so as to map out a functional model of the relationship between alterations to cell cycle control and changes to multicellularity phenotypes. Multiple possible interactions are examined, with the causal link and model of the relationship between the multicellular passenger phenotype and the selectable quiescence-release phenotype being well-supported. There are extensive controls demonstrating the separation between the 'passenger' multicellular phenotype and the cell cycle regulation phenotypes examined, including haploid/diploid strains with different multicellular phenotypes but similar cell cycle regulation phenotypes, and phenocopy strains in which downstream enzymes are deleted rather than key central regulators.

      Weaknesses:

      My only concerns about these results relate to the focus on selection on cell cycle control being examined in a model of multicellularity with key core cell cycle mutations rather than in a wild-type background, as this is a somewhat artificial system.

      I believe, however, that the authors convincingly make their case that this work on the multicellular phenotypes of yeast represents a potent proof-of-concept that simple multicellularity can be driven into existence or selected for as a passenger phenotype due to pleiotropic effects of mutations under selection from real-world ecological pressures. They are able to connect this phenotype back to known mutations of particular cell cycle regulators (RB) in other multicellular lineages and demonstrate that ecologically relevant changes to the cell cycle are connected to multicellular phenotypes. As a proof of concept of the connection between these phenotypes, rather than a study of a particular event in the past of a living lineage, it makes a strong case.

      A longstanding question in the field of multicellularity is the selective pressures that can drive simple multicellularity into existence and then act on simple multicells to drive their increased size and complexity. This work brings to the table tangible evidence of the possibility that, instead of being selected for on its own, simple multicellularity can be a side-effect of selection on other key phenotypes.

      This separates the question of the origins of multicellularity and the forces that drive its further evolution. This separation can reframe how the field is studied, especially in the context of the apparent dichotomy between dozens of origins of 'simple' multicellularity across the tree of life and a few origins of 'complex' multicellularity in the history of Earth. Especially in light of other evidence that multicellularity is connected to changes in cell cycle regulation, I believe that this is an important insight that will alter the way we think about the origins of this key evolutionary transition.

      We thank the reviewers for their insightful comments on our work.

      We agree with reviewer #1 that further experiments would be needed to figure out how the observations done on lab strains can apply to yeast in various ecological conditions and particularly in the wild. We here provide a proof of principle that multicellularity selection can arise as a side-effect. It obviously does not prove that it took place during yeast evolution, but we would like to emphasize that resource fluctuations are very common in ecological conditions, making it highly likely that the environmental conditions necessary for the selection of the side effects described have arisen.

      We agree with reviewer #2 that our work on yeast strains is “somewhat artificial” as often the case with model organisms under laboratory conditions. Importantly though, we showed that the effect found with the cln3 knock-out mutation can be phenocopied by overexpression of WHI5 (encoding the yeast equivalent of Rb). We propose that variations in the levels of cell cycle regulators during evolution may have played a role in multicellularity selection as a side effect. We agree that this is merely a hypothesis to explain the selection of multicellularity (just like predator escape) and that there is no direct evidence that this occurred in the history of the lineage. Nevertheless, our work provides a first evidence that such a selection of multicellularity as a side effect could be possible, and gives a framework to understand how multicellularity can persist in the wild, even when it is not the primary target of selection.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      As mentioned in my public review, I very much appreciate this work, its interpretation for early multicellularity as an example opposite to the assumed cost of multicellular phenotypes, and the robust design behind the premise and claims. Therefore, my suggestions below are mostly aimed at improving the readability and data presentation.

      (1) In the abstract, Lines 24-27 (the last sentence): This statement is worded too generally and therefore reads as too strong. I think the authors' work provides an example that multicellularity itself does not need to be beneficial all the time - this is really exciting and makes sense! However, there is a substantial body of work showing the origin and maintenance of multicellularity for its direct benefits. Relative to that body of work, this represents a special case, and therefore, while we should definitely reconsider the view that "multicellularity always comes at a cell-level fitness cost," we cannot overgeneralize these findings. Please consider reframing this statement.

      Done, now line 25 (addition of “in some cases”)

      (2) Line 48 (Introduction): "This mostly concerns two major regulators, RB and Cyclin D." Which organisms are you referring to? Please specify.

      Done.

      (3) In the Introduction, there are at least three sentences that need citations: L57-58, L59-60, and L65. For instance, I do not know what makes CLN3 the yeast functional equivalent of RB, and I wanted to verify this claim, but no references are cited. Please ensure citations are provided throughout the manuscript.

      Done: ref 11,12 and 13 were added

      (4) This is my main request regarding data collection and presentation. The authors share some microscopy images of mutant strains in Figure 2 for different purposes (e.g., Figure 2B compares the fraction of budded cells between two genotypes). However, I would appreciate seeing a collected microscopy figure showcasing the phenotypes of all genotypes that went into competition experiments, including the planktonic (WT lab strain) yeast, either where they appear or in a supplementary figure, all presented with the same magnification and scale to make them comparable. Because cell size, shape, and multicellular phenotype are all key aspects of the competition experiments, being able to see all those genotypes/phenotypes would prepare the reader to make predictions about the fitness assays and other experiments.

      Done Supplementary Figure 1 B-E were added

      (5) Related to my previous point, I would appreciate seeing cell size measurements for the different genotypes (both single cells of planktonic genotypes and single cells forming multicellular clusters). Cell size is a key trait that directly impacts the results shown in the paper, and summary statistics comparing them would be helpful for interpreting the results.

      Done Supplementary Figure 1 F was added

      (6) In competition experiments, the authors mix unicellular and multicellular yeast clusters at 50/50 and measure the fraction of a phenotype of interest (usually the % of snowflake). It took me a while to understand what is being counted under the "% snowflake yeast" category. This is because, while each cell in unicellular yeast should be counted as one unit, one can count a snowflake yeast composed of 50 cells as 50 units or as 1 unit. Please clearly state what is being counted for the Y-axis labeled "% of snowflake yeast" (or relabel those Y-axes in plots to make this clear).

      Done: Added in figure legend 1A and Y-axes of competition figures

      (7) I recommend editing the genotype labels in figures (see, for instance, Figure 1B, C, D). In Figure 1B, the bars are labeled as "CLN3/CLN3 co-culture" or "cln3Δ/cln3Δ co-culture," etc. These are actually co-cultures of SF vs. PK (with or without a CLN3 copy). Please consider using more representative labels that will be easier for readers to understand.

      Done: this has been changed in all concerned figures

      (8) In the Results, L225, you begin referring to AMN1368D as AMN1. I suggest using the full allelic form throughout the text so it will be clear each time that you are referring to that specific allele, as I was confused about whether you were discussing the allele or the gene AMN1 itself.

      This has been changed throughout the text.

      (9) Discussion, Lines 250-252, states that this is a "situation that is likely to happen very often under ecological conditions." Are there any examples you can cite?

      Done, as also requested by reviewer #2 (now line 256-7)

      (10) Lines 272-275 contain a strong, general statement suggesting that co-evolution of cell cycle regulation and multicellularity could be more general (which is acceptable as speculation). However, the suggestion that this co-evolution could have "started very early in the evolution of eukaryotic cells" is too speculative. I would recommend sticking with the alternative, suggesting that the link between the two phenotypes may be a case of convergent evolution.

      Done

      (11) Lines 278-279 are both vague and too bold. The text mentions a link between cancer and multicellularity and then extends this link through cell cycle regulators. Without explaining the connection between cancer and multicellularity and then trying to link it to cell cycle regulators, all in a few words without background, this sentence is too vague. Please consider deleting this or spending more time clearly explaining the link, which would at best still be speculative.

      These speculative sentences were removed.

      (12) First, I wanted to note that I highlighted Lines 284-287, as this passage is clearly written and provides a nice argument. I also wonder if you could mention that your work shows simple multicellular cluster formation should not always come at a cost, contrary to the general assumption in the literature, and add a few citations to support that claim. This would highlight how significant this work is within the broader multicellularity literature.

      Changed in discussion (now line 242-4 with additional references 30 and 31)

      (13) I recommend labeling the genotype of your "quintuple mutant" in Figure 3. You can refer to it as the quintuple mutant in the text, but I had to go back and forth to see what those mutations were when trying to think about potential genetic interactions. Even the legend of Figure 3 does not specify the genotype and refers to it only as the "quintuple mutant."

      Now explicitly stated in the title of the figure

      Reviewer #2 (Recommendations for the authors):

      I find the presented research to be of high quality, with very important implications. I have suggestions for improvement of the manuscript, but they are largely stylistic, with one paper that I believe deserves citation regarding the proteins involved. I see little need for additional experiments or analysis, just a clearer description of the results and their significance.

      (1) Line 62: Yeast CLN3 definitely performs the same role as cyclin D in the cell cycle, but has an unclear phylogenetic relationship with the rest of the cyclins. See Cross, Buchler, & Skotheim 2011 ("Evolution of networks and sequences in eukaryotic cell cycle control"). This reference also covers the functional relationship between RB and Whi5, referred to in nearby sentences, as does Medina, Walsh, and Buchler 2019 ("Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain").

      The reference has been added

      (2) Line 69: Is the question whether the evolution of G1/S regulation favoring multicellularity the question, or the two of them being connected such that the evolution of one can affect the other?

      It is clearly the first of the two questions.

      (3) Line 73: Comma after Ace2.

      Done

      (4) Line 76: It would be clearer to specify that snowflake and ACE2 yeast were co-cultured without settling selection or other selection that explicitly favors multicellularity, unlike in experiments where multicellular evolution is observed, as in Ratcliff publications.

      This is now specified.

      (5) Line 80: Specify which phenotypes observed for ace2 mutants are observed, specifically, both the multicellularity and the release from quiescence.

      Done

      (6) Line 146: This observation should be noted as another indication that the multicellular phenotype is not behind the selective pressure, because it is so different between unicells and multicells.

      Overall, you have very strong evidence that this is the case, and emphasizing this would benefit the paper!

      Done.

      (7) Line 151: specify that you are maintaining yeast in proliferation in coculture.

      Done.

      (8) Line 181: This is another key experiment showing that the multicellular phenotype is not the causal reason for the change in quiescence. It might make things clearer to bring all these confirmatory experiments together, particularly the haploids and the sonicated single cells.

      This is now clearly stated line 195.

      (9) Line 225: The choice of referring to the non-laboratory strain as the 'AMN1' wild type default may be confusing to readers, who may treat the genetic background you are using as the ground truth wild type. I recommend throughout the paper always specifying the allele's amino acid to avoid any confusion.

      The genotype is now clearly presented throughout the text.

      (10) Line 238: I would continue to specify that the multicellular phenotype has no selective advantage, specifically when no selection for size is applied.

      See added sentence Line 242-4 (revised version)

      (11) Line 243: I would say that the evolution of cell cycle regulation may interact with the multicellular phenotype.

      This was changed (now line 248)

      (12) Line 244: Strike 'indeed' and the 'the' before AMN1 and ACE2.

      Done

      (13) Line 252: Suggest some ecological conditions under which quiescence exit is likely, such as boom and bust or moving from rotting fruit to rotting fruit.

      Done

      (14) Line 267: Are you suggesting that the specific genes AMN1 and ACE2 had particular effects on actual organisms in the past, or that it represents a broad pattern of evolution in which multicellularity could be more broadly related to exit from quiescence? I believe it is the latter, and I think that should be clearer.

      Modified as suggested

      (15) Line 280: In this paragraph, I think that the point being made could be slightly clearer - if I am not mistaken, you are making the distinction between the appearance of multicellularity and its refinement under selection, and that the former may be more common than previously believed, given this proof of concept. I think this can be made clearer. Furthermore, it is worth noting that all experiments that show effects of the multicellular phenotype are in mutant backgrounds, and explaining why this is still relevant to wild organisms. It might be taken by some as indicating that the multicellular phenotypes are not relevant to a wild population, but the connection to known RB mutations in known multicellular lineages and the fact that it is connected to a very key aspect of cell cycle regulation, I think, overcomes this issue, and this should be made clear.

      Our study reveals a genetic link between multicellularity and Whi5 and Cln3, two important G1/S cell cycle regulators. Similar genetic interactions have been observed in phylogenetically distant species, reinforcing the idea that the interplay between cell cycle regulation and multicellularity is a general feature and not a mere artifact of mutant background.

      The neutral fitness effect of multicellularity in wild-type backgrounds is particularly of interest. By being maintained as a side effect of selection on fundamental cellular processes, the neutral effect of multicellularity may have provided “an evolutionary scheme” for its repeated emergence throughout the tree of life. As such, the "passenger selection" hypothesis fits well with the observations of phenotypic reversibility and facultative multicellularity, despite varying and specific selective pressures. Our work thus gives a framework to understand how multicellularity can persist in the wild, even when it is not the primary target of selection.

      (16) Line 314: What promoters are they driven by?

      Specified

      (17) Line 336: What was the culture volume, and the volume transferred?

      Specified

      (18) Line 362: How was the proportion of blue-stained cells scored? Manually, or with an imaging software cutoff?

      Specified

      (19) Figure 1: I think that the full genotypes of each strain should be specified, either in the legend or the key of the figure, rather than always specifying the ACE2 genotype and other mutations separately.

      Done as requested by reviewer #1

      (20) Figure 2E, 2F: Same as Figure 1, regarding genotypes.

      Done

    1. Author response:

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

      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. Please see lines 111-120.

      (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. As we had 5 treatment groups, and intended to generate a minimum of 8 litters of offspring per treatment group, this resulted in over 40 litters in total. In order to dissect these litters appropriately, and in a timely fashion, we had to stagger their generation over time. As such, this resulted in utilising our males at different ages/durations on the diet. However, in all our statistical analysis, we factored in the duration of time on the diet, which also acted as a proxy measure of paternal age. We also ensured that we staggered the generation of litters in each diet group so that any age effects were experienced across all paternal regimens.

      We have revised the manuscript to acknowledge this fact and to highlight that the duration of time on any diet was factored into the statistical analysis.

      (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 apologies 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, inclusion of siblings and correction for multiple testing.

      Reviewer #1 (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.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors have done an immense amount of work, which should be commended. In addition to the public review, I have a few suggestions for improvement.

      (1) To further explore the weight discrepancy between the males subjected to diet alteration and those on the control diet, further details about the intake and provision of the diets would be beneficial. Seeing as the fat mass was increased in males fed a WD, do you have information on where the weight 'loss' originated from?

      We thank the Reviewer for their insight into the changes in male body weight. We agree that the differences in total body weight verses the amount of adipose tissue, is intriguing. Unfortunately, we were unable to monitor the food intake of our animals for two main reasons. The first was that for animal welfare considerations, all our males were initially group housed prior to mating. This meant that typically, males were housed in groups of 4 during the initial feeding (pre-mating) period. Males were only housed singly upon them being used for mating. As such, it was not possible to obtain food consumption data for individual males.

      A second limitation arose due to the high extend of males who were fed the Western Diet effectively shredding the diet. This meant that it was not possible to weight the food to obtain a crude idea of how much they were consuming. The reason for this shredding is not clear to us. All mice received environmental enrichment, as we did not observed this behaviour for our control or low protein diet fed males.

      With regards to the weight of the other organs, we did not observe and significant overall changes in organ weight, or weight relative to body weight. Unfortunately, we did not have access to, or conduct any whole body scanning, such as DEXA, which would have given more insight into the body composition of our mice.

      (2) The testicular abnormalities and gene expression findings are linked nicely to the offspring's story. This is not as compelling for other findings, including the gut microbiome changes, which are not discussed in the context of the fetoplacental outcomes. More discussion of the potential impact of paternal changes on fetal outcomes would strengthen claims that these findings are impactful.

      We thank the Reviewer for their comments and suggestion. Our caution with connecting the gut microbiota to offspring development is that, to the best of our understanding, there is little data with regards to its effect on post-fertilisation development. While there is data showing that the microbiome can produce compounds and metabolites that can affect sperm quality and metabolism, lipid composition and testicular morphology, the connection with post-fertilisation development is limited. Additionally, as we saw no difference in fundamental fertility, as measured by changes in litter size, we propose that there no overall changes in the ability of the sperm from our experimental males to reach, fertilise and support development.

      However, we acknowledge the Reviewers comments on strengthening the manuscript and so have included some additional text within the Discussion to highlight the links between the microbiome and male reproductive fitness. Please see lines 337-348.

      (3) It is clarified in the methods that n=8 males were used in the study, but different nnumbers are shown for some parameters. It would improve transparency for the reader if it were clarified whether these differences result from missing data or from the removal of statistical outliers.

      The Reviewer is correct that while 8 males were initially placed on their respective diets, for some of the analyses, the n-number is less than 8. In some instances, for example the analysis of total body fat (Fig. 1D), data was unfortunately not collected during an initial round of dissections. As such, the n number here is only 6 in each group. Additionally, due to the high cost associated with sequencing the microbiome for 5 groups, we decided to only sequence 6 samples per group. However, we do not feel that this impacts significantly on the overall focus of the data presented.

      (4) Despite this, you may have been underpowered to detect differences in some parameters, for example, the placental stereology. Alternative approaches, such as immunostaining with whole-section quantification, may be more sensitive to detect subtle changes. Alternatively, have you considered using smaller grids for improved sensitivity of the stereological analysis?

      We thank the Reviewer for their insight into the data and their suggestion for immunostaining. We agree with the Reviewers that a greater number of samples would have strengthened our analyses. However, we are not in the possession of further samples which have been processed in the correct manner for additional stereological analysis. We are hoping to conduct further placental analyses based on our RNA-Seq data, but this will require the generation of new samples.

      (5) It would be easier to interpret the figures if it were clear which datasets were analysed using non-parametric tests. Were Figure 2F, 2G, 6A, 6E, and 6I are shown differently for that reason, perhaps? It would improve transparency if non-normally distributed data are shown as medians, as that's what's being compared in a non-parametric test.

      We apologies for any confusion regarding the analysis of our data. The Reviewer is correct that the data in 2F and 2G were analysed using a non-parametric test. We have now made this clearer in the legend to the figure highlighting which data sets were analysed by ANOVA or Kruskal–Wallis test. We have also done this for the other figure legends where appropriate. With regard to Figure 6, the data presented in Panels A, E and I were intended to show the range of data extending above and below the 90th and 10th centiles of the CD fetuses. As such, we felt that violin plots were the most appropriate way to display these data.

      (6) Supplemental Figure 1 seems to be missing.

      We apologise sincerely for the lack of inclusion of Supplemental Figure 1. We will ensure that it is included in our resubmission

      (7) Line 523 states that samples with RIN < 7 were used for microarray analysis. Do the authors mean RIN > 7?

      We thank the Reviewer for identifying our mistake. The Reviewer is correct that this should have been a RIN >7. We have now corrected this.

      (8) It is mentioned in lines 603-604 that paraffin shrinkage was accounted for. It could be useful to describe how this was done.

      We have revised the text within the Materials and Methods to provide additional clarity on how we compensated for the shrinkage due to the paraffin processing.

      In the revised Methods we have added a brief “Shrinkage correction” subsection describing how paraffin-embedding shrinkage was quantified for each placenta individually. Specifically, we now state that post-embedding placental volume was estimated using the Cavalieri Principle on systematic and uniformly-random sampled H&E sections, and a per-placenta volume shrinkage coefficient (k<sub>V</sub> = V<sub>post</sub>/V<sub>pre</sub>) was calculated.

      We have also added the equations showing how this coefficient was used to correct compartment volumes and the derived surface area estimates (surface area calculated from S<sub>v</sub> and the corresponding shrinkage-corrected placenta volume). Please see lines 618-644.

      (9) This may be due to the generation of the reviewer PDF, but Figure 4E and 4H are illegible in our version of the manuscript.

      We apologies for the lower resolution with these figures and the difficulty in seeing the information presented. We have created revised versions of these figures which we hope are of higher quality and clarity.

      (10) What do the stars represent in Figure 6A, E, I - compared to what, controls?

      The Reviewer is correct that the asterisks in Figures 6A, E and I represent differences in the proportion of fetuses either above or below the 90th and 10th centile of the CD fetuses respectively. As such, in panel A, for both the LPD and MD-LPD groups, there are significantly more fetuses who are below the 10th centile of the CD group. Similarly, in panel E, there are significantly more placentas in the LPD group that have a weight above the 90th centile of the CD group. We have revised the graphs to make these differences, and their comparisons clearer.

      Reviewer #2 (Recommendations for the authors):

      Some Recommendations for improving the writing and presentation, and minor corrections to the text and figures:

      (1) Please describe Wnt signaling in the Abstract.

      The Abstract has been amended to provide some additional text regarding Wnt signalling. Please see lines 60-63.

      (2) Page 6, line 134: A brief explanation of why measuring the inhibin beta-A chain should be included.

      The text within this section has been amended to include a brief description of the role of Inhibin β-A chain on testicular function. Please see lines 135-139.

      (3) The methodology used for Tnf determination is missing and should be described.

      We apologies for the lack of detail regarding our analysis of serum Tnf in our males. This has now been included. Please see lines 479-480.

      (4) It is important to mention that free fatty acid levels in the MD-WD group were similar to those in the CD group, although they remained comparable to the WD group.

      We agree with the Reviewer and have amended the text to indicate that there was no difference in the FFA profile of the MD-WD males to either the CD or WD males. Please see lines 147-148.

      (5) Figure 2 presents both metabolic parameters and bacterial profile analyses. Although the authors appear to relate these outcomes, clarity would be improved by presenting them in separate figures.

      As requested, we have now presented these data as two separate Figures

      (6) Figure 3H: The data suggest that the decrease in the number of spermatogonia (PLZF⁺) observed in the LPD and WD groups was prevented when the diets were supplemented with methyl donors.

      (7) However, the description and interpretation of this result (or of a neutral effect) are missing.

      We agree with the Reviewer in their interpretation of the PLZF+ data. We have indicated this in the text within the Results and Discussion sections. Please see lines 177-178 and lines.

      (8) Line 284: Please check the abbreviation for MD-LPD.

      We thank the Reviewer for identifying this typographical mistake. This has now been corrected to state MD-LPD and not MDL.

      (9) Line 285: Please check the lettering in the text and in Figure 6H-K.

      We thank the Reviewer for identifying this typographical mistake. This has now been corrected to state the panels are Figure 9H-K, as we have split the original Figure 2 into two figures.

    1. Author response:

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

      eLife Assessment

      The study presents important insights into the regulation of muscle hypertrophy, regulated by Muscle Ankyrin Repeat Proteins (MARPs) and mTOR. The methods are overall solid and complementary, with only minor limitations. Overall, the findings will be of interest for both muscle-biology specialists and the broader mechanobiology community.

      We thank the editors for their interest in our manuscript. Below we respond to the reviewer’s comments. Based on these comments we made extensive textual revisions throughout the manuscript, and we added additional analyses to the revised results.

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors employ diaphragm denervation in rats and mice to study titin‑based mechanosensing and longitudinal muscle hypertrophy. By integrating bulk RNA‑seq, proteomics, and phosphoproteomics, they map the stretch‑responsive signalling landscape, uncovering robust induction of the muscle‑ankyrin‑repeat proteins (MARP1‑3) together with enhanced phosphorylation of titin's N2A element. Genetic ablation of MARPs in mice amplifies longitudinal fibre growth and is accompanied by activation of the mTOR pathway, whereas systemic rapamycin treatment suppresses the hypertrophic response, highlighting mTORC1 as a key downstream effector of titin/MARP signalling.

      Strengths:

      The authors address a clear biological question: "how titin‑associated factors translate mechanical stretch into longitudinal fibre growth" using a unique and clinically relevant animal model of diaphragm denervation. Using a comprehensive multiomics approach, the authors identify MARPs as potential mediators of these effects and use a genetic mouse model to provide compelling evidence supporting causality. Additionally, connecting these findings to rapamycin, a drug widely used clinically, further increases the relevance and potential impact of the study.

      We thank the reviewer for their kind words and critical review of our manuscript. The roles of the MARP proteins are diverse and form an intriguing target for further study.

      Weaknesses:

      There are several areas where the manuscript could be substantially improved.

      (1) The statistical analysis of multi-omics data needs clarification. Typically, analyses across multiple experimental groups require controlling the false discovery rate (FDR) simultaneously to avoid reporting false-positive findings. It would be very helpful if the authors could specify whether adjusted p-values were calculated using a multi-factorial statistical model (e.g., ~group) or through separate pairwise contrasts.

      We agree with the reviewer that the description of the statistical analysis could be improved. We report the q-values in the supplemental data tables to correct for false positive data, the p-values reflect pairwise comparisons. Statistical testing was performed on whole proteomes or phospho-proteomes, making for very stringent testing (please also see reply to reviewer 2, response 5). Unbiased quantitative proteomics functions primarily as a screen, in-solution digestion of muscle proteins yields comparatively few peptides making population adjusted p-value calculation very stringent, suggesting no/few differences in expression. Hence, we compared RNAseq to proteome data to isolate consistently differential proteins. We have revised the method section (lines 745-746) to include clarifications of the FDR analysis.

      (2) (A)There are three separate points regarding MARP3 that could be improved. First, the authors report that MARP3-KO mice exhibit smaller increases in muscle mass after diaphragm denervation compared to wild-type mice (a -13% difference), indicating MARP3 likely promotes rather than attenuates hypertrophy. However, the manuscript currently states the opposite (lines 215-216); this interpretation should be revisited. (B) Second, it would be valuable if the authors could provide data showing whether MARP3 transcript or protein levels change response to denervation - if they do not, discussing mechanisms behind the observed phenotype would help clarify the findings. (C) Finally, given that some MARP-KO mice already exhibit baseline differences, employing and reporting the full two-way ANOVA (including genotype × treatment interaction) would allow a direct statistical assessment of whether MARP deficiency modifies the muscle's response to stretch. This analysis would help clearly resolve any existing ambiguity.

      (A) Compared to wildtype mice, MARP3 KO mice exhibit baseline diaphragm hypertrophy. This suggests that MARP3 may normally restrain hypertrophy under basal conditions. However, in response to UDD, MARP3 KO mice display an attenuated hypertrophic response, which could be interpreted as MARP3 promoting hypertrophy under stress conditions, as noted by the reviewer. The relationship between MARP3 and metabolism remains incompletely understood, but prior studies indicate that loss of MARP3 enhances glucose tolerance and insulin sensitivity (PMID: 12456686), suggesting that MARP3 may act as a negative regulator of metabolic signaling. Both glucose and insulin can activate the PI3K pathway to promote hypertrophy (PMID: 16679293), which may contribute to the baseline hypertrophy observed in MARP3 KO diaphragms. In addition, MARP3 deficiency has been associated with activation of AMPK signaling (PMID: 26398569). AMPK is a key regulator of metabolic pathways and a well-established inhibitor of hypertrophic signaling, in part through suppression of mTOR activity, and is also responsive to mechanical stimuli (PMID: 18556591). Thus, increased AMPK activity in MARP3 KO mice may limit hypertrophy in response to UDD. Supporting this, our phospho-proteomics data indicate increased activation of the AMPK β-subunit following UDD, suggesting a potential role for AMPK signaling in stretch-induced hypertrophy. Based on these considerations, we have removed the statement that MARP3 attenuates hypertrophy and instead incorporated the potential role of AMPK signaling into the Discussion (lines 354–355). While the present study focuses on the triple MARP KO model, future work will examine the specific contributions of individual MARP proteins to muscle hypertrophy.

      (B) MARP3 (Ankrd23) upregulation at the RNA level was detected by RNA-seq in rat diaphragm following both UDD and BDD (Supplemental Tables 1 and 2). This is consistent with our prior findings in mice, where western blot analysis showed increased MARP3 protein expression following UDD (PMID: 29978560). We note that reliable detection of MARP3 protein remains technically challenging due to limited availability of specific antibodies.

      (C) We agree with the reviewer and have added the results of the two-way ANOVA to the figures (see updated Figure 4). The three MARP proteins exhibit differential effects on diaphragm hypertrophy, supporting their role as modulators of stretch-induced hypertrophy.

      (3) The current presentation of multi-omics data is somewhat difficult to follow, making it challenging to determine whether observed changes occur at the transcript or protein level due to inconsistent gene/protein naming and capitalization (e.g., proper forms are mTOR, p70 S6K, 4E-BP1). Clearly organizing and presenting transcript and protein-level changes side-by-side, especially for key molecules discussed in later experiments, would make the data more accessible and provide clearer insights into the biology of titin-mediated mechanosensing.

      We agree with the reviewer that naming conventions between gene and protein can be hard to follow. We kept the names for titin-associated proteins as some have multiple protein names and the most common names is shown here. However, we made the suggested changes for the mTOR related proteins (for example, see figure 5).

      (4) The current analysis relies on total protein measurements downstream of mTOR, yet mTOR's primary mode of action is to change phosphorylation status. Because the authors have already generated a phosphoproteomic dataset, it would be very helpful to report - or at least comment on - whether known mTOR target phosphosites were detected and how they respond to denervation and rapamycin. Including even a brief summary of canonical sites such as S6K1 Thr389 or 4E - BP1 Thr37/46 would make the link between mTOR activity and hypertrophy much clearer.

      We agree with the reviewer that the mTOR data requires more work to ascertain its function in regulating hypertrophy following UDD. We investigated S6K1 Thr389 or 4E BP1 Thr37/46 in both the phosphoproteomic dataset and by western blot. These sites do not appear in phosphoproteome mass spectrometry (supplemental data table 13) and 4E BP1 Thr37/46 was unchanged by western blot (not shown). The S6K1 Thr389 antibody was aspecific in our hands, but Norrby et al (PMID: 22657251) saw increased levels by 6-days UDD. Hence the mTOR aspect of this study is quite complex, suggesting mTOR plays a major role in UDD hypertrophy, but potentially through an alternative activation pathway from what is classically described for muscle hypertrophy. We are investigating the mTOR mechanism further focusing on mTOR’s role in regulating longitudinal hypertrophy with potential connection to titin signaling and hope to publish this in the next few years. We revised the discussion to include canonical mTOR activation in hypertrophy, please see lines 388-392.

      (5) Finally, since rapamycin blocks only a subset of mTOR signalling, a brief discussion that distinguishes rapamycin‑sensitive from rapamycin‑insensitive pathways would be valuable. Clarifying whether diaphragm stretch relies exclusively on the sensitive branch or also engages the resistant branch would place the results in a broader mTOR context and deepen the mechanistic narrative.

      We agree with the reviewer that distinguishing between rapamycin-sensitive and -insensitive mTOR signaling adds useful context to the interpretation of stretch-induced hypertrophy. Rapamycin primarily inhibits mTORC1, whereas mTORC2 is generally considered rapamycin-insensitive, although prolonged or high-dose exposure can also affect mTORC2 activity. Our data indicate that UDD induces a form of hypertrophy that is sensitive to rapamycin, supporting a prominent role for mTORC1 in this process. However, we cannot exclude the possibility that rapamycin-insensitive pathways, including mTORC2 signaling, also contribute. Notably, denervation itself may influence mTORC2 activity, which could complicate the distinction between stretch- and denervation-mediated signaling. Given these considerations, we have added a brief discussion to acknowledge potential contributions of rapamycin-insensitive mTOR signaling (lines 379-384). A more comprehensive dissection of mTORC1 versus mTORC2 signaling in this context will require targeted approaches and falls beyond the scope of the present study.

      Reviewer #1 (Recommendations for the authors):

      Minor comments:

      (6) The manuscript notes that KEGG analysis "confirmed" the GO‑term findings. Because KEGG pathways and GO terms describe different types of biological information, it might be clearer simply to present them as complementary lines of evidence rather than one validating the other.

      We agree and modified the text accordingly. “Concurrently, KEGG PATHWAY database searches (Supplemental data Table 6) indicated that the DEG’s are involved in muscle remodeling.” See lines 166-169.

      (7) Figure 2's legend mentions a two‑way ANOVA, but the specific factors tested are not specified. Listing those two factors would help readers interpret the statistics more easily.

      The two-way ANOVA refers to the violin plot in figure 2E and tests the difference of the 2 surgical modalities sham vs UDD and sham vs BDD. Sham groups were combined in the graphs for easy comparison. We clarified the text of figure legend 2.

      (8) The Methods briefly describe phosphopeptide enrichment, but additional details on the criteria for site identification - such as the localisation algorithm, probability cut‑off, and FDR thresholds - would make the phosphoproteomics section more transparent and reproducible.

      Please see the updated method section, lines 756-765

      Reviewer #2 (Public review):

      Summary:

      Muscle hypertrophy is a major regulator of human health and performance. Here, van der Pilj and colleagues assess the role of the giant elastic protein, titin, in regulating the longitudinal hypertrophy of diaphragm muscles following denervation. Interestingly, the authors find an early hypertrophic response, with 30% new serial sarcomeres added within 6 days, followed by subsequent muscle atrophy. Using RBM20 mutant mice, which express a more compliant titin, the authors discovered that this longitudinal hypertrophy is mediated via titin mechanosensing. Through an omics approach, it is suggested that the Muscle ankyrin proteins may regulate this approach. Genetic ablation of MARPs 1-3 blocks the hypertrophic response, although single knockouts are more variable, suggesting extensive complementation between these titin binding proteins. Finally, it is found through the administration of rapamycin that the mTOR signalling pathway plays a role in longitudinal hypertrophic growth.

      Strengths:

      This paper is well written and uses an impressive suite of genetic mouse models to address this interesting question of what drives longitudinal muscle growth.

      We appreciate the reviewer’s kind words on our manuscript and their critical review of our work. A potential separate mechanism governing cross-sectional versus longitudinal hypertrophy is of great interest and something we aim to address in future manuscripts.

      Weaknesses:

      While the findings are of interest, they lack sufficient mechanistic detail in the current state to separate cross-sectional versus longitudinal hypertrophy. The authors have excellent tools such as the RBM20 model to functionally dissect mTOR signalling to these processes. It is also unclear if this process is unique to the diaphragm or is conserved across other muscle groups during eccentric contractions.

      Reviewer #2 (Recommendations for the authors):

      (1) Cross-sectional hypertrophy characterization: The paper emphasizes longitudinal hypertrophy but does not quantify the contribution of radial (cross-sectional) hypertrophy to the total mass increase. Given that the denervated costal diaphragm shows ~50% increase in mass (Figure 1B) but there is only ~30% fiber lengthening, it is important to determine the proportion attributable to fiber diameter changes. Histological analysis of muscle fiber cross-sectional area would clarify the relative contributions of longitudinal versus radial hypertrophy to the overall mass phenotype.

      We agree with the reviewer that radial hypertrophy is an important mechanism for muscle weight gain in UDD. In previous work we characterized both the radial and longitudinal hypertrophy response in 6-day UDD and found that ~20% of the mass gain seen in UDD is radial hypertrophy (PMID: 29978560). We reference this paper in the discussion section, line 277-278. Doing a full histological work-up of UDD diaphragm would be interesting but falls outside the scope of this manuscript. Our focus was to characterize longitudinal hypertrophy by addition of sarcomeres in series and provide insight into titin’s role in regulating longitudinal hypertrophy. We hope that the reviewer agrees with this approach.

      (2) Titin isoform expression analysis: At line 103, the authors propose that longitudinal hypertrophy reduces strain on titin by decreasing fractional sarcomere extension. However, this hypothesis does not exclude the possibility of isoform switching to a less elastic titin variant, which may compensate for changes in mechanical stress. The RNA-sequencing data should be analyzed for titin exon usage patterns between sham and UDD to determine whether changes in isoform composition (e.g., PEVK region splicing) accompany longitudinal hypertrophy. If isoform switching occurs, this represents an alternative or complementary mechanism to sarcomere addition.

      We analyzed titin exon usage in rat following both UDD and BDD. Increases in sarcomeres in series associated with UDD show modest changes in titin exon usage, though not significant by population adjusted p-values. The denervation effect of BDD did show changes in splicing, indicating lower inclusion of PEVK encoding exons, suggesting a stiffening of the titin molecules. Stiffening of titin molecules might be protective for the fully paralyzed diaphragm and preserve muscle mass. This would align with our prior publication (PMID: 29978560) which showed that stiffer titin generated more radial hypertrophy in response to UDD. In response to the reviewer’s comment, we added the splicing data to the supplemental data as new figure 2 and briefly address titin splicing in the results section, see lines 121-125.

      (3) The comparison of 3-day unilateral diaphragm denervation (UDD) and bilateral diaphragm denervation (BDD) in rats (Figure 1D-E) is used to argue that hypertrophic signaling is stretch-dependent rather than denervation-dependent. However, this interpretation requires clarification. In mice, hypertrophy is detectable as early as 1 day post-UDD, whereas the 3-day BDD protocol may drive an accelerated hypertrophic-to-atrophic remodelling process given the severity of the model. Moreover, longitudinal and global muscle hypertrophy may operate through distinct mechanisms: denervation could suppress longitudinal hypertrophy through a separate pathway while promoting or delaying cross-sectional hypertrophy. The authors should acknowledge that the current evidence does not fully exclude denervation-dependent mechanisms and should consider extended BDD time points or additional mechanistic studies to clarify this distinction.

      UDD and BDD are both denervation models and hypertrophy occurs in the denervated costal of UDD operated animals. Stretch is thus the mechanical difference between UDD and BDD and thus the trigger for hypertrophy signaling. At the denervation signaling level both models should in principle be comparable and are unlikely to play different roles between UDD and BDD, except that UDD also induces a more potent hypertrophy signaling profile on top of the atrophy program. That said, BDD is a more severe model and respiration rate is depressed compared to UDD where respiration rate is elevated. BDD rats also engage in abdominal breathing, which mildly stretches the diaphragm. Hypoxia is likely to play a stronger role in BDD than UDD and could thus further enhance the atrophy profile of BDD. We agree with the reviewer that more work is needed to elucidate the BDD remodeling response, however UDD induced stretch is the main driver of longitudinal hypertrophy. In response to the reviewer’s comment, we have added clarifying text to the discussion, lines 286-292.

      The potential for there being two independent mechanisms for both radial and longitudinal hypertrophy is of great interest to us. We foresee that dissecting out these differences will require a cell culture-based approach and will aid in avoiding the complexity of overlapping denervation and hypertrophy signals as seen in this manuscript.

      (4) Characterization of RBM20 models: The RBM20 experiments rely on the assumption that increased titin compliance reduces stretch sensitivity. However, the paper provides minimal baseline characterization of the diaphragms. Specifically: (a) What are the sarcomere lengths in RBM20-deficient diaphragms at rest and under stretch? (b) How does the passive force-length relationship differ between wildtype and RBM20-deficient diaphragm muscles? and (c) Would RBM20-deficient muscles, despite having longer sarcomeres at baseline, actually experience sufficient strain to activate mechanosensing? These data are necessary to interpret why RBM20-deficient mice show attenuated mass gain rather than none (as in BDD) during UDD (Supplemental Figure 2A-C). Additionally, what would the authors hypothesize would happen if rapamycin were used in RMB20 UDD models? It appears to be an attractive experimental approach to separate potential mTOR contributions to longitudinal versus cross-sectional hypertrophy.

      We agree with the reviewer that more work is needed on Rbm20 deficient mice and rats to elucidate their response to stretch. Part of this characterization has previously been published (PMID: 29978560) and Rbm20 splice-deficient mice have reduced passive stiffness in the diaphragm and show a robust mechanosensing response to UDD. Rbm20 splice-deficient mice also show a similar increase in longitudinal hypertrophy, but a blunted radial hypertrophy in response to 6-days UDD. The main reason for not expanding on these mice/rats further was the added complexity of Rbm20 splicing multiple targets that could affect hypertrophy signaling, for example LDB3 (ZASP) and FLNC (Filamin C) are both associated with hypertrophic cardiomyopathy. Hence for the purpose of this manuscript we showed mice and rats having a similar response to UDD, hypertrophy wise, and that titin stiffness (reduced in Rbm20-deficient animals) affects hypertrophy at the diaphragm mass level.

      Testing rapamycin on Rbm20-deficient animals could be interesting, however the complexities of also changing splicing of non-titin targets will make interpretation of mTOR signaling difficult. Perhaps an alternative approach would be to generate a titin mouse model with more compliant titin (e.g. increase the size of the PEVK segment), a model we are considering for future studies. TtnΔ112-158 mice, deleting a large portion of the PEVK region (PMID: 30565562) show increases in sarcomere number. We would expect a model with more PEVK to thus show a reduction in the number of sarcomeres in series. We discuss the role of titin stiffness in the discussion and how titin stiffness ties to longitudinal hypertrophy, please see lines 302-314.

      (5) Statistical analysis and multiple hypothesis correction: The proteomic analyses appear to employ a nominal p-value threshold (p < 0.05) without correction for multiple comparisons or false discovery rate (FDR) control. This is particularly concerning given the large number of comparisons. For example, the authors report 142 titin phosphorylation sites significantly different between sham and UDD at p < 0.05 (approximately 20% of ~700 identified sites). However, with proper FDR correction (adjusted p < 0.05), only 14 sites remain significant - a 90% reduction. This discrepancy is critical for the discussion on titin N2A phosphorylation sites pS9459 and pS9520, where only pS9520 achieves statistical significance after FDR adjustment. The authors should justify their choice of statistical thresholds and reanalyze key findings using FDR-corrected p-values. Additionally, the phosphoproteomics dataset should be screened for duplicate phosphosite identifications to ensure each site is counted only once.

      Reviewer 1 has voiced similar concerns, and we have thus expanded the methodology to explain the statistical tests used to analyze the data and the process of establishing Z-scores of isobaric peptides for the same phospho-sites (see lines 756-765). Our statistical analysis covers all detected peptides, when we only analyze the titin peptides: pS9459 is only significant in t-test, likely due to large variation in isobaric peptides. pS9520 is significant in both independent t-test and FDR. We changed figure 3D to show the fold change instead of the previous Z-score for more intuitive interpretation.

      Minor comments:

      (6) Line 52: "thesarcomeres" should read "the sarcomeres".

      A space has been added, please see line 52.

      (7) Line 52: "half-sarcomer" should read "half-sarcomere"

      Spelling has been corrected, please see line 52.

      (8) Figure clarity: Figure 1 (B-C) presents mouse data, while Figure 1 (D-E) presents rat data. This distinction should be clearly labeled in the figure legend or on the axes to prevent misinterpretation, particularly for readers unfamiliar with the experimental design.

      We added the species to the y-axis of revised figure 1B-E and added additional clarification in the figure legend.

      (9) Supplementary tables: When reporting statistical comparisons in the supplementary tables, please consider including the directionality of the statistical tests (e.g., which group was higher or lower) alongside p-values. This will facilitate interpretation without requiring reference to the main text figures.

      We agree with the reviewer and added statistical direction as a new column next to the p-values, please see the revised supplemental tables.

      (10) Given the interesting divergent findings in MARPtKO versus single knockouts, it would be interesting to assess by immunofluorescence the association of each MARP with the N2A region of titin following UDD.

      We agree with the reviewer that localization is important. Miller et al (PMID: 14583192) previously localized MARP1-3 to the N2A segment by immuno-EM and our work previously localized MARP1 to N2A using SR-SIM (PMID: 29978560). We will further investigate MARPs binding to the N2A region in an upcoming study that we intend to publish soon.

    1. Author response:

      Reviewer #1 (Public review):

      Weaknesses:

      This is a challenging hypothesis that would require some additional experimental controls. The pathway dissection, while extensive, is sometimes approached in unconvincing ways, and the results are not always evident to judge or interpret. Technically, the western blots and transcriptomic analyses require notable improvements.

      We would like to thank the reviewer for the careful and patient examination of the issues identified in our manuscript. The poor quality of some of the Western blot bands in Figure 4 may have been caused by inappropriate electrophoresis conditions during the Western blot experiments. In the revised manuscript, we will optimize the electrophoresis conditions to obtain higher-quality protein bands and update the quantitative data. Regarding the quantification format, we believe that heatmaps provide a more intuitive representation of trends in protein expression across different treatment groups. This approach more accurately reflects the results of our biological replicates than simply analyzing the significance of differences in the grayscale values of protein bands. For the analysis of transcriptomic data, we will conduct a more detailed analysis of signal pathway enrichment and the identified differentially expressed genes to ensure that predicted genes are excluded from our current results and redundant data presentation is removed.

      Regarding additional experimental controls, such as incorporating experimental data under blue light treatment conditions as a control for red light. While exploring the optimal red light irradiation dose at the cellular level, we simultaneously conducted experiments on the effects of blue light irradiation at the same dose on keratinocyte activity. The results indicated that as the blue light irradiation dose increased (0–160 J/cm<sup>2</sup>), the keratinocyte activity exhibited a dose-dependent decline. This indicates that blue light is phototoxic to keratinocytes. The relevant experimental results have already been published in our previous study (Communications Biology 2024, doi: 10.1038/s42003-024-06973-1). Taken together with the data from our study, this demonstrates that the anti-aging effects of red light reported in the current manuscript are indeed driven by red light.

      Reviewer #2 (Public review):

      Weaknesses:

      The paper does not evolve to use the mechanistic discoveries of the manuscript to help our community to identify the mechanism of photobiomodulation, which is not known so far.

      I would like to draw attention to a recently published paper by Herrera et al. (FEBS Letters 2025, doi:10.1002/1873-3468.70195), which shows that red light (660 nm) stimulates mitochondrial fatty acid oxidation in keratinocytes via AMPK‑dependent phosphorylation of ACC, without altering expression of electron transport chain complexes. I believe this paper is highly complementary to the current study.

      Herrera et al. demonstrate that red light increases basal, ATP-linked, and maximal oxygen consumption rates in keratinocytes specifically through enhanced fatty acid oxidation (inhibited by etomoxir). This independently validates the central finding of the current manuscript, i.e., red light boosts lipid metabolism, strengthening the robustness of this concept.

      While the current manuscript focuses on the SIRT4-MCD axis, Herrera et al. identify AMPK phosphorylation and ACC inhibition as key effectors. The authors can integrate and expand their discussion, since SIRT4 downregulation may converge on AMPK activation, or they may represent parallel, reinforcing mechanisms. This would enrich the mechanistic model and open new hypotheses.

      The mechanism of photobiomodulation: Herrera et al. explicitly challenge the prevailing paradigm that red light acts solely via cytochrome c oxidase (by showing long-lasting effects, unchanged OXPHOS protein levels, and no difference in permeabilised cells). The current finding (red light acts through SIRT4 downregulation, i.e., not direct enzymatic activation) aligns perfectly with Herrera´s critique.

      Long-term metabolic effects-Herrera et al. show that a single red light exposure elevates oxygen consumption for up to 2 days. The current study focuses on changes at 12-24 h. Their data extend the time window and suggest that the metabolic reprogramming you describe may persist longer than currently discussed, which is clinically relevant.

      Discussing Herrera et al.'s results would not only acknowledge independent, corroborating evidence but would also allow the authors to position their SIRT4-centric mechanism within a broader, emerging understanding of red-light photobiomodulation.

      We would like to thank the reviewer for providing us with constructive suggestions for discussion. Our results showed that under red light conditions, both glycolipid and lipid metabolism were activated in keratinocytes, and cellular metabolic flux increased. The activation of lipid metabolism directly led to an increase in metabolism-associated H3K9ac and drove the upregulation of anti-aging-related genes; we believe this is key to the anti-aging effects of red light. Mechanistic analysis combining proteomics and acetylation proteomics revealed that red light significantly downregulated SIRT4 expression and increased the acetylation of MCD, a protein regulated by SIRT4 that governs cellular fatty acid oxidation rates. Through validation using cell-level knockdown and inhibitors, we confirmed that SIRT4 inhibition exerts anti-aging effects in vitro and that inhibiting MCD function under red light conditions suppresses H3K9ac. These results establish the role of the SIRT4-MCD signalling axis in mediating the anti-aging effects of red light.

      The study by Herrera et al. included a substantial body of validation data confirming the role of red light in promoting fatty acid oxidation, providing robust empirical support for our research. Furthermore, Herrera et al. revealed that red light-induced fatty acid oxidation depends on AMPK and ACC phosphorylation. This mechanism of red-light photobiomodulation may refute the notion that its bio-regulatory effects rely solely on the action of mitochondrial cytochrome c oxidase. Furthermore, together with our study revealing that red light exerts anti-aging photobiomodulatory effects via the SIRT4-MCD signalling axis, these findings independently confirm that red light regulates cellular fatty acid oxidation, thereby demonstrating the pivotal role of activated fatty acid oxidation in the bio-regulatory effects of red light. In the revised manuscript, we will include a discussion on the potential link between the red light-driven downregulation of SIRT4 and the phosphorylation of AMPK/ACC. This will be of positive value in elucidating how SIRT4 exerts its anti-aging effects by regulating lipid metabolism, as well as in explaining the possible mechanisms by which red light downregulates SIRT4.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript has several strengths, including a technically comprehensive approach that combines mouse genetics, electrophysiology, live imaging in assembloids, and human organoid models, providing a rich and multifaceted dataset. Cross-species validation through the parallel use of mouse and human systems strengthens the generality of the observed phenotypes and increases relevance to human neurodevelopment.

      Consistent phenotypic observations across systems show that ARHGEF6 loss affects migration, neurite morphology, growth cone structure, and neuronal survival, supporting a coherent role in cytoskeletal regulation.

      There is clear evidence for developmental defects, including reduced interneuron numbers, increased apoptosis in the ganglionic eminences, and migration deficits, all well supported by quantitative analyses. Also, there is a high-quality electrophysiological characterization that demonstrates reduced firing in interneurons, providing a well-controlled functional phenotype.

      Strengths:

      The manuscript has several strengths, including a technically comprehensive approach that combines mouse genetics, electrophysiology, live imaging in assembloids, and human organoid models, providing a rich and multifaceted dataset. Cross-species validation through the parallel use of mouse and human systems strengthens the generality of the observed phenotypes and increases relevance to human neurodevelopment.

      Consistent phenotypic observations across systems show that ARHGEF6 loss affects migration, neurite morphology, growth cone structure, and neuronal survival, supporting a coherent role in cytoskeletal regulation.

      There is clear evidence for developmental defects, including reduced interneuron numbers, increased apoptosis in the ganglionic eminences, and migration deficits, all well supported by quantitative analyses. Also, there is a high-quality electrophysiological characterization that demonstrates reduced firing in interneurons, providing a well-controlled functional phenotype.

      We thank the reviewer for their positive and thoughtful assessment of our manuscript. We appreciate their recognition of the technical breadth of the study, including the integration of mouse genetics, electrophysiology, live imaging in assembloids, and human organoid models. We are also grateful that the reviewer highlights the value of our cross-species approach, as a major goal of the study was to determine whether ARHGEF6 loss produces convergent developmental and cellular phenotypes in both mouse and human systems.

      Weaknesses:

      Despite the strengths mentioned above, the study has some conceptual and experimental weaknesses that reduce its impact. The mechanistic insight is limited, as the research does not directly establish how ARHGEF6 regulates downstream signaling pathways.

      We appreciate the reviewer’s constructive comment. We agree that, although our data establish a phenotypic link between ARHGEF6 loss and interneuron development, they do not directly dissect the molecular mechanisms underlying the observed defects. Our interpretation that the mutant phenotype involves dysregulation of cytoskeletal dynamics is based on the directly observed defects in actin polymerization and organization in neural progenitor cells and neuronal growth cones respectively, and is consistent with the abnormalities observed in neurite morphology and neuronal migration. This interpretation is further supported by the established role of Arhgef6 as a regulator of the small Rho GTPases Rac1 and Cdc42. Previous evidence shows that Arhgef6 loss reduces the activity of both GTPases and deregulates the expression of the cytoskeletal regulators Pak1–3, Limk1, and Cofilin in the mouse brain (Ramakers et al., 2012). Moreover, spine abnormalities in Arhgef6-knockdown ex vivo slice cultures can be rescued by expressing the active form of Pak3, a downstream effector of Rac1 and Cdc42 (Node-Langlois et al., 2006). Together, these findings support a model in which the loss of the protein affects development through cytoskeletal dysregulation, likely involving altered Rho GTPase signalling. We nevertheless agree that further experiments would be required to establish a direct causal relationship between ARHGEF6 loss, Rho GTPase activity, cytoskeletal dysregulation, and the interneuron phenotypes described here. We will therefore revise the manuscript to clarify that this mechanistic link remains an interpretation supported by our data and the literature, rather than a direct demonstration within the present study.

      Also, there is insufficient evidence for interneuron specificity; although the central claim is that ARHGEF6 plays a selective role in interneurons, the data do not adequately exclude the possibility that the observed effects reflect broader neuronal defects. The study lacks critical controls across cell types, as several phenotypes observed in organoids and progenitors, including apoptosis, reduced neuronal output, and altered morphology, could also affect multiple neuronal populations without being directly tested.

      We agree that the current data do not exclude the possibility of alterations in other neuronal lineages, specifically the excitatory lineage. With regard to this, we would like to emphasize that the investigation of excitatory cell phenotypes was beyond the scope of the present study, as this aspect has previously been examined by Ramakers et al., 2012 and Node-Langlois et al., 2006, particularly in the context of hippocampal pyramidal cells, which are among the few cell types showing consistent expression of the gene in the adult mouse brain (Allen Brain Atlas; Yao et al., 2021). In this context, it is interesting to note that, in Ramakers et al., 2012 (Figure S1), MAP2 immunostaining of hippocampal formations revealed comparable distribution and intensity of neuronal cell bodies and dendrites throughout the hippocampus of both wild-type and Arhgef6-KO animals. With regard to morphological maturation of excitatory cells, whereas we observe a simplification of interneuron morphology in both mouse and human models, Ramakers et al., 2012 reported increased dendritic arborization complexity in hippocampal pyramidal cells. With regard to migration, a direct comparison with excitatory neurons would be intrinsically difficult, as excitatory and inhibitory neurons undergo highly distinct migratory processes and are therefore not directly comparable. We greatly appreciate the reviewer’s comment, as it gives us the opportunity to better discuss the relationship between our findings and previous studies in the Discussion. We will revise the manuscript and avoid implying that the phenotype observed is exclusive to interneurons.

      Furthermore, the data are predominantly descriptive, with many results remaining correlative and failing to establish causal relationships.

      We agree that our study primarily establishes a phenotypic framework and does not fully resolve the causal hierarchy among altered survival, migration, cytoskeletal morphology, and intrinsic excitability. We will revise the manuscript to make this limitation explicit, avoiding statements that imply direct causality beyond the data presented.

      Some more comments:

      (1) Given that ARHGEF6 is a guanine nucleotide exchange factor for Rac1 and Cdc42, the absence of direct measurements of GTPase activity or downstream signaling represents a significant gap. The interpretation that the observed phenotypes are mediated through specific cytoskeletal pathways, therefore, remains inferential.

      We appreciate the comment. The interpretation that our phenotype involves dysregulated cytoskeletal dynamics is based on the observed defects in actin polymerization and F-actin organization in neuronal growth cones and is consistent with the abnormalities in neurite morphology and neuronal migration. We will explicitly state in the Discussion that, since we did not directly measure Rac1 and Cdc42 activity levels in our models, our hypothesis regarding the involvement of this molecular pathway in the establishment of the observed phenotype therefore remains inferential, despite being supported by the current literature.

      (2) The manuscript repeatedly interprets the findings as interneuron-specific. However, several key observations are not demonstrated to be restricted to IN. Without direct comparison to excitatory neurons or other cell types, it is difficult to conclude that ARHGEF6 plays a selective role in interneurons rather than a more general role in neuronal development. The well-done analysis of the transcriptomic dataset is not sufficient to claim IN specificity. This issue is particularly important for the interpretation of the human organoid experiments, where reductions in SOX2⁺ progenitors and NEUN⁺ neurons, as well as increased apoptosis, could reflect global developmental defects. Similarly, in the mouse experiments, the reduction in GAD67⁺ cells is compelling, but it is not shown whether other neuronal populations are also affected.

      As previously mentioned, we understand the reviewer’s concern regarding the specificity of the observed phenotypes in interneurons and agree that the claims should be tempered. However, it is important to note that the interpretation of the human organoid experiments should be reconsidered. The use of specifically ventralized MGE-like organoids allowed us to assess the cell-autonomous nature of defects such as the reduction in inhibitory progenitors’ neuronal output, the increased apoptosis, and the morphological abnormalities of inhibitory neurons. We will acknowledge in the Discussion the limitations of the study with regard to assessing the cell-autonomous nature of the observed migration defects.

      (3) The study provides a strong phenotypic description but limited causal resolution. For example, migration defects, altered growth cone morphology, and reduced branching are all consistent with impaired cytoskeletal regulation, but the links between these phenotypes are not directly established. Likewise, while the electrophysiological data convincingly show reduced firing in interneurons, the connection between altered cytoskeletal dynamics and intrinsic excitability is not explored.

      The observed migration defects, altered growth-cone morphology, and reduced branching are consistent with impaired cytoskeletal regulation. However, we acknowledge that the mechanistic links among these phenotypes remain to be directly demonstrated. Similarly, although our electrophysiological data show reduced firing in ARHGEF6-KO interneurons, the present study does not provide direct evidence linking impaired excitability to altered cytoskeletal dynamics. In the latter case, we think that the underlying mechanisms should be further investigated at the subcellular level, particularly with respect to cytoskeleton-mediated intracellular trafficking and localization and distribution of ion channels. One limitation of the present study, which may have masked electrophysiological alterations associated with differences in membrane composition (current Figure S1D–H), is that different interneuron subtypes with distinct intrinsic properties were pooled together in the analysis. We will expand the Discussion to address these limitations.

      (4) Several aspects of data presentation could be improved. In multiple figures (e.g., Figure 1A, D; Figure 4 and Video S1, 2), the images are difficult to interpret due to high cellular density, limited magnification, or lack of clear annotation. In some cases, it is not fully clear how quantifications were performed or which regions were analyzed. Improving the visual clarity with arrows, boxes, and high-magnification inserts of the data would strengthen confidence in the conclusions.

      We would like to thank the reviewer for pointing this out. We agree that some images and videos would benefit from clearer annotation. In the revised manuscript, we will add high-magnification insets, arrows or boxes highlighting the relevant regions/cells, and clearer descriptions of the quantified regions. We will also improve legends and video labels to indicate genotype, region, and tracked cells.

      Reviewer #2 (Public review):

      The authors investigate the impact of the deletion of the small GTPase regulator ARHGEF6 on the development and physiology of interneurons. Using public databases, they first show that ARHGEF6 is enriched in interneurons or in areas that give rise to them, both in development and adulthood, in humans and mice. Using a complete KO mouse previously reported, and using a GAD67-GFP reporter mice line, they show that in the adult mouse cortex and hippocampus, there is a notorious reduction GFP+ cells. These mice show increased apoptotic cells at different timepoints and areas of the brain during development. In the developing cortex of ARHGEF6-KO mice, there are fewer IN in all layers of the developing cortex, and cells present processes not correctly oriented. IN from the hippocampus in culture show reduced excitability and impaired neurite branching. The authors then established isogenic hiPSCs lines to study ARHGEF6 deletion in human cells and differentiated ventral forebrain neurons, to find interneuron-related and non-related phenotypes. Most importantly, human interneurons grown in organoids show reduced branching and altered growth cone morphology. The authors claim that the novel interneuron phenotypes found in these models can explain, in part, the human intellectual disabilities associated with mutations in this protein. The study is well conducted and opens new avenues of research not only for the role of small GTPases regulation in early nervous system development, but also for how interneuron deficiencies impact a wider range of intellectual disability syndromes found in humans.

      We appreciate the reviewer’s positive evaluation of our manuscript and their recognition of this work’s potential to expand the focus of intellectual disability research on the development and function of the inhibitory system. We are particularly encouraged that the reviewer highlights the strength of our combined mouse and human cellular models, as well as the relevance of the interneuron-related phenotypes we identify across systems.

      However, most conclusions of the present version would be strengthened after considering the following comments:

      Major comments:

      (1) The reported biological processes evaluated at different developmental stages may be directly or indirectly related to ARHGEF6 function itself. As a model of a hereditary disease, full organism gene deletion is valid, since the human patients suffer from that condition as well. However, to investigate the roles of a protein, complete deletions may not be very accurate since they can give rise to phenotypes that are only indirectly related to the protein function itself. Most conclusions of the present manuscript should either be discussed in this regard or add evidence for a direct role of the protein. One such evidence is typically performed with acute knockdowns in culture, or in developing brains by in utero electroporation. For example, Figure 1C shows that the principal excitatory neurons in the hippocampus do not express ARHGEF6. However, most electrophysiological and behavioral evidence of defects in ARHGEF6-KO mice arises from evaluating these cells (Ramakers et al., 2012). I am not suggesting that either previous or actual evidence is wrong. But I believe readers would benefit from a clear distinction (or add caution notes) between a functional consequence of the deletion (that can be months away and in other cells than the actual molecular defect) and a true cell biological function of the protein under study. In favor of the authors, this is a concern with most conclusions derived from KO organisms.

      We agree with the reviewer that phenotypes observed in constitutive knockout models may, in some contexts, reflect indirect or compensatory consequences of long-term gene loss. Conditional and/or inducible knockout or knockdown approaches can certainly help dissect the nature of the observed defects and better define the effects of gene ablation at different developmental stages or in specific cell types. However, in the context of our study, it is important to note that the experiments performed in ventralized MGE-like organoids allowed us to assess the cell-autonomous nature of very early developmental defects in the inhibitory lineage, in isolation from other cell types. These defects include reduced neuronal output from inhibitory progenitors, increased apoptosis, and morphological abnormalities in inhibitory neurons. Therefore, the phenotypes reported here are less likely to reflect effects originating in, or indirectly caused by, cell types that do not express Arhgef6.

      With regard to Figure 1C, we state in the Results that “among excitatory populations, only CA3 pyramidal neurons and mossy cells exhibited expression levels comparable to those observed in inhibitory clusters (Figure 1D, Table S2),” thereby not neglecting the potential effect of the lack of a functional protein in these populations.

      (2) Figure 1E-G H I. All conclusions are made with a GAD67-GFP reporter, which is a very powerful and reliable tool for large-scale screening. All the conclusions of the paper would be strengthened if some immunohistochemical staining in the same areas of specific markers for interneurons would be added as supporting complementary evidence.

      We appreciate the insightful comment of the reviewer. Additional validation using established interneuronal markers will further strengthen the GAD67-eGFP analysis. We will perform complementary stainings (e.g., PVALB and CCK) and quantifications and include these data as a Supplementary Figure.

      (3) Cell death in development: It is surprising that the high amount of TUNEL staining during development does not translate into gross histological changes in the adult brain (studied elsewhere). Can authors discuss possible explanations?

      We appreciate the thoughtful consideration of our findings. We think that possible explanations include partial compensatory mechanisms during development, which may mitigate the long-term anatomical consequences of increased cell death. In addition, the phenotype may be restricted to specific neuronal populations or developmental windows, thereby producing functional alterations without necessarily resulting in overt macroanatomical defects. Thus, although increased developmental cell death may contribute to altered circuit assembly and neuronal output, it may not be sufficient to produce gross histological changes detectable at the adult brain level.

      (4) Section 4 (Figures 2F-J) - The authors present this staining as an analysis of migration. Normally, migration studies are performed with a "pulse-chase" paradigm, where a single cohort is labeled and then followed over time (normally by in utero electroporation of a fluorescent protein). Tissue is then fixed at different time points, and migration can be followed. On the contrary, the evidence is from a single point, in an experimental setting in which all Gad67 IN are stained, and hence, one cannot imply a defect in migration. The differences between WT and ARHGEF6-KO are obvious and interesting; it is just that they cannot be solely attributed to a problem in migration.

      Also, a true phenotype of migration in the current setting should have found that the cells that failed to migrate are accumulated in deeper layers. My impression is that the changes in IN per layer are easier explained by total cell number, rather than migration. Perhaps evaluating earlier timepoints could clarify this.

      We appreciate the reviewer’s suggestion to implement an additional time point in the in vivo migration analysis. Since an earlier in vivo time point would most likely not reveal migration-related defects, as most cells would still be confined to the ganglionic eminence (Liaci et al., 2022), we will include analyses performed at a later developmental time point as supplementary evidence. We will also revise the wording to clarify that the fixed-tissue data show altered distribution and orientation of GAD67-eGFP-positive interneurons, which are consistent with impaired migratory behavior when considered together with the in vitro live-imaging data. At the same time, we will acknowledge that reduced interneuron survival and/or neuronal output may also contribute to the observed phenotype.

      (5) It is known that ARHGEF6 deletion produces severe F-actin phenotypes in neurons. Have the authors confirmed in their hippocampal cultures GAD67 cells ALSO have these phenotypes? Stress fibers in somas, growth cones, and actin patches along neurites.

      We did not directly assess F-actin organization in GAD67-eGFP murine primary cultures. Direct analyses of F-actin organization, growth-cone morphology, and cytoskeletal organization were performed only in the human system. To further assess this phenotype, we will perform phalloidin staining on GAD67-eGFP brain sections to evaluate F-actin organization in interneurons in vivo.

      (6) Section 4. The authors present data for deficient migration of the GFP-labeled interneurons. Is it possible to assess, in the same sections, whether other cell types are also affected? Although the hypothesis that ARHGEF6 deletion will have an impact in IN is well rooted in expression data, by assessing other cell types, one can even include a positive control or evidence for a cell-autonomous phenotype.

      We thank the reviewer for their thoughtful suggestions. We agree that extending the analysis to additional cell types would provide further insight into the specificity of the phenotype; however, a comprehensive evaluation of all neuronal populations falls beyond the scope of this research. The use of ventralized MGE-like organoids enabled us to examine whether key defects were cell-autonomous, including the reduced neuronal output of inhibitory progenitors, increased apoptosis, and abnormal inhibitory-neuron morphology.

      (7) ARHGEDF6 deletion has an important impact on organoid development (size, shape, etc). Have the authors analysed whether these organoids produced fewer interneurons?

      We would like to clarify that the organoids analyzed in the study are ventral MGE-like organoids and therefore the reduction in neuronal output (current Figure 4K) primarily reflects the ventral/interneuron lineage in this model.

      (8) In assembloids, the differences in migration parameters are very small between WT and ARHGEF6-KO, which reinforces that perhaps what is observed in the different layers of cortex during mouse development is likely not entirely due to migration, as concluded.

      We agree that the migration parameters in assembloids should not be interpreted in isolation. We will revise the text to emphasize that the reduction in the number of interneurons observed in the adult brains is part of a broader pattern that also includes altered neuronal output and reduced viability.

      (9) To properly weigh the present evidence -interneuron deficits- using the ARHGEF6-KO model, authors should include a deeper discussion in light of much work that has been done using these mice. How does the finding of a diminished IN population in the brain of these mice explain the large amount of electrophysiological and behavioral evidence produced before with these animals? Perhaps the most important work to discuss these aspects is the initial ARHGEF6-KO report by Ramakers and colleagues (2012), but there are others.

      We appreciate the reviewer’s emphasis on the importance of framing our findings within the broader context of the existing literature. We will expand the Discussion to better integrate previous work on ARHGEF6-KO mice. Specifically, we will discuss how reduced interneuron number and altered interneuronal function may contribute to previously reported electrophysiological and behavioral phenotypes, acting in concert with previously described alterations in excitatory neurons and synaptic plasticity (Ramakers et al., 2012).

      Minor comments:

      (1) Figure 1A. It looks clear that the GE shows the highest expression of ARHGEF6; however, the reader needs the reference levels where the log2 expression is calculated. What are the reference levels?

      We would like to thank the reviewer for pointing this out. We will clarify in the caption that the log2(RPKM+1) expression values are shown as absolute values and are not relative to a reference condition.

      (2) Have the authors compared the number of GAD67-eGFP cells in the hippocampal cultures between WT and ARHGEF6-KO mice?

      We did not rely on total GAD67-eGFP counts in dissociated hippocampal cultures because differences could reflect initial plating composition, survival, and maturation. In our experience, the MGE-like organoid system provides a more controlled in vitro context to assess neuronal output in the ventral lineage.

      (3) Section 3, as a caution note, authors should mention that it is not possible to know from the evidence provided which cells are dying.

      We agree with the reviewer and will add a cautionary statement noting that TUNEL staining alone does not identify the precise dying cell type. We will clarify that increased cell death in the ganglionic eminence and MGE-like organoids is consistent with a prominent involvement of the ventral/inhibitory lineage, while acknowledging the limits of the assay.

      (4) In the dorsal-ventral assembloids, it is expected that the ventral organoid would contain lots of GFP expression compared to the dorsal, but in the image shown (Figure 5A) both parts of the assembloid seem to have the same amount and distribution of GFP. How is that possible?

      We appreciate the thoughtful comment of the reviewer. After two weeks of fusion, a considerable number of interneurons are expected to have migrated from the ventral to the dorsal compartment of the assembloid (Birey et al., 2017; Sloan et al., 2018). In terms of distribution, we think that current Figure 5A shows a gradient of eGFP-positive cells within the dorsal compartment, with the number of labeled cells decreasing as the distance from the fusion interface between the two organoids increases. By contrast, a comparable gradient is not evident in the ventral compartment, where several labeled neurons remain present even in regions distal to the fusion site.

      Reviewer #3 (Public review):

      Summary:

      ARHGEF6 is a RAC1/CDC42 guanine nucleotide exchange factor that has been proposed to be associated with X-linked intellectual disability, but its relevance to the pathology is not well established. ARHGEF6 has been assigned a role in spine density and plasticity of hippocampal pyramidal neurons, but nothing is known about its role in interneuron development. Here, the authors show that ARHGEF6 is expressed early in development in the inhibitory lineage during the peak of interneuron generation and migration. The aim of the study is therefore to investigate whether, in addition to its role in pyramidal neurons, ARHGEF6 could play a role in inhibitory neuron development. Using both ARHGEF6-KO mice and organoids from ARHGEF6-KO hiPSCs, the authors show that ARHGEF6 plays a critical role in interneuron development and function

      Strengths:

      The major strength of the paper is the very detailed analysis of the role of ARHGEF6 using two different systems: ARHGEF6-KO mice and deletion of ARHGEF6 in human iPSC-derived organoids. Strikingly, deletion of ARHGEF6 in both systems induces similar defects such as an increase in apoptosis, reduced neuronal output, impaired neuronal morphology, and disrupted migratory dynamics. This compelling evidence demonstrates that ARHGEF6, in addition to its already well-described role in spine formation and plasticity, is playing a crucial role during embryonic development through its function in interneurons.

      We thank the reviewer for this positive assessment of our work and for highlighting the strength of our combined in vivo and human iPSC-derived organoid approaches. We are pleased that the reviewer recognizes the consistency of the phenotypes observed across both systems and acknowledges that our findings support a crucial role, during early stages of embryonic development, for a protein previously thought to be relevant primarily in the synaptic context.

      Weaknesses:

      (1) In Figure 1, the authors show that ARHGEF6 is expressed in different regions of the brain, including the interneuron lineage, and that depletion of ARHGEF6 reduces the number of GABAergic neurons in the adult cortex and hippocampus. To try to better characterize this defect, the authors in Figure 2 investigate whether deletion of ARHGEF6 affects interneuron migration and survival during embryonic development. To do so, ARHGEF6 ko mice were crossed with the GAD67-eGFP reporter line to follow the inhibitory lineage. The authors analyse apoptosis using TUNEL staining, and show that it is significantly increased in the ganglion eminence of ARHGEF6-KO E14.5 embryos. The authors claim that this is not the case in the cortex. However, the image shown in Figure 2A really suggests that staining is increased. Which part of the neocortex is analysed for quantification? This should be clarified.

      We would like to thank the reviewer for pointing this out. The region analyzed was the same as that used to assess GAD67-eGFP-positive cells in Figure 2F. We will clarify the exact neocortical region used for TUNEL quantification and revise the figure and legend to make the analyzed area explicit. We will also analyze additional animals to improve the accuracy of the analysis.

      (2) In Figure 2F-J, the authors investigate the migration of interneurons by analysing the GAD67-eGFP staining, and clearly show that the migratory abilities of the depleted neurons are reduced. However, the authors do not discuss the fact that, because depletion of ARHGEF6 increases apoptosis, there are fewer neurons available for migration. This is important for the interpretation of the data. This point should be clarified.

      We appreciate this comment and believe that it is particularly relevant to the interpretation of the data shown in Figure 2F–G. We will clarify the limited interpretation of this specific analysis in the Results section. The altered directionality observed in vivo, together with evidence of impaired migratory behavior obtained through in vitro live imaging, supports the possibility that altered migratory dynamics contribute to the phenotype, although increased apoptosis and reduced neuronal output may also contribute.

      (3) In Supplementary Figure S2, the authors describe the establishment of the ARHGEF6-KO human iPSC line and test the ability of these cells to undergo correct development, especially for the generation of neural progenitor cells. I was wondering why the authors do not present the data of both control and ARHGEF6-KO cells.

      We thank the reviewer for pointing this out. All staining reported in the organoids and assembloids in this paper shows that the WT ATCC-DYS0100 cell line, as well as the mutant, efficiently differentiates into neuronal tissue. The Supplementary Figure was intended to validate the impact of the mutation on the ability of the iPSC line to retain its differentiation capacity as a preliminary step before proceeding with organoid differentiation. We will integrate stainings for NPC markers on the WT line in the Supplementary Figure.

      (4) At the molecular level, how ARHGEF6 depletion could affect neuronal survival is missing. In addition, as ARHGEF6 is a GEF for RAC1 and Cdc42 amongst other GEFs, I would have expected that the authors test how RAC1 activity (and Cdc42) is affected in ARHGEF6-depleted brains and in ARHGEF6-KO organoids. The measure of phalloidin staining and the anisotropy index are not really meaningful.

      We appreciate the thoughtful comment of the reviewer. Previous evidence already shows that Arhgef6 loss reduces the activity of both GTPases and deregulates the expression of the cytoskeletal regulators Pak1–3, Limk1, and Cofilin in the mouse brain (Ramakers et al., 2012). Regarding organoids, we agree that direct RAC1/CDC42 activity measurements would have strengthened the molecular mechanism. We will revise the manuscript to avoid implying that our phalloidin-based measurements alone establish the underlying dysregulated molecular pathway.

      (5) The authors show that ARHGEF6-KO forebrain organoids were markedly smaller compared to their isogenic controls, and their study suggests that ARHGEF6 expression impacts progenitor maintenance and neurogenesis. Despite representing only a minority of the total neuronal population, I was wondering whether ARHGEF6-KO mice present brain morphology defects such as microcephaly.

      We appreciate the comment. We did not perform a morphometric analysis for microcephaly in the present study. We will add this limitation to the Discussion and note that gross brain morphology changes were not reported in the previously published ARHGEF6-KO mouse characterization (Ramakers et al., 2012). We will also clarify that the smaller organoid phenotype may reflect developmental defects that may reflect developmental defects that are not fully compensated in a reductionist in vitro model and therefore do not necessarily imply overt microcephaly in vivo.

      References

      Allen Institute for Brain Science. Allen Mouse Brain Atlas: Arhgef6 ISH data. Available from: Allen Brain Map.

      Birey, F., Andersen, J., Makinson, C. D., Islam, S., Wei, W., Huber, N., Fan, H. C., Metzler, K. R. C., Panagiotakos, G., Thom, N., O’Rourke, N. A., Steinmetz, L. M., Bernstein, J. A., Hallmayer, J., Huguenard, J. R., & Pașca, S. P. (2017). Assembly of functionally integrated human forebrain spheroids. Nature, 545(7652), 54–59. https://doi.org/10.1038/nature22330

      Liaci, C., Camera, M., Zamboni, V., Sarò, G., Ammoni, A., Parmigiani, E., Ponzoni, L., Hidisoglu, E., Chiantia, G., Marcantoni, A., Giustetto, M., Tomagra, G., Carabelli, V., Torelli, F., Sala, M., Yanagawa, Y., Obata, K., Hirsch, E., & Merlo, G. R. (2022). Loss of ARHGAP15 affects the directional control of migrating interneurons in the embryonic cortex and increases susceptibility to epilepsy. Frontiers in Cell and Developmental Biology, 10, 875468. https://doi.org/10.3389/fcell.2022.875468

      Nodé-Langlois, R., Muller, D., & Boda, B. (2006). Sequential implication of the mental retardation proteins ARHGEF6 and PAK3 in spine morphogenesis. Journal of Cell Science, 119(23), 4986–4993. https://doi.org/10.1242/jcs.03273

      Pelkey, K. A., Chittajallu, R., Craig, M. T., Tricoire, L., Wester, J. C., & McBain, C. J. (2017). Hippocampal GABAergic inhibitory interneurons. Physiological Reviews, 97(4), 1619–1747. https://doi.org/10.1152/physrev.00007.2017

      Ramakers, G. J. A., Wolfer, D., Rosenberger, G., Kuchenbecker, K., Kreienkamp, H.-J., Prange-Kiel, J., Rune, G., Richter, K., Langnaese, K., Masneuf, S., Bösl, M. R., Fischer, K.-D., Krugers, H. J., Lipp, H.-P., van Galen, E., & Kutsche, K. (2012). Dysregulation of Rho GTPases in the αPix/Arhgef6 mouse model of X-linked intellectual disability is paralleled by impaired structural and synaptic plasticity and cognitive deficits. Human Molecular Genetics, 21(2), 268–286. https://doi.org/10.1093/hmg/ddr457

      Sloan, S. A., Andersen, J., Pașca, A. M., Birey, F., & Pașca, S. P. (2018). Generation and assembly of human brain region-specific three-dimensional cultures. Nature Protocols, 13(9), 2062–2085. https://doi.org/10.1038/s41596-018-0032-7

      Yao, Z., Nguyen, T. N., van Velthoven, C. T. J., Goldy, J., Sedeno-Cortes, A. E., Baftizadeh, F., Bertagnolli, D., Casper, T., Chiang, M., Crichton, K., Ding, S.-L., Fong, O., Garren, E., Glandon, A., Gouwens, N. W., Gray, J., Graybuck, L. T., Hawrylycz, M. J., Hirschstein, D., … Zeng, H. (2021). A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell, 184(12), 3222–3241.e26. https://doi.org/10.1016/j.cell.2021.04.021

    1. Author response:

      We sincerely thank the reviewers and editors for the thorough, constructive, and insightful comments, which have greatly helped us improve the accuracy, clarity, and rigor of the manuscript. We acknowledge that the current version has several limitations, including insufficient contextualization with other model systems and lack of critical synthesis. These important weaknesses will be comprehensively addressed in a future revised version of the review.

      For the present revision, we have focused exclusively on correcting objective errors, factual inaccuracies, and citation mistakes as pointed out by the reviewers. All specific factual and reference issues raised by Reviewer 2 and Reviewer 3 have been carefully corrected in the revised manuscript, including inaccurate statements, incorrect citations, missing references, and inconsistent descriptions of zebrafish clock genes, photoreception, and physiological functions.

      We appreciate the reviewers’ thoughtful suggestions regarding the conceptual depth, comparative context, critical synthesis, and expanded discussion of sleep and model limitations. While we fully agree that these aspects would significantly strengthen the review, we plan to systematically incorporate these broader conceptual improvements in a future, more substantial revision.

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Evidence, reproducibility and clarity):

      Summary

      Sheidaei and colleagues report a novel and potentially important role for an early mitotic actomyosinbased mechanism, PANEM contraction, in promoting timely congression of chromosomes located at the nuclear periphery, particularly those in polar positions. The manuscript will interest researchers studying cell division, cytoskeletal dynamics, and motor proteins. Although some data overlap with the group's prior work, the authors extend those findings by optimizing key perturbations and performing more detailed analyses of chromosome movements, which together provide a clearer mechanistic explanation. The study also builds naturally on recent ideas from other groups about how chromosome positioning influences both early and later mitotic movements.

      In its current form, however, the manuscript is not acceptable for publication. It suffers from major organizational problems, an overcrowded and confusing Results section and figures, and a lack of essential experimental controls and contextual discussion. These deficiencies make it difficult to evaluate the data and the authors' conclusions. A substantial structural revision is required to improve clarity and persuasiveness. In addition, several key control experiments and more conceptual context are needed to establish the specificity and relevance of PANEM relative to other microtubule- and actin-based mitotic mechanisms. Testing PANEM in additional cell lines or contexts would also strengthen the claim. I therefore recommend Major Revision, addressing the structural, conceptual, and experimental issues detailed below.

      Major Comments

      A. Structural overhaul and figure reorganization

      The Results section is overly dense, lacks clear structure, and includes descriptive content that belongs in the Methods. Many figure panels should be moved to Supplementary Materials. A substantial reorganization is required to transform the manuscript into a focused, "Reports"-type article.

      Move methodological and descriptive details (e.g., especially from the second Results subheading and Figure 2) to the Methods or Supplementary Materials.

      In these parts, we define four phases of kinetochore motion in early mitosis. Without such a description in the main text, readers would be confused about subsequent analyses. Figure 2 is also important to show examples of how the four phases develop. Although we respect this suggestion from the reviewer, we would like to keep these parts in the main text and main figure.

      Remove repetitive statements that simply restate that later phenotypes arise as consequences of delayed Phase 1 (applicable to subheadings 3 onward).

      As suggested, we have removed the statement for the delayed start of Phase 2 for peripheral kinetochores in azBB-treated cells (Page 9, second paragraph). We have also simplified the statement for the delayed start of Phase 3 and Phase 4 to avoid repetition (Page 9, third paragraph; Page 10, second paragraph).

      Figure 4I: This panel is currently unclear and should be drastically simplified.

      Following this suggestion, we simplified Figure 4I by removing the column of ‘Start’, which is easily deduced from the ‘Duration’ results and therefore does not provide much new information.

      I recommend to reorganize figures as follows:

      Figure I: Keep as single figure but simplify. Figure 1D and 1E could be combined, move unnormalized SCV to supplementary materials. Same goes for 1F.

      We have reorganized Figure 1, as suggested, and moved unnormalized data to supplemental materials.

      New Figure 2: Combine current Figures 2A, 3A, 3C, 3D, 4C, 4F, and 4H to illustrate how PANEM contraction facilitates initial interactions of peripheral chromosomes with spindle microtubules which increases speed of congression initiation.

      If we were to follow this suggestion, we would lose Figure 2B, D, Figure 3B and Figure 4A, where examples of kinetochore motions are shown in images and 3D diagrams. The new Figure would mostly consist of only graphs. Without examples of images and 3D diagrams, readers would have difficulty understanding the study. Although we respect this suggestion from the reviewer, we would like to keep Figures 2, 3 and 4, as they are (except for making Figure 4I simpler; see above).

      New Figure 3: Combine current Figures 5A, 5C, 5D, 5F, 6B, 6C, and lower panels of 4H to show how

      PANEM contraction repositions polar chromosomes and reduces chromosome volume in early mitosis to enable rapid initiation of congression.

      If we were to follow this suggestion, we would lose Figure 5B and Figure 6A, where examples of kinetochore/chromosome dynamics are shown in images and 3D diagrams. For the same reason as above, we would like to keep Figure 5 and 6 as they are, although we respect this suggestion from the reviewer.

      New Figure 4: Combine Figures 7A, 7B, 7D, 7E, 7F, expanded Supplementary Figure S7, and new data to demonstrate that PANEM actively pushes peripheral chromosomes inward which is important for efficient chromosome congression in diverse cellular contexts.

      We have conducted new experiments to demonstrate the role of PANEM in diverse cellular contexts, as detailed below. We have combined the new results with the original Figure S7 to create Figure 8 in line with this suggestion.

      On the other hand, in our view, combining Figure 7A-E and the extended Figure S7 would be confusing because the two parts address different topics. Although we respect this suggestion from the reviewer, we would like to keep Figure 7 and the extended Figure S7 (i.e. Figure 8) separate.

      B. Specificity and redundancy of actin perturbation

      To establish the specificity and relevance of PANEM, the authors should include or discuss appropriate controls:

      Apply global actin inhibitors (e.g., cytochalasin D, latrunculin A) to disrupt the entire actin cytoskeleton. These perturbations strongly affect mitotic rounding and cytokinesis but only modestly influence early chromosome movements, as reported previously (Lancaster et al., 2013; Dewey et al., 2017; Koprivec et al., 2025). The minimal effect of global inhibition must be addressed when proposing a localized actomyosin mechanism. Comment if the apparent differences in this approach and one that the authors were using arises due to different cell types.

      We did experiments along this line, using a dominant-negative LINC construct, in our previous study (Booth et al eLife 2019). LINC-DN should more specifically remove/reduce PANEM than the global actin inhibitors mentioned above. LINC-DN attenuated the reduction of CSV soon after NEBD and increased the number of polar chromosomes (Booth et al eLife 2019); i.e. in this regard, the outcome was similar to azBB treatment in the current study. One can expect that global actin inhibitors would also inhibit the PANEM formation and show effects similar to LINC-DN. By contrast, the indicated references reported that global actin inhibitors strongly affect mitotic rounding and cytokinesis but only modestly influence early chromosome movements, as the reviewer noted. One possibility is that such differences may have arisen from different cell types – this could be important, especially given that some cells form the PANEM and others do not (Figure 8A). A second possibility is that cytokinesis, mitotic rounding and PANEM formation may rely on actin polymerization to different extents. For example, the same concentration of global actin polymerization inhibitors may affect cytokinesis, but may still allow PANEM formation to proceed without observable effects on early chromosome movements. As suggested, we discussed this topic in the Discussion (page 16, third paragraph).

      Clarify why spindle-associated actin, especially near centrosomes, as reported in prior studies using human cultured cells (Kita et al., 2019; Plessner et al., 2019; Aquino-Perez et al., 2024), was not observed in this study. The Myosin-10 and actin were also observed close to centrosomes during mitosis in X.laevis mitotic spindles (Woolner et al., 2008). Possible explanations include differences in fixation, probe selection, imaging methods, or cell type. Note that some actin probes (e.g., phalloidin) poorly penetrate internal actin, and certain antibodies require harsh extraction protocols. Comment on possibility that interference with a pool of Myo10 at the centrosomes is important for effects on congression.

      As the reviewer implies, we cannot rule out that we could not detect actin associated with the spindle or centrosomes because of the difference in methods or cell lines between the current study and the literature mentioned by the reviewer. We have therefore moderated our claim in the Discussion that ‘we did not detect any actin network inside the nucleus, on the spindle or between chromosomes’ by adding ‘at least, using the method and the cell line in the current study’ to this statement (Page 14, second paragraph). We have also cited the three references mentioned by the reviewer in the Discussion (Page 14, second paragraph). Regarding Myosin10, azBB (blebbistatin variant) should have negligible effects on class-X myosin, including Myosin-10 (Limouze et al 2004 [PMID 15548862]). It is therefore unlikely that the effects of azBB that we observed in the current study are due to the inhibition of Myosin-10. We have cited Woolner et al 2008 and another paper and discussed this topic in the Discussion (Page 14, second paragraph).

      C. Expansion of PANEM functional analysis

      To strengthen the conclusions and broaden the study beyond the group's previous work, PANEM function should be tested in additional contexts (some may be considered optional but important for broader impact): [underlined by authors]

      Test PANEM function in at least one additional cell line that displays PANEM to rule out cell-line-specific effects.

      As suggested, we have studied the effect of PANEM contraction in cell lines other than U2OS. We have found that when PANEM contraction was inhibited, the reduction in chromosome scattering was diminished in RPE1 cells (new Figure 8B, C). Moreover, we have found that inhibition of PANEM contraction increased polar chromosomes during prometaphase/ metaphase in RPE1 and HCT116 cells (which form PANEM), but not in HeLa cells (which do not form PANEM) (new Figure 8D, E). These results suggest that the effects of PANEM contraction, originally observed in U2OS cells, are also present in other cell lines (RPE1 and HCT116) that form PANEM.

      Examine higher-ploidy or binucleated cells to determine whether multiple PANEM contractions are coordinated and if PANEM contraction contributes more in cells of higher ploidies or specific nuclear morphologies.

      This is an interesting suggestion, but it takes lots of time to conduct such a study, and it goes beyond the scope of this paper.

      Investigate dependency on nuclear shape or lamina stiffness; test whether PANEM force transmission requires a rigid nuclear remnant.

      This is an interesting suggestion, but it takes lots of time to conduct such a study, and it goes beyond the scope of this paper.

      Analyze PANEM's contribution under mild microtubule perturbations that are known to induce congression problems (e.g., low-dose nocodazole).

      In the current study, we found that PANEM contraction affects chromosome motions in Phase 1 and Phase 3 but not Phase 2 or Phase 4. Mild microtubule perturbation itself could affect chromosome motions in all four Phases. We do not think it would be so informative to study what additional effects the reduced PANEM contraction shows when combined with mild microtubule perturbation.

      Evaluate PANEM contraction role in unsynchronized U2OS cells, where centrosome separation can occur before NEBD in a subset of cells (Koprivec et al., 2025), and in other cell types with variable spindle elongation timing.

      Following this suggestion, we first investigated the timing of spindle elongation, relative to NEBD, in asynchronous U2OS cells (Figure 8 – figure supplement 3). We imaged cells every 5 min (it was difficult to reasonably observe enough mitotic cells using a shorter interval). Most of the cells showed no significant change in the spindle length (distance between two spindle poles) after (or around) NEBD [e.g. Cell 1 in A] or a mild reduction in it [e.g. Cell 2 in A]. Only a small number of cells (2-3 out of 26) showed a mild increase in the spindle length after (or around) NEBD [e.g. Cell 3 in A]. Because the spindle elongation after NEBD was rare and mild, it was difficult to address how the timing of spindle elongation affects the effect of PANEM on reducing chromosome scattering and on chromosome relocation from polar regions. We explained this result and discussed this topic in the Discussion section.

      Quantify not only the percentage of affected cells after azBB but also the number of chromosomes per cell with congression defects in the current and future experiments.

      It is tricky to count the number of chromosomes because they frequently overlap. Counting kinetochores is more feasible, but kinetochore signals show some non-specific background (e.g. those outside of the nucleus in prophase). We therefore quantified the chromosome volume at polar regions in azBB-treated cells (Figure 6C).

      D. Conceptual integration in Introduction and Discussion

      The manuscript should better situate its findings within the context of early mitotic chromosome movements:

      Clearly state in the Introduction and elaborate in the Discussion that initiation of congression is coupled to biorientation (Vukušić & Tolić, 2025). This provides essential context for how PANEM-mediated nuclear volume reduction supports efficient congression of polar chromosomes.

      It has been a widely accepted view in the field that chromosome congression precedes biorientation, since the publication in 2006 (Kapoor et al Science 2006). Very recently, this view has been challenged by the new publication (Vukušić & Tolić, Nat comm 2025), as indicated by this reviewer. We have mentioned this new model and discussed the new interpretation of our results based on this new model, in the Discussion (page 15; ‘It has been a widely accepted view…’).

      To explain the new interpretation of our results more clearly, we have a new diagram as a supplemental figure (Figure 9 – figure supplement 1) in the revised manuscript.

      Explain that PANEM is most critical for polar chromosomes because their peripheral positions are unfavorable for rapid biorientation (Barišić et al., 2014; Vukušić & Tolić, 2025).

      We have included such a statement in the Discussion, as a part of the new interpretation of our results based on the new model that chromosome biorientation precedes congression (see above). We have also cited the indicated two papers.

      Discuss how cell lines lacking PANEM (e.g., HeLa and others) nonetheless achieve efficient congression, and what alternative mechanisms compensate in the absence of PANEM. For example, it is well established that cells congress chromosomes after monastrol or nocodazole washout, which essentially bypasses the contribution of PANEM contraction.

      Following this suggestion, we discussed three possible mechanisms that could compensate for a lack of PANEM and facilitate kinetochore-MT interaction and chromosome congression, based on previous literature (Page 17): 1) the enhanced assembly rate of spindle MTs may facilitate kinetochore-MT interactions in N-CIN+ cancer cells, 2) chromosome biorientation may precede congression more frequently to promote the congression towards the spindle midplane, and 3) the balance between CENP-E, Dynein and chromokinesin’s activities may incline to greater chromosome-arm ejection forces towards the spindle midplane.

      Minor Comments

      These issues are more easily addressable but will significantly improve clarity and presentation.

      Introduction

      Remove the reference to Figure 1A in the Introduction. The portion of Figure 1 and related text that recapitulates the authors' previous work should be incorporated into the Introduction, not the Results.

      As suggested in the second sentence of this comment, we have moved most of the second paragraph of the first section of Results to Introduction (Page 4) and cited Figure 1A and 1B in Introduction. We would like to keep the reference to Figure 1A in the Introduction, because showing the PANEM images at the beginning of the manuscript would help readers’ understanding of our study. In addition, citing Figure 1A in the Introduction is more consistent with the suggestion in the second sentence of this comment.

      Results (by subheading)

      First subheading: When introducing the ~8-minute early mitotic interval, cite additional studies that have characterized this period: Magidson et al., 2011 (Cell); Renda et al., 2022 (Cell Reports); Koprivec et al., 2025 (bioRxiv); Vukušić & Tolić, 2025 (Nat Commun); Barišić et al., 2013 (Nat Cell Biol).

      As suggested, we cited these references at the indicated part of the first section of the Results (page 5).

      Second subheading: Cite key reviews and foundational research on kinetochore architecture and sequential chromosome movement during early mitosis: Mussachio & Desai, 2017 (Biology); Itoh et al., 2018 (Sci Rep); Magidson et al., 2011 (Cell); Vukušić & Tolić, 2025 (Nat Commun); Koprivec et al., 2025 (bioRxiv); Rieder & Alexander, 1990 (J Cell Biol); Skibbens et al., 1993 (J Cell Biol); Kapoor et al., 2006 (Science); Armond et al., 2015 (PLoS Comput Biol); Jaqaman et al., 2010 (J Cell Biol).

      Rieder & Alexander, 1990 (J Cell Biol) and Kapoor et al., 2006 (Science) have already been cited in the second section of the Results in the original manuscript. We agree that all other references should be cited in this manuscript, and they are now cited in the Introduction and/or Discussion where they fit best (e.g. Mussachio & Desai 2017 reviews the kinetochore in general and is therefore best cited in the Introduction).

      Third subheading: Clarify why some kinetochores on Figure 3A appear outside the white boundaries if these boundaries are intended to represent the nuclear envelope.

      We interpret that these are background signals in the cytoplasm, which do not come from kinetochores, because 1) before NEBD, they were outside of the nucleus, and 2) after NEBD, they did not show any characteristic kinetochore motions such as those towards a spindle pole (Phase 2) and the spindle mid-plane (Phase 4). We have commented on these background signals in the legend for Figure 3A.

      Fourth subheading: Note that congression speed is lower for centrally located kinetochores because they achieve biorientation more rapidly (Barišić et al., 2013, Nat Cell Biol; Vukušić & Tolić, 2025, Nat Commun).

      Relevant to this comment, there was an error regarding the congression speed of central kinetochores (original Figure 4H). The congression speed of peripheral kinetochores was shown correctly, but for central kinetochores it was shown incorrectly with µm per time interval (30s) shown, rather than µm per minute. We amended this error in the revised manuscript (new Figure 4H). Based on the corrected data, the speed of congression is similar between peripheral and central kinetochores. The original Figure 3G (the speed of poleward motion for central kinetochores) had a similar error, which we have also corrected in the revised manuscript. We apologize for these errors and the confusion it may have caused.

      Regarding this comment, if biorientation is achieved more rapidly for central kinetochores, Phase 3 (rather than congression speed) would be shorter for central kinetochores. Indeed, Phase 3 is slightly shorter for central kinetochores (control) than for peripheral kinetochores (control) (Figure 4C), but the difference is not statistically significant (t test; p\=0.21).

      Fifth subheading: Cite studies on polar chromosome movements: Klaasen et al., 2022 (Nature); Koprivec et al., 2025 (bioRxiv). Clarify that Figure 5F displays only those kinetochores that initiated directed congression movements.

      These two references have already been cited and discussed in this Result section of our original manuscript. However, considering this suggestion, we have discussed more about polar chromosome movements reported by Koprivec et al (page 11). Meanwhile, the reviewer is correct about Figure 5F, and we have clarified this point in the Figure 5F legend.

      Sixth subheading (currently in Discussion): Move the final paragraph of the Discussion into the Results and expand it with preliminary analyses linking PANEM contraction to congression efficiency across untreated cell types or under mild nocodazole treatment.

      As suggested, we have moved the final paragraph of the Discussion in the original manuscript to make a new final section in the Results in the revised manuscript. Moreover, as suggested, we have studied the outcome of inhibiting PANEM contraction in cell lines other than U2OS (Figure 8 B–E), and have described the new results to the new final section in the Results.

      Discussion

      1. When discussing cortical actin, cite key reviews on its presence and function during mitosis: Kunda & Baum, 2009 (Trends Cell Biol); Pollard & O'Shaughnessy, 2019 (Annu Rev Biochem); Di Pietro et al., 2016 (EMBO Rep).

      As suggested, we have cited all these review papers in the Discussion (page 17), and mentioned the role of the cortical actin on the spindle orientation and positioning (Kunda & Baum, 2009; Di Pietro et al., 2016), as well as the function of the actomyosin ring on cytokinesis (Pollard & O'Shaughnessy, 2019).

      Significance

      Advance

      This study's main strength is its novel and potentially important demonstration that contraction of PANEM, a peripheral actomyosin network that operates contracts early mitosis, contributes to the timely initiation of chromosome congression, especially for polar chromosomes. While PANEM itself was previously described by this group, this manuscript provides new mechanistic evidence, improved perturbations, and detailed chromosome tracking. To my knowledge, no prior studies have mechanistically connected this contraction to polar chromosome congression in this level of detail. The work complements dominant microtubule-centric models of chromosome congression and introduces actomyosin-based forces as a cooperating system during very early mitosis. However, the impact of the study is currently limited by major organizational issues, insufficient controls, and incomplete contextualization within existing literature. Addressing these issues will substantially improve clarity and credibility. [underlined by authors]

      We have addressed the underlined criticisms as detailed above.

      Audience

      Primary audience of this study will be researchers working in cell division, mitosis, cytoskeleton dynamics, and motor proteins. The findings may interest also the wider cell biology community, particularly those studying chromosome segregation fidelity, spindle mechanics, and cytoskeletal crosstalk. If validated and clarified, the concept of PANEM could be integrated into textbooks and models of chromosome congression and could inform studies on mitotic errors and cancer cell mechanics.

      Expertise

      My expertise lies in kinetochore-microtubule interactions, spindle mechanics, chromosome congression, and mitotic signaling pathways.

      Reviewer #2 (Evidence, reproducibility and clarity):

      In this manuscript, Sheidaei et al. reported on their study of chromosome congression during the early stages of mitotic spindle assembly. Building on their previous study (ref. #15, Booth et al., Elife, 2019), they focused on the exact role of the actin-myosin-based contraction of the nuclear envelope. First, they addressed a technical issue from their previous study, finding a way to specifically impair the actomyosin contraction of the nuclear membrane without affecting the contraction of the plasma membrane. This allowed them to study the former more specifically. They then tracked individual kinetochores to reveal which were affected by nuclear membrane contraction and at what stage of displacement towards the metaphase plate. The investigation is rigorous, with all the necessary controls performed. The images are of high quality. The analyses are accurate and supported by convincing quantifications. In summary, they found that peripheral chromosomes, which are close to the nuclear membrane, are more influenced by nuclear membrane contraction than internal chromosomes. They discovered that nuclear membrane contraction primarily contributes to the initial displacement of peripheral chromosomes by moving them towards the microtubules. The microtubules then become the sole contributors to their motion towards the pole and subsequently the midplane. This step is particularly critical for the outermost chromosomes, which are located behind the spindle pole and are most likely to be missegregated.

      Significance

      While the conclusions are somewhat intuitive and could be considered incremental with regard to previous works, they are solid and improve our understanding of mitotic fidelity. The authors had already reported the overall role of nuclear membrane contraction in reducing chromosome missegregation in their previous study, as mentioned fairly and transparently in the text. However, the reason for this is now described in more detail with solid quantification. Overall, this is good-quality work which does not drastically change our understanding of chromosome congression, but contributes to improving it. Personally, I am surprised by the impact of such a small contraction (of around one micron) on the proper capture of chromosomes and wonder whether the signalling associated with the contraction has a local impact on microtubule dynamics. However, investigating this point is clearly beyond the scope of this study, which can be published as it is. [underlined by authors]

      The suggested topic (underlined) is intriguing. However, we agree with the reviewer that it is beyond the scope of this paper. The reviewer recommends publication of our manuscript as it is.

      Reviewer #3:

      Sheidaei et al., report how chromosomes are brought to positions that facilitate kinetochore-microtubule interactions during mitosis. The study focusses on an important early step of the highly orchestrated chromosome segregation process. Studying kinetochore capture during early prophase is extremely difficult due to kinetochore crowding but the team has taken up the challenge by classifying the types of kinetochore movements, carefully marking kinetochore positions in early mitosis and linking these to map their fate/next-positions over time. The work is an excellent addition to the field as most of the literature has thus far focussed on tracking kinetochore in slightly later stages of mitosis. The authors show that the PANEM facilitates chromosome positioning towards the interior of the newly forming spindle, which in turn facilitates chromosome congression - in the absence of PANEM chromosomes end up in unfavourable locations, and they fail to form proper kinetochore-microtubule interactions. The work highlights the perinuclear actomyosin network in early mitosis (PANEM) as a key spatial and temporal element of chromosome congression which precedes the segregation process.

      Major points

      (1) The complexity of tracking has been managed by classifying kinetochore movements into 4 categories, considering motions towards or away from the spindle mid-plane. While this is a very creative solution in most cases, there may be some difficult phases that involve movement in both directions or no dominant direction (eg Phase3-like). It is unclear if all kinetochores go through phase1, 2, 3 and 4 in a sequential or a few deviate from this pattern. A comment on this would be helpful. Also, it may be interesting to compare those that deviate from the sequence, and ask how they recover in the presence and absence of azBB.

      To respond to this comment, we would like to first clarify how we selected kinetochores for our analysis. We selected kinetochores that can be individually tracked. If kinetochore tracking was difficult (before the start of Phase 4 in control and azBB-treated cells or before observing the extended Phase 3 in azBB-treated cells) because of kinetochore crowding, we did not choose such kinetochores. For example, related to the next comment of this Reviewer, we did not include kinetochores close to spindle poles (within 4 µm) at NEBD in our analysis for the following two reasons: First, these kinetochores often did not show clear and rapid movements towards a spindle pole, which we used to define Phase 2. Second, although we referred to kinetochore co-localization with a microtubule signal for the start of Phase 2, this was difficult for kinetochores close to spindle poles because of a high density of microtubules. As requested, we have added this comment to the Method section (page 25).

      With the above selection, all selected kinetochores without azBB treatment (control) showed the poleward motion (Phase 2) and congression (Phase 4) in this order, though their extents were varied among kinetochores. All selected kinetochores with azBB treatment also showed the poleward motion (Phase 2), and some of them showed congression (Phase 4) after Phase 2. Then, Phase 1 and Phase 3 were defined as intervals between NEBD and Phase 2 and between Phase 2 and Phase 4, respectively. If no Phase 4 was observed with azBB, we judged that Phase 3 continued till the end of tracking. We have added this comment to the Method section (page 25-26).

      (2) Would peripheral kinetochore close to poles behave differently compared to peripheral kinetochore close to the midplane (figure S4)? In figure 3D, are they separated? If not, would it look different?

      Since we did not include kinetochores close to spindle poles (at NEBD), for which it was difficult to define Phase 2 (see our response to the above major point 1), in our analysis, the suggested comparison is not feasible.

      (3) Uncongressed polar chromosomes (eg., CENPE inhibited cells) are known to promote tumbling of the spindle. In figure 5B with polar chromosomes, it will be helpful to indicate how the authors decouple spindle pole movements from individual kinetochore movements.

      In contrast to CENPE-inhibited cells, azBB-treated cells did not show much tumbling of the spindle, though both cells showed uncongressed polar chromosomes. The reason for this difference may be fewer uncongressed polar chromosomes in azBB-treated cells. There were still modest spindle motions in azBB-treated cells. However, because kinetochore motions were assessed relative to a spindle pole (and other reference points on the spindle) in our study (Figure 2A, C), the modest spindle motions were offset in our analyses of kinetochore motions. We have clarified the underlined part in the Method section (page 24).

      (4) The work has high quality manual tracking of objects in early mitosis- if this would be made available to the field, it can help build AI models for tracking. The authors could consider depositing the tracking data and increasing the impact of their work.

      As suggested, we have included kinetochore tracking data as supplemental data in the revised manuscript (Figure 3 – source data 1–4; Figure 5 – source data 1, 2).

      Minor points

      (1) It will be helpful for readers to see how many kinetochores/cell were considered in the tracking studies. Figure legends show kinetochore numbers but not cell numbers.

      As suggested, we have now mentioned the number of cells, where the kinetochore motions were analyzed, in the legends for Figures 3, 4, 5, and supplemental figures.

      (2) Discussion point: If cells had not separated their centrosomes before NEBD, would PANEM still be effective? Perhaps the cancer cell lines or examples as shown in Figure 6A have some clues here.

      Following this suggestion, we first investigated the timing of spindle elongation, relative to NEBD, in asynchronous U2OS cells (Figure 8 – figure supplement 3). We imaged cells every 5 min (it was difficult to reasonably observe enough mitotic cells using a shorter interval). Most of the cells showed no significant change in the spindle length (distance between two spindle poles) after (or around) NEBD [e.g. Cell 1 in A] or a mild reduction in it [e.g. Cell 2 in A]. Only a small number of cells (2-3 out of 26) showed a mild increase in the spindle length after (or around) NEBD [e.g. Cell 3 in A]. Because the spindle elongation after NEBD was rare and mild, it was difficult to address how the timing of spindle elongation affects the effect of PANEM on reducing chromosome scattering and on chromosome relocation from polar regions. We explained this result and discussed this topic in the Discussion section.

      (3) Figure 7 cartoon shows misalignment leading to missegregation. It may be useful to consider this in the context of the centrosome directed kinetochore movements via pivoting microtubules. Is this process blocked in azBB-treated cells?

      We understand that the Reviewer refers to the kinetochore pivoting mechanism around a spindle pole, which was recently reported by the Tolic group (Koprivec et al., 2026). Such a pivoting mechanism would work only when the spindle elongates (i.e. the distance between spindle poles is enlarged) after NEBD. Therefore, to address this Reviewer’s question, we tried to assess how PANEM contraction contributes to relocating polar chromosomes when the spindle elongates before or after NEBD in asynchronous U2OS cells (i.e. in the situation where the kinetochore pivoting mechanism is applied or not), as we noted above in response to Point 2. However, spindle elongation after NEBD was rare and mild, and we were unable to address this issue (see our response to Point 2). We discussed this matter in the Discussion section.

      (4) Are all the N-CIN- lines with PANEM highly sensitive to azBB? In other words, is PANEM essential for normal congression in some of these lines.

      Because blebbistatin could kill cells by inhibiting cytokinesis, the blebbistatin sensitivity of cell growth may not necessarily reflect how essential the PANEM contraction is for chromosome congression.

      Instead, we addressed more directly how essential the PANEM contraction is for chromosome congression. We analyzed chromosome congression in RPE1 and HCT116 cells (both are NCIN-) in the presence and absence of pnBB, the inhibitor of PANEM contraction (new Figure 8D, E). With pnBB, these cells showed congression defects, suggesting that the PANEM contraction is essential for chromosome congression in these N-CIN- cells.

      (5) Are congression times delayed in lines that naturally lack PANEM?

      For example, it takes 10-20 min for HeLa cells (lacking PANEM) to complete chromosome congression after the NEBD (Bancroft et al 2025: https://doi.org/10.1242/jcs.163659). This is not significantly different from the time (8-18 min) for chromosome congression we observed in U2OS cells (which form PANEM). We assume that cells lacking PANEM have developed a compensatory mechanism for efficient chromosome congression – we have discussed possible compensatory mechanisms in the last paragraph of the Discussion (page 17).

      (6) Page 23 "we first identified the end of congression" how does this relate to kinetochore oscillations that move kinetochores away from the metaphase plate?

      The start of kinetochore oscillation was defined as the end of Phase 4 if we could track the kinetochore until that point. In some cases where the kinetochore became close to the midplane (< 2.5 µm), it was not possible to track it further due to kinetochore crowding around the spindle mid-plane – in such cases, the end of Phase 4 was assigned as the end of tracking. These definitions were not necessarily clear in the original manuscript. Moreover, in the original manuscript, it was not clearly stated that the end of Phase 4 was defined in the same way for both non-polar and polar kinetochores. We have now clarified these points in the Method section (page 25).

      (7) Are spindle pole distances (spindle sizes) different in early and late mitotic cells (4min vs 6min after NEBD) in control vs azBB-treated cells? Please comment on Figure S2E (mean distance) in the context of when phase 4 is completed. Does spindle size return to normal after congression?

      In Figure S2E (Figure 1 – figure supplement 6 in the revised manuscript), we did not observe a significant difference in the spindle-pole distance (the spindle size) between control and azBBtreated cells at any individual time points. The smallest p-value was 0.094 at 6.0 min. As suggested, we have explained this in the legend for this supplementary figure. Completion of Phase 4 is highly variable across different kinetochores within the same cell; thus, a general comment on its completion timing in cells is not feasible.

      Significance:

      The current work builds upon their previous work, in which the authors demonstrated that an actomyosin network forms on the cytoplasmic side of the nuclear envelope during prophase. This work explains how the network facilitates chromosome capture and congression by tracking motions of individual kinetochores during early mitosis. The findings can be broadly useful for cell division and the cytoskeletal fields.

    1. Author response:

      Thank you for your decision letter with the public review and the recommendations. While we are delighted that the referees feel the work is addressing an outstanding and important issue, they have raised concerns regarding the strength of the support. We will address all the concerns in full in a revised manuscript in the due course. Please find below a couple of general points regarding the referees’ concerns and a proposal as to how we plan to address them.

      (1) The idea of the manuscript is to present a plausible solution for a long-standing question in the field of mitochondrial biology and evolution. The fact that the identified solution to the origin of AAC transporters is a remote structural homolog (as you will see in our later detailed response that it is better than any other sequence/structure available till date) is to be expected. If the actual similarities were any better than what we have identified (with a special case of circular permutation), they could have been identified by other simpler structural homology search methodologies.

      (2) A recurrent and strong disagreement of the reviewers on the findings presented in this manuscript is rooted on the fact that the structural and sequence relatedness between AAC and CysZ detected in this work are so weak that they can be co-incidental and not an actual evolutionary link. Based on the above, we now searched carefully in all available structural databases such as SCOP, CATH, ECOD etc. whether the above fold link has been noted by others independently. We notice that in the ECOD (Evolutionary Classification of Protein Domains) database only AAC and CysZ are grouped together under a single Possible homology group (X) called ‘Mitochondrial ADP/ATP carrier-like’. The ECOD database contains hierarchical classification of protein domains organized according to their evolutionary relationships and the server is maintained by Prof. Nick Grishin at The University of Texas Southwestern Medical Center.

      Link to ECOD database: http://prodata.swmed.edu/ecod/index_af2_pdb.php

      Reference: Cheng H, Schaeffer RD, Liao Y, Kinch LN, Pei J, et al. (2014) ECOD: An Evolutionary Classification of Protein Domains. PLOS Computational Biology 10(12): e1003926. https://doi.org/10.1371/journal.pcbi.1003926

      Therefore, our study and the independent findings of the ECOD database team together offers greater confidence on the proposed remote evolutionary relationship between AAC and CysZ, and that the structural and sequence similarity we report in the manuscript are not a mere co-incidence. We will also incorporate the details of possible evolutionary relationship between AAC and CysZ identified in the ECOD database in the revised version of manuscript.

      (3) One point we would like to stress is that considering all the similarities identified, it very unlikely falls into the class of ‘convergent evolution’. We will make this point explicit in the revised version.

      (4) Lastly, while we totally agree that the similarities are in the twilight zone, considering the importance of the problem, we feel that our work would induce researchers from the field of protein design to attempt possible interconversion of the two distantly related transporters thus providing an experimental rationale for the evolution of these transporters.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Renard, Ukrow et al. applied their recently published computational pipeline (CHROMAS) to the skin of Euprymna berryi and Sepia officinalis to track the dynamics of cephalopod chromatophore expansion. By segmenting each chromatophore into radial slices and analyzing the co-expansion of slices across regions of the skin, they inferred the motor control underlying chromatophore groups.

      Strengths:

      The authors demonstrate that most motor units of cephalopod skin include a subregion of multiple chromatophores, creating "virtual chromatophores" in between the fixed chromatophores. This is an interesting concept that challenges prevailing models of chromatophore organization, and raises interesting possibilities for how chromatophore arrays may be patterned during development.

      This study introduces new analyses of cephalopod skin that will be valuable for the quantitative study of cephalopod behavior.

      Weaknesses:

      The authors chose to image spontaneous skin changes in sedated animals, rather than visually-evoked skin changes in awake, freely-moving animals. Spontaneous chromatophore changes tend to be small shimmers of expansion and contraction, rather than obvious, sizable expansions. This may make it more challenging to distinguish truly co-occurring expansions from background activity. The authors don't provide any raw data (videos) of the skin, so it is difficult to independently assess the robustness of the inferred chromatophore groupings.

      The patch-clamp experiments in E. berryi are used to test the validity of their approach for inferring motor units. The stimulations evoke expansions of sub-regions of each chromatophore, creating "virtual chromatophores" as predicted from the behavioral analysis. However, the authors were not able to predict these specific motor units from behavioral analysis before confirming them with patch-clamp, limiting the strength of the validation. It would be informative to quantify the results of the patch-clamp experiments - are the inferred motor units of similar sizes to those predicted from behavior?

      The authors report testing multiple experimental conditions (e.g., age, size, behavioral stimuli, sedation, head-fixation, and lighting), but only a small subset of these data are presented. It is difficult to determine which conditions were used for which experiments, and the manuscript would benefit from pooling data from multiple experiments to draw general conclusions about the motor control of cephalopod skin.

      The authors use a different clustering algorithm for E. berryi and S. officinalis, but do not discuss why different clustering approaches were required for the two species.

      Impact:

      The authors use their computational pipeline to generate a number of interesting predictions about chromatophore control, including motor unit size, their spatial distribution within the skin, and the independent control of subregions within individual chromatophores by putatively distinct motor neurons. While these observations are interesting, the current data do not yet fully support them.

      The CHROMAS tool is likely to be valuable to the field, given the need for quantitative frameworks in cephalopod biology. The predictions outlined here provide a useful foundation for future experimental investigation.

      We thank the reviewer for the thoughtful and detailed evaluation of our work and for recognizing the potential of the CHROMAS pipeline for studying chromatophore control.

      We agree that some aspects of the manuscript required clarification and additional explanation, and we have revised the text accordingly. We also now provide access to representative raw video recordings in the Data Availability section. In the E. berryi patch-clamp experiments, single motor neurons evoked expansions of sub-regions of chromatophores, consistent with the “virtual chromatophore” concept. We have now quantified the size of motor units across patch-clamp sessions, and the results show that the inferred motor-unit sizes broadly match those predicted from behavioral recordings, supporting the validity of our approach.

      We agree that pooling data across individuals would provide valuable insight into variability across animals. In practice, we recorded chromatophore activity from several animals (14 Euprymna berryi and 12 Sepia officinalis) under different experimental conditions during development of the experimental pipeline. However, acquiring long, stable, artifact-free recordings suitable for motor unit analysis is technically challenging. We now clarify this point in the manuscript. Specifically, we explain that multiple animals were recorded during pipeline development, while the analyses presented focus on recordings with the highest signal quality. We anticipate that the framework introduced here will enable future studies to collect larger datasets and compare motor unit organization across individuals, developmental stages, and species.

      HDBSCAN was used for E. berryi during initial exploratory analyses, and Affinity Propagation was adopted for S. officinalis because it better captured the correlation structure of those recordings. We did not re-analyze the E. berryi data with Affinity Propagation, and the implications of algorithm choice are now discussed in the Discussion.

      Reviewer #2 (Public review):

      Summary:

      Overall, this is an excellent paper, making use of a newly developed system for monitoring the behaviour of chromatophores in the skin of (mostly) free-swimming bobtail squid and European cuttlefish. The manuscript is very well-written, clearly presented and very well-structured. The central finding, that individual chromatophores are connected to multiple motor neurones, is not new. Novelty instead comes from the ability to measure the actuation of chromatophore sections across wide areas of skin in free-swimming animals, showing the diversity of local motor units and reinforcing the notion that individual chromatophores are not necessarily the individual units of colour change, but rather local motor units that cover multiple neighbour and near-neighbour chromatophore muscles. This is an excellent finding and one that will shape our understanding of the neural control of cephalopod skin colour.

      Strengths:

      The methodological approach to collecting large amounts of data about local variations in the expansion of sections of chromatophores is exciting, and the analysis pipeline for clustering sections of chromatophores whose spontaneous activity correlated over time is powerful and exciting.

      Weaknesses:

      Some minor edits and typographical errors need correcting. I also had some concerns that the preparation for the electrophysiological section of the manuscript complies with the journal's ethical requirements, so I would urge that this be carefully checked.

      We thank the reviewer for the positive evaluation of our work and for recognizing the value of the methodological approach and the clarity of the manuscript.

      We have carefully reviewed the manuscript and corrected minor typographical errors.

      Regarding the ethical considerations raised for the electrophysiological experiments, we have carefully verified that the experimental procedures comply with the journal's ethical requirements and relevant institutional guidelines.

      Reviewer #3 (Public review):

      Summary:

      This study uses high-resolution videography and a custom computer-vision pipeline to dissect the motor control of cephalopod chromatophores in Euprymna berryi and Sepia officinalis. By quantifying anisotropic chromatophore deformations and applying dimensionality reduction methods, the authors infer that individual chromatophores can be a part of multiple motor units. Clustering analyses reveal putative motor units that often span multiple chromatophores, with diverse and overlapping geometries. Chromatophore expansion dynamics are faster and more stereotyped than relaxation, consistent with active neural contraction followed by passive recoil. Together, the results show that chromatophores function not as uniform pixels but as fractionated, coordinately controlled elements that enable flexible pattern generation

      Strengths:

      The authors present compelling, direct evidence that a). chromatophore deformations are anisotropic, and indirect evidence that b) individual chromatophores can be split across multiple putative motor units. This evidence is provided through data collected over large spatial scales, but also at a sub-chromatophore resolution. This combination of scale and resolution is not possible using traditional neuroanatomical and physiological approaches alone.

      The authors also develop a new non-invasive, image analysis approach to extract information about chromatophore deformation across large spatial scales on the organism's body. In principle, this approach is applicable across species and may allow for further comparative characterization of chromatophore motor control. It is therefore a promising new tool and useful resource for the community.

      Weaknesses:

      An important weakness of the work is that the methods the authors develop can only be applied during resting, spontaneous 'flickering' activity of chromatophores. The inability to reliably apply their technique during any kind of realistic camouflage is a large limitation, as it means this method cannot be used to study the dynamics of motor control during realistic camouflage behaviors.

      Another weakness of this paper is the rather limited electrophysiological validation of the computational findings. The authors present only one electrophysiology experiment in E. berryi, the species that they used only for 'methodological development' and not for detailed characterization. A complementary electrophysiological experiment in S. officinalis, or some visualization of neuron morphology confirming that motor neurons do indeed project to multiple chromatophores, would strengthen the generalizability of their computational analysis. This would be particularly pertinent to validate the author's claim that some motor units contain chromatophores that are quite distant from one another on the animal.

      Overall, the authors' technical contributions and method development are an important advance. This work serves as an excellent proof of concept that their method can extract useful information about chromatophore motor control. Further validation of their method is needed to fully trust the fine-scale conclusions drawn about the distribution and composition of multi-innervated chromatophores. Furthermore, the authors raise many interesting ideas about developmental constraints on circuit wiring and potential adaptive significance of multi-innervated chromatophores for certain features of camouflage patterning. Their method may be able to help resolve some of these questions in the future if it is refined and applied across developmental stages, regions of the animal, and across species

      We thank the reviewer for their thoughtful evaluation and for recognizing the potential of the computational approach introduced in this study.

      Regarding the focus on spontaneous chromatophore activity, we have clarified earlier in the Results section why these events are necessary to isolate individual muscle activations. While large camouflage patterns are visually striking, they involve the coordinated activation of many groups of chromatophores by premotor circuits simultaneously, making the identification of individual motor units, our goal here, impossible. Our approach can, however, also be applied during active behavior, including camouflage; the questions addressed there would be different, focusing on how multiple motor units are coordinated to generate the resulting skin patterns, rather than resolving the structure of single motor units. This could be challenging if the patterns of premotor control are highly variable, thus making the detection of meaningful or interpretable motion correlations difficult. This remains to be tested.

      We also acknowledge that electrophysiological validation remains limited. Patch-clamp experiments were performed in Euprymna berryi to test predictions generated by the computational analysis, and these experiments confirmed that activation of single motor neurons can produce anisotropic expansion of chromatophore subregions. We now provide the associated datasets in the Data Availability section. We agree that complementary electrophysiological or anatomical experiments in Sepia officinalis would further strengthen the conclusions. Such experiments represent an important direction for future work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      General points:

      (1) Given all the experimental conditions and animals tested, the manuscript would be much stronger if the figures represented pooled data from many animals and experiments (e.g. Figure 1C).

      We agree that pooling data from multiple animals would strengthen the manuscript. In practice, we tested these experimental conditions across several animals (14 Euprymna berryi and 12 Sepia officinalis), but we selected the segments shown in the figures for their minimal artifacts and errors. Acquiring high-quality, stable recordings of this type is extremely challenging, and the presented data represents the clearest examples suitable for analysis and visualization. We hope that in the future these methods will enable not only the collection of a larger, high-quality dataset, but also comparisons across individuals, ages, species, and different regions of the mantle.

      (2) It's very unclear what animals were used for each experiment:

      (a) E. berryi: L677 states that 14 animals were filmed, and L684 implies that non-sedated individuals were used in addition to sedated animals, but it appears all the data is from a single E. berryi with sedation?

      The original wording was unclear, so we modified the sentence for clarity. The Methods now specify that 14 animals were filmed to refine the experimental pipeline and explore different conditions, while the data presented in the Results are from a single lightly sedated individual chosen for quality and stability of chromatophore activity.

      (b) S. officinalis: L692 onwards states that lots of different conditions and animals were explored, but only minimal data from a couple of animals is described in the figures. L156 states that all (?) the data comes from one head-fixed animal and one sedated and head-fixed animal. L549: The conclusion states that the pipeline was used in freely moving animals, but it appears that all of the S. officinalis were head-fixed? This is very confusing. Rather than describing the conditions of every experiment ever performed, the manuscript would benefit from explicitly stating the experimental conditions used for each figure.

      The original text was unclear. We have clarified in the manuscript which animals and experimental conditions were used for the analyses in each figure. To clarify, E. berryi was recorded without head fixation, whereas S. officinalis data were obtained under head-fixed conditions. We did film 11 S. officinalis without head fixation, and data can in principle be extracted from these recordings. Head fixation was used both to minimize visual artifacts and to enable longer, stable recordings, which was important for capturing the highest level of apparent noise in motor unit activation—information that is critical for our analyses of motor-unit organization, though not necessary for studies of broader camouflage patterns. Our computational pipeline enables large-scale analyses that would be very difficult or impossible with traditional electrophysiology, not that all data were acquired from freely behaving animals. While fully unconstrained recordings remain technically challenging due to optical and logistical constraints, we maintain that our approach provides a valid framework for analyzing freely behaving animals.

      (c) Additionally, there is a claim that the sedated condition represents the unsedated one (e.g. L151 and L643), but no data is shown to support this. L173 references Figure 6d as evidence, but 6d doesn't exist. Only L210 provides sedation/no sedation statistics for the number of components per motor unit. However, in L643 it says "and motor unit organization remained unchanged". This data needs to be shown to include that statement.

      Reference to the inexistant 6d figure was removed. L170 provides statistics for the number of principal components per chromatophore, and L210 provides statistics for the number of components per MU. We do not think a sub-figure is necessary. We, however, agree that L643 “motor unit organisation” is potentially misleading as we only compared the number of chromatophores belonging to a single MU and not the MU shape or distribution. Changed “organization” to “size (in chromatophores)”.

      (3) The text needs considerable revision. There are many typos (including multiple instances of "refs" instead of the actual references being inserted). These issues make the manuscript much more difficult to evaluate.

      Our apologies. We have now added the missing refs.

      (4) It is not clear how convincing the chromatophore groups are. For instance, Figure 4h could alternatively be interpreted as a group of 5 chromatophores in a motor group that happen to co-vary with a sixth one at a great distance. Without seeing some of the raw data (videos), it's difficult to assess how convincing it is that these chromatophores belong to the same group. I recommend analyzing: when multiple chromatophores expand together, what is the likelihood that other chromatophores also happen to expand at the same time (given the frequency that they're all changing shape spontaneously)?

      We appreciate the reviewer’s concern. Chromatophores are assigned to the same cluster because their activity, or that of their slices, covaries consistently over time. It is, of course, possible that what appears as a single motor unit may reflect two or more motor neurons acting simultaneously during the recording. Longer video segments increase confidence in the integrity of inferred motor units, but in the absence of a ground truth for motor unit spatial organization in this species at this age, it is difficult to quantify the likelihood that two motor units are being conflated. Raw video data is provided in the Data Availability section. We note, however, that most of the time motor units cannot be readily discerned by eye, because individual chromatophores and their constituent slices fluctuate continuously, and motor-unit correlations are subtle and distributed across multiple chromatophores.

      (5) The rationale for focusing on spontaneous activity is introduced relatively late in the manuscript and would benefit from being stated earlier. Examples should be provided of what this looks like (as opposed to regular chromatophore expansion). It would be valuable to see measurements across many experiments of how expanded the chromatophores are - what is the change in surface area? And what is the frequency of expansion for each chromatophore?

      Thank you for the remark. This is true. We have added a paragraph at the beginning of the Results section to clarify the rationale for focusing on spontaneous activity.

      This section now reads:

      “Because our primary aim was to describe the composition and coordination of chromatophore motor units, it was important to examine animals in the absence of the descending commands that occur during active behavior. Spontaneous activity, typically mild and “noisy” was thus ideal to enable measurements of the motion correlations between chromatophores that reflected shared motor neuron drive, rather than shared correlations due to upstream motor neuron groupings by premotor circuits.”

      We added an example of video recording of spontaneous activity in our Data Availability section.

      While quantifying expansion magnitude and frequency across experiments would indeed be valuable, these questions fall outside the primary focus of the present study, which centers on resolving motor unit organization. In the section “Dynamics of chromatophore expansion and contraction,” we analyze the speed of expansion and contraction to demonstrate that such kinetic features can be reliably detected with the temporal resolution of our video imaging approach. By isolating single muscle activations, we establish a methodological framework that can be used in future work to quantify expansion amplitude, rate of change and frequency across preparations.

      (6) Chromatophore expansion was only measured in anesthetized E. berryi, and L679 states that chromatophore expansion was triggered by shining light on the skin. However, light-mediated chromatophore expansion may be mediated by a different mechanism, so chromatophore correlations do not necessarily reflect the underlying motor control.

      We agree that there is, in principle, a theoretical risk of direct light-mediated activation of chromatophores. Yet, the kinetics of this light mediated activation are very different, and are the object of a separate, on-going investigation by our groups. In our experiments, the illumination was applied to the whole animal rather than locally to the skin, ensuring that all chromatophores and the eyes were exposed to the same light source. By transitioning from darkness to light, we created a window in which chromatophores were partially expanded—both fully contracted and fully expanded states would show little to no decorrelation. Within this window, we observed spontaneous fluctuations in chromatophore activity, which formed the basis for our correlation analyses. To our knowledge, direct light-mediated expansion of chromatophores has not been reported in E. berryi although it may exist there. Finally, the size, shape, and orientation of the inferred motor units align with electrophysiological evidence, supporting the validity of our motor unit inferences.

      (7) Some figures might be better suited for the supplement. For instance, it's not clear what the significance of Figure 5 is (it's not currently sufficiently justified in the text).

      We have clarified the purpose of Fig. 5 in both the Results and Discussion sections. In the Results, we now explain that events are separated by amplitude to show that expansion–contraction kinetics can be reliably measured across a full range of chromatophore events, validating the precision of our videographic approach. In the Discussion, we highlight that this precision allows measurement of radial muscle speeds and opens avenues to study chromatophore biomechanics, including the contributions of intertwined forces such as radial muscles, elastic pigment sacs, and intercellular coupling.

      (8) Multiple chromatophores can belong to multiple clusters - this study reveals that this is because subsections of a chromatophore are controlled separately. But do the same sections (slices) of chromatophores ever belong to multiple clusters?

      Yes, it is possible. Dubas (1985) used videographic recordings to show that the same chromatophore muscle fibers could be activated by stimulation of different nerve bundles, supporting Florey’s (1969) electrophysiological evidence for polyneuronal excitatory innervation. From Dubas: "Usually, different muscle fibres were recruited by each nerve but sometimes a single muscle fibre responded to stimulation of each nerve. Variations of the stimulus voltage also produced gradation of the amplitude of shortening of individual muscle fibres. This supports the evidence above for multiple innervation of single muscle fibres."

      The petal-like distribution of motor-neuron influence shows overlapping territories, suggesting that some chromatophore sections may be influenced by multiple neurons. However, this overlap could arise from polyinnervation of individual muscles, the presence of gap junctions between muscles, or passive mechanical coupling due to the elastic properties of the pigment sac.

      The petal-like distribution of motor-neuron influence shows overlapping territories, suggesting that some chromatophore sections may be influenced by multiple neurons. However, this overlap could arise from polyinnervation of individual muscles, the presence of gap junctions between muscles, or passive mechanical coupling due to the elastic properties of the pigment sac.

      With the present approach, it is not possible to disentangle the relative contributions of these mechanisms, which will require targeted physiological or anatomical experiments. For this reason, we adopted a hard clustering approach for individual chromatophore slices.

      (9) All time should be labeled in seconds, not in frames, and all distances should be measured in um or mm, not in pixels.

      We chose to present figures in pixels and frames to reflect the native units of our recordings and analyses, which preserves fidelity and reproducibility of the computational pipeline. For biological interpretation, corresponding values are converted to µm in the main text, providing the relevant real-world scale. A scale for conversion is provided in the figure legend.

      Specific comments:

      (1) L36: I'm not sure the description of virtual chromatophores here is clear enough to make sense to a more general audience.

      Addressed. We retained the concept of ‘virtual chromatophores’ in the abstract and added a brief clarifying phrase to indicate that these are functional groupings of adjacent chromatophore territories that act as single units.

      (2) L50: "Rimmed by" - consider rephrasing.

      Addressed. Replaced with “surrounded”.

      (3) L64: "refs" - actual references aren't inserted. There are multiple other examples of this.

      Addressed. Added missing references.

      (4) L100: This section could use rewriting. Some of the text reads more like a figure legend.

      Addressed. We have streamlined the main text to reduce redundancy with the figure legend.

      (5) L101: Consider the opening sentence/s providing a more general introduction to the question and approach.

      Addressed.

      (6) L104: This implies that the data presented are from 14 animals of many ages. This is only relevant if the pooled data is analyzed and presented.

      We agree that the original phrasing was ambiguous. We have modified the sentence for clarity, and explain in the Methods that 14 animals were filmed to refine the pipeline and explore experimental conditions, while the analyses shown are from a single animal.

      (7) L111: HDBSCAN should be defined.

      Addressed. The acronym has been expanded.

      (8) L173: Figure 6D doesn't exist.

      Addressed. Reference to the inexistent 6d figure was removed.

      (9) L193: "excluding negative (contraction) phases" This phrase requires clarification.

      Addressed. Added “see Methods” in the legend and added clarification on the reasoning in Methods.

      (10) L204: Should explain why the switch to affinity-propagation clustering was made when a different method was used for E. berryi.

      Addressed in discussion.

      (11) Figure 3: I recommend including a diagram or image of a whole cuttlefish and showing what the corresponding imaging area was in relation to the animal so the reader gets an intuitive sense of scale.

      Thank you. We have added a supplementary figure to give the reader a sense of scale.

      (12) L221/Fig 3b: These colors are supposed to represent clusters of 3 to 5 chromatophores? The clusters look much bigger.

      The figure shows clusters of 3 to 5 chromatophores, but many adjacent clusters were assigned the same color. We have changed the colors to remove this ambiguity.

      (13) Figure 3c: This would be more powerful if it represented the combined data of many experiments to draw a general conclusion. Also, shouldn't these cluster sizes match those in 2e, e.g. they get as big as 40?

      We assume the reviewer is referring to a comparison between Figures 3c and 2e. For visualization purposes, the graph in 3c was truncated to display over 90% of the data, which explains why the largest clusters appear smaller than in 2e. We modified the legend accordingly. We agree that the results would be strengthened by pooling data from additional experiments; however, acquiring high-quality, artifact-free recordings suitable for motor unit analysis is extremely challenging. We hope that our framework will enable future studies to extend this analysis.

      (14) Figure 4: I would show some of these examples earlier, to give the reader an intuitive sense of the data and claims (though it doesn't need its own figure - provide a couple of examples, and the diagram of how much of the mantle you're sampling) then put the rest in the supplement, and include some videos too.

      We agree that providing spatial context is important for readers to develop an intuitive understanding of the dataset. However, introducing examples of motor units earlier in the manuscript would, in our view, interrupt the logical progression of the Results, where motor unit identification builds on prior analyses. To address the reviewer’s concern, we have added a new supplementary figure (Fig. S1) illustrating the size and location of the sampled mantle region. In addition, we now provide representative videos in the Data Availability section to give readers direct visual access to the underlying dynamics.

      (15) Figure 4f: Is the location of the split color in each dot accurate? It's surprising that each one is split down the middle, and the pink side is always on the right - this is unintuitive given where the motor neuron is likely to be located.

      The dots and half dots represent the membership of a chromatophore to a particular cluster.

      (16) Figure 5: I didn't find this figure sufficiently justified in the text. I would move this to the supplement.

      Addressed in General point #7.

      (17) L350: States that 12 animals were patched, but the data isn't shown. It's important to show all of this data (some of which can be in the supplement).

      Addressed. We provided the data in the Data Availability Section.

      (18) Figure 5: I would quantify how many chromatophores were in each motor group across all the recording sessions, and compare this to the equivalent behavioral analysis.

      We assume the reviewer means Fig. 6. We calculated and stated the size of motor units across patching sessions.

      (19) Figure 5c: I recommend labeling each panel with a different number so you can refer to specific data.

      We assume the reviewer means Fig. 6c. We consider the figure layout clear enough to allow readers to follow the data without additional panel numbers.

      (20) L379: Typo: repeat of "quantitative"

      Addressed.

      (21) L576: Salinity should be 33-36 ppt, not %

      Addressed.

      (22) L877: The salinity units are sg? That should be stated. Though I would use the same units for salinity throughout.

      Addressed.

      Overall, this work introduces a potentially valuable quantitative framework for studying chromatophore dynamics. Addressing the points above would substantially strengthen the manuscript and clarify the scope and support for its conclusions.

      We thank the reviewer for these many helpful comments.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 64 - missing references for chromatophore colour with age.

      Addressed. Added missing refs.

      (2) Line 64-65 - would be good to have a little more detail about what is meant by 'migrating through the skin'. Is this a lateral process, or depth in the skin?

      Addressed. Changed “migrating in the thickness..” with “through the thickness..” to emphasize verticality.

      (3) Line 72 - typo, should read '...individual and groups...'

      Addressed.

      (4) Remove 'In Fig 1, ...' from line 104.

      Addressed.

      (5) Figure 1 - It's unclear why some chromatophores are uncoloured with a red dot in the centre. Are these chromatophores that do not share a cluster with neighbours? If so, wouldn't it make more sense to colour the chromatophore with a unique colour of its own? Or, at the very least, make a note in the caption to indicate that all white chromatophores are not clustered with neighbours.

      Segmented chromatophores are shown in white, with coloured slices highlighting cluster membership. Uncoloured slices represent outliers. Addressed in the figure legend.

      (6) Line 119 - the concept of a 'closed virtual chromatophore' needs a few more words of explanation. The way I interpret the text as it is, is that the motor units driving colour change are not necessarily the individual chromatophores, but a motor region containing a mixture of whole and partial chromatophores innervated by the same motor neuron. If this is the case, a few extra words of description would help here to remove any ambiguity as I think this is an important concept for the paper.

      Addressed. We added a sentence clarifying the concept.

      (7) Line 173 - Figure 6d doesn't exist in the paper. Was a different panel intended? If so, please make sure to number the figures in order of appearance in the manuscript.

      Reference to the inexistent figure 6d was removed.

      (8) Figure 3b is very difficult to see. Perhaps consider lightening the background image. Please also indicate whether the individual colours refer to individual clusters. If this is the case, then some of these clusters look much larger than the 3-5 suggested in the caption.

      This issue has been corrected.

      (9) Line 210 - remove the bold type.

      Addressed.

      (10) Line 211 - please specify which 'two groups' you are referring to here. Presumably, this is anaesthetised and non-anaesthetised.

      Addressed.

      (11) I think that the text is missing any indication of the pixel sizes involved in extracting slice metrics, particularly from the S. officinalis data. It would be great to include some data on how many pixels span the radius of an expanded chromatophore. There is some small indication of this in Figure 2a, but a panel or two with details about the pixel size of S. officinalis chromatophores and their slices would be welcome. This would help with the judgment of the robustness of the resolution of the analysis. Looking at the y-axis in Figure 5a, there is some indication that the chromatophore radius is only 1 to 8 pixels. Is this the case?

      Figure 5a doesn’t show chromatophore radius but instead the relative change in peak amplitude during an expansion event. At that point the chromatophore has likely a larger radius as you sum the baseline radius of the chromatophore + the size of the peak.

      (12) Line 246-7 - reword this sentence to avoid referring to Figure 3d in the narrative. Include it in parentheses instead.

      Addressed.

      (13) Lines 408 and 409 - missing references.

      Addressed.

      (14) Line 576 - salinity should be reported in parts per thousand, not per cent.

      Addressed.

      (15) Line 593 - how were animals <50mm fed?

      Animals smaller than 50 mm were fed Neomysis spp. or small Palaemonetes spp., as noted a few lines above the description for animals larger than 50 mm.

      (16) Line 847 - typo - '...putative motor units' ramifications...'

      Addressed.

      (17) Line 854 - better to write out the [chrom_id, label] info as narrative text rather than using the variable names.

      Addressed.

      (18) Line 876 - two typos '...were reared in an artificial...'

      Addressed.

      (19) Line 877 - please use the same salinity metric as used in the earlier part of the methods.

      Addressed.

      (20) Section 898-910 - equipment details would ideally include the location of the company. E.g. (BX51W1, Olympus, Tokyo, Japan).

      Addressed.

      Reviewer #3 (Recommendations for the authors):

      I am left with a number of questions that arise from the authors' work, some of which the authors themselves briefly mention in the technical limitations section.

      (1) In relation to the first weakness, do the authors know if the recruitment patterns they identify are likely to be the same when octopi perform visually-mediated camouflage to their environment?

      Thank you for this comment. We assume the reviewer is referring to S. officinalis. There seems to be a misunderstanding: our approach is designed to reveal the smallest independent functional units—motor units—that together generate skin patterns. The technique is fully applicable to an animal displaying camouflage, but the results would necessarily differ. Camouflage patterns are composed of relatively large shapes compared to individual motor units and arise from the coordinated activation of multiple units. Disentangling motor units requires decorrelated activity, whereas visually-evoked camouflage inherently drives correlated motor-unit activation by premotor control. To use an analogy, if our goal were to map the distribution and wiring of pixels on a screen, it would be more informative to broadcast a noise signal rather than display coherent images, as the noise produces decorrelated activity that allows the underlying structure to be resolved. We have clarified this important point in the early results section.

      (2) The authors provide indirect evidence that motor neurons innervate multiple chromatophores. Can sets of radial muscles within a chromatophore be innervated by multiple motor neurons? Is there neuroanatomical evidence or experiments that could perhaps shed light on this?

      Addressed above. Same question as #1(8).

      (3) Are multi-innervated chromatophores evenly distributed across the octopus's body? For instance, could the authors compare chromatophore recruitment over multiple patches on the animal from multiple regions?

      At present, we do not have sufficient data to quantitatively compare motor-unit structure or the distribution of multi-innervated chromatophores across different body regions of cuttlefish. However, we would not necessarily expect uniformity across the skin, as distinct body regions are associated with characteristic pattern elements (e.g., the white square on the central mantle or the thicker zebra stripes along the sides). It is therefore plausible that different motor-unit geometries and densities are differentially represented across regions to support these region-specific patterns. Future recordings spanning multiple patches and body locations will be required to test this question directly.

      (4) Relatedly, is there any idea of whether chromatophore size or age corresponds with the number of motor units within a single chromatophore?

      At present, our analyses are limited to single developmental time points, and we therefore cannot directly assess whether chromatophore size or age correlates with the number of motor neurons innervating an individual chromatophore. However, this is a question that our analysis framework is explicitly designed to address. Our custom pipeline, CHROMAS, (Ukrow, Renard et al., 2025) includes tools for longitudinal image alignment that allow chromatophores to be tracked within the same animal across development. Applying these scripts to developmental datasets enables future analyses linking chromatophore growth or age to changes in the motor innervation of single chromatophores.

      I understand that a full resolution to the issues raised above may require substantial additional experiments. At a minimum, further discussion of these points with integration of existing literature would elevate the paper.

    1. Author response:

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

      Reviewer #1 (Public review):

      (1) The rationale behind averaging sentence embeddings across multiple transformer models (with different architectures and training objectives) is unclear. These transformer-based models have different training paradigms and model architectures, which may result in misaligned semantic spaces. The averaging operation may dilute the distinct sentence representations learned by each model, potentially weakening the overall semantic encoding for sentences. Please clarify this choice or cite supporting methodology.

      The reviewer questions the rationale for averaging sentence embeddings across different models. However, our method involves computing correlations separately for each model, then averaging the correlations. We apologize for the confusion. We have clarified this on page 3:

      “Results for the ‘Transformers’ model are computed by computing correlations separately for five different transformer models and then taking a simple average of these correlations. Results for each individual transformer are presented in Supplementary Information Figure S2.”

      (2) All structure-sensitive models discussed incorporate semantics to some extent. Including a purely syntactic baseline, such as a model based on context-free grammar, would help confirm the importance of syntactic structures.

      Following the suggestion, we have implemented two syntactic models and discuss the results on page 10:

      “We also found that purely syntactic models based on constituency parses (see Benepar and CFG) show poor correlations with brain activity (see Supplementary Information Figure S2). Examining the corresponding RSA matrices (see Figure S1), this seems to be due to such models being overly sensitive to syntactic form, and relatively insensitive to which words are assigned to different nodes within the syntactic tree. This is most evident for the edit-distance similarity metric, and to a lesser extent also for the subtree similarity metric. This finding highlights the value of hybrid approaches designed to appropriately balance sensitivity to lexical, syntactic, and compositional information in representing semantic information at the sentence level.”

      (3) In Figure 2, human behavioral judgments show weak correlations with neural data, and even fall below those of computational models, suggesting the behavioral judgments may not reflect the sentence structures in a brain-like way. This discrepancy between behavioral and neural data should be clarified, as it affects the interpretation of the results.

      While the behavioural judgements are made by different participants and involve a different task than the neuroimaging results, nonetheless we agree the difference is surprising and warrants more detailed consideration. We have included a more detailed discussion of this issue on page 11:

      “Our study has several limitations. First, we found a surprisingly low correlation between behavioural ratings and brain activations (see Figure 2). This may be partly explained by differences in task structure. In the behavioural experiment, participants viewed many pairs of related sentences, and were explicitly asked to pay attention to differences in the words of each sentence. In contrast, in the fMRI task, participants read one sentence at a time without an explicit comparison. In addition, we suspect that presentation of so many sentence pairs with highly similar structures may have biased the way in which participants rated sentence similarity. Modifications to the behavioural task to mitigate these aspects may reduce the divergence between behavioural and brain findings.”

      (4) To better contextualize model and neural performance, sentence similarity should be anchored to a notion of semantic "ground truth", such as the matrix shown in Figure 1a. Comparing this reference with human judgments, brain responses, and model similarities would help establish an upper bound.

      While our design matrix served as the basis for constructing a set of stimuli with systematic modifications, we respectfully suggest that it should not be regarded as a ‘semantic ground truth’. Sentence pairs within each category will not have the same degrees of semantic similarity since the words and context differ across sentences in a graded manner. Furthermore, while we anticipated ‘different’ sentence pairs would be less similar than ‘swapped’ sentence pairs, and that within each of the six block diagonals the ‘modified’ or ‘substituted’ sentence pairs would be the most similar, we did not have any prediction about the magnitude of these differences. Our goal was to construct a set of sentence pairs which spanned a range of semantic similarities, and allowed for dissociation between lexical similarity and overall similarity in meaning. The design matrix is not intended to represent a ‘ground truth’ that human judgements or brain representations would be expected to conform with.

      (5) The structure of this paper is confusing. For instance, Figure 5 is cited early but appears much later. Reordering sections and figures would enhance readability.

      We agree that placement of figures was not ideal in the previous draft. We have reworked the manuscript so that all figures appear closer to their mention in the text, and the figure (now Figure 3) appears in the correct order. We have also substantially revised the discussion, and included subheadings to help guide the reader through the various different issues we include.

      (6) While the analysis is broad and comprehensive, it lacks depth in some respects. For instance, it remains unclear what specific insights are gained from comparing across brain regions (e.g., whole brain, language network, and other subregions). Similarly, the results of simple-average and group-average RSA appear quite similar and may not advance the interpretation.

      We included both analyses in line with our preregistration, and also because we believe the fact that two distinct approaches to analyzing the data yield similar results strengthens our conclusions.

      (7) While explaining the grid-like pattern due to sentence length is important, this part feels somewhat disconnected from the central question of this paper (word order). It might be better placed in supplementary material.

      We believe that the grid-like pattern in the RSA results is an important unexpected finding that warrants discussion in the main manuscript.

      Reviewer #1 (Recommendations for the authors):

      (1) Consider including a purely syntactic baseline model. For instance, parse each sentence into a constituency tree and compute tree edit distances between pairs of trees. This would allow you to construct a sentence similarity matrix based solely on syntactic structure, and may clarify the role of syntax in sentence representations.

      See our response to Public Review comment 2.

      (2) Instead of averaging embeddings across different transformer-based models, I recommend reporting RSA results for each model individually. For instance, compare one sentence-level model (e.g., SentBERT or SimCSE) and one general-purpose language model (e.g., GPT-2 or Llama).

      See our response to Public Review comment 1.

      (3) I suggest revisiting the structure of the Results section to improve the clarity and impact of your key findings. Consider which results are most central to the paper's claims and ensure they are presented in the main text. Less central analyses (e.g., the analysis on the grid-like pattern) might be better suited for the supplementary information. Presenting behavioral results prior to neuroimaging results could also improve logical flow by first validating model similarity estimates behaviorally.

      As mentioned in our response to Public Review comment 5, we have revised the ordering of the figures to improve the flow of the main manuscript. We believe that the grid-like pattern in the RSA results is an important unexpected finding that warrants discussion in the main manuscript. In addition, we believe that presenting the neuroimaging results first is appropriate as this is the primary and most important contribution of our study.

      Reviewer #2 (Public review):

      (1) The stimuli are not fully controlled for lexical content across conditions. Residual lexical differences between sentences could still influence both brain and model similarity patterns. To more cleanly isolate syntactic effects, it would be useful to systematically vary only a single structural element while keeping all other lexical content constant (e.g., the boy kicked the ball / the ball kicked the boy). It would be better to engage more with the minimal pair paradigm, which is widely used in large language model probing research.

      The reviewer rightly argues that our stimuli do not fully control for lexical content across conditions, and that a more appropriate paradigm may be to utilise minimal pairs in which only a single variable of interest (such as sentence structure) is modified. We agree that most of our sentence pairs do not constitute minimal pairs; however, this was not our objective. Our study design aimed to synthesise traditional minimal pair approaches with more recent research paradigms using naturalistic stimuli. As such, we selected stimuli which are more complex and contain more variable features than traditional minimal pair studies, but which also are tailored to highlight differences which are of particular theoretical interest.

      Because we are interested in comparing the effects of multiple sentence elements and semantic roles, a systematic pairwise comparison of minimal pairs is not necessarily optimal. Instead, we designed our stimuli to leverage the advantage of fMRI in that we can measure the brain representations corresponding to each sentence, and hence can conduct a full series of pairwise comparisons of sentence representations. We do not claim this approach to be universally superior to a minimal pair approach, but we do believe our novel approach provides additional insights and a new perspective on semantic representation relative to minimal pair studies.

      We have added the following paragraph on pages 9-10 contrasting our approach to previous minimal-pair studies:

      “Another approach that has seen widespread use is the presentation of minimal sentence pairs that differ only in one specified aspect, for example, interchanging subject and object in a sentence (Frankland 2015, Wang 2016, Frankland 2020, Giglio 2024), or altering adjective-noun phrases to influence composition (Graves 2010, Schell 2017, Fyshe 2019, Ciapparelli 2025). Our approach is an extension of these approaches utilising more naturalistic and complex sentences, designed to facilitate comparison of a wider range of structural manipulations (see Table 1). In more completely characterising the representational structure of various computational models in response to different structural contrasts, we can more comprehensively evaluate their adequacy as models of semantic processing in the brain.”

      (2) The comparisons are done across fundamentally different model types, including static embeddings, graph-based parsers, and transformers. The inherent differences in dimensionality and training objectives might make the conclusion drawn from RSA inconclusive. Transformer embeddings typically occupy much higher-dimensional, anisotropic representational spaces, and their similarity structure may reflect richer, more heterogeneous information than models explicitly encoding semantic roles. A lower RSA correlation in this study does not necessarily imply that transformers fail to encode syntactic information; rather, they may represent additional aspects of meaning or context that diverge from the narrow structural contrasts probed here.

      The reviewer notes that low RSA correlations do not necessarily imply that transformers fail to encode syntactic information. We acknowledge this in our discussion (page 10), where we also highlight that our focus is not on whether transformers encode such information, but rather what transformer representations can tell us about how sentence structure is represented in the brain. Our results indicate that transformer embeddings do not have the same geometric properties as brain representations of sentence meaning, at least for certain types of sentences where lexical information is insufficient to determine overall meaning.

      The reviewer also notes that transformer embeddings are highly anisotropic; however, we adjust for this by normalising each feature as discussed on page 14. Finally, the reviewer notes that the transformers we examine differ in architecture and training objectives. This is not critical for our study because we are not seeking to determine which architecture or training objectives are best. Our goal is simply to compare a range of approaches and see which, if any, have similar sentence representations to those formed by the brain. In fact, our results indicate that architecture and training regime make relatively little difference for our stimuli, as shown by the pattern of results for all models in Figure S2.

      (3) The interpretation of the RSA correlation largely depends on the understanding of models. The authors suggest that because hybrid models correlate better than transformers, this implies that transformers are inferior at representing syntax. However, this is not a direct test of syntactic ability. Transformers may encode syntactic information, but it may not be expressed in a way that aligns with the RSA paradigm or the chosen stimuli. RSA does not reveal what the model encodes, and the models might achieve a good correlation for non-syntactic reasons (e.g., length of sentence, orthographic similarity, lexical features).

      The reviewer argues that RSA correlations do not measure the extent to which a model encodes syntactic information. This is very similar to the previous point. We do not claim that our results show that transformers do not encode syntactic information. Rather, our claim is that sentence embeddings derived from transformers have different geometric properties to brain representations, and that brain representations are better described by models explicitly representing key semantic roles. From this we conclude that, at least for the sentences we present, the brain is highly sensitive to semantic roles in a way that transformer representations are not (at least to the same extent). We have clarified this in a modified paragraph on page 11:

      “We emphasise that our results do not show that transformers fail to represent syntactic or semantic role information. Indeed, large language models show clear capabilities of correctly interpreting sentence structure (Chang 2024), and probing studies have found that transformers represent information about syntax and word order (Clark 2019, Manning 2020). This is consistent with our finding that directly prompting GPT-4 to rate sentence similarity yields very high correlations with human judgements (see Supplementary Information Figure S3). Nonetheless, the fact that transformers can encode and utilise structural information to perform linguistic tasks does not mean that they effectively utilise this information to construct a brain-like representation of sentence meaning.”

      We also respectfully disagree with the reviewer’s suggestions that sentence length and orthographic or lexical similarities may drive model correlations with brain activity. As we discuss on page 19, we explicitly control for differences in sentence length when computing correlations. Our process for constructing our sentence set also controls for lexical similarity by generating pairs of sentences with all or mostly the same words but different orderings. We did not explicitly address orthographic similarity, but this will be strongly correlated with lexical similarity.

      Reviewer #2 (Recommendations for the authors):

      (1) Model dimensionality: the interpretability of cosine similarity diminishes as the dimensionality increases, and there are some math tricks to work around it. To make a fair comparison among models with different dimensionalities, it would be better to apply some dimensionality-insensitive distance metrics.

      We thank the reviewer for this suggestion. We repeated all vector-based similarity calculations using the Dimension Insensitive Euclidean Metric (DIEM). As shown in Figure S9, the results are broadly similar, though with overall somewhat lower brain correlations for most transformers compared to cosine similarity.

      (2) Depending on the scope of the current study, if the authors would like to establish whether transformers are inferior to graph-based models in representing syntax, a linear classifier using the model embeddings would be sufficient. I think this would be a more direct assessment of model syntax ability than correlation with brain data.

      As we discuss in our previous responses, our objective in this study was not to assess how well transformers can represent syntax. Rather, the goal was to assess whether internal transformer representations have similar geometric properties to patterns of brain activation. Our results indicate that transformers do represent sentence structure, but in a different manner to the human brain.

      Reviewer #3 (Public review):

      (1) The interpretation of findings is nuanced. Although Transformers underperform as brain models on the critical subsets of controlled sentences, a Transformer outperforms all other models when evaluated on the union of all sentences when both word-level content and structure vary. Transformers also yield equivalent or better models of human behavioral data. Thus, although Transformers have demonstrable flaws as human models, which are pinpointed here, in the general case, (some) Transformers are more human-like than the other models considered.

      The reviewer argues that we overstate some of our conclusions, as several transformers achieve higher brain correlations than the hybrid model when computed over all sentence pairs, as well as on the behavioural data. In response, we first note that our primary interest in this paper is on the block diagonal sentence pairs, as these were specifically designed to interrogate how different models represent sentence structure. The comparison with all sentence pairs is presented for comparison but is not our primary focus on this paper, as also reflected in the pre-registered prediction that our VerbNet-CN hybrid model would show higher brain correlations than transformers over this block diagonal subset.

      Second, we have included a new analysis in the revised manuscript (Figure S9) where we compute brain correlations controlling for the pattern of similarities observed in the primary visual cortex (averaged over participants), as a way to control for visual similarity. This added control substantially reduces the brain correlations of the transformers, such that they all have lower correlations than VerbNet-CN and AMR-smatch even over the set of all sentence pairs. We provide interpretation of this result in the discussion.

      Third, we would like to note one of the disadvantages of transformers as a model of mind or brain representations is that they are largely a ‘black box’ whose workings are poorly understood. One advantage of hybrid models like our simple semantic role model is that they can be much easier to interpret, thereby enabling them to be used to determine which features are most important for brain representations of sentence meaning, and what mechanisms are used to combine individual words into a full sentence. Given their relative simplicity and interpretability, we believe hybrid models have considerable value as scientific tools, even in cases where they achieve comparable correlations to transformers. We have added a short discussion of this issue in the revised manuscript (page 10).

      (2) There may be confounds between the critical sentence structure manipulations and visual representations of sentence stimuli. This is inconvenient because activation in brain regions that process semantics tends to partially correlate with visual cortex representations, and computational models tend to reflect the number of words/tokens/elements in sentences. Although the study commendably controls for confounds associated with sentence length, there could still be residual effects that remain. For instance, the Graph model correlates most strongly with the visual cortex despite these sentence length controls.

      We agree with the reviewer that this is a potential confound. As noted in the previous response, we have implemented a new control analysis in which we directly control for visual similarities as reflected in participant-averaged similarities of primary visual cortex activations in response to all stimuli. These results are shown in Figures S8-S11 in the SI. We show that transformer correlations are reduced much more than graph and hybrid models with this control. Also, we note that the AMR-smatch graph model shows high correlations with other brain regions even after removing correlations with the visual cortex (Figure S10). This indicates that the model represents a range of sentence features, including both superficial visual or length-related features, as well as semantic features that are represented in common with language and other cortical regions.

      (3) Sentence similarity computations are emphasized as the basis for unifying comparative analyses of graph structures and vector data. A strength of this approach is that correlation is not always the ideal similarity metric. However, a weakness is that similarity computations are not unified across models. This has practical consequences here because different similarity metrics applied to the same model produce positive or negative correlations with brain data.

      The reviewer notes that the method for computing similarities differs between the vector-based (mean and transformer) models, and the hybrid and syntax-based models, thereby potentially adding an additional confound to our results. We agree that this is a potential limitation, and our correlations should always be understood as applying to a model paired with a similarity metric. However, we believe that this is mostly unavoidable when comparing different formalisms. In the revised manuscript we have incorporated an entirely new similarity metric for vector-based models (DIEM similarity), as well as an extended discussion of the effect of different similarity metrics for graph and hybrid models.

      Reviewer #3 (Recommendations for the authors):

      (1) Compute separate RSAs on each sentence pair type (especially Swapped), to quantify how each sentence type manipulation contributed to the divergence between model and brain. Although the manuscript is already brimming with analyses, I think squeezing this in would be helpful because the results currently rely on qualitative inspection of group-average scatter plots to interpret how sentence pair manipulations contributed to the divergence between Transformers and humans. The Swapped condition would appear to be the centrepiece of the title and manuscript, and potentially the only condition for which confounds associated with the surface form of sentence are controlled for (because sentences should be the same words in different orders). Thus, this analysis might see to the inconvenient visual cortex correlations in Figures 3d/e.

      We respectfully disagree that computing separate RSA for each sentence pair type would be a useful additional analysis. The motivation for the construction of our stimulus set was to provide a range of variants of a given base sentence that alter the semantic meaning and lexical content (somewhat) independently. The purpose of the ‘modified’ sentences, for instance, is to construct sentences with a similar overall meaning but lower lexical similarity due to the inclusion of many modifier words. It is precisely the comparisons across the different pair types that provide information about how each model represents sentence semantics, so restricting an analysis to only a single subset would not be very informative. Another problem with this approach is that it would dramatically reduce the number of sentence pairs analysed, thereby decreasing statistical power. In the revised manuscript we have provided additional details regarding the motivation and rationale for how our stimulus set of 108 sentences was constructed, which should help to elucidate this point more clearly. The following excerpt is from page 3:

      “Within each of the six subsets, we begin with a base sentence such as `the cameraman brought the equipment to the director', which we then systematically modified in various ways to create different combinations of lexical and compositional similarity, in order to dissociate these two aspects of meaning (see Table 1 for further details).”

      (2) Explaining the motivation for the sentence stimulus types. I appreciated the careful design of the dataset, but I couldn't immediately work out the motivation for all the different sentence types, and why this selection was ideal to identify divergences with Transformers. For instance, given the goal of (approximately) controlling for lexical similarity whilst varying sentence meaning, I couldn't immediately see why stimulus blocks weren't all built from rearranging the same content words (as in the Swapped condition). The negative RSA correlation with the Mean model also made me stop and think - it seems like the more similar the words in a sentence, the more different their structure, and vice versa, but I wasn't clear that this was a design feature. Thus, a few extra words motivating the conditions could be helpful for the reader, and these might helpfully lead them to anticipate the negative RSA correlation.

      As noted in the previous response, in the revised manuscript we have expanded our explanation of the rationale for the construction of our 108 sentences. In particular, Table 1 in the methods section now includes two additional columns which summarise the intended combinations of lexical and overall sentence similarity which our sentence pairs are intended to satisfy.

      (3) Explanation for why different implementations and similarity computations between variants of ostensibly equivalent Graph / Hybrid models yielded widely divergent positive vs negative brain correlations, despite both positively capturing behavioural ratings. This might incorporate a brief intuitive explanation of how Graph model similarities were computed (e.g., what SMATCH and WWLK do). In light of the above, why do different similarity algorithms applied to the Graph model yield positive and negative correlations on the same brain (e.g., Figure S2 - Graph / Graph-WL a,b, diag-pairs). Same goes for why Hybrid and Hybrid-AMR yielded positive vs negative correlations (e.g., Figure S2 - Graph / Graph-WL a,b, diag-pairs). Acknowledge that the brain results are sensitive to similarity computations in the Discussion.

      We appreciate this suggestion. We have added an extended consideration of these issues to the discussion (pages 10-11), as well as some additional details regarding the differences between the Smatch and WWLK metrics in the methods section (page 17).

      (4) Acknowledgement and explanation of why the human similarity ratings were poor at explaining brain data in Figure 2a,b (right column diag-pairs). The poor behaviour vs brain match is indirectly implied in the Discussion as "the comparison between behavioural and fMRI data is somewhat difficult owing to the difference in task structure." However, I would suggest being upfront and explicitly mentioning and explaining the poor brain match in Figures 2a and b, because the reader will notice and wonder - especially because the models correlate strongly with the behavioural data without the models doing the human behavioral task (though this could be a possibility, see later).’

      As suggested, we have included a passing reference to this in the presentation of our main results in page 5, and a lengthier discussion on page 11:

      “Our study has several limitations. First, we found a surprisingly low correlation between behavioural ratings and brain activations (see Figure 2). This may be partly explained by differences in task structure. In the behavioural experiment, participants viewed many pairs of related sentences, and were explicitly asked to pay attention to differences in the words of each sentence. In contrast, in the fMRI task participants (who were not the same as the behavioural task participants) read one sentence at a time without an explicit comparison. In addition, we suspect that presentation of so many sentence pairs with highly similar structures may have biased the way in which participants rated sentence similarity. Modifications to the behavioural task to mitigate these aspects may reduce the divergence between behavioural and brain findings.”

      (5) Brief explanation of why model vs brain correlations tended to be strongest in the visual cortex (Figure 3d,e). Currently, this issue is only mentioned in passing, however, it seems worthy of further comment.

      We appreciate the reviewer for highlighting this issue. We have added discussion of the potential for visual confounds to several points in the revised manuscript, including the ‘Neuroscience of semantics’ subsection on page 11. As noted, we have also added a new analysis in which we compute correlations controlling for the average RSA similarities of the primary visual cortex. We find that this additional control significantly reduces correlations for most transformer models, but only has a more modest reduction on the correlations for most of the graph and hybrid models, particularly VerbNet-CN (see Figures S8-S11).

      (6) Softening/clarifying some statements that could be misconstrued as suggesting Transformers were universally inferior models. Statements made in the Abstract/Discussion initially came over to me as implying that Transformers were universally inferior models when compared to the Graph/Hybrid models - but this appears only to be true when one looks at analyses conducted within block diagonal sentence subsets. Otherwise, when analyses are conducted on all sentences (between and within blocks, Figure 5) Llama 3 L2 provides by far the strongest brain model. Transformers also appear to yield the strongest accounts of the behavioural data, whether tested on block diagonal or all sentence pairs (Figure S3). To remedy this, I would suggest softening some statements in the Abstract/Discussion that could be misconstrued as suggesting that Transformers were universally inferior. I would also suggest explicitly acknowledging that when the entire dataset was analyzed, Transformers were most accurate, and that (some) Transformers best accounted for the behavioural data.

      We agree that there was some lack of precision in certain sections of the previous draft regarding the conclusions to be drawn regarding the representational capacities of transformers. We have revised the abstract and conclusion to better reflect our intended message, which is that transformers certainly can represent sentence structure and semantic roles, but that the way in which they do this (through vector representations in their hidden layers) is significantly different to how such features are represented in the human brain. In particular, we have included this new text on page 10:

      “We emphasise that our results do not show that transformers fail to represent syntactic or semantic role information. Indeed, large language models show clear capabilities of correctly interpreting sentence structure, and probing studies have found that transformers represent information about syntax and word order. This is consistent with our finding that directly prompting GPT-4 to rate sentence similarity yields very high correlations with human judgements (see Figure S3). Nonetheless, the fact that transformers can encode and utilise structural information to perform linguistic tasks does not mean that they effectively utilise this information to construct a brain-like representation of sentence meaning.

      (7) Given that GPT-4 was already deployed to parse semantic roles for the hybrid model, and GPT-4 should be able to generate reasonable similarity ratings between sentence pairs, it struck me that an interesting addendum could be to use GPT-4 similarities derived from the human behavioral task to interpret both brain and human behavioral data. This might also help support the case for conducting analyses within a similarity-based framework.

      We appreciate this suggestion. We have added this model (GPT-4 ratings of sentence similarity) to the revised manuscript (see Figures S1-S3).

      Other changes

      As noted by reviewer 3, the full set of sentence pairs was missing from the previous draft. They have been added to the SI of the revised manuscript.

      We have renamed the Graph and Hybrid models in the manuscript to AMR-Smatch and Verbnet-CN respectively, for greater clarity as to which models these terms refer to, and also to better differentiate from the newly added constituency parse graph models.

      We have thoroughly revised the discussion section, incorporating feedback from all reviewers regarding areas needing additional depth.

      We have added subsections to the discussion to aid the reader navigating the now lengthier section.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      This rigorous and creative study uses an elegant combination of metabolomics, transcriptomics, and budding yeast molecular genetics to discover that (i) activating AMPK to maintain mitochondrial respiration fueled by cytosolic Acetyl CoA and (ii) increasing fatty acid synthesis independent of respiration drive independent pathways that increase the fitness of replicatively-aged budding yeast cells, albeit without increasing their lifespan. This work will be of interest to scientists in the field of aging and metabolism. Some clarifications in the text would address the following concerns, which would increase the impact of the study:

      (1) What does activation of AMPK (via PGDP-Sak1 expression) do to the replicative lifespan? How many bud scars, in general, do the subpopulations that are older - yet have less Tom70 (increased mitochondrial fitness) - have, after the 48 hrs time point that they are examining? How many divisions occurred in this 48hr time period - i.e. is it long enough to have all cells reach the end of their replicative lifespan? This information is important to rule out that a subset of the mutant cells just divided faster and hence had more divisions within 48 hrs (growing faster and living longer are different things). Having identical growth curves doesn't indicate per se that they all divide at the same rate, as there may be a subpopulation that divides faster and a subpopulation that doesn't grow so well.

      Increasing AMPK activity increases replicative lifespan [PMID: 25869125], but given our finding that AMPK activation splits the population, such replicative lifespan assays are hard to interpret. Bud scar counts have a similar issue. Hence we restricted the lifespan and bud scar analyses to wt and A2A which are more homogenous (Figures S2 B and E). A2A cells at 48h have ~25% more bud scars than wt cells. Yes, by 48h most of the cells have lost viability (Figure 2E). The reviewer is correct that you can't properly compare the lifespan curves if the cells divide at different rates, hence our follow-up test of wt at 48h vs A2A at 40h viability after we had confirmed that these timepoints captured cells at equivalent replicative ages (Figure 2D,E). This shows that viability of A2A is slightly lower than wt at matched age, indicating a slightly shorter lifespan.

      (2) A2A cells do not have an extended replicative lifespan (RLS) but show an increase in the "low senescence" population (Figure 2). If the cells are not becoming senescent, why don't they have longer RLS? Not having a longer lifespan seems inconsistent with the statement that "bud scar counting confirmed that A2A cells reach a higher age than wild type", which comes back to how many times the cells can divide in the 48hr timepoint studied and their rate of cell division? Also, the lifespan curve shown is plotted against time, not cell division number, which does not take into account different division times of cells within the population (described above). It would be much more useful to show standard lifespan curves showing cell division numbers per lifespan per cell.

      Our observation that cells can reach the end of life without senescing is consistent with other studies that have studied the life course of individual cells by microscopy [PMID: 31291577, 32675375]. These studies always highlight some proportion of the cells that reach the end of life with no or minimal senescence, though this fraction varies with the experimental system. The question of why cells lose viability without senescing is a complete unknown in the field, but reflects a wider lack of consensus as to why yeast lose viability with replicative age.

      We are wary about making strong statements on lifespan for exactly the reason the reviewer picks out. In liquid culture we can only assess viability over time, and it is clear from the comparison of liquid and solid media lifespans performed by the Gottschling lab [PMID: 19652178] that culture system has a huge effect on lifespan, with cells in classical microdissection-based lifespan assays living far longer than they do in liquid. This of course means that classical microdissection assays are not very useful for A2A so we are left with an unsatisfactory approximation. We have therefore restricted our conclusion on lifespan to simply say that lifespan of A2A cells is not extended which our data in Figures 2D,E,S2B does support (see also answer to Q1), and therefore with the majority of A2A cells showing low senescence marks and high fitness at 48h we can conclude that lifespan and fitness loss must be separable.

      We will note these limitations of lifespan measurements in the manuscript.

      (3) Increased "fitness" of the old cells is implied from the increased size of the colonies that the old cells can make. However, this is a measure of the fitness of the daughters per se, not the old mother cells. Are the old mothers just passing on healthier mitochondria and more lipids to the daughters, such that they can divide more times? If the aged cells have an "increased fitness", why don't they divide more times themselves (i.e. live longer?).

      Yes, colony growth speed is defined by daughter cell replication, and as long as the daughters and subsequent generations divide at the same rate irrespective of whether they come from a young or old mothers then the size of the colony after 24 hours varies based on the time it took the initial mother to produce a daughter. This is what the assay really measures. We note that aged wildtype mothers often do not divide at all in the first 24 hours after being put on an agar plate (hence the tiny reported colony size), even though they do eventually produce a daughter which then forms a colony, whereas A2A cells tend to produce the first daughter rapidly whether young or old. It is known that daughters of aged wildtype mothers also divide slower, which will also contribute to differences in colony size, and this may well result from a lipid and/or mitochondrial contribution, but the primary driver of colony size in 24 hours is the time the mother took to initially divide. We will add this detail to the manuscript.

      As noted above, the mechanistic basis of lifespan is unknown, but although senescence can shorten lifespan, our work and that of others shows that lifespan is still limited in the absence of senescence.

      (4) The statement is made that "these experiments define two classes of aging cells with distinct metabolic needs, coherent with the model of two aging trajectories previously proposed (referencing Nan Hao's work)". However, the big difference here is that in Nan Hao's work, their two aging trajectories influenced the length of lifespan, but that does not appear to be the case here. That distinction should be made clear. Perhaps the authors could also speculate as to why the A2A yeast stops dividing after presumably the same number of cell divisions, even though they have an activated AMPK and activated fatty acid synthesis pathway.

      We will add this distinction. As noted above, we are wary of making strong statements regarding lifespan as the assays we can do in liquid culture are limited. We are therefore similarly wary about speculating about causes for the lack of lifespan difference because in reality all we can do is rule out a big effect. We would love to speculate on why the A2A cells don't have an extended lifespan, but at this point we don't have any good ideas on this point!

      (5) I am a bit confused by the use of the word "senescence" by this lab here and in their previous growth on galactose studies. If yeast don't senesce, which is usually defined as an irreversible arrest of the cell cycle where cells stop dividing, shouldn't the yeast that do not senesce still be dividing and hence have a longer lifespan? Should a different term be used rather than senescence? Such as "fitness late in life". The authors giving their definition of senescence may help reduce this apparent contradiction.

      We completely agree, this is confusing and noted this distinction in the Introduction. Use of the term senescence to mean a loss of fitness late in life in yeast stems from the classical definition of senescence as applied to whole organisms. However, the term senescence as applied to cells has a more specific meaning in terms of the cell cycle as the reviewer notes. As an individual S. cerevisiae is both a cell and an organism, the terminology clashes. However, the marker we largely employ (Tom70-GFP) which in our hands is a very good proxy for fitness was originally defined as marking the senescence entry point (SEP), so overall we feel we can't avoid the term.

      Reviewer #2 (Public review):

      Summary:

      In this study, the authors investigate how cytosolic acetyl-CoA metabolism influences replicative aging in budding yeast. They propose that acetyl-CoA regulates aging through three major pathways: (1) mitochondrial transport to support mitochondrial function, (2) fatty acid synthesis, and (3) global protein acetylation. The data show that AMPK activation promotes mitochondrial import of acetyl-CoA and partially mitigates mitochondrial decline in a subset of aging cells.

      Furthermore, the engineered A2A strain, which enhances mitochondrial acetyl-CoA utilization while relieving inhibition of fatty acid synthesis, increases the proportion of cells exhibiting a "low senescence" phenotype.

      Overall, this is a thoughtful and potentially impactful study that advances our understanding of metab to olic control of aging. Addressing the points below, particularly by refining interpretations and, where feasible, incorporating additional analyses, will further strengthen the manuscript and its conclusions.

      Strengths:

      The study has several notable strengths. It addresses an important question by shifting the focus from lifespan to preservation of late-life fitness, which is highly relevant to aging biology. The work integrates metabolic, genetic, and functional analyses to link cytosolic acetyl-CoA flux with distinct aging outcomes, and the engineering of the A2A strain provides a clear and elegant demonstration of how coordinated pathway modulation can improve cellular fitness.

      Weaknesses:

      (1) While the manuscript focuses on mitochondrial transport and fatty acid synthesis, cytosolic acetyl-CoA is also a key regulator of histone acetylation and chromatin silencing. It would strengthen the study to consider whether acetyl-CoA depletion contributes to improved fitness through enhanced rDNA silencing. Given the well-established role of rDNA instability in yeast aging, additional experiments examining rDNA silencing and stability would be valuable. For example, monitoring rDNA copy number changes (not necessarily ERCs) under AMPK activation, oleic acid supplementation, and in the A2A strain, similar to approaches used in the authors' prior work, would help clarify whether chromatin regulation contributes to the observed phenotypes.

      We have data addressing this point that we will add to the manuscript. In short, we see no difference in gene expression from Sir2-repressed sub-telomeric regions or MAT loci, but the genome-wide gene expression dysregulation associated with age is partially suppressed in PGPD-SAK1. However, A2A does not suppress this further, so it is not critical for the suppression of senescence in A2A though we are following this up. ERC accumulation is higher in A2A at 48h, consistent with the cells being older, meaning that ERCs are unlinked to senescence onset as we have previously reported. There is a strong upregulation of transcripts from Sir2-repressed rDNA intergenic spacers with age in all genotypes, but we attribute this simply to the copy number increase of these regions on ERCs rather than a defect in silencing. We have previously looked for heritable changes in rDNA copy number arising during ageing and found (to our surprise) absolutely nothing, so we don't expect any changes under these conditions.

      (2) The current data do not fully distinguish whether AMPK activation and oleic acid supplementation act on distinct subpopulations of aging cells. An alternative explanation is that oleic acid supplementation enhances mitochondrial function and acts additively with AMPK activation, thereby increasing the fraction of cells in the "low senescence" state. Since this distinction is not central to the main conclusions, I suggest softening the language around subpopulation specificity. Emphasizing instead that the A2A strain coordinately modulates multiple branches of acetyl-CoA metabolism to improve late-life fitness would maintain the strength of the central message without overinterpretation.

      We agree that oleic acid and the lipids produced downstream of Acc1 in A2A may improve late life fitness via enhanced mitochondrial function, and in support of this Oxygen Consumption Rate is marginally (though significantly) higher in A2A than PGPD-SAK1. We will add this data to the manuscript. However, we disagree with the interpretation of an additive effect as we report throughout the study that AMPK activation and lipid biosynthesis/supplementation affect different sub-populations of cells. We do not observe populations of intermediate senescence cells, rather by flow cytometry and fitness assays we observe individual cells in binary low senescence or high senescence states.

      (3) The manuscript proposes that lipid starvation and excess acetyl-CoA are major drivers of senescence in distinct subpopulations of wild-type aging cells. This conclusion is not yet fully supported by the presented data. Direct measurements of age-dependent divergence in acetyl-CoA and fatty acid levels at the single-cell level would be needed to substantiate this model. Based on the current evidence, a more conservative interpretation would be that aging cells exhibit differential sensitivity to perturbations in acetyl-CoA and lipid metabolism. Accordingly, I recommend revising the statement in the Abstract ("We further implicate lipid starvation and excess acetyl coenzyme A availability as major drivers of senescence...") and the corresponding discussion text to better align with the data.

      We agree and will adjust the abstract to make it clearer that the lipid starvation / excess acetyl coA interpretation is a model.

      Reviewer #3 (Public review):

      Summary:

      These findings suggest that PGPD-SAK1 yeast show a subpopulation with lowered TOM70-GFP expression in high bud scar staining aged cells. Deletion of CAT2 or MLS1 reduces this effect. A PGPD-SAK1 acc1S1157A double mutant (called "A2A" here) shows an even larger effect of lowered tom70 expression in high bud scar staining aged cells. Utilization of various additional mutants involved in acetyl-CoA transport, carnitine shuttle, respiration, etc., leads the authors to conclude that these shifts in TOM70-GFP in aged cells are linked to the AMPK-fatty acid metabolic regulatory system.

      Strengths:

      These extensive and clearly described experiments reveal interesting changes in TOM70-GFP intensity in subsets of aged yeast in several mutants eventually identified as linked to the AMPK-fatty acid metabolic regulatory system.

      Weaknesses:

      (1) 3 biological replicates for mRNASeq is low.

      Thank you for pointing this out. We performed another replicate after posting the initial preprint but didn’t update the figure in the eLIFe-reviewed version. We will add this to the scatter plots and analysis in Figure 1, the findings have not changed.

      (2) While "Traditional conceptions of ageing implicate a progressive accumulation of damage leading to systemic degradation in performance until death, with evolutionary pressures acting to maximise early life fitness and fecundity at the expense of ageing health." is tangential perhaps to the data and conclusions of the study, both claims of this sentence are at best controversial, and the manuscript is no weaker for their omission.

      We actually feel that this sentence is very important to the message of the manuscript, which is that ageing does not necessarily have to involve a loss of fitness before death. Ageing is often described as the progressive wearing out of components leading to decline and death (with an old car often used as an analogy); in the ageing field this is certainly controversial, but outside the field this remains the normal understanding. We think it is important to state this widely held viewpoint with which our findings are hard to reconcile.

      Our interpretation that yeast are bet-hedging as a population growth strategy and this drives ageing in the long term is a classic antagonistic pleiotropy - we will add this term (from the citation that is already in the manuscript) and clarify in the discussion to make it obvious why we are introducing this concept in the introduction.

      (3) The statement that "Here, we determine the basis of senescence and fitness loss in replicatively ageing yeast" is a bit strong as a summary of the present careful work presented here. If the authors had created yeast mutants that retained fitness indefinitely, this would be a more appropriate strength of claim to summarize the work.

      Indeed - we will refine this sentence.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this work the authors investigate the molecular dynamics of MinD, a component of the Bacillus subtilis Min system, in vitro and in vivo. In Escherichia coli the Min system is highly dynamic and displays rapid pole to pole oscillation whereby a time average minimum of the Min proteins at mid cell is established. However, in B. subtilis, this is not the case, and there is no MinE present. MinD in B. subtilis dynamically relocalizes from the poles to division sites, and binds to MinC and MinJ, which mediates its interaction with DivIVA. This paper reports biochemical characterization of B. subtilis MinD in vitro and dynamics of MinD variants in vivo, providing mechanistic insight into the mechanism of dynamic localization.

      Strengths:

      In the current study, the authors perform a detailed biochemical characterization of the in vitro ATPase activity of MinD and demonstrate that rapid hydrolysis is elicited by adding phospholipids. They further show using a collection of substitution mutants of MinD that both monomers and dimers bind to the membrane, and ATP occupancy changes the on and off rates. Identification, quantification, and tracking of discrete Halo-MinD populations was nicely done and showed that mutations in MinD alter dynamic localization, correlating with PL binding on and off rates in vitro.

      In the revised manuscript, the authors now demonstrate localization and tracking data for minC and minJ deletion strains, which suggest that MinJ impacts MinD membrane cycling, but MinC does not. Additional in vitro work showed that the PDZ domain of MinJ modifies MinD ATP hydrolysis rates, and the authors propose that MinJ may promote MinD dimer formation.

      Weaknesses of the revised version: No major weaknesses.

      We thank this reviewer for the positive evaluation of our manuscript and the precise summary of our findings.

      Reviewer #2 (Public review):

      Summary:

      Feddersen & Bramkamp determined important characteristics of how MinD protein binds/dissociates to/from the membrane, and dimerizes in relation to its ATPase activity. The presented data clearly shows the differences in function of MinD homologs from B. subtilis and E. coli.

      Strengths:

      The work presents well-executed experiments that lead to interesting conclusions and a new model of how Min system works during B. subtilis mid-cell division. Importantly, this model is supported by in vitro characterization of well-chosen mutants in the functional domains of MinD. Outstandingly, most of the in vitro data are confirmed by single-molecule localization microscopy.

      Weaknesses:

      The authors immobilized liposomes, for which they used E. coli total lipids, to measure ATPase activity and liposome association and dissociation of B. subtilis MinD. For these experiments would be more suitable to use B. subtilis total lipids as more biologically relevant data could be gained.

      Although the work is in detail and nicely compares the function of B. subtilis Min system with E. coli Min system, it lacks the comparison of the Min system function in other rod-shaped Gram-positive bacteria. I would suggest including in the Discussion the complexity of other Min systems. Especially, this complexity is seen in other rod-shaped and spore formers such as Clostridial species in which one of these Min systems or both are present, an oscillating E. coli Min system type and more static as in B. subtilis.

      Comments on revisions:

      I'm satisfied with the authors response to my private recommendation points. However, I thought that they would also respond to my points mentioned in Public Review part, weaknesses as shown above and update the revised version accordingly.

      We are very grateful to the reviewer for the positive comments and fully agree with the points raised. Due to the overall length of the manuscript, we initially omitted a discussion of the complexity of the Min system in certain Firmicutes. However, we agree that this aspect should be considered. Accordingly, we have now added a dedicated paragraph to the Discussion section addressing this point.

      We also agree that investigating different lipid compositions, including native membranes from Bacillus subtilis, represents a logical next step to further elucidate the influence of lipids on the MinD activity cycle. However, we consider this to constitute a separate project and therefore beyond the scope of the present study.

      Recommendations for the authors:

      Reviewing Editors:

      Some minor corrections are requested-the addition of a bit more details about the complexity of Min systems in other bacteria in particular to the discussion as suggested by Reviewer 2 would be very much appreciated.

      We thank the editors for their positive assessment and the clear recommendations. We have now added a dedicated paragraph to the Discussion section addressing the complexity of the Min system in Clostridioides.

      Reviewer #1 (Recommendations for the authors):

      The following corrections are requested:

      Abstract - Line 29 - Remove the word "solely" from this statement of the abstract. It would be wise to not be so rigid for a biological system that is only partially characterized and to allow for the possibility that biological factors, including local concentrations and/or other molecules, may yet be discovered to impact MinD activation under certain conditions.

      We agree and have amended the text to avoid a to restrictive statement.

      Line 38 - Remove "do not require any unknown protein component" for the reason stated above. Currently, the experiments recapitulate activation suggesting the membrane binding and release controls dynamics without additional factors. This allows for the possibility that biological factors may yet be shown to impact MinD activation under certain conditions.

      We agree and have change the text.

      Discussion - Line 526 - Thermus thermophilus is misspelt.

      Corrected.

    1. Author response:

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

      eLife Assessment

      This study reports a dynamic association/dissociation between malate dehydrogenase (MDH1) and citrate synthase (CIT1) in Saccharomyces cerevisiae under different metabolic conditions that control TCA pathway flux rate. The research question is timely, the use of the NanoBiT split-luciferase system to monitor protein-protein interactions is innovative, and the significance of the findings is valuable. However, the strength of evidence needed to support the conclusions was found to be incomplete based on a lack of critical control and mechanistic experiments.

      We thank the editor for this thoughtful assessment of our work. We are encouraged that the research question, experimental approach, and overall significance were viewed positively.

      To address the concern regarding the strength of evidence, we have implemented additional controls in the revised manuscript. Specifically, we have repeated all MDH1CIT1 interaction measurements alongside strains expressing full-length NanoLUC fusion proteins to assess MDH1 and CIT1 protein abundance. The resulting data, now included as supplementary figures (Figure 2 – figure supplement 2, Figure 2 – figure supplement 3, Figure 3 – figure supplement 1, Figure 4 – figure supplement 2), demonstrate the reproducibility of the findings and indicate that the observed changes in MDH1-CIT1 interaction are not attributable to protein abundance variations.

      We agree that a detailed mechanistic dissection of how the MDH1–CIT1 complex influences metabolic pathway flux is an essential piece of evidence for establishing the functions of the metabolon. However, such analyses require extensive additional investigation beyond the scope of the present study. Accordingly, we have clarified the aims of this work in the revised manuscript to emphasize that our primary objective is to characterize the dynamic behavior of the MDH1–CIT1 interaction under different metabolic conditions and to identify key factors associated with its regulation.

      We believe these revisions strengthen the rigor of the study, better define its scope, and provide a solid foundation for future mechanistic investigations.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study by the Obata group characterizes the dynamics of the canonical malate dehydrogenase-citrate synthase metabolon in yeast.

      Strengths:

      The study is well-written and appears to give clear demonstrations of this phenomenon.

      Studies of the dynamics of metabolon formation are rare; if the authors can address the concern detailed below, then they have provided such for one of the canonical metabolons in nature.

      We sincerely thank the reviewer for their positive assessment and for recognizing the value of our study in characterizing the dynamics of the MDH1-CIT1 metabolon. We appreciate the recognition that studies of metabolon dynamics are rare and that our work provides a clear demonstration of this phenomenon for a canonical metabolon. We have carefully addressed the methodological concerns regarding the NanoBiT system as detailed below to further strengthen the evidence for our findings.

      Weaknesses:

      There is a fundamental issue with the study, which is that the authors do not provide enough support or information concerning the split luciferase system that they use.

      We agree that a detailed description of the NanoBiT system is essential to ensure the reliability of the methodology. As suggested, we have added a dedicated paragraph to the Introduction (Lines 90–103) to clarify these technical aspects, supported by the foundational work of Dixon et al. (2016).

      Is the binding reversible or not? How the data is interpreted is massively influenced by this fact.

      Yes, the NanoBiT system is specifically designed to be reversible. The intrinsic affinity of the subunits is low (K<sub>D</sub> = 190 μM), and the association and dissociation rate constants (k<sub>on</sub> = 500 M<sup>-1</sup>s <sup>-1</sup>, k<sub>off</sub> = 0.2 s<sup>-1</sup>) are well outside the range of typical protein-protein interactions (Dixon et al., 2016). These kinetics ensure that the assembly and disassembly of the luminescent complex are dictated solely by the interaction characteristics of the target proteins (MDH1 and CIT1) and not by the tags themselves. This allows for real-time monitoring of both the association and dissociation phases.

      What are the pros and cons of this method in comparison to, for example, FLIM-FRET?

      We have now explicitly addressed the pros and cons of our methodology compared to fluorescence-based systems:

      Pros: The NanoLUC-based reporter is 150 times brighter than conventional luciferases and has a significantly higher dynamic range (Hall et al 2016), allowing detection of weak transient interactions. Importantly for this study, fluorescence-based methods such as FLIM-FRET and BRET are difficult to implement in yeast microplate assays due to the high levels of cellular autofluorescence. NanoBiT bypasses this issue, providing a high signal-tonoise ratio.

      Cons: Unlike FRET, NanoBiT requires the application of a substrate (furimazine). We did not include this disadvantage in the manuscript because it is not critical in a yeast study. Furimazine can be applied directly to the medium and readily permeates cells.

      The authors state that the method is semi-quantitative - can they document this?

      The semi-quantitative nature of the system is supported by its high dynamic range and the linear relationship between the luminescence signal and the amount of protein complex formed, as documented in Dixon et al. (2016). By using this system in a microplate setting, we were able to monitor relative increases or decreases in interaction levels over time across multiple metabolic conditions, providing a robust comparative analysis of metabolon dynamics.

      All of the conclusions are based on the quality of this method. I know that it has been used by others, but at least some preliminary documentation to address these questions is required.

      We acknowledge the reviewer’s concern regarding the reliance on the NanoBiT system. To ensure the reliability of our conclusions, we have included several lines of evidence to validate the method and demonstrate that the observed luminescence signals accurately reflect protein-protein interaction dynamics.

      To confirm the NanoBiT results using an independent biochemical approach, we performed an in vivo pull-down assay following glucose addition (Figure 2 – figure supplement 1A). The results demonstrate a reduction in the physical association between MDH1 and CIT1. This biochemical validation directly supports the reduction in interaction observed with the NanoBiT system during the Crabtree effect.

      We have provided protein abundance data for both MDH1 and CIT1 across the experimental conditions (Figure 2 – figure supplement 1&3; Figure 3 – figure supplement 1; Figure 4 – figure supplement 2). These results show only minor changes in protein levels, confirming that the fluctuations in the NanoBiT signal are independent of protein expression and represent genuine changes in metabolon assembly.

      To ensure the findings are reproducible, we have included MDH1-CIT1 interaction results from repeated independent experiments (Figure 2 – figure supplement 1&3; Figure 3 – figure supplement 1; Figure 4 – figure supplement 1). The consistency of the results across these trials confirms the robustness of the system in monitoring the metabolic regulation of this complex.

      We hope that these additional experimental validations, alongside the detailed technical description based on the established properties of the NanoBiT system (Dixon et al., 2016; Hall et al., 2012), provide the necessary documentation to satisfy the reviewer’s concerns regarding the quality and reliability of the method.

      Reviewer #2 (Public review):

      This study explores the dynamic association between malate dehydrogenase (MDH1) and citrate synthase (CIT1) in Saccharomyces cerevisiae, with the aim of linking this interaction to respiratory metabolism. Utilizing a NanoBiT split-luciferase system, the authors monitor protein-protein interactions in vivo under various metabolic conditions.

      Major Concerns:

      (1) NanoBiT Signal May Reflect Protein Abundance Rather Than Interaction Strength

      In Figure 1C, the authors report increased MDH1-CIT1 interaction under respiratory (acetate) conditions and decreased interaction during fermentation (glucose), as indicated by NanoBiT luminescence. However, this signal appears to correlate strongly with the expression levels of MDH1 and CIT1, raising the possibility that the observed luminescence reflects protein abundance rather than specific interaction dynamics. To resolve this, NanoBiT signals should be normalized to the expression levels of both proteins to distinguish between abundance-driven and interaction-driven changes.

      We agree that distinguishing between abundance-driven and interaction-driven changes is vital. To address this, we have included new data showing the relative protein levels of MDH1 and CIT1 across all experimental conditions. The protein levels were assessed using yeast lines expressing these proteins tagged with full-length NanoLUC luciferase (Figure 2 – figure supplement 1&3, Figure 3 - figure supplement 1, Figure 4 – figure supplement 2). Using the luminescence data of these relative protein levels, we have included plots showing normalized interaction index (Figure 2 – figure supplement 1G & 3D,H,L; Figure 3 - figure supplement 1D,H,L P; Figure 4 – figure supplement 1D,H,L). This index was calculated by dividing the NanoBiT interaction signal by the product of the relative abundances of both proteins:

      In this formula, NanoBiT, MDH1, and CIT1 are the relative luminescence levels at each time point. This analysis clarified that the changes in the interaction signal significantly exceeded the fluctuations in protein levels, confirming that the dynamics are interactionspecific and not abundance-driven. To provide the most direct and transparent representation of the experimental measurements, we have chosen to keep the raw RLU data in the main figures and have moved the data related to protein abundance and normalization to figure supplements.

      (2) Lack of Causal Evidence

      The study presents a series of metabolic perturbation experiments (e.g., arsenite, AOA, antimycin A, malonate) and correlates changes in metabolite levels with NanoBiT signals. However, these data are correlative and do not establish a functional role for the MDH1CIT1 interaction in metabolic regulation. To demonstrate causality, the authors should implement approaches to specifically disrupt the MDH1-CIT1 interaction. One strategy could involve using a 15-residue peptide (Pept1) derived from the Pro354-Pro366 region of CIT1, previously shown to mediate the interaction, or introducing the cit1Δ3 (Arg362Glu) mutation, which perturbs binding. Metabolic flux analysis using ^13C-labeled glucose and mitochondrial respiration assays (e.g., Seahorse) could then assess functional consequences.

      We agree with the reviewer that the current dataset correlates metabolon assembly with metabolic states rather than establishing a direct causal proof of its functional role in regulating pathway flux.

      However, the primary objective of this manuscript was to establish the dynamic nature of the MDH1-CIT1 metabolon and to demonstrate the causal relationship between the changes in cellular conditions and metabolon dynamics through in vitro and in vivo assessments. Demonstrating that this canonical multienzyme complex undergoes reversible assembly and disassembly in vivo represents a major advance, as metabolon dynamics is a critical, yet previously unrevealed, factor involved in metabolic regulation. We aimed to define the specific environmental triggers that govern these dynamics, providing the necessary foundation for defining the functions of metabolons.

      We completely agree that establishing causality using interaction-deficient mutants coupled with metabolic flux analysis is another critical experiment to establish the functions of the TCA cycle metabolon. We have, in fact, been conducting these precise metabolic flux analyses on CIT1 mutants with disrupted interaction with MDH1. Because the functional consequences of complex disruption involve wide-reaching metabolic rerouting that requires extensive data presentation and modeling, this work forms a separate, comprehensive follow-up study that is currently in preparation for submission in the near future.

      To address this limitation in the current manuscript, we have carefully reviewed and revised the Abstract, Results, Discussion, and Conclusion sections (Lines 19-22; 205; 322-327; 341-342; 458-466). We have removed any language that may have inadvertently implied direct causality. We now explicitly state that our findings indicate the relationship between metabolon dynamics and respiratory conditions, and we have added a clear statement noting that the direct effects of this assembly on metabolic flux are the focus of our forthcoming studies.

      (3) Absence of Protein Expression Controls Under Perturbation Conditions

      In experiments involving acetate, arsenite, AOA, antimycin A, and malonate, the authors infer changes in MDH1-CIT1 association based solely on NanoBiT signals. However, no accompanying data are provided on MDH1 and CIT1 protein levels under these conditions. This omission weakens the conclusions, as altered expression rather than interaction strength could underlie the observed luminescence changes. Immunoblotting or quantitative proteomics should be used to confirm constant protein expression across conditions.

      In response to your first concern, we have now performed protein expression assessments for all experiments, including the perturbation conditions, such as acetate, arsenite, AOA (Figure 3 – figure supplement 1), antimycin A, cyanide, and malonate (Figure 4 – figure supplement 2). The results demonstrate that the protein levels of MDH1 and CIT1 remain relatively stable throughout these treatments and do not correlate with the large changes observed in the interaction signals. This is also demonstrated by the normalized interaction index, which confirms that the shifts in luminescence are driven by the dynamic assembly and disassembly of the MDH1-CIT1 metabolon rather than changes in protein concentrations.

      Conclusion:

      Although the central question is compelling and the use of NanoBiT in live cells is a strength, the manuscript requires additional experimental rigor. Specifically, normalization of interaction signals, introduction of causative perturbations, and validation of protein expression are essential to substantiate the study's claims.

      We sincerely thank the reviewer for recognizing the value of our central question and the strength of the live-cell NanoBiT system, as well as for your rigorous critique that has strengthened this manuscript. To address the concerns regarding experimental rigor, we have now provided extensive validation of MDH1 and CIT1 protein expression across all experimental conditions using yeast lines tagged with the full-length NanoLUC luciferase. These data demonstrate relatively stable protein expression, allowing us to calculate a normalized interaction index that substantiates that the observed luminescence shifts are driven by dynamic metabolon assembly rather than protein concentration. Regarding causative perturbations, we agree that introducing interaction-deficient mutants coupled with isotopic flux analysis is the critical next step to establish functional consequences. Because defining these pathway-wide rerouting events requires extensive modeling, this work will be reported in a follow-up study currently in preparation. Accordingly, we have carefully revised the manuscript to remove language implying direct causality, explicitly framing metabolon dynamics as an integral factor in metabolic regulation closely related to pathway activity and cellular metabolic states. We believe these new quantitative controls, normalizations, and textual clarifications thoroughly address the need for additional rigor and solidly substantiate our findings.

      Reviewer #3 (Public review):

      Summary:

      Metabolons are multisubunit complexes that promote the physical association of sequential enzymes within a metabolic pathway. Such complexes are proposed to increase metabolic flux and efficiency by channeling reaction intermediates between enzymes. The TCA cycle enzymes malate dehydrogenase (MDH1) and citrate synthase (CIT1) have been linked to metabolon formation, yet the conditions under which these enzymes interact, and whether such interactions are dynamic in response to metabolic cues, remain unclear, particularly in the native cellular context. This study uses a nanoBIT protein-protein interaction assay to map the dynamic behavior of the MDH1-CIT1 interaction in response to multiple metabolic stimuli and challenges in yeast. Beyond mapping these interactions in real time, the authors also performed GC-MS metabolomics to map whole-cell metabolite alterations across experimental conditions. Finally, the authors use microscale thermophoresis to determine components that alter the MDH1-CIT1 interaction in vitro. Collectively, the authors synthesize their collected data into a model in which the MDH1CIT1 metabolon dissociates in conditions of low respiratory flux, and is stimulated during conditions of high respiratory flux. While their data largely support these models, some key exceptions are found that suggest this model is likely oversimplified and will require further work to understand the complexities associated with MDH1-CIT1 interaction dynamics. Nonetheless, the authors put forth an interesting and timely toolkit to begin to understand the interaction kinetics and dynamics of key metabolic enzymes that should serve as a platform to begin disentangling these important yet understudied aspects of metabolic regulation.

      We thank the reviewer for this thoughtful and constructive summary of our work. We appreciate the recognition of the novelty and utility of our experimental approach and the integrated analysis of MDH1–CIT1 interaction dynamics.

      We agree with the reviewer that, although our data largely support a model in which MDH1– CIT1 interaction correlates with respiratory activity, there are conditions that do not fully conform to this simplified framework. In the revised manuscript, we have addressed these apparent inconsistencies by providing detailed interpretations of the counterintuitive observations (e.g., ETC inhibition) and emphasizing that the MDH1–CIT1 interaction is modulated by changes in the mitochondrial matrix microenvironment associated with respiratory activity.

      Furthermore, we have revised the Discussion to highlight that the regulation of the MDH1– CIT1 interaction is likely multifactorial, involving the combined effects of pH, metabolites, and other unknown factors, which together enable fine-tuning of metabolic flux in fluctuating environments. This expanded perspective is now more clarified.

      We agree that identifying the precise molecular determinants of MDH1–CIT1 interaction dynamics will require additional mechanistic studies, such as systematic analyses using yeast mutants. While these experiments are an important next step, they are beyond the scope of the present study. We anticipate that the toolkit and framework established here will facilitate such future investigations.

      Strengths:

      (1) The authors address an important question: how do metabolon-associated proteinprotein interactions change across altered metabolic conditions?

      (2) The development and validation of the MDH1-CIT1 nanoBIT assay provides an important tool to allow the quantification of this protein-protein interaction in vivo. Importantly, the authors demonstrate that the assay allows kinetic and real time assessment of these protein interactions, which reveal interesting and dynamic behavior across conditions.

      (3) The use of classic biochemical techniques to confirm that pH and various metabolites can alter the MDH1-CIT1 interaction in vitro is rigorous and supports the model put forth by the authors.

      We thank the reviewer for these positive and encouraging comments. We are pleased that the importance of the research question, the development of the MDH1–CIT1 NanoBiT assay, and the integration of in vivo and in vitro approaches were recognized. We especially appreciate the acknowledgment of the assay’s ability to capture dynamic and kinetic changes in protein–protein interactions, as well as the support provided by the biochemical analyses. We hope that the experimental framework established in this study will serve as a useful platform for further investigations into metabolon dynamics and metabolic regulation.

      Weaknesses:

      (1) Some of the data collected seem to be merely reported rather than synthesized and interpreted for the reader.

      We agree that explicitly synthesizing these findings is essential for clarity. To improve this, we have revised the Results section to include concise summary statements at the conclusion of each major experimental paragraph (Lines 190-191, 201, 218-219, 229-231, 241-242, 272-274, 282-283; 291-293). These additions interpret the data in relation to our main hypothesis. The discussion section was thoroughly revised to more precisely explain the logic supporting the model (Lines 381-393; 433-443, 458-466). Additionally, to bring together the entire dataset, we introduced a new summary schematic (Figure 6A). This figure visually and conceptually integrates our diverse findings, covering metabolic treatments, pH fluctuations, and complex metabolite profiles, showing how these signals work together to control multienzyme complex assembly.

      This is particularly true for data that seem to reflect more complex trends, such as the GCMS experiments that map metabolites across multiple experiments, or treatments that show somewhat counterintuitive results, such as the antimycin A treatment, which promotes rather than disrupts the MDH1-CIT1 interaction.

      We agree that our complex datasets, including the metabolomics and the seemingly counterintuitive Antimycin A results, required deeper synthesis. To clarify the broader metabolic trends, we have added Figure 6A to visually map which factors, specifically pH, malate, fumarate, and aspartate, most consistently align with complex assembly. We revised the Discussion (Lines 390-393, 439-443) to explicitly conclude that no single variable predominantly governs the interaction, but it is coordinately regulated by multiple microenvironmental cues.

      Regarding the Antimycin A (and other ETC inhibitors) discrepancy, where the interaction is enhanced despite suppressed respiration, we have expanded our interpretation (Lines 346–358) to explain this as a transient response that is not directly reflected by steadystate respiratory activity. Specifically, we propose that acute perturbations of the mitochondrial matrix microenvironment, particularly changes in pH, temporarily promote MDH1–CIT1 interaction. Thus, under these conditions, transient microenvironmental changes can dominate over steady-state respiratory output in regulating metabolon assembly.

      The discussion paragraph about the imperfect relationship between pH and interaction has been revised to highlight our conclusion that mitochondrial matrix pH can be a contributing factor rather than the primary regulator (Lines 386-393).

      (2) Some of the assertions put forth in the manuscript are not substantiated by the data presented, and the authors are at times overly reliant on previous findings from the literature to support their claims. This is particularly notable for claims about "TCA cycle flux"; the authors do not perform flux analysis anywhere in their study and should be cautious when insinuating correlations between their observations and "flux".

      We appreciate the reviewer’s careful evaluation of our terminology and fully agree that claims regarding "flux" should be reserved for studies that employ direct isotopic flux measurements. In response to this constructive feedback, we have thoroughly reviewed the manuscript to ensure that our assertions are substantiated by the presented experimental data. We have carefully evaluated the use of the term "flux" throughout the Abstract, Introduction, and Discussion, replacing it with more accurate phrases such as "pathway activity," "respiratory activity," or "mitochondrial respiration" depending on the specific context (Lines 11; 20-21; 50; 111-112; 322-327; 329; 345; 349-350; 442-443; 458466).

      We also removed a paragraph discussing the potential role of the MDH1-CIT1 metabolon in the malate-aspartate shuttle (Line 361). We realized the paragraph is highly speculative, and our data do not directly support the hypothesis. The influence of the MDH1-CIT1 on the malate-aspartate shuttle is a major finding of the upcoming manuscript reporting its effects in metabolic network flux. We apologize for mixing up the results of two separate studies.

      Furthermore, we have revised our conclusions to avoid over-reliance on prior literature in making causal claims. We now explicitly frame the dynamic assembly of the MDH1-CIT1 metabolon as an integral factor in metabolic regulation, closely related to cellular metabolic states, rather than stating that it controls pathway flux (Lines 454-462). We believe these textual revisions accurately align our claims with our current observations and remove any unsubstantiated assertions.

      (3) The manuscript presentation could be improved. For figures, at times, the axes do not have intuitive labels (example, Figure 1A), data points and details about the number of samples analyzed are missing (bar graphs and box plots), and molecular weight markers are not reported on western blots. The authors refer to the figures out of order in the text, which makes the manuscript challenging to navigate as a reader.

      We thank the reviewer for these helpful suggestions to improve the clarity and presentation of the manuscript. We have made several revisions accordingly.

      First, axis labels have been revised throughout the figures to improve clarity and make them more intuitive. Second, we have added the number of biological replicates to the figure captions and updated bar graphs and box plots to display individual data points. Third, to improve the transparency of the immunoblot data, we have included molecular weight marker position in Figure 1C and corresponding full gel images in a new Figure 1 – figure supplement 2. Other immunoblot images have been moved to Figure 2 – figure supplement 1 since they lack molecular marker images.

      In addition, we have reorganized the figure panel labeling and corresponding text to improve the flow of the Results section. Specifically, figure subpanels are now arranged according to the measured parameters rather than treatment conditions, and the relevant sections describing TCA cycle manipulation and ETC inhibition have been revised to follow this updated figure order (Lines 208–231; 251–274). These changes improve the readability and logical progression of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The grammar in the abstract in the sentence which states called metabolon. This needs to be fixed.

      We thank the reviewer for pointing this out. We have revised the sentence in the Abstract to improve clarity. The revised sentence reads: “The tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase (MDH1) and citrate synthase (CIT1) form a multienzyme complex, referred to as a metabolon, that channels intermediate oxaloacetate between their reaction centers.” (Lines 7-9)

      Reviewer #3 (Recommendations for the authors):

      Major points:

      (1) Much of the data reported in this manuscript reads as a summary of what was found, rather than distilling what the trends in the data mean or how they support the proposed model.

      We thank the reviewer for this comment. This concern overlaps with your previous point (Weakness 1), which we have addressed through revisions to improve synthesis and clarity. Specifically, we have added concise summary statements at the end of each major experimental section (Lines 190-191, 201, 218-219, 229-231, 241-242, 272-274, 282-283; 291-293), and we have included a new summary schematic (Figure 6A) that integrates the findings to illustrate how metabolic conditions and mitochondrial microenvironments relat to MDH1–CIT1 interaction. Together, these revisions improve the interpretation and clarify how the results support our model.

      For instance, in Figure 3, the authors use one metabolic treatment to activate the TCA cycle and two to inhibit the TCA cycle. In Figure 3M, GC-MS data are reported for select metabolites across these three conditions, as well as a control condition. However, these metabolites don't follow clean "trends" according to the predictions; as one example, malate is down in the TCA active (acetate) and one TCA inhibited condition (arsenite), whereas it is elevated in the second TCA inhibited (aminooxyacetate) condition. As an additional example, glutamate is down in the arsenite (inhibited) condition, slightly down in the acetate (activated) condition, but is unchanged in the AOA (inhibited) condition. Similar variability is seen in Figure 4M. What do these discrepancies mean? How do they support the model? As written, these data bring forth more questions than they answer.

      We appreciate the reviewer’s careful analysis of the metabolomics data in Figures 2E, 3M, and 4M. The reviewer notes that the levels of certain metabolites show complex patterns that do not simply reflect overall TCA cycle activity. We have acknowledged that our metabolomics dataset is a valuable resource for the research community and have added a brief paragraph to emphasize the complex metabolic phenotypes resulting from chemical treatments (Lines 422-431).

      As mentioned in the paragraph, this complexity is biologically expected. It is likely from the distinct primary targets of each inhibitor, such as arsenite affecting redox-sensitive enzymes and AOA disrupting the malate-aspartate shuttle, as well as off-target effects and the adaptive reorganization of intersecting metabolic networks to bypass local blockades. Rather than viewing these diverse metabolic phenotypes as discrepancies, we leveraged them to uncouple general respiratory suppression from specific metabolite pools, allowing us to independently assess their relationship with metabolon assembly.

      Furthermore, we note that our GC-MS analysis measures whole-cell metabolite levels, which represent the sum of multiple subcellular compartments and may not precisely reflect localized concentrations within the mitochondrial matrix that is directly affected by the TCA cycle. The description of this limitation of whole-cell metabolomics has been revised in Lines 417-420.

      (2) Why do the authors propose that antimycin A increases the interaction between MDH1 and CIT1 despite decreasing respiratory activity? Given the generalities proposed in Figure 6, this is important to address.

      We thank the reviewer for this comment. This point overlaps with Weakness 1, where we have addressed the apparent discrepancy associated with antimycin A (and other ETC inhibitors). Briefly, we have expanded our interpretation (Lines 349–360) to explain this effect as a transient response that is not directly aligned with steady-state respiratory activity. We propose that acute perturbations of the mitochondrial matrix microenvironment, particularly changes in pH, temporarily promote MDH1–CIT1 interaction. In addition, we have revised the Discussion (Lines 386–404) to clarify that mitochondrial matrix pH acts as a contributing factor rather than the primary regulator of the interaction. Together, these revisions reconcile the ETC inhibition by antimycin A with the overall model presented in Figure 6.

      (3) The authors use acetate to "activate" the TCA cycle; do other non-fermentable carbon sources also promote the MDH1-CIT1 interaction?

      We thank the reviewer for this insightful question. We have tested additional nonfermentable carbon sources and found that they did not significantly affect MDH1–CIT1 interaction (Figure 3—figure supplement 1). We note that raffinose present in the medium likely provides a baseline carbon source supporting oxidative metabolism, which may limit the observable effects of these treatments (Lines 149-150).

      In addition, we performed a new experiment using ethanol. While ethanol treatment enhanced the MDH1–CIT1 interaction signal, it also increased the abundance of MDH1 and CIT1, resulting in a reduced interaction index. Because ethanol induces protein accumulation under our experimental conditions, this result is not straightforward to interpret. We have included this observation and its interpretation in the revised manuscript (Lines 208–211).

      (4) The authors show that the MDH1-CIT1 interaction is sensitive to pH. Is the MDH1-CIT1 interaction affected by uncouplers in vivo?

      We thank the reviewer for suggesting a meaningful experiment. We performed a new experiment examining the effect of the uncoupler CCCP on MDH1–CIT1 interaction in vivo (Figure 4—figure supplement 4). We found that CCCP treatment increased the interaction signal, consistent with the idea that acidification of the mitochondrial matrix promotes MDH1–CIT1 association.

      However, we observe that CCCP treatment also decreased the luciferase signals from MDH1 and CIT1 fused to full-length NanoLUC in an abnormal way, making it harder to interpret the interaction index. Therefore, although these results support a possible role for pH in regulating the interaction, they should be viewed with caution and included as a figure supplement. This experiment and its interpretation have been added to the revised manuscript (Lines 276–283).

      (5) NADH is a potent suppressor of many enzymes within the TCA cycle, including MDH1 and CIT1. Can the authors modulate mitochondrial NADH through genetic manipulation of Ndi1, or through overexpression of mito-Lb-NOX (PMID: 27124460)?

      We thank the reviewer for this insightful suggestion. We agree that the mitochondrial NADH is a potential regulator of the MDH1-CIT1 interaction as it is a potent suppressor of many TCA cycle enzymes, and indeed, we have previously shown that NADH inhibit the MDH-CS interaction in vitro (Omini et al 2021 PMID: 34548590). For this reason, we investigated the mitochondrial matrix redox state that is related to the NADH levels in the current study. The reviewer’s proposed strategy of using targeted genetic tools like mito-Lb-NOX or Ndi1 manipulation to specifically influence the NADH level is an elegant approach to isolate this variable. However, implementing this system requires generating, optimizing, and validating new yeast strains that harbor the targeted NADH-modulating constructs alongside NanoBiT and full-length NanoLUC sensor systems. Because this extensive strain engineering and subsequent live-cell validation fall outside a feasible timeframe for the current manuscript revision, we must respectfully defer these experiments. We view the precise manipulation of the mitochondrial redox state via tools like mito-Lb-NOX as a complementary approach for our future work to systematically pinpoint the individual regulatory factors. We have expanded our Discussion (Lines 417-420; 462-465) to highlight the targeted genetic manipulation of the possible regulatory factors including the NADH pool, as a critical future direction for dissecting these dynamics.

      (6) The authors should correct their figures:

      (a) Axes should be easy to interpret on graphs.

      (b) Individual datapoints should be shown on bar graphs and box plots. Minimally, the number of samples evaluated should be reported.

      (c) Molecular weight markers should be reported on blots.

      We thank the reviewer for these helpful suggestions. Points (a) and (b) overlap with Weakness 3, which we have addressed through revisions to improve figure clarity and data presentation. Specifically, axis labels have been revised to be more intuitive, the number of samples is now reported in the figure captions, and bar and box plots have been updated to include individual data points. For time-course data, we retained point-line plots, as alternative formats (e.g., bar or box plots) would reduce clarity due to the density of time points.

      For point (c), we have added molecular weight markers to the immunoblot data where available (Figure 1C). In the time-course experiment in the original Figure 2, molecular weight markers were absent from the gel images. Although we are confident in the identity of the detected signals, we have moved these data to a figure supplement (Figure 2—figure supplement 1C) to reflect this limitation. Similarly, the corresponding Co-IP data are now presented as a figure supplement (Figure 2—figure supplement 1A).

      Minor points:

      (1) In the last paragraph before the results, the authors refer to "the fluorescent biosensors", but start the paragraph discussing the nanoBIT PPI. After reading the manuscript, these seem to be distinct experimental setups, but that was not evident in the first read through of the paper.

      We thank the reviewer for pointing out this source of confusion. We apologize for the lack of clarity in distinguishing between the experimental approaches. In this study, the NanoBiT system was used to measure MDH1–CIT1 interaction, whereas fluorescent biosensors were used to assess mitochondrial matrix pH, redox state, and ATP levels. We have revised the paragraph to more clearly distinguish these methodologies and their respective roles in the study (Lines 105–112).

      (2) As mentioned above, referring to multiple figures out of order within the manuscript is very jarring for the reader. The authors should consider reworking the narrative or figures to be presented in order.

      We thank the reviewer for this comment. This concern overlaps with the previous comment regarding figure organization, which we have addressed by revising both the figure labeling and the corresponding text. Specifically, figure subpanels have been reorganized to follow the measured parameters rather than treatment conditions, and the Results sections describing TCA cycle manipulation and ETC inhibition have been revised to follow the updated figure order (Lines 208–231; 251–274). These changes improve the logical flow and readability of the manuscript.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      This study investigated how visuospatial attention influences the way people build simplified mental representations to support planning and decision-making. Using computational modeling and virtual maze navigation, the authors examined whether spatial proximity and the spatial arrangement of obstacles determine which elements are included in participants' internal models of a task. The study developed and tested an extension of the value-guided construal (VGC) model that incorporates features of spatial attention for selecting simpler task mental representation.

      Strengths:

      (1) Original Perspective:

      The study introduces an explicit attentional component to established models of planning, offering an approach that bridges perception, attention, and decisionmaking.

      (2) Methodological Approach:

      The combination of computational modeling, behavioral data, and eye-tracking provides converging measures to assess the relationship between attention and planning representations.

      (3) Cross-validated data:

      The study relies on the analysis of three separate datasets, two already published and an additional novel one. This allows for cross-validation of the findings and enhances the robustness of the evidence.

      (4) Focus on Individual Differences:

      Reports of how individual variability in attentional "spillover" correlates with the sparsity of task representations and spatial proximity add depth to the analysis.

      We thank the Reviewer for their overall positive assessment of our work and their helpful comments. We have addressed each point below.

      Weaknesses:

      (1) Clarity of the VGC model and behavioral task:

      The exposition of the VGC model lacks sufficient detail for non-expert readers. It is not clear how this model infers which maze obstacles are relevant or irrelevant for planning, nor how the maze tasks specifically operationalize "planning" versus other cognitive processes.

      The method for classifying obstacles as relevant or irrelevant to the task and connecting metacognitive awareness (i.e., participants' reports of noticing obstacles) to attentional capture is not well justified. The rationale for why awareness serves as a valid attention proxy, as opposed to behavioral or neurophysiological markers, should be clearer.

      We thank the reviewer for urging further clarity here. Our work builds closely on the previous maze navigation paradigm and VGC model developed and reported by Ho et al. Nature (2022). We directly adopted variants of their maze stimuli, computational model and obstacle awareness measures, and married these with an investigation of the role of visuospatial attention. We agree that it would be useful for the reader to have a more in-depth description of the paradigm and model, and how it operationalises planning, without needing to refer back to the original Ho et al. paper. We have now added additional explanatory sections to the Introduction and Methods as follows:

      On page 4:

      “One elegant approach to forming such a simplified representation is to adaptively select the granularity of information required to complete the task (Ho et al., 2022), known as value-guided construal (VGC). Unlike previous accounts, which model human planning as a search over all items (e.g.., tube lines), the VGC model predicts that a cognitively limited decision-maker selects a manageable subset of information over which to plan— i.e., a task representation—balancing utility and complexity (Ho et al., 2022). In our example, the VGC algorithm would plan over a few relevant tube lines rather than planning over all possible stations. To select the representation that achieves the best balance between utility and complexity, the model searches across all possible combinations of tube lines, computing the value (i.e., the plan’s utility minus its cost) of each representation for planning a specific journey. The algorithm then selects the representation with the highest value, which ensures that an ideal observer selects a representation which only includes the items (i.e., tube lines) that lead to successful planning while excluding as many items as possible to keep the plan as simple as possible. For our purposes, items included in the representation are considered taskrelevant, while items that are not represented are considered task-irrelevant. This algorithm, therefore, provides a normative standard of an efficient plan to which we can compare people’s actual plans.”

      On page 6:

      “We operationalized planning using a maze navigation paradigm, akin to our tube-related example, where participants were required to plan a route through the maze, avoiding obstacles that blocked their path. Obstacles predicted by the sVGC model to be included in the representation were considered task-relevant.”

      “At the end of every trial, participants reported their awareness of specific obstacles (see Methods for details). The level of awareness reported for different obstacles provides a read-out of what features of the environment individuals were subjectively representing while solving a particular maze. While other markers of attention and awareness (for instance, behavioural or neurophysiological variables) could also be used, here we focused on direct awareness reports in order to relate our findings both to those of Ho and colleagues and to the subjective awareness reports used in consciousness science (e.g. the Perceptual Awareness Scale (Barnett et al., 2024; Overgaard & Sandberg, 2021; Ramsøy & Overgaard, 2004; Samaha et al., 2015)). Participants were instructed to maintain central fixation while planning (see dataset dSC 1), in line with previous empirical work using this task (Ho et al., 2022).”

      To visualize our effects, we binarized the predictions of the sVGC model such that obstacles with a marginalized probability greater than 0.5 were considered taskrelevant, while other obstacles were considered task-irrelevant (e.g., Figure 2b). We now clarify this point in the caption of Figure 2.

      (2) Attention framework:

      The account of attention is largely limited to the "spotlight" model. When solving a maze, participants trace the correct trail, following it mentally with their overt or covert attention. In this perspective, relevant concepts are also rooted in attention literature pertaining to object-based attention using tasks like curve tracing (e.g., Pooresmaeili & Roelfsema, 2014) and to mental maze solving (e.g., Wong & Scholl, 2024), which may be highly relevant and add nuance to the current work. This view of attention may be more pertinent to the task than models of simultaneously tracking multiple objects cited here. Prior work (notably from the Roelfsema group) indicates that attentional engagement in curve-tracing tasks may be a continuous, bottom-up process that progressively spreads along a trajectory, in time and space, rather than a "spotlight" that simply travels along the path. The spread of attention depends on the spatial proximity to distractors - a point that could also be pertinent to the findings here.

      Moreover, the tracing of a "solution" trail in a maze may be spontaneous and not only a top-down voluntary operation (Wong & Scholl, 2024), a finding that requires a more careful framing of the link to conscious perception discussed in the manuscript.

      Conceptualizing attention as a spatial spotlight may therefore oversimplify its role in navigation and planning. Perhaps the observed attentional modulation reflects a perceptual stage of building the trail in the maze rather than a filter for a later representation for more efficient decision making and planning. A fuller discussion of whether the current model and data can distinguish between these frameworks would benefit readers.

      We thank the reviewer for highlighting relevant findings in the attention literature that were missing from our discussion. We fully agree that a complete account of the interplay of planning, navigation, and attention is likely to recruit the kind of curvetracing processes highlighted by the reviewer. However, we emphasise that our current focus is not on the process of navigation through a maze, but on the process of construing the maze itself. In other words, we are focused not on how people represent their path from A to B, but how they represent the maze itself, which they then use as a basis for planning between A and B. The VGC model predicts that a subset of obstacles will be included in this construal. We think that a spotlight model is a good starting point for this work, because attention is being deployed across the whole maze stimulus, and then becomes attached to particular objects located in particular positions. This is a distinct process from that involved in navigating the path itself. Accordingly, our stimuli were designed such that task-relevant obstacles could be presented either proximally or distally to the optimal path (e.g., Figure 1a and Supplemental Figures S1-6). An obstacle that blocks any possible path on one side of the maze is task-relevant but located a long way from the optimal path. The results of Ho and colleagues’ (2022) third experiment demonstrate how task-relevant yet distal obstacles are better remembered than task-irrelevant proximal obstacles (see Figure 4 of Ho et al., 2022). We also observed that obstacles further away from the navigation path were often represented by participants (see Figures S1-6), which cannot be explained by curve tracing alone.

      While these results cannot definitively rule out the possibility that participants automatically trace the path while also construing the maze, they suggest that the value-guided construal process is an independent predictor of participants’ representations beyond proximity to the navigated path. To make this distinction clearer, we now cite the papers alluded to by the reviewer, in the Discussion on pages 28-29, while also acknowledging the potential for investigating attention during the navigation process itself:

      “Future work may also wish to examine the relevance of visuospatial attention for the navigation process itself in this task. While our present findings speak to how individuals perceive the maze while planning, it remains unclear how attention is deployed during navigation along a path, such as how object-based attention progressively spreads along trajectories in time and space(Pooresmaeili & Roelfsema, 2014; Wong & Scholl, 2024).”

      There is also one additional nuance to the current spotlight model that we were inspired to consider by the reviewer’s comment. This is the idea that attentional effects may spread within or along the obstacles themselves. We cannot explore this in the current data because we asked for awareness of the entire obstacles, not parts of obstacles, but it may be possible to explore this in future work, for instance, with eye tracking measures.

      More generally, the growth-cone (i.e., zoom lens) model of attention for curve tracing proposed by Roelfsema and colleagues shares considerable similarities with the spotlight of attention model. Both models argue for the grouping of spatially proximal items based on attention. While the growth-cone model argues for varying sizes of zoom lenses (i.e., receptive fields of neurons) that facilitate the tracing of proximal items, both models predict that spatially proximal items are preferentially processed together because of attention. Indeed, the spotlight model could model these varying zoom lenses by altering the width of the attentional spotlight dynamically across the visual scene based on the spatial proximity of obstacles. Following related comments by Reviewer 2, we now investigate inter-individual differences in the attentional spotlight of participants and observed that these differences significantly predict participants’ mental representations (see Attentional spotlight model of task representations). We have now updated the Discussion to include consideration of these alternative model frameworks:

      On page 27:

      “Second, in the current work we were unable to distinguish whether these attentional effects are driven by a fixed spotlight of attention, or whether attention operates akin to a zoom lens, shifting the ‘width’ of the focus of attention according to the task demands (Eriksen & St. James, 1986; Müller et al., 2003; Schad & Engbert, 2012). The latter view would be consistent with growth-cone models of attention in which the focus of attention expands and contracts in accordance with task demands, mirroring the various receptive field sizes in the visual hierarchy (Pooresmaeili et al., 2014; Pooresmaeili & Roelfsema, 2014). In partial support of this idea, we found significant inter-individual differences in the width of participants’ attentional spotlight (Figure S11). It is also possible that attention is deployed within or along parts of obstacles, rather than on entire obstacles. Future work using naturalistic measures of eye movements may be able to address these questions.”

      (3) Lateralization of attention:

      The analysis considers whether relevant information is distributed bilaterally or unilaterally across the visual display, but does not sufficiently address evidence for attentional asymmetries across the left and right visual fields due to hemispheric specialization (e.g., Bartolomeo & Seidel Malkinson, 2019). Whether effects differ for left versus right hemifield arrangements is not made explicit in the presented findings.

      We thank the reviewer for this suggestion. To address this point, we fitted a three-way interaction model between VGC model prediction, lateralization index, and side (left vs right hemifield). We did not find evidence for the three-way effect (β= 0.01, SE= 0.02, 95% CI [-0.03, 0.04], p = 0.738; ΔBIC = 58.30 in favour of the null effect; see table below), suggesting that the side to which participants lateralized their attention did not influence their task representations. This result is now reported on page 12:

      “This effect did not vary significantly as a function of the specific hemifield (i.e., left vs right) in which task-relevant information was presented (β= 0.01, SE= 0.02, 95% CI [-0.03, 0.04], p = 0.738; ΔBIC = 58.30 in favour of the null effect; see table S14).”

      We also explored inter-individual differences in participants’ tendency to lateralize their attention (see also the next point). We observed that participants tended to lateralize their attention slightly more to the right-hand side for non-lateralized maze stimuli, despite the normative sVGC model predicting that participants should not lateralize their attention for these stimuli (Figure 3c). These results may speak to potential asymmetries in lateralization, but given the exploratory nature of these analyses, they should be verified and replicated in future work.

      (4) Individual differences:

      Individual differences in attentional modulation are a strength of the work, but similar analyses exploring individual variation in lateralization effects could provide further insight, and the lack of such analyses may mask important effects.

      Thank you for this suggestion. In new analyses, we explored whether i) participants exhibited differences in their tendency to lateralize their awareness reports, and ii) whether the degree to which they tended to lateralize their awareness predicted their performance on a separate set of maze stimuli. In short, we observed substantial variation in participants’ tendency to lateralize their awareness (Figure S11) and found that this tendency reflected an inter-individual difference which was stable across maze types. We report these new findings on pages 14-16.

      “Inter-individual variation in lateralization of attention

      Next, we investigated participants’ tendency to pay attention to obstacles within a single hemifield (left vs right) regardless of the sVGC model predictions. To do so, we computed an awareness lateralization index (ALI) based on participants’ self-reported awareness reports of obstacles on each trial (Figure 3a). Large positive values indicate that participants were preferentially aware of the right hemifield, whereas negative values indicate preferential awareness of the left hemifield. Values close to zero indicate that participants paid attention to both hemifields equally (see Methods for details). We observed that participants’ tendency to lateralize their awareness varied greatly across the Ho datasets 1 and 2 (Figure 3b); some participants preferentially paid attention to a single hemifield, regardless of whether the sVGC model predictions were lateralized. For the dSC1 dataset, we observed that on some trials, participants significantly lateralized their awareness (|ALI| > 0.5; Figure 3c) even though the sVGC model predictions were non-lateralized. These findings suggest that participants’ tendency to pay attention to a single hemifield may represent an observable inter-individual difference in how they allocate their awareness to form task construals.”

      “To further explore these inter-individual differences, we tested whether participants’ tendencies to lateralize their attention to a single hemifield was consistent across trials and maze stimuli. We observed that participants’ tendency to lateralize their attention to a single hemifield was similar for left and right lateralized maze stimuli (Spearman ⍴= 0.72, Figure 3d). This suggests that participants who preferentially attended to a single hemifield did so regardless of which hemifield they should attend to. More consequentially, the tendency for participants to lateralize their awareness on maze stimuli whose model predictions were also lateralized linearly correlated with participants’ tendency to lateralize their attention on non-lateralized maze stimuli (Spearman ⍴= 0.88, Figure 3d). Taken together, these findings emphasize that some individuals tend to preferentially attend to a single hemifield when planning. This tendency, importantly, represents an inter-individual difference in how participants allocate their attention across various maze types.”

      (5) Distinction between overt and covert attention:

      The current report at times equates eye movement patterns with the locus of attention. However, attention can be covertly shifted without corresponding gaze changes (see, for example, Pooresmaeili & Roelfsema, 2014).

      We fully agree, and thank the reviewer for prompting further reflection on this distinction. In the online experiments run by Ho and colleagues (i.e., datasets Ho1 and Ho2), participants’ eye movements were not tracked, and therefore, they could not disambiguate whether participants were engaging in covert or overt attention to sample maze obstacles. In our third experiment (i.e., dataset dSC1), we both recorded eye movements and explicitly instructed participants to fixate centrally while viewing the maze. This ensured that participants oriented their attention only covertly during planning (see Figure S13-14).

      We now elaborate on this important distinction in the Results section of the manuscript, page 12:

      “In addition, we monitored participants’ eye movements in dataset dSC 1 to ensure that attention shifts would be covert as opposed to overt—a distinction which could not be determined in the online samples of datasets Ho 1 and 2.”

      On page 28:

      “Importantly, while the visuospatial attention effects observed in the Ho 1 and 2 datasets are likely driven by both covert and overt shifts in attention, the findings presented in experiment 3 (i.e., dSC1 dataset) rule out the contribution of overt shifts in attention through the use of eye tracking (see Figure S13-14)(Carrasco, 2011; Pooresmaeili & Roelfsema, 2014).”

      The implications for interpreting the relationship between eye movement, memory, and attention in this setting are not fully addressed. The potential dynamics of attention along a maze trajectory and their impact on lateralization analysis would benefit from further clarification.

      We thank the reviewer for urging more clarity here. The attentional dynamics we document in our study concern how people perceive / construe the maze itself, rather than how they deploy their attention to guide active navigation. We have now sought to make this distinction clear at a number of points in the paper. The core idea is that attention acts as an early filter to select which obstacles are part of a task construal, which then affects both awareness and memory.

      We have now clarified the focus of our study in the introduction on pages 5-7:

      “Our focus in this study was to examine how participants perceive and represent their environment (the maze stimulus). This is a distinct process to how participants orient their attention during navigation itself, which is not part of our current study. To do so, we harness classical signatures of attentional selection to characterise how visuospatial attention shapes awareness of maze obstacles during planning.” … “Our focus in the present study was to examine attentional effects on participants’ perception of the maze stimulus. We did not quantify how individuals deploy their attention in the phase in which they were navigating through the maze.”

      We did not explicitly test for memory effects in our new experiments, but Ho and colleagues demonstrated that the sVGC model predicted not only awareness reports, but also participants’ memory of obstacles (see Ho et al., 2022). Indeed, task representations computed from memory or awareness reports were strikingly similar in their experiments (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness). In relation to eye movements, we refer the reviewer back to our previous response, which details how eye movements were measured and controlled during maze construal.

      Figure 1 legend (b) --> (c)

      We have corrected this typo in the figure caption.

      Reviewer #2 (Public review):

      Summary:

      Castanheira et al. investigate the role of spatial attention for planning during three maze navigation experiments (one new experiment and two existing datasets). Effective planning in complex situations requires the construction of simplified representations of the task at hand. The authors find that these mental representations (as assessed by conscious awareness) of a given stimulus are influenced by (spatially) surrounding stimuli. Individual participants varied in the degree to which attention influenced their task representations, and this attentional effect correlated with the sparsity of representations (as measured by the range of awareness reports across all stimuli). Spatially grouping taskrelevant information on either the left or right side of the maze led to mental representations more similar to optimal representations predicted by the valueguided construal (VGC) model - a normative model describing a theoretical approach to simplifying complex task information. Finally, the authors propose an update to this model, incorporating an attentional spotlight component; the revised descriptive model predicts empirical task representations better than the original (normative) VGC model.

      Strengths:

      The novelty of this study lies in the proposal and investigation of a cognitive mechanism through which a normative model like value-guided construal can enable human planning. After proposing attention as this mechanism, the authors make concrete hypotheses about mismatches between the VGC predictions and real human behavior, which are experimentally validated. Thus, not only does this study describe a possible mechanism for simplification of task information for planning, but the authors also propose a descriptive model, revising VGC to incorporate this attentional component.

      A strength of this paper is the variety of investigative approaches: analysis of existing data, novel experiment, and a computational approach to predict experimental findings from a theoretical model. Analyzing pre-existing datasets increases the size of the participant cohort and strengthens the authors' conclusions. Meanwhile, comparing the predictions of the existing normative model and the authors' own refined model is a clever approach to substantiate their claims. In addition, the authors describe several crucial controls, which are key to the interpretability of their results. In particular, the eye tracking results were critical.

      In summary, this paper constitutes an important step toward a more complete understanding of the human ability to plan.

      We thank the Reviewer for their thoughtful and positive assessment of our findings. We also appreciate the constructive feedback on our methodology, which we believe has substantially improved our manuscript.

      Weaknesses:

      (1) There is a critical conceptual gap in the study and its interpretation, mainly due to the reliance on a self-report metric of awareness (rather than an objective measure of behavioral performance).

      a. Awareness is tested by a 9-point self-report scale. It is currently unclear why awareness of task-irrelevant obstacles in this task would necessarily compromise optimal planning. There is no indication of whether self-reported awareness affects performance (e.g., navigation path distance, time to complete the maze, number of errors). Such behavioral evidence of planning would be more compelling.

      We thank the reviewer for prompting further reflection on the connection between construal and navigation performance. We wish to emphasise that the primary focus of our study was on measuring and modeling participants’ task construals using perceptual awareness judgments, building on the methods developed by Ho and colleagues, rather than on navigation performance itself. However, as the reviewer points out, there is a natural relationship between construal and performance – if you represent the wrong obstacles, plans may be disrupted.

      To explore the relationship between task construals and performance on the navigation task we first regressed out the effects of the sVGC model on participants’ awareness reports and computed the mean squared residuals for each trial. We then used these values to predict participants’ navigation response times on each trial. We observed a significant negative relationship, suggesting that on trials where participants’ representations showed greater deviations from the normative model, they were in fact faster at navigating the mazes. This relationship was surprising, and at odds with the initial idea that adhering to normative VGC aids in task performance. However, we think that this direction of effect may make sense if one considers that a large part of the actual construal (rather than the normative prediction) in our data was in fact driven by effects such as lateralisation which are not accounted for by the sVGC model. If one is faster at harnessing inductive biases such as lateralisation, then one may be faster to complete the maze but also show a greater deviation from the predictions of the original model.

      To further explore these effects, we next focused on the distinction between lateralised and non-lateralised mazes. Here, we reasoned that the initial phase of lateralised attentional selection would lead to lateralised mazes being easier to navigate than nonlateralised ones. We conducted new analyses to determine whether participants navigated lateralized maze stimuli faster and with fewer moves than maze stimuli with non-lateralized model predictions. As detailed in Methods, we excluded trials in which participants significantly deviated from the optimal number of moves (9 or more moves) and took longer than 20 seconds to solve the maze. In line with our interpretation that attention operates as an inductive bias, participants were faster and deviated less from the optimal path on lateralized compared to non-lateralized mazes.

      We now report these new results on navigation performance on pages 20-21:

      “Maze navigation performance

      The previous analyses focused on participants’ task representations during planning. We next sought to explore links between participants’ task representations and maze navigation performance. Participants performed the maze navigation task near-ceiling: they solved 95% of maze stimuli in under 20 seconds, with minimal deviation from the optimal path (i.e., 9 moves or fewer). Notwithstanding this limited variance in task performance, we explored whether participants’ task construals may have impacted their navigation speed. To do so, we first regressed out the effects of the sVGC model from participants’ awareness reports and used the mean squared residuals for each trial to predict response times (see Methods for details). Surprisingly, we observed a negative relationship between mean squared residual variance and response times (β = -0.31, SE = 0.05, 95% CI [-0.41, -0.21], p < 0.001), indicating that participants were faster on trials where the sVGC model explained less variance in their awareness reports. In other words, trials in which participants deviated more from the sVGC model predictions were solved faster. We note that one reason for this may be the strong influence of the lateralisation effect on navigation performance (see paragraph below), which itself is not part of the sVGC model prediction.”

      “We then explored whether participant performance differed between lateralised and nonlateralised mazes. Here, we reasoned that the initial phase of lateralised attentional selection would lead to lateralised mazes being easier to navigate than non-lateralised ones. Consistent with this hypothesis, participants were faster (β = -0.04, SE = 5.91*10<sup>3</sup>, 95% CI [-0.06, -0.03], p< 0.001) and followed the optimal path more closely (β = -0.59, SE = 0.09, 95% CI [-0.78, -0.40], p< 0.001) when maze stimuli were more lateralized.”

      And in the Discussion section, on page 23:

      “Mental representations and task performance

      We observed that participants were faster and deviated less from the optimal path on maze stimuli that were lateralized. This effect is not predicted by the original sVGC model but dovetails with the interpretation that early visuospatial attention operates as an inductive bias to guide the formation of simplified task representations. Surprisingly, we also observed that participants were faster to navigate mazes on trials where their simplified task representation deviated from the sVGC model prediction. We interpret this seemingly contradictory finding in the following way: there are several factors beyond the sVGC model – including, for instance, maze lateralisation – that predict both construal and performance on the maze navigation task. Further work is needed to understand how inductive biases such as lateralisation shape both construal and performance, and the real-world benefits that such strategies might afford for naturalistic stimuli.”

      b. Relatedly, it would have been more convincing to have an objective measure of awareness, for instance, how the presence or absence of a "task-irrelevant" obstacle affects performance (e.g., change navigation path distance or time to complete the maze), or whether participants can accurately recall the location of obstacles.

      We thank the reviewer for prompting further reflection on the validity and robustness of our awareness measures. We emphasise however that our focus is not (primarily) on maze navigation performance, but on task construal, which as noted in our previous response may come apart from navigation performance for a variety of reasons. Our primary goal is to measure participants’ subjective awareness of the maze as a marker of their idiosyncratic (conscious) mental representation on each trial. In doing so, we build on a rich tradition of measuring subjective awareness in consciousness and perception science (for instance, work using the Perceptual Awareness Scale, or detection judgments). In this sense, we think our awareness scale (following Ho et al.) represents a valid and straightforward way of assessing our target psychological construct. However, we also agree with the Reviewer that convergent evidence from other measures is always valuable. In Ho and colleagues’ original paper, they developed a variant of the maze task where participants had to recall the location of obstacles, as well as rate their awareness (Exp 3) and a variant in which participants could hover their mouse over hidden obstacles in the maze to reveal their location – an online metric of attentional deployment (Exp 4). These data afforded us the opportunity to validate the awareness reports against an objective measure of recall, as suggested by the Reviewer. In reanalysing these data, we observed that the obstacle awareness and memory/hover measures were strikingly correlated within two independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness). These re-analyses are now reported on page 22 of our manuscript, to highlight the convergent validity of the awareness metric:

      “Finally, we examined the convergent validity of participants’ awareness reports by reanalyzing the memory recall data reported in Ho and colleagues’ experiment(Ho et al., 2022). We reasoned that participants should demonstrate similar task representations regardless of the measure used to probe the construal. In line with this prediction, we observed that the obstacle awareness reports and memory/hover measures were strikingly correlated within three independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness; see Tables S18 and S19).”

      c. Consequently, I'm not sure that we can conclude that the spatial context does impact participants' ability to plan spatial navigation or to "incorporate taskrelevant information into their construal". We know that the spatial context affects subjective (self-reported) awareness, but the authors do not present evidence that spatial context affects behavioral performance.

      Following the line of argument above, we think it’s important to separate out task construal (the simplified representation of the maze, measured by awareness reports), and the impact of this on navigation and other aspects of behaviour. The awareness reports (and other convergent measures) show that task-relevant information (as predicted by the VGC) is incorporated into the construal, a process which is modulated by spatial context. These are the key targets of our modeling. Whether this impacts performance is a distinct question, and one that we now address in our response to point a above.

      d. Another concern that may complicate interpretation is the following: Figure 3c shows improved VGC model predictions (steeper slope) for mazes with greater lateralization. However, there are notable outliers in these plots, where a high lateralization index does not correspond to good model performance. There is currently no discussion/explanation of these cases.

      The Reviewer astutely points out some outliers in our analysis. While on average lateralized maze stimuli are represented more closely to the sVGC model, there are indeed some noticeable outlier mazes. These mazes represent stimuli in which participants tended to lateralize their attention to the ‘wrong hemifield’—e.g., participants were more aware of obstacles in the right hemifield despite sVGC model predicting that obstacles on the left hemifield were task-relevant. We believe this explains the poor sVGC model fits on these trials. We note, however, that on average participants were capable of attending to the correct hemifield without explicit instructions (i.e., 9 out of 12 mazes).

      We have now included a discussion of these outliers in the results section of the paper on page 12:

      “We note that for three maze stimuli whose model predictions were lateralized there was nevertheless a poor fit to the sVGC model (see Figure 2c, right panel). These outliers correspond to maze stimuli where participants, on average, lateralized their attention to the incorrect hemifield (i.e., the opposite hemifield to that predicted by the sVGC model).”

      (2) I noticed an issue with clarity regarding task-relevance. It is currently not fully clear which obstacles are "task irrelevant". Also, the term is used inconsistently, sometimes conflating with "awareness". For example, in the "Attentional spotlight model of task representations" section, the authors state that "taskrelevant information becomes less relevant when surrounded by task-irrelevant information". But they really mean that participants become less aware of those task-relevant obstacles. I assume task-relevance is an objective characteristic related to maze organization, not to a participant's construal. Indeed, the following paragraph provides evidence of model predictions of awareness.

      We apologize for any confusion regarding the terminology of our manuscript. We indeed use the terms task-relevant and task-irrelevant to refer to obstacles that are objectively predicted by the normative sVGC model or the attentional spotlight model to be included in (>0.5) or excluded from (<0.5) task construals, respectively. This designation reflects the predictions from the computational model and does not reflect participants’ reported awareness. We then ran linear hierarchical models to predict participants’ awareness reports from these model predictions. The Reviewer is correct that the task-relevance of obstacles is indeed related to the maze’s organization, and not related to participants’ subjective reports of awareness. We have now clarified this point throughout the manuscript to better emphasize the difference between the model predictions of taskrelevance and participants’ subjective reports.

      On page 17:

      “To achieve this, we computed the predictions of the existing VGC model for each obstacle’s task relevance in a given maze, and averaged these predictions within an attentional spotlight of 3 squares (Figure 4a & S8, see Methods for details). This process yielded novel model predictions, whereby some obstacles which were once predicted as task-irrelevant by the normative sVGC are now predicted as task-relevant by the attentional spotlight model. We depict the effects of this spatial spotlight in Figure 4a: task-irrelevant stimuli (plotted in grey; see middle left obstacle) neighbouring taskrelevant obstacles (plotted in orange) become more task-relevant, whereas taskrelevant information becomes less relevant when surrounded by task-irrelevant information (see bottom right orange obstacle). This deviation in model predictions from the normative sVGC model was used to predict participants’ awareness reports. We hypothesized that this spotlight-VGC model would predict participants’ reports better than the original VGC model, which does not account for spatial attention.”

      (3) The behavioral paradigm has some distinct disadvantages, and the validity of the task is not backed up by behavioral data.

      a. I understand the need for central fixation, but it also makes the task less naturalistic.

      The fixation cross was required on every trial such that participants could maintain central fixation for our eye tracking experiment. While this design is less naturalistic, it allows us to examine the eye movements of participants. Requiring participants to fixate during the ‘planning’ phase of the experiment allowed us to isolate the effects of covert attention from changes in awareness due to overt shifts in attention. In other words, differences in participants’ awareness reports in the 3rd experiment cannot be explained by longer fixation times to specific obstacles.

      b. The task with its top-down grid view does not seem to mimic real human navigation. Though this grid may be similar to mental maps we form for navigation, the sensory stimuli corresponding to possible paths and to spatial context during real-life navigation are very different.

      We agree with the reviewer that while our task is engaging for participants and simple to follow, it does not mimic naturalistic navigation in humans. There is a natural tension in computational / experimental work in cognitive science in wanting to build closely on previous results and paradigms, while ensuring that results can generalise to real-world contexts. Here, our choice of paradigm and measures was closely built on previous papers using this task from Ho and colleagues (2022, 2023). While preparing this response, we learnt that the MIT group had also harnessed this same task to develop a novel dynamic variant of the VGC model (Chen et al., 2026) called the Just in Time model (JIT). The advantage of building on this prior work is that we are able to iteratively refine and expand the VGC approach, and (in our case) bring it into closer contact with work on modeling the deployment of spatial attention in human vision. The top-down aspect of the maze notably facilitated the study of the spatial deployment of attention. We now discuss the novel dynamic variant of the VGC model in our paper on page 27:

      “We close by reflecting on opportunities for further work in this area. First, an important next step is to explore the process by which task representations are formed, and how inductive biases might affect the process of task construal. The sVGC model is a normative model of the optimal task representation. Since it’s construction involves an exhaustive calculation over possible paths, it is not a plausible basis for a model of the psychological process by which participants actually construct task representations. More recently a process model of task construal has been proposed, the Just in Time model (JIT). The hypothesis of the JIT model is that participants’ task representations are built up over time by iteratively simulating possible paths through the maze, affording insight into the construal process (Chen et al., 2026). In future work, it would be of interest to ask whether the attentional effects we observe in our experiments could be meshed with a dynamic JIT account of construal. We speculate that visuospatial attention may operate as an early filter, limiting the space of potential construals based on coarse spatial features of the environment, constraining a dynamic selection of obstacles. Brain imaging techniques with high time resolution, such as M/EEG, may be able to shed further light on how task representations are formed as participants plan.”

      c. Behavioral performance is not reported, so it is unknown whether participants are able to properly complete the task. The task seems pretty difficult to navigate, especially when the obstacles disappear, and in combination with the central fixation.

      Behavioural performance is now reported in response to point 1a above.

      d. There is no discussion of whether/how this navigation task generalizes to other forms of planning.

      We fully agree that an important next step would be to generalise our results on construal to naturalistic forms of planning – for instance, using immersive VR mazes, and or investigating cognitive rather than perceptual construals. We have now added a line to this effect to the Discussion on page 28.

      “An important next step to further our understanding of task representations would be to extend the current paradigm to other forms of planning and more naturalistic tasks, such as navigating immersive virtual reality (VR) environments, planning over cognitive rather than perceptual representations (e.g. planning over an abstract space), or internallyguided planning based on working memory.”

      Reviewer #2 (Recommendations for the authors):

      (1) There are, of course, benefits to simple tasks like the ones described, but it would be interesting to compare the results to a possible experiment in which a top-down grid/map is used for planning, but then task execution is carried out in a simulated environment corresponding to the map. Also, perhaps beyond the scope of the questions addressed in this paper, but I am curious how unexpected obstacles affect representations. For instance, if participants plan based on a topdown map and then begin "real" navigation but encounter an unexpected obstacle that was not indicated on the map, does this modulate representations/awareness of future obstacles (near vs. far)?

      We fully agree that all of these lines of investigation would be super interesting to pursue in future studies, and we have added a line to the discussion to that effect on page 28:

      “An important next step to further our understanding of task representations would be to extend the current paradigm to other forms of planning and more naturalistic tasks, such as navigating immersive virtual reality (VR) environments, planning over cognitive rather than perceptual representations (e.g.. planning over an abstract space), or internallyguided planning based on working memory.”

      (2) Regarding self-reported awareness as a metric, an additional experiment could ask participants to recreate the maze (identify locations of obstacles after they disappear). This would be a more objective measure of awareness.

      Yes indeed, and as described above, this was a metric used by Ho and colleagues in their previous experiment. As we describe in more detail above, the task representations obtained via memory or awareness reports demonstrated striking similarity (⍴ = 0.86).

      (3) What is meant by "all possible orientations of the maze" in this Methods sentence: "For dataset dSC 1, participants solved each of these 24 mazes four times (i.e., all possible orientations of the maze)"?

      We thank the Reviewer for prompting more clarity here. We vertically and horizontally reversed mazes (i.e., left-right flipped) such that participants could not predict the location of the goal or start location. In this way, each maze stimulus had four potential orientations. This resulted in 96 trials of 24 unique mazes. We have clarified this point in the Methods section on page 30:

      Maze stimuli were vertically and horizontally reversed (i.e., left-right flipped) such that participants could not predict the location of the start or goal location. This resulted in four potential orientations of each maze across all 24 mazes, 96 trials in total.

      (4) For lateralization, it was unclear until reading the Methods that the lateralization index was calculated using the VGC-predicted level of taskrelevance. From the main text and Figure 2, I assumed you were just counting the number of task-relevant obstacles on each side, rather than also quantifying relevance. I understood after reading the Methods, but this could be clarified further.

      We agree with the Reviewer that this was not evident from the text. We have now updated the Results section of the manuscript to clarify this point on page 11:

      “To test this hypothesis, we derived a measure of task-relevant lateralization inspired by the attention literature (Ghafari et al., 2024; Keefe & Störmer, 2021; Vollebregt et al., 2015) (Figure 2a). Specifically, we separated maze stimuli across the vertical meridian and computed the ratio of task-relevant information presented on the left versus right side derived from the sVGC model. For example, the maze shown in Figure 2a has twice the amount of task-relevant information presented in the left hemifield than in the right (lat. Index= 1/3). A lateralization index of 0.0 indicates that both hemifields contain equal amounts of task-relevant information (i.e., non-lateralized). The lateralization index was computed using the continuous VGC predictions for each obstacle (see Methods).”

      (5) The explanation in the Methods of how the width of the attentional spotlight was chosen references Figure 1b and Supplementary Figure S2, but it seems that Supplementary Figure S8 explains this more in the caption. Also, I don't see how Figure S2 supports this.

      We apologize for this typo. The explanation of how we selected the width of the attentional spotlight should indeed reference supplemental Figure 15 (previously Figure S8). We have now corrected this and elaborated on this choice in the Methods section on page 35:

      “We fixed the ‘width’ of the attentional spotlight to a distance of 3 squares based on the observation that the two neighbouring obstacles positively predicted the awareness of a probe. We observed that the mean and median distance between neighbouring obstacles of the 2nd rank (i.e., second closest) was 3 squares away for all mazes (Figure S15). We therefore opted to fix the value of the attention spotlight to 3 squares based on these observations. Future work utilizing this model should consider the statistics of their maze stimuli when deciding on the ‘width’ of the attentional spotlight.”

      (6) The attentional spotlight width was assumed to be 3 squares, based on the linear regression predictions of the effect of neighboring obstacles on stimulus awareness. Given the individual differences across participants, it would be interesting to choose a different attentional spotlight size for each participant. Would a participant-specific attentional spotlight width improve the predictions of the spotlight-VGC model?

      The Reviewer highlights a very interesting question: do individuals vary in terms of their attentional spotlight? To test this hypothesis, we first estimated the size of the attentional spotlight for each individual based on lateralized maze stimuli, and then used this to generate personalized attentional spotlight model predictions for each subject based on these values (Figure S11). We restricted this analysis to the dSC1 dataset, where we had substantially more trials (96 in total).

      In brief, we observed that indeed the personalized spotlight model fit participants’ awareness reports better than both a normative sVGC model and a group-level attentional spotlight model. We interpret these findings with some caution as i) a subset of individuals had flat attentional slopes and therefore were excluded from these analyses, and ii) we believe we require additional trials to ensure a robust model fit at the individual level. While our results are encouraging, we hope future investigations into inter-individual differences will extend these findings.

      We have included these additional analyses in the main text.

      On page 18:

      “To further explore inter-individual differences in task construal, we tested whether adjusting the attentional spotlight width to each participant’s awareness reports improved the predictions of the attentional spotlight model. To do so, we first determined the width attentional spotlight of each individual in the dSC1 dataset based on lateralized maze stimuli. We then generated person-specific attentional spotlight model predictions for the non-lateralized maze stimuli to avoid overfitting the data (Figure S11). We note that 7 participants had either flat attentional slopes or negative beta coefficients, which prevented the selection of an appropriate attentional spotlight width (see Methods for details). We observed a significant improvement in model fit for the person-specific attentional spotlight model relative to both the group-level attentional spotlight model (ΔBIC= -1487.39) and the normative sVGC model (ΔBIC= -1655.29). While the limited trial numbers per participant in our current dataset warrants caution in interpreting these findings, these findings do encourage further research on inter-individual differences in attentional deployment during planning.”

      On pages 23-24:

      “Inter-individual differences in attention

      We also observed considerable inter-individual differences in attentional effects across participants (Figure 1c). While some participants were strongly influenced by the spatial context of neighbouring stimuli, others showed more limited evidence for an attentional effect (Figure 1b). Inter-individual differences in attention predicted the sparsity of participants’ simplified representations: participants with larger attention effects exhibited sparser representations. Moreover, these inter-individual differences in effects of spatial proximity could be incorporated into the attentional spotlight model by varying the width of the spotlight, resulting in better model predictions.”

      “Beyond these spatial proximity effects, we also observed that participants varied in their tendency to lateralize their attention to a single hemifield (Figure 3). This tendency was observed across all three datasets, including on maze stimuli whose value-guided model predictions were not lateralized. This suggests that although a strategy of allocating attention is sub-optimal for these maze stimuli, some individuals preferentially attend to a single hemifield in a heuristic-like fashion. This tendency to attend to a single hemifield was a robust inter-individual difference across maze stimuli (Figure 3d), and dovetails with individual-level variation in spatial proximity effects. Taken together, these findings offer novel insights into how people vary in the ways they allocate spatial attention to solve complex problems. Future research could explore how these individual differences constrain performance on other tasks that require planning and search in highdimensional spaces.”

      On page 17 of the Supplemental Materials:

      (7) The supplementary text about lateralization effects, above Supplementary Table S8, references Table S6, but it is Table S6 does not seem to display lateralization results.

      We thank the Reviewer for pointing out this typo: we now refer to the correct supplementary table (S9).

      (8) Why does it matter that "the maze stimuli were not designed to test horizontalmeridian lateralization effects"? What is the effect on power? Is it because there is not a good enough range in lateralization indices? It would be good to clarify, or just remove that explanation, since the cortical retinotopy explanation seems more convincing.

      We did not specifically design the maze stimuli such that there is an equal number of obstacles above and below the horizontal meridian. As such, the lateralization index derived along the horizontal meridian does not control for the number of obstacles in each hemifield, which may influence participants’ awareness reports. In contrast, we designed maze stimuli such that this would not be a concern for the vertical meridian. We have clarified this point in the discussion on page 27.

      “Third, while we observed clear lateralization effects along the vertical meridian (i.e., left vs right hemifield), effects along the horizontal meridian were less clear (i.e., above vs below; see Table S15-16). One potential explanation of this asymmetry is the retinotopic organization of the cortex, in which spatially adjacent stimuli can be retinotopically distant if presented on the opposite side of the vertical (but not horizontal) meridian, facilitating distractor inhibition. Importantly, while the visuospatial attention effects observed in the Ho 1 and 2 datasets are likely driven by both covert and overt shifts in attention, the findings presented in experiment 3 (i.e., dSC1 dataset) rule out the contribution of overt shifts in attention through the use of eye tracking (see Figure S13-14)(Carrasco, 2011; Pooresmaeili & Roelfsema, 2014).”

      (9) For Figure 2c, it would be helpful to directly state what each dot and line mean.

      We updated the caption of Figure 2c to clarify what we are plotting: each point represents an obstacle, and each line the linear fit for a maze stimulus.

      “Each point represents an obstacle in a maze, and each line represents the model fit for that specific maze stimulus.”

      (10) Figures and wording imply there is only a single probe obstacle per trial, but methods and model imply that participants are asked to report awareness for every obstacle. This should be clarified.

      We apologize for any confusion regarding the methodology of our study. The Reviewer is correct that participants reported their awareness of every obstacle presented on a given trial. We have clarified this in the Results section of the manuscript on page 7:

      “Note, participants reported their awareness of every obstacle presented on a given trial.”

      We have also updated the caption of Figure 1 to clarify this point:

      “Once participants finished navigating the maze, they were asked to report their awareness of every obstacle presented on a given trial in a random order.”

      (11) What is the reason for the exclusion of participants (33 for experiment 1 and 26 for experiment 2)?

      Participants were excluded from the Ho et al. datasets 1 and 2 based on their preregistered exclusion criteria, as detailed in the Methods section of their paper. In short, trials were excluded if participants took longer than 20 seconds to complete the trial, or if they spent longer than 5 seconds in the initial state. Participants were excluded if less than 80% of trials remained after reaction time exclusions or if they failed 2 out of 3 comprehension checks. We have elaborated on this point in the Methods section on page 31.

      “Participants were excluded from analyses based on pre-registered exclusion criteria as detailed in (Ho et al., 2022). In short, participants were excluded if 20% or more of their trials were removed based on reaction times, or if they failed 2 out of 3 comprehension checks.”

      (12) The supplemental figures are not referenced in order, and some are not referenced at all; this should be fixed.

      We thank the Reviewer for pointing this out and have reorganized our Supplementary materials accordingly.

      Reviewer #3 (Public review):

      Summary:

      The authors build on a recent computational model of planning, the "value-guided construal" framework by Ho et al. (2022), which proposes that people plan by constructing simple models of a task, such as by attending to a subset of obstacles in a maze. They analyze both published experimental data and new experimental data from a task in which participants report attention to objects in mazes. The authors find that attention to objects is affected by spatial proximity to other objects (i.e., attentional overspill) as well as whether relevant objects are lateralized to the same hemifield. To account for these results, the authors propose a "spotlight-VGC" model, in which, after calculating attention scores based on the original VGC model, attention to objects is enhanced based on distance. They find that this model better explains participant responses when objects are lateralized to different hemifields. These results demonstrate complex interactions between filtering of task-relevant information and more classical signatures of attentional selection.

      Strengths:

      (1) The paper builds on existing modeling work in a novel manner and integrates classic results on attention into the computational framework.

      (2) The authors report new and extensive analyses of existing data that shed light on additional sources of systematic variability in responses related to attentional spillover effects

      (3) They collect new data using new stimuli in the original paradigm that directly test predictions related to the lateralization of task-relevant information, including eye tracking data that allows them to control for possible confounds.

      (4) The extended model (spotlight-VGC) provides a formal account of these new results.

      We thank the Reviewer for their positive assessment of our manuscript and their insightful comments, which has improved the clarity of our findings.

      Weaknesses:

      (1) The spotlight-VGC model has a free parameter - the "width" of the attentional spotlight. This seems to have been fixed to be 3 squares. It would be good if the authors could describe a more principled procedure for selecting the width so that others can use the model in other contexts.

      Our choice for this parameter was informed by the spatial effects reported in Figure 1b. We observed that the two closest neighbouring obstacles to a probe had similar awareness (i.e., positive beta weights). We therefore compute the mean and median distances between obstacle pairs that were the second closest obstacle to a probe. This distance was 3 squares away, as depicted in Figure S15. We fixed the width of the attentional spotlight across all studies based on this observation. We agree that future research utilizing this model may need to tune this hyperparameter depending on the mean distance between a probe and its neighbours.

      We have clarified this point in the methods section on page 35:

      “We fixed the ‘width’ of the attentional spotlight to a distance of 3 squares based on the observation that the two neighbouring obstacles positively predicted the awareness of a probe. We observed that the mean and median distance between neighbouring obstacles of the 2nd rank (i.e., second closest) was 3 squares away for all mazes (Figure S15). We therefore opted to fix the value of the attention spotlight to 3 squares based on these observations. Future work utilizing this model should consider the statistics of their maze stimuli when deciding on the ‘width’ of the attentional spotlight.”

      Following the suggestion of Reviewer 2 point 6, we now also explored inter-individual differences in this parameter. To do so, we first used the lateralized mazes in the dSC1 dataset to determine the optimal width of the attentional spotlight for each individual.

      Then, we used this spotlight to derive model predictions for each person. We observed that these personalized attentional spotlight model predictions fit participants’ awareness reports on non-lateralized mazes better than the fixed-width spotlight model. We believe this preliminary result suggests the importance of modelling inter-individual differences in attentional deployment during planning. We report these effects on page 17.

      (2) Have the authors considered other ways in which factors such as attentional spillover and lateralization could be incorporated into the model? The spotlightVGC model, as presented, involves first computing VGC predictions and only afterwards computing spillover. This seems psychologically implausible, since it supposes that the "optimal" representation is first formed and then it gets corrupted. Is there a way to integrate these biases directly into the VGC framework, perhaps as a prior on construals? The authors gesture towards this when they talk about "inductive biases", but this is not formalized.

      We thank the reviewer for bringing up this very important point. We think that a full computational treatment of the inductive bias would be a distinct project, but now seek to expand our discussion on the mechanisms by which representations could be formed. In this context, we specifically highlight novel computational work from the MIT group that was published as a preprint in the time since we submitted our paper, and which proposes a new process account of construal, the “Just in Time” (JIT) model. We also elaborate on a possible mechanism by which visuospatial attention may aid the dynamics of the construal process. In short, we agree with the reviewer that spatial attention may bias individuals to search over a subset of potential representations based on low-level spatial characteristics of the obstacles (e.g., their spatial spread in the visual field), prior to (or in concert with) a dynamic JIT-like selection process. We now elaborate on these possibilities on pages 27-28:

      “We close by reflecting on opportunities for further work in this area. First, an important next step is to explore the process by which task representations are formed, and how inductive biases might affect the process of task construal. The sVGC model is a normative model of the optimal task representation. Since it’s construction involves an exhaustive calculation over possible paths, it is not a plausible basis for a model of the psychological process by which participants actually construct task representations. More recently a process model of task construal has been proposed, the Just in Time model (JIT). The hypothesis of the JIT model is that participants’ task representations are built up over time by iteratively simulating possible paths through the maze, affording insight into the construal process (Chen et al., 2026). In future work, it would be of interest to ask whether the attentional effects we observe in our experiments could be meshed with a dynamic JIT account of construal. We speculate that visuospatial attention may operate as an early filter, limiting the space of potential construals based on coarse spatial features of the environment, constraining a dynamic selection of obstacles. Brain imaging techniques with high time resolution, such as M/EEG, may be able to shed further light on how task representations are formed as participants plan.”

      […]

      “Fourth, it will also be necessary to elaborate on how bottom-up and top-down aspects of attentional selection are combined to guide complex task representations and plans. Foundational questions remain unanswered, for instance: can multiple spatial locations be preferentially selected at once, i.e. are there multiple spotlights (Awh & Pashler, 2000; McMains & Somers, 2004; Pylyshyn & Storm, 1988; Shaw & Shaw, 1977)? There is also discourse on how spatial attention may move from one location to another: are the intervening visual regions between attended locations similarly selected (Dubois et al., 2009; Kr & Np, 1999; McMains & Somers, 2004, 2005)? Our findings tentatively suggest that individuals are able to attend to disparate spatial regions to form sparse task representations, yet there is substantial variability in how individuals orient their attention during the task. The present paradigm and computational modelling, in conjunction with carefully designed stimuli, may help resolve these outstanding questions.”

      (3) Can the authors rule out that the lateralization effects are the result of memory biases since the main measure used is a self-report of attention?

      We thank the reviewer for bringing up this important point. In our experiments, we sought to measure participants’ subjective awareness of the maze stimuli as a readout of their conscious task representation on each trial. This approach marries an extensive literature on measures of perceptual awareness in consciousness science (e.g., using the Perceptual Awareness Scale) with computational models of planning. Participants’ memory of (their awareness of) the obstacles is inherent to this approach, but just as with similar approaches in consciousness science (e.g. measures of iconic memory in the Sperling paradigm), we think it provides a reasonably “online” measure of awareness. It’s important of course to ensure that results obtained with awareness reports are not idiosyncratic, and generalise to other approaches to quantifying task representations.

      To further bolster the convergent validity of our awareness measure, we reanalyzed the data from Ho and colleagues. In their original paper, they developed a variant of the maze-navigation task where participants were asked to recall the location of obstacles as well as report their awareness (Exp 3) and a third variant of the task where participants could hover their cursors over hidden obstacles to reveal their locations (Exp 4). These data allowed us to validate the awareness reports against objective measures of recall and mouse-tracking data. We observed that the subjective awareness reports of participants were strikingly correlated with recall/hover measures across two independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness). We believe these findings validate participants’ awareness reports. These findings are now reported on page 22 of the manuscript.

      “Finally, we examined the convergent validity of participants’ awareness reports by reanalyzing the memory recall data reported in Ho and colleagues’ experiment (Ho et al., 2022). We reasoned that participants should demonstrate similar task representations regardless of the measure used to probe the construal. In line with this prediction, we observed that the obstacle awareness reports and memory/hover measures were strikingly correlated within three independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness; see Tables S18 and S19).”

    1. Author response:

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

      Reviewer #1 (Public review)

      Summary:

      In this manuscript the authors derive a mean-field model for a network of Hodgkin-Huxley neurons retaining the equations for ion exchange between the intracellular and extracellular space.

      The mean-field model derived in this work relies on approximations and heuristic arguments that, on the one hand, allow a closed-form derivation of the mean-field equations, and on the other hand restrict its validity to a limited regime of activity corresponding to quasi-synchronous neuronal populations. Therefore, rather than an exact mean-field representation, the model provides a description of a mesoscopic population of connected neurons driven by ion exchange dynamics.

      Strengths:

      The idea of deriving a mean-field model which relates the slow-timescale biophysical mechanism of ion exchange and transportation in the brain to the fast-timescale electrical activities of large neuronal ensembles.

      Weaknesses:

      The idea underlying this work is not completely implemented in practice.

      The derived mean field model do not show a one-to-one correspondence with the neural network simulations, except in strongly synchronous regimes. The agreement with the in vitro experiment is hardly evident, both for the mean-field model and for the network model. The assumptions made to derive the closed-form equations of the mean field model have not been justified by any biological reason, they just allow for the mathematical derivation. The final form of the mean-field equations do not clarify whether or not microscopic variables are used together with macroscopic variables in an inconsistent mixture.

      Comments on revisions:

      The main weaknesses I listed in the first report are still present, since the authors did not answer my questions on a solid basis. I report the list for completeness:

      (1) It seems that the reduction methodology that is employed is not the most suitable one for the single-neuron model they are considering.

      (2) The formulation of the mean-field derivation is unnecessarily complicated. It could be heavily simplified by following previously published approaches to derive biologically realistic neural masses.

      (3) The model seems to work only for highly synchronized situations and not for the standard asynchronous evolution usually observed in neural circuits.

      Therefore, my statement remains unchanged.

      Reviewer #2 (Public review)

      Summary:

      The authors aiming in developing a neural mass model characterized by few collective variables mimicking the dynamics of a network of Hodgkin - Huxley neurons encompassing ion-exchange mechanisms. They describe in details the derivation of the mean-field model , then they compare experimental results obtained for the hippocampus of a mice with the neural network simulations and the mean-field results. Furthermore, they report a bifurcation analysis of the developed model and simulation of a small network containing various coupled neural masses, somehow moving towards the simulation of an entire connectome.

      Strengths:

      The author attempts to develop a mean-field model for a globally coupled network of heterogeneous Hodgkin-Huxley neurons with explicit ion exchange mechanism between the cell interior and exterior.

      Weaknesses:

      (1) They do not employ the reduction methodology more suited for the single neuron model they consider.

      (2) Their derivation of the neural mass model is based on several assumptions, and not all well justified.

      (3) Their formulation of the mean-field derivation is unnecessary complicated, it can be strongly simplified by following previously published approaches to derive biologically realistic neural masses.

      (4) Their model seems to work only for highly synchronized situations and not for the standard asynchronous evolution usually observed in neural circuits.

      General Statements:

      The authors honestly declared the many limitations of their approach, once assumed this the results of the mean-field are somehow inconsistent with the neural network simulations as expected.

      The authors suggest to employ this model for the simulations on the whole connectome to follow seizure propagation, however I believe that a simpler model, as the Epileptor, remains superior in this respect to this model. That indeed includes biophysical parameters but their correspondence with the ones employed in the network dynamics remain elusive, due to the many assumptions required to derive this mean field model. Furthermore it is more complicated than the Epileptor, I do not think that the present model will be largely employed by the community.

      Comments on revisions:

      The authors have corrected mistakes present in the manuscript and put a correct list of references.

      However, they refuse

      (1) To simplify the formulation of the model, the model contains unnecessary complications, as I have clearly written in my report, the authors agree, but they do not want to change the formulation;

      (2) To derive the mean field model in a simpler way, as possible, and as I asked many times in my Referee report, this would help the readers to understand the important aspect of the derivation, without not needed and confusing complicated formulations;

      (3) To compare direct simulations of the network with neural mass results in sub-section "Bifurcation analysis: emergent network states and multistability" to show bistability, as I asked.

      As a matter of fact the performed modifications do not solve my previous doubts on the validity of the results reported in the manuscript.

      Therefore, my previous assessments remain valid.

      We thank the editors and the two reviewers for their continued engagement with our manuscript. The three weaknesses retained from the first round are essentially identical between the two public reviews:

      (i) The reduction methodology is not the most suitable for the single-neuron model we consider;

      (ii) The mean-field derivation is unnecessarily complicated;

      (iii) The model works only in highly synchronous regimes and does not reproduce the asynchronous evolution typical of neural circuits.

      Both reviewers explicitly note that their assessments remain unchanged and we have decided not to alter the formulation of the model. We use this response to state—on the public record—exactly where we agree with the reviewers, where we disagree, and why.

      On point (i): the reduction methodology.

      We fully agree with the reviewers' technical observation: the Ott–Antonsen / Lorentzian-ansatz reduction in the form introduced by Montbrió, Pazó and Roxin (2015) is exact for canonical Type I neurons (QIF), whose membrane-potential equation is quadratic, and is not directly applicable to a Type II / Hodgkin–Huxley-type neuron whose voltage dynamics is cubic-like. On this point there is no disagreement.

      Where we differ is in the conclusion the reviewers draw from this observation. The reviewers read our work as applying an inappropriate reduction methodology to an inappropriate neuron model. We instead positioned our work, from the outset, as an extension of that methodology: we keep the biophysically detailed Hodgkin–Huxley substrate (because it is the only level at which extracellular ion concentrations, depolarization block, bursting and seizure-like events are biophysically grounded), and we adapt the reduction by approximating the cubic voltage nullcline as a piece-wise quadratic with two parabolas of opposite curvature. This is explicitly an approximate, not exact, mean-field. The Lorentzian ansatz is then applied on each branch of the piece-wise quadratic, with the limitations of this construction analyzed in the manuscript.

      The reviewers' alternative—starting from a Type I canonical model and grafting on biophysical features—would indeed yield an exact mean-field, but it would forfeit precisely what motivates our work: a tractable mesoscopic description in which the slow variables are physiologically interpretable ion concentrations rather than phenomenological parameters. The trade-off is that we give up exact rigour in order to construct a bridge between the Montbrió-style next-generation neural mass models on one side and the Epileptor on the other, with the additional benefit that the parameters of the resulting neural mass retain a biophysical correspondence (e.g., [K<sup>+</sup>]_bath, Δ[K<sup>+</sup>]_int, [K<sup>+</sup>]_g, the gating variable n) that the Epileptor does not afford.

      We therefore respectfully maintain our position: the methodology is not "the wrong reduction for a Type II neuron"; it is an extended reduction designed to be applicable beyond the Type I case, with explicitly characterized validity.

      On point (ii): the formulation is unnecessarily complicated.

      We agree with the reviewers that, given the assumptions we ultimately adopt, namely that the gating variable n and the potassium concentrations Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are treated as collective (mesoscopic) variables shared by the population, with n a function of the average membrane potential, the closed neural mass equations could be reached by the more direct path used by Guerreiro et al. (2022) and the related literature (R1–R7). In the revised manuscript we now state this explicitly, and we note that the same five-dimensional system arises under either derivation.

      Our choice to follow Chen and Campbell (2022) is motivated by the fact that it makes each approximation visible at the point where it is invoked. In particular, it exposes the moment-closure step (Eq. 19), the vanishing-flux boundary condition (Eq. 28), and the locations where microscopic and mesoscopic variables enter the description. We believe that for a reader trying to extend our framework, for instance to a setting with partial heterogeneity in the slow variables, or with stochastic gating, this is the more useful presentation. We have added a remark stating that the simpler Guerreiro-type derivation reaches the same equations under our assumptions, so that readers can take whichever route they find clearer.

      On point (iii): the model only works in highly synchronous regimes.

      Here we partially agree and partially disagree, and we would like the partial disagreement to appear on the public record.

      We agree that the Lorentzian ansatz is, strictly, valid in regimes where the population's membrane potential distribution is unimodal, that is, when essentially all neurons sit on the same side of the threshold V*. Where we disagree is with the implication that the mean-field model fails outside the strongly synchronous regime. The supplementary analysis in Fig. S2, added in the previous round, quantifies the error introduced by the first-moment approximation of n as a collective variable across the full range of [K<sup>+</sup>]_bath values, spanning quiescent, bursting, seizure-like, sustained ictal and depolarization-block dynamics. The fraction of neurons whose gating variable deviates from the population mean is below 2% for the parameters used throughout the manuscript, and the error becomes appreciable only during the brief transitions between sub- and supra-threshold states. These are precisely the moments at which the population is genuinely bimodal and the single-Lorentzian assumption is theoretically expected to leak. In other words, the error peaks coincide with the moments where our derivation tells us in advance that the assumption is locally invalid; the model "knows where it fails." Away from these transitions, the mean-field tracks the population average across all dynamical regimes shown in Fig. 3, not only in the most strongly synchronized ones.

      This is, in our view, the strongest argument we can make: we are not claiming exactness, and we are not unaware of the limitations. We have characterized them analytically (the construction of the piece-wise Lorentzian, and the theoretical reason a closed solution exists only when the two branches collapse onto one), and we have characterized them numerically (Fig. S2). The deviations are bounded, their location in parameter space is well identified, and they coincide with transitions where the underlying assumption is locally violated. We believe this constitutes a controlled approximation rather than an uncontrolled one, and we would like this distinction to be visible to readers of the Reviewed Preprint.

      We note, in this connection, that the reviewers' preferred reference point, the next-generation neural mass model of Montbrió et al. (2015), which is exact and one-to-one with its underlying network, is exact precisely because the underlying network is a network of QIF neurons. The corresponding statement for a network of Hodgkin–Huxley-type neurons with explicit ion exchange does not, to our knowledge, exist in closed form, and may not exist at all. The relevant question is therefore not whether our model matches the exactness of the QIF case, but whether the controlled approximation we provide is useful. Given the qualitative agreement with neural-network simulations across the full range of [K<sup>+</sup>]_bath, the qualitative agreement with the in vitro recordings, and the recovery of the expected bifurcation structure with new emergent regimes, we believe the answer is yes.

      Other outstanding points in the review.

      Reviewer 2 reiterates the view that the Epileptor remains superior for whole-connectome seizure-propagation simulations because it is simpler and better characterized. We do not dispute that the Epileptor is more thoroughly analyzed and more parsimonious. The complementarity we propose is not a replacement but a parameter-grounding, as the Epileptor's phenomenological parameters (excitability, slow permittivity) acquire, in the present framework, an interpretation in terms of measurable biophysical quantities (extracellular potassium, intracellular potassium variation, glial buffering).

      We thank the reviewers and editors once again for their careful reading, and we are grateful that the points of disagreement have been sharpened to a state where readers can judge them transparently.


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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors derive a mean-field model for a network of Hodgkin-Huxley neurons retaining the equations for ion exchange between the intracellular and extracellular space.

      The mean-field model derived in this work relies on approximations and heuristic arguments that, on the one hand, allow a closed-form derivation of the mean-field equations, and on the other hand restrict its validity to a limited regime of activity corresponding to quasi-synchronous neuronal populations. Therefore, rather than an exact mean-field representation, the model provides a description of a mesoscopic population of connected neurons driven by ion exchange dynamics.

      We agree with the reviewer's characterization. Our manuscript describes the derivation as relying on "approximations and heuristic arguments" and states that "the derivation is not exact"; what we provide is a controlled, approximate mesoscopic description in which the slow variables are physiologically interpretable ion concentrations rather than phenomenological parameters. An exact closed-form thermodynamic limit is, to our knowledge, available only for canonical Type I (QIF) networks (Montbrió, Pazó and Roxin, 2015) and a few of their extensions; it is not currently known for a Hodgkin–Huxley-type network with explicit ion-exchange dynamics. We acknowledge that the original description of the regime of validity may have caused confusion on this point, and in the revised manuscript we have therefore replaced the looser formulation "strongly synchronous regimes" by the more accurate "regimes where the membrane-potential distribution is unimodal and can be reasonably approximated by a Lorentzian" throughout the manuscript.

      Strengths:

      The idea of deriving a mean-field model that relates the slow-timescale biophysical mechanism of ion exchange and transportation in the brain to the fast-timescale electrical activities of large neuronal ensembles.

      We thank the reviewer for recognizing the motivation behind our work. This explicit coupling between slow biophysical ion dynamics and fast electrical activity is precisely the feature we tried to preserve in the reduction, even at the cost of giving up exactness.

      Weaknesses:

      The idea underlying this work is not completely implemented in practice.

      We address this general statement through the four specific sub-points the reviewer raises in the paragraph that follows.

      The derived mean field model does not show a one-to-one correspondence with the neural network simulations, except in strongly synchronous regimes.

      We partially agree and partially disagree. We agree that the Lorentzian ansatz is strictly valid where the membrane-potential distribution is unimodal, i.e. when essentially all neurons sit on the same side of the threshold V*. We disagree with the implication that the mean-field fails outside this regime. To make this claim quantitative, we added a new supplementary figure (Fig. S2) that quantifies the deviation of individual neurons' gating variables from the population mean across the full range of [K<sup>+</sup>]_bath values—quiescent, bursting, seizure-like, sustained ictal and depolarization-block dynamics. The fraction of deviating neurons is below 2% for the parameters used in the manuscript, with localized peaks only during the brief, genuinely bimodal transitions between sub- and supra-threshold states—precisely the moments at which the theory predicts the assumption to be locally invalid. Away from these transitions, the mean-field tracks the population average across all dynamical regimes shown in Fig. 3, not only in the strongly synchronized ones.

      The agreement with the in vitro experiment is hardly evident, both for the mean-field model and for the network model.

      We acknowledge that the experimental and simulated traces in the original Fig. 4 did not match quantitatively; this was never our intention. The figure and its caption have been reorganized in the revised manuscript to frame the comparison as qualitative: we aim to demonstrate the shared structure i.e., the slow modulation of fast population activity by extracellular potassium fluctuations, rather than to claim a quantitative fit.

      We also added two clarifications that account for the residual differences: (i) the network simulations were intentionally run with rescaled biophysical parameters (membrane capacitance, gating time constants) to keep the computational cost feasible, a standard practice when the goal is to validate dynamical mechanisms rather than absolute timescales; (ii) the in vitro LFP recordings were AC-coupled, so the slow DC components visible in the mean-field traces are filtered out at acquisition.

      The assumptions made to derive the closed-form equations of the mean-field model have not been justified by any biological reason, they just allow for the mathematical derivation.

      We agree that the modelling assumptions were scattered through the original derivation. In the revised manuscript, the three core assumptions are stated explicitly at the point of derivation: (i) the gating variable n is treated as a collective, population-averaged variable; (ii) the potassium concentrations Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are homogeneous across the population, biophysically justified by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforces near-instantaneous equilibration at the mesoscopic scale; (iii) no heterogeneity is assumed at the level of ion dynamics. The meaning of "locally homogeneous" is now defined explicitly.

      On the biophysical motivation of the in vitro perturbation used in the experiment, we have added a new Methods subsection that explains how low extracellular Mg<sup>2+</sup> unblocks NMDARs and abolishes the divalent-cation stabilisation of the resting membrane potential, depolarising hippocampal neurons and increasing the driving force for outward K<sup>+</sup> currents. This provides a biophysical link between the experimental perturbation and the model's main control parameter, the extracellular potassium concentration. We also added a reference to the well-established model of epileptic discharges that underpins the experiment.

      The final form of the mean-field equations does not clarify whether or not microscopic variables are used together with macroscopic variables in an inconsistent mixture.

      We now explicitly acknowledge that in the spiking-network simulations the gating variable n is microscopic (each neuron has its own n_i), whereas in the mean-field derivation it is treated as mesoscopic and shared by the population. This asymmetry between modalities is discussed both in the Results and in the Limitations sections, and is identified as a likely source of some of the discrepancy between the two modalities.

      We have also made the notation in Eqs. (36)–(37) consistent (firing rate r used throughout, full current-based dV/dt̄ restored) and fixed the typos and broken equation/reference labels that contributed to the impression of inconsistency (Eqs. 18, 28, 29; the Fig. 2(c) [K<sup>+</sup>] bath label; the lost reference at line 696).

      Reviewer #2 (Public review):

      Summary:

      The authors aim to develop a neural mass model characterized by a few collective variables mimicking the dynamics of a network of Hodgkin – Huxley neurons encompassing ion-exchange mechanisms. They describe in detail the derivation of the mean-field model, then they compare experimental results obtained for the hippocampus of a mouse with the neural network simulations and the mean-field results. Furthermore, they report a bifurcation analysis of the developed model and simulation of a small network containing various coupled neural masses, somehow moving towards the simulation of an entire connectome.

      We thank the reviewer for the accurate summary of the manuscript's structure and aims.

      Strengths:

      The author attempts to develop a mean-field model for a globally coupled network of heterogeneous Hodgkin-Huxley neurons with an explicit ion exchange mechanism between the cell interior and exterior.

      We thank the reviewer for recognizing this objective. The retention of Hodgkin–Huxley dynamics with explicit ion exchange is precisely the feature that distinguishes our framework from QIF-based reductions, and it is what enables the slow variables of the resulting mean-field to retain a direct biophysical interpretation.

      Weaknesses:

      (1) It seems that the reduction methodology that is employed is not the most suitable one for the single-neuron model they are considering.

      We agree, on technical grounds, with the observation: the Ott–Antonsen / Lorentzian-ansatz reduction is exact for canonical Type I neurons (QIF) and is not directly applicable to a Type II Hodgkin–Huxley-type neuron with a cubic-like voltage nullcline. Where we differ is in the conclusion. We did not apply an inappropriate reduction to an inappropriate neuron; we deliberately extended the methodology by approximating the cubic nullcline as a piece-wise quadratic with two parabolas of opposite curvature, and then applying the Lorentzian ansatz on each branch. The result is an explicitly approximate, biophysically grounded mean-field, with its regime of validity stated and quantified (Fig. S2).

      To make this positioning explicit, we have added a paragraph to the Introduction that situates our work within the next-generation neural mass literature (Byrne et al. 2020; Montbrió, Pazó & Roxin 2015; Guerreiro et al. 2022; Forrester et al. 2024; Perl et al. 2023; Gerster et al. 2021; and works on short-term plasticity, adaptation, conductance-based reductions,

      spike-timing-dependent plasticity, random connectivity and noise) and clarifies that we see our contribution as complementary to these approaches, not as a competitor to the exact QIF reductions.

      (2) The authors' derivation of the neural mass model is based on several assumptions, and not all well justified.

      We agree that, in the original submission, the modelling assumptions were scattered through the derivation. In the revised manuscript, the three core assumptions are stated explicitly at the point of derivation: (i) the gating variable n is treated as a collective population-averaged variable; (ii) the potassium concentrations Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are homogeneous across the population, biophysically justified by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforces near-instantaneous equilibration at the mesoscopic scale; (iii) no heterogeneity at the level of ion dynamics is assumed. The meaning of "locally homogeneous" is now defined explicitly. In addition, we have added Fig. S2, which quantifies numerically the error introduced by the moment-closure assumption (deviation below 2% for the parameters used in the manuscript).

      (3) The formulation of the mean-field derivation is unnecessarily complicated. It could be heavily simplified by following previously published approaches to derive biologically realistic neural masses.

      We agree that, under the assumptions ultimately adopted in our model—namely that n, Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are mesoscopic—the final five-dimensional system can be reached by the more direct path used by Guerreiro et al. (2022) and the related literature. We now state this explicitly in the revised manuscript and note that the same system arises under either derivation, so that the reader can take whichever route they find clearer. Our choice to retain the Chen and Campbell (2022) formalism is pedagogical: it exposes the moment-closure step (Eq. 19), the vanishing-flux boundary condition (Eq. 28), and the locations where microscopic versus mesoscopic variables enter the description, which is the more useful presentation for a reader wishing to extend the framework (e.g. to partial heterogeneity in the slow variables or to stochastic gating). We also made the notation in Eqs. (36)–(37) consistent (firing rate r used throughout, full current-based dV/dt̄ restored) and fixed a number of typos and broken equation/reference labels.

      (4) The model seems to work only for highly synchronized situations and not for the standard asynchronous evolution usually observed in neural circuits.

      We partially agree and partially disagree. We agree that the Lorentzian ansatz is strictly valid where the membrane-potential distribution is unimodal; we have replaced "strongly synchronous regimes" by this more accurate formulation throughout the manuscript. We disagree, however, with the implication that the mean-field is useful only in those regimes. Fig. S2, added in this revision, explicitly quantifies the deviation across all dynamical regimes (quiescent, bursting, seizure-like, sustained ictal and depolarization-block dynamics): it remains below 2% for the parameters used in the manuscript, with localized peaks only during the brief sub-to-supra-threshold transitions where the population is genuinely bimodal. Away from these transitions, the mean-field tracks the population average across all dynamical regimes shown in Fig. 3.

      General Statements:

      The authors honestly declared the many limitations of their approach. It is assumed that the results of the mean-field are somehow inconsistent with the neural network simulations as expected.

      We thank the reviewer for acknowledging that the limitations are honestly declared. As detailed above and quantified in Fig. S2, the deviation from the network simulations is bounded and well characterized; it is not assumed but measured.

      The authors suggest employing this model for the simulations on the whole connectome to follow seizure propagation, however, I believe that the Epileptor remains superior in this respect to this model. That indeed includes biophysical parameters but their correspondence with the ones employed in the network dynamics remains elusive, due to the many assumptions required to derive this mean-field model. Furthermore, it is more complicated than the Epileptor, I do not think that the present model will be largely employed by the community.

      We do not propose our model as a direct replacement for the Epileptor and we do not dispute that the Epileptor is more thoroughly analyzed and more parsimonious. The complementarity we propose is not a replacement but a parameter-grounding: the Epileptor's phenomenological parameters (excitability, slow permittivity) acquire, in our framework, a concrete interpretation in terms of measurable biophysical variables (extracellular potassium, intracellular potassium variation, glial buffering). Retaining the Hodgkin–Huxley substrate is essential to ground these variables biophysically.

      To make this complementarity more visible, the Limitations and Discussion section has been expanded to discuss the choice of a purely excitatory network as a first step (with excitatory–inhibitory generalizations available via the synaptic reversal potential) and to point to additional biological ingredients (calcium and other ions, plastic synapses, random connectivity and noise, adaptation, spike-timing-dependent plasticity) that the framework can accommodate, with reference to the next-generation neural mass literature.

      We thank the reviewers and editors for their careful reading. We hope this public response makes our reasoning, the limits of our approach, and the concrete revisions made in this round transparent.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In general, the writing is scattered. Every time a model is introduced, one starts from the general formulation only to find that a very simplified case is used with respect to that formulation, which is very confusing. Authors need to reduce unnecessary formulations that confuse the reader and make it clear which formulations are actually used.

      We thank the reviewer for this comment and understand the concern regarding the balance between general formulations and specific approximations. Our intention in including the more general equations and derivations (e.g., Eq. 7 and others) was pedagogical — to ensure completeness and transparency in the modeling steps, especially for readers less familiar with mean-field reductions of biophysically detailed models. These general forms also serve to clarify the assumptions underlying the simplifications we employ. In the latest version, we improved the clarity of core equations (e.g., Eq. 37), which form the basis of all simulations presented (see details below, in the answer to question 14).

      (2) The Introduction would benefit from a wider view of the literature. The literature on exact mean field models (i.e. derived from the Lorentzian Ansatz) has flourished in the last years. In particular, it would be worth considering the following papers, where exact neural mass models are applied to perform whole-brain and large-scale brain simulations:

      Forrester, M., Petros, S., Cattell, O., Lai, Y. M., O'Dea, R. D., Sotiropoulos, S., & Coombes, S. (2024). Whole brain functional connectivity: Insights from next generation neural mass modelling incorporating electrical synapses. PLOS Computational Biology, 20(12), e1012647.

      Perl, Y. S., Zamora-Lopez, G., Montbrio, E., Monge-Asensio, M., Vohryzek, J., Fittipaldi, S.,

      Campo, C. G., Moguilner, S., Ibanez, A., Tagliazucchi, E., Yeo, B. T. T., Kringelbach, M. L., & Deco, G. (2023). The impact of regional heterogeneity in whole-brain dynamics in the presence of oscillations. Network Neuroscience, 7(2), 632-660.

      Byrne, Aine, James Ross, Rachel Nicks, and Stephen Coombes. "Mean-field models for EEG/MEG: from oscillations to waves." Brain topography 35, no. 1 (2022): 36-53.

      Gerster, M., Taher, H., Skoch, A., Hlinka, J., Guye, M., Bartolomei, F.,... & Olmi, S. (2021). Patient-specific network connectivity combined with a next generation neural mass model to test clinical hypothesis of seizure propagation. Frontiers in Systems Neuroscience, 15, 675272.

      Byrne, Aine, Reuben D. O'Dea, Michael Forrester, James Ross, and Stephen Coombes. "Next-generation neural mass and field modeling." Journal of neurophysiology 123, no. 2 (2020): 726-742.

      Benitez-Stulz, Sophie, Samy Castro, Gregory Dumont, Boris Gutkin, and Demian Battaglia. "Compensating functional connectivity changes due to structural connectivity damage via modifications of local dynamics." bioRxiv (2024): 2024-05.

      We have added the following paragraph:

      “Recently, a class of these models, called next-generation neural mass models [42], has been developed based on an analytical approach introduced by [25] that allowed for the exact derivation of mean field parameters for a population of quadratic integrate-and-fire (QIF) neurons. These can be linked to EEG/MEG oscillations [43], including epipeltic seizures [43], and have been used to study various aspects of the whole-brain dynamics such as the low-dimensional manifold of the resting state [45,46], aging [47] and neural signatures of consciousness [48].”

      We have also modified the preceding paragraph of the introduction that now reads:

      “At the mesoscopic level, the observable properties of a neuronal ensemble are generally explained by statistical physics formalism of mean-field theory [19-22]. Mean-field models demonstrated a predictive value for studying the mesoscopic dynamics of neuronal populations [23], providing statistical descriptions of neuronal networks [2, 19, 24-29], which can be used to address questions related to network-level mechanisms [12, 24, 30].

      In general, neural mass models have a low enough number of parameters to be tractable and provide general intuitions regarding mechanisms underlying complex neuronal activity [31-36]. For example, statistical population measures, such as the firing rate, can be used to assess mesoscopic dynamics [1, 7, 31, 36-41].”

      (3) Moreover, conductance-based models have been already implemented in neural mass models not only in references [69, 71, 95], but also in:

      Guerreiro, I. C., Di Volo, M., & Gutkin, B. (2023). A new generation of reduction methods for networks of neurons with complex dynamic phenotypes.

      Capone, C., Di Volo, M., Romagnoni, A., Mattia, M., & Destexhe, A. (2019). State-dependent mean-field formalism to model different activity states in conductance-based networks of spiking neurons. Physical Review E, 100(6), 062413.

      We have added the following sentence:

      “Moreover, conductance-based couplings between the spiking neurons have been already implemented in neural mass models [58, 59, 91, 93, 121], but without an extracellular exchange mechanism.”

      (4) Sec. 1.1 As previously established in the literature, a system of all-to-all coupled neuronal equations can be solved exactly in the thermodynamic limit (i.e., infinite neurons limit) if the single neuron membrane potential equation is a quadratic function and if the instantaneous distribution of membrane potentials of neurons in a population is described by a Lorentzian [Montbrió, E., Pazó, D. & Roxin, A. Physical Review X 5 (2), 021028 (2015)]. This means that the thermodynamic limit can be performed for a Canonical Type I model like the quadratic integrate-and-fire.

      What is the biological justification and the reason to approximate a different neuron type (a type II neuron model), whose membrane potential equation resembles a cubic function, with a quadratic function? The fact that it can be solved in the quadratic approximation is not, in my opinion, a sufficient justification. It would be more correct to start from a type I neuron at the microscopic level with a quadratic function and then provide additional biological features.

      We thank the reviewer for raising this important point. We respectfully disagree with the notion that starting from a canonical Type I model (such as the quadratic integrate-and-fire neuron) would be a more biologically grounded approach. While the quadratic form is analytically convenient, it does not capture certain key features of neuronal excitability particularly those related to bursting, seizure-like events, and depolarization block which are closely tied to the cubic-like nullcline geometry arising in Hodgkin–Huxley-type models, especially in the presence of slow ion dynamics.

      Our work seeks to bridge biophysical realism with analytical tractability. The step-wise quadratic approximation we employ is specifically designed to mimic the cubic membrane potential profile that emerges from the full ion-exchange dynamics. While the Lorentzian Ansatz is not strictly justified in this case from first principles, we show that it yields a workable and biologically interpretable mean-field description, which aligns with single-neuron dynamics, population simulations, and even in vitro observations. To our knowledge, this is a novel contribution that extends mean-field modeling beyond currently available approaches, which are often restricted to simplified or phenomenological neuron models.

      In this context, using a quadratic approximation is not merely a mathematical convenience — it is a means to retain key dynamical features of more realistic (non-Type I) neurons within a tractable framework, enabling insights into complex behaviors like multistability and pathological bursting.

      (5) Sec. 1.2 As shown in Figure 3, the mean-field equations do not show a one-to-one correspondence with the neural network simulations, except in strongly synchronous regimes. This represents a strong limitation in the model, especially because exact neural mass models (as shown in Reference [23]) perfectly fit the dynamics of the underlying network model both in the asynchronous and in the synchronized regime.

      We appreciate the reviewer’s observation and acknowledge that our original description may have caused confusion. The model's validity is not strictly limited to strongly synchronous regimes, but rather to regimes where the distribution of membrane potentials across the neuronal population remains unimodal and can be reasonably approximated by a Lorentzian. This includes but is not restricted to—highly synchronized states.

      We agree that this distinction is important and have clarified it in the revised manuscript (e.g., “in strongly synchronous regimes” —> “in regimes where the membrane potentials' distribution is unimodal and can be reasonably approximated by a Lorentzian”).

      In contrast to exact mean-field reductions based on quadratic integrate-and-fire neurons (e.g., [23]), our model originates from a biophysically grounded HH-type neuron with ion exchange dynamics, and necessarily involves heuristic approximations to achieve a closed-form mean-field description. While this results in a less exact correspondence with network simulations in more heterogeneous or bimodal states, our goal was to retain biological interpretability and account for phenomena such as ion-driven bursting and seizure-like transitions, which are not captured by standard QIF-based neural masses.

      We see our contribution as complementary to existing exact reductions — offering a biophysically grounded alternative that remains tractable and informative in a relevant class of unimodal, mesoscopic dynamical regimes.

      (6) Sec. 1.3 In this section the authors show the comparison between in vitro experiments and simulations with both the network model and the neural mass model (Figure 4, panels a,b,c). The qualitative agreement that is supposed to be shown is hardly evident. The shape of the signals is different as is the type of bursting. The only agreement results in the fact that there are repeated spiking events at successive times in a periodic manner. However, the time scale of the simulations is different for neural network simulation and mean-field experiment, making it difficult to compare them. While the period of the bursting event is around 2 min for mean field simulation (in according with experiments), the time scale of the network simulation is 60 times smaller, thus meaning that we are considering completely different mechanisms and phenomena. The justification given by the authors, that "the parameters were modified to simulate shorter fluctuations (in the network of Hodgkin-Huxley neurons) for computational efficiency" is inappropriate.

      The poor agreement turns out to be even worse in the comparison between experiments and mean-field simulations shown in panels d and e of Figure 4. While the mean field simulation is characterized by a periodic behaviour both in the mean membrane potential and in the external potassium concentration, the in-vitro traces are not periodic and show an increasing irregular activity of the extracellular LFP in correspondence with increasing external potassium concentration.

      How it is possible to justify the implementation of this model if the working hypotheses are not supported by the results? The worst agreement of the network simulations with the experiments reinforces the doubt raised in the previous point: what is the reasoning underlying the choice of Hodgkin-Huxley as a single neuron model?

      We thank the reviewer for this detailed critique. We acknowledge that the comparisons in Figure 4 involve limitations and we now provide a clearer rationale and context in the revised manuscript. First, we emphasize that our intention is not to claim a quantitative match between the experimental and simulated traces, but rather to demonstrate that our model grounded in biophysical mechanisms such as ion exchange is capable of qualitatively reproducing a key feature observed experimentally: the slow modulation of neuronal activity by extracellular potassium concentration. For example, both in vitro (Fig. 4a, 4d) and in our simulations (Fig. 4b, 4e), bursts of activity ride on slower oscillations of potassium, and the interplay of fast and slow dynamics is central to both.

      Regarding the discrepancy in timescales between the neural network and mean-field simulations: the network simulations were intentionally run with accelerated dynamics by rescaling biophysical parameters (e.g., membrane capacitance and gating time constants) to keep the computational cost feasible. We now clarify in the manuscript that this choice is standard practice in computational modeling when the primary goal is to validate dynamical mechanisms rather than replicate absolute timescales.

      On the shape of LFP signals: the experimental recordings were AC-coupled, and the DC components associated with slower shifts in membrane potential such as those modeled in the mean-field simulations are not captured in those recordings. This limits the visibility of key features like the underlying potential jumps. Additionally, no claim is made regarding a specific bursting classification in either data or simulation.

      We agree that the experimental trace in Fig. 4d shows more complex, non-periodic dynamics (e.g., slowing burst frequency and irregularity), which are not captured by our current deterministic model. These differences could plausibly arise from additional physiological processes (e.g., stochastic transitions between metastable regimes or variability in ion regulation) that are not modeled here. In future work, such phenomena may be captured by introducing noise or parameter variability (see, e.g., Saggio et al., A taxonomy of seizure dynamotypes , elife 2020), or by allowing the parabola coefficients in the nullcline approximation to vary dynamically.

      Finally, regarding the choice of a Hodgkin–Huxley-type neuron: this model allows us to incorporate a biophysical description of ion exchange, which is central to the phenomena we study. While modeling the spiking mechanisms explicitly precludes certain mathematical simplifications available to very simplified neuron models with reset, it enables direct links between mesoscopic dynamics and measurable quantities such as extracellular potassium an essential objective of our work. To summarize, we rearranged Fig4:

      Potassium can have periodic behavior with V bursting riding on top (Fig.4 a). The model also shows this behavior at different timescales (Fig. b,c,e).

      AC LFP recording is filtered so we might not see the V jump during the bursts (because we do not have DC recordings). No claim about bursting class here.

      Potassium can also have more complex behavior (e.g., slowing down of burst frequency Fig.4.d), that the deterministic model do not show, but maybe exploring dynamical parameters (e.g., from parabolas or K_bath) or with added noise allowing to jump between regimes (reference Saggio et al. eLife 2020).

      (7) Sec. 1.5 Here six neural masses are coupled via long-range structural connections with random weights. Simulations of the system are shown for two different values of the global coupling parameter (G = 0 and G = 100). How many realisations of the network have been considered?

      We thank the reviewer for pointing this out. The presented simulation was intended as a proof-of-concept demonstration to illustrate the model’s capacity to support network-level propagation of pathological activity. For this purpose, we considered a single representative realization of the structural connectivity with random weights. Given the deterministic nature of the model and the qualitative focus of the demonstration, additional realizations do not qualitatively change the observed behavior — namely, the transition from localized to network-wide bursting as coupling strength increases. We have now clarified this in the revised manuscript.

      “This simulation serves as a proof of concept to illustrate how local pathological activity can propagate through a network depending on the strength of coupling. We used a single representative realization of randomly weighted structural connectivity. While we did not perform a systematic exploration of different realizations or coupling strengths, we observed that the qualitative behavior namely, the emergence of network-wide bursting beyond a critical coupling threshold remains robust across similar setups. The model is compatible with empirical connectome data and can be readily extended to simulations using realistic brain network architectures.”

      In future applications involving data-driven network architectures or variability analyses, we agree that exploring multiple realizations or empirical connectomes will be valuable.

      How do the results depend on the different choices of the random weights? What is the dependence of the emergent dynamics on G? What kind of dynamics can be observed varying smoothly the parameter G (e.g. from 0 to 100)?

      This section serves as a proof of concept to show that pathological activity in one node can propagate through the network when coupling is strong. We used a single random weight configuration and did not systematically explore variations in G or connectivity. While richer dynamics likely emerge across intermediate values of G, a full parameter sweep is beyond the scope of this study. We clarify this in the revised text (see answer above).

      (8) Sec. 2.1 In the description of the experiment it is mentioned that only Mg^{2+} is varied. What is the role played by Mg^{2+} variation in influencing the external potassium concentration variation? How the experiment can be linked to the model? How the hypothesis of introducing an equation for the potassium concentration current in the microscopic model is supported by the experiment and vice-versa?

      We thank the reviewer for this question. We have added a new subsection in the Methods explaining the.agnesium removal as a mean to influence the external potassium dynamics:

      “The membrane of hippocampal neurons is equipped with N-methyl-D-aspartate type glutamate receptors (NMDARs). These receptors have a very high affinity for glutamate and can, in principle, be activated by ambient glutamate present at low concentrations in the brain extracellular fluid (ECF). Under normal physiological conditions, this activation does not occur because extracellular magnesium ions (Mg<sup>2+</sup>) block the NMDAR channel at membrane potentials more negative than about –50 mV; this voltage-dependent block prevents receptor activation at rest. When extracellular magnesium is removed, the block is relieved, allowing NMDARs to be activated, leading to neuronal depolarization toward the action potential threshold [117].”

      “In addition, as a divalent cation, Mg<sup>2+</sup> interacts with the negatively charged neuronal membrane, contributing to the stabilization of the resting membrane potential. Lowering extracellular magnesium concentration disrupts this effect, resulting in membrane depolarization [118].”

      “Consequently, magnesium removal not only facilitates NMDAR-dependent depolarization, but also directly depolarizes neurons. This depolarization increases the driving force for outward potassium currents through K<sup>+</sup> channels, meaning that variations in Mg<sup>2+</sup> can indirectly influence external potassium dynamics during neuronal activity.”

      (9) Sec. 2.6 The modified version of the continuity equation has been derived following Reference [95], where the authors consider a network of Izhikevich neurons, and each neuron is modelled by a two-dimensional system consisting of a quadratic integrate and fire equation plus an equation that implements spike frequency adaptation. In particular, in [95] the authors achieve a closed set of mean-field equations with the inclusion of the mean-field dynamics of the adaptation variable by using a Lorentzian ansatz combined with the moment closure approach. The moment closure condition is also assumed in the present manuscript (Eq. 19). Under which assumptions is the implementation of the moment closure condition justified?

      We are thankful to the reviewer (and also to the R2) for pointing out to the validity of the justification of the assumptions that we have used in our formalism. We hence agree that the moment closure is not a sufficient justification for assuming that V depends on the mean n, which is neccessary for the derivation of Eq. 20, but in addition we need the assumption that n can be treated as a collective variable as it is done in the works mentioned by the reviewer 2. In addition we have performed numerical simulations of the full system to calculate the error term introduced by this approximation, and the results in the new Fig. S2 show that this is below 2% for each of the different dynamical regimes.

      We have hence modified the justification for Eq. (19) reading:

      “Next we assume a first-order moment closure condition for the variable n [59], justified by the numerical simulations of the full network (see Fig. S2) which show that for most of the neurons (close to 99 \% for the value of ∆ same as in the other simulations) the mean of the population is well capturing the behavior of the single neurons [122]. Finally, putting together these factors and assuming that n can be treated as a collective variable for each neuron (see Limitations of the model} section) we arrive to ” and also

      “The validity of the first moment closure, Eqs. (19), as in [59], is supported by the numerical simulations, which show that, both, during the silent regime and when seizure-like events occur, n<sub>i</sub> for most neurons track the network averaged ⟨n | V, η⟩. In particular, it is less than 2% of the neurons that fire while the mean is low, and vice-versa, Fig. S2. In less synchronized scenarios (larger ∆ or smaller J), however, this value would increase, but the mean would always capture the qualitative behaviour of the population.”

      This is also now explicitly mentioned in the following paragraph:

      “Unlike the mean membrane potential ⟨V⟩ and the firing rate (r), which can be explicitly derived from the continuity equation under the Lorentzian assumption, the expression for ⟨n(t)⟩ in Eq. (26) is formal. In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore, ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      (10) Considering also the comments reported above, I think that it would make more sense to start from an Izhikevich neuron model as microscopic model and add the equations for the ionic currents as mesoscopic variables (i.e. written as population average variables), instead of starting from the Hodgkin-Huxley single neuron model and trying to make hardly justifiable approximations and simplifications.

      We respectfully disagree. While the Izhikevich model is computationally efficient, it lacks the biophysical detail required to capture key ion-driven mechanisms such as depolarization block, slow ion accumulation, and specific burst-initiation dynamics all of which are central to our study. The Hodgkin–Huxley framework, despite requiring approximation, provides the necessary physiological grounding to link microscopic ion exchange with emergent population behavior.

      (11) Sec. 2.7 What is the advantage of using six more parameters to fit, like R-,R+,c-,c+,I-,I+?

      This is in contradiction with the spirit of deriving a mean-field model, where the number of parameters should be reduced. What is the advantage of this mean-field derivation with respect to other mean-field derivations of Hodgkin-Huxley neurons, like the one in Reference [9]?

      The additional parameters (R±, c±, I±) are not arbitrary they compactly parametrize the cubic-like nonlinearity of the membrane potential dynamics in our stepwise-quadratic approximation. This trade-off allows us to preserve essential biophysical features of HH neurons (e.g., bursting regimes, depolarization block) within a tractable analytic framework. Compared to alternative approaches like in ref. [9], which focus on phenomenological reductions and do not yield an ODE system, our model offers more direct interpretability in terms of ion dynamics, providing a closer link between microscopic mechanisms and mesoscopic activity patterns.

      (12) Sec. 2.11 The derivation of the mean-field dynamics for the gating variable is rather heavy and difficult to follow. This section could be simplified, whilst also better explaining the underlying approximations and the validity of these approximations, which is currently missing.

      We agree that the derivation is technical, but we chose to retain it for transparency, as it follows the Chen and Campbell approach and makes key approximations such as moment closure explicit. We have now added a clarification that n is treated as a collective variable We hope that the current level of detail helps readers understand the assumptions underlying the gating variable dynamics.

      (13) Sec. 2.12 The derivation of Eqs. (36) is quite confusing and needs to be re-written in a clearer form. Why are both the variables x and r present in these equations, since they are proportional according to Eq. (25)?

      We thank the reviewer for pointing this out. We have adjusted the equations to improve clarity and now consistently express the firing rate in terms of a single variable. This removes the redundancy and simplifies the presentation.

      (14) Sec. 2.13 The derivation of Eqs. (37) is quite confusing and needs to be rewritten in a clearer form.

      Both the auxiliary variable x and the firing rate r are present in this equation, the same as in Eq. (36). Therefore it is presented as a set of equations for the auxiliary variable x and for the physical variable V. Moreover in the equation for dV/dt, the quadratic term in V has disappeared and it is not clear to me which are the variables corresponding to I- and I+. In particular, in Eqs. (36) there are two different current terms I-,I+ for the two equations related to dy/dt. In Eqs. (37) there is a single term (I_{cl} +I_{Na}+I_K+I_{pump})/C_m which is identical for both equations related to dV/dt. I was expecting two different terms also in Eqs. (37).

      We appreciate the reviewer’s close reading. To improve clarity, we now express the dynamics in terms of the firing rate r, replacing \dot{x} with \dot{r} in both Eq. (36) and Eq. (37) to avoid confusion.

      As for the current terms: in Eq. (37), we reverse the stepwise quadratic approximation and reintroduce the original ionic currents from Eq. (16). This is why the expressions involving I_{\text{cl}}, I_{\text{Na}}, I_K, and I_{\text{pump}} appear as a single summed term in \dot{V}, rather than the split I_-,I_+ terms used in the stepwise approximation. We now clarify this in the text.

      We also write V as \bar{V} to clarify that it refers to the average membrane potential for the neuronal population. Finally, we wrote the final equation in a more compact form to improve clarity (new Eq.38).

      (15) Moreover, while the equation for the gating variable n can be considered as a differential equation for a mesoscopic variable since n depends on average values only, it is not clear to me if the remaining variables 𝛥[K+]_{int}, [K+]_g can be considered mesoscopic or not. Since Eqs. (37) represent a mean-field model, I expect every variable to be a mean-field variable. This could be easily achievable for the extracellular potassium concentration, but I do not understand how a site-specific microscopic variable like the intracellular potassium concentration variation can be automatically inserted in a set of mean-field equations without any averaging or intermediate steps. This is a crucial point to be clarified for the validity of the neural mass equations.

      We thank the reviewer for raising this important point. In our model, we assume spatial homogeneity at the mesoscopic scale, meaning that ion concentrations — both intra- and extracellular — are uniformly distributed across the population. As a result, variables such as \Delta[K^+]_{\text{int}}, Δ[K+]int and [K+]g are treated as population-level averages, consistent with the mean-field framework.

      Moreover, the rate of change of intracellular potassium is tightly coupled to extracellular dynamics via ion exchange mechanisms, justifying its inclusion as a slow, mesoscopic variable. We now clarify this modeling assumption explicitly in the text.

      “By locally homogeneous, we mean that all neurons in the population are assumed to share the same extracellular and intracellular ionic environment and are connected with identical coupling rules, allowing us to treat the population as uniform with respect to ion dynamics and connectivity.”

      “These slow variables are in addition considered to be mesoscopic, meaning they are identical for every neuron in the population.”

      Minor points:

      (1) Figure 2, panel d. Please detail the variable on the y-axis, which is not reported in the figure.

      Done

      (2) Eq. (15) is cited in many parts of the manuscript, while it seems to me it would be more appropriate to reference Eq. (2). Is this a mistake or is there a reason to cite Eq. (15)?

      The reviewer is correct, we have had a wrong equation label, which we have now corrected.

      (3) Figure 4 Would it be possible to show enlargements of the mean membrane potential traces to directly compare the different bursting types shown by the simulation of the different models?

      The panel d already contains enlarged part of the membrane potential traces. For the rest, going back to the Q6, we want to stress again that our intention is not to claim a quantitative match between the experimental and simulated traces.

      (4) Figure 5 In the caption the author refers to "the generic model, single neuron model, and epileptor model". Could you please better explain the models referred to and why they are mentioned? Are the generic model and the single neuron model those that are presented in the Materials and Methods section? Or do you refer to completely different models, as for the epileptor?

      We have removed the reference to the generic model (we had in mind the canonical model for seizures by Saggio et al. 2017), since it is not mentioned in the paper, and we have clarified that the single neuron model and epileptor model, which were used to simulate seizure like events.

      (5) Sec 2.5 As already stated above, the authors need to reduce unnecessary formulations that confuse the reader. Here, for example, Eqs. (6) and (7) are unnecessary, in view of the fact that delta spikes are used (Eq. 8).

      We thank the reviewer for the suggestion, but we disagree, and we think it is better to start the derivations from the more general case, as done with Eqs. 6-7.

      (6) Sec. 2.6 Could you please better explain why in Eqs. (15) and (16), the variable V0 is introduced, while before and after this, the variable V is used?

      We thank the reviewer for the comment. In Eqs. (15) and (16), \dot{V}_0 denotes the free term of the membrane potential equation, i.e., the component driven solely by the intrinsic ionic currents and excluding the synaptic input I_syn. Only this \dot{V}_0 term (a function rather than an independent variable) is approximated by the piece-wise quadratic expression in Eq.(21). In contrast, the variable V represents the membrane–potential variable, which dynamics is obtained by combining \dot{V}_0 with the synaptic current contribution I_syn. In summary, there is no independent variable V_0; only the function \dot{V}_0 is introduced to represent the intrinsic (non-synaptic) component of the membrane–potential dynamics. We have now clarified this in the text.

      (7) In the square brackets of the r.h.s. of Eq. (18), for all the intermediate steps, it appears G^n(V,n) ϱ^V, while there should be G^n(V,n) ϱ^n.

      We thank the reviewer for catching this typo. We have corrected this in the revised manuscript.

      (8) Sec. 2.8 Here the authors affirm that "a double-Lorentzian (or a piece-wise Lorentzian) could be a suitable form for ρ^V (t, V | η). However, it is not clear under which conditions such an assumption would allow a solution to the continuity equation". What are the problems underlying the implementation of the double Lorentzian? It seems to be a more correct form than the single Lorentzian actually implemented.

      We thank the reviewer for this thoughtful question. In principle, a double-Lorentzian ansatz for \rho^V can indeed be implemented in several reasonable ways–for example, by enforcing that the combined area of the two Lorentzian components is normalized to one (to preserve the probabilistic interpretation) and by imposing smoothness constraints at their boundaries. However, despite exploring these implementations, we were unable to obtain non-trivial solutions of the continuity equation under this parametrization. The only solvable case we found is the degenerate one in which the two Lorentzians collapse onto each other (i.e., (x_- = x_+) and (y_- = y_+)), which reduces the ansatz to the single-Lorentzian form used in the manuscript. For this reason, although the double-Lorentzian is conceptually appealing, it did not yield practically useful solutions within our framework.

      (9) Eq. (28). The symbols used for the flux (especially those used in the second-to-last step once the inner integration is performed) are confusing and it is difficult to understand what they mean.

      We thank the reviewer for noting this issue. The problem was due to a LaTeX typo that prevented the vertical lines—indicating that the flux is evaluated at specific points—from rendering correctly. We have now corrected this.

      (10) Eq. (29) In the third step there are some misprints that impair comprehension.

      We thank the reviewer for noting this. We have corrected these misprints in the revised version.

      (11) Line 696. The reference is not displayed.

      Fixed.

      Reviewer #2 (Recommendations for the authors):

      As a really general remark, this manuscript is written in a confusing manner, the authors present their model in a general formulation and their analysis in a complicated way that in the end is not needed, as I will explain in detail in the following.

      Another general question is why the authors want to employ the neural mass reduction methodology developed in [23] to obtain exact mean-field evolution for quadratic neurons (like the quadratic integrate and fire (QIF)) for a model that reveals a cubic dependence on the membrane potential, as the FizhHugh-Nagumo neuron (that indeed is a 2d reduction of the Hodkgin-Huxley model), to obtain an approximate neural mass model that somehow works qualitatively only for synchronized dynamics? Why not use another approach more suited to derive the neural mass model for cubic nonlinearity, as the one suggested in [33] and [69] by Di Volo and co-authors? What is the rationale behind the choice of the authors?

      We appreciate the reviewer’s critical feedback and the opportunity to clarify our methodological choices. Our decision to base the mean-field model on Hodgkin–Huxley-type neurons stems from the need to retain ion channel dynamics, which are essential to capture the coupling between membrane activity and extracellular ionic concentrations. This biophysical link is central to our study and cannot be achieved using more abstract neuron models such as QIF or FitzHugh-Nagumo alone.

      Regarding the mean-field reduction method: while the Ott-Antonsen/Lorentzian framework is indeed exact for QIF neurons, we adopted a stepwise quadratic approximation to apply a similar formalism to the cubic-like dynamics of the HH model. This choice enables us to analytically capture a rich set of behaviors, including bursting, depolarization block, and seizure-like dynamics, in a tractable mean-field system.

      We considered the approach of Di Volo and colleagues [33, 69], but their methodology is tailored to asynchronous irregular regimes, whereas our model is specifically designed to capture dynamics in quasi-synchronous or bursting regimes — including epileptiform activity — which are not covered by the assumptions of the Di Volo framework.

      We now clarify these modeling choices more explicitly in the revised manuscript.

      "Unlike phenomenological or reduced models, the Hodgkin–Huxley framework allows us to retain explicit ion exchange dynamics, which are essential for linking membrane behavior to extracellular potassium fluctuations. This level of biophysical detail is crucial for modeling pathological regimes such as seizure onset and propagation."

      Furthermore, the derivation of the neural mass equations is unnecessarily complicated, as a matter of fact, they approximate all the variables (except the membrane potentials of the single neurons) as collective variables (i.e. the gating variable and the potassium concentration) common to all the neurons. The neural network model for which they derive the neural mass model presents microscopic evolutions of the membrane potential cubic-like plus other global variables equal for all neurons, that depend on collective variables such as the mean membrane potential or the mean firing rate. Once clarified, the derivation of the neural mass model is much simpler, and it is not necessary to follow the approach reported in Reference [95] [Chen, L. & Campbell, S. A. Exact mean-field models for spiking neural networks with adaptation. Journal of Computational Neuroscience 50 (4), 445-469 (2022)] which is unnecessarily complicated. The authors can follow a much simpler methodology as explained by Guerriero et al in Reference [R6] (cited below) where the authors consider the same model studied in [95]. Such a methodology has been applied in many cases already, to introduce realistic aspects in the neural mass model [23] (see References [R1-R7] below). I strongly encourage the authors to reformulate their approach in a simpler and clearer manner, by following the approach reported in [R1-R7]. The manuscript will become more readable and it will gain in comprehension.

      We thank the reviewer for this helpful suggestion. We agree that, given the assumptions made in our derivation (i.e., shared gating and ion concentration variables across neurons), the mean-field equations could alternatively be obtained using the simpler methodology proposed by Guerriero et al. [R6] and related works [R1–R7]. However, we chose to follow the derivation presented by Chen and Campbell [95] because it makes the approximations (e.g., moment closure, flux boundary assumptions) explicit and generalizable to future extensions. However, we also acknowledge that the assumption of n to be treated as a collective variable is needed, and for clarity, we have now added a remark in the manuscript indicating that the same result could be recovered more directly using the approach of Guerriero et al.

      “We note that, under the assumption of globally shared gating and ion concentration variables across the neuronal population, the resulting mean-field equations can also be derived using simpler methods as proposed by Guerriero et al [58]. In this work, we follow the more general formalism of Chen and Campbell [59], which makes the role of key approximations (e.g., moment closure, vanishing flux at boundaries) explicit. This also facilitates potential generalizations to settings with partial heterogeneity or dynamic gating distributions.”

      “Finally, putting together these factors and assuming that n can be treated as a collective variable for each neuron”

      “Unlike the mean membrane potential ⟨V⟩ and the firing rate (r), which can be explicitly derived from the continuity equation under the Lorentzian assumption, the expression for ⟨n(t)⟩ in Eq. (26) is formal. In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore, ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      Now I will examine in detail all the manuscript and report comments/remarks/suggestions numbered as (Q#) on how to improve the present manuscript to render it easier to read and more comprehensible, these are not minor remarks, just detailed ones.

      Introduction

      (Q1) The Introduction section needs a part devoted to the reduction methodology developed in [23] for QIF neurons and a presentation of previous works dealing with the introduction of biologically realistic aspects in the neural mass model derived in [23]. Here is a non exhaustive list of such papers concerning the introduction of the following realistic aspects in the neural mass developed in [23]:

      (I) short-term synaptic plasticity :

      [R1] Exact neural mass model for synaptic-based working memory H Taher, A Torcini, S Olmi, PLOS Computational Biology 16 (12), e1008533 (2020)

      [R2] Bursting in a next generation neural mass model with synaptic dynamics: a slow-fast approach H Taher, D Avitabile, M Desroches, Nonlinear Dynamics 108 (4), 4261-4285 (2022)

      [R3] Mean-field approximations of networks of spiking neurons with short-term synaptic plasticity R Gast, K Thomas R, H Schmidt, Physical Review E 104 (4), 044310 (2021)

      (II) spike frequency adaptation:

      [R4] Gast, Richard, Helmut Schmidt, Thomas R. Knösche. "A mean-field description of bursting dynamics in spiking neural networks with short-term adaptation." Neural computation 32.9 (2020): 1615-1634.

      [R5] Population spiking and bursting in next-generation neural masses with spike-frequency adaptation, A Ferrara, D Angulo-Garcia, A Torcini, S Olmi, Physical Review E 107 (2), 024311 (2023).

      (III) conductance-based neuron with a slow current (Izekievic model):

      [R6] A new generation of reduction methods for networks of neurons with complex dynamic phenotypes,IC Guerreiro, M Di Volo, B Gutkin, preprint arxiv: 2206.10370 (2022)

      (IV) spike timing-dependent plasticity:

      [R7] Mean-field approximations with adaptive coupling for networks with spike-timing-dependent plasticity, B Duchet, C Bick, Á Byrne, Neural computation 35 (9), 1481-1528 (2023).

      (V) random connectivity and noise:

      [R8] Mean-field models of populations of quadratic integrate-and-fire neurons with noise on the basis of the circular cumulant approach

      DS Goldobin Chaos: An Interdisciplinary Journal of Nonlinear Science 31 (8) (2021)

      [R9] A reduction methodology for fluctuation-driven population dynamics DS Goldobin, M Di Volo, A Torcini, Phys. Rev. Lett. 127, 038301 (2021)

      [R10] Shot noise in next-generation neural mass models for finite-size networks VV Klinshov, SY Kirillov Physical Review E 106 (6), L062302 (2022)

      I think the authors should refer in the introduction to these previous papers, where realistic biological aspects have been already introduced in the neural mass model developed in [23].

      We have added a whole pragaraph devoted to the next-generation neural mass models and in particular to the other works introducing biological realism in this class of models:

      “Recently, a class of these models, called next-generation neural mass models [42], has been developed based on an analytical approach introduced by [25] that allowed for the exact derivation of mean field parameters for a population of quadratic integrate-and-fire (QIF) neurons. These can be linked to EEG/MEG oscillations [43], including epipeltic seizures [44], and have been used to study various aspects of the whole-brain dynamics such as the low-dimensional manifold of the resting state [45, 46], aging [47] and neural sig natures of consciousness [48]. Number of works dealt with the introduction of biologically realistic aspects in the mostly phenomenological neural mass model derived in [25]. These included short-term synaptic plasticity [49–51], spike frequency adaptation [52, 53], spike timing-dependent plasticity [54], synaptic delay [29], random connectivity and noise [55–57], as well as an extension of the conductance-based neurons with a recovery variable [58–60].”

      (Q2) Line 117 - Please specify what you mean by locally homogeneous, here.

      Thank you for allowing us the opportunity to clarify this. We now report:

      "By locally homogeneous, we mean that all neurons in the population are assumed to share the same extracellular and intracellular ionic environment and are connected with identical coupling rules, allowing us to treat the population as uniform with respect to ion dynamics and connectivity."

      (Q3) In this sub-section the authors should clarify all the hypotheses they employ to derive the neural mass models, not only the Lorentzian approximation they did for a cubic model, but also the fact that they assume that the gating variable n is a global variable as well as that the potassium concentration are assumed to be the same for all neurons, that they assume no heterogeneity at this level. This is a fundamental aspect that should be clarified at this stage already.

      We thank the reviewer for this important observation. We agree and have revised the text in the derivation section to explicitly state all key assumptions. Specifically, we now clarify that:

      (1) The gating variable n is treated as a population-average (global) variable;

      (2) The potassium concentrations Δ[K+]int and [K+]g are assumed to be homogeneous across the neuronal population; and (3) No heterogeneity is assumed at the level of the ion dynamics.

      This assumption is biophysically motivated: ion concentrations — particularly extracellular potassium — tend to redistribute rapidly due to diffusion and electrochemical forces, leading to an effectively well-mixed environment at the mesoscopic scale. As such, assigning separate compartments to individual neurons is not justified in this modeling context. We now explicitly note this in the manuscript to avoid ambiguity.

      “3) We assume that the potassium concentrations, both intracellular(\( \Delta[K^+]_{\text{int}} \)) and extracellular (through the buffering variable \( [K^+]_g \)), are homogeneous across the neuronal population. This is justified physiologically by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforce near-instantaneous equilibration at the mesoscopic scale. As such, assigning separate compartments to each neuron is neither practical nor biologically meaningful in this context. We assume that the potassium concentrations, both intracellular (\( \Delta[K^+]_{\text{int}} \)) and extracellular (through the buffering variable \( [K^+]_g \)), are homogeneous across the neuronal population. This is justified physiologically by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforce near-instantaneous equilibration at the mesoscopic scale. As such, assigning separate compartments to each neuron is neither practical nor biologically meaningful in this context; 4) We assume that the gating variable n, which governs potassium conductance, can be treated as a population-averaged variable. This allows us to describe the neuronal ensemble using a reduced set of collective (mean-field) variables.”

      Comparison with neural network simulations

      (Q4) The comparison the authors perform between the microscopic model and the neural mass is misleading, From what the authors wrote it seems that you are considering 4 variables for each neuron in the network model (this is unclear from how the model is written in Eq (9)), I guess one for the membrane potential, one for the gating variable and two for the potassium concentration. However, this is not the network model for which the neural mass has been developed, the neural mass has been obtained for a network made of N + 3 variables (N membrane potentials and 3 collective variables for gate, and potassium concentrations) this is a sort of mesoscopic network models, analogously to what done previously in references [R1,R3,R4] above and others. If the authors would compare their neural mass with this mesoscopic model the agreement among the two would be improved.

      We agree with reviewer’s observation and we now acknowledge this issue in the Results and in the Limitations. We have already modified the text to explicitly state that for the mean filed derivations n is treated as a collective variable and we have added the following statements:

      “Also note that the gating variable n is treated as microscopic in the neural network, while in the derivations for the mean-field it is considered as a mesoscopic and identical for the whole population. This is likely responsible for some of the discrepancies between the two modalities.”

      “Moreover, the discrepancy between the two modalities would have likely been smaller if for the neural network we also adopted a gating variable that is mesoscopic and identical across the spiking neurons, as in similar works [49–51]. However, here we demonstrate the validity of the mean-field approximation even for the more natural, microscopic representation of the gating variable in the neural network.”

      Comparison with in vitro experiments

      (Q5) Experiment -- The experiment is performed in vitro on the intact Hippocampus of mice between postnatal days P5-P7. It is known [R1] that neuronal activity at an early developmental stage is provided in the Hippocampus by a network primarily driven by synchronized GABA_A that provides an excitatory action and generates giant depolarizing potentials (GDPs) [R11]. However, GDPs have frequencies in the range of 1 Hz - 0.1 Hz, not matching the oscillation frequencies reported by the authors. I have several questions here:

      (E1) At this stage P5-P7 are the interactions among neurons essentially excitatory? Or not, please explain why, Are the oscillations reported by the authors somehow related to GDPs? The depolarizing action of GABAergic transmission and the presence of GDPs during early rodent brain development, as described by Ben-Ari and some others researchers, are characteristics commonly observed in ex vivo brain preparations, but are not evident under physiological in vivo conditions (see doi: 10.3389/fphar.2012.00065).

      In our preparation—intact mouse hippocampus—GABAergic synaptic transmission is not depolarizing. This is evidenced by the fact that inhibition of ionotropic GABA_A receptors with bicuculline triggers interictal-like discharges, which are routinely used as a model of epileptiform activity (see doi: 10.1016/j.nbd.2014.12.013). Therefore, in our experiments at P5–P7, neuronal interactions are not purely excitatory, and the observed low Mg2+ induced oscillations are not related to GDP.

      (E2) What is the nature of the oscillations reported by the authors in Figure 4 ? Which is their origin, please explain in the text of the paper clearly.

      The model of epileptic discharges presented in our study was first introduced over 20 years ago and has since become a well-established paradigm for screening potential antiepileptic drugs and research on the mechanism of epileptic seizure. A detailed description of this model can be found in doi: 10.1046/j.1460-9568.2002.02143.x, and its pharmacological properties are reviewed in doi: 10.1046/j.1528-1157.2003.19503.x. These references have now been added to the manuscript for clarity.

      We have added the following:

      “The model of epileptic discharges presented in our study was first introduced over 20 years ago [115] and has since become a well-established paradigm for screening potential antiepileptic drugs and research on the mechanism of epileptic seizure [116].”

      (E3) How exactly does the concentration of extracellular potassium ions change, this is not clear even in Methods, please clarify.

      [R11] Excitatory actions of GABA during development: the nature of the nurture Y Ben-Ari, Nature Reviews Neuroscience 3 (9), 728-739 (2002).

      We have now added a new Subsection in the methods explaining how we use Mg2+ variation to influence the external potasium variation.

      “The membrane of hippocampal neurons is equipped with N-methyl-D aspartate type glutamate receptors (NMDARs). These receptors have a very high affinity for glutamate and can, in principle, be activated by ambient glutamate present at low concentrations in the brain extracellular fluid (ECF).Under normal physiological conditions, this activation does not occur because extracellular magnesium ions (Mg<sup>2+</sup>) block the NMDAR channel at membrane potentials more negative than about –50 mV; this voltage-dependent block prevents receptor activation at rest. When extracellular magnesium is removed, the block is relieved, allowing NMDARs to be activated, leading to neuronal depolarization toward the action potential threshold [117]. In addition, as a divalent cation, Mg<sup>2+</sup> interacts with the negatively charged neuronal membrane, contributing to the stabilization of the resting membrane potential. Lowering extracellular magnesium concentration disrupts this effect, resulting in membrane depolarization [118]”

      “Consequently, magnesium removal not only facilitates NMDAR-dependent depolarization, but also directly depolarizes neurons. This depolarization increases the driving force for outward potassium currents through K<sup>+</sup> channels, meaning that variations in Mg<sup>2+</sup> can indirectly influence external potassium dynamics during neuronal activity.”

      (Q6) Lines 187-191 and Figure 4 -- The authors wrote : "In Figure 4.c we show the membrane potential and external potassium for a simulation of N = 3000 coupled HH-like neurons showing a similar behavior, although the parameters were modified to simulate shorter fluctuations for computational efficiency." This sentence is unclear. What is clear from Figure 4 is that the network simulations gave rise to collective oscillations on a completely different scale seconds with respect to minutes and also the profile of the potassium concentration has a clearly different evolution. From Figure 4 one can conclude that network simulations have nothing to do with the neural mass evolution and the experiment. I think the authors should better clarify and describe the results reported in Figure 4.

      We thank the reviewer for the observation. We have revised the relevant section of the manuscript to clarify the interpretation of Figure 4 and avoid any implication of quantitative matching. As stated in our response to Reviewer 1 (comment 6), the comparison is intended to highlight the shared qualitative structure across experimental data, the neural mass model, and the network simulation — specifically, the modulation of fast bursting by slow extracellular potassium fluctuations. The difference in timescale in the network simulation arises from rescaled parameters used for computational efficiency. We now explicitly state this and have updated the figure caption and accompanying text accordingly to reflect these points.

      (Q7) Why do the authors consider a purely excitatory network to describe the experimental results? What is the reason for this choice? Why they do not consider as usual balanced excitatory- inhibitory networks? Please clarify this point.

      We thank the reviewer for raising this point. We chose to model a purely excitatory network as a first step in isolating the role of extracellular potassium dynamics in generating population-level bursting. This allows us to focus on the ion-driven modulation mechanisms without introducing additional complexity from inhibitory feedback. Similar modeling choices have been made in previous studies of bursting and seizure-like dynamics (e.g., Gutkin et al.,), where inhibition is omitted to emphasize intrinsic or modulatory mechanisms. We acknowledge that incorporating inhibitory populations is an important next step for capturing a broader range of dynamics, but for the current study, the excitatory-only network provides a minimal and interpretable framework aligned with our focus.

      (Q8) By comparing Figures 4 (a) and (b) it seems that the bursting activity observed in the experiment and in the mean-field simulations seem quite different, originating from different mechanisms and bifurcations, Can the authors comment on this?

      We thank the reviewer for this important observation. We have reorganized the presentation of Figure 4 and revised the accompanying text to better clarify the nature of the comparison (see also our response to Reviewer 1, point 6). Our aim is not to claim that the experimental and simulated bursts arise from identical bifurcation mechanisms, but rather to highlight shared qualitative features — in particular, slow modulation of population activity by extracellular potassium. We now also comment on the potential role of more complex or noise-driven bifurcations (see Saggio et al. 2020) in shaping experimental bursting dynamics, which are not fully captured by the current deterministic model.

      Bifurcation analysis: emergent network states and multistability

      (Q9) This sub-section will gain interest by reporting simulations of the network and of the neural mass model presenting bistable dynamics.

      We agree with the reviewer that this would be an important addition, but we believe that it goes beyond the scope of this work (for the computational reasons among others) and it remains for future work. We have however updated the bifurcation analysis section.

      Limitations of the model

      (Q10) Lines 276- 280 -- I think that the parameters c+,c_,R+,R_ depend not only on the slow variables, potassium concentrations but also on the actual value of the gate variable n. This should be stressed.

      We thank the reviewer for this helpful observation. We agree and have clarified in the revised manuscript. This reflects the mean-field assumption that n is treated as a collective variable, and we now make this dependency explicit in the text.

      “Furthermore, the parabola coefficients c_-,c_+, R_-, R_+ were fixed as constants, however, these coefficients could be made functions of the slow variables and the gating variable, which might unveil new dynamical regimes and extend the validity of the thermodynamic limit beyond the regimes described in this work. Also, in the case of constant values, an in-depth exploration of the parameter space is required to fully characterize the model and its bifurcation structure.”

      (Q11) The authors wrote: " Other limiting assumptions are the moment closure condition (19) and the assumptions that the functions (3) averaged across the neuronal population can be expressed as functions of the average membrane potential V and gating variable n (which is only true in the cases where the functions (3) can be reasonably approximated as linear functions in a range of V and n." Apart from that a parenthesis is lacking, I think that this last aspect has been already taken into account when performing the fit with 2 parabolas to the sum of the currents, or not? In case, please specify.

      We thank the reviewer for catching the missing parenthesis — this has been corrected in the revised manuscript. Regarding the modeling point: the two-parabola fit applies specifically to the membrane potential dynamics and captures the nonlinear dependence of the total current on V (eq.16). In contrast, the moment closure assumption involves approximating averages of nonlinear functions of both V and n, such as those appearing in the gating dynamics (e.g., n∞(V)). This is not directly accounted for by the parabola approximation, but is handled separately via the mean-field approximation of G^n as a function of the average variables (eq.15).

      (Q12) A limitation that should be stressed is that the authors in the neural mass model consider the gate variable and the potassium concentrations, as global variable equal for all neurons, and where n depends on the mena membrane potential, to write that the moment closure (19) is a limiting assumption is honestly too clear, please be explicit here.

      We have now the following two statements:

      “These slow variables are in addition considered to be mesoscopic, meaning they are identical for every neuron in the population.”

      “In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore, ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      Discussion

      (Q13) The authors could discuss in this section the further biological ingredients they can introduce in their neural mass based on the previous works [R1-R9] that have already shown how to include plastic synapses, random connectivity, noise, adaptation, spike-timing-dependent plasticity, etc and which of these ingredients they consider more relevant for the whole brain dynamics.

      In order not to repeat the same statements from the Introduction, we have now addded the following sentence:

      “This approach, taking into account key biophysical details, offers a first step in considering the role of the glia in neural tissue excitability. Following this direction, other ions, such as calcium should be taken into consideration, as well as other effects such as plastic synapses, random connectivity, noise, adaptation, spike-timing-dependent plasticity, as already discussed in the Introduction.”

      (Q14) The authors should also discuss why they limited their analysis to purely excitatory networks, and what would change by including excitatory-inhibitory interactions in each single mass and across neural masses, if this makes sense or not.

      As stated in our response to Q7, we chose to focus on purely excitatory networks as a first step to isolate and study the core role of extracellular potassium dynamics in driving bursting behavior. This modeling choice allows for a minimal system where the interaction between intrinsic ionic mechanisms and network coupling is most transparent.

      We also note that excitatory and inhibitory effects can be modeled within the same formalism by adjusting the synaptic reversal potential — for example, $E_{syn}=0$mV for excitatory, and $E_{syn}=-80$mV for inhibitory interactions. Including inhibitory populations would introduce additional complexity and richer dynamical regimes (e.g., oscillatory instabilities, balance states), which are certainly of interest but beyond the scope of this study.

      Materials and Methods

      (Q15) Fig.2 - I think a plus is lost in panel (c) where it should be [K+bath];

      Thank you. We corrected the figure.

      (Q16) Caption of Figure 2- the authors wrote: "In the case where the derivative of the membrane potential is zero for V > V ⋆ (e.g., if the cubic function is shifted up by adding a constant current to the membrane potential derivative), the population is described by the red distribution in the steady state, and the continuity equation is governed by the negative parabola equation." This sentence is unclear, the authors mean in the case where the derivative of the membrane potential crosses zero at V > V*? Please clarify.

      We thank the reviewer for pointing this out. Yes, we refer to the case where the membrane potential derivative crosses zero at a point V>V∗. We have clarified this in the revised figure caption.

      (Q17) Lines 558-562 -- Eqs (6) and (7) are examples of unnecessary complications of which this manuscript is full of. Since the authors do not consider any synaptic dynamics and homogenous (equal) couplings, these equations are not needed, I strongly recommend removing Eqs (6) and (7) and limiting to the expression reported in Eq (8), which indeed should also be corrected see next remark.

      We appreciate the reviewer’s concern regarding clarity. As mentioned in our response to Reviewer 1, the inclusion of Eqs. (6) and (7) was intentional and serves a pedagogical purpose — to present the general structure of the network interactions before introducing simplifying assumptions. While we agree that Eq. (8) suffices for the simulations considered in this manuscript, we believe that showing the more general form helps clarify the model’s extensibility, for instance to cases with heterogeneous coupling or synaptic dynamics.

      (Q18) Eq (8) - line 562 - Since the authors assume no synaptic evolution, i.e. instantaneous post-synaptic potentials, they can clarify that Eq (8) represents the population firing rate that later will be one of the fundamental variables of the neural mass model and call it r, as in the following. Furthermore, $s_i$ does not depend on the neuron index $i$ in a fully coupled network with homogenous coupling, as in the present case, this quantity is the same for all neurons. Please drop the index and call it r since it is the population firing rate.

      We thank the reviewer for this useful suggestion. We now clarify in the text that under the assumptions of all-to-all homogeneous coupling and no synaptic dynamics, s_i is identical for all neurons and can be interpreted as the population firing rate r. This connection is made explicit in the revised manuscript.

      “Under the assumption of instantaneous synaptic transmission and homogeneous all-to-all coupling, the synaptic activation variable (s<sub>i</sub>) is the same for all neurons and corresponds to the population firing rate, which we denote by (r)”

      (Q19) Line 564-567 - Here the network model is incomplete, it is not sufficient that the authors report the evolution equation for the membrane potential Eq (9). They should report the evolution equation for the gate variable n and for the potassium concentration as done in Eq (1). This request is fundamental because it is unclear from the present formulation which are the variables that are microscopic (associated with the single neuron evolution) and which are global (common to all the neurons). This is a fundamental aspect and it should be clarified. I guess that n will depend on the neuron index $i$, while the potassium concentration it is unclear how the authors will consider them, global or local. I guess that the internal density should depend on the neuron index $i$ or not ? Anyway, I would like to know exactly which network model has been simulated e.g. to obtain the results reported in Figure 3.

      We thank the reviewer for this essential clarification request. In the revised manuscript, we now explicitly state the full network model, including the evolution equations for the gating variable n_i and potassium variables. While in some simulations we consider the full microscopic model involving 4N variables (where each neuron has its own V_i ,n_i ,Δ[K+]int_i ,[K+]g_i), for the mean-field reduction and mesoscopic comparisons we assume that the gating and potassium variables are shared across neurons. This assumption is consistent with prior work (e.g., Chen & Campbell) and is biophysically justified in the case of potassium due to its fast spatial equilibration in extracellular space. We also now mention this explicitly in the Limitations.

      (Q20) Continuity equation - Lines 568 - 597 - This part can be largely simplified and rewritten, as a matter of fact, the authors consider the gate variable n, the potassium concentrations as global (collective variables) depending on mean field values of <V> they can directly start from eq 20, by stating that they assume that the other variables (n, $\Delta[K^+]_{int}$, $[K^+]_g$) are collective variables, common to all the neurons, and that depends only on mean field variables as <V> or r. This has been done in many previous cases since the Ott-Antonsen Ansatz can be applied whenever the potential evolution is driven by quadratic terms and in the presence of mean field variables, the first indication of this was reported in 1993 by Watanabe and Strogatz for phase oscillators :

      [R12] Watanabe, Shinya, and Steven H. Strogatz. "Integrability of a globally coupled oscillator array." Physical review letters 70.16 (1993): 2391.

      Anyway, this approach has been previously employed to derive a neural mass model for networks of QIF neurons in the presence of various further neuronal variables (ranging from slow currents to plastic evolution of the couplings) describing more biologically realistic situations, see references [R1-R7] above. I strongly encourage the authors to reformulate their approach in a simpler and clearer manner, particularly interesting is for them the article [R6] by Guerriero et al, the authors examine exactly the same model as in Ref [95] [Chen, L. & Campbell, S. A. Exact mean-field models for spiking neural networks with adaptation. Journal of Computational Neuroscience 50 (4), 445-469 (2022)]. However, they solve the problem in a much more simple way, I encourage the authors to follow this approach.

      We thank the reviewer for the constructive suggestion. We acknowledge that, under the assumption that n, Δ[K+]int , and [K+]g are collective variables shared across the neuronal population, one could directly begin from Eq. (20) and proceed using the simpler approaches found in Guerriero et al. [R6] or related works [R1–R7]. However, we chose to retain the Chen & Campbell formalism, with additional clarification regarding the mesoscopic nature of the gatin variable, as it explicitly highlights the key approximations used in the derivation, which may be beneficial for readers seeking to extend the method. See also general response to reviewer 2 at the beginning.

      (Q21) Eq (26) -- I do not think the authors can estimate explicitly <n(t)> from the equation (26), as they do for the mean membrane potential and the firing rate. This is just a formal expression representing a collective variable, I do not think that <n> will coincide with the average of the values of n_i for each neuron. Please discuss this point, and in this case show that <n> indeed coincides with the average of all of the values of the single neuron gate variable n_i.

      We thank the reviewer for raising this important point. We agree that Eq. (26) is more formal than operational, as ⟨n(t)⟩ is not directly derived from the continuity equation in the same way as ⟨V⟩ or the firing rate r. Rather, it reflects our mean-field assumption that the gating variable evolves as a collective population-averaged quantity, governed by the dynamics of the average membrane potential. In our formulation, n is treated as a global variable shared across neurons, and thus ⟨n(t)⟩ effectively is the gating variable in the neural mass model — rather than the result of averaging heterogeneous n_i. We have clarified this distinction in the text to avoid suggesting that Eq. (26) provides an explicit estimate of microscopic gating dynamics.

      “Unlike the mean membrane potential ⟨V⟩ and the firing rate (r)>, which can be explicitly derived from the continuity equation under the Lorentzian assumption, the expression for ⟨n(t)⟩ in Eq. (26) is formal. In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      (Q22) Mean-field dynamics for the gating variable - All this sub-section is in my opinion not useful, if the authors assume from the beginning that <n(t)> is a global variable. Indeed in the end they write for <n(t)> the evolution equation Eq (30) which is the same equation as for the single neuron gate variable (1) but for the mean values of n and <V>. I suggest removing this sub-section.

      We thank the reviewer for this suggestion. We agree that, under the assumption that n is a global collective variable, the resulting equation for ⟨n(t)⟩\langle n(t) \rangle⟨n(t)⟩ is equivalent in form to the single-neuron gating equation, driven by the average membrane potential. However, we chose to retain this subsection to explicitly demonstrate how the gating dynamics enter into the mean-field formulation, especially for readers less familiar with this type of reduction. This step also mirrors the structure of the derivation used for other state variables in the model and maintains clarity for potential extensions where n may not be strictly global.

      (Q23) Line 696 - here an equation reference is lost.

      Thank you for pointing this out. We have corrected the text and restored the missing equation reference in the revised manuscript.

      (Q24) Eqs (36) -(37) -- Since the variables r and x entered in Eq (36) are essentially the same as Eq (25), apart from a constant R/pi, the use of two different names complicated in a useless manner an already complicated expression, Please decide to use everywhere r or x and then proceed consequently this applies also to Eq (37). This will also allow us to rewrite the equation in x or r in a more compact form.

      As noted in our response to Reviewer 1, point 14, we have revised Eq. (37) to ensure consistency in notation by replacing x with r throughout.

      (Q25) Eq (37) - This equation is written in a manner that is not careful enough, apart from that the authors are passed now from (x,y) to (pi*r/R,V) , therefore they should substitute everywhere x with r. Furthermore, the equation for the derivative of V is confusing, the authors should use the same approximate expression employed in eq (36) that makes explicit the quadratic dependence on V itself, otherwise, I believe that the equation is incorrect.

      In the same response to Reviewer 1, point 14, we also clarified the expression for \dot{V} in Eq. (37), we reintroduced the full current-based formulation (as in Eq. 16), reversing the quadratic approximation used earlier. This is now explicitly stated in the text, and we have improved the equation presentation to avoid confusion.

      (Q26) Eq (37) below line 708 - From this expression, it is clear that the gate variable n and the potassium variables are ruled exactly by the same equations as for the single neuron Eq (1) and that the Lorentzian Ansatz enter only in the rewriting of the evolution of the membrane potentials of the neurons in the network. In the end, the authors are doing exactly the same approximation made by many other authors [R1-R7], that these variables are collective, i.e. they are the same for all neurons, and in particular n=n(V) is a function of the mean membrane potential V. The mean field model that the authors derive corresponds to a microscopic model where the single neurons are heterogenous only in the intrinsic currents $\eta_i$, but they are all driven by collective variables, like n(V) and the potassium variables that are identical for all neurons. This should be clarified.

      We agree with the conclusion by the reviewer, and as seen through the previous responses, we now explicitly acknowledge the fact that n and the two slow variables are considered as a mesoscopic variables for the mean-field derivation, while for the spiking network, n remains microscopic.

    1. Author response:

      We are writing to provide our provisional response to the public reviews. We note that the reviewers’ comments focus primarily on strengthening technical rigor and quantitative interpretation. We have designed the planned revisions to directly address the reviewers’ major concerns and to strengthen the study’s evidentiary basis. We plan to submit a revised manuscript for the final Version of Record.

      For clarity, we summarize below the major new experiments and analyses that address the reviewers’ primary concerns:

      (1)Validation of Tracking Parameters (Reviewers 1 & 3): We will re-analyze our single molecule tracking data with tighter gap-time allowances (0 seconds) to demonstrate the robustness of our interpretations of short- and long-lived kinetics. We will also generate a supplementary movie with binding trajectories superimposed directly on detected molecules to visually confirm tracking robustness.

      (2) Photobleaching & Two-State Controls (Reviewers 1 & 3): We will report per-cell photobleaching lifetimes derived from our global fluorescence decay. To strengthen this analysis, we will include supplementary measurements using a H2B-HaloTag control under matched imaging conditions and perform single-molecule tracking of GATA2 zinc-finger deletion mutants (N-terminal, C-terminal, and double) as a binding-deficient functional control.

      (3) Protein Expression & Labeling Efficiency (Reviewers 1 & 2): To address concerns about transgene expression and competition with endogenous proteins, we will quantify Halo-GATA2 levels in G1E-ER4 and HPC7 cells and SNAP-GATA2 levels in primary cells using standardized titration methods with established Halo-CTCF and SNAP-RPB1 reference systems.

      (4) Integration of SMT and CUT&Tag (Reviewer 3): We have conducted a quantitative foldchange analysis of our existing CUT&Tag dataset to complement our single-molecule kinetics.

      However, as detailed in our specific response below (R3 point 5), we emphasize that directly integrating population-level genomic occupancy measurements with single-cell kinetic measurements is not straightforward. We will therefore frame the relationship between these datasets as a conceptual consistency check rather than a strict quantitative integration. This quantitative analysis supports and refines the Early-restricted peak set, identifying a high confidence strict subset consistent with the broader presence/absence-defined set described in Figure 5 of the manuscript (see Author response images 1–3 and our response to R3 point 7).

      (5) Characterization of the GATA2-SNAP Mouse (Reviewer 3): We have characterized hematopoietic populations in the homozygous knock-in mouse, including lymphoid (CD3<sup>+</sup>/CD4<sup>+</sup>/CD8<sup>+</sup>/B220<sup>+</sup>/CD19<sup>+</sup>), myeloid (CD11b<sup>+</sup>/Gr1<sup>+</sup>), and erythroid (Ter119<sup>+</sup>) compartments. These data, presented in Author response image 4, indicate that normal mature hematopoietic output is preserved across genotypes. Statistical caveats are described in the corresponding figure legend and in our response to R3 point 8.

      Public Reviews:

      Reviewer 1 (Public review):

      (1) Two binding states: justification and controls

      The authors propose two states of GATA2 binding. Are there only two states? Some longbinding duration distributions here are very long-tailed (e.g., Figure 2D middle), suggesting a possible third state. The authors must explain how they determined that two states provide the best fit and how they classified short versus long binding. Controls should be included for long-lived and short-lived binding (e.g., histone proteins, HaloTag-NLS, or a binding-deficient GATA2 mutant).

      Agreed in part; we will attempt the requested binding-deficient control using existing GATA2 deletion constructs, complemented by GRID and H2B-HaloTag controls.

      We will clarify that the two-state framework is an operational model rather than a claim that GATA2 can occupy only two physical states. This approach is widely used in SMT studies of chromatin-associated transcription factors and transcription machinery (Gebhardt et al., 2013; Liu et al., 2014; Hansen et al., 2017; Kenworthy et al., 2022). In particular, Ling et al. (Science, 2026) recently used two-exponential survival-probability fitting across 58 Halotagged transcription-associated proteins to distinguish transient and stable chromatin-binding populations, while explicitly noting that the simplified two-state model provides a tractable framework even when the underlying physical behavior may be more heterogeneous.

      We agree that our current two-state model may under-represent the diversity of GATA2 chromatin-binding populations in single cells. However, even within this simplified framework, the existing analysis already indicates increased upper-tail dispersion of kinetic measurements (e.g., residence time and/or percentage of stable events) at the single-cell level in early erythroid cells. To support the goodness-of-fit metrics from our two-state fitting, as Reviewer 3 recommends, we will provide a supplementary table containing confidence intervals for the rate parameters and an F-test metric describing the differences between one- and two-state fits.

      To determine whether additional binding states exist, we will perform GRID (Genuine Rate Identification from Distributions), which does not bias the model toward a particular number of states and, in our experience across multiple proteins, yields fits with 3-5 binding populations. However, we have found that in many cases, GRID requires aggregating binding events from multiple cells to achieve consistently robust fits for the populations of relatively rare, long-lived (>~30 sec) binding events. Therefore, GRID will assess whether additional populations exist, but we will lose the ability to analyze changes in the cell populations at the single-cell level.

      We will include the multi-state analysis as a new supplementary figure. We will additionally clarify in the Results and Methods exactly how short- and long-lived binding events are classified (1-second threshold consistent with prior single-molecule frameworks for transcription-factor chromatin interactions; Gebhardt et al., 2013; Liu et al., 2014; Kenworthy et al., 2022) and direct the reviewer to these passages.

      For the requested controls, we will include H2B-HaloTag imaging under matched conditions as a long-lived reference for both photobleaching correction and as a positive control for stable chromatin association, addressing R1 point 2 and R3 point 1 simultaneously.

      We will also attempt to address the reviewer’s request for a binding-deficient control. We have lentiviral constructs in hand that encode GATA2 with a C-terminal zinc-finger deletion (which removes the primary DNA-binding domain), an N-terminal zinc-finger deletion, and a double deletion. We will perform single-molecule tracking of these mutants in the engineered cell systems and test whether removing GATA2’s specific DNA-binding capacity produces the predicted reduction in long-lived chromatin engagement, providing a functional perturbation control. The interpretation of these experiments will depend on the mutants expressing and localizing appropriately, which we will validate before drawing kinetic conclusions. We note that an analogous binding-deficient mutant cannot be examined in the physiological context of the Gata2SNAP knock-in mouse, and we will frame the cell-line mutant analyses accordingly. Together with GRID and the H2B-HaloTag control, these mutants provide complementary lines of validation for the two-state kinetic framework.

      (2) Photophysical and focal-plane artifacts

      The authors should exclude contributions from (i) photobleaching, (ii) blinking, and (iii) Z-axis motion. Describe and quantify the photobleaching correction. Provide analyses or controls that distinguish true dissociation events from photophysical blinking/bleaching or axial motion.

      Agreed.

      We will substantially expand the methodological description and provide three new pieces of supplementary analysis:

      - Photobleaching: A per-cell photobleaching-rate distribution will be plotted for each cell type and differentiation stage, and photobleach-corrected residence-time values will be reported alongside apparent values in the relevant figures. We will also perform H2B-HaloTag imaging under matched illumination, exposure, and dye conditions in each cell line as a longlived chromatin-bound reference, establishing per-cell-type bleach lifetimes to which the GATA2 measurements can be referenced. This approach follows recent SMT precedent in which H2B decay was used to correct residence-time measurements for photobleaching, chromatin and nuclear motion, microscope drift, defocalization, and dye photophysics (Ling et al., Science 2026). The right-censoring photobleach-correction model used in our analysis will be described in detail in the revised Methods, including parameter values and per-cell handling.

      - Blinking: The STRAP single-particle tracking pipeline already accommodates fluorophore blinking when linking trajectories across successive frames, following the multiple-targettracing framework of Sergé et al. (Nature Methods, 2008). This use of short gap-frame allowances to avoid artificially splitting trajectories due to fluorophore blinking or transient defocalization is consistent with recent live-cell SMT studies of chromatin-associated factors (Ling et al., Science 2026). We will add an explicit statement to the Methods describing how blinking-tolerant linkage parameters are set, and we will reanalyze representative datasets

      with stricter maximum off-frame settings to ensure this parameter does not drive our conclusions (also addressing R3 point 6).

      - Z-axis motion: Given our 500-ms exposure and the ~500-nm axial detection range of the HiLo configuration, axial loss is expected to be a minor contributor. We will quantify this indirectly by plotting, as a supplementary analysis, the maximum in-plane 2D spatial exploration of each binding trajectory, defined as the long-axis diameter of the 2D trajectory envelope. Although this does not directly measure z-position, it serves as a control for large apparent displacements that could reflect molecules moving out of the HiLo detection volume and demonstrates that observed dissociation events are not dominated by axial drift.

      Representative photobleaching traces from individual cells (lowest, highest, and median bleach rates) will be included to support the single-molecule interpretation (also addresses R1 point 5).

      (3) HILO illumination and nuclear region sampled

      HiLo is sensitive to illumination angle: slight changes sample different nuclear regions. Explain how the HiLo angle was controlled and confirmed comparable across cells and conditions.

      Agreed.

      We will add a Methods subsection describing our HiLo illumination procedure. In brief, we started at a TIRF-supercritical angle and reduced it toward epifluorescence just enough to achieve high imaging depth while minimizing out-of-focus background signal. Within each biological system (cell line or primary cells), the TIRF angle was held constant across Basal, Early, and Late conditions to ensure direct comparability of kinetic measurements across stages.

      (4) Quantification of event counts and long-binding durations

      The number of binding events and the duration of long-binding events are influenced by imaging conditions. Provide a more detailed analysis of how these variables were controlled and assess the sensitivity of the results to detection and tracking parameters.

      Agreed.

      We will (i) normalize per-cell binding-event counts to nuclear cross-sectional area (extracted from the segmented nuclear masks already in the STRAP pipeline) to control for differences in nuclear size; (ii) report the tracking-parameter sensitivity sweep described above; and (iii) confirm in the revised Methods that all imaging conditions (laser power, exposure, dye concentration, sample preparation) were held constant across stages and cell types, consistent with the existing manuscript text. Per the Reviewing Editor’s guidance, the planned labeling-efficiency and absolute-molecule-quantification experiments will further constrain the interpretation of binding-event counts across conditions.

      (5) Evidence that spots are single molecules

      Provide evidence that spots represent single molecules.

      Agreed.

      We will include a small number of per-event intensity traces from our STRAP tracking output, selected to illustrate the single-step photobleaching behavior characteristic of single-molecule emission (intensity remains approximately constant during the binding event and then drops to background in a single step). The nuclear-fluorescence measurements from the planned labeling-titration experiment will also allow us to confirm that bound-spot densities are consistent with single-molecule occupancy at the labeled fraction used for tracking.

      (6) Description of the spot-analysis pipeline

      The Methods should include a detailed STRAP pipeline description.

      Partially agreed; the existing STRAP reference is appropriate, but the Methods will be expanded.

      STRAP (Haque & Coleman, 2025) is a consolidated, automated implementation of two well-established, previously published frameworks: SLIMfast / multipletarget tracing (Sergé et al., 2008) and evalSPT (Normanno et al., 2015), both of which are cited in the original manuscript. We will expand the Methods to describe the parameter set used in our analysis (detection thresholds, linking radii, gap-frame allowance, photobleaching correction model) so that readers can assess the analysis without referring exclusively to the STRAP manuscript and code repository, while preserving the cited STRAP reference for the full algorithmic description. We respectfully suggest that a complete pipeline description duplicating Haque & Coleman (2025) would not be appropriate in a primary research article.

      (7) Differences among cell systems

      The three cell systems yield notably different results. Provide a more detailed explanation for these differences.

      Agreed.

      We will also explicitly describe the caveats of the engineered systems versus the native GATA2-SNAP primary-cell system, in which endogenous GATA2-SNAP remains under physiological regulation. Specifically, we will discuss how variables such as the GATA1null background, ectopic forced nuclear import of GATA1-ERT, and ectopic GATA2-Halo in G1E-ER4 cells, as well as ectopic GATA2-Halo, endogenous GATA1, and cytokine signaling in HPC7 cells, likely contribute to the observed differences in signatures.

      Reviewer 2 (Public review):

      (1) Expression levels of the GATA2-HaloTag transgene

      Determine the expression levels of the GATA2-HaloTag transgene over the course of differentiation under the conditions used for single-molecule imaging.

      Agreed.

      This is the central concern flagged by the Reviewing Editor. For each cell line (G1E-ER4 and HPC7), we will (i) measure total nuclear GATA2-Halo fluorescence per cell under matched acquisition conditions and (ii) convert this fluorescence intensity to absolute molecules per cell using a Halo-CTCF/U2OS reference standard (Cattoglio et al., 2019; absolute CTCF abundance quantification applied previously by our group). This will provide per-cell GATA2Halo molecule counts at each differentiation stage (Basal, Early, Late). For the primary GATA2SNAP cells, we will perform the analogous comparison against a SNAP-RPB1/U2OS standard.

      (2) Fraction of molecules labeled

      Carry out a titration of the HaloTag ligand and compare the amount of labeled protein under single-molecule imaging conditions to that of saturating labeling.

      Agreed.

      We will perform HaloTag-ligand and SNAP-tag-ligand titrations in each cell type, comparing nuclear fluorescence under the limiting-label conditions used for single-molecule tracking with that under saturating labeling. This will yield a per-cell-type labeled fraction and allow us to confirm that comparisons of binding-event counts across conditions are not confounded by differences in labeling efficiency. The labeled-fraction values will be reported in a new supplementary figure and incorporated into our quantification of binding-event rates.

      (3) Robust single-particle tracking

      Show images of particle trajectories or movies superimposing trajectories on imaging data.

      Agreed.

      We will generate visualizations of selected long-lived binding events with single-particle trajectories overlaid on the imaging data — using a multi-frame color overlay (e.g., five sequential frames in distinct colors superimposed) so that linkage of the spot across frames is visually unambiguous — and include them as a new supplementary figure or movie. Examples will be drawn from each cell system to demonstrate consistent tracking quality.

      Reviewer 3 (Public review):

      (1) Photobleaching correction; per-cell bleach lifetimes

      Report the per-stage (or per-cell) photobleaching lifetimes and the photobleachcorrected residence time values alongside apparent values, ideally with an H2B-Halo control.

      Agreed.

      Addressed by the photobleach-rate distribution and H2B-HaloTag control analyses described under R1 point 2. The supplementary figure will explicitly compare per-cell bleach lifetimes across stages, report photobleach-corrected residence-time values alongside apparent values and include H2B-HaloTag controls under matched conditions in each cell line.

      (2) Mechanistic differences across systems

      The three systems show qualitatively different signatures: residence time change in G1EER4, bound fraction expansion in HPC7 and primary cells. Reporting an on-rate proxy alongside k_off would help.

      Agreed.

      Addressed by the cross-system kinetic framing described under R1 point 7 and by the GRID state-spectrum analysis described under R1 point 1. We will explicitly frame the three systems in terms of underlying kinetic mechanism in both Results and Discussion, following the conceptual distinction emphasized by Ling et al. (Science 2026) in which residence time reports binding stability once engaged, whereas changes in bound fraction or event frequency can indicate altered association/recruitment efficiency. In this framework, the G1E-ER4 residencetime signature is consistent with reduced dissociation (a longer-lived bound state), while the longlived-fraction expansion in HPC7 and primary cells is consistent with an increased target-search efficiency or specific-binding-competent pool. Alongside the GRID-derived state-spectrum analysis, we will report an apparent engagement-rate proxy calculated as binding events per unit imaging time normalized to detectable molecule number; this proxy is an approximation, not a direct k_on measurement, as accurate determination of k_on from single-molecule tracking requires concentration-dependent on-rate experiments that are outside the scope of the present study. We thank the reviewer for this suggestion, which we agree sharpens rather than alters the central message.

      (3) Per-cell GATA2 concentration and the uncoupling claim

      Quantify total nuclear GATA2-Halo signal per cell across stages; for primary cells, a western blot or quantitative immunofluorescence on flow-sorted populations would make the uncoupling argument more defensible.

      Agreed.

      For the cell lines, the per-cell nuclear GATA2-Halo quantification described in our response to R2 point 1 addresses this point.

      For primary cells, where the biological claim is strongest, we will exploit the endogenous Gata2SNAP knock-in itself as a quantitative reporter of total GATA2 protein. Specifically, we will label flow-sorted CD71/Ter119 populations from Gata2-SNAP mouse bone marrow with SNAP-Cell 647-SiR at saturating concentration in a parallel acquisition to the limiting-label single-molecule tracking experiment. Total nuclear SNAP-GATA2 fluorescence at saturating labeling provides a measure of endogenous GATA2 abundance per cell at each erythroid stage, in the same chemistry used for our single-molecule measurements, and will be benchmarked against a SNAPRPB1/U2OS reference standard for absolute molecule counting. This approach (i) measures the protein of interest in the labeling chemistry already established in this study; (ii) avoids reliance on quantitative immunofluorescence, which we have not been able to validate under our flowsorted-cell conditions; and (iii) extends the same analytical framework — saturating versus limiting labeling, with U2OS reference standards — across cell lines and primary cells. Quantitative western blotting on flow-sorted populations remains an alternative we will consider if specifically requested by the reviewers.

      (4) Single-cell distribution analysis

      Distribution-based statistics (K-S test, mixture model) rather than (or alongside) meanbased ANOVA, particularly for the Early populations, which look potentially bimodal.

      Agreed.

      We will perform Kolmogorov–Smirnov and Gaussian mixture model analyses of the single-cell long-lived fraction and residence-time distributions across stages, reporting these alongside the existing Welch ANOVA results in a new supplementary figure. This analysis is consistent with the conceptual framework cited in the manuscript (Wheat et al., 2020; Palii et al., 2019) for probabilistic hematopoietic transitions and may reveal subpopulation structure underlying the Early-stage signal. The GRID analysis further complements this by formally testing whether multi-state mixture models are statistically preferred at each stage. However, GRID analysis requires aggregating binding events across cells, which limits our ability to monitor changes in population dispersion at the single-cell level.

      (5) Quantitative integration of CUT&Tag with SMT

      Attempt a back-of-the-envelope calculation of whether the residence-time or fraction changes are quantitatively consistent with the acquisition of the 1,167 Early-restricted sites.

      Partially agreed; will attempt an order-of-magnitude framing.

      We thank the reviewer for this thoughtful suggestion. We agree that more explicit framing of the quantitative relationship between the two datasets will strengthen the integration. We will add a paragraph to the Discussion presenting an order-of-magnitude calculation linking the observed residence-time and long-lived-fraction changes to the steady-state occupancy increase predicted at competent regulatory sites, with explicit caveats regarding (i) the inherently semi-quantitative nature of CUT&Tag signal and (ii) the assumptions required to translate population-averaged occupancy into the genome-wide site count observed. For the G1EER4 cells, we observe relatively minor shifts in population-mean behavior as single-cell dispersion increases. Therefore, it may be difficult to directly link population-based measurements (e.g. CUT&Tag) with single-cell kinetic measurements (SPT). This distinction between occupancy and dynamics is consistent with recent systematic SMT analysis of the eukaryotic transcription machinery, in which factors appearing persistently associated in ensemble genomic assays were shown to exchange on second-scale timescales in living cells (Ling et al., Science 2026), emphasizing that population genomic occupancy and single-molecule residence time are complementary but not directly interchangeable measurements. Closing this gap rigorously is a major hurdle for the field and will require substantial technology development on quantitative single-cell CUT&Tag occupancy measurements. We will therefore frame our analysis as a consistency check rather than a strict quantitative integration. The reviewer notes that this analysis “does not change the central message; it sharpens it,” and we agree.

      (6) Short-lived kinetic interpretation and tracking parameters

      The 1.5 s gap allowance is long relative to the short-lived residence times in primary cells. A sensitivity analysis with tighter gap parameters would help. Also clarify how slowing of search reconciles with increased binding events at Early.

      Agreed.

      Addressed by the tracking-parameter sensitivity analysis described under R1 point 2. We apologize for the lack of clarity in our original description of the gap allowance. Our current maximum off-frame parameter is set to 2 frames, corresponding to a 0.5-s gap allowance. We will rerun the tracking analysis on representative datasets using a maximum off-frame parameter of 1, corresponding to no missed frames, and will report the resulting residence-time distributions alongside the original analysis to demonstrate robustness. We will also clarify in the Results and Discussion how changes in short-lived binding kinetics are reconciled with the increase in detectable binding events at the Early stage, drawing on the apparent engagement-rate proxy interpreted alongside the GRID-derived state-spectrum analysis.

      (7) CUT&Tag peak definition and quantitative analysis

      Report (a) signal intensity distribution at the 1,167 sites across stages (scatter or density plot beyond the heatmap) or (b) differential binding analysis (e.g., DESeq2). State replicate count and overlap of Early-restricted sets across replicates.

      Agreed; normalized fold-change analysis completed, with replicate-aware differential binding analysis planned if additional replicates are generated.

      We have performed a normalized count-based fold-change analysis of the union peak set from the existing GATA2 CUT&Tag dataset (14,468 peaks) using the goodpeaks framework previously used in our group, yielding per-peak log2 fold-change values and discrete dynamicstatus calls (Gained / Lost / Unchanged at |log2FC| ≥ 2) for each of the two transitions (Basal → Early at 0 vs 2 h, and Early → Late at 2 vs 24 h). This provides a conservative quantitative complement to the presence/absence peak-calling analysis presented in Figure 5; if additional replicate data are generated, we will perform replicate-aware differential binding analysis (DiffBind/DESeq2; Love et al., 2014; Stark & Brown, 2011) and report replicate overlap. This analysis addresses option (b) of the reviewer’s request and also enables the visualization requested in option (a) as a cross-stage scatter (Author response image 1). We present the quantitative analysis as a supplement to the presence/absence-defined Early-restricted set in Figure 5 of the manuscript, providing two orthogonal lines of evidence for the same biology. We note that the CUT&Tag experiments were initially performed as a validation step to confirm that the tagged GATA2-Halo constructs recapitulate endogenous chromatin-binding behavior, including appropriate genomic localization and expected GATA switch dynamics. This validation supports the conclusion that the observed single-molecule kinetics reflect physiologically relevant GATA2 engagement. Having established this, we subsequently extended the dataset to perform the quantitative analyses presented here.

      Quantitative findings.

      - 384 peaks were Gained (|log2FC| ≥ 2) at the Basal → Early transition.

      - 1,006 peaks were Lost over the same transition.

      - 178 peaks were Gained at Basal → Early and subsequently Lost at Early → Late, defining the strict differentially-restricted Early set (Author response image 1, red points). This set represents the higher-confidence subset of the manuscript’s broader presence/absence-defined Earlyrestricted set (n = 1,167; defined as MACS2 peaks at q < 0.01 present at Early but absent at Basal and Late).

      - 200 peaks were Gained at Early and retained at Late, indicating stable acquisition.

      - 49 peaks were acquired only at the Late stage.

      The discrepancy between the broader presence/absence set (1,167) and the strict differential set (178) reflects the analytical choice the reviewer raised: presence/absence calls based on a peaksignificance threshold are sensitive to near-threshold peaks, whereas differential analysis with a fold-change cutoff captures only sites with quantitatively pronounced stage-restricted enrichment. We interpret these as two complementary definitions: the broader set captures all peaks meeting a stage-specific peak-calling criterion, and the strict subset isolates the most quantitatively dynamic core of that population.

      Importantly, the three named example loci shown in Figure 5D of the manuscript — Nono (promoter-proximal), Nr3c1 (intron 2), and Gata3 (distal intergenic) — all survive the strict differential criterion (each shows |log<sup>2</sub>FC| ≥ 2 in both transitions, consistent with a clean Gainedthen-Lost signature). The published example panel therefore represents the high-confidence intersection of both definitions, supporting the robustness of the manuscript’s selected illustrative cases.

      We will explicitly state the number of CUT&Tag replicates per stage in the revised Methods and figure legends. Where the differential analysis is currently based on a single replicate per stage, we will explicitly note this and treat the strict subset as a conservative confirmatory analysis. An additional replicate is under consideration for the full revision, and if performed, overlap of Earlyrestricted calls across replicates will be reported.

      Motif cross-validation against a matched-GC background using HOMER and/or MEME-ChIP is planned for the strict differential subset and will be reported alongside the original SeqPos analysis in the revised Figure 5F or its supplement.

      Author response image 1.

      Cross-stage log<sub>2</sub> fold-change scatter for GATA2 CUT&Tag peaks. Each point represents a single peak in the union peak set (n = 14,468). The x-axis shows the log2 fold change from Basal (0 h) to Early (2 h); the y-axis shows the log2 fold change from Early (2 h) to Late (24 h). The sign convention follows the field-standard direction (positive log2FC = increased signal at the later time point). Peaks are colored by dynamic-status classification: unchanged/other (gray; n = 9,794); Lost at Early (blue; n = 109); Gained at Early and retained at Late (orange; n = 200); acquired only at Late (teal; n = 49); and Early-restricted, defined as Gained at Early and Lost at Late with |log2FC| ≥ 2 in both transitions (red; n = 178). The Early-restricted population occupies the lower-right quadrant, consistent with a transient kinetic peak of GATA2 binding.

      Author response image 2.

      Density representation of GATA2 CUT&Tag peak dynamics with Early-restricted peaks highlighted.

      Author response image 2 is shown for illustrative reference and is not annotated with a separate legend; it presents the same data as Author response image 1 in a hexbin density format to emphasize the bulk of unchanged peaks at the origin and the spatial separation of the Early-restricted set.

      Author response image 3.

      Genomic-annotation comparison of newly acquired GATA2 binding at Early. Stacked-bar comparison of genomic annotations (ChIPseeker classification) for two definitions of the newly acquired GATA2 peaks at the Early erythroid stage: all peaks Gained at Basal → Early (orange; n = 384) and the strict Early-restricted subset (Gained then Lost; red; n = 178). Annotation categories shown: Promoter (≤1 kb of TSS), Intron, Distal Intergenic, and Other (Exon, 5′/3′ UTR, Downstream). Both peak sets contain substantial promoter-proximal and distal/intronic components, consistent with the two-subclass model described in Figure 5E–G of the manuscript (GATA2-only promoter-proximal peaks with GATA/RUNX motifs, and GATA2/GATA1 cobound distal peaks with composite GATA/E-box motifs). The strict subset shows a higher proportion of intronic and distal-intergenic sites and a lower proportion of promoter-proximal sites than the full Gained set; this difference will be discussed transparently in the revised Results. Motif analysis (HOMER/MEME-ChIP, planned for the full revision) will be performed on both peak sets to confirm that the GATA/RUNX and GATA/E-box subclass signatures are preserved.

      (8) Knock-in mouse hematopoietic validation

      A brief characterization of basic hematopoietic parameters in homozygotes (CBC, LSK/HSPC frequencies, or colony assays) would confirm the tagged allele is physiological.

      Agreed; data acquired and analyzed.

      We have characterized mature trilineage hematopoietic populations in whole bone marrow from wild-type, heterozygous (Gata2Het), and homozygous (Gata2Homo) Gata2-SNAP knock-in mice (n = 5 per genotype). Bone marrow cells were stained for myeloid (CD11b<sup>+</sup> Gr1<sup>+</sup>), lymphoid (CD3<sup>+</sup>/CD4<sup>+</sup>/CD8<sup>+</sup>/B220<sup>+</sup>/CD19<sup>+</sup>), and erythroid (Ter119<sup>+</sup>) markers and analyzed by flow cytometry. Lineage frequencies are shown as percentages of live bone marrow cells in a new Figure Supplement in the revised manuscript.

      For myeloid and erythroid populations, omnibus one-way ANOVA detected no significant differences across genotypes (Myeloid: F(2,12) = 2.616, P = 0.1140; Erythroid: F(2,12) = 0.4943, P = 0.6219). Dunnett’s multiple-comparisons test against the WT control did not detect significant pairwise differences for either knock-in genotype (Myeloid: WT vs Het P = 0.1351, WT vs Homo P = 0.9926; Erythroid: WT vs Het P = 0.7017, WT vs Homo P = 0.9602).

      For the lymphoid compartment, although the omnibus ANOVA reached significance (F(2,12) = 6.690, P = 0.0112), no pairwise comparison against WT remained significant after multiplecomparisons correction (Dunnett’s adjusted P values: WT vs Het = 0.1217; WT vs Homo = 0.2078). We therefore interpret this result conservatively. Brown-Forsythe and Bartlett’s tests showed no significant differences in variance across genotypes (P = 0.1423 and P = 0.0908), so the result is not attributable to unequal variances. We do not interpret these data as indicating an unambiguous lymphoid phenotype in either heterozygous or homozygous Gata2-SNAP mice; this interpretation is consistent with the broader pattern across all three lineages, in which no pairwise comparison against WT survives multiple-comparisons correction. We will note in the figure legend and in the Results text that more granular HSPC-compartment analysis (LSK, MPP, lineage-restricted progenitor frequencies) and a complete blood count (CBC) remain valuable directions for future characterization of this resource and will be considered for the full revision if specifically requested.

      Author response image 4.

      Bone marrow trilineage frequencies in Gata2-SNAP knock-in mice. Bone marrow was harvested from the femurs and tibias of wild-type (WT), heterozygous (Gata2Het), and homozygous (Gata2Homo) Gata2-SNAP knock-in mice (n = 5 per genotype; mixed sex; 12–14 weeks). After ACK lysis, cells were stained for myeloid (CD11b<sup>+</sup> Gr1<sup>+</sup>), lymphoid (CD3<sup>+</sup>/CD4<sup>+</sup>/CD8<sup>+</sup>/B220<sup>+</sup>/CD19<sup>+</sup>), and erythroid (Ter119<sup>+</sup>) markers and analyzed by flow cytometry. Each dot represents one mouse, and horizontal bars indicate genotype means. Statistical results: Myeloid: ANOVA F(2,12) = 2.616, P = 0.1140; Dunnett’s adjusted P values WT vs Het = 0.1351, WT vs Homo = 0.9926. Lymphoid: ANOVA F(2,12) = 6.690, P = 0.0112 (omnibus); Dunnett’s adjusted P values WT vs Het = 0.1217, WT vs Homo = 0.2078. Erythroid: ANOVA F(2,12) = 0.4943, P = 0.6219; Dunnett’s adjusted P values WT vs Het = 0.7017, WT vs Homo = 0.9602. Brown-Forsythe and Bartlett’s tests for unequal variance were non-significant in all three lineages. Although the lymphoid omnibus ANOVA reached nominal significance, no pairwise comparison with WT remained significant after multiple-comparison correction; we therefore interpret this result conservatively (see response to R3 point 8).

      Summary

      We thank the editors and the three reviewers for the constructive and detailed assessment. The planned revisions consist of:

      - Four new experiments [planned] (HaloTag/SNAP labeling efficiency and absolute molecule counts via U2OS reference standards; H2B-HaloTag photobleaching reference; percell quantification of total endogenous GATA2 in flow-sorted primary Gata2-SNAP populations via saturating SNAP-tag labeling, benchmarked against a SNAP-RPB1/U2OS reference standard; single-molecule tracking of GATA2 N-terminal, C-terminal, and double zinc-finger deletion mutants in the engineered cell systems as a binding-deficient functional control).

      - Six analyses of existing data (GRID multi-state fitting [planned]; per-cell bleach-rate distributions and photobleach-corrected residence times [planned]; tracking-parameter sensitivity [planned]; nuclear-area normalization and total-displacement controls [planned]; normalized fold-change CUT&Tag analysis [completed; motif cross-validation planned], presented in Author response images 1–3; distribution-based single-cell statistics [planned]).

      - One previously-acquired dataset [completed] (trilineage hematopoietic flow cytometry of homozygous Gata2-SNAP knock-in mice; presented in Author response image 4 with full statistical detail).

      - Substantial revisions to text and figures [planned] to address statistical reporting, methodological description, mechanistic framing of cross-system differences, and refinement of the Figure 6 schematic.

      With respect to the requested binding-deficient single-molecule control, we will attempt to address this directly using sequence-validated lentiviral constructs in hand encoding GATA2 mutants lacking the C-terminal zinc finger, the N-terminal zinc finger, or both. These mutant analyses will be complemented by GRID multi-state analysis and H2B-HaloTag controls, providing converging lines of validation for the two-state kinetic framework. We note that an analogous mutant cannot be examined in the physiological context of the Gata2-SNAP knock-in mouse, and we will frame the cell-line mutant analyses accordingly.

      We believe these revisions directly address the editors’ specific guidance regarding labeling efficiency and methodological clarification. We thank the editors and reviewers for their time and look forward to submitting the revised manuscript.

      References cited in this response:

      References listed below are cited in this provisional response in support of the planned analyses and methodology.

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      Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature Communications, 10(1), 1930. https://doi.org/10.1038/s41467-019-09982-5

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    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      This manuscript is very interesting and timely. By introducing the critical effects of desolvation barriers and solvent (water)-separated minima into the implicit-solvent potentials (of mean force, PMFs) for coarse-grained molecular dynamics simulations of biomolecular liquid-liquid phase separation (LLPS), this work fills a gap that should be apparent to researchers of protein folding in the past couple of decades but has so far escaped deserved attention such that these basic features of aqueous solvation have seldom, though not never, been invoked in recent studies of biomolecular condensates. Although the present paper deals almost exclusively with homopolymers, this work can be a foundation for the future development of a new, more physical coarse-grained interaction scheme for simulating amino acid sequence-dependent effects, which I presume is the authors' ongoing or next endeavor. The results presented in this manuscript are highly valuable.

      We thank the reviewer for all the insightful comments.

      However, there is room for improvement in the authors' description of (i) the broader impact of effects of desolvation barrier and solvent-separated minimum in the thermodynamics of biomolecular condensates, especially with regard to the ramifications on hydrostatic pressure-dependent effects; (ii) the physical implication of using a 20-parameter hydropathy scale rather than a 210-parameter pairwise amino acid interaction scheme; and (iii) temperature-dependent effects, including the authors' discussion of "enthalpic" and "entropic" contributions. In all these aspects, the authors' discussion should be put in a more comprehensive context of the existing literature. At a few other places, the description of the methods and results should be clarified as well. Accordingly, the authors should revise the manuscript to address the following items thoroughly within the revised manuscript (not merely in the response letter) with the additional references mentioned below included in the revised discussion:

      (1) In several places, e.g., on line 77 (p.2), the authors appear to suggest that "implicit-solvent representation" is the origin of the deficiency in commonly utilized coarse-grained potentials that this study is aiming to rectify. But desolvation barriers and solvent-separated minima are also features of implicit-solvent representations; they are just features that should be incorporated in more accurate implicit-solvent potentials. This point is stated quite clearly and accurately in the Abstract (p.1) but not consistently in the rest of the text. The authors should check the entire text carefully to ensure that a coherent, accurate perspective is presented.

      We thank the reviewer for the insightful comment and suggestion. In this work, rather than departing from the implicit‑solvent modeling framework, our intention is to incorporate the desolvation effect within the implicit solvent model framework. In the revised manuscript, we will revise the text to ensure this point is presented clearly and consistently throughout the paper.

      (2) In the discussion of the importance of desolvation barriers and solvent-separated minima in the Introduction (pp.1-3), connections should be drawn to recent works that utilize these PMF features to rationalize hydrostatic pressure (P)-modulated effects on biomolecular LLPS, including the P-dependent reentrant phase separation of alpha elastin; see Cinar et al. (2019) Chem Eur J 25:13049 (https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/chem.201902210) and references therein, especially discussions around Figures 10, 11 & 13 in this reference.

      We thank the reviewer for bringing these references to our attention. The hydrostatic pressure modulated effects on LLPS provide important context for understanding the physical significance of desolvation barriers and solvent‑separated minima. In the revised manuscript, we will expand the literature discussion by incorporating previous studies on pressure‑modulated phase separation.

      (3) In the lower panels of Figures 2D, E (p.5), what do the differently colored small circles in the double-minimum free energy profiles represent? Does the color shading have the same meaning as that in the upper panels? If so, what do the positions of the circles on the free energy profile represent? The authors should clarify this.

      We thank the reviewer for the suggestion to improve the clarity of the figure. In the lower panels of Figures 2D and 2E, the colored dots were intended solely as a qualitative illustration of the populations of residue‑pair configurations along the effective energy surface. Their colors are not related to the color scale used in the phase diagrams shown in the upper panels. We will modify the color scheme to improve clarity.

      (4) The discussion regarding entropy and enthalpy around Figure 2 is quite confusing as it stands. What do the authors mean exactly by the association of entropy or enthalpy with the desolvation barrier of the solvent-separated minimum? Are they referring to conformational entropy?

      We apologize for the confusion. When the desolvation barrier is high, configurations with inter‑residue distances corresponding to the barrier region become difficult to access, thereby reducing the conformational entropy of the condensed phase. This interpretation is supported by Figure 2—figure supplement 1C, where increasing the desolvation barrier decreases the population in the barrier region of the radial distribution function, indicating that fewer residue‑pair configurations are sampled there. In contrast, increasing the depth of the solvent‑separated minimum makes the condensed phase more energetically favorable. In the revised manuscript, we will incorporate this discussion to improve clarity.

      (5) Do the authors assume that the PMF (effective implicit-solvent potential) is a purely enthalpic term? It appears to be the authors' assumption. If so, the assumption has to be stated clearly in their discussion of "entropy" vs "enthalpy" around Figure 2.

      We thank the reviewer for highlighting this important point. In this work, the PMF profile is constructed from atomistic simulation results, and thus both entropic and enthalpic contributions shape the overall PMF. In the revised manuscript, we will clarify that the PMF represents a free‑energy profile along the intermolecular distance and therefore incorporates enthalpic and entropic contributions from the solute, solvent, and configurational degrees of freedom.

      (6) Closely related to points 3-5 above, it should be stated clearly that the "temperature" used in the authors' simulations does not represent experimental temperature if the authors are using purely enthalpic effective potentials because PMFs are in fact temperature-dependent. This clarification is necessary to avoid misunderstanding. In this regard, it should be noted that temperature-dependent effective interactions have been used for modeling biomolecular condensates in analytical theory (Lin, Song, Forman-Kay & Chan, J Mol Liq 2017, already in the citation list) as well as in coarse-grained molecular dynamics simulations [Dignon et al. (2019) ACS Cent Sci 5:821-830 (https://pubs.acs.org/doi/10.1021/acscentsci.9b00102); Chakravarti & Joseph (2025) Protein Sci 34:e70284 (https://onlinelibrary.wiley.com/doi/10.1002/pro.70284)]. The latter two studies, not cited currently, are particularly relevant and thus should be cited because the authors may wish to incorporate temperature-dependent features in their ongoing or future effort in constructing a more comprehensive coarse-grained interaction scheme for biomolecular LLPS simulation.

      We thank the reviewer for raising this important point. We agree that PMFs and the corresponding effective interactions should be temperature dependent, and therefore the simulation temperature in our current temperature-independent CG potential cannot be interpreted as a fully quantitative experimental temperature. In the revised manuscript, we will clarify the above point. We will also expand the discussion to include previous studies that introduced temperature-dependent effective interactions in analytical theories and coarse-grained simulations of biomolecular condensates.

      (7) In tackling "entropy" vs "enthalpy", it should be noted that the temperature dependence of the effective interactions entails an entropic contribution (which is itself temperature dependent) in addition to conformational entropy. As for the effective potential with desolvation barrier and solvent-separated minimum, it should be noted that the decomposition into entropic and enthalpic contributions at the direct contact, desolvation barrier, and solvent-separated minimum can be dramatically different, see, e.g., MaCallum et al. (2007) PNAS 104:6206-6210 (https://www.pnas.org/doi/full/10.1073/pnas.0605859104) and references therein.

      We agree that a temperature‑dependent PMF includes entropic contributions beyond the configurational entropy discussed around Figure 2. In the present manuscript, our discussion of entropy in that context refers specifically to the reduced accessible configurational space of residue‑pair states in the coarse‑grained ensemble, rather than to a full thermodynamic decomposition of the PMF. In the revised manuscript, we will make this distinction explicit. We will also note that the direct‑contact minimum, desolvation barrier, and solvent‑separated minimum may each have distinct enthalpic and entropic components, and that resolving these components would require additional temperature‑dependent PMF calculations. We will discuss this as a limitation of the current model and as a direction for future parameterization.

      (8) P.7, line 340: The proportionality relation follows directly from the standard Flory-Huggins result T_c = T chi(T)/chi_c, thus the proportionality constant is exactly 1/chi_c. Is this the standard relation that the authors are invoking here? The authors should clarify this.

      We thank the reviewer for pointing this out. Yes, our argument uses the condition that chi_c is fixed at the critical point for a given chain length. We will revise the text to explicitly state this relation and add the missing intermediate step, so that the proportionality used in the manuscript is clearer.

      (9) The study on dynamic consequences on pp.8-11 is interesting, but clarifications are necessary:

      (i) The vertical schematic in Figure 4A should be explained in detail in its entirety. As it stands, no explanation is provided either in the figure caption or in the text. In particular, what does "elasticity driven" refer to?

      (ii) The top snapshot in Figure 4A is labeled t_sim = 0 ns. Does it mean that the snapshot shown is the only chain configuration that the authors used to start the simulation, and that the snapshot does NOT represent the result of any time evolution, no matter how short the duration is? However, if that is the case, why is this snapshot identified with spinodal decomposition if it is not the product of a time evolution from a more homogeneous configuration?

      (iii) Related to (ii) - do the rectangular boxes shown represent the entire simulation box or just part of the box containing the polymer chains? One would imagine that if the top snapshot represents spinodal decomposition, the simulation would have been started at a more uniform distribution a short time prior? Why is this not the case?

      (iv) What precisely do the small yellow beads and black-colored springs in the zoom-in image of Figure 4E represent?

      We thank the reviewer for pointing out these unclear issues in Figure 4. In the revised manuscript, we will better explain the vertical schematic in Figure 4A, including the progression from the early growth of density fluctuations, to intermediate kinetic arrest, and finally to late-stage coarsening. We will also clarify that “elasticity driven” refers to the resistance to domain deformation caused by transient inter-chain network connectivity. We will clarify that t_sim = 0 denotes the time immediately after the temperature quench from the high-temperature homogeneous state to the low-temperature two-phase region. This snapshot is the post-quench initial configuration, while spinodal decomposition refers to the subsequent amplification of density fluctuations after the quench. The displayed snapshot is one representative trajectory, not the only initial configuration used in the simulations. The quantitative kinetic analysis was averaged over multiple independent trajectories. The rectangular box represents the entire simulation box. Although the system was equilibrated at high temperature before the quench, instantaneous density fluctuations remain, so the initial configuration is not perfectly uniform. In Figure 4E, the yellow beads represent interacting residue pairs. The black springs schematically represent the transient elastic network formed by these interactions, rather than a precise structural model.

      (10) In discussing dynamic effects, it is useful to draw connections to related works on the effect of chain flexibility on "aging" of condensate [Biswas & Potoyan (2024) PRX 45:9222-9245 (https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.2.023011)] and characterization of viscoelasticity in simulations of biomolecular condensates [Tejedor et al. (2023) J Phys Chem B 127:4441-4459 (https://pubs.acs.org/doi/10.1021/acs.jpcb.3c01292)], as the effects of desolvation can be explored further based on these prior works.

      We thank the reviewer for this helpful suggestion. In the revised Discussion, we will cite and discuss the related studies on condensate aging and viscoelasticity, including the effects of chain flexibility, sticker lifetime, desolvation, and transient network formation on condensate material properties. These works provide an important context for interpreting our dynamic results. We will clarify that desolvation may influence condensate dynamics not only by slowing local rearrangements, but also by modulating transient network connectivity, kinetic arrest, and viscoelastic relaxation.

      (11) Much of the present study is based on the original HPS formulation of Dignon et al. (2018). In this regard and also in anticipation of future development of improved interaction schemes, several issues should be stated and discussed, even if briefly:

      (i) The original HPS model has a basic shortcoming in accounting for the relative interaction strengths of, among others, arginine vs lysine residues [Das et al. (2020) PNAS 117:28795-28805 (https://www.pnas.org/doi/10.1073/pnas.2008122117)].

      (ii) Compared to 210-parameter pairwise interaction schemes, such as KH in Dignon et al. (2018) and Joseph et al. (2021), the 20-parameter interaction scheme is likely too restrictive to account for pairwise amino acid residue interactions [Wessén et al. (2022) J Phys Chem B 45:9222-9245 (https://pubs.acs.org/doi/10.1021/acs.jpcb.2c06181)].

      (iii) The height of the desolvation barrier may vary significantly for different amino acid residue pairs, see, e.g., Figure 11 of Cinar et al. (2019) mentioned above (and references therein). The authors should discuss these nuances in the revised version. They may also wish to take them into consideration in future investigations.

      We thank the reviewer for highlighting these important limitations of the original HPS-based framework. We agree that a 20‑parameter hydropathy‑scale model has limitation in fully capturing residue‑pair‑specific interactions, including well‑established differences such as those between arginine and lysine. In the revised manuscript, we will explicitly discuss this limitation and cite the suggested studies on residue‑specific and pairwise interaction schemes. We also agree that desolvation barriers and solvent‑separated minima are likely to depend on amino‑acid pair identity. In the present work, we employ a simplified, residue‑independent desolvation parameterization to isolate the general thermodynamic and kinetic consequences of desolvation in coarse‑grained LLPS simulations. In the revised Discussion, we will clarify this scope and emphasize that developing residue‑pair‑specific desolvation parameters, potentially within a 210‑parameter interaction framework, is an important direction for future work.

      Reviewer #2 (Public review):

      Summary:

      This manuscript addresses an important and timely question in the molecular simulation of biomolecular condensates. Most residue-level coarse-grained models used for IDP phase separation employ implicit solvent and represent effective interactions through relatively simple pairwise potentials. While these models have been very useful, they usually do not explicitly distinguish direct contacts from solvent-separated interactions, nor do they include an energetic barrier associated with water removal. This manuscript attempts to address that limitation by introducing desolvation-inspired terms into coarse-grained models and examining their consequences for phase behavior, chain conformations, dense-phase packing, and dynamics.

      Strengths:

      The central idea is physically well motivated. Using a simple homopolymer model, the authors show that increasing the desolvation barrier suppresses phase separation, whereas stabilizing solvent-separated contacts enhances phase separation. They further show that solvent-separated interactions can reduce dense-phase over-compaction, which is a meaningful result given the known challenges in obtaining both accurate single-chain dimensions and realistic dense-phase properties from the same coarse-grained model. The finding that desolvation-like terms can reshape dense-phase packing without simply rescaling the overall interaction strength is interesting and could be useful for future model development. I also found the attempt to connect conformational changes across dilute and dense phases with thermal distance from the critical point to be intriguing. The dynamic analysis, including the FRAP-like simulations and the discussion of kinetic arrest during coarsening, adds another useful dimension to the work.

      We thank the reviewer for all these positive and constructive assessment and comments. We are encouraged that the reviewer found the central idea physically well motivated and recognized the value of introducing desolvation-inspired terms to distinguish direct contacts, solvent-separated interactions, and the energetic barrier associated with water removal in coarse-grained models of biomolecular condensates.

      Weaknesses:

      At the same time, there are several places where the manuscript would benefit from more careful framing. First, the desolvation terms are still effective coarse-grained parameters rather than a direct representation of water molecules. The language sometimes gives the impression that desolvation is being treated explicitly, whereas the model introduces desolvation-inspired effective interactions into an implicit-solvent framework.

      We agree that the current wording should more clearly reflect the nature of our model. The desolvation terms introduced in this work are effective coarse-grained interaction terms rather than an explicit molecular representation of water. In the revised manuscript, we will carefully revise the language throughout the article to describe the model as incorporating desolvation-inspired effective interactions within an implicit-solvent coarse-grained framework.

      Second, the conformational analysis is interesting, but the broader context of prior work on dilute-to-dense phase conformational reorganization of IDPs could be more clearly discussed. This would help clarify what is new in the present work, whether it is the conformational change itself, its dependence on desolvation terms, or the proposed scaling with distance from the critical point.

      We appreciate this suggestion. In the revised manuscript, we will place the conformational analysis in the context of prior work and discuss the observed conformational changes more explicitly from the perspective of desolvation-inspired interactions. We will also clarify the assumptions behind the scaling relation between conformational change and thermal distance from the critical point.

      Third, the dynamic results are potentially useful, but the manuscript should more clearly articulate what is nontrivial beyond the expected slowing of local rearrangements by an added barrier in the potential.

      We thank the reviewer for the suggestion. In the revised manuscript, we will clarify which aspects of the observed dynamics can be directly expected from the added desolvation barrier and which trends arise from the combined effects of desolvation on packing density, chain mobility, kinetic arrest, and coarsening.

      We again thank the editors and reviewers for their constructive comments and suggestions. We believe that the planned revisions will improve the precision of the model description, clarify the physical interpretation of the desolvation-inspired terms, expand the relevant literature context, and better define the scope and limitations of the current framework.

    1. Author response:

      We thank the Reviewers for their time and effort reviewing our manuscript, we are particularly thankful for the literature recommendations of Reviewer 1, and the analysis ideas of Reviewer 2.

      We are glad that both Reviewers agree that the method we developed provides value to the field. We furthermore agree that our theoretical claims and conclusions could be supported by further analyses. Thus, we primarily plan to focus on this.

      We plan to strengthen our statements by:

      - Comparing our metrics to those of alternative learning processes and hypotheses

      - Additional analyses, including ones using standardized learning scores, collapsed saccade likelihoods for learning-dependent and not-learning-dependent saccades, angular deviations instead of the binary update variable, and a breakdown of high-probability triplets into ones that end with a pattern element or a random one.

      - Adding further information regarding saccades, trials without saccades, and saccade starting points.

      Furthermore, we plan to strengthen our Methods section: some of the Reviewers’ points potentially stem from our unclear description of the ASRT task, thus, the Task & Procedure section needs deeper and clearer explanations. Lastly, we will extend the Introduction, citing the literature recommended in the reviews, which indeed could provide further depth.

    1. Author response:

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

      eLife Assessment

      This study presents valuable findings on the relationship between nutrient availability and NAD/NADH levels, which in turn regulate biomass production in cancer cells. The authors provide solid evidence to support their claims, offering insight into why it is difficult to predict which nutrients limit cancer cell growth: both cell type and nutrient availability together determine the oxidative capacity that constrains the synthesis of various metabolic intermediates. The manuscript will be of interest to researchers working in cancer and cell metabolism.

      We thank the eLife Editor for evaluating our manuscript and for the positive comments.

      Reviewer #1 (Public review):

      Summary:

      This manuscript investigates how cellular NAD/NADH ratios are controlled in cancer cell lines in vitro. The authors build on previous work, which shows that serine synthesis is sensitive to NAD/NADH ratios and PHGDH expression. Here, the authors demonstrate that serine synthesis is variable across a panel of cell lines, even when controlling for expression of serine synthesis enzymes such as PHGDH. The authors show that cellular NAD/NADH ratios correlate with the ability to synthesize serine and grow in serine-deprived environments when PHGDH levels remain constant. Investigating this variability in NAD/NADH ratios, the authors find that the cells that can positively respond to serine deprivation are able to increase oxygen consumption and cellular NAD/NADH ratios. Cells that do not increase oxygen consumption in response to serine deprivation do not increase NAD/NADH ratios and cannot grow well without serine. The authors go on to show that in cells with the ability to increase oxygen consumption upon serine deprivation, PHGDH expression alone is sufficient to fully restore growth-serine; in cells that cannot increase oxygen consumption, both PHGDH expression and interventions to increase NAD/NADH ratios are required to increase growth. Thus, cells need both PHGDH and NAD/NADH increases to maximize serine synthesis in response to serine deprivation. The authors previously showed that lipid synthesis likewise requires NAD regeneration. Interestingly, one cell line that does not increase oxygen consumption in response to serine limitation tends to increase oxygen consumption in response to lipid deprivation; accordingly, depriving this cell line of lipids increases the synthesis of serine. Together, these findings show that how cells respond to nutrient deprivation is highly variable and that the response to nutrient deprivation (for example, whether or not oxygen consumption is increased) will determine how well cells tolerate depletion of nutrients with related biosynthetic constraints. This work sheds light on the complexity of cancer cell metabolism and helps to explain why it is difficult to predict which nutrients will be limiting to any cancer cell type or environment.

      Strengths:

      (1) The authors use multiple interventions to manipulate NAD/NADH ratios in cells.

      (2) Experiments are well controlled and appropriately interpreted.

      Weaknesses:

      Overall the data support the conclusions of the manuscript. I have only two minor comments and suggestions:

      We thank Reviewer 1 for their insightful comments, which have helped us improve the manuscript.

      (1) Figure 2B/C: data are presented as relative to +serine, which shows how some cells respond to -serine, but may also be of interest to see how absolute (not relative) NAD/NADH levels correlate with serine synthesis and serine-independent proliferation. In other words, is it the dynamic increase in the ratio that is most important, or the absolute level of the ratio?

      We thank Reviewer 1 for raising this point about whether it is the absolute NAD+/NADH ratio, or the change in NAD+/NADH ratio, that is important for increasing serine synthesis and allowing proliferation under serine depleted conditions. We reported relative ratios for accessibility to a general audience, but agree that this information is informative and should be presented. We assessed the NAD+/NADH ratio using an enzymatic assay, which does not directly measure absolute concentrations of NAD+ or NADH (PMID: 26232225). However, we previously confirmed the assay is in the same linear range for both NAD+ and NADH, and thus is valid for assessing the NAD+/NADH ratio. We now provide the unnormalized NAD+/NADH ratio data in Supplementary Figure 2G of the revised manuscript. This shows that the considered cells exhibit a range of NAD+/NADH ratios, and redox responsive cells do not cluster in having a higher or lower NAD+/NADH ratio.

      To more formally answer Reviewer 1’s question about whether the absolute ratio or change in ratio is important for increasing serine synthesis, we measured the correlation coefficient between the unnormalized NAD+/NADH ratios and the proliferation rate of all examined cancer cells cultured with or without serine. These data are presented in Author response image 1. Of note, we find that there is a significant positive correlation between the raw values of the measured NAD+/NADH ratio and proliferation rate in both serine-replete (r = .371) and serine depleted (r = .562) conditions. However, this correlation is not strong, and when examining the cancer cells whose proliferation in serine depleted conditions cannot be fully explained by serine synthesis enzyme expression (Calu6, 8988T, A549, MIA PaCa-2, H1299, and HCT116), there is no significant correlation between the raw NAD+/NADH ratio and proliferation rate in serine depleted conditions. The association between the relative change in the NAD+/NADH ratio and proliferation rate is much stronger upon serine deprivation (r = .571), as presented in Figure 2C of the revised manuscript. This suggests that the dynamic increase in the ratio is more tightly linked to the change in serine synthesis rate and proliferation in serine depleted environments, and we discuss this point in the revised manuscript with the following text:

      “Of note, whether the NAD+/NADH ratio of a cell was more or less oxidized in serine-replete conditions was not predictive of response to serine withdrawal (Supplementary Figure 2G).” (Lines 163-165)

      Author response image 1.

      Correlations between unnormalized NAD+/NADH ratios and cell proliferation rates between (A) all cancer cells examined (Calu6, MCF7, MDA-MB-231, A549, 8988T, MIA PaCa-2, A375, H1299, HCT116, MDA-MB-231 with PHGDH overexpression) in serine-replete conditions, (B) all cancer cells examined in serine depleted conditions, and (C) select cancer cells (labeled in gray) where serine synthesis enzyme protein expression does not fully explain proliferation in serine depleted conditions. Pearson correlation coefficient and P values were calculated by simple linear regression, *p<0.05, **p<0.01. Data shown are means of three biological replicates ± SD.

      (2) Line 177-178: the authors write, "We hypothesized that the elevated NAD+/NADH ratio represented a cellular response to make the NAD+/NADH ratio more oxidized to enable serine synthesis". I recommend modest edits to avoid anthropomorphizing. It is possible that the ratio responds for reasons yet to be determined and not necessarily because the cell is deliberately trying to enable serine synthesis.

      We thank Reviewer 1 for raising this point. We agree that our data do not show whether the ratio is elevated for the deliberate purpose of enabling serine synthesis and have edited the text accordingly with the following edit to that line of the revised manuscript:

      “We hypothesized that a more oxidized NAD+/NADH ratio could support greater serine synthesis and thus sought to identify the processes that increase the NAD+/NADH ratio in some but not all cancer cells.” (Lines 190-192)

      Reviewer #2 (Public review):

      In the manuscript "Cancer cells differentially modulate mitochondrial respiration to alter redox state and enable biomass synthesis in nutrient-limited environments", Chang et al investigate how cancer cells respond to the limitation of certain environmental nutrients by regulating the cellular NAD+/NADH ratio. They focus on serine and lipid metabolism, pathways known to be controlled by the NAD+/NADH ratio, and propose that changes in mitochondrial respiration in response to deprivation of these nutrients can influence the NAD+/NADH ratio, thereby impacting biomass synthesis.

      While the study is descriptive in nature and does not investigate specific molecular mechanisms that explain the crosstalk between nutrient availability and mitochondrial redox changes, the experimental component is robust, and the conclusions are well supported by the results. Some suggestions could further refine the conclusions and enhance the quality of the manuscript.

      We thank Reviewer 2 for their time and for their suggestions to improve the manuscript.

      Main critiques:

      (1) Throughout the manuscript, the authors utilise the number of cell doublings per day as an endpoint readout of cell proliferation. It would be advisable to include a quantification of the cell number and to display the proliferation rate over time. This would provide valuable insights into the timeline of cellular responses and avoid potential confounding effects associated with the use of Sulforhodamine B dye, an indirect measure of cell proliferation based on protein content, which may be influenced by some of the interventions. Furthermore, it will help determine whether specific treatments reduce cellular doublings resulting from cell death. This concern is particularly evident in treatments with rotenone, e.g., Fig. 1G, where the increase in doublings could be attributed to cell death.

      We thank the reviewer for this suggestion and agree that assessment of cell count provides additional information beyond Sulforhodamine B dye as an indirect measure of proliferation. To address this, we directly measured cell number over time using Incucyte Live-Cell imaging analysis applied to A549 and H1299 cells cultured with or without serine for 72 hours. Consistent with results using sulforhodamine B, A549 cells doubled at a rate of 0.874 per day and H1299 cells doubled at a rate of 1.034 per day in serine-replete conditions. In serine depleted conditions, A549 cells doubled at a rate of 0.205 per day while H1299 cells doubled at a rate of 0.544 per day. We have added the cell number measurements over time as well as the corresponding calculated doublings per day in Supplementary Figure 2D and Supplementary Figure 2E of the revised manuscript.

      We also agree with Reviewer 2 that serine deprivation and rotenone treatment could potentially impact cell viability, which might confound phenotypes, including NAD+/NADH ratio measurements. To assess whether serine deprivation and rotenone treatment cause cell death, we measured cell viability using Sytox Green after exposing cells to these conditions for 72 hours. We find that there is indeed more cell death in cells cultured without serine at most concentrations of rotenone. However, cell death did not exceed 4% in any of the conditions tested, suggesting this is not a major contributor to the cell doubling phenotypes. These data are now presented in Supplementary Figure 1C of the revised manuscript. However, in light of Reviewer 2’s comments, along with a comment from Reviewer 3 about whether rotenone induces ROS and cellular stress responses, we have decided to remove the proliferation data involving rotenone that were in Figure 1F and 1G of the original manuscript. The rationale is that the potential confounding impacts of rotenone on viability make interpreting the proliferation data difficult. Instead, we have focused Figure 1 of the revised manuscript on the observation that there is specifically a correlation between the cell NAD+/NADH ratio and serine synthesis.

      (2) The authors propose a model in which the deprivation of extracellular nutrients impacts mitochondrial respiration, which in turn increases the NAD+/NADH ratio and ultimately affects metabolic biosynthetic pathways that occur in the cytosol, such as serine biosynthesis. The mechanism by which nutrient availability is sensed and transmitted across different cellular compartments to regulate mitochondrial redox status remains unclear. This concern is particularly relevant for serine metabolism, as its synthesis occurs in the cytosol, but the authors connect it to mitochondrial respiration. Compartment-specific measurements of NAD+/NADH ratio would help to understand to what extent the redox state is affected by nutrients in the mitochondria and in the cytoplasm (see also minor critiques point 2). Moreover, the use of the genetic tool LbNox could be employed to manipulate the NAD+/NADH ratio in a compartmentspecific manner, while also avoiding the toxicity of certain compounds, such as rotenone. This set of experiments would add depth to the investigation, which might otherwise appear too descriptive.

      (A) Compartment-specific measurements of NAD+/NADH ratio would help to understand to what extent the redox state is affected by nutrients in the mitochondria and in the cytoplasm

      The question of how nutrient availability is sensed and transmitted across cellular compartments to impact mitochondrial respiration is important. However, rigorous assessment of compartment-specific metabolism is quite challenging, as we are not aware of tools to accurately measure redox ratios in a compartment-specific manner. Direct assessment of cofactor levels in subcellular compartments requires long isolation times and are unlikely to be accurate (PMID: 27565352). Rapid immunopurification of mitochondria has been used to estimate metabolite levels and ratios, but accurate measurements are hindered by rapid oxidation of NADH to NAD+. The use of fluorescence lifetime imaging (FLIM) to monitor NADH levels does not allow for accurate monitoring of the NAD+/NADH ratio as NAD+ cannot be visualized and NADH cannot be distinguished from NADPH. Additionally, the resolution of FLIM to interrogate compartment-specific signals is limited (PMID: 38594590). Fluorescent sensors, such as SoNar, have been used to image the NAD+/NADH ratio in compartments, though SoNar is sensitive to pH changes, which vary across compartments, and it has been argued that these sensors are more suitable for qualitative, not quantitative, changes in the NAD+/NADH ratio (PMIDs: 25955212, 29181426). It has also been argued that sensors are not amenable to measurement of mitochondrial ratios, as the predicted ratios are too reduced for the range of the sensors. Given these technical limitations, we opted to attempt a rapid subcellular fractionation (~25 second process to separate cytoplasm and mitochondria) followed by enzyme-based measurements of the NAD+/NADH ratio (PMID: 36883551), acknowledging the limitations of this approach. We find that across both A549 and H1299 cells, the mitochondrial NAD+/NADH ratio is lower than the cytosolic NAD+/NADH ratio, as expected. Using this approach, we find that in A549 cells, serine depletion leads to a decreased cytosolic NAD+/NADH ratio compared to serine-replete conditions while having no impact on the mitochondrial NAD+/NADH ratio. On the other hand, serine depletion leads to an elevated cytosolic NAD+/NADH ratio in H1299 cells while also having no impact on the mitochondrial NAD+/NADH ratio. In parallel, we used extracellular pyruvate exposure as a positive control, which should support cytosolic NAD+ regeneration, and rotenone as a negative control, which should suppress mitochondrial NAD+ regeneration. We show that pyruvate led to an elevated cytosolic NAD+/NADH ratio whereas rotenone treatment led to a decreased cytosolic NAD+/NADH ratio. Despite rotenone inhibiting complex I of the electron transport chain, we did not observe a change in the mitochondrial NAD+/NADH ratio (Author response image 2). This likely indicates that this assay is not sensitive enough to detect changes in mitochondrial NAD+/NADH, and we opted not to include these data in the revised manuscript given the limitations of the approach.

      Author response image 2.

      Rapid subcellular fractionation to examine compartment-specific NAD+/NADH ratios. (A) Cytosolic and mitochondrial NAD+/NADH ratios of A549 cells grown with or without serine for 24 hours, n=3. (B) Cytosolic and mitochondrial NAD+/NADH ratios of H1299 cells grown with or without serine for 24 hours, n=3. (C) Cytosolic and mitochondrial NAD+/NADH ratios of H1299 cells treated with either 1 mM pyruvate or 50 nM rotenone for 24 hours, n=3. P-values were calculated using a Student’s t-test, *p<0.05, **p<0.01. Data shown are means ± SD.

      We nevertheless draw the following conclusions from these data:

      (1) Changes to mitochondrial NAD+/NADH either do not occur or are not captured with this approach. Even rotenone treatment, which inhibits complex I and might be expected to change mitochondrial redox state, does not change the measured mitochondrial NAD+/NADH ratio.

      (2) The whole cell NAD+/NADH ratio most likely reflects changes in the cytosolic NAD+/NADH ratio. While observing no impact on the mitochondrial NAD+/NADH ratio after rotenone treatment, we still find the cytosolic NAD+/NADH ratio is decreased. Moreover, both pyruvate and serine depletion led to an elevated cytosolic NAD+/NADH ratio in H1299 cells, which we observe at the whole cell level.

      (3) H1299 cells depleted of serine elevate the cytosolic NAD+/NADH ratio, while rotenone treatment decreased the cytosolic NAD+/NADH ratio despite changes in mitochondrial respiration. This suggests that redox shuttles, such as the malate aspartate shuttle, play a role in communicating changes in mitochondrial redox dynamics to the cytoplasm. We test this hypothesis as described in response to Reviewer 2, point B, below.

      (B) The mechanism by which nutrient availability is sensed and transmitted across different cellular compartments to regulate mitochondrial redox status remains unclear

      Multiple known shuttles are involved in exchanging redox equivalents between the mitochondria and the cytosol. It is likely that multiple shuttles are involved, or could be involved in the right context, but one major shuttle is the malate aspartate shuttle (MAS), and the MAS has been shown previously to support de novo serine synthesis (PMID: 37647199). Thus, we hypothesized that the MAS is involved in the response involving elevated mitochondrial respiration in H1299 cells to increase the whole cell NAD+/NADH ratio upon serine deprivation. To test this, we used CRISPR/Cas9 to generate H1299 cells lacking MAS components GOT1, MDH1, or GOT2 and measured the cell NAD+/NADH ratio. We did not knock out MDH2 given its integral role in the TCA cycle. We find that when MDH1 and GOT2 are knocked-out, H1299 cells no longer exhibit elevated whole cell NAD+/NADH ratios upon serine deprivation. Consistently, removing MDH1 and GOT2 also blunted the increase in oxygen consumption as well as the increase in serine synthesis upon serine deprivation. This suggests that MDH1 and GOT2 activity though the MAS support the process by which mitochondrial NAD+ regeneration is transmitted to the cytoplasm to support serine synthesis. We have added these data as Supplementary Figure 7 in the revised manuscript.

      (C) Moreover, the use of the genetic tool LbNox could be employed to manipulate the NAD+/NADH ratio in a compartment-specific manner

      We thank Reviewer 2 for the suggestion to consider whether LbNOX might be used to manipulate the NAD+/NADH ratio in a compartment-specific manner. We expressed LbNOX in both the cytoplasm and the mitochondria of A549 (serine non-responsive) cells. We predicted that if LbNOX expression, either in the cytoplasm or the mitochondria, affected the NAD+/NADH ratio, proliferation in serine depleted conditions might be improved. However, we found that expressing LbNOX in the cytoplasm or the mitochondria of A549 cells had no effect on the NAD+/NADH ratio. Thus, LbNOX expression in either compartment also did not change proliferation in serine depleted conditions. These data are consistent with the known limitations of this genetic tool. While LbNOX can increase NADH oxidation in response to some interventions like rotenone, it does not necessarily change the NAD+/NADH ratio of unperturbed cells. This was reported in the original description of LbNOX (PMID: 27124460). We confirmed that LbNOX was successfully expressed via immunoblotting, and also confirmed that LbNOX functioned by showing either cytoplasmic or mitochondrial LbNOX expression improves cell proliferation following complex I inhibition. Thus, expressing LbNOX in A549 cells is not informative for understanding compartment specific metabolism following serine deprivation. Nevertheless, as this question is likely to come up for other readers, we have included these data as Supplementary Figure 6 in the revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      Minor critiques:

      (1) It seems clear from the authors' data that the response to serine depletion in terms of cell proliferation is not determined exclusively by PHGDH levels. It would be useful to measure the levels of the other two enzymes in the serine synthesis pathway and also to measure serine uptake under normal conditions in the different groups of cells. This information could provide some insight into the different responses of cancer cell lines to serine deprivation.

      (A) It would be useful to measure the levels of the other two enzymes in the serine synthesis pathway

      Reviewer 2 raises a fair point, and we agree that measuring levels of other enzymes in the serine synthesis pathway is informative. Thus, we measured the expression of phosphoserine aminotransferase 1 (PSAT1) and phosphoserine phosphatase (PSPH) across all cancer cells examined and find that, similar to PHGDH protein expression, PSAT1 and PSPH protein expression is lower in many cancer cells that are more sensitive to serine withdrawal (e.g. MCF7). However, among the cancer cells where PHGDH protein expression did not explain the response to serine withdrawal, the protein expression of PSAT1 and PSPH also did not explain how well the cells proliferate without environmental serine. These data have been included in Supplementary Figure 2B of the revised manuscript.

      Of note, we measured serine synthesis enzyme expression for the six cancer cell lines whose proliferation in serine depleted conditions better correlated with a change in the NAD+/NADH ratio than it did with PHGDH expression: Calu6, 8988T, A549, MIA PaCa2, H1299, and HCT116. For these cells, we correlated proliferation upon serine depletion with PHGDH, PSAT1, and PSPH protein expression and found that interestingly, there was a significant negative correlation between PHGDH protein expression and proliferation upon serine deprivation. This was not observed for PSAT1 expression, and a statistically significant positive correlation between proliferation and PSPH protein expression was noted, though the variation in PSPH protein expression was large. We have added these correlation data to the revised manuscript as Supplementary Figure 2F.

      (B) It would be useful to measure…serine uptake under normal conditions in the different groups of cells

      Per the Reviewer’s request, we performed absolute quantification of serine uptake rates in serine-replete conditions for three serine “non-responder” cancer cells (Calu6, 8988T, A549) and three serine “responder” cancer cells (MIA PaCa-2, H1299, HCT116). We did not observe a notable difference in serine uptake rate and whether cells responded to serine deprivation. Additionally, with the exception of 8988T cells having a higher serine uptake rate than the other cells, there was no statistical difference in serine uptake across the cancer cells tested (Author response image 3).

      Author response image 3.

      Basal serine uptake rate of exponentially growing cells in serine replete conditions. Serine levels were measured using GC MS before and after 24 hours of serine depletion and normalized by area under the growth curve (PMID: 26954548). P-values were calculated using one-way ANOVA followed by a post-hoc Tukey HSD test, *p<0.05, **p<0.01

      (2) The authors experimentally demonstrated that some cancer cells respond to serine depletion with an increase in mitochondrial respiration, but the molecular mechanism behind this is not addressed. There is some evidence in the literature showing that serine acts as an activator of the glycolytic enzyme PKM, which is coherent with an increased mitochondrial respiration in the absence of serine (PMID: 23064226). The authors could discuss their findings in the context of this paper. Additionally, they could provide some insights about baseline mitochondrial activity in the different cell lines. Indeed, it seems that "redox responsive cells" might have an overall increased basal OCR.

      We appreciate the suggestion that pyruvate kinase M (PKM) may mediate the elevation in mitochondrial respiration in response to serine depletion. Given that serine is an allosteric activator of PKM, and PKM suppression can increase mitochondrial OCR, we discuss this possibility in the Discussion section of the revised manuscript using the following text:

      “Interestingly, serine is an allosteric activator of the glycolytic enzyme pyruvate kinase, which converts phosphoenolpyruvate to pyruvate and generates ATP (Chaneton, 2012). Thus, decreased environment serine availability in addition to differences in pyruvate kinase activity may yield lower glycolytic ATP, resulting in greater mitochondrial respiration in serine redox responder cancer cells.” (Lines 443-447)

      Additionally, we appreciate the reviewer’s observation that redox responsive cells may have an overall increased basal respiration rate. We directly measured mitochondrial dependent oxygen consumption in the same assay to test whether redox responsive cells exhibit higher mitochondrial respiration. We find that while the redox responsive H1299 and MIA-PaCa2 cells have higher mitochondrial respiration than non-responsive cells, HCT116 cells that are also redox responsive to serine deprivation, did not exhibit higher mitochondrial respiration compared to redox non-responsive Calu6, 8988T, and A549 cells (Author response image 4). However, when comparing redox non-responders versus responders as a whole, there was a statistically significant difference in basal OCR. Together, this suggests that basal mitochondrial respiration rate in serine-replete conditions may be related in some cases to whether cancer cells elevate mitochondrial respiration and the NAD+/NADH ratio upon serine deprivation, but this cannot be the full explanation given the HCT116 cell data. We also acknowledge the reviewer’s statement that we do not understand the molecular mechanism by which respiration responds to serine deprivation and explicitly state this in the revised manuscript.

      Author response image 4.

      Basal Oxygen consumption rate (OCR) of cancer cells in serine-replete conditions. (A) Kinetic OCR measurements of cancer cells before and after rotenone and anti-mycin injection, n=8. Data shown are means ± SD. (B) Quantified mitochondrial OCR (removing residual OCR), n=8. Values are averages obtained over three measurements. P-values were calculated via nested ANOVA, ****p<0.001

      (3) There is a discrepancy between the basal values of the OCR from the same cell lines in different experiments, i.e., Figure 3A and Supp. Figure 3C, or in different experiments, Figure 3A, Figure 5E, and Figure 6A. The authors need to comment on/clarify that. Moreover, authors are encouraged to show ECAR values to support the conclusion that lactate production is not differentially affected by serine depletion, and thus, does not contribute to the increase in the NAD+/NADH ratio.

      We recognize the differences in basal OCR values across different experiments. Given experiment-to-experiment variation and the need for different cartridges for each Seahorse experiment, we have found that measured OCR values using Seahorse assays vary across experiments despite the same conditions. Additionally, while we aim to seed the same number of cells per assay, cell seeding and cell quantification after each Seahorse assay can contribute to variation. Given this variability on a per-assay basis, we performed a singular experiment across all examined cancer cell lines considered to minimize variation in oxygen sensor calibration and address the reviewer question about whether absolute differences might contribute to response. These data are shown in Author response image 4.

      Regarding the reviewer’s request to present ECAR data, we note that measuring ECAR is dependent on using unbuffered media and for this reason do not routinely measure ECAR. Our concern is that removing serum from the culture conditions can impact OCR measurements, and we instead prioritized maintaining the same media composition across all sets of experiments (i.e., cell proliferation assays, NAD+/NADH assays, kinetic tracing assays, and OCR measurements). Additionally, we point out that ECAR does not directly measure lactate. We refer the Reviewer to data included in the manuscript where GC-MS was used to directly measure lactate secretion over time for cells cultured with or without serine. These data are presented as Supplementary Figure 3B in the revised manuscript.

      (4) There seems to be also a discrepancy between the levels of M+2 citrate and the fraction labelled (Figure 5C versus Supplementary Figure 6C) in the H1299 cell line upon serine depletion, whereby the M+2 fraction seems unexpectedly lower in serinedeprived cells. In those conditions, H1299 cells showed an increased mitochondrial respiration, which is consistent with increased total citrate levels. This could be explained by a faster TCA cycle activity and the presence of higher-order isotopologues of citrate upon serine starvation. Is this the case? Showing the abundance of the different citrate isotopologues and their contribution to the total pool would help to interpret the results.

      We thank Reviewer 2 for this thoughtful comment regarding the discrepancy between M+2 citrate produced (normalized ion counts per cell) versus fraction of the total intracellular citrate pool that is M+2 labeled in serine depleted H1299 cells. In our kinetic U-<sup>13</sup>C-glucose tracing experiments, where we performed isotope labeling for up to 15 minutes, we only see a greater presence of M+3 citrate from fully labeled glucose without robust changes in M+4, M+5, or M+6 citrate (Author response image 5). An elevated M+3 citrate could represent pyruvate carboxylase activity, where M+3 labeled pyruvate is converted to M+3 oxaloacetate that then reacts with unlabeled acetyl-CoA to generate M+3 citrate.

      We also find that the total citrate pool in H1299 cells is elevated upon serine depletion (see Supplementary Figure 6C in the original manuscript). Thus, the fractional contribution of an isotope to the citrate pool may decrease despite an increase in the amount of the particular isotope. In the original manuscript, we included data from kinetic U-<sup>13</sup>C-glutamine tracing in H1299 cells cultured with or without serine (Supplementary Figure 6I,J of the original manuscript). We find that H1299 cells depleted of serine exhibit greater M+4 citrate (via oxidative decarboxylation) and greater M+5 citrate (via reductive carboxylation) compared to serine-replete H1299 cells. Thus, one other potential explanation for why M+2 citrate from kinetic U-<sup>13</sup>C-glucose tracing represents a lower fraction of the total citrate pool in serine depleted H1299 cells is because there is a larger contribution from glutamine to the citrate pool. While there was no difference in the fraction of the citrate pool that consists of M+4 citrate, there was a greater fraction of the citrate pool labeled by M+5 citrate upon kinetic U-<sup>13</sup>C-glutamine tracing in serine depleted H1299 cells (see Author response image 6A, B). There was also a greater fraction of the citrate pool from M+6 citrate upon kinetic U-<sup>3</sup>C-glutamine tracing in serine depleted H1299 cells (Author response image 6C). This would require M+3 pyruvate labeling from glutamine, which may be due to malic enzyme, which converts M+4 malate to M+3 pyruvate. M+3 pyruvate may also be formed by PEPCK, which could convert M+4 oxaloacetate to M+3 phosphoenolpyruvate, leading to M+3 pyruvate. While understanding the source of M+6 citrate from glutamine is out of the scope of this study, it may highlight an interesting metabolic shift in H1299 cells depleted of serine that could elevate the total intracellular citrate pool.

      Author response image 5.

      Citrate isotopologues (A. M+3; B. M+4; C. M+5; D. M+6) from kinetic U-<sup>13</sup>C-glucose tracing in H1299 cells depleted of serine for 24 hours. For all measurements, citrate values were normalized to internal norvaline standard and cell number for each condition, n=3. Data shown are means ± SD.

      Author response image 6.

      Fraction of the citrate pool labeled by U-<sup>13</sup>C-glutamine in H1299 cells depleted of serine for 24 hours. (A) Fraction of the total citrate pool that is M+4 citrate (formed via oxidative decarboxylation), n=3. (B) Fraction of the total citrate pool that is M+5 citrate (formed via reductive carboxylation), n=3. (C) Fraction of the total citrate pool that is M+6 citrate, n=3. Data shown are means ± SD.

      (5) The lipid depletion part of the paper seems to be somewhat tangential. The effect of lipid depletion on the NAD+/NADH ratio in A549 cells is modest, and the effects of dual serine and lipid depletion on OCR and NAD+/NADH ratio are not consistent. Moreover, if the authors want to show that these different nutritional environments affect lipid synthesis, apart from glucose incorporation into citrate, they would need to show actual carbon incorporation into palmitate, probably at longer time points.

      We apologize for the lack of clarity for how mitochondrial respiration and the NAD+/NADH ratio play a role in governing glucose oxidation to citrate. To better highlight our logic and rationale for investigating alterations in NAD+/NADH homeostasis and citrate synthesis under lipid depletion, we have added the following text to the revised manuscript:

      “Oxidative biosynthetic reactions other than serine synthesis can also be constrained by the NAD+/NADH ratio. For example, cancer cells deprived of environmental lipids increase oxidative citrate production, and we have previously found that citrate synthesis, either through glucose oxidation or glutamine oxidation, is limited by NAD+ availability (Li, 2022) (Figure 5A, Supplementary Figure 8A). Thus, we sought to uncover whether the increase in the cell NAD+/NADH ratio by mitochondrial respiration in response to serine withdrawal specifically supports greater serine synthesis or also leads to greater oxidative citrate production.” (Lines 307-313)

      While we have previously shown that alterations to the NAD+/NADH ratio can modify both citrate production and palmitate synthesis under lipid depleted conditions (PMID: 35739397), we agree with Reviewer 2 that no conclusion can be made about lipid synthesis without direct measurements and have revised the manuscript accordingly.

      (6) In Figure 6C-6F, showing the results of the controls (+serine +lipids) will help to clarify the extent to which serine and citrate synthesis rates are affected by the different interventions.

      We thank the reviewer for the comment. Because we specifically asked how dual serine and lipid starvation impacted either serine or citrate synthesis compared to singular nutrient deprivation alone, we performed the experiments focusing on these conditions. We felt that conducting an experiment that specifically targeted our question would be make the findings more accessible as we had compared the +serine +lipid conditions to either serine or lipid depletion alone earlier in our manuscript (Figure 2D and Figure 5G,H of the revised manuscript).

      Reviewer #3 (Public review):

      Summary:

      The manuscript by Chang and colleagues provides new insights into how cancer cells adapt their metabolism under nutrient-deprived conditions. They find cells respond differentially to serine and lipid deprivation via oxidising the cell redox state, which enables biomass synthesis and cell proliferation. They identified mitochondrial respiration as the major mechanism that dictates the endogenous NAD+/NADH ratio. By incorporating a dual stress paradigm, serine and lipid deprivation, the study further suggests that the NAD+/NADH ratio can serve as a link to orchestrate the complex interplay between multiple nutrient changes in the tumour microenvironment.

      Strengths:

      A novel aspect of this study is the idea that cancer cells are not uniformly passive victims of nutrient limitation; some can actively invoke endogenous NAD+ regeneration to combat nutrient stress. The conclusion is well-supported by comparing multiple cell lines from different tissues and genetic backgrounds, which improves generalizability. While most of the smaller conclusions align with common reasoning and expectations, the step-by-step deduction that leads to a novel 'big picture' is commendable. Another notable strength is the integration of dual stress (lipid and serine deprivation), which better mimics the complex tumor microenvironment with multiple nutrient fluctuations, raising the translational potential of these findings. The observation that lipid-deprived cells can stimulate serine synthesis and support proliferation in a subset of cancer cell lines offers a novel perspective on metabolic plasticity under starvation conditions.

      We thank Reviewer 3 for their time and for their comments to help us improve the manuscript. We also thank them for highlighting the strengths and significance of our findings.

      Weaknesses:

      (1) Although the authors derive a novel and valuable overarching concept, the presentation of this "big picture" is not clearly articulated, making it less accessible to readers outside the immediate field. It would greatly enhance the manuscript to include a clearer summary of the overarching model and its implications. Additionally, discussing the potential clinical significance and applications of the findings would increase the relevance and broader impact of the work. Finally, the manuscript's clarity and credibility are undermined by inconsistent figure labeling and the lack of statistical analysis, particularly for the Western blot data.

      (A) It would greatly enhance the manuscript to include a clearer summary of the overarching model and its implications. Additionally, discussing the potential clinical significance and applications of the findings would increase the relevance and broader impact of the work.

      We appreciate Reviewer 3’s suggestion to help clarify the findings of this study. To better articulate our overarching model, we have added the following text to the end of the Results section of the revised manuscript

      “Taken together, we propose a model where environmental nutrient availability can impact mitochondrial respiration based on the specific cancer. Because mitochondrial respiration is a major pathway that regenerates NAD<sup>+</sup>, changes to mitochondrial respiration can alter the cell NAD+/NADH ratio, influencing the activity of major NAD<sup>+</sup>-requiring metabolic reactions such as serine synthesis and citrate synthesis that can be important for proliferation. We further propose that changes to the cell NAD+/NADH ratio can impact all oxidative biosynthetic reactions if the enzyme machinery is present, but that specificity for how the cell NAD+/NADH ratio changes is dependent on both cell-intrinsic factors and cellextrinsic factors (Figure 7)." (Lines 396-404)

      Additionally, a new model figure was added as Figure 7 in the revised manuscript, which may help with understanding for a general audience.

      To better highlight the potential clinical significance of these findings, we have added the following at the end of the Discussion section of the revised manuscript:

      “Better understanding the mechanisms cells use to alter respiration and adjust the NAD+/NADH ratio in response to available nutrients could inform the complex interplay between cell-intrinsic and cell-extrinsic factors that determine cancer metabolic dependencies. This is particularly important to consider when targeting metabolism for cancer treatment. Many newer therapies targeting metabolism have not been successful in part because of metabolic plasticity to nutrient shifts (Amoedo, 2017; Fendt, 2020; Xiao, 2023). Co-targeting mitochondrial function limits metabolic adaptations and may also help predict the tissue nutrient conditions that result in pathway dependencies for specific cancers. Thus, better understanding how the cell NAD+/NADH ratio responds to nutrient levels in different cancers could improve selection of patients for cancer therapies that impact metabolism.” (Lines 483-492)

      (B) “…the manuscript's clarity and credibility are undermined by inconsistent figure labeling and the lack of statistical analysis, particularly for the Western blot data.”

      We apologize to the reviewer for any inconsistency in data presentation. To address the comment related to inconsistent figure labeling, we ensured all figures in the revised manuscript are labeled to allow readers to recognize what cell lines are used, what conditions are tested, what parameters are measured, and how the data may or may not be normalized. To address the reviewer’s comments about lack of statistical analysis, in the revised manuscript we ensured that statistical analyses are included for data presented in each figure, when appropriate. We also include a section titled “Statistics and Reproducibility” in the Methods section. In our revised manuscript, we have ensured that the p-value threshold is consistent throughout all figures, and have removed “ns” across the manuscript for consistency as suggested by Reviewer 3 in their minor comments. We also removed any explicit p-values included in figures where the p-values were close to reaching the threshold for significance (a=0.05). We have also performed additional statistical analyses where needed, including adding the pvalues for linear regression analyses, and ensured new data added to the revised manuscript also included appropriate statistical analyses.

      For western blot data, we show representative immunoblots. However, we measured PHGDH, PSAT1, and PSPH protein expression in three biological replicates across examined cancer cells and quantified the average serine synthesis protein expression from each replicate performed with error bars that denote standard deviation (see Author response image 7). We performed a nested ANOVA to examine whether there was a statistically significant difference in PHGDH, PSAT1, and PSPH protein expression between non-responder and responder cancer cells. Interestingly, as noted in our response to Reviewer 2, we find a significant negative association between PHGDH protein expression and response to serine deprivation among the six cancer cells where PHGDH protein expression did not explain proliferation upon serine depletion.

      Author response image 7.

      Serine synthesis enzyme protein expression in serine-replete and serine depleted cancer cells. (A) Immunoblots examining the expression of PHGDH, PSAT1, and PSPH in cancer cells as shown. HSP90 was used as a loading control. Data are from two separate biological replicates. (B) Mean levels of PHGDH, PSAT1, and PSPH normalized to loading control HSP90 across cancer cells from three separate biological replicates. Yellow denotes cancer cells that do not elevate mitochondrial respiration in response to serine depletion (non-responders). Blue denotes cancer cells that do elevate mitochondrial respiration in response to serine depletion (responders). P-values were calculated with nested ANOVA comparing non-responders and responders, **p<0.01

      (2) While this study identifies changes in serine synthesis, mitochondrial respiration, PHGDH protein levels, and NAD+/NADH ratio in different cell lines, some of these relationships appear correlative rather than causally established (Figure 2; Figure 5; Figure 6). Some claims are thus overinterpreted. For example, the co-occurrence of increased NAD+/NADH ratio and citrate levels under lipid deprivation in A549 cells does not establish causality (Figure 5). Direct perturbation experiments that manipulate NAD+/NADH and assess downstream effects on citrate synthesis would substantially strengthen the conclusions.

      We agree with Reviewer 3 that corresponding changes in proliferation, mitochondrial respiration, and serine synthesis are correlated to the NAD+/NADH ratio. As shown in Figure 4, we perturbed the NAD+/NADH ratio with FCCP and rotenone to measure downstream effects on serine synthesis. We also agree with the reviewer that doing similar experiments in the lipid depletion condition would highlight the relationship between the NAD+/NADH ratio and citrate synthesis. However, we point out that these experiments were already published in a manuscript from our group specifically showing that the NAD+/NADH ratio is limiting for citrate synthesis (PMID: 35739397). In that manuscript, the NAD+/NADH ratio was perturbed using electron transport chain inhibitors, including complex I inhibitors, which decreases the cell NAD+/NADH ratio. Exogenous electron acceptors were used to rescue the NAD+/NADH ratio, and under those conditions, cell proliferation, the NAD+/NADH ratio, and glucose and glutamine oxidation to citrate were measured with and without lipid depletion. We showed that decreasing the NAD+/NADH ratio decreases citrate synthesis through both glucose and glutamine oxidation and also affects palmitate synthesis. We could rescue citrate and palmitate synthesis by supplementing cells with exogenous electron acceptors. We also show that expressing cytosolic or mitochondrial NADH oxidase (LbNOX; PMID: 27124460) in mitochondrial complex I-inhibited cells rescues proliferation in lipid depleted conditions and that LbNOX expression raises oxidative citrate production at baseline. Given the extensive prior work showing the relationship between the NAD+/NADH ratio, oxidative citrate synthesis, and palmitate synthesis, efforts to repeat these same experiments for this manuscript were not warranted. We do show in the current manuscript that treating cells with AKB or FCCP, which raises the NAD+/NADH ratio, also increases glucose oxidation to citrate (Figure 5D of the original and revised manuscripts). We did this to confirm that the elevated M+2 citrate production from glucose in serine starved H1299 cells was related to an increase in the NAD+/NADH ratio as opposed to a specific response to serine depletion.

      The study focuses predominantly on mitochondrial respiration as a source of NAD+ regeneration. However, it will also be interesting to check other significant pathways, such as NAD+ salvage, which have been implicated in supporting serine biosynthesis. In addition, the subcellular distribution of NAD+ may distinguish whether some cells are truly redox-unresponsive. Mitochondrial NAD+ regeneration might counteract the cytosolic NAD+ consumption, rendering a relatively stable intracellular NAD+/NADH ratio. The malate-aspartate shuttle can be an interesting aspect.

      (A) The role of NAD+ salvage and serine biosynthesis

      Per the reviewer’s request, we investigated whether NAD+ salvage might be involved in supporting serine synthesis. Specifically, the reviewer comments highlight an interesting question about whether NAD+ salvage may differentially contribute to serine synthesis between cancer cells that elevate mitochondrial respiration in response to serine depletion and cancer cells that do not change mitochondrial respiration in response to serine depletion. Specifically, we wondered whether cancer cells that do not elevate mitochondrial respiration in response to serine depletion depend more on NAD+ salvage to support proliferation in serine depleted conditions. To test this, we treated A549 and H1299 cells in serine depleted conditions with increasing doses of the nicotinamide phosphoribosyltransferase (NAMPT) inhibitor FK866. However, we found no statistically significant difference in sensitivity to FK866 upon serine depletion in these cells based on ANCOVA analysis (p=0.9332). Interestingly, we observe that A549 cells are more sensitive to FK866 treatment than H1299 cells in serine-replete media conditions (ANCOVA analysis, p=0.0004). This suggests that A549 cells at baseline may have greater dependence on NAD+ salvage compared to H1299 cells, though this is not specific to the response to serine depletion. We then asked whether nicotinamide mononucleotide (NMN), the product of NAMPT and the immediate precursor to NAD+ in the salvage pathway, would rescue the proliferation of A549 cells cultured without serine. We find that adding 100 µM NMN, a concentration that can impact PHGDHdriven serine synthesis (PMID: 30157431), does not change proliferation of A549 cells cultured without serine, unlike supplementing cells with AKB or FCCP, which increase NADH oxidation to NAD+. Together, these data suggest that NAD+ salvage does not play a major role in differentiating the redox response to serine deprivation between responder and non-responder cells. We have added these data as Supplementary Figure 3C,D of the revised manuscript.

      (B) The role of the malate-aspartate shuttle and serine biosynthesis

      The MAS has been shown to play an important role in serine synthesis (PMID: 37647199) and may facilitate elevation in mitochondrial respiration in response to serine depletion. As stated in response to Reviewer 2, measuring subcellular compartmentspecific NAD+/NADH ratios accurately is not feasible, so we utilized a functional approach to interrogate the role of compartmentalization. Specifically, we tested a role for the malate-aspartate shuttle (MAS). Using CRISPR/Cas9, we generated GOT1, MDH1, and GOT2 deleted H1299 cells. We did not knock out MDH2 given its integral role in the TCA cycle. Using the knockout lines, we measured the whole cell NAD+/NADH ratio and found that MDH1 and GOT2 KO cells no longer exhibited an elevated cell NAD+/NADH ratio upon serine depletion compared to non-targeting controls (NTC). Consistently, MDH1 and GOT2 KO cells did not elevate OCR upon serine deprivation, nor did they exhibit greater serine synthesis rates compared to NTC cells. This suggests that MDH1 and GOT2 activity support the process by which mitochondrial NAD+ regeneration provides cytosolic NAD+ to support serine synthesis. We next asked whether MAS protein expression differed between cells that elevate respiration in response to serine depletion and cells that do not. While enzyme expression is not equivalent to activity, we wondered whether MAS protein expression would be lower in cells that do not increase their mitochondrial respiration upon serine depletion. However, we observed no major difference in GOT1, GOT2, MDH1, or MDH2 protein expression across the cancer cells examined (Author response image 8). Further experimentation is needed to measure MAS activity across lines and may reveal a mechanism by which mitochondrial respiration is governed by nutrient availability, such as levels of environmental serine.

      Author response image 8.

      Protein expression of the malate aspartate shuttle enzymes GOT1, MDH1, GOT2, and MDH2 in cancer cells cultured without serine for 24 hours. Membranes were first probed for GOT1 or GOT2 then stripped and re-probed for MDH1 or MDH2.

      (3) The authors should acknowledge the limitations of short-term isotope tracing in their experimental design. Differences in metabolic rates across cell lines can affect the kinetics of metabolite labeling, limiting the direct comparability of metabolic fluxes between them. As a result, observed changes may reflect transient adaptations rather than stable metabolic reprogramming. It is important to clarify that the study primarily captures short-term responses, and the conclusions may not extrapolate to longer-term adaptations or protein-level changes under sustained nutrient stress.

      We thank the reviewer for this comment. We apologize for any confusion around experimental approaches. We agree that in the case of acute changes in nutrient availability at the start of kinetic isotope tracing, the observed changes may reflect transient adaptations. However, cells are exposed to conditions for 24 hours prior to performing kinetic tracing. This approach allows us to examine changes that occurred in response to the nutrient condition, not acute changes. Additionally, we add fresh, prewarmed treatment media at least two hours prior to commencing kinetic isotope tracing. Upon analysis of kinetic isotope tracing, we examine whether cells were at metabolic steady state by monitoring metabolite levels over the course of tracing. For example, in the kinetic glucose tracing experiments in serine depleted cells, total serine levels are relatively stable throughout the experiment, and we find that total serine levels are greater in H1299 cells after 24 hours of serine starvation. Data showing total metabolite pools over the course of tracing are shown in the Supplementary Figures (for example, see Supplementary Figure 8C-H in the revised manuscript). The period of treatment prior to the start of kinetic isotope tracing is described in the figure legends and further detailed in the “Kinetic U-<sup>13</sup>C-Glucose Isotope Tracing Experiments” section of the Methods in the revised manuscript. To improve clarity, we added a kinetic graph showing total serine levels over time in Supplementary Figure 2I of the revised manuscript as this can address whether synthesis rates are captured while cells are at metabolic steady state. We also discuss these considerations better in the revised manuscript with the following text:

      “Importantly, we confirmed kinetic U-<sup>13</sup>C-glucose tracing was performed at metabolic steady state by ensuring metabolite levels were stable at each collected time point (Supplementary Figure 2I)” (Lines 178-180).

      Reviewer #3 (Recommendations for the authors):

      It is important to note that, in many cases, the data show only trends rather than statistically significant differences, or, if significance testing was performed, the results are not clearly labeled. For example, in Figure 1B, no p value was denoted in the figure, and the scale bar is quite high, precluding the conclusion that "AKB and rotenone dosedependently increased and decreased the cell NAD+/NADH ratio". In Figure 2E, no pvalue was shown to support the result that "H1299 cells had higher serine level than A549 cells". Inconsistencies in how significance is denoted across figures (e.g., asterisks vs. numerical values; "ns" vs. no label) make interpretation difficult. Marginal significance (e.g., p = 0.06 in Figure B) can be reported explicitly, but all figures should clearly denote whether comparisons are significant or not. Conclusions drawn from nonsignificant trends should be appropriately stated.

      We thank Reviewer 3 for this important comment and for highlighting specific instances where the manuscript could be improved. Please see response to Reviewer 3, Major Comment 1B. We also agree with Reviewer 3 that it is integral to ensure that conclusions made from non-significant trends are appropriately stated. For example, we explicitly mention that there was no statistically significant difference between the serine synthesis rate of A549 cells depleted of serine versus A549 cells depleted of both serine and lipids (Line 375). As another example, we changed the phrase “Moreover lipid depletion led to a greater fraction of total serine derived from glucose in serine depleted A549 cells” to “Moreover, lipid depletion appeared to lead to a greater fraction…” (Line 376).

      Western blot data supporting PHGDH expression variability across cell lines (e.g., Supplementary Figure 2B, 3E) appear to rely on single experiments. At least three biological replicates are required to substantiate claims about discordance between PHGDH levels and serine sensitivity. Supplementary Figure 4G presents overexpression validation based on a single Western blot without quantification. Including statistical validation from biological replicates would strengthen this point.

      We thank Reviewer 3 for this suggestion. Western blots were repeated 3 times, although data from a representative blot is shown. Please see response to Reviewer 3, Major Comment 1B.

      Certain data visualizations (e.g., Figure 2C) lack annotation indicating which data points correspond to which cell lines, limiting interpretability. All figures should include clear labels, consistent statistical notation, and complete legends. The author uses different color labels (redox-responsive (blue) and unresponsive (yellow) cell lines), which provides mechanistic clarity; however, this classification was not consistently used across the manuscript (e.g., Figures 2d and 2e). To further improve reader comprehension, consider adding conceptual schematic diagrams before each main result section to illustrate experimental logic, and a final diagram summarizing the proposed mechanism.

      We apologize for any unclear data presentation. In the revised manuscript we have added greater clarity around what cell lines are used in each experiment and have added explicit labeling to specify cancer cell lines in Figure 2C of the revised manuscript. Throughout, we have ensured that any serine redox non-responder cell lines are labeled in yellow while serine redox non-responder cell lines are labeled in blue. We have also ensured that any lipid redox responder cells are labeled in green while lipid redox non-responder cells are labeled in dark purple, a change from the original manuscript. Finally, we have also added a schematic to summarize the proposed model in Figure 7 of the revised manuscript.

      Although the authors provide justification for using H1299 and A549 as representative cell lines to study serine depletion, it remains unclear whether these two lines are equally suitable for investigating lipid depletion. Additional rationale or supporting data would help clarify their appropriateness for the lipid-related experiments.

      We thank Reviewer 3 for this suggestion. We opted to study H1299 and A549 cells under lipid deprivation to assess their responses in relation to the response to serine deprivation. We specifically wanted to know whether these findings related to serine deprivation applied to other nutrient depleted conditions. We clarify this logic in the revised manuscript by adding the following text:

      “Oxidative biosynthetic reactions other than serine synthesis can also be constrained by the NAD+/NADH ratio. For example, cancer cells deprived of environmental lipids increase oxidative citrate production, and we have previously found that citrate synthesis, either through glucose oxidation or glutamine oxidation, is limited by NAD+ availability (Li, 2022) (Figure 5A, Supplementary Figure 8A). Thus, we sought to uncover whether the increase in the cell NAD+/NADH ratio by mitochondrial respiration in response to serine withdrawal specifically supports greater serine synthesis or also leads to greater oxidative citrate production.” (Lines 307-313)

      We have also included more detailed justification for focusing our studies on A549 and H1299 to study serine depletion by adding the following statements to the manuscript:

      “We performed focused comparisons between A549 and H1299 cells because they exhibit differences in proliferation upon serine deprivation that are not explained by PHGDH protein expression, demonstrate differing responses of the cell NAD+/NADH ratio upon serine deprivation, and have similar basal proliferation rates.” (Lines 171-175)

      The concentration of serine in replete media should be explicitly stated and justified. If the intention is to mimic physiological conditions, alignment with human plasma levels would increase translational relevance.

      We agree that explicitly stating the concentration of serine in replete media is important. In the revised manuscript, we explicitly state that DMEM contains 400 uM of serine and that we use this concentration for serine-replete conditions (Line 102). While an important application of our manuscript is to better explain metabolic changes that can occur in physiologic conditions, we acknowledge that we did not test levels found in different tissues. Rather, by examining extreme conditions of high and low serine, we hoped to dissect how cells adapt to nutrient conditions, and testing the more subtle responses based on tissue serine levels will require a dedicated study.

      Rotenone may elevate ROS levels and trigger cellular stress responses, potentially confounding proliferation assays. The authors should validate that concentrations used do not induce cytotoxicity or excessive oxidative stress, and ideally measure ROS levels to support interpretation.

      We thank Reviewer 3 for raising this important point. We explicitly measured cell viability with the doses of rotenone used in this manuscript in cells cultured with or without serine. We find that rotenone dose-dependently increases cytotoxicity in A549 cells grown in serine-replete conditions in a statistically significant manner as calculated by simple linear regression. However, the cytotoxicity from rotenone is low (at most 4% in serine depleted conditions) and does not explain differences to rotenone sensitivity with respect to serine synthesis. These data have been added to Supplementary Figure 1C of the revised manuscript.

      Evidence for lipid depletion can enhance serine synthesis in A549 cells is inadequate, for the marginal difference in NAD+/NADH ratio and slight increase of M+3 serine levels. The statement "any perturbation that increases the NAD+/NADH ratio led to both elevated serine and citrate production, regardless of what nutrient was depleted from the environment" (introduction section) should be reworded.

      We thank Reviewer 3 for this suggestion. We have changed the above statement to the following:

      “Lastly, we find that any perturbation that increases the NAD+/NADH ratio, including lipid deprivation, could paradoxically improve the proliferation of cells in serine depleted conditions.” (Lines 90-92).

    1. Author response:

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

      eLife Assessment

      The nematode C. elegans is an ideal model in which to achieve the ambitious goal of a genome-wide atlas of protein expression and localization. In this paper, the authors explore the utility of a new and efficient method for labeling proteins with fluorescent tags, evaluating its potential to be the basis for a larger, genome-wide effort that is likely to be very useful for the community. While the evidence for the method itself is solid, carrying out this project at a large scale will require significant additional feasibility studies.

      We appreciate the editor’s recognition that the evidence for our method is solid and that a genome-wide protein atlas in C. elegans would be highly valuable to the community. However, we respectfully disagree that “significant additional feasibility studies” are required. Take the yeast proteome-wide GFP tagging project (Huh et al., Nature 2003). It achieved ~75% coverage of ~6,000 proteins directly from an established protocol without any prior significant feasibility studies, at least to our knowledge. While the C. elegans genome is 3 times in size, we would argue that our tagging protocol may even be less labor intensive as it does not involve any cloning and the screening is visual, requiring no molecular biology skills. Reviewer 3 notes: ‘They also provide convincing evidence that labelling the whole proteome is an achievable goal with relatively limited resources and time.’

      Our pilot study validates all key parameters for genome-wide scaling: editing efficiency at novel loci with untested reagents, viability of tagged worms, and detectability of multiple spectrally separated fluorophores across expression ranges. These address the core technical, biological, and practical challenges of large-scale endogenous tagging in a multicellular organism, leaving no fundamental barriers in our view.

      The proposed cost and timeline align quite favorably with established large-scale consortium projects: e.g., ENCODE pilot analyzed 1% of the human genome at ~$55 million over 4 years; Mouse Knockout Consortium scaled to ~20,000 genes over 20 years (ongoing) with ~$100 million; Human Protein Atlas mapped ~87% of proteins with antibodies in fixed cells (through much more labor intensive methods) over 20+ years at >$100 million. With ~8% of C. elegans genes already tagged (WormTagDB) and labs already tagging entire gene classes (PMID: 40463100), scaling our protocol to the proteome is feasible, potentially covering the genome in 5-6 years by a single lab or faster with distributed effort at a reagent cost of merely $2.2 million. The main barriers now are funding commitment and assembling collaborators, not further feasibility testing.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Eroglu and Hobert demonstrate that injecting CRISPR guides and repair constructs to target three genes at a time, tagging each with a different fluorescent protein, and selecting which gene to tag with which fluorophore based on genes' expression levels, can improve the efficiency of gene tagging.

      Strengths:

      This manuscript demonstrates that three genes can be targeted efficiently with three different fluorophores. It also presents some practical considerations, like using the fluorophore least complicated by agar/worm autofluorescence for genes with low expression levels, and cost calculations if the same methods were used on all genes.

      Weaknesses:

      Eroglu has demonstrated in a previous publication that single-stranded DNA injection can increase the efficiency of CRISPR in C. elegans while inserting two fluorescent proteins and a co-CRISPR marker into three loci. The current work is, therefore, an incremental advance. In general, I applaud the authors' willingness to think ahead to how whole proteome tagging might be accomplished, but I predict that the advance here will be one of many small advances that will get the field to that goal.

      Our manuscript indeed builds on prior multiplex editing (including our own co-CRISPR work), but the manuscript's primary contribution is not a novel technical breakthrough per se. Instead, our main goal was to pilot and strategize a feasible path to whole-proteome tagging in C. elegans and, most critically, test the following key parameters: (1) success rate of triple pools with prior untested reagents at novel targets; (2) utility of fluorophores across expression levels; (3) major effects on tagged protein function. In prior multiplexing, we used two targets which we already knew could be edited quite efficiently, with the 3rd target a point mutation with nearly 100% efficiency. Thus, it was not at all clear that picking 3 random genes and replacing the 3rd highly efficient locus with another less efficient large insertion would work or be sufficiently scalable for thousands of novel genes with unvalidated reagents at first pass.

      The title vastly oversells the advance in my view, and the first sentence of the Discussion seems a more apt summary of the key advance here.

      Some injections target genes on the same chromosome together, which will create unnecessary issues when doing necessary backcrossing, especially if the mutation rate is increased by CRISPR.

      We disagree with the reviewer’s assessment of the need for backcrossing, for two reasons: (1) Prior studies have shown that off-target mutations are not a serious concern in C. elegans (reviewed in PMID: 26336798). For instance, WGS of strains after CRISPR/Cas9 found negligible off-target effects (PMID: 25249454, PMID: 30420468 – using similar RNP/ssDNA method and multiple guides; PMID: 23979577, PMID: 27650892 using other methods). Targeted sequencing studies have reported similar findings, using various CRISPR/Cas9 methods, with essentially no mutations at sites other than the intended target (PMID: 23995389; PMID: 23817069). (2) If the goal is to tag the entire genome, the introduction of backcrossing should not reasonably be a routine part of the initial tagging.

      Lastly, if one really does want to backcross, the existence of tags on the same chromosome is actually an advantage because it permits selection for recombinants with wild-type chromosomes.

      Also, the need for backcrossing and perhaps sequencing made me wonder if injecting 3 together really is helpful vs targeting each gene separately, since only 5 worms need to be injected.

      Apart from our disagreement regarding backcrossing, we are puzzled by the reviewer’s comment. Why would one do single tagging at a time, rather than triple tagging if the whole point is to scale up tagging? It is important to keep in mind that the rate limiting step for tagging the whole genome is the number of injections that can be done per day. Since there is no cloning to generate the repair templates/guides and all other reagents are commercially available and not sample specific, these can be prepared quite rapidly. Being able to isolate multiple lines (together or independently) from the same injection increases throughput 3-fold and in our view does not provide any disadvantages as individual tags can be isolated independently if desired.

      Beyond the numerous technical advantages pooling provides (also lower cost and throughput for making injection mixes as well as imaging), our results show that it yields epistemic benefits as well: we would never have noted the subcellular pattern in Fig. 6B, C with different sets of mitochondria being marked by different mitochondrial proteins had we imaged them separately or even aligned to a pan-mitochondrial landmark. As we mentioned in the discussion, grouping proteins predicted to localize to the same compartment together can simultaneously test how uniform or differentiated such compartments are during the screen.

      The limited utility of current blue fluorescent proteins makes me wonder if it's worth using at all at this stage, before there are better blue (or far red) fluorescent proteins.

      We do not think that the utility of current BFPs is that limiting. At least the theoretical brightness of mTagBFP2 is comparable to that of EGFP (PMID: 30886412), which was useful for the bulk of currently tagged proteins. Due to modestly higher autofluorescence in the blue spectrum, the practical brightness is somewhat less ideal, but we have shown that many proteins are expressed high enough to be detected quite well with mTagBFP2 by eye at low magnification. We also note that many tags that are not visible by eye under a dissection scope become visible with long exposure cameras of widefield microscopes or modern confocal (GaAsP) detectors, so the list of genes detectable with mTagBFP2 is likely to be much higher. We routinely use mTagBFP2 to super-resolve subnuclear structures with endogenous tags (e.g., in the nucleolus), with some tags having lower annotated FPKMs than the genes tested here.

      Some literature reviews, particularly in the Introduction and Abstract, rely too much on recent examples from the authors' laboratory instead of presenting the state of the field. I'd like to have known what exactly has been done with simultaneous injection targeting multiple loci more thoroughly, comparing what has been accomplished to date by various laboratories' advances to date.

      We are not sure what the reviewer is referring to. In the Abstract, we do not refer to any literature. In the Introduction, we cite 28 papers, 6 of those from our lab (4 of which providing examples of protein tags). We do not believe that this can be fairly called an unbalanced presentation of the state of the field.

      This being said, we have gladly expanded our Introduction to provide more background on co-CRISPRing. Labs have routinely used co-conversion (“coCRISPR”) markers for picking out their intended edits (e.g., point mutations or insertions), as it has been shown by multiple groups that a CRISPR/Cas9 edit at one locus correlates with efficiency at other simultaneous targets (PMID: 25161212). Generally, making point mutations with the Cas9/RNP protocol is highly efficient, especially at specific loci such as dpy-10. However, multiple FP-sized insertions have not been routinely attempted. We and only one other group have successfully attempted it using previously working targets and reagents (e.g., 28% in PMID: 26187122). Importantly, the efficiency of such multiple insertions has never been assessed at scale and using entirely untested reagents at novel sites – critical parameters to determine for a whole genome approach. So, we test here (1) the efficiency of triple insertions and (2) the chance of getting them with new and untested guides and reagents.

      In our view, since we have to use some injection/coCRISPR marker anyway for those genes which are not expressed at dissecting-scope visible levels (likely most genes), using highly expressed intended targets as improvised markers in a pooled approach makes our approach much more efficient. It allows us to find the worms with the highest chance of yielding CRISPR insertions, which we can screen with higher power methods for the dimmer targets, while enabling us to co-isolate other intended targets. Insertions, being often heterozygous in F1, can be segregated independently if desired, or homozygosed together to facilitate maintenance then outcrossed individually by those interested in studying specific genes in more detail.

      In the revised version of this manuscript, we now discuss some of these points in the introduction section:

      “Currently, around 1554 proteins representing 8% of the proteome are estimated to have been endogenously tagged (Leyhr et al., 2025). However, at current rates, tagging the proteome is projected to take around 100 years and likely involve numerous duplicate attempts on a small number of commonly studied proteins (Leyhr et al., 2025). It will thus be crucial for the field to coordinate tagging efforts and scale up tagging protocols to enable coverage of the entire genome at a reasonable timescale and cost. Given the number of injections is a major time-limiting factor, pooling multiple injections into one would at minimum cut tagging time by a factor of 3. In C. elegans, screening for novel CRISPR/Cas9-induced genomic edits is already facilitated either by use of co-injection markers (i.e., plasmids that form extrachromosomal arrays) that yield phenotypes or fluorescence in progeny of successfully injected worms, or co-editing well characterized loci using established and highly efficient reagents which likewise yield visible phenotypes. In the latter approach, termed “co-CRISPR”, worms edited at the marker locus are most likely to also carry the intended edit (Arribere et al., 2014). Recent methods for CRISPR/Cas9 mediated genomic insertions have pushed efficiencies to sufficient levels to simultaneously insert multiple fluorophores (e.g., mNeonGreen and mScarlet) as well as a co-CRISPR marker (dpy-10) at three independent loci in a single injection (Eroglu et al., 2023; Paix et al., 2015). These attempts pooled reagents previously established to work efficiently and targeted genes that were known to yield functional fusion proteins when tagged. Thus, while in principle current methods could allow tagging of at least 3 independent loci in one injection if a co-CRISPR marker is omitted, it is not known to what extent such an approach could be generalized across the genome with previously unvalidated reagents (i.e., guides and repair template homology arms) at novel loci to yield functional tags”

      Reviewer #2 (Public review):

      The manuscript by Eroglu and Hobert presents a set of strains each harboring up to three fluorescently tagged endogenous proteins. While there is technically nothing wrong with the method and the images are beautiful, we struggled to appreciate the advance of this work - who is this paper for?

      We consider this paper to have two purposes: (1) motivate the community to come together to consider such genome-wide tagging approach; (2) provide a reference point for funding agencies that such an aim is not unreasonable and will provide novel interesting insights.

      As a technical method, the advance is minimal since the first author had already demonstrated that three mutations (fluorophore insertion and co-CRISPR marker) could be introduced simultaneously.

      We agree that the basic principle is similar. However, it was not clear that triple pooling three novel large edits would work, given the numbers in our original paper or that it would be scalable.

      The dpy-10 coCRISPR marker previously used is a highly efficient single site, with close to 100% hit rate. We also knew in the earlier study that the two pooled insertions already worked quite efficiently and did not disrupt the function of targeted proteins. Exchanging these plus dpy-10 for three novel tags was not guaranteed to succeed for many potential reasons, including both biological and technical. For instance, such a “marker free” approach necessitates that a significant number of targets in the genome should be expressed highly enough to be visible by fluorescence stereomicroscopy when tagged with current best fluorophores. The chance of disrupting gene function by tagging was also not explored in detail in C. elegans, nor whether one untested guide is generally sufficient. We think that establishing these parameters was meaningful and necessary for the goal of whole genome tagging. We have clarified some of these points in the text.

      As a pilot for creating genome-scale resources, it is not clear whether three different fluorophores in one animal, while elegantly designed and implemented, will be desired by the broader community. 

      The usage of three different fluorophores is largely driven by the ability to co-inject and therefore cut injection effort by a factor of three. Moreover, having all three fluorophores together facilitates imaging and maintenance. Lastly, co-labeling has the potential to reveal unexpected patterns of co-localization or lack thereof (example: two mitochondrial proteins that we found to not have overlapping distribution). We clarified this point in the revised text in both the results and discussion.

      Finally, the interpretation of the patterns observed in the created lines is somewhat lacking. A Table with all the observations must be included. This can replace the descriptions of the observations with the different lines, which could be somewhat laborious for the reader, and are often wrong. There are numerous mistaken expectations of protein expression here, but two examples include:

      We are not convinced that our expectations are mistaken. Below we respond to the reviewer’s specific examples, and we are open to hear from the reviewer about additional cases.

      (1) The expectation that ACDH-10 is enriched in the intestine and epidermal tissues (hypodermis).

      There are multiple paralogs of this protein (see WormPaths or WormFlux) that may share functions in different tissues. There is also no reason to assume that fatty acid metabolism does not occur in other tissues (including the germline). Finally, there are no published studies about this enzyme, so we really don't know for sure what it's doing.

      The expression of acdh-10 is annotated in multiple scRNA datasets as intestine and epidermal enriched (CeNGEN/Taylor et al. 2021, highest in epidermis; Ghaddar et al 2023 highest in intestine). We did not mean to imply that fatty acid metabolism does not occur in the gonad, nor that a paralog of acdh-10 could not be performing the same function in tissues where acdh-10 is not expressed.

      However, this raises an important question: why have different paralogs doing the same thing? Duplicate genes with the same function are generally not evolutionarily stable (PMID: 11073452, PMID: 24659815). That there are such striking tissue specific expression patterns of an essential or widely expressed protein class suggests that paralogs of the gene likely differ in some meaningful parameter that might align with tissue-specific functional needs or regulation. The reviewer’s statement that ‘there are no published studies about this enzyme, so we really don't know for sure what it's doing’ is in fact an excellent demonstration of our point; finding out where the duplicates are expressed can provide a starting point to uncover potential differences between the paralogs. At the very least it can delineate to what degree paralogs diverge in their expression across the proteome and identify which such cases merit further study. In a more ideal scenario, prior information of protein function could indicate that the involved pathway requires tissue specific regulation.

      (2) The expectation that HXK-1 is ubiquitously expressed.

      Three paralogous enzymes are all associated with the same reaction, and we have shown that these three function redundantly in vivo, perhaps in different tissues (PMID: 40011787).

      The cited paper (PMID: 40011787) does not show where they are expressed. We discussed redundancy/paralogs above in point 1, and in our view the same applies here. They may perform the same reaction but are likely to differ in some meaningful way, be it regulation or rate of activity, for them to be stably maintained as functional genes over evolution.

      Moreover, single-cell RNA-seq data (PMID: 38816550) also show enrichment of hxk-1 in gonadal sheath cells.

      The Ghaddar et al. and CeNGEN/Taylor et al. datasets do not show this. The scRNA paper cited (PMID: 38816550) also shows enrichment in neurons, pharynx, coelomocyte and germ cells which we did not note. In our view, these in fact further support our goals: often, transcript datasets alone (frequently used to infer tissue function) do not sufficiently predict protein expression. One can post hoc find an scRNA-seq dataset that aligns somewhat with our protein observations, but how does one know which to trust a priori? Disagreements between transcript datasets will ultimately require resolution at the protein level, in our view.

      To clarify these points, we added the following to the discussion section:

      “We also noted unexpected cell type dependent distributions of proteins involved in broadly important metabolic processes such as ACDH-10, which was depleted from the germline compared to other tissues, and HXK-1, which was highly enriched in the gonadal sheath. Notably, for these as well as other cases, scRNA-seq datasets were not sufficient to deduce a priori the observed cell type specific differences at the protein level. Importantly, many genes encoding metabolic enzymes including acdh-10 and hxk-1 have paralogs that likely perform similar catalytic functions. Yet, duplicate genes with identical functions are generally not evolutionarily stable (Adler et al., 2014; Lynch and Conery, 2000); thus such genes are likely to differ in some meaningful parameter (e.g., regulation or activity) that might align with tissue-specific functional needs. Fully annotating the expression patterns of paralogs at the protein level could indicate which tissues require unique metabolic needs and indicate which paralogous genes have undergone sub- versus neo-functionalization. For those proteins that are less functionally understood, unexpected distributions might indicate which merit further study.”

      The table should have at least the following information: gene/protein name - Wormbase ID - TPM levels of single cell data assigned to tissues for L2, L4, and adult (all published) - tissues in which expression is observed in the lines presented by the authors.

      We added some of this information such as annotated expression levels in young adults from various scRNA datasets (but not larval datasets as we did not image these). We note that each of these studies use different pipelines and report different metrics (scaled TPM/Z-score versus Seurat average expression versus TPM), so comparisons between them are not informative unless they are integrated and analyzed together.

      Reviewer #3 (Public review):

      Summary:

      The authors argue that establishing the expression pattern and subcellular localisation of an animal's proteome will highlight many hypotheses for further study. To make this point and show feasibility, they developed a pipeline to knock in DNA encoding fluorescent tags into C. elegans genes.

      Strengths:

      The authors effectively make the points above. For example, they provide evidence of two populations of mitochondria in the C. elegans germline that differ qualitatively in the proteins they express. They also provide convincing evidence that labelling the whole proteome is an achievable goal with relatively limited resources and time.

      We appreciate the referee’s recognition that whole proteome tagging is feasible.

      Weaknesses:

      Cell biology in C. elegans is challenging because of the small size of many of its cells, notably neurons. This can make establishing the sub-cellular localisation of a fluorescently tagged protein, or co-localizing it with another protein, tricky. The authors point out in their introduction that advances in light microscopy, such as diSPIM, STED, and ISM (a close relative of SIM), have increased the resolution of light microscopy. They also point out that recent advances in expansion microscopy can similarly help overcome the resolution limit.

      (1) Have the authors investigated if the three fluorescent tags they use are appropriate for super-resolution microscopy of C. elegans, e.g., STED or SIM? Would Elektra be better than mTAGBFP2? How does mScarlet3-S2 compare to mScarlet 3?

      All three tags work for ISM (i.e., Airyscan). We previously tried Electra (not for the genes tested here) but could not isolate positive tags. Given Electra is not that much brighter on paper than mTagBFP2 we did not pursue it further, though we recognize that these may simply have been unlucky injections. mScarlet3-S2 is quite a bit dimmer than mScarlet3 on paper – the advantage is that it has higher photostability. In our view, the limiting factor will be having FPs that are bright enough to screen, image and scale to the whole genome, so brightness will likely provide an advantage over photostability at this stage.

      (2) Have the authors investigated what tags could be used in expansion microscopy - that is, which retain antigenicity or even fluorescence after the protocol is applied? It may be useful to add different epitope tags to the knock-in cassettes for this purpose.

      mSG and mSc3 retain fluorescence after fixing with formaldehyde. We have not tested mTagBFP2 fluorescence in fixed worms. We agree that adding different epitope tags would be useful.

      The paper is fine as it stands. The experiments above could add value to it and future-proof it, but are not essential. If the experiments are not attempted, the authors could refer to the points above in the discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Merged figures appear saturated, and use colors that won't work for red-green colorblind viewers. 

      For all figures, we also show individual channels separately, which is common practice for making fluorescence images accessible to colorblind readers (PMID: 33788834). Figures highlighting non-overlap like 6B and C are already in accessible colors when merged (blue/green) and include a numerical quantification. 3-color RGB images preserve the greatest information for the highest number of individuals.

      (2) Targeting ubiquitously expressed genes as a proof of concept gives me some concern that this might underestimate the challenges that may be experienced with less widely expressed genes.

      While the genes were predicted to be ubiquitously expressed, many were not in practice, like HXK-1 and F54C8.1, which were also among the lower expressed genes on our list and highly cell type restricted. As discussed, the more tissue restricted a gene, the likelier that bulk RNA levels underestimate expression. Such genes are therefore more likely to be detected in a specific tissue. We routinely isolate tissue restricted endogenous tags, including those expressed in only a few neurons, with bulk FPKMs lower than the ranges tested in this manuscript.

      (3) Some results are not shown or referenced (autofluorescence, for example, is shown using a schematic in Figure 1C).

      We now provide representative images alongside what would be expected to be observed by eye during screening.

      (4) It would be useful to describe how to recover worms from what is shown in Figure 1A. 

      In the revised version, we added the following in the caption for Fig. 1A:

      “Selected worms expressing the brighter tag can be screened for dimmer tags by higher magnification and long exposure imaging. Worms can be recovered directly from slides if immobilized by levamisole as described (Ghanta et al., 2021). Alternatively, single hermaphrodite worms can be isolated, allowed to lay eggs, then screened.”

      (5) A blue bar of data must be missing from Figure 3B injection pool 5.

      As stated in the text, “All but one tag (cox-6B::mTagBFP2) was visible in the F1 generation of injected P0 animals, and these were subsequently isolated among F2 worms positive for the other tags in the pool.”

      To clarify that data points are not unintentionally omitted, we added the following text to the caption of Fig. 3B:

      “For group 5 including cox-6B::mTagBFP2, worms with detectable levels of mTagBFP2 fluorescence were not recovered in the F1 generation but were isolated among progeny of F1s positive for mStayGold and mScarlet3; we were thus unable to quantify efficiency for this locus at F1.”

      (6) Some expression or localization patterns were unexpected, but complications like germline silencing and protein mislocalization, with a small fraction localizing normally and rescuing function, were not presented as possibilities. Viability is used to confirm function, but without presenting whether this means 100% viability, less, or just the ability to maintain a strain.

      We already do discuss mislocalization and functionality issues in the Discussion, as well as tradeoffs of alternate methods. Any existing method to observe biological molecules, be it protein, RNA or DNA, has multiple drawbacks and sources of artifacts, which are unlikely to be fully eliminated in the foreseeable future.

      In regard to germline silencing of endogenously tagged genes in C. elegans, there is actually very little evidence for this. Collectively, various labs have now generated over 200 reporter alleles of germline-expressed genes (WormTagDB), with robust expression throughout the germline and retention of function. Likewise, numerous of our tags across fluorophores showed robust germline expressions including EEF-1A.1::mTagBFP2, Y22D7AL.10::mStayGold, and HAT-1::mScarlet3. In fact, overall transcript levels generally tended to underestimate germline enrichment at the protein level. We note that single-copy transgenes driven by eef-1A.1/eft-3 promoter by itself are frequently not expressed in the germline (PMID: 31064766); that we could detect EEF-1A.1 robustly in the germline when tagged endogenously is evidence that silencing is unlikely to be a widespread concern, and at the least less of a concern than single copy transgenes. We appreciate that for a transgene, presence/absence of specific sequence elements and genomic loci play a role in expression, but an endogenous tag captures all such information at a given locus.

      Indeed, we found only two reports of endogenous tags being silenced in the germline, the first being a novel tag (not fluorophore) which initially prevented expression at the tagged locus (PMID: 30109984), but after making changes to the sequence to avoid silencing signals the authors could rescue expression and thereafter saw robust expression in various novel contexts with this tag. The second example (PMID: 34547227) leaves open the possibility that germline repression of that particular gene might be a part of its endogenous regulation.

      Nevertheless, given it is probably rare if occurs at all, it will likely take a large scale tagging effort to uncover such cases at sufficient numbers to study. In our view, this further justifies tagging at large, ideally genomic, scales. If we do discover that there are numerous annotated germline proteins which we don’t observe by tagging, that would be interesting to study on its own.

      (7) Halotag is presented in the Discussion as a small tag, but it is bigger than GFP.

      Thank you for catching this. We have removed the discussion of Halotag. Given the comparable size to FPs, it would be unlikely to alleviate issues of tag functionality.

      (8) It would be useful to include FPKMs and viability percentages in Table 1.

      FPKM is included in column 6, but the title for this column is cut off. In the revised table FPKM values are now shown more clearly across stages.

      We did not quantify viability percentage. In our view it does not yield an informative metric when there is little information about the protein’s required dosage for function, which was the case for most proteins here. A haplosufficient gene might yield a full brood size even if 50% of protein function is lost; conversely, a highly dose sensitive protein could yield penetrant and severe inviability with mild perturbation of function. It also is not actionable information at this stage if there is no alternate tagging strategy as a baseline of comparison. The worms we picked to image all have viable embryos as adults, so in those individuals the genes were likely to be sufficiently expressed and functional.

      (9) Because establishing that a guide works well is a limiting step for many CRISPR experiments (once a guide works well, it's easy to inject 5 worms and get lines), I wondered if testing that for many genes is what is really needed in the field at this stage. 

      Guide quality is rarely an issue in C. elegans, as for all the genes here we tried only one guide, all of which were previously untested. We now clarified this in the discussion section:

      “Notably, we find that previously untested guide RNAs and homology arms perform exceptionally well at novel loci, as we only tested one set of reagents for each locus which yielded satisfactory tagging rates.”

      (10) For a manuscript where the injection is so central to what was done, I was surprised to read in the Acknowledgments that all of the injections were done by someone who is not included as an author.

      We are likewise surprised by such a comment but gladly clarify: Chi Chen has been with us as an expert microinjection specialist for more than 25 years and her very important technical contributions have been acknowledged in many dozen papers. Multiple authorship guidelines, including COPE’s and ICMJE’s, state that technical contributions alone do not qualify for authorship.

      Reviewer #2 (Recommendations for the authors):

      (1) We would encourage the authors to provide systematic validation of the reported insertions. The manuscript reports that 24 of 30 tags were isolated and visible, but does not clearly state whether each isolated line was confirmed by sequence‑level validation to be correctly in‑frame and free of unintended mutations at the target locus.

      We appreciate the reviewer’s concerns on fidelity. These parameters have been assessed in prior published work (e.g., PMID: 30504364, PMID: 34748534) and in our hands are in the range of 80% whenever we sequence non-fluorescent tags of similar sizes. The efficiencies we observed are high enough that one can expect to recover numerous worms with the exact intended sequence for each target, though we would argue mutations within the FP reporter are less likely to matter if it retains high fluorescence.

      (2) The manuscript presents aggregated success counts (e.g., 8/10 mTagBFP2 tags, 9/10 mStayGold, 7/10 mScarlet3) and useful narrative descriptions of injection outcomes. We also suggest including per‑locus success rates.

      Figure 3B shows per locus success rate and source data is provided for this figure. Each dot is an individual injection and the Y axis is per locus rate. We now worded this more clearly in the figure’s caption.

      “Total insertion efficiencies per locus for the indicated targets across injection pools.”

      (3) For pools that required re‑injection after initial failures, we would like to see a description of the specific changes that were made to the injection mixes or procedures (e.g., new repair template prep, different Cas9 reagent lot, guide redesign). This will be useful troubleshooting information for others.

      We re-made the exact same injection mix but with nanodrop to ensure the purity of the repair templates as assessed by absorbance ratios (A260/230 and A260/280) were sufficient after each purification step. No other changes were made. This is now specified in the methods section in the following way:

      “For re-runs of pools 4, 6 and 10 which failed initially, we regenerated the repair templates and ensured that after each column purification, the A260/230 ratio of the purified DNA was ≥2.2 and A260/280 was 1.8 ± 0.05 when measured with a Nanodrop spectrophotometer.”

      (4) The authors state that the fluorophore sequences are codon-optimized for C. elegans. We suggest they provide the exact donor/tag sequences, specifically state whether the fluorophore sequences contain any synthetic/artificial introns, or whether other sequence modifications (e.g., silent PAM‑disrupting mutations) were included in the donor templates. 

      This information is provided in Supplementary Table 1.

      (5) Page 3: Include a reference for "The C. elegans genome encodes around 20,000 genes" 

      We added a reference to the most recent release of the genome (WS237, May 2013). Spieth et al., 2014.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors aimed to uncover novel therapeutic vulnerabilities in APC-mutant colorectal cancer (CRC), which constitutes the majority of CRC cases. They hypothesized that modulating oxygen-sensing pathways (via PHD inhibition) could disrupt adaptive stress responses in these tumours.

      Strengths:

      The study employs a powerful, two-pronged approach to identify Molidustat's targets. By using both Thermal Proteome Profiling (TPP) and an orthogonal chemical proteomic competition assay, the authors provide compelling evidence that GSTP1 is a genuine, direct off-target, effectively addressing the common limitation of indirect effects in proteomic screens.

      Weaknesses:

      (1) In Figure 1, the current data rely on a single guide RNA (sgRNA). To make the data solid, at least two independent sgRNAs targeting different regions of PHD2 should be used.

      We thank the reviewer for raising this. Clarity on the CRISPR strategy was missing from the original submission and we have now added the following to the Methods (Page 4). We did not use a single sgRNA. PHD2 was targeted with a pool of three chemically modified crRNAs:

      (IDT Alt-R; target sequences: 5'-TACAACCAGCATATGCTACA, 5'GTGGCTGCCGAAGCCGAGCC, 5'-GATAAGATCACCTGGATCGA)

      Delivered as in vitro assembled ribonucleoprotein complexes with high-fidelity Cas9. This format has been reported to achieve high on-target efficiency while minimising off-target cutting [1,2] such that any residual stochastic off-target events are distributed across the population and are not expected to manifest as a coherent phenotype at the population level. Working with pooled, unselected knockouts rather than single-cell clones also avoids the confounds of clonal heterogeneity that normally motivate the use of multiple independent guides and rescue experiments in single-clone workflows. We have previously validated this approach for GSTP1 knockout in a separate single-cell proteomics study [3], where loss of GSTP1 protein was observed in over 90% of single cells and GSTP1 was the most significantly altered protein between sgControl and sgGSTP1 populations.

      (2) Figure 3E: Asn205 site should be mutated to prove that whether Molidustat inhibits GSTP1 activity via Asn205 or not.

      This is a good suggestion, and we explored it in silico before concluding it was not tractable. We used PyMol mutagenesis to model Molidustat binding to GSTP1 variants at the predicted contact residues: Asn205 was mutated to Ala, Gly and Ser; Trp39 (predicted to hydrogen-bond Molidustat) was mutated to Ala, Phe and Thr; and a Tyr8Phe/Asn205Ser double mutant was also modelled. In every case, Molidustat reoriented within the active site and adopted an alternative hydrogen-bonding configuration (most commonly with Tyr8), yielding a docking score equal to or better than binding to native GSTP1 (Author response image 1– Author response image 4). The model therefore does not predict any single or double point mutant that would ablate Molidustat binding in a clean, interpretable way, and we could not design a rational loss-of-interaction mutant on this basis. Given this limitation, and that definitive mapping of the binding interface would require co-crystallography, which is beyond the scope of the present study, we have moved the docking model to the supplement and flagged it as predictive rather than definitive.

      Author response image 1.

      Molidustat in native GSTP1

      Author response image 2.

      Molidustat docking with mutated GSTP1, Asn205 mutated to Gln205

      Author response image 3.

      Molidustat docking with mutated GSTP1, Tyr39 mutated to Phe39

      Author response image 4.

      Molidustat docking with mutated GSTP1, Asn205 mutated to Ser205 and Tyr8 mutated to Phe8

      (3) Figure 5B and 5C: The metabolic imbalance phenotype observed upon dual knockout of PHD2 and GSTP1 requires rescue experiments to confirm on-target specificity.

      We thank the reviewer for this important point and agree that rescue experiments could represent the most direct demonstration of on-target specificity for the metabolic phenotype observed in Figures 5B and 5C. These rescue experiments are necessary when working with single clones, as they allow for comparing a knock-out clone with a reconstituted pool and sidestep the issue of clonal heterogeneity.

      In our case, we think that there is no advantage to doing so, as we work with pooled knockouts, so any clonal heterogeneity is diluted in the pool.

      One could even make the case that such a rescue experiment would introduce additional artefacts. Combined loss of PHD2 and GSTP1 leads to reduced cellular viability, with decreased proliferation and increased apoptosis, consistent with a synthetic lethal interaction. To devise a rescue experiment, we would have to isolate a single-cell clone (the pool is not a complete 100% knock out, WT cells would outgrow the knock out cells). The isolation of such a clone that has overcome the anti-proliferative insult of the double knockout is likely to have a phenotype distinct from the original, pooled population, as would the rescued have from the WT cells. For these reasons, we have not performed rescue experiments in the current study. We have added the absence of a rescue as a limitation to the study in the discussion

      “While genetic rescue experiments would provide definitive confirmation of on-target specificity, the pronounced loss-of-fitness and apoptotic phenotype observed upon combined PHD2 and GSTP1 loss limited the feasibility of establishing stable rescued double-knockout populations, and therefore represents a limitation of the current study.”

      Reviewer #2 (Public review):

      Summary:

      The authors aimed to determine Molidustat targets and the potential utility of these findings. They clearly demonstrate that Molidustat interferes with GSTP1 and some other proteins on top of PHD2. They also demonstrate that PHD2 deletion is not sufficient to recapitulate Molidustat effects in cells and proteomes. Finally, they demonstrate synthetic lethality in organoids for Molidustat and APC deletion.

      Strengths:

      The data on Molidustat proteomes, GSTP1 binding, inhibition and metabolic health of organoids is really clear. All biochemical, docking and omic data are really strong. The potential impact of these findings could be the use of Molidustat in APC null tumours and awareness of potential off-target effects.

      Weaknesses:

      A main but minor weakness is that Molidustat also inhibits other PHDs, although these are less expressed. PHD1 has been shown to control the cell cycle and be expressed in the colon, where it is needed for viability. Although this does not explain the lack of effect of other PHD inhibitors, it does warrant some discussion. The use of MTT is not very good to detect viability when it measures metabolism; this also needs to be discussed and perhaps supplemented with colony or cell number measurements.

      Great point, for this reason, we have assayed apoptosis throughout. In addition, we have added a clonogenicity assay with APC organoids. Organoid cells were treated with an acute dose of Molidustat. We subsequently measured the level of Lgr5 (a stem cell marker) and of the ability of the cells to generate organoids (these data have been added as Figure 5 F-G.)

      Reviewer #3 (Public review):

      In this paper, the authors revealed that Molidustat can induce a dose-dependent increase in Caspase-3/7 activity in the HT29 cell line, which is an APC-mutant colorectal cancer cell line. More importantly, they found that targeting PHD2 alone cannot cause cell death. By using thermal proteome profiling (TPP) and orthogonal chemical proteomic competition assays, they determined GTSP1 as a previously undiscovered off-target of Molidustat. They also revealed that combined PHD2 and GSTP1 loss leads to an increase in intracellular ROS and apoptosis. Moreover, they evaluated the effects of Molidustat in colonic organoids and showed that

      Molidustat has a high selectivity for colonic organoids with activated WNT signaling and/or KRAS pathway alterations, and this effect is not reproduced by hydroxylase inhibition alone, providing a new potential approach to targeting both PHD2 and GTSP1 for the treatment of APC-mutant CRC.

      Specific comments:

      (1) What is the possible molecular mechanism of dual GSTP1/PHD2 loss, inducing cell death?

      This is an important question. Our data support a model in which combined loss of GSTP1 and PHD2 disrupts cellular redox homeostasis, leading to accumulation of reactive oxygen species, increased GSSG/GSH ratios, and depletion of antioxidant buffering capacity. This redox imbalance is accompanied by downregulation of pro-survival pathways. In this context, activation of apoptotic signalling, as evidenced by increased caspase-3/7 activity and proteomic enrichment of apoptosis-associated pathways, contributes to the observed cell death phenotype.

      While apoptosis is supported by our data, the magnitude of oxidative stress suggests that additional oxidative stress-associated cell death mechanisms may also contribute. We have clarified this point in the Discussion (Page 11).

      (2) Can the authors mutate the binding site of Molidustat on GTSP1 to verify the in silico docking results?

      This is a very important question. Currently, the model is of limited value. Reviewer 1 had a similar question. Can we refer you to Reviewer 1, question 2.

      (3) Evidence for Molidustat inhibiting PHD2 activity or stabilising HIF-1α should be provided.

      We thank the reviewer for this suggestion. Data showing HIF-1α stabilisation and evidence of downstream signalling is now added to Supplementary Figure 1.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      I only have minor suggestions:

      Molidustat also inhibits other PHDs, although these are less expressed. PHD1 has been shown to control the cell cycle and be expressed in the colon, where it is needed for viability. Although this does not explain the lack of effect of other PHD inhibitors, it does warrant some discussion. The use of MTT is not very good to detect viability when it measures metabolism; this also needs to be discussed and perhaps supplemented with colony or cell number measurements.

      This is correct, PHD1 is of particular interest, given the effects inhibition/knock-out has on the inflamed colon. We have added a new paragraph to the Discussion (Page 13) that addresses the isoform selectivity of Molidustat. We note that, although developed as a PHD2 inhibitor, Molidustat retains appreciable activity against PHD1 and PHD3 [4], and we discuss the non-redundant and in some contexts opposing roles of PHD1 and PHD2 in the colon, PHD1 loss is protective in DSS colitis [5] and restrains colitis-associated tumour growth, whereas PHD2 loss in the tumour and stroma is reported to inhibit metastasis and treatment response [6]. We further note that this pattern of isoform engagement is shared with other pan-PHD inhibitors that did not phenocopy Molidustat in our screens, indicating that PHD isoform profile alone is insufficient to explain Molidustat’s distinctive activity and pointing to GSTP1 off-target engagement as the key distinguishing feature. We argue that localised colonic delivery (as discussed earlier in the Discussion) would concentrate drug at the APC-mutant epithelium while limiting systemic exposure.

      We fully agree with the reviewer, MTT measures metabolic activity/NADH levels rather than viability in the strict sense, and that this is particularly relevant for a compound that perturbs redox metabolism. We have added a clonogenicity assay in APC organoids (Fig. 5 F-G) to supplement the MTT and Cleaved Caspase 3 assays already present in the manuscript.

      (1) Lee, J. K. et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat. Commun. 9, (2018).

      (2) Sakovina, L., Vokhtantsev, I., Vorobyeva, M., Vorobyev, P. & Novopashina, D. Improving Stability and Specificity of CRISPR/Cas9 System by Selective Modification of Guide RNAs with 2′-fluoro and Locked Nucleic Acid Nucleotides. Int. J. Mol. Sci. 23, (2022).

      (3) Makar, A. N., Holkham, J., Lilla, S., Wilkinson, S. & von Kriegsheim, A. Overcoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity. Preprint at https://doi.org/10.1101/2025.03.10.642380 (2025).

      (4) Flamme, I. et al. Mimicking hypoxia to treat anemia: HIF-stabilizer BAY 85-3934 (molidustat) stimulates erythropoietin production without hypertensive effects. PLoS One 9, (2014).

      (5) Tambuwala, M. M. et al. Loss of prolyl hydroxylase-1 protects against colitis through reduced epithelial cell apoptosis and increased barrier function. Gastroenterology 139, (2010).

      (6) Leite de Oliveira, R. et al. Gene-Targeting of Phd2 Improves Tumor Response to Chemotherapy and Prevents Side-Toxicity. Cancer Cell 22, (2012).

    1. Author response:

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

      eLife Assessment

      This study used pupillometry to provide an objective assessment of a form of synesthesia in which people see additional color when reading numbers. It provides convincing evidence that subjective color ratings are matched by changes in pupil size that recapitulate brightnessmediated changes when exposed to the real color. The work provides a valuable contribution to the literature on both synesthetic perception and the use of pupillometry to probe perception and related psychological processes.

      We were pleased to learn that our manuscript was of interest to the reviewers and the editor. We thank the reviewers for their useful feedback and have addressed all their comments in the revised version. We here give the most prominent changes as quotes.

      We thank all reviewers and for their very helpful input.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Knowing that small pupil-size variations accompany brightness variations (even when these are illusory), the authors asked whether pupil constrictions would accompany the synesthetic perception of a brighter color (compared with a darker one), induced by the presentation of a blackwhite character. This grapheme-colour synesthesia is only experienced by a few participants, sixteen of whom were enrolled in this study. The results reliably showed that a relative pupil constriction would "betray" the perception of a brighter color in these participants, while no such effect would be observed in control participants who were asked to report a color in association with each grapheme, even though they did not perceive any.

      Strengths:

      The main strength of the study lies in its combination of psychophysics (brightness ratings) and pupillometry, which allowed for showing clear-cut results.

      Weaknesses:

      Some relatively minor weaknesses concern the ancillary analyses, which tackle secondary questions and are not entirely convincing.

      (1) The linear mixed model approach is a powerful way to identify important variables, but it does not clarify whether the key factors are between-subject or between-trial variations. Some variables are inherently defined at a subject level (e.g., PA scores), others are not. I would strongly recommend an alternative visualisation of the results to examine inter-individual variability.

      Visualizing the highly idiosyncratic effects is indeed challenging. Addressing R1’s point 4 and a point brought up by R2, we updated all figures to now visualize pupil size in millimeters instead of arbitrary units. Furthermore, we added a supplementary figure (supplementary figure 4) that visualizes pupil size change without demeaning (please see reply to point 4).

      To get a better grasp of the interaction between lightness and coupling strength, we further included the supplementary figure 5 that splits by lightness and coupling strength in synesthetes.

      Furthermore, as this review and response will be publicly available, Author response image 1 provides participant-mean traces per lightness bin in addition to the overall means and hopefully makes the stability/variability of effects visually clearer (in addition to the strip plots that attempt this for the average response).

      Author response image 1.

      We hope that these additional visualizations make the effects of interest more transparent. Ultimately, however, the LME figure likely provides the information best, albeit at the cost of complexity.

      (2) It is not clear why taking the first derivative of pupil size in Figure 5 would isolate the effect of arousal, eliminating those of luminance and contrast changes (in fact, one could argue for the opposite, since arousal effects are generally constant for extended periods of time while contrast effects are typically more local and transient).

      First, please note that the results in 2.3.1 cannot be explained by task or context effects such as luminance and contrast: the exact same active color reporting task (same task and context) was presented to synesthetes and non-synesthetes.

      Indeed, the reviewer is correct that the first derivative does not eliminate other concurrent pupil-driving effects, that was expressed wrongly in our original text. Indeed, any stimulus-locked effect, such as the luminance and contrast effects, but also the effort effect will reflect similarly in the derivative measure.

      We did take the derivative because pupil responses driven by other non-trial related activity, such as increasing tiredness or excitement over the course of trials differ almost by necessity between participants, thus creating variability. However, these effects are most likely happening at a slower timescale and thus show less in the derivative measure. Accordingly in past research, we previously found clearer response-locked effects in the past when using a derivative measure (Douze et al., 2025; Ten Brink et al., 2024). This way, we also hoped to get rid of such variability that happens between participants for this between participant analysis.

      Even if we were to use the same baseline corrected analysis, we would arrive at the same conclusion: we here directly compared baseline-corrected pupil sizes by taking individual differences into account (using a LME). In other words, we tested for the same question, but not relying on the derivative. We thus compared baseline-corrected pupil sizes using over-time LMEs. Group (active control vs. synesthete) gained significance between ~1.7s and 3s, aligning with the derivative-based result.

      Author response image 2.

      t-values of a per-time point LME predicting pupil response from group (synesthete/active control) Group reached significance.

      In sum, we deem the derivative more powerful/more appropriate in this context, but the interpretation of findings does not hinge on that analysis choice (as can be seen in the Author response image 2).

      We corrected the claims on the derivative as a measure cleaning out other effects that indeed was oversimplified as it stood. We now write:

      “Mental effort presents in task-evoked pupil dilations, yet other factors simultaneously affect the pupil, such as luminance and contrast changes at trial onset, as well as slower trends across the session (e.g., fatigue). To reduce the influence of these slower, non-trial-locked fluctuations while retaining the trial-evoked dynamics, we calculated the first derivative of the pupil time course to assess the velocity of pupillary changes (Butterworth filter, 18 Hz, order 3, 2.5 Hz lowpass, following our previous works [60, 61]).”

      Douze, B. T., Ten Brink, A. F., Dijkerman, H. C., & Strauch, C. (2025). Pupil responses objectively index pharmacologically altered tactile sensitivity. Cortex, 193, 90-104.

      Ten Brink, A. F., Heiner, I., Dijkerman, H. C., & Strauch, C. (2024). Pupil dilation reveals the intensity of touch. Psychophysiology, 61(6), e14538.

      (3) It is a pity that responses to physical brightness modulations were only measured in the synesthete group, not in controls, as this would have allowed for ruling out differences in pupil reactivity across the two populations.

      The reviewer is correct that this would allow additional comparisons, but argue that light responses in healthy control samples are very well documented and stereotypical. For instance, Bergamin & Kardon (2003) provide very systematic latency estimations, for low-luminance change stimuli in the realm of about 320ms that can accelerate to about 250ms for very strong luminance changes. Our relatively small luminance increments should thus be expected in this range. Indeed, this also well describes the response latencies we observed in synesthetes when exposed to the colored disks. While there is no detailed information about participants in Bergamin & Kardon (2003), data from previous studies shows very similar pupil light response profiles in a healthy student control population that matches our synesthetes well demographically (Strauch, Romein et al., 2022 Figure 2a, exact same lab as for the present study; Koevoet et al., 2025 Figure 3a). See also the further responses, baseline pupil size in millimeters across groups did not differ.

      Together, we can safely conclude that pupil light responses in synesthetes are not different from pupil light responses in controls. We agree with the reviewer that this is a sensible point to also make in the manuscript:

      “Specifically, pupil size first responded significantly to physical luminance after 330 ms (see Supplementary Figure 7 for per-timepoint LME; in line with response latencies of similar control populations, see Bergamin & Kardon [52], Koevoet et al. [40], and Strauch et al. [53]), but only responded significantly to synesthetic lightness at about 870 ms (see also Figure 3c vs e and Figure 4 for per-timepoint LME)”.

      Bergamin, O., & Kardon, R. H. (2003). Latency of the pupil light reflex: sample rate, stimulus intensity, and variation in normal subjects. Investigative Ophthalmology & Visual Science, 44(4), 1546-1554.

      Koevoet, D., Naber, M., Strauch, C. & Van der Stigchel, S. Presaccadic Attention Shifts Up-and Downwards: Evidence From the Pupil Light Response. Psychophysiology 62, e70047 (2025).

      Strauch, C., Romein, C., Naber, M., Van der Stigchel, S., & Ten Brink, A. F. (2022). The orienting response drives pseudoneglect—Evidence from an objective pupillometric method. Cortex, 151, 259-271.

      (4) Another concern is with the visualisation of the pupil traces in Figure 3 (main results); these were heavily pre-processed (per-participant demeaned), losing any feature besides the effect of interest and generating the unrealistic expectation that perception of dark/bright colors generate a net dilation/constriction of the pupil - whereas perception-related modulations of pupil size are always relative and generally small compared to the numerous other effects registered in pupil size. It would be far better to see the actual profiles, preserving the unfolding of dilations and constrictions over time, especially since these are further analysed in Figures 4 and 5.

      Indeed, the expectation that any dark synesthetic experience would lead to pupil dilation whereas any bright synesthetic experience would lead to constriction is not warranted – it would only do that relative to the counterfactual of not having that experience.

      Many factors affect the pupillary signal at the same time, and often differently across individuals (think of tiredness etc.), making merely baseline corrected traces seemingly noisy. Our visualization highlights that there is a systematic part to that variation that lies in the synesthetic brightness experience.

      Visualizing the effects of idiosyncratic experiences, varying within and between participants is challenging. For the theoretical insight brought about through our paper in Figure 4 (synesthesia being sensory in nature), demeaning is favorable in our opinion as it isolates the effect of interest in visualization. However, for methodological reasons and to better show effect sizes etc., there is certainly use in additional transparency. We now thus provide non-demeaned traces in the supplementary material as the reviewer suggested and also refer to these in the main manuscript. Furthermore, all figures are now provided in millimeters, with all pupil related analysis being rerun and updated to this end (without qualitative changes to the results). This should further rectify possibly inflated expectations about the absolute size of effects and allows to put effects into perspective across studies. We now added:

      “Pupillary data were transformed from arbitrary eyelink units to millimeters using a conversion factor obtained with an artificial eye (see Hayes & Petrov, 2016).”

      Hayes, T. R., & Petrov, A. A. (2016). Mapping and correcting the influence of gaze position on pupil size measurements. Behavior research methods, 48(2), 510-527.

      Impact:

      Despite these weaknesses, and especially if they are adequately addressed in the review, this work is likely to improve our understanding of synesthesia, providing a new tool to quantify the subjective sensations; an interesting potential extension would be using pupillometry for tracking changes over time of the synesthetic experiences, opening up the possibility to evaluate the importance of learning for this peculiar experience.

      We were happy to read our manuscript was evaluated this positively and hope that our replies can address the remaining smaller concerns and make findings more transparent to the readers.

      Reviewer #2 (Public review):

      Synesthesia is a neurological condition where stimulation of one sensory channel leads to involuntary, automatic, and consistent experience of another, unrelated percept. For example, Sir Francis Galton (1880, Nature) famously described the robust tendency of some individuals (synesthetes) to associate numerals with a distinct color. Ever since, synesthesia has continued to attract a broad interest in the cognitive neurosciences in light of its implications for the study of domains such as perception, consciousness, and brain connectivity, among others.

      Strauch, Leenaars, and Rouw measured pupil size in a group of 16 grapheme-color synesthetes and two matched control groups. The participants were presented with gray digits - that is, visual stimuli having identical physical properties in terms of brightness. Each participant subsequently rated the corresponding evoked color and brightness: unlike controls, synesthetes did so in a very consistent and reliable fashion. Accordingly, this was also shown in their pupils: despite the same objective luminance, digits associated with brighter percepts caused their pupils to constrict, and digits associated with darker percepts caused their pupils to dilate more than controls. These results highlight how crossmodal correspondences are deeply rooted in synesthetes, and put forward pupillometry as a particularly appealing biomarker for some phenomenological experience (at least those grounded in "brightness").

      Further strengths of the technique are its temporal resolution and its responsiveness to several constructs. Across several tasks, the authors show, for example, that responses to synesthetic light are somewhat slower than responses to real light (i.e., they are likely mediated), but at the same time faster than responses to mental imagery. The role of mental imagery can also be reasonably dismissed when considering the second feature of pupil size: its responsiveness to mental effort and cognitive load. The pupils tend to dilate with demanding, challenging tasks, and this was the case when control participants were asked to report the color of a digit for which they did not consistently experience a synesthetic association. The same task was, instead, seemingly effortless for synesthetes, again speaking in favor of the automaticity of number-color correspondences in their case.

      Overall, the findings by Strauch, Leenaars, and Rouw are highly significant for the field and likely to be impactful. The strength of their evidence, when accounting for the relatively small sample size and the inherent variability of both phenomenology (color perception and subjective reporting) and physiology (pupil size), is adequate and sufficiently convincing.

      We were glad to read this overall very positive assessment of our work and thank the reviewer for the additional non-public suggestions for improvements.

      Reviewer #3 (Public review):

      Summary:

      In the present study, the authors examined pupillary responses to uncolored stimuli (number graphemes) among number-color synesthetes and non-synesthetes. After seeing a digit, the synesthetes and active control participants were asked to indicate which color they perceived using three dimensions of hue, saturation, and lightness. The lightness values were the primary independent variable for follow-up analyses. To see how the pupil responded to psychologically "bright" and "dark" digits, the authors split the reported lightness values at the median and plotted them. The synesthetes showed a pupillary constriction to digits they perceived as bright and dilation to digits they perceived as dark. Active control participants did not show that effect. In a subsequent block, only the synesthetes were shown the colors they reported perceiving as colored discs. Their pupillary responses were similar. The authors also found that the differences in pupillary responses between light and dark perceptions (with digits) were only slightly delayed in their onset to the perception of a colored disc, and therefore, the color perception accompanying a digit is unlikely to be effortful or a retrieved association, but occurs rather automatically.

      Strengths:

      The authors employed a well-controlled and designed quasi-experiment comparing colorgrapheme synesthetes to non-synesthetes and showed convincingly that the color perceptions accompanying graphemes alter the physical perception of brightness. They also made a reasoned attempt to rule out the possibility that color associations are occurring effortfully via retrieved associations.

      We appreciate the positive assessment and useful suggestions for revision.

      Weaknesses:

      There are some areas in which the implications of these findings could be elaborated upon. I had the following questions:

      (1) Are the pupillary responses among synesthetes, which objectively do not seem to match the degree of physical stimulation entering the retina, in any way maladaptive for eye functioning? I understand the constriction/dilation of the pupil to not only benefit visual acuity but also to protect the retina from damage. Are synesthetes at any risk of retinal damage due to over-dilation of the pupil to brighter stimuli? Or are these effects of a magnitude that is too small to matter? As reported in arbitrary units, it was hard to know how large these effects were in terms of measurable changes in dilation (e.g., millimeters).

      This is an interesting point. Some argue that pupil size changes in a mid-range mildly affect optics thus affecting detection performance, contrast perception, and depth of field (Eberhardt et al., 2022, Mathôt & Ivanov 2019, Ruuskanen, Boehler, & Mathôt, 2025), rather than serving a protective role for the retina (Mathôt, 2018). Indeed, any effects reported here were quite small. We agree with the reviewer that this can be made more accessible by reporting effects in millimeters. We thus now adjusted all figures accordingly and write in the methods section:

      “Pupillary data were transformed from arbitrary eyelink units to millimeters using a conversion factor obtained with an artificial eye (see Hayes & Petrov, 2016).”

      Note that even the largest effects here (those elicited by physical luminance change in block 2 for the synesthetes) only caused differences in pupil size of about 0.3mm. This lies below the maximal pupil dilations observable in response maximal effort (about 0.5mm), for instance, and substantially below the full range of pupil size changes elicited through strong luminance stimulation (several millimeters). We therefore deem the changes in pupil size as obtained in our study too minor to be practically maladaptive for optics/perception.

      Eberhardt, L. V., Strauch, C., Hartmann, T. S., & Huckauf, A. (2022). Increasing pupil size is associated with improved detection performance in the periphery. Attention, perception, & psychophysics, 84(1), 138-149.

      Hayes, T. R., & Petrov, A. A. (2016). Mapping and correcting the influence of gaze position on pupil size measurements. Behavior research methods, 48(2), 510-527.

      Mathôt, S., & Ivanov, Y. (2019). The effect of pupil size and peripheral brightness on detection and discrimination performance. PeerJ, 7, e8220.

      Mathôt, S. (2018). Pupillometry: Psychology, physiology, and function. Journal of cognition, 1(1), 16.

      Ruuskanen, V., Boehler, C. N., & Mathôt, S. (2025). The Interplay of Spontaneous Pupil-Size Fluctuations and EEG Power in Near-Threshold Detection. Psychophysiology, 62(3), e70035.

      (2) Likewise, is the automatic synesthetic merging of two percepts something that could be learned such that natural synesthetes and "artificial" synesthetes would look similar? For example, if a group of non-synesthetic participants were to learn a color-grapheme association to automaticity, would you expect their pupillary responses to the graphemes look similar to the synesthetes'? If so (or if not), what would this tell us anything about the phenomenology of synesthesia?

      We find this question most interesting. Likely, different synesthesia researchers wouldn’t even fully agree on the most plausible answers to these questions. Training studies have shown that nonsynesthetes can be trained to associate particular colors to particular graphemes, as revealed in the synesthetic Stroop effect: interference effects of the learned color onto reporting the typeface color of the grapheme. The degree to which non-synesthetes can be trained to become similar to synesthetes is however still topic of debate.

      We now discuss as follows:

      “Future studies could examine to what degree training a non-synesthete to associate specific colors to particular inducers (e.g., digits), can provide similar patterns of results as genuine synesthesia (Bor et al., 2014, Colizoli et al., 2012, Rothen & Meier, 2014). Could learning produce similar brightness-related pupil effects in non-synesthetes? Similarly, would effort-linked responses diminish with increased training duration? The perhaps most interesting question relates to response latencies: Would a trained participant ever be able to produce brightnessrelated pupil effects as fast as a synesthete?”

      Bor, D., Rothen, N., Schwartzman, D. J., Clayton, S., & Seth, A. K. (2014). Adults can be trained to acquire synesthetic experiences. Scientific reports, 4(1), 7089.

      Colizoli, O., Murre, J. M., & Rouw, R. (2012). Pseudo-synesthesia through reading books with colored letters. PloS one, 7(6), e39799.

      Rothen, N., & Meier, B. (2014). Acquiring synaesthesia: insights from training studies. Frontiers in human neuroscience, 8, 109.

      (3) Do the synesthetic perceptions of digit graphemes merge in a sensible way? For example, if a synesthete sees a particular color with the digit 1, and a different color with the digit 9, what do they perceive when they see 19? or 1-9, or 1 9? Is there color blending, or an altogether different color perception?

      This is a very interesting question indeed. While each synesthete will have their own specific expression of synesthesia, there are regularities in how a combination of digits evokes synesthetic color. First, if asked about the color of a specific digit, each digit keeps its own color, as the color of a digit is linked to the identity of the digit (Dixon et al., 2006). Context effects are however possible, in particular when context alters the interpretation of the digit (Myles et al., 2003). A particularly common context in a multi-digit number is a dominant first digit, spreading its color to the subsequent digits in the number. However, as the digit color is linked to digit identity, what does ‘not’ happen is a mixing of colors into a qualitatively new color; for example, a yellow "1" and blue "9" do not merge into a green "19".

      Dixon, M. J., Smilek, D., Duffy, P. L., Zanna, M. P., & Merikle, P. M. (2006). The role of meaning in grapheme-colour synaesthesia. Cortex, 42(2), 243-252.

      Myles, K. M., Dixon, M. J., Smilek, D., & Merikle, P. M. (2003). Seeing double: The role of meaning in alphanumeric-colour synaesthesia. Brain and Cognition, 53(2), 342-345.

      Many thanks for the constructive assessment of our work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I am not sure I'd use the term 'cross-modal' given that the case considered here (graphemecolor) is purely visual.

      The reviewer is absolutely right: the term 'cross-modal' has a historical background rather than reflecting an exact factual accuracy. The term is still commonly used however, as it readily reflects how the induced additional experience is always of a different (sub)type than the inducing experience. There is a cross-over between experiences that might occur within the same sensory modality, or even induce awareness of a particular concept. But key to synesthesia is the crossover experience as the inducer and concurrent are different (sub)types of experiences. For example, seeing a letter can evoke a synesthetic experience of seeing a color, or evoke awareness of a particular gender or personality of that letter, but does not evoke another letter. To remain consistent with literature, we refer to 'cross-modality' when explaining the link to previous literature, but generally switched to using 'cross-over experience':

      “Therefore, synesthesia might provide a unique window into how the brain’s constructive processes can generate additional, conscious content, in cross-over experiences, often across modalities, going all the way down to the level of sensory phenomenology.”

      We adjusted throughout the manuscript accordingly.

      (2) I would not recommend focusing the introduction on the problem of qualia; this is a much more general and complex question than the one addressed in the study; the space of the introduction may be better used to present the actual object of study, giving a better picture of the synesthetic phenomenon and of previous work aimed at characterising it (behavioural, including PA scores and consistency measures, and neuroimaging). It is important to discuss how the pupillometric approach differs from the previously adopted neuroimaging techniques and what it can add to those.

      We agree that qualia is a very general and complex question. However, we respectfully disagree that this complex question is not the object of the study. What is remarkable about synesthesia is not the presence of an additional perceptual association per se, but the presence of a specific perceptual experience. As illustration, think of a test where an unconscious color association to the word 'banana' was tested. While a generic 'yellow' could semantically be linked and would likely be obtained in the (e.g. priming) experimental results, a follow-up question of picking on a color wheel the exact shade of yellow to this association, or describing the perceptual sensation of the color, would be non-sensical to the participants.

      This sharply contrasts with the current study: synesthetes, but not non-synesthetes, indicate a perceptual sensation of additional colors, and subsequently indeed the sensory properties of this percept (experienced brightness) affects the objective reflection of this sensation (pupil size) in synesthetes but not in non-synesthetes. In our view, the presence of additional qualia is key in understanding what sets synesthetic apart from non-synesthete associations, including so-called cross-modal correspondences (unconscious consistent associations across modalities, common to us all). We even believe that the reported qualia is what makes synesthesia so interesting in the first place. We now more clearly explain this link to qualia better in the introduction.

      "The most remarkable aspect of synesthesia is the subjective perceptual phenomenology of the induced colors, setting these sensations apart from color memory, thought, or amodal association. The contrast between synesthetes and non-synesthetes can thus offer an interesting doorway into examining qualia, the subjective perceptual phenomenology or first person (what's-it-like) perspective."

      We also improved the explanation of the synesthetic phenomenon, including a more detailed characterisation of behavioural measures (including consistency scores) and added neuroimaging studies. These changes have been incorporated into the text in response to previous comments (point 1- reviewer 1).

      Please note that we have chosen not to include more detailed discussion of PA scores. Our results show a trend but do not allow for a conclusive interpretation on PA scores, and we feel that placing greater emphasis on this topic might therefore be confusing or even misleading. Still, it would be a very interesting topic for follow-up research to examine how alterations in characteristics of the synesthetic experience influence pupil responses.

      The different synesthesia types all share the defining characteristics of an additional conscious and consistent experience. Synesthetes can verbally report their additional experience, and synesthetic sensations can be measured in behavioral paradigms such as the ’synesthetic Stroop’ effect, or brain activation patterns in sensory cortex [15]. Furthermore, test-retest paradigms show how synesthetic, but not non-synesthetic associations are highly specific and consistent [16-18]. Thus, over the past decades, research has established synesthesia as a ’real’ condition that can reliably be identified using behavior, neurophysiology, and neuroimaging [11, 13, 15–21]. The most remarkable aspect of synesthesia is the subjective perceptual phenomenology of the induced additional sensation, i.e., color in grapheme-color synesthesia. This sets synesthetic sensations apart from (color) memory, thought, or amodal association. Synesthesia can thus offer an interesting doorway into examining qualia, the subjective perceptual phenomenology or first person (what’s-it-like) perspective.

      We now discuss the pupillometric approach as it differs from the previously adopted neuroimaging techniques as follows:

      “Compared to neuroimaging studies [12,15,51], pupillometry may offer a more direct window into synesthetic phenomenology, as the directionality between pupil light reflex and perceived brightness is straightforward. Finally, improved understanding of the underlying processes can be obtained by contrasting responses to perceived versus actual (physical) brightness, given that the pupil light reflex is a well-characterised reflex arc involving few inferential steps.

      This adds to the explanation that was already present on how the current approach differs from previous techniques, and what it can add to those techniques:

      "Instead, current paradigms capturing synesthesia employ objective measures, but fail to capture its phenomenology [16, 17, 21, 23]."

      (3) There are a few typos and word repetitions.

      Many thanks – we identified typos and repetitions after another set of careful reads and hope to have eradicated them completely now.

      Reviewer #2 (Recommendations for the authors):

      I am overall very supportive of this work, but addressing the following points may enrich it further:

      (1) Paragraph 2.2.1. Here, models do not seem to compare synesthetes versus controls but rather assess the effects of interest separately in the two groups. The fact that experimental effects are significant in synesthetes, but not in controls, does not tell us much about differences between groups. Controls (e.g., Figure 3) do show a similar trend, albeit clearly smaller. There is one passage in which this issue appears to be tackled (page 10): "Critically, in an LME ran on synesthetes and controls and using only graphemes and the interaction of group and lightness as predictors, we found lightness to predict pupil size in synesthetes (t = -2.754, p = 0.006), but not controls (t = -1.134, p = 0.257)." But I am not sure that the reported statistics belong to the interaction - they seem to refer to the lightness effect within each group, not the difference.

      This is an important point, power for between-group comparisons is inherently limited for n = 16 per group (while still feasible for overall responses, things become trickier when less trials remain). A simple model of pupil ~ grapheme + group * lightness_scaled + (1 | participant) shows no significant interaction (despite one group showing the effect and the other not showing the effect significantly). The additional negative effect for group is in line with the effort-related effect reported later in the manuscript. Where does this leave us? Based on the lightness responses alone, the group difference can be characterized as a quantitative distinction, but the degree in which it is also a qualitative distinction cannot clearly be determined from current data. We revised the manuscript to make sure that such an interaction is not implied/ point to the absence of the significance of that interaction.

      The sensory nature of synesthetic color is supported by within-synesthete analyses, where coupling strength parametrically modulates the lightness-pupil relationship in a theoretically predicted manner. Importantly, the effort-related findings provide a complementary and statistically robust group comparison: synesthetes and controls performing the identical colorreporting task showed significantly different pupil dilation rates, directly demonstrating that the two groups differ in how they access color information. Together, these two independent pupillometric signatures, one tracking perceptual quality, one tracking effort, converge on the same conclusion and mutually reinforce the interpretation that synesthetic color constitutes genuine sensory phenomenology.

      Author response image 3.

      We now make this more explicit in the manuscript as follows:

      “We found significant modulations of pupil size by the lightness of the grapheme's synesthetic color - sustained and in the to-be-expected time window. Specifically, the pupil constricted more for brighter reported colors, and dilated more for darker reported colors, as predicted (Average pupil size 800-4000ms, t = -3.601, p < 0.001). In an LME ran for synesthetes and controls and using only graphemes and lightness as predictors, we found lightness to predict pupil size in synesthetes (t = 2.844, p = 0.004), but not controls (t = 0.606, p = 0.544). However, when taking group as interacting factor in a joint LME, there was no interaction of lightness and group (t = -0.949 p = 0.342).”

      and

      “For controls a separate model was run, now without the PA score as predictor (not assessed for controls). Neither lightness (t = -0.815, p = 0.415), coupling strength (t = 0.438, p = 0.661), nor their interaction gained significance (t = -1.058, p = 0.290; all for average pupil size between 800 ms and 4000 ms). Critically, we also ran a LME with the three-way interaction of coupling strength, group, and lightness (Wilkinson notation: pupil = grapheme + group + lightness * group + coupling strength * lightness * group + (1 | participant)). This analysis revealed a significant three-way interaction between lightness, coupling strength, and group (F = 3.86, p = .021), indicating that the lightness × coupling strength effect on pupil size was not equivalent across groups. Decomposing this interaction by group, the lightness × coupling strength slope was significant in synesthetes (t = 2.59, p = .010) but not in controls (t=-1.01, p=.311), suggesting that reported lightness and its coupling strength were more consistently related to pupil size in synesthetes than in controls. Note however, that this decomposition does not directly test whether the two slopes significantly differ from each other, however. Lastly, pupil size was marginally larger in controls than in synesthetes (t = 1.94, p = .062; see later sections for more in-depth analyses)”

      (2) The authors choose to analyze pupil size in arbitrary eye tracker units. This is fine, although I would recommend assessing and reporting whether the average pupil size (e.g., during the baseline) is roughly comparable between groups. The size of the effects may be difficult to compare between groups in the presence of very different baseline pupil size.

      Please see Author response image 4 for Baseline pupil sizes per group in millimeters. There were no differences between groups.

      Author response image 4.

      F2, 45) = 0.707, p = 0.499 (One-way Anova).

      We now write:

      “Baseline pupil sizes did not differ between groups (F(2, 45) = 0.707, p = 0.499).”

      We agree with the reviewer that millimeters are a more intuitive measure and updated all figures throughout manuscript and supplementary materials accordingly. We also briefly added to signal processing that this conversion was applied.

      “Pupillary data were transformed from arbitrary eyelink units to millimeters using a conversion factor obtained with an artificial eye (see Hayes & Petrov, 2016).”

      Hayes, T. R., & Petrov, A. A. (2016). Mapping and correcting the influence of gaze position on pupil size measurements. Behavior research methods, 48(2), 510-527.

      (3) If I understand correctly, the main task counted 120 trials overall (12 per digit). It seems, however, that only 3 and 4 participants remained with at least 50 trials (or 25 per median split by lightness) after preprocessing. This appears to be quite a massive data loss: is there a reason behind it? Please also clarify: the overall percentage of discarded trials; whether the median split by lightness was computed on all responses or only on those of the remaining, valid trials.

      This is an important point for clarification indeed. The exclusion of participants in Figure 3 applies only to that particular visualization, not to the statistical analyses. The linear mixed effects models (LMEs) used all available valid trials from all participants, with no participant-level exclusions. The figure-specific threshold (≥25 trials per median-split bin) was applied purely for display clarity, as plotting participants with very few trials per bin would produce unreliable/noisy and thus visually misleading traces (as we note in the figure caption and point readers to Supplementary Figure 1, which shows the same visualization without any exclusions).

      Since the paradigm required participants to repeat discarded trials until 120 valid trials were collected, all participants thus contributed exactly 120 valid trials to the analyses. There was therefore no data loss at the analysis level for the LME that is central to the claims of the manuscript (albeit more complex to grasp than the t-tests between bins).

      Why were there sometimes so little trials per brightness bin?

      First, participants differed in how dark or bright (synesthetic or forced-report) colors were overall, meaning that differing proportions thereof would fall above or below the 0.5 cutoff that overall, well represented the sample (but not necessarily every single participant). Note that this median split was not performed per individual but across all color reports to allow an apples-to-apples comparison.

      Second, participants often reported colors that differed in Hue and Saturation, but not Lightness. This is in line with synesthetes picking certain colors more often than others, as compared with non-synesthetes (Rouw & Root, 2019; Ward et al., 2025).

      We now include a new Supplementary Figure that visualizes responses on the Hue and Saturation dimensions of HSL space for both synesthetes and controls; fully saturated reports appear on the outer edge. We refer to the supplementary figure in the caption of Figure 2 as follows:

      "See Supplementary Figure 1 for color reports on the hue and saturation axes.”

      Rouw, R., & Root, N. B. (2019). Distinct colours in the ‘synaesthetic colour palette’. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1787).

      Ward, J., Maciel, S., Rouw, R., Simner, J., & Root, N. (2025). Synaesthesia is linked to differences in music preference and musical sophistication and a distinctive pattern of sound-color associations. Psychology of Music, 53(3), 453-473.

      Minor points:

      (1) "Building on this evidence, we hypothesized that the cross modal color phenomenology in synesthesia can, if truly sensory in nature, could likewise be (...)" -> may need rephrasing (can/could).

      Many thanks, fixed.

      (2) Caption of Figure 1: "Block 2 (synesthetes only): a colored disk and gray central patch, matching the average indicated color per digit, and the number and luminance of pixels of said digit were presented to assess externally triggered light responses." -> I find this sentence a bit hard to follow; perhaps consider rephrasing it.

      Agreed, we rephrased to:

      Block 2 (synesthetes only): a colored disk was presented, colored according to the synesthete's average indicated color for that digit. At its center sat a gray patch matching the luminance and pixel area of the original digit from Block 1, together allowing assessment of externally triggered light responses.

      (3) Figure 2 b: Consider truncating the y-axis to 1 if that improves the visualization.

      We adjusted the axis accordingly and added a bit more detail in the caption for the interpretation of the measure.

      (4) Caption of Figure 3 points to "see Supplementary Figure 1", but it should probably be SF2.

      Many thanks for spotting, all references to supplementary figures have been checked and are corrected now.

      Elvio Blini

      Reviewer #3 (Recommendations for the authors):

      (1) As a minor comment, there are some terms that felt overused in the manuscript. For example, the words "extraordinary" and "exceptional" were used multiple times throughout. I believe I understand the authors to mean them in their descriptive sense (i.e., outside the realm of typical experience), but in context, those words make it seem like they are touting their own experiment as "exceptional" or "extraordinary," which I don't believe was their intention.

      We agree. We removed words such as exceptional and extraordinary when they do not directly refer to the sensation throughout the manuscript (which is indeed how we intended to use it). We hope that this removes unnecessary and convoluting hyperbole.

      (2) It seemed counterintuitive to me that the color consistency score would be reverse-coded. In this case, the scores actually seem to indicate inconsistency, rather than consistency. Perhaps the raw scores can be inverted for a more intuitive interpretation that aligns with the terminology. I understand that they were following a previous publication in their method (Rothen et al., 2013).

      This manner of coding is counter-intuitive indeed. However, there are both logical and practical reasons to this approach. Importantly, this is indeed the standard way of reporting color consistency in synesthesia research (Carmichael et al., 2015; Eagleman et al., 2007; Root et al., 2025; Rothen et al., 2013). The calculation is based on a simple logic; a higher number reflects a larger distance in color space. An additional advantage is the clear and intuitive zero- reference: a score of zero implies choosing the exact same color. Finally, it intuitively reflects the distinction between synesthetes and non-synesthetes; there is by definition little variation across synesthetes (visualized at the bottom of the graph), then a 'cut-off line' (if consistency is used as diagnostic tool), and then the height of the range shows how large the range in consistency is, in that particular sample of non-synesthetes. In a way we therefore inherit a confusing definition/standard, but changing it would lead to new confusion instead. We now specifically clarify this in the caption as follows:

      “Note that higher consistency is reflected in lower color distance, hence lower values [17].”

      Carmichael, D.A., Down, M.P., Shillcock, R.C., Eagleman, D.M., Simner, J., 2015. Validating a standardised test battery for synesthesia: does the synesthesia battery reliably detect synesthesia? Conscious. Cogn. 33, 375–385

      Eagleman, D.M., Kagan, A.D., Nelson, S.S., Sagaram, D., Sarma, A.K., 2007. A standardized test battery for the study of synesthesia. J. Neurosci. Methods 159 (1), 139–145.

      Root, N., Chkhaidze, A., Melero, H., Sidoro -Dorso, A., Volberg, G., Zhang, Y., & Rouw, R. (2025). How “diagnostic” criteria interact to shape synesthetic behavior: The role of self-report and test–retest consistency in synesthesia research. Consciousness and Cognition, 129, 103819.

      Rothen, N., Seth, A.K., Witzel, C., Ward, J., 2013. Diagnosing synaesthesia with online colour pickers: maximising sensitivity and specificity. J. Neurosci. Methods 215 (1), 156–160.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      This work compiles a comprehensive atlas of ncORFs across mammalian tissues and cell types, derived from reanalysis of ~400 public ribosome profiling datasets. The authors then evaluate cross-species conservation and functional signatures, proposing that evolutionarily ancient ncORFs tend to have higher translation potential, stronger expression, and closer relationships with canonical coding sequences.

      Strengths:

      In general, the study provides a large-scale and timely resource of annotated ncORFs, which could be broadly useful for the community. The authors collected ~400 public ribosome profiling datasets for annotations of ncORFs, which, to my best knowledge, is the largest collection of data for such a purpose. The catalog could facilitate future investigations into ncORF biology and broaden understanding of the coding potential of the "non-coding" genome.

      We thank the reviewer for the positive evaluation of our manuscript and for recognizing the significance of our contribution.

      Weaknesses:

      Based on the ncORF catalog, some of the analyses were not properly done. Some of the results are descriptive.

      (1) Bias and representations of the data source. Public ribo-seq datasets are unevenly distributed across tissues and cell lines, raising concerns about heterogeneity and underrepresentation of certain contexts. This may limit the generalizability of the catalog.

      We agree with the reviewer that the uneven distribution of public Ribo-seq datasets across tissues can inevitably introduce bias in the ncORF composition of our catalog. This bias is likely more pronounced in humans due to the narrower tissue coverage. We have addressed this point in the Discussion section of the revised manuscript.

      (2) The discussion on modular domains of ncORFs is unclear, and the claim that they may originate via TErelated mechanisms is not well supported. Stronger evidence or clearer reasoning is needed.

      We thank the reviewer for highlighting this point. We have revised the manuscript to more clearly explain the rationale behind our analysis of ncORF modular domains and have adopted more cautious language regarding their potential transposable element–related origins, limiting interpretations to what is directly supported by the data.

      (3) The conservation comparisons are not fully convincing. Figure S7 shows only mild differences between ncORFs and CDS, and statistical significance is not clearly demonstrated.

      Comparisons with other non-coding RNAs should be added, and overlapping sequences between ncORFs and CDS should be excluded to avoid bias.

      We thank the reviewer for this comment and apologize for the lack of clarity in the original figure. Both CDSs and ncORFs show significant deviation from zero Gnocchi scores (two-sided Wilcoxon signed-rank tests), which is now stated explicitly in the revised legend and text. CDS-overlapping ncORFs were already excluded in the original analysis; this has been clarified to avoid confusion.

      As suggested, we have added lncRNAs for comparison. ncORFs display modestly higher Gnocchi scores than lncRNAs, and this difference persists when restricting the analysis to lncRNA-derived ncORFs and their corresponding full-length lncRNAs (see revised Fig. S7). These additions strengthen the conservation comparison while controlling for transcript context.

      (4) Figure 3 indicates that some ncORFs are subject to evolutionary constraints. This is not surprising. The authors should provide further analyses on more detailed features of these "conserved" ncORFs vs. the "non-conserved" ones. Some pretty informative works have been done in Drosophila, worms, mice, and humans. Figure 3 suggests some ncORFs are under evolutionary constraint, but this is not unexpected. More granular analyses contrasting "conserved" versus "non-conserved" ncORFs would be informative. In fact, small ORFs, especially uORFs, have been extensively studied for their functions and cross-species conservation. The authors should explicitly show what is new here in their analyses.

      We thank the reviewer for this insightful comment. We agree that cross-species conservation of ncORFs (particularly uORFs) has been extensively investigated in prior studies, including our own.

      However, most prior analyses have focused on conservation of start codons or overall ORF integrity, which does not distinguish selection acting on translational activity from selection acting on the encoded peptide sequence itself. In contrast, our analysis leverages codon-level periodic PhyloP signals across the full ORF. The observed three-nucleotide periodicity is consistent with selective constraint at the amino acid level, rather than merely preservation of initiation sites or translational potential. Furthermore, our newly developed branch-length statistic uncovers lineage-restricted conservation patterns among ncORFs, enabling resolution of evolutionary dynamics not captured by conventional conservation metrics.

      Thus, while the existence of conserved ncORFs is not unexpected, the conceptual advance of our study lies in demonstrating that a subset exhibits coding-like evolutionary constraint consistent with selection on their peptide products, as well as revealing lineage-specific conservation patterns. We have clarified this distinction in the revised Discussion.

      (5) Translation levels are reported using RPF counts. However, translation efficiency (normalized by RNA expression) is a more appropriate measure to account for expression heterogeneity.

      We agree that translation efficiency (TE), which normalizes ribosome footprint counts by RNA abundance, is in principle an appropriate metric. We initially calculated TE and compared ncORFs with CDSs. However, we found that TE estimates for short ncORFs were substantially inflated by RPF enrichment near start and stop codons, leading to unstable and potentially misleading values.

      For CDSs, this bias is commonly addressed by excluding the first and last 10 to 20 codons when quantifying RPF density. This strategy is not feasible for ncORFs because of their short length. We therefore used RPF counts in the final analysis, applying stringent positional filtering. Only RPFs whose P sites fall within the ORF body, excluding start and stop codons, were counted. RPFs overlapping the ORF but with P sites outside the annotated frame, likely derived from adjacent ORFs or initiation or termination pausing, were excluded.

      TE and RPF counts both measure translation but capture different aspects. TE reflects ribosome density relative to transcript abundance, whereas RPF counts quantify overall ribosome engagement. Given the short lengths of ncORFs, count-based quantification provides a more robust and conservative estimate of their translational activity.

      (6) The correlation analyses between ncORF translation levels and PhyloCSF are confusing and largely descriptive. These sections need sharper framing and clearer conclusions.

      We thank the reviewer for this comment. We agree that the original presentation lacked clear framing. The relationship between PhyloCSF scores and mean ncORF translation levels across tissues is influenced by both evolutionary age and tissue specificity. Older ncORFs with higher coding potential tend to exhibit stronger tissue-restricted expression. As a result, their mean translation levels across all tissues appear lower, not because they are weakly translated, but because their translation is concentrated in specific tissues. This point is addressed in the revised manuscript.

      (7) Public ribo-seq datasets, generated by different research labs, are known for their strong batch effects. Representations of tissues and cells are also very unbalanced. Therefore, the co-translation analysis between ncORFs and canonical CDS is not well controlled. This should be done by referring to a recent large-scale ribo-seq meta-analysis (Nat Biotechnol. 2025. doi: 10.1038/s41587-025-02718-5).

      We thank the reviewer for highlighting this important study and for raising concerns regarding batch effects and tissue imbalance in public Ribo-seq datasets. We are aware that public Ribo-seq data generated by different laboratories are subject to substantial batch effects. During the ncORF annotation phase, we applied stringent quality-control criteria to minimize technical variability. For the co-translation analysis, inclusion criteria were relaxed to increase tissue and cell-type coverage. To partially mitigate representation bias, libraries derived from the same tissue or cell type were merged when quantifying ORF translation levels, thereby reducing overrepresentation from heavily sampled contexts.

      Nevertheless, we acknowledge that these measures cannot completely eliminate batch effects or imbalance inherent to public datasets. We agree that co-translation analysis would benefit from uniformly processed, high-quality datasets generated under standardized protocols with balanced tissue representation, representing a valuable direction for future research.

      Reviewer #2 (Public review):

      Summary:

      Chang et al. attempted to analyze a large number of ribo-seq datasets through a standardized pipeline, identifying novel non-canonical ORFs and elucidating their evolutionary and expression characteristics.

      Strengths:

      (1) The datasets analyzed by the authors are sufficiently comprehensive, and the use of standardized pipelines ensures excellent analytical consistency.

      (2) Their analyses of ORF evolution and co-expression further deepen our understanding of these ORFs.

      We thank the reviewer for the positive evaluation of our manuscript. It is encouraging to know that the analytical framework was found to be sound and appropriate.

      Weaknesses:

      (1) The authors primarily conducted analyses through bioinformatics, lacking sufficient wet-lab experimental evidence.

      We thank the reviewer for this comment and acknowledge this limitation. We agree that functional validation through wet-lab experiments would provide important mechanistic insight into individual ncORFs. However, this study was designed as a systematic, genome-wide computational analysis to characterize translated ncORFs across species and tissues. Our objective was to define global patterns of translation, conservation, and structural features using large-scale datasets. Given the breadth and scale of these analyses, experimental validation of specific ncORFs falls beyond the scope of the current study. We have clarified this point in the dicussion and noted that our results provide a framework for future targeted experimental investigation.

      (2) Regarding the evolution of non-canonical ORFs, a considerable amount of prior work already exists. The authors need to further clarify what new insights and discoveries they have made based on the analysis of such a large dataset.

      We thank the reviewer for this suggestion. Similar concerns were also raised by Reviewer #1. In response, we have revised the Discussion to more clearly delineate the conceptual advances enabled by our large-scale dataset.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Several aspects of the downstream analyses would benefit from additional refinement. The heterogeneity and tissue imbalance inherent in public Ribo-seq datasets introduce potential biases in ncORF detection and inferences about co-translation. Given the breadth of the dataset, it would also be informative to quantify how consistently the newly identified ncORFs are detected across samples-distinguishing those observed broadly across tissues, those enriched in specific contexts, and those detected in only a few datasets. Such stratification would help differentiate reproducibly translated ORFs from candidates requiring further validation.

      We thank the editor for the helpful comments. We agree that heterogeneity and tissue imbalance in public Ribo-seq datasets can influence ncORF detection and downstream interpretations. We have added discussion of this limitation in the revised manuscript.

      Detection of ncORF translation depends not only on biological activity but also on sequencing depth and data quality. Although all ncORFs reported here were reproducibly identified by multiple methods across independent libraries, we agree that those detected in a larger number of datasets represent stronger candidates for functional validation. Accordingly, we now report the number of methods and libraries in which each ncORF was detected in the final catalog (Supplementary Table 3). Overall, 22.3–26.3% of ncORFs were detected in more than 10 libraries, whereas more than half were observed in only two to five libraries (Fig. S1B), enabling clearer stratification of broadly translated versus more context-specific candidates.

      Some evolutionary and functional interpretations are largely descriptive or consistent with established findings for small ORFs, and the authors should more clearly articulate what is novel in their analyses. The criteria separating "young," "old," and "ancient" ORFs require clearer definition, and conservation analyses would be strengthened by improved statistical rigor and explicit exclusion of regions overlapping annotated coding sequences. Evidence for modular domain features or transposable element-related origins is limited and warrants either stronger support or more cautious framing. Proteomics validation is currently minimal and could be substantially reinforced using existing public MS resources.

      We thank the reviewer for these constructive comments. In the revised manuscript, we more clearly delineate the novel insights derived from our evolutionary analyses of ncORFs, distinguishing them from established findings on small ORFs.

      We have clarified the criteria used to classify ORFs by evolutionary age in figure 6E and refined the terminology describing “young,” “old,” and “ancient” categories to ensure precise definition. The conservation analyses have been strengthened through more rigorous statistical treatment and by explicitly excluding regions overlapping annotated coding sequences.

      With respect to modular domain features and potential transposable element–related origins, we have adopted more cautious language and limited our interpretations to what is directly supported by the data. Finally, we acknowledge that current proteomic validation remains limited and have clarified this point in the manuscript while outlining the potential for future integration of large-scale public mass spectrometry datasets in Discussion.

      The authors additionally report an interesting observation that many ncORFs on mRNA co-translate with the main CDS of the same gene. Because canonical models often posit that uORF translation suppresses downstream CDS translation, further analysis would be valuable. In particular, it would be useful to determine whether patterns of co-translation differ among ORF types or evolutionary categories and to discuss possible regulatory mechanisms underlying these relationships.

      We thank the editor for this thoughtful comment. As noted in our response to Reviewer #2, uORF–CDS co-translation does not contradict the canonical model in which uORFs repress downstream CDS translation. Co-translation reflects concurrent ribosome occupancy, whereas repression concerns the fraction of initiating ribosomes that ultimately reach and translate the CDS. Following the editor’s suggestion, we further examined whether co-translation patterns differ across ORF types or evolutionary categories. We found that ncORFs co-translating with their corresponding main CDSs are predominantly uORFs. However, these uORFs do not show statistically significant differences in conservation metrics or evolutionary age compared with other non-overlapping uORFs. Thus, we did not detect clear subtype- or age-specific distinctions among co-translating ncORFs. We have clarified these analyses in the revised manuscript.

      Addressing these points would enhance the precision, interpretability, and robustness of the study's conclusions.

      Reviewer #2 (Recommendations for the authors):

      (1) The authors developed and refined a standardized pipeline to analyze nearly 400 ribo-seq datasets, identifying over 10,000 novel non-canonical ORFs in both human and mouse samples. Given the scale of this analysis, it is intriguing to consider how many of the newly identified non-canonical ORFs are consistently detected across multiple sample types (conservatively expressed ORFs), how many are restricted to specific tissues/ or tissue-specific ORFs), and how many were detected in only a single or very few samples (ORFs requiring further validation). Providing these data could offer new insights into understanding ORF translation.

      Thanks for this constructive suggestion. This information has been presented in the revised Supplementary Table 3 and in a newly added supplementary figure (Fig. S1B), which together provide a clearer overview of ncORF detection consistency and context specificity.

      (2) The authors' validation of MS data lacks specific details in the paper. Regarding the MS-supported ORF mentioned in Lane 117, which dataset's MS data is being referenced? Or does it refer to the content in Reference 20? At present, substantial research exists in both public general proteomics studies (e.g., CPTAC) and MS investigations targeting non-canonical ORFs. We recommend the authors incorporate additional MS data or public MS-based databases to strengthen validation in this area (PMID: 34129944, 39794466, 37823596,39413795).

      We thank the reviewer for this comment and for the helpful suggestions. The MS-supported ORFs mentioned in line 117 refer to the compilation reported in Reference 20, which integrates evidence from multiple independent proteomics studies. In addition, we examined MS-supported ORFs curated by GENCODE and PeptideAtlas, which are shown in Fig. 1E.

      We agree that incorporating additional MS datasets would further strengthen validation of ncORFs. Studies cited by the reviewer and recent community efforts such as the GENCODE and PeptideAtlas analyses (PMID: 39314370) provide valuable examples in this direction. However, performing a comprehensive reanalysis of more than 95,000 public human MS runs is computationally demanding and currently infeasible for our group given resource and funding constraints.

      To our knowledge, ongoing community-wide initiatives are working toward more comprehensive catalogs of translated human ncORFs. Large-scale, exhaustive MS searches will be particularly effective once a community consensus annotation framework for ncORFs is established. We have added discussion of these limitations and future directions in the revised manuscript.

      (3) The authors classified ncORFs into three groups-"Ancient," "Young," and "Old"-based on their origin nodes. However, both the "Young" and 'Old' groups appear to be "mammalian-specific," yet the specific criteria for their division remain unclear. It is recommended to more clearly define in the figure legend or main text how "Young" and "Old" are categorized (e.g., based on specific evolutionary nodes or distance thresholds from nodes to the end) to avoid reader confusion.

      In Fig. 5, “old” and “young” were intended as qualitative descriptors of relative evolutionary age based on the position of ncORF origination nodes along the phylogeny, as indicated on the x-axis. They were not meant to represent discrete categories. To avoid confusion, we have revised the manuscript to use “older” and “younger” throughout when referring to relative age differences. A binary classification is used only in Fig. 6E, where ncORFs are grouped into ancient (pre-mammalian) and younger (mammalian-specific) categories. This distinction is clearly defined in both the main text and the corresponding figure legend.

      (4) The authors observed an intriguing phenomenon: ncORFs on mRNA tend to co-translate with the main CDS of the same gene. However, the conventional view holds that uORF translation often inhibits the translation of the main CDS. I suggest the authors could refine their analysis in this section further. For instance, do different types of ORFs or ORFs at different evolutionary levels exhibit distinct levels of cotranslation with the main CDS? Additionally, while observing this phenomenon, the authors should also propose hypotheses regarding the regulatory mechanisms involved in these processes.

      We thank the reviewer for these constructive suggestions. After excluding CDS-overlapping ORFs, we identified 258 human and 128 mouse ncORFs that co-translate with their corresponding main CDSs. With the exception of 10 human dORFs, all remaining cases were uORFs. We compared these cotranslating ncORFs with other non-overlapping uORFs and dORFs but did not detect statistically significant differences in evolutionary age and conservation metrics. Because no clear distinguishing features emerged, we did not include these results in the manuscript.

      Importantly, the observation of uORF–CDS co-translation does not contradict the established repressive role of uORFs. Co-translation reflects concurrent ribosome occupancy, whereas repression concerns the proportion of initiating ribosomes that ultimately translate the CDS. For example, if two ribosomes initiate within a given interval and one translates the uORF while one translates the CDS, CDS output is reduced by 50% relative to a uORF-free transcript. If four ribosomes initiate under the same repressive regime, two may translate the uORF and two the CDS. In this case, absolute translation of both ORFs increases, while the fractional repression remains unchanged. Thus, co-translation is compatible with a regulatory model in which uORFs reduce CDS translation efficiency without abolishing it. This has been clarified in the revised manuscript.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) All outcomes are attributed specifically to L6b neurons, but the genetic manipulation is not specific to L6b neurons. The authors acknowledge this as a limitation, but in my view, this global manipulation is more than a limitation - it affects the overall interpretations of the data. The Hoerder-Suabedissen et al., 2018 paper shows sparse, but also dense, expression of Drd1a+ neurons in brain regions outside of the L6b. Given this issue, the results are largely overstated throughout the paper.

      We appreciate the reviewer’s careful reading and concern that some of our statements may have overstated the implications of our data. The Drd1a Cre mouse model used (FK164) has a relatively selective expression of Drd1a Cre in cortex, but indeed some expression is seen subcortically. This is an acknowledged limitation which is now explicitly addressed in the revised manuscript.

      (2) It is not clear to me that the "silencing" of Drd1a+ neurons was verified.

      In our previous publications, we showed confirmation of the loss of regulated synaptic vesicle release from the Cre-positive neuronal population (Marques-Smith et al., 2016; Hoerder-Suabedissen et al., 2018; Messore et al., 2024). This has now been described in the revised manuscript.

      (3) There were various discrepancies (and potentially misattributions) between the stated significant differences in Supplementary Table T1 data and Figure 3a & S2 spectral plots. This issue makes it difficult to effectively evaluate the main text and stated outcomes.

      We thank the reviewer for their careful attention to the statistical analyses and for noting the inconsistencies in how the results of the spectral analysis were presented: in the text we described two-way ANOVAs with according posthoc tests but in the figures significance markers were positioned based on multiple t tests. We have now carefully revised the spectral results and implemented a consistent approach in statistical reporting and spectral plots. We have updated Supplementary Table T1, Figure 3a and S2 to ensure that all statistics are presented consistently throughout the manuscript, i.e. with two-way ANOVAs and accompanying posthoc tests. Please note that we performed all spectral analyses in the range between 0.5 and 128 Hz (excluding the range between 49-51.5 Hz due to electrical noise from the power grid) but only plot the range between 0.5-30 Hz as the spectral bands most relevant for sleep neurophysiology are contained in this range.

      Related, the authors stated that post hoc comparisons of EEG spectral frequency bins were not corrected for multiple testing. Instead, significance was only denoted if changes in at least two consecutive frequency bins were significant. However, there are multiple plots in which a single significance marker is placed over an isolated bin (i.e., 4c, 6, S5, S6). Unless each marker is equivalent to 2 consecutive frequency bins, these markers should be removed from the plots. Otherwise, please define the frequency and size of these markers in the main text.

      In line with the previous comment, we have adjusted markers to reflect the results from posthoc tests after two-way ANOVAs.Please note that Figure 6 and the related supplementary figures S5 and S6 have now been removed from the manuscript, as careful re-analysis indicated that the sample size was too low to support a strong conclusion regarding the comparison of orexin effects between genotypes. We stated in the text that we would only include posthoc significance when at least two consecutive bins were significant, but this was indeed not supported in our figure, where each marker reflects one 0.25 Hz bin. We have now adjusted our code to ensure that only markers are plotted when at least two consecutive bins are significant in bin-wise posthoc comparisons.

      (4) A rainbow color scale, as in Figure 3, we've now learned, can be misleading and difficult to interpret. The viridis color scale or a different diverging color scale are good alternatives.

      Thank you for pointing this out, we have adjusted the colour scale.

      (5) How much time elapsed between vehicle/orexin A & B infusions?

      There were 2-4 non-infusions days between infusions. We have added this information to methods.

      (6) For Figure 6, there are statistical discrepancies between the main text and the plots (pg. 10):

      (a) The text claims post hoc differences for relative ORXA frontal EEG, but there are no significance markers on the plot.

      (b) The text states that there were no post hoc differences for the relative ORXA occipital EEG, but significance markers are on the plot.

      (c) The main test for the relative ORXB frontal EEG was not significant, but there are post hoc significance markers on the plot.

      (d) For relative ORXB occipital EEG, there are significant markers on the plot outside of the stated range in the text.

      We agree with the reviewer, and we decided to exclude this figure from the manuscript as the sample size for some key comparisons was too low to support any strong conclusions and therefore presenting this analysis is potentially misleading. We explain the rationale for excluding this analyses in the revised manuscript.

      (7) Some important details are only available in figure captions, making it difficult to understand the main text. For example, when describing Figure 3c in the main text on page 7, it is not clear what type of transitions are being discussed without reading the figure caption. Likewise, a "decrease," "shift," and "change" are mentioned, but relative to what? Similar comment for the EEG theta activity description on pages 7 - 8. Please add relevant details to the main text.

      We have adjusted the wording in the main text to reflect more precisely which comparisons are shown in the figures.

      (8) Statistical comparisons for data in Figure 3e, post hoc analyses for data in Figure S7a-b REM data, and post hoc analyses for Figure S7c (not b) occipital EEG should be included to support differences claims. Please denote these differences on the respective plots.

      Please note that the previously named Supplementary Figures S5 and S6 have been removed from the manuscript, and that the Supplementary Figure S7 in this comment refers to the figure currently named Supplementary Figure S5.

      We have added the statistical comparisons for Figure 3e, Supplementary Figure S5A and Figure S5b to the results section. In Figure S5c, there was an overall genotype difference, but there was no significant time x genotype interaction, so we have not performed posthoc tests and did not plot posthoc significance markers for this figure. We have adjusted the wording in the results section to make this clearer. We have adjusted the reference to the figure S5c which was incorrect, thank you for your careful attention.

      (9) In the subsection titled "Layer 6b mediates effects of orexin on vigilance states (pg. 8)," there does not seem to be any stated differences between control and L6b silenced mice. A more accurate subtitle is needed.

      We agree with the reviewer and the title of this sub-section has now been changed accordingly.

      Reviewer #2 (Public review):

      Weaknesses:

      (1) Although the authors used a highly selective approach to silence layer 6b neurons, the observed changes in EEG oscillations cannot be solely attributed to layer 6b neurons because of the ICV route for orexin administration.

      We thank the reviewer for this important comment. The ICV route of orexin administration cannot guarantee that only cortical Drd1a-Cre–expressing neurons are reached by orexin, and the Drd1a-Cre driver line is highly selective but not entirely specific for layer 6b neurons (see also response to reviewer #1, comment 1). We have therefore changed the wording of the stated effects and addressed this consideration in the Limitations section of the manuscript. Please note that, as mentioned above, Figure 6 has now been excluded from the manuscript.

      (2) The rationale for using only male rats is not provided.

      We thank the reviewer for highlighting this omission. We now provide the rationale for using only male mice in the methods section as follows: “In the current study, only male mice were used, because our experimental protocol precluded the possibility of accurately monitoring the oestrous cycle, which has marked effects on brain activity, arousal and vigilance states. We therefore decided to use male mice only for the current study but are planning to use both sexes in future work.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Better descriptions of L6b connectivity will improve clarity in the second paragraph of the Introduction (pg. 3). For example, it is not explicitly stated that L6b projects to L5 before the authors describe L5. Therefore, the L5 description seems irrelevant.

      We thank the reviewer for this request for clarification. We mention the connectivity between L6b and L5 because L5 pyramidal neurons have recently been found to play a key role in sleep-wake regulation (Krone et al., Nat. Neurosci. 2021; Honjo et al., 2025; Wasilczuk et al, 2025; Krone et al., 2025). We have now amended the corresponding section of the introduction to emphasise the potential functional relevance of this connection as follows:

      “L5, the major output layer of the cortex, is also bidirectionally communicative with higher order thalamic nuclei (Hoerder-Suabedissen et al., 2018) as well as layer 5 pyramidal neurons (Zolnik et al., 2024). Since several subtypes of L5 pyramidal neurons have recently been shown to play important roles in distinct aspects of sleep-wake regulation (Krone et al., 2021, 2025; Hong et al. 2023; Wasilczuk et al. 2025; Honjo et al., 2025; Chouafeev et al., 2025); depth of anaesthesia (Wasilczuk et al. 2025), and the influence of stress on sleep (Chouafeev et al. 2025) the projections of orexin-sensitive L6b to L5 pyramidal neurons may be a key circuitry in the top-down regulation of brain states.”

      (2) There are plots where the y-axis tick label appears to be offset from the tick mark (4a, S5b, S6a).

      Thank you for spotting this graphical issue. We have removed the y-axis tick labels from Figure 4a to avoid confusion. Please note that we decided to remove Figure S5 and Figure S6, because after careful re-analysis we concluded that the group size was too small to draw conclusions on orexin spectra and that any results could be potentially misleading.

      (3) The 2-h time constant, I believe, is depicted in Figure 4H (not 4G).

      Thank you for spotting this. We have corrected the figure legends accordingly and double-checked that Figure 4G depicts the 2-h time constant and Figure 4H the 6-h time constant.

      (4) "...although there was an indication of a higher absolute theta-peak power in layer 6b silenced mice (Figure S6)," pg. 10. It is not clear to me how the data lead to this conclusion.

      Thank you for identifying this inconsistency, which resulted from a preliminary statistical analysis subsequently corrected. We have now improved the statistical analysis of spectral data (for more details see comments to both reviewers in public response) and removed this statement, which in fact is no longer supported by the data.

      (5) Exclusion of female mice is not listed as a limitation.

      We now discuss this limitation as follows:

      “In the current study, only male mice were used, because our experimental protocol precluded the possibility of accurately monitoring the oestrous cycle, which has marked effects on brain activity, arousal and vigilance states. We therefore decided to use male mice only for the current study but are planning to use both sexes in future work.”

      (6) A brief description of why Cplx3 and Tbr1 antibodies are being used will be helpful to include in the Methods (pg. 21) in addition to what is in the figure caption.

      We have added the following information to the methods section to clarify why we used these two antibodies: “rabbit α-Cplx3 to distinguish between L6a and L6b” “mouse α-Tbr1 to identify the L5-6 boundary”

      (7) Including a label/title for the Figure 2c spectral plots will be helpful. It is not immediately clear if these are light period & dark period data or frontal & occipital data.

      Thank you for pointing this out, we have updated the figure legend to clarify what is shown on this Figure

      Similar comments for S2 and S3a plots. Including a state label on the plots will be helpful in addition to the caption description.

      We have now added the state labels for Figure panels S2 and S3a for improved clarity.

      Reviewer #2 (Recommendations for the authors):

      This is a soundly conducted and well-written study that enhances our understanding of the cortical control of states of consciousness. I do not have any major concerns, but would like the authors to consider some alternate possibilities as suggested in my comments below:

      We thank the reviewer for this positive assessment of our manuscript and the helpful suggestions.

      (1) Given that the inactivation of layer6b neurons did not affect the time spent in sleep-wake states, to me it appears that these neurons likely have a role in creating the background neural conditions/oscillations supportive of an activated state rather than a direct role in behavioral state control.

      We completely agree with the reviewer and have made the wording more consistent throughout the manuscript, now using “brain state control” rather than “behavioural state control” to clarify that the main effect observed in the L6b-silenced mouse model is a change in spectral characteristics reflecting brain oscillations, rather than effects on vigilance states, which were modest.

      (2) Does the observed shift in REM sleep-related theta-peak frequency in the occipital derivation suggest changes in local neural processes, or could it be just a matter of better signal detection because theta is most prominent at or around the hippocampal region, which is approximately the location of occipital electrodes in this study.

      The source of the shift in REM sleep–related theta peak frequency in the occipital derivation cannot be established with EEG recordings alone. Additional intracortical or intrahippocampal recordings would be necessary to distinguish between the two possible explanations proposed by the reviewer. We have discussed this further in the revised manuscript.

      (3) Orexinergic system innervates multiple subcortical sites and widely covers the cortex too, because of which the effect of ICV orexins cannot be attributed to just layer6b neurons as described in the manuscript ("Layer 6b mediates effects of orexin on brain activity.").

      We agree with the reviewer that this is a limitation. We have now adjusted the subtitle of the paragraph describing the results from the ICV administration of orexin and further mention this important consideration in the ‘limitations’ section of the discussion.

      (4) While the current study is focused on sleep-wake mechanisms, the findings reported here have much broader implications for behavioral and/or brain state arousal and provide a mechanistic bridge between different states of consciousness, including general anesthesia. Therefore, the authors may consider tying these findings with the recent work on the role of the prefrontal cortex in arousal from general anesthesia and slow-wave sleep (PMID: 35436248, PMID: 29937348, PMID: 33328847).

      We thank the reviewer for this excellent recommendation. We are now citing these papers in the revised manuscript.

      (5) It's up to the authors, but I do not see the need for the section on Clinical Implications. It's very speculative, and it makes the entire discussion section heavy.<br />

      We have considerably shortened the discussion of potential clinical implications to make the manuscript more concise.

      (6) Figure 1: It's difficult to compare the EEG power the way figures are set up right now. I think it would enhance clarity if the authors separate the plots based on state and show power from the control and silenced neuronal group in the same plot. Also, the colors are too similar (essentially a shade of green/blue) to provide effective visual resolution. This is especially true in panel d. Please consider changing the color scheme.

      This comment seems to refer to Figure 2 and subsequent figures with analysis of vigilance states and EEG spectra (Figure 1 contains histological images). We have selected the colour scheme for colour-blind individuals. Therefore, the main difference is in the saturation, not the colour of the plots. We have tested the visibility of the colour scheme on a high-resolution screen with the original image files and can reassure the reviewer that the genotype differences, which are slightly blurred in the reduced-resolution figures provided within the combined text file for the review process, are easily distinguishable in the final figure quality.

      (7) I don't understand the y-axis scale in Figure 1. How can this be 500% and if it is, then 500% of what?

      This comment also seems to refer to the analysis of slow wave activity (SWA) in Figure 2 rather than to Figure 1 (histology figure). The percentage of SWA is normalised to the average SWA across the recording. Since NREM sleep is characterised by considerably higher SWA than wakefulness and REM sleep, the level of SWA during NREM sleep is in the range of 200-300%, and can be even higher after long wake episodes which are followed by a rebound of NREM sleep SWA. Hence, the upper limit of the y-axis in these (and subsequent) plots of SWA is 500% (of the average SWA). We have amended the figure legend to clarify that SWA is presented here as percentage of average SWA across the recording.

    1. Author response:

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

      eLife Assessment

      In this potentially valuable computational study, the authors conducted atomistic and coarsegrained simulations to probe the temperature-dependent phase behaviors of ELF3, a disordered component of the evening complex in plant. The results aim to highlight the role of polyQ tracts in modulating the temperature sensitivity. The level of evidence is considered incomplete, due to the lack of systematic calibration of the coarse-grained model and limited statistical uncertainty analysis, especially considering the relatively subtle nature of the differences due to temperature change.

      We agree that the subtle temperature dependence of ELF3-PrD condensation requires rigorous uncertainty reporting and careful interpretation of CG predictions. In the revised manuscript we therefore (i) report mean ± SEM across independent replicas for all CG observables and provide full time series in the Supplementary Information, and (ii) expand our CG analysis beyond cluster counting to include condensate stability (size), lifetime, internal mobility (D, α), dynamic heterogeneity (van Hove), and structural descriptors (anisotropy, singlechain compaction/density). These additions strengthen the robustness of the conclusions and even enable physical explanations of recent experimental measurements on ELF3-PrD condensates.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript explores the role of the Evening Complex (EC), specifically focusing on ELF3, a disordered protein component of the EC, and its temperature-dependent phase behavior. The study highlights the role of polyQ tracts in modulating temperature-sensitive condensate formation and provides a combination of computational approaches, including REST2 simulations and coarse-grained Martini simulations, to investigate how polyQ tract length and sequence context influence this behavior.

      Strengths:

      The study addresses a key question in plant biology - how temperature influences circadian clock-mediated growth regulation through protein phase behavior. The manuscript introduces the novel finding that polyQ tract length modulates the temperature-dependent formation of helices and condensates.

      Weaknesses:

      (1) Coarse-Grained Simulation Results Not Supported by Data:

      The results presented in Figure 6A of the manuscript do not seem to show a clear trend in the number of clusters formed as a function of polyQ tract length. This is particularly evident in the comparison between 0Q and 7Q polyQ lengths, which display statistically similar values in terms of the number of clusters. The lack of distinction between these values raises questions about the sensitivity of the coarse-grained simulations to polyQ tract length, which the authors claim as a key modulator of condensate formation. This discrepancy weakens the argument that polyQ length directly impacts the clustering behavior in the simulations.

      Suggested Analysis:

      A more detailed statistical analysis should be performed to assess whether the observed differences between polyQ lengths are significant. This could involve hypothesis testing or the use of error bars in the graphs to better communicate the variability in the data.

      Additionally, the authors should examine whether there are other features, such as cluster shape or internal structure, that might differentiate between different polyQ lengths, even if the total number of clusters is similar.

      We agree that the number of clusters in Fig. 6A does not show a strong or monotonic dependence on polyQ length (e.g., 0Q vs 7Q can overlap within uncertainty). The cluster number is highly sensitive to coarsening kinetics and rapidly approaches a late-time plateau, and therefore is not our primary discriminator of variant-dependent condensation behavior.

      To address the reviewer’s request for statistical rigor and additional differentiating features, we have revised the analysis in two ways. First, we now report mean ± SEM across independent replicas for all key CG observables and provide full replicate time series in the Supplementary Information to make variability and convergence/coarsening explicit.

      Second, we shift our main CG conclusions away from “cluster number” and toward more diagnostic observables of condensate robustness and material state, including: (i) stability via the late-time mean largest-cluster size, (ii) persistence/lifetime via the fraction of frames with largest cluster size greater than 50, (iii) internal dynamics via MSD-derived DDD and anomalous exponent ααα, (iv) dynamic heterogeneity via self van Hove distributions relative to a Gaussian reference, and (v) morphology/internal structure via κ<sup>2</sup> and Rg distributions.

      Notably, the κ<sup>2</sup>/Rg distributions are broadly overlapping at 300 K, indicating that in our system variant differences are expressed more strongly in stability/persistence and internal dynamics (D/α/van Hove) than in a large shift in single-chain compaction at this temperature.

      This revised framing also aligns our interpretation with the experimental picture put forward by Huntin et al -- polyQ length modestly affects onset-like behavior but more strongly tunes condensed-phase regimes and dynamics.

      Relevant revisions have been made in the Results and the Discussion sections.

      (2) Inconsistency in Cluster Size Across Temperatures (Figure 6B):

      The results in Figure 6B show a striking difference in the size of the largest cluster between temperatures of 290K and 300K. This abrupt shift in behavior lacks a clear mechanistic explanation. Typically, phase transitions driven by temperature are more gradual, unless there is some underlying structural or chemical shift that the authors have not accounted for. Without a clear explanation, this sudden change in behavior reduces confidence in the simulation Results.

      Suggested Analysis:

      The authors should explore possible explanations for the dramatic difference in cluster size between 290K and 300K. For example, they could investigate whether specific interactions (such as the breaking or formation of hydrogen bonds or hydrophobic contacts) might explain the behavior at higher temperatures.

      It is important to check whether the coarse-grained simulation model has been adequately parameterized and scaled for accurate temperature dependence. Atomistic simulations of monomers and dimers with varying polyQ tract lengths could be used to fine-tune the coarsegrained model, ensuring it accurately reflects molecular behavior. The gross estimate of a 10% scaling factor might be insufficient and could lead to inaccurate representations of cluster formation.

      We agree that the apparently sharp change in largest-cluster size between 290 K and 300 K requires clearer interpretation. In the revised manuscript, we clarify that this behavior does not imply an abrupt thermodynamic phase transition; rather, in a finite (~100-chain) simulation box, the largest cluster size is sensitive to both (i) proximity to a coexistence boundary and (ii) coarsening kinetics. Consistent with this, all systems rapidly coarsen early and then approach a late-time plateau, so the dominant cluster size can change steeply when conditions shift the balance between one system-spanning droplet versus multiple long-lived subclusters.

      To distinguish “true loss of condensation” from “differences in coarsening state,” we added replica-averaged stability and persistence metrics (mean ± SEM) and full time series. Importantly, the condensate lifetime (fraction of frames with largest aggregate-population > 50) is ~1 at both 290 K and 300 K, indicating that both temperatures correspond to a persistently condensed regime, not intermittent nucleation/dissolution. We therefore interpret the smaller dominant cluster at 290 K as reflecting slower coarsening / stronger kinetic arrest, where reduced chain mobility delays merger/annealing into a single large droplet within the simulated time window, leaving a larger satellite/dispersed population despite sustained condensation.

      We further support this interpretation with mechanistic and dynamical analyses added in the revision. As temperature increases from 290 K to 300 K, we observe increased internal mobility (higher effective diffusivity, D) that would accelerate rearrangements and coalescence. In parallel, contact/desolvation analyses show progressive loss of protein-water contacts and gain of protein-protein contacts as clusters mature, and a residue-resolved comparison indicates net contact increases at 300 K relative to 290 K concentrated in aromatic-rich “sticker” regions, consistent with a strengthened intermolecular contact network that promotes more complete annealing at 300 K.

      (We address the reviewer’s points regarding Martini temperature scaling/parameterization together with points (3)-(4) below.)

      (3) Scaling of Coarse-Grained Model with Atomistic Simulations:

      As mentioned, the coarse-grained model used in the study may not have been properly scaled against atomistic data. A simple scaling factor of 10% may not be appropriate for accurately capturing the behavior of polyQ tracts across different lengths, especially considering their sensitivity to subtle changes in temperature. Without rigorous validation against atomistic simulations, the coarse-grained model's predictions could be skewed.

      (4) To address this, the authors should compare the coarse-grained model with atomistic simulations of monomeric and dimeric forms of ELF3 with different polyQ tract lengths. By comparing key structural parameters (e.g., radius of gyration, contact maps, and clustering propensity), the authors could adjust the coarse-grained model to more accurately reflect the atomistic behavior. The authors have wealth of atomistic simulation data that could afford such benchmarking and identification of scaling factor

      Additionally, the authors should investigate whether the assumed scaling factor of 10% is appropriate for each polyQ length or whether it needs to be refined based on specific properties, such as the number of hydrophobic interactions or secondary structure stability.

      We agree that temperature-dependent CG predictions must be interpreted carefully and that the interaction balance should be justified. In the revision, we therefore clarify both our calibration choice and the scope of inference.

      We use Martini 3 with a single, literature-motivated adjustment: protein-water Lennard-Jones interactions are strengthened by 10 percent, following an established strategy shown to improve IDP/multidomain protein behavior in Martini 3. This scaling is applied uniformly to all residues, polyQ lengths, and temperatures to avoid introducing construct-specific parameters and to preserve a controlled comparison across variants.

      We emphasize that our CG simulations are used in a comparative manner (how stability/dynamics/structure change with temperature and polyQ length under a fixed model), and we do not claim a quantitatively exact phase boundary or transition temperature for ELF3. In this spirit, and consistent with how Martini 3 has been used in prior work to probe thermally varying properties across temperature windows (while acknowledging documented limits to temperature transferability), we treat the temperature sweep as a comparative probe rather than an absolute calibration (https://doi.org/10.1063/5.0221199, 10.1021/acscentsci.5c00755, https://doi.org/10.1038/s41592-021-01098-3). Accordingly, we report replica uncertainty (mean ± SEM) for all CG observables and restrict conclusions to qualitative trends that are robust to replicate variability.

      Finally, while we do not undertake a full ELF3-specific reparameterization, we include qualitative checks linking atomistic and CG behavior: the CG model reproduces the same qualitative features of single-chain reorganization inferred from atomistic simulations — notably the radiusof-gyration (Fig. S8) and the rearrangement/exposure of aromatic “sticker” regions that correlate with strengthened intermolecular contacts in the condensate. We emphasize that these comparisons are intended as qualitative sanity checks on trend direction, not as a quantitative validation or calibration of an absolute phase boundary.

      (5) Lack of Analysis for Liquid-Like Behavior in Phase Separation:

      The simulations presented in the manuscript do not analyze the liquid-like behavior of ELF3 condensates, which is a key characteristic of liquid-liquid phase separation (LLPS). In LLPS systems, condensates are often dynamic, with chains exchanging between clusters, indicating liquid-like rather than solid-like behavior. The authors fail to probe this crucial aspect, which is necessary to support the claim that ELF3 undergoes phase separation.

      Suggested Analysis:

      The authors should conduct additional analyses to probe the liquid-like nature of the clusters formed by ELF3. One approach would be to analyze the dynamics of chain exchange between clusters, measuring how frequently chains leave one cluster and join another over time. This analysis would reveal whether the condensates behave as liquid- like, dynamic structures or more static, solid-like aggregates.

      Additionally, the temperature dependence of these exchange dynamics should be investigated. In true liquid-liquid phase separation, the rate of chain exchange is often sensitive to temperature. Observing how this rate changes between 290K and 300K, for instance, could help explain the abrupt shift in cluster size seen in Figure 6B.

      The authors should also analyze whether the internal structures of the condensates are consistent with a liquid-like phase. For example, radial distribution functions and contact lifetimes could be calculated to reveal whether the clusters exhibit liquid-like organization.

      We thank the reviewer for highlighting that liquid-like behavior is a key diagnostic for LLPS. We agree that our original manuscript did not explicitly quantify condensate material properties. In the revision, we therefore add several complementary analyses and figures that directly probe whether the condensed state in our simulations is liquid-like versus dynamically arrested, and how this depends on temperature and polyQ length.

      (i) Condensate persistence vs temperature (stability and lifetime).

      We now quantify two replica-averaged metrics with uncertainty (mean ± SEM): (a) stability, defined as the mean largest-cluster size over a late-time analysis window, and (b) lifetime, defined as the fraction of frames in which the dominant cluster exceeds a fixed size threshold. These results are shown in the new figures “Stability (Mean cluster size)” and “Lifetime (P [size > 50])”. In our system, both 290 K and 300 K correspond to a persistently condensed regime (lifetime ≈ 1 across variants), whereas at 340 K the lifetime drops substantially (≈0.3-0.5 depending on variant), indicating intermittent condensation / partial dissolution at high temperature. This directly demonstrates temperature-dependent persistence of the condensed state and clarifies that the key qualitative change at high temperature is loss of stability and intermittency, rather than a purely static cluster-size difference.

      (ii) Internal mobility and viscoelasticity (D and α).

      To probe liquid-like dynamics within the condensed state, we compute internal Mean squared displacement (MSD) and extract an effective internal diffusivity D(T) and anomalous exponent α(T) (new figures FIG X). In our system, D increases systematically with temperature for all variants, confirming that internal rearrangements accelerate at higher temperature. At the same time, α remains strongly subdiffusive (α ≈ 0.3-0.5), indicating constrained, non-Fickian motion rather than simple liquid diffusion. Importantly, we also observe variant-dependent mobility: around 300-320 K, 0Q exhibits markedly lower D than 19Q, consistent with stronger kinetic arrest in 0Q even when both variants are condensed. Together, these dynamics metrics show that our condensates are not ideal liquids, but instead occupy a viscoelastic / dynamically slowed regime with clear temperature dependence.

      (ii) Dynamic heterogeneity (self van Hove).

      We additionally compute the self van Hove displacement distributions (Fig. SX). In our system, the van Hove distributions deviate from a Gaussian reference matched to the MSD, with an excess of near-zero displacements relative to a simple Gaussian model. This non-Gaussian displacement statistics is consistent with heterogeneous/caging-like dynamics inside the condensed phase, further supporting a viscoelastic (gel-like) rather than purely liquid material state at the timescales accessible to simulation.

      (iv) Internal structure and morphology (Rg and anisotropy).

      Finally, we add structural descriptors as requested. The new Rg distribution and shape anisotropy (κ<sup>2</sup>) violin plots quantify single-chain compaction and heterogeneity in morphology within the condensed phase. In our system these structural distributions are broadly overlapping at 300 K, indicating that differences among variants are more strongly expressed in dynamics (D/α/van Hove) and stability/lifetime, rather than in a large change in single-chain compaction at this temperature. We report these results transparently and include them in the SI as additional mechanistic context.

      We now explicitly frame our CG condensed phases as viscoelastic/dynamically slowed condensates rather than assuming fully liquid droplets. This interpretation is consistent with experimental observations on ELF3 PrLD that report very slow recovery/gel-like behavior under some conditions (i.e., condensates can age into low-mobility hydrogel states).

      (6) Lack of justification of polydispersity of polyQ:

      The authors don't provide any rationale for choice of different copies of polyQ used in the manuscript for their chain- growth simulation studies. It will be more apt if it can be motivated via some precedent experimental observations.

      We agree and have clarified our rationale in the revised manuscript. ELF3’s polyQ tract is a naturally polymorphic short tandem repeat in Arabidopsis, reported to vary from roughly ~7 to ~29 glutamines in natural populations, and this variation has been linked to ELF3-dependent phenotypes and temperature-responsive growth (Undurraga et al.; Jung et al.). Importantly, recent ELF3 PrLD thermosensing/condensation experiments explicitly compare multiple polyQ lengths (including Q0, short/WT-like constructs such as Q7, and expanded tracts around ~Q20) and show that polyQ length tunes temperature-responsive phase behavior and condensate properties (Jung et al.; Hutin et al.).

      Accordingly, for our chain-growth ensembles we chose a small, experimentally motivated set that brackets this range - 0Q (deletion), 7Q (WT-like short), and expanded lengths 13Q and 19Q (with 19Q closely matching the ~Q20 construct used experimentally), so that our simulations map onto established constructs and naturally occurring variation rather than arbitrary copy numbers.

      The manuscript draft has been modified in the Results and Methods sections.

      Jung J-H. et al. A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis. Nature (2020).

      Undurraga S. et al. Background-dependent effects of polyglutamine variation in the Arabidopsis thaliana gene ELF3. PNAS (2012), DOI: 10.1073/pnas.1211021109.

      Hutin S. et al. Phase separation and molecular ordering of the prion-like domain of the Arabidopsis thermosensory protein EARLY FLOWERING 3. PNAS (2023).

      (7) Lack of initiative to connect to Experiments:

      While the computational models and simulations provide robust theoretical insights, the absence of direct experimental validation weakens the overall impact of the manuscript. For example, experimental data on how specific mutations in the polyQ tract influence ELF3 behavior in vivo would significantly bolster the authors' claims. The manuscript would benefit from either citing existing experimental studies that corroborate these findings or from suggesting future experimental directions.

      We agree that our original submission did not make the experimental connections explicit enough, and we have strengthened this in the revision by (i) explicitly anchoring our results to published ELF3 thermosensing/condensation measurements and (ii) articulating concrete, experimentally testable mechanistic predictions that follow from the simulations.

      (i) Explicit connection to published experimental benchmarks: We now cite and discuss key experimental studies that directly probe ELF3 temperature responsiveness and polyQ effects. Jung et al. demonstrated temperature-triggered ELF3 condensation/speckle formation in vivo and showed that polyQ length modulates thermoresponsive behavior. More recently, Hutin et al. compared ELF3 PrLD constructs spanning polyQ lengths (e.g., Q0, Q7, and ~Q20) and reported temperature-triggered phase separation, condition-dependent condensed-phase regimes (droplet-like versus more arrested/gel-/hydrogel-like), and reduced mobility/immobile fractions quantified by FRAP in some regimes. In the revised manuscript we explicitly map these observations onto our results: our coarse-grained simulations capture temperature-dependent condensation propensity, while our added condensate dynamics analyses (MSD-derived internal mobility DDD, anomalous exponent α\alphaα, and self van Hove displacement statistics) indicate dynamically slowed/heterogeneous condensates rather than assuming ideal liquid droplets—consistent with experimentally observed slow FRAP recovery and arrested behavior under some conditions.

      (ii) Mechanistic Connections: While existing experiments establish that ELF3 condensation is temperature-triggered and tuned by polyQ length, they cannot directly resolve the molecular interaction changes that drive these macroscopic readouts. We therefore emphasize that our atomistic and coarse-grained analyses provide a mechanistic interpretation: temperature shifts reorganize and expose “sticker”-rich regions (notably aromatics), strengthening intermolecular contact networks that tune condensate stability and material properties. This framing aligns our conclusions with the experimental picture that polyQ length has modest effects on onset-like behavior but more strongly tunes condensed-phase robustness and dynamics (persistence, internal mobility, and arrest) across temperature

      The modifications relevant to this are in the Discussion section.

      Reviewer #2 (Public review):

      Summary:

      The authors aimed to explore how a key protein in the circadian clock of plants, ELF3, responds to temperature changes by forming molecular condensates. They focused on understanding the role of a specific region of the protein, a polyQ tract, in promoting temperature-sensitive structural changes and regulating the formation of condensates. Through a series of computational simulations, they sought to uncover the molecular basis for ELF3's temperature responsiveness and its broader implications for plant growth and adaptation to environmental conditions.

      Strengths:

      The study's strength lies in its focus on an important biological question: how plants sense and respond to temperature changes at the molecular level. The authors employed a variety of computational techniques, including coarse-grained simulations, to explore the role of specific molecular features in this process. These methods provide a multi-scale view of protein behavior and offer valuable insights into how molecular structures may influence biological function.

      Weaknesses:

      However, there are notable weaknesses in the evidence provided. While the authors present trends in molecular changes, such as shifts in helical propensity and the formation of condensates, these results seem subtle and are not strongly substantiated by statistical analysis. The lack of error bars in the figures makes it difficult to distinguish between meaningful signals and potential noise in the data. Furthermore, the temperature-sensitive behavior appears to be influenced more by chain length than by sequence-specific effects of the polyQ region, raising questions about whether the findings truly capture the molecular mechanisms responsible for temperature sensing. Additionally, some simulations, particularly those related to the formation of condensates, do not appear fully converged, which casts further doubt on the robustness of the results.

      We appreciate the reviewer’s concerns regarding statistical support, sequence specificity, and convergence. In the revised manuscript we (i) report replicate-averaged means with uncertainty (mean ± SEM) for all key observables and add error bars/shaded bands to the relevant figures, (ii) provide the full time series plots in the Supplementary Information to make variability and equilibration transparent, and (iii) revise our interpretation to emphasize that polyQ length has only modest effects on onset-like metrics but more strongly tunes condensate stability and material state (lifetime, internal mobility (D), subdiffusion exponent (α), and non-Gaussian van Hove signatures). This revised framing is consistent with recent ELF3 PrLD experiments showing that polyQ variation can subtly affect onset while substantially modulating condensed-phase behavior and dynamics. Relevant changes to the main text have been made in the Results and Discussion section.

      Additional Context for Readers:

      Readers should interpret the results with caution, especially regarding the molecular mechanisms proposed for temperature sensing. While the study presents interesting trends, the evidence is not definitive, and the findings may be more reflective of general protein behavior (such as the effect of chain length on condensate formation) than specific sequence-driven responses to temperature. Further experimental studies and more converged simulations will be necessary to fully understand the role of ELF3 in temperature regulation.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I already have listed my possible recommendations for authors for revising their manuscript in the review. By addressing these issues, the authors could significantly improve the robustness of their conclusions and provide stronger evidence for ELF3's role in temperature-responsive phase separation.

    1. Author Response:

      Reviewer #1 (Public review):

      Summary:

      The authors present a novel approach to subcellular spatial proteomics by combining laser microdissection with expansion microscopy and LC-MS/MS analysis (SPEx). They implement two different workflows for LMD and LC-MS/MS quantification:

      (1)The standard approach, where an area of interest is cut out by LMD, subjected to proteomics analysis, and compared to the rest of the cell without the dissected ROI.

      (2) The subtraction approach, where ROIs are removed, and the remaining cellular material is compared to samples containing both the surrounding material and the ROI.

      The authors assess the technique by applying it to subcellular targets of various sizes, volumes, and protein compositions such as the nucleus, nucleoli, and Golgi. They demonstrate that SPEx can identify proteins enriched or reduced in ROIs.

      Strengths:

      The broad, relatively easy, and inexpensive applicability of this approach to potentially many cell types and subcellular areas of interest provides an exciting alternative to subcellular fractionation, native immunoprecipitation, or genetically encoded proximity labeling constructs. Moreover, by visually selecting ROIs for subsequent analysis, subcellular context or organelle morphology can be taken into account, as discussed by the authors in the discussion section.

      Weaknesses:

      While strongly supporting the sharing of this approach, we have a number of comments and questions that will improve the impact of the manuscript:

      We thank the reviewer for the careful evaluation of our manuscript and the generally positive assessment. We plan on improving our manuscript based on the reviewers’ comments.

      (1) General:

      a) The manuscript would benefit from restructuring and language revision. In its current form, the writing is sometimes dense and verbose (in particular, the Results section). This makes it difficult to follow the authors' arguments.

      We will improve readability and clarity of the results section in the revised manuscript.

      b) The authors mention the possibility of selecting organelles based on morphology. This is left for the discussion, but it seems like a missed opportunity - the authors could compare individual organelles in different morphological states, e.g., connected vs. fragmented mitochondria.

      The authors agree with the reviewers’ assessment that investigating proteome of organelles based on morphology or cellular state is an exciting application of SPEx. While we plan experiments along this line in the future, we think that these experiments are beyond the scope of this manuscript, which is meant to describe the method and its general usefulness.

      (2) Technical:

      a) Why do the authors strive and optimize for a 10x expansion factor? Is SPEx compatible with a more standard 4x expansion, as e.g., used in the classic U-ExM approach (https://www.nature.com/articles/s41592-018-0238-1)? This could be added to the discussion.

      We aimed for 10x expansion solely because our ultimate goal is to cut out very small structures. Isolating structures as small as nucleoli would not be as reliable with a lower expansion factor (i.e. 4x) expansion. We did not assess the compatibility with U-ExM. We would assume that SPEx would also work with U-ExM as expansion method; omitting protease treatment, however. Still, we performed pilots with just 4x expansion (using TREx) in the early stages of optimization. We were able to isolate single cells and obtain similar protein coverage as with 10x expansion. We will further clarify our motivation to use 10x expansion in the discussion.

      We would also like to point out whether to U-ExM the standard method or not is rather subjective. Even though TREx was published three years later, it is also very widely used. The original expansion microscopy method was published three years prior to U-ExM.

      b) The U-ExM approach shows improved ultrastructural preservation when using 3%FA with 0.1% glutaraldehyde fixation (GA). Is SPEx compatible with the use of low amounts of GA for fixation?

      We tried different fixation methods in the early stages of this study (where expansion was not yet close to 10x). We saw a mild negative effect of GA on the expansion factor, so we avoided it in the later experiments since it also did not seem necessary to preserve the structure of our organelles of interest. However, the use of GA would generally be compatible with SPEx, potentially at the cost of a mild negative effect on expansion factor (see Author response image 1) and proteome coverage. We can add this information to the discussion.

      Author response image 1.

      Fixation methods mini-screen. Cells were fixed with the indicated reagents for 10 minutes at 37°C. After TREx expansion, the diameter of the nucleus was measured (A) and the resulting expansion factor compared to the non-expanded control was determined (B).

      Related to the above, was the anchoring efficiency reduced only to achieve a 10x expansion factor or does this additionally affect the proteome coverage?

      We solely lowered the anchoring in order to allow for higher expansion factors. In earlier pilots we performed proteomic analysis on samples that were just expanded 4x using standard TREx expansion (also using the original anchoring strategy from the TREx publication, consisting of 0.2 mg/ml AcX for overnight at RT). We presented the results of this pilot in Fig S1A. We still detected over 2,000 proteins from 10 cells, a coverage, which is highly similar to what we found in the final experiments (Figure 2F), in which the anchoring was lower yielding 10x expansion. Based on these data, we hypothesize that anchoring (and expansion factor!) has a negligible impact on protein coverage. We will clarify this in the manuscript.

      d) Have the authors considered using alternative anchoring approaches, such as GMA (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0291506#pone.0291506.s001), which potentially increase the amount of sample retained in the hydrogel, thus allowing for better proteome coverage? This could be added to the discussion.

      We did not use alternative anchoring approaches. We modified the TREx protocol to fit our purposes and since this was sufficient, we did not explore alternatives. However, using anchoring approaches, in which higher amounts of sample could be retained in the gel might be beneficial for the proteomics coverage. We will keep this suggestion in mind for future experiments. Thank you for the suggestion!

      e) The limitation of the approach to near-2D samples should be mentioned, and alternative approaches for more 3D samples could be discussed.

      The authors agree that SPEx is limited to near-2D samples at this point. We suggest that SPEx is applicable for 3D samples (e.g. in tissues) by performing cryosectioning. TREx has been shown to be compatible with sectioned tissue (Damstra et al., 2022). We will elaborate this in the discussion.

      f) How are peptides that are directly anchored to the hydrogel dealt with during LC-MS/MS analysis? Are they excluded, or can they be identified during the spectral search? The latter would allow us to get a deeper structural understanding of how proteins are actually anchored into hydrogels, which so far has not been assessed.

      The reviewer raises an interesting point. In general, peptides carrying the anchoring modification are analysed by LC-MS, but we did not include these specific modifications in the database search. Overall, we assumed that the labeling would be low and stochastic and hence should, if at all, only minimally affect the detection of peptides. Nevertheless, in response to the reviewers’ comment, we searched the MS data again for the crosslinking reagent linked to lysine residues. However, we could not get any confident hit for any peptide containing this modification. Since we cannot exclude that the modification precludes the identification of the corresponding peptides, we compared the number peptides generated by trypsin cleavage after arginine and lysine. As the human genome contains similar proportions of both amino acids, one would expect similar numbers of both peptide types being identified. Any modifications of lysine by the anchoring reagent used, would prevent tryptic cleavage and thus reduce the number of lysine peptides. As shown in Author response image 2, the number of lysine terminating is only slightly lower compared to arginine terminating peptides. Notably, the proteomics results of a different fixed human tissue sample directly extracted by laser capture micro dissection without expansion showed a very similar lysine to arginine peptide ratio. This indicates that the large majority of lysine residues is not modified and affected by the hydrogel anchoring.

      Author response image 2.

      Number of peptides identified either terminating with lysine (K) or arginine (R) across all samples shown in Figure 5F.

      An alternative approach to address this question would be to investigate if the peptide coverage of proteins detected by SPEx is enriched for peptides representing the folded core of proteins as opposed to the surface-exposed regions, which likely get more anchored into the hydrogel.

      Because of the negligible amounts of modified peptides, we did not investigate this potential bias of surface-exposed versus folded-core peptides.

      g) Same question regarding peptides with NHS labeling. Can they be identified, or do they just compete for ionization and thus negatively affect coverage and dynamic range of the LC-MS/MS approach?

      The reviewer raises a similar point as above for another lysine labeling used during the SPEx protocol. Again, we specifically looked for this modification by re-searching the raw MS data, but still could not identify any peptides, carrying this modification on a lysine residue. Even though we cannot exclude that this rather large modification prevents detection, considering the high number of lysine terminating peptides in our dataset (see Figure 2), we would expect that also this labeling step is stochastic and affects only a minor proportion of the proteins.

      h) How are the primary and secondary antibodies affecting the proteomics analysis identified as contaminants?

      We thank the reviewer for this comment. Since antibodies bind to proteins in a non-covalent manner, they will be released during the denaturing steps of the protocol. Of course, the antibodies will stay in the sample, be digested and analyzed and could, if very abundant, affect the analysis of the proteins from the samples. To check this possibility, we re-searched the MS data including the sequences of the antibodies used. To our surprise, we could not detect any peptides of these antibodies. This suggests that the concentrations of the antibodies used are much lower than those of the sample proteins and thus should not have any impact on the proteomics results.  We interpret this result also as a benefit of our method compared to organellar-IP.

      i) Have the authors observed differences in proteomics coverage of only antibody vs NHS-labeling? Depending on the questions above, could pure antibody-based labeling increase proteomic coverage?

      We did not perform this comparative analysis, since we always used NHS dyes. In the experiments presented in this manuscript, NHS dyes allowed easy visualization of the whole cell without the use of antibodies. This NHS staining was essential for this particular setup for sample acquisition. We cut out entire cells, cells lacking the nucleus and cells lacking the Golgi apparatus, which served as critical controls. However, other ways of detecting cell boundaries could be used to avoid NHS staining. As shown above, both, the anchor and NHS labeling are likewise sparse and stochastic. Moreover, we could not detect any impact of the antibody labeling to our results. Thus, we assume that both labeling procedures could be used.

      Reviewer #2 (Public review):

      Summary:

      This study introduces a method that combines physical expansion of cells, imaging-guided isolation of defined regions, and protein identification to enable compartment-resolved analysis of protein composition at the subcellular scale. The authors aim to address a central limitation in existing approaches, namely the loss of spatial information during sample preparation or the indirect nature of proximity-based labeling methods. Using several cellular compartments as examples, they demonstrate that their approach can recover compartment-enriched protein sets and identify candidate proteins with previously unassigned localization.

      Strengths:

      A major strength of this work is the conceptual simplicity and accessibility of the approach. By combining established techniques in a modular way, the method avoids the need for genetic manipulation or specialized labeling strategies, making it broadly adaptable across experimental systems. The ability to directly select regions of interest based on imaging represents a clear advantage over indirect enrichment strategies and allows flexible targeting of both membrane-bound and non-membrane-bound compartments.

      The experimental design is also a strong aspect of the study. The use of complementary comparison strategies-analyzing isolated compartments alongside matched "subtracted" controls-provides an internal framework for assessing enrichment and depletion, increasing confidence in spatial assignment. The application of the method across multiple organelles of different sizes and properties demonstrates versatility, and the reported specificity for several compartments is encouraging. In particular, the ability to profile small and biochemically challenging structures highlights a potentially important niche for the approach.

      Weaknesses:

      Despite these strengths, several methodological limitations constrain the interpretation of the results. The most important relates to spatial accuracy in three dimensions. While lateral resolution is improved through physical expansion, the lack of depth resolution introduces uncertainty regarding contributions from structures above and below the selected region. Although the authors argue that this does not substantially affect specificity, the current evidence is largely indirect, and a more rigorous quantification of potential contamination would strengthen this conclusion.

      Quantitative interpretation also remains challenging. Because the measurements reflect total protein abundance rather than local concentration, differences in compartment size and protein density can influence enrichment values, particularly for small structures embedded within larger volumes. This issue is evident in the analysis of smaller compartments and complicates direct comparison across conditions. Additional normalization or modeling would help clarify how to interpret these measurements.

      Another limitation concerns variability in the expansion process and its downstream consequences. Differences in expansion factor across samples may affect the definition of regions of interest and introduce variability in sampling, yet the impact of this variability is not fully explored. Similarly, the use of a modified chemical treatment to preserve proteins for downstream analysis is central to the workflow but is not extensively validated with respect to preservation of spatial organization.

      While the identification of previously unannotated proteins is an appealing aspect of the study, validation is limited to a small number of examples, and broader support from independent datasets or literature context is lacking. In addition, the study primarily focuses on steady-state measurements in a single cell type, and therefore does not yet demonstrate the ability of the method to capture dynamic or condition-dependent changes in protein localization.

      Finally, the positioning of the method relative to existing approaches could be more clearly articulated. Although qualitative comparisons are provided, a more systematic and quantitative benchmarking against alternative strategies would help readers better understand the specific advantages and trade-offs.

      We thank the reviewer for the careful evaluation of the manuscript and for the constructive feedback. We think the reviewer raises valid points and will address them in the revised manuscript.

      Reviewer #3 (Public review):

      Franziscus et al. describe an elegant approach for spatially specific proteome analysis. To achieve this, they expand fixed cells and subsequently use a laser to micro-dissect a region of interest, which is then analyzed by mass spectrometry.

      They demonstrate the effectiveness of their approach by analyzing the nucleus, nucleolus, and the Golgi, and benchmark their hits against previous datasets for these organelles.

      The manuscript is very well written and nicely guides the reader through the applied methods. The presented data is convincing, and I do not see the need for additional experimental verification of the protocol. The only minor concern is the novelty of the method and the presentation. A combination of expansion, laser microdissection, and proteomics has been applied in the past (PMID: 36450705, PMID: 39477916). In the manuscript, one of these studies is cited, though it does not become clear that this approach is already described. However, Franziscus et al. describe the approach better and make it more accessible to the reader, especially since the other studies described this methodology in combination with tissue expansion and not in combination with single cell expansion as it is done here. I would ask the authors to be clearer in the introduction about what others have already done and what their contribution is here. In general, I am convinced that the community will benefit from the presented protocol to analyze organelle proteomics in detail.

      We thank the reviewer for the careful evaluation of our manuscript and overwhelmingly positive assessment. We apologize for the omission of the mentioned citations, and will adjust the introduction to make it clearer what has already been done and what the advance our method provides.

      References

      Damstra HG, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. 2022. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 11:e73775. DOI: https://doi.org/10.7554/eLife.73775

      Gambarotto D, Hamel V, Guichard P. 2021. Ultrastructure expansion microscopy (U-ExM). Methods in Cell Biology 161:57–81. DOI: https://doi.org/10.1016/bs.mcb.2020.05.006, PMID: 33478697

      Liffner B, Silva TLA e., Vega-Rodriguez J, Absalon S. 2024. Mosquito Tissue Ultrastructure-Expansion Microscopy (MoTissU-ExM) enables ultrastructural and anatomical analysis of malaria parasites and their mosquito. BMC Methods 1:13. DOI: https://doi.org/10.1186/s44330-024-00013-4

    1. Author response:

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

      We thank the editor and reviewers for their constructive questions, valuable feedback, and for approving our manuscript. We truly appreciate the opportunity to improve our work based on their insightful comments. Before addressing the editor’s and each referee’s remarks individually, we provide below a point-by-point response summarizing the revisions made.

      Duplication of control groups across experiments

      We appreciate the reviewers’ concern regarding the potential duplication of control groups. In the revised manuscript, we have explicitly clarified that independent groups of control mice were used for each experiment. These details are now clearly indicated in the Materials and Methods section to avoid any ambiguity and to reinforce the rigor of our experimental design (Page 15, Line 453-455): “Furthermore, knockout animals and those treated with pharmacological inhibitors or neutralizing antibodies shared the same control groups (chow and HFCD), as required by the animal ethics committee.”

      Validation of the MASLD model

      To strengthen the metabolic characterization of our MASLD model, we have now included additional parameters, including liver weight, Picrosirius staining and blood glucose measurements. These data are presented as new graphs in the revised manuscript and support the metabolic relevance of the HFCD diet model (Figure Suplementary S1). The corresponding description has been added to the Results section (Page 5, Lines 116-117) as follows: “Mice fed HFCD showed no increase in liver weight and collagen deposition as evidenced by Picrosirius staining (Fig. S1A and Fig. S1C)”

      Assessment of liver injury in RagKO and anti-NK1.1 mice

      We fully agree that assessment of liver injury is essential for these models. For mice treated with antiNK1.1, ALT levels are shown in Figure 4G, confirming increased liver injury after treatment. Regarding Rag⁻/⁻ mice, the animals exhibit exacerbation of liver injury when fed a HFCD diet and challenged with LPS (Page 7, Lines 183–184). The corresponding description has been added to the Results section (Page 7, Lines 175-176) as follows: “Interestingly, Rag1-deficient animals under the HFCD remained susceptible to the LPS challenge (Fig. 4C) with exacerbation of liver injury (Fig. 4D) ”

      Discussion of limitations

      We have expanded the Discussion section to provide a more comprehensive and balanced perspective on the limitations of our model and experimental approach (Page 13-14, Lines 401–414) “Our study presents several limitations that should be acknowledged and discussed. First, we cannot entirely rule out the possibility that our mice deficient in pro-inflammatory components exhibit reduced responsiveness to LPS. However, our ex vivo analyses using splenocytes from these animals revealed a preserved cytokine production following LPS stimulation. These results suggest that the in vivo differences observed are primarily driven by the MAFLD condition rather than by intrinsic defects in LPS sensitivity. Second, the absence of publicly available single-cell RNA-seq datasets from MAFLD subjects under endotoxemic or septic conditions limited our ability to perform direct translational comparisons. To overcome this, we analyzed existing MAFLD patients and experimental MAFLD datasets, which consistently demonstrated upregulation of IFN-y and TNF-α inflammatory pathways in MALFD. In line with these findings, our murine model revealed TNF-α⁺ myeloid and IFN-y⁺ NK cell populations, thereby reinforcing the validity and translational relevance of our results.”. This revision highlights the constraints of the MASLD model, the inherent variability among in vivo experiments, and the interpretative limitations related to immunodeficient mouse strains.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In Figure 4 the authors are showing the number of IFN+ positive CD4, CD8, and NK 1.1+ cells. Could they show from total IFNg production, how much it goes specifically on NK cells and how much on other cell populations since NK1.1 is NK but also NKT and gamma delta T cell marker? Also, in Figure 2E the authors see a substantial increase in IFNg signal in T cells.

      While we did not specifically assess IFNγ production in NKT cells or other minor populations, our data indicate that the NK1.1+CD3+ cells (NKT cells) cited in Page 7, Lines  188-192 were essentially absent in the liver tissue of LPS-challenged animals, as shown in Supplementary Figures 3C and S10. The corresponding description has been added to the Results section (Page 7, Lines 188-192) as follows: “We observed that the number of NK cells increased in the liver tissue of PBS-treated MAFLD mice compared with mice fed a control diet (Fig. 4E). LPS challenge increased the accumulation of NK1.1+CD3− NK cells in the liver tissue of MAFLD mice and the absence of NK1.1+CD3+ NKT cells (Fig. S3C and 4E)”.

      This absence was consistent across all experimental conditions, corroborating our focus on NK1.1+CD3− cells as the primary source of NK1.1-associated IFNγ production. Furthermore, data demonstrated in Figure 2E illustrate the presence of IFNγ primarily in NK cells. Therefore, the observed IFNγ signal, attributed to NK1.1+ cells, predominantly reflects conventional NK cells, with minimal contribution from NKT or γδ T cells.

      (2) In Figure 4C, the authors state that the results suggest that T and B cells do not contribute to susceptibility to LPS challenge. However, they observe a drop in survival compared to chow+LPS. Are the authors certain there is no statistical significance there?

      The observed decrease in survival is consistent with our expectations, as T and B cells are not the primary source of interferon-gamma (IFNγ) in this context. Even in their absence, animals remain susceptible to LPS challenge due to the presence of other IFNγ-producing cells that drive the observed lethality. We have carefully re-examined the statistical analysis and confirm that it was correctly performed.  

      (3) Since the survival curve and rate are exactly the same (60%) in Figures 3F, 3G, 4C, 4F, 5G, and 5H I would just like to double-check that the authors used different controls for each experiment.

      The number of mice used in each experiment was carefully determined to ensure sufficient statistical power while fully complying with the limits established by our institutional Animal Ethics Committee. To minimize animal use, the same control group was shared across multiple survival experiments. Despite using shared controls, the total number of animals per experimental group was adequate to produce robust and reproducible survival outcomes. All groups were properly randomized, and the shared control data were rigorously incorporated into statistical analyses. This strategy allowed us to maintain both ethical standards and the scientific rigor of our findings.

      (4) In Figure 5 the authors are saying that it is neutrophils but not monocytes mediate susceptibility of animals with NAFLD to endotoxemia. However, CXCR2i depletion and CCR2 knock out mice affect both monocytes/macrophages and neutrophils. And in Figures 5E, 5G, and 5H they see that a) LPS+CXCR2i decreases liver damage more than LPS+anti Ly6G, b) HFCD mice challenged with LPS and treated with anti-LY6G do not rescue survival to levels of CHOW LPS and c) anti Ly6G treatment helps less than CXCR2i. Therefore, from both knock out mice and depletion experiments the authors can conclude that most likely monocytes (but potentially also other cells) together with neutrophils are substantial for the development of endotoxemic shock in choline-deficient high-fat diet model.

      While neutrophils express CCR2, our data clearly show that CCR2 deficiency does not impair neutrophil migration, as demonstrated in Supplemental Figures 5A and 5B (added to the manuscript, page 8, lines 213–217). The corresponding description has been added to the Results section (Page 8, Lines 213217) as follows: ``Interestingly, animals deficient in monocyte migration (CCR2-/-) showed a high mortality rate compared to wild type after LPS challenge and neutrophil migration is not altered (Fig. 5SA and Fig. 5SB)``, In contrast, CCR2 deficiency primarily affects monocyte recruitment, yet in our experimental conditions, monocyte depletion or CCR2 knockout did not significantly alter the severity of endotoxemic shock, indicating that monocytes play a minimal role in mediating susceptibility in HFCD-fed mice.

      To specifically investigate neutrophils, we used pharmacological blockade of CXCR2 to inhibit migration and antibody-mediated neutrophil depletion. Both approaches have consistently demonstrated that neutrophils are critical factors in endotoxemic shock.

      These findings support our conclusion that neutrophils are the primary cellular contributors to susceptibility in HFCD-fed mice during endotoxemia, with monocytes making a negligible contribution under the tested conditions.

      (6) In Figure 6A (but also others with PD-L1) did the authors do isotype control? And can they show how much of PD1+ population goes on neutrophils, and how much on all the other populations?

      To address this issue, we performed additional analyses to assess the distribution of PD-L1 expression on CD45+CD11B+ leukocytes. These new results, detailed on Page 9, lines 245-250, and now presented in Supplemental Figure 6, demonstrate that PD-L1 expression is predominantly enriched in neutrophils compared to other immune subsets. This observation further reinforces our conclusion that neutrophils represent a major source of PD-L1 in our experimental model.

      To ensure the robustness of these findings, we also included FMO controls for PD-L1 staining in the newly added Supplemental Figure S6. These controls validate the specificity of our gating strategy and confirm the reliability of the detected PD-L1 signal. The corresponding description has been added to the Results section (Page 9, Lines 245-250) as follows: ``First, we observed that only the MAFLD diet caused a significant increase in PD-L1 expression in CD45+CD11b+ leukocytes after LPS challenge (Fig. S6C). We observed that within this population, neutrophils predominate in their expression when compared to monocytes (Fig. 6SA, Fig. 6SB, and Fig. 6SD). Furthermore, PD-L+1 neutrophils showed an exacerbated migration of PD-L1+ neutrophils towards the liver (Fig. 6A and 6B)”

      (7) In Figure 6D it is interesting that there is not an increase in PD-L1+ neutrophils in LPS HFCD IFNg+/+ mice in comparison to LPS chow IFNg+/+ mice, since those should be like WT mice (Figure 6A going from 50% to 97%) and so an increase should be seen?

      The apparent difference between Figures 6A and 6D likely reflects inter-experimental variability rather than a biological discrepancy. Although the absolute percentages of PD-L1⁺ neutrophils varied slightly among independent experiments, the overall phenotype and trend were consistently maintained namely, that PD-L1 expression on neutrophils is enhanced in response to LPS stimulation and modulated by IFNγ signaling. Thus, the data shown in Figure 6D are representative of this consistent phenotype despite minor quantitative variation.

      (8) In Figure 7 do the authors have isotype control for TNFa because gating seems a bit random so an isotype control graph would help a lot as supplementary information, in order to make the figure more persuasive

      To address the concern regarding gating in Figure 7, we have included the FMO showing TNFα as a histogram Supplementary Figure 8gG. These control reaffirm the accuracy and reliability of our gating strategy for TNFα, further supporting the robustness of our data. The corresponding description has been added to the Results section (Page 9, Lines 272-274) as follows:`` We observed an exacerbated TNF-α expression by PD-L1+ neutrophils from MAFLD when compared to control chow animals (Fig. 7A, Fig. 7B, Fig. 7D, and Fig8SG).

      (9) Figure 6C IFNg+/+ mice on CHOW +LPS is same as Figure 8E mice chow +LPS but just with different numbers. Can the authors explain this?

      Although the data points in Figures 6C and 8E may appear similar, we confirm that they originate from entirely independent experiments and represent distinct datasets. To enhance clarity and avoid any potential confusion, we have adjusted the figure presentation and sizing in the revised manuscript. These changes make it clear that the datasets, while comparable, are derived from separate experimental replicates.

      (10) Figure 1E chow B6+LPS is the same as Figure 5D B6+LPS but should they be different since those should be two different experiments?

      We confirm that Figures 1E and 5D correspond to data obtained from independent experiments. Although the experimental conditions were similar, each dataset was generated and analyzed separately to ensure the reproducibility and robustness of our results.

      Reviewer #2 (Recommendations for the authors):

      (1) Why did you look at kidney injury in Figure 1D? I think this should be explained a little.

      We assessed kidney injury alongside ALT, a marker of liver damage, because both the liver and kidneys are among the primary organs affected during sepsis and endotoxemia. This rationale has been added to the manuscript (page 5, lines 129–131): “Remarkably, compared to the Chow group, HFCD mice exposed to LPS did not show greater changes in other organs commonly affected by endotoxemia, such as the kidneys (Figure 1D).” By evaluating markers of injury in both organs, we aimed to determine whether our physiopathological condition was liver-specific or indicative of broader systemic injury.

      (2) I know Figure 2C isn't your data, but why are there so few NK cells, considering NK cells are a resident liver cell type? Doesn't that also bring into question some of your data if there are so few NK cells? And the IFNG expression (2E) looks to mostly come from T-cells (CD8?).

      The data shown in Figure 2C were reanalyzed from a separate NAFLD model based on a 60% high-fat diet. Although this model differs from ours, the observed low number of NK cells is consistent with expectations for animals subjected solely to a hyperlipidic diet, which primarily provides an inflammatory stimulus that promotes recruitment rather than maintaining high baseline NK cell numbers.

      In our experimental model, these observations align with published data. Specifically, liver tissue from NAFLD animals typically exhibits low baseline NK cell numbers, but upon LPS challenge, there is a marked increase in NK cell recruitment to the liver. This dynamic illustrates the interplay between dietinduced inflammation and immune cell recruitment in our experimental context and supports the interpretation of our IFNγ data.

      (3) In your methods, I think you didn't explain something. You said LPS was administered to 56 week old mice, but that HFCD diet was started in 5-6 week old mice and lasted 2 weeks, then LPS was administered. So LPS administration happened when the mice were 7-8 weeks old, right?

      We thank the reviewer for pointing out this inconsistency in our Methods section. The reviewer is correct: the HFCD diet was initiated in 5–6-week-old mice, and LPS was administered after 2 weeks on the diet, such that LPS challenge occurred when the mice were 7–8 weeks old.

      We have revised the Methods section (add page 15-16, lines 474–480).  to clarify this timeline and ensure it is accurately described in the manuscript. The corresponding description has been added to the Materials and Methods section (Page 14, Lines 436-442) as follows: “Lipopolysaccharide (LPS; Escherichia coli (O111:B4), L2630, Sigma-Aldrich, St. Louis, MO, USA) was administered intraperitoneally (i.p.; 10 mg/kg) in C57BL/6, CCR2 -/-, IFN-/-, and TNFR1R2 -/- mice. The HFCD was initiated in 5–6 week-old mice, and LPS was administered after 2 weeks on the diet, meaning that LPS administration occurred when the mice were 7–8 weeks old, with body weights ranging from 22 to 26 g. LPS was previously solubilized in sterile saline and frozen at -70°C. The animals were euthanized 6 hours after LPS administration”.

      (4) Throughout the manuscript, I would consider changing the term NAFLD to something else. I think HFCD diet is a closer model to NASH, so there needs to be some discussion on that. And the field is changing these terms, so NAFLD is now MASLD and NASH is now MASH.

      We appreciate the reviewer’s comment regarding the terminology and disease classification. In our experimental conditions, the animals were subjected to a high-fat, choline-deficient (HFCD) diet for only two weeks, a period considered very early in the progression of diet-induced liver disease. At this stage, histological analysis revealed lipid accumulation in hepatocytes without evidence of hepatocellular injury, inflammation, or fibrosis. Therefore, our model more closely resembles the metabolic-associated fatty liver disease (MAFLD, formerly NAFLD) stage rather than the more advanced metabolic-associated steatohepatitis (MASH, formerly NASH).

      Indeed, prolonged exposure to HFCD diets, typically 8 to 16 weeks, is required to induce the inflammatory and fibrotic features characteristic of MASH. Since our objective was to study the initial metabolic and immune alterations preceding overt liver injury, we believe that using the term MAFLD more accurately reflects the pathological stage represented in our model. Accordingly, we have revised the text to align with the updated nomenclature and disease context.

      (6) I am concerned about over interpretation of the publicly available RNA-seq data in Figure 2. This data comes from human NAFLD patients with unknown endotoxemia and mouse models using a traditional high-fat diet model. So it is hard to compare these very disparate datasets to yours. Also, if these datasets have elevated IFNG, why does your model require LPS injection?

      We thank the reviewer for their thoughtful comments regarding the interpretation of the RNA-seq data presented in Figure 2. We would like to clarify that the human NAFLD datasets referenced in our study do not specifically include patients with endotoxemia; rather, they focus on individuals with NAFLD alone.

      Comparing data from human and murine MAFLD models, we observed that NK cells, T cells, and neutrophils are present and contribute to the hepatic inflammatory environment. Our reanalysis indicates that the elevations of IFNγ and TNF in NAFLD are primarily derived from NK cells, T cells, and myeloid cells, respectively.

      In our experimental model, LPS administration was used to evaluate whether these immune populations particularly NK cells are further potentiated under a hyperinflammatory state, leading to exacerbated IFNγ production. This approach allows us to determine whether increased IFNγ contributes to worsening outcomes in NAFLD, providing mechanistic insights that cannot be obtained from static human or traditional mouse datasets alone.

      (7) The zoom-ins for the histology (for example, Figure 1E) don't look right compared to the dotted square. The shape and area expanded don't match. And the cells in the zoom-in don't look exactly the same either.

      We have thoroughly re-examined the histological sections and the corresponding zoom-ins, including the example in Figure 1E. Upon verification, we confirm that the zoom-ins accurately represent the highlighted areas indicated by the dotted squares. The apparent discrepancies in shape or cellular appearance are likely due to minor differences in orientation or cropping during figure preparation. Nevertheless, the content and regions depicted are consistent with the original sections.  

      (8) Did the authors measure myeloid infiltration in the CCR2-/- mice? Did you measure Neutrophil infiltration in the TNF-Receptor KO mice?

      Analysis of CD45+ cell migration in CCR2 knockout mice, as shown in Supplemental Figure 5C and 5D, demonstrates that the absence of CCR2 does not impair overall leukocyte migration. Similarly, assessment of neutrophil migration in TNF receptor (TNFR1/2) knockout mice, presented in Supplemental Figure 8A, shows that neutrophil trafficking is not affected in these animals. These results indicate that the respective knockouts do not compromise the migration of the analyzed immune populations, supporting the interpretations presented in our study.

      (9) Regarding Methods for RNA-seq Analysis. Was the Mitochondrial percentage cutoff 0.8%, because that seems low. And was there not a Padj or FDR cutoff for the differential expression?

      The mitochondrial percentage in our scRNA-seq analysis reflects the proportion of mitochondrial gene expression per cell, which serves as a quality control metric. A low mitochondrial gene expression percentage, such as the 0.8% cutoff used here, is indicative of highly viable cells.

      For differential gene expression analysis, we employed the FindMarkers function in Seurat with standard parameters: adjusted p-value (Padj) < 0.05 and log2 fold change > 0.25 for upregulated genes, and adjusted p-value < 0.05 with log2 fold change < -0.25 for downregulated genes. These thresholds ensure robust identification of differentially expressed genes while balancing sensitivity and specificity.

      (10) Regarding Methods for Flow Cytometry. How were IFNG and TNF staining performed? Was this an intracellular stain? Did you need to block secretion? TNF and IFNG antibodies have the same fluorophore (PE), so were these stainings and analyses performed separately?

      Six hours after LPS challenge, non-parenchymal liver cells were isolated using Percoll gradient centrifugation. Because the animals were in a hyperinflammatory state induced by LPS, no in vitro stimulation was performed; all staining was carried out immediately after cell isolation. Detection of IFNγ and TNF was performed via intracellular staining using the Foxp3 staining kit (eBioscience). Due to both antibodies being conjugated to PE, IFN-γ and TNF-α staining and analyses were conducted in separate experiments. These distinct staining protocols and analyses are detailed in Supplemental Figures 10 and 11. The corresponding description has been added to the Materials and Methods section (Page 16, Lines 490-493) as follows: ``As animals were already in a hyperinflammatory state, no additional in vitro stimulation was required. Intracellular detection of IFN-γ and TNF-α was conducted using the Foxp3 staining kit (eBioscience). Since both antibodies were conjugated to PE, staining and analyses were performed in separate experiments``

      Reviewer #3 (Recommendations for the authors):

      (1) Achieving an NAFLD model/disease is the starting point of this study. I understand that a two-week HFCD diet period was applied due to the decrease in lymphocyte numbers. Was it enough to initiate NAFLD then? Or is it a milder metabolic disease? Which parameters have been evaluated to accept this model as a NAFLD model?

      Indeed, the two-week HFCD diet induces an early-stage form of NAFLD, characterized by initial fat accumulation in the liver without significant hepatic injury. While this represents a milder metabolic phenotype, it is sufficient to study the inflammatory and immune responses associated with NAFLD. To validate this model, we assessed multiple parameters: liver weight, blood glucose levels, and collagen deposition. These measurements confirmed the presence of early-stage NAFLD features in the animals, providing a relevant and reliable context for investigating susceptibility to endotoxemia and immune cell dynamics. They are shown in Figure Suplementary 1 and the text was included in the manuscript (Page 5, Lines 116-117): “Mice fed HFCD showed no increase in liver weight and collagen deposition as evidenced by Picrosirius staining (Fig. S1A and Fig. S1C) ”.

      (2) It is true that the CD274 gene (encoding PD-L1) and the IFNGR2 gene, corresponding to the IFNγ receptor, are among the upregulated genes when authors analyzed the publicly available RNAseq data but they are not the most significantly elevated genes. What is the reasoning behind this cherrypicking? Why are other high DEGs not analyzed but these two are analyzed?

      We highlighted the expression of the IFN-γ receptor (IFNGR2) and CD274 (encoding PD-L1) in the publicly available RNA-seq data to align and corroborate these findings with the key results observed later in our study. To avoid redundancy, we chose to present these genes in the initial figures as they are directly relevant to the subsequent analyses. Regarding the broader analysis of human RNA-seq data, our primary objective was to identify enriched biological processes and pathways, which served as a foundation for the focus and direction of this study.

      (3) Figures 3C-3G: I understand that IFNg-/- and NFR1R2a-/- mice are not showing elevated liver damage but it may simply be because of the non-responsiveness to the LPS challenge. I suggest using a different challenge or recovery experiments with the cytokines to show that the challenge is successful and results are caused by NAFLD, truly. The same goes for Figure 6: Looking at Figure 6D one may think that IFNg deficiency alters the LPS response independent of the diet condition (or NAFLD condition).

      We appreciate the reviewer’s insightful comment and fully understand the concern regarding the potential non-responsiveness of IFN-γ⁻/⁻ and TNFR1R2a⁻/⁻ mice to the LPS challenge. To address this point and confirm that these knockout animals are indeed responsive to LPS stimulation, we conducted an additional set of ex vivo experiments.

      Specifically, WT and cytokine-deficient (IFN-γ⁻/⁻) mice were fed either Chow or HFCD for two weeks, after which spleens were collected, and splenocytes were challenged in vitro with LPS. We then quantified TNF, IFN, and IL-6 production to confirm that these mice are capable of mounting cytokine responses upon LPS stimulation.

      Due to current breeding limitations and a temporary issue in colony maintenance of TNF-deficient mice, we were unable to include TNFR1R2a⁻/⁻ animals in this additional experiment. Nevertheless, we prioritized performing the analysis with the available knockout line to avoid leaving this important point unaddressed.

      These additional data demonstrate that IFN-γ-deficient mice remain responsive to LPS, reinforcing that the differences observed in vivo are related to the NAFLD condition rather than a lack of LPS responsiveness.

      (4) Figure 1 vs Figure 4: Rag-/- mice seem more susceptible to LPS-derived death even after normal conditions. But If I compare the survival data between Figure 1 and Figure 4, Rag-/- HFCD diet mice seem to be doing better than wt mice after LPS treatment. (1 day survival vs 2 days survival). How do you explain these different outcomes?

      We thank the reviewer for this insightful question regarding the survival data in Figures 1 and 4. Although there is a one-day difference in survival outcomes, Rag-/- mice consistently exhibit increased susceptibility to LPS-induced mortality can influence the exact survival timing. Nonetheless, across all experiments, Rag-/- mice display a reproducible phenotype of heightened sensitivity to LPS challenge, which is supported by multiple independent observations in our study.

      (5) How do you explain Figure 4J in connection to the observation presented with Figure 7: TNFa tissue levels, even though significant, seem very similar between the conditions?

      We would like to clarify that the animals in this study are in a metabolic syndrome state, with early-stage NAFLD characterized by hepatic fat accumulation without significant tissue injury, as shown in Figure 1C.

      Under these conditions, the LPS challenge triggers an exacerbated inflammatory response, leading to increased secretion of IFN-γ and TNF-α, primarily from NK cells and neutrophils. While TNFα levels may appear visually similar across conditions, the HFCD mice exhibit a heightened predisposition for an amplified immune response compared to chow-fed mice. This difference is consistent with the functional outcomes observed in our study and highlights the diet-specific sensitization of the immune system.

    1. Author response:

      We will extend and clarify the text of the paper according to the suggestions of the reviewers. In particular we will extend the description and discussion of the calcium chelator approach, re-patching and multiple probability fluctuation analysis. We will also include in the Results section that volume-averaged calcium signals were measured and extend the description about measurement of the resting calcium and variability between boutons. Literature will be included and discussed as suggested.

      In order to avoid any misunderstandings, we will also make it clearer that recordings from

      L5PN – L5PN synapses in S1 were published in our preceding papers (Bornschein et al., 2019a, b), but that these data were partially reanalyzed for the comparison with recordings from L5PN – L5PN synapses in PFC (this paper). We will also emphasize that the recordings from L2/3 to L5PN synapses in S1 and PFC were made directly in the present study. We will include a supplementary table, which explicitly shows for each figure which data are from Bornschein et al. (2019a, b) and which data were obtained in the present study. 

      We will consider all points of the reviewers and the recommendations of the editors in detail in the revised manuscript and/or our pointwise response.

      We recognized one factual error in the public reviews:

      Reviewer 2, point 7: “Methods: The authors use Student's t-test for data comparison. The authors should verify that the data distribution was indeed normal, e.g. by using a Shapiro-Wilk test. If this is not the case, non-parametric tests should be used.”

      A detailed description of the statistics, including test for normality, is given in the Methods section. In particular we wrote in the Methods: “Normality was tested using the Shapiro-Wilk Test. (…) To compare pre- and post-treatment data the paired t-test or the Wilcoxon signed rank test (WSR) was used, depending on the distribution of the data. (…)”

      To further emphasize that the data was tested for normal distribution, we have also extended the description of the statistical tests in the figure legends.

      Bornschein G, Brachtendorf S, Schmidt H (2019a) Developmental increase of neocortical  presynaptic efficacy via maturation of vesicle replenishment. Front Synaptic Neurosci 11:36.

      Bornschein G, Eilers J, Schmidt H (2019b) Neocortical high probability release sites are formed by distinct Ca2+ channel-to-release sensor topographies during development. Cell Rep 28:1410-1418 e1414.

    1. Author response:

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

      We thank the editors and reviewers for their assessment of this manuscript, and for the positive words highlighting the value of undertaking evaluation of small molecule drugs for snakebite in the neotropics, inclusive of the quality of this work and the value of the validated screening pipeline. We completely agree that the next steps for this work will be to evaluate the preclinical efficacy of the identified drugs in mouse models, though this considerable undertaking will form the basis of future work. Critically, the pipeline that we describe herein facilitates the selection of the most appropriate candidates to progress into such mouse studies, aligning with the 3Rs principles for minimising the need for animal research. The comment around insufficient venom characterisation seems somewhat misplaced – the objective of this project was not to characterise the venoms used, but to evaluate the in vitro inhibition of venom toxin family activities and identify the potential utility of specific repurposed drugs as therapeutics for snakebite in the neotropics. Venom characterisation of the diverse samples used in this project would represent an entire project and manuscript in its own right. We are pleased that the reviewers highlight the gap in research on serine protease inhibitors and the value this paper has in highlighting that more research is required in this area to identify a candidate that is more suitable for future clinical use than nafamostat.


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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Small molecule therapeutics for snakebite have received a lot of attention for their potential to close the gap between bite and treatment, where antivenom is not immediately available.

      Strengths:

      There has been a lot of focus on Africa, Asia, and India, but very little work related to neotropical regions. The authors seek to begin filling this gap in the preclinical literature. The authors use well-developed methods for preclinical assessment.

      Weaknesses:

      A clearer and more focused discussion of the limitations of the overall present work would be desirable (e.g. protection vs. rescue, why marimastat over prinomastat for in vivo assays when both have been through clinical trials for other indications; real-world feasibility of nafamostat, which has a half-life of 1-2 minutes compared to camostat, which has a half-life of hours). All of this could be improved in a revision.

      We thank the reviewer for their shared opinion of the potential value of small molecules as snakebite envenoming therapeutics and their insight on the gap in focus in the neotropics, which this manuscript aims to address.

      Our work in this manuscript included standard practice of pre-incubation between drug and venom for all in vitro studies, and sequential (i.e. not co-incubation) administration in the egg model. In our revised manuscript we will make these distinctions clearer. Use of a ‘rescue’ approach in the in vitro assays is not feasible due to the rapid destruction of the substrates used for assay readouts. The clearest rationale for the use of rescue models relates to their power within in vivo preclinical models (i.e. murine envenoming models) which, following the in vitro characterisations presented in this paper, are the logical next step for evaluating small molecule drugs for inhibiting neotropical snake venoms.

      Although both marimastat and prinomastat are repurposed drugs that have undergone clinical evaluation for other indications, marimastat has been more extensively characterised preclinically than prinomastat for snakebite, and will soon enter Phase II clinical trial evaluation for this indication (https://www.ddw-online.com/ophirex-to-produce-snake-venom-inhibitor-for-lstm-study-40669-202602/). Marimastat also has a longer half-life in humans of 8-10 hours (Millar et al. 1998), compared to prinomastat (2-5h, Hande et al. 2004). We will more clearly highlight the rationale for selecting marimastat in the revised manuscript.

      Although we appreciate the reviewer’s point regarding the short half-life of nafamostat (which is typically given by continuous iv infusion due to its short half-life), in the manuscript we have already stated that we do not recommend the progression of nafamostat as a snake venom serine protease (SVSP) inhibitor candidate due its low efficacy and off target effects. We highlight the need for the community to identify other serine protease inhibitors that might have utility for snakebite.

      Reviewer #2 (Public review):

      Summary:

      The authors set out to test whether a defined set of small molecules can lessen damaging effects caused by venoms from several Bothrops species, and whether these effects are consistent enough to suggest a broadly applicable approach. They present a cross-venom dataset spanning in-vitro activity readouts and blood-based functional outcomes, and include a chicken embryo model to explore whether venom inhibition can translate into improved survival. The central message is that certain small molecules can reduce specific venom-driven effects across multiple samples, providing a comparative resource for the field and a basis for prioritizing future validation.

      Strengths:

      The main value of this work is the breadth and structure of the dataset, which places multiple venoms and multiple readouts into a single, comparable framework that should be useful for readers evaluating patterns across samples. The experimental flow is generally coherent, moving from activity measurements to functional outcomes and then to an in-vivo test, which helps the reader understand how the authors link mechanism-oriented assays to more integrated endpoints. The manuscript also provides practical information for the community by highlighting which readouts appear most consistently affected across venoms, which can help guide hypothesis generation and study design in follow-up work.

      Weaknesses:

      Several aspects of the study design and framing reduce the confidence with which readers can translate the findings beyond the specific experimental context presented. The evidence base is strongest in controlled in-vitro settings, while the bridge to real-world effectiveness remains limited, particularly for understanding performance under conditions that better reflect delayed treatment and systemic exposure. As a result, the manuscript is best interpreted as a well-organized comparative screening study with promising signals, rather than a definitive demonstration of a broadly effective, deployable intervention.

      We appreciate the reviewer’s opinion on the thorough and logical workflow we present in this manuscript and the value this pipeline providers the field for future and parallel work. We agree with the reviewer that this provides a well-organized comparative screening study applicable to different snake species or therapeutics. In relation to the comment on this manuscript being a definitive demonstration of a broadly effective, deployable intervention we agree with their opinion and are happy to clarify that while the evidence presented in this manuscript is promising, there is much work still to do before such molecules are ready for deployment for treating snakebite. Ultimately, this manuscript supports the growing evidence of the promising utility of marimastat and varespladib, and extends this evidence to neotropical snake venoms in a comparative manner. The next step will be to evaluate the efficacy of these molecules within in vivo murine preclinical models, which will be crucial for further supporting the evidence base for onward translation.

      Reviewer #3 (Public review):

      In this work, the authors wanted to evaluate repurposed small molecule inhibitors for the treatment of envenomation by snakes of the Bothrops genus; one of the most medically relevant in the Americas. I believe the objectives of the research were clearly achieved, and compelling evidence for the ability of these molecules to neutralize enzymatic and toxic activities of metalloproteinases and phospholipases in all the tested venoms is provided. Furthermore, the work highlights the limited efficacy of the tested serine protease inhibitor, suggesting a need for drug discovery campaigns to address toxicity caused by this protein family. The methods are well designed and performed, and the use of both in vitro and in vivo methodologies makes this a thorough and robust work.

      These results are extremely relevant, since they take us one step further to a potential orally administered snakebite treatment. The existence of such a treatment could improve the outcomes for thousands of snakebite victims worldwide. I have a few comments and questions that I hope will be useful to the authors:

      We thank the author for their high regard for the purpose and execution of this work. Their insight in relation to questions are supportive for an improved manuscript and discussion points for the field.

      During the introduction, the authors mention that small-molecule inhibitors can neutralize the localized tissue damage via cytotoxicity of some venoms, and cite PLA2s, SVMPs and/or cytotoxic 3FTxs as the main causing agents of this pathology. I am not aware of any direct effect described by small molecule inhibitors on cytotoxic 3FTxs alone. Has this been observed at all? Or is it more likely that the small molecule inhibitors act on the enzymatic toxins only, preventing synergistic effects with 3FTxs?

      We apologise for this error on our behalf. While inhibitory molecules have been described for cytotoxic 3FTxs, these are not small molecules as alluded to in the previous version of the manuscript. We have amended this text in our revised manuscript.

      I think it would be relevant to address the effects of non-enzymatic PLA2s, such as myotoxin II, which have been described in detail within Bothrops venoms. I believe there is some evidence of Varespladib also having a neutralizing effect on the myotoxicity caused by these non-enzymatic PLA2s. I suggest adding a comment about the contribution of these toxins in the discussion or in the section where PLA2 activity of the venoms is compared. In my opinion, right now it seems like these were overlooked.

      We thank the reviewer for highlighting this point. We agree that this is highly relevant and would benefit from discussion in the revised manuscript given the nature of our assays and the non-enzymatic mechanism of action of certain Bothrops PLA<sub>2</sub>s. We have added this to the discussion.

      Regarding Marimastat and the other MP inhibitors, are there any studies showing that they don't have an effect on endogenous MPs? I understand they have been approved for human use before, but is there any indication that they would not have an effect at the doses that would be required to treat envenomation?

      Most matrix metalloproteinases inhibitors will act on endogenous MPs to at least some extent (variable potency on different MMPs). Marimastat has demonstrated activity against endogenous metalloproteinases, including MMP1, which was hypothesised to cause severe joint pain when used chronically (i.e. frequent dosing over many weeks) for indications such as cancer, though this effect was reversible within 8 weeks of cessation of drug administration (Wojtowicz-Praga, 1998). Thus long-term use of matrix metalloproteinases inhibitors can cause safety concerns. However, the anticipated duration of dosing for snakebite, which is an acute life-threatening condition, is a few days. It is therefore unlikely that prior safety concerns observed following chronic dosing in cancer studies would apply to its potential use as a snakebite field therapy.

      Regarding the quenched fluorescence substrate used for enzymatic activity. Is there a possibility that some of the SVMPs would not act on this substrate, and therefore their activity or neutralization is not observed? Would it be relevant to test other substrates, such as gelatin, collagen, or even specific clotting factors?

      It has been observed that certain SVMPs (specifically several PI SVMPs) are not active against this ES010 substrate in vitro. The substrate used in the in vitro SVMP assay is reported by the manufacturer as a substrate for a wide range of MMPs which target the extracellular matrix components mentioned by the reviewer, i.e. collagenases and gelatinases as well as matrilysins, stromelysins and elastate. This in vitro assay combined with the coagulation assays are complementary in covering the main targets of SVMPs (ECM and clotting cascade), prior to haemorrhagic assessment in the egg model. Thus, we are confident that activity for the broad range of SVMP isoforms will be captured through the screening pipeline we have developed.

      Finally, could the authors comment or provide some bibliography regarding the translatability of the chicken embryo model in the context of envenomation?

      Our current model is based on an earlier egg embryo model (Sells et al. 1997, Sells et al. 1998 and Sells et al. 2000) which described good correlations (p<0.01) with the standard WHO murine preclinical envenoming model. These studies have assessed correlations for minimal haemorrhagic doses (MHDs), LD50s and ED50s in both models for a selection of viper venoms. As chicken embryos at day 6 of development have incomplete neural arcs, the model is not well suited for assessing neurotoxic effects, but can be effectively used for addressing venom-induced haemorrhage and lethality and for testing therapeutics. In addition, a more recent study (Yusuf et al. 2023) reported almost identical LD50s for the venom of Bitis arietans between the two in vivo approaches. The model is also being pursued as a preclinical testing model by an antivenom manufacturer with the focus of reducing the use of rodents in batch release testing (Verity et al. 2021). We will provide further clarification on the rationale for using the egg model, including the supportive references outlined above, in the revised manuscript.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The manuscript provides a useful comparative dataset across multiple Bothrops venoms and supports SVMP inhibition as a broadly effective lever in the authors in-vitro work. However, the strength of the 'pan-Bothrops' and translational claims is currently limited by insufficient characterization of the exact venom samples tested and by experimental designs that fall in clinically realistic rescue.

      Major comments:

      (1) The venoms used in this study are historical batches and are not formally characterized beyond SDS-PAGE and literature summaries, despite well-known intra- and inter-population venom variability; this weakens the generalization of the conclusions.

      To address this comment, we have increased clarity on our venom sources being historic, Due to the historic source locality is not available beyond country of origin, with the exception of B. lanceolatus which is endemic to Martinique. Figure 1 also makes clear that we agree with the reviewer that the variation is high within Bothrops species. We discuss this variation on the limitations in our sampling for making broad conclusions throughout the first paragraph of the discussion, with the final sentence stating Future proteomic characterisations of the specific venom samples used in this study, which were all sourced from a historical collection (except for B. lanceolatus), would be informative in this regard. Although venom composition of our samples has not been characterised, the focus of the manuscript is the characterisation of the whole venom functional activity through a wide ranging screening pipeline, and the generalisation of our findings is supported by the diversity of the venom samples (i.e. several species) despite them not being characterised (which is not critical for the focus of the study).

      (2) On a technical comment, the venom inhibition assays appear to rely on drug-first or preincubation conditions, which can easily overestimate efficacy compared with real snakebite envenomation, where toxins distribute and engage targets rapidly. Here, a translational gap is the clinical feasibility of the 'repurposed' inhibitors, as it is unclear whether the drugs central to the conclusions (especially marimastat, prinomastat and varespladib) are realistically available or stocked in hospitals or could be deployed in regions where Bothrops envenoming occurs. I think that the manuscript should clearly distinguish this from candidates with a plausible access and delivery pathway.

      Our work in this manuscript includes standard practice of pre-incubation between drug and venom for all in vitro studies, and sequential (i.e. not co-incubation) administration in the egg model. None of our methods administer drug-first. Throughout the methods and figure legends we have made these distinctions clearer. Use of a ‘rescue’ approach in the in vitro assays is not feasible due to the rapid destruction of the substrates used for assay readouts. The clearest rationale for the use of rescue models relates to their power within in vivo preclinical models (i.e. murine envenoming models), which would be the next step for this research programme.

      While the evidence presented in this manuscript is promising, there is much work still to do before such molecules are ready for deployment for treating snakebite, inclusive of the requirement to complete clinical trials, cost-benefit analysis and policy change and manufacturing/distribution feasibility assessments. Ultimately, this manuscript supports the growing evidence of the promising utility of marimastat and varespladib, and extends this evidence to neotropical snake venoms in a comparative manner. The next step will be to evaluate the efficacy of these molecules within rescue in vivo murine preclinical models, which will be crucial for further supporting the evidence base for onward translation. To further support this point we have included an additional section to the manuscript discussing the current preclinical and clinical progression of prinomastat and marimastat, which also incorporates the public comment on selection of marimastat over prinomastat.

      (3) In my opinion, the Nafamostat results and discussion need reframing, given weak SVSP inhibition and intrinsic anticoagulant behavior at 5 µM. Excluding it from certain analyses undermines interpretability, and it may be more appropriate to include it throughout as an explicit negative control condition (showing its baseline anticoagulant effect) rather than omitting it.

      Although we understand the reviewers opinion here, we disagree and believe that including nafomastat as a ‘negative control’ may present a negative reflection on the benefit that an efficacious serine protease inhibitor could provide. Furthermore, as the intrinsic anticoagulant effect of nafamostat cannot be de-coupled from direct SVSP toxin inhibition we were unable to interpret the activity which undermines the results. This can be seen in Figure 3b, which demonstrates that a false positive result would occur. For the serine protease assay, we do clearly discuss the lack of efficacy and justification of why EC<sub>50</sub> testing wasn’t appropriate within the guidance of our screening protocols.

      In the manuscript we have now further justified our approach in relation to the limitations of nafamostat as a snake venom serine protease (SVSP) inhibitor candidate due its low efficacy and off target effects. We highlight the need for the community to identify other serine protease inhibitors that might have utility for snakebite.

      (4) The data presentation needs consistent statistical analyses (currently absent for multiple key figures, including Figures 2, 3, 4, 6 and 7) and a clearer explanation for the dose of venom and drugs you choose. For example, Figure 3 relies on a fixed 5 µM drug concentration and very different venom amounts (50-100-250 ng), but it is not discussed whether such exposures are achievable in vivo, or how these concentrations map onto expected pharmacokinetics in patients. Likewise, Bothrops venoms can contain both pro- and anticoagulant activities, so the authors should justify how their framework accounts for anticoagulant components and why the observed plasma phenotypes are interpreted as they are

      In relation to the reviewers comment on the need for consistent analysis we thank the reviewer for flagging this and have now included these in figures 3, 4, 6 and 7. However, Figure 2 is presented to display the variation between all the venoms and ultimately used to select the most relevant doses for the latter inhibition experiments, therefore statistical analysis is not relevant for this figure. The updated statistical analysis now includes the following, which has been included in the relevant figure legends and results sections;

      Figure 3 - Bars indicate significant results (p = <0.05) identified through one-way ANOVA with Dunnett’s multiple comparisons test to the DMSO control

      Figure 4 - two-way ANOVA with Šídák's multiple comparisons test of each venom control compared to the matched venom treated with inhibitor

      Figure 6 – the CT and MCF data were analysed independently using one-way ANOVA with Tukey’s multiple comparisons test

      Figure 7 - Log-rank test (Mantel-Cox) with Holm- Šídák's multiple comparisons test against treatment vs venom-only control

      We have ensured that all figure legends clearly indicate the venom and drug dose to aid the clarity which the reviewer requested.

      The comment Figure 3 relies on a fixed 5 µM drug concentration and very different venom amounts (50-100-250 ng), but it is not discussed whether such exposures are achievable in vivo, or how these concentrations map onto expected pharmacokinetics in patients. is an understandable query however, in vitro assessment such as those carried out in this manuscript are not designed to directly inform pharmacokinetic/pharmacodynmanic interpretations, largely because they do not replicate real world envenoming (i.e. preincubation would not occur between a venom and treatment). This is why, as stated, follow on preclinical and clinical assessments are needed for onward progression of these inhibitors to inform dosing regimens that might achieve the necessary exposures required for in vivo venom neutralisation. That being said, PK/PD work has been initiated within Phase I trials, for example with DMPS Abouyannis et al. 2025 demonstrated a plasma exposure of >10 µg/mL for single doses of 1,200 mg and higher. This is equivalent to 80 µM, which although is lower than the EC<sub>50</sub> for some venoms in the clotting assay (Figure 3J), the venom dose (50 to 250 ng/ 50 µL, i.e. 1,000 to 5,000 ng/µL) is estimated to be >1000 times higher than a natural envenoming by Bothrops atrox at less than 1 ng/mL in serum (https://doi.org/10.1016/j.toxicon.2022.09.010). These extrapolations therefore indicate that the doses selected in our studies would have human clinical relevance.

      Finally, in terms of anticoagulant venom effects - these would be observed in our experimental approach either as reduced kinetic responses in the plasma clotting assay (as observed with nafamostat in Figure 3B) or as a prolonged clotting time in the thromboelastography assay (Figure 6). As stated in the results section Comparison of coagulation profiles, all of the venoms tested presented with a procoagulant effect. If underlying anticoagulant activity from PLA<sub>2</sub> toxins was to arise after inhibition of the procoagulant toxins (i.e. SVMPs by marimastat), as has been seen for certain other snake venoms previously, this would result in a percentage inhibition far greater than 100% in the plasma assay (Figure 3C to I) or as a prolonged clotting time in the thromboelastography assay. These described anticoagulant profiles were not observed with any venom tested in this study.

      (5) Finally, the in vivo evidence is limited to a chicken embryo model. To support your hypothesis, a conventional mouse model with delayed post-envenomation dosing (24-36 h monitoring) is needed to address both safety/toxicity and post-exposure efficacy, and to define a realistic therapeutic window, especially because venom toxins act very quickly and the timing of administration is central to the clinical utility of any small-molecule approach.

      We agree with the reviewer that the next important step for this research activity is utilising murine preclinical models to validate the in vitro and preliminary in vivo findings described in this manuscript. However, as stated above, this study provides the initial evidence base that the promising utility of marimastat, DMPS and varespladib as repurposed snakebite drugs extends to a range of neotropical viper venoms. Evaluating the safety, efficacy (both precincubation and rescue approaches) and PK/PD relationships to inform optimal dosing strategies of these molecules will be crucial next steps for the field. However, these activities are far from trivial and will take several years of additional research, and therefore fall outside the scope of this initial manuscript.

      To address the concern related to the evidence is limited to a chicken embryo model, we have included additional sentences to discuss the wider use of the egg model within snakebite research and related translation to murine studies.

      Minor comments:

      (1) Figure 2D: How do you discuss the fact that "no venom" has SVSP activity?

      The data for all in vitro assays in Figure 2 is presented as AUC from the raw data (absorbance or fluorescence), for consistency across assay. Therefore, all assays (B to D) have background signal in the absence of venom. The SVSP assay has a greater background signal.

      (2) For better understanding, I would suggest adding a dedicated column in Figure 4A with Nafamostat SVSP data reported as "N/D" where applicable.

      As stated in the results, due to the weak inhibitory activity EC<sub>50</sub> assessment was not justified, therefore adding this column would be redundant.

      (3) The introduction is too long relative to the experimental content and would benefit from tightening to sharpen the motivation and unmet need.

      We thank the reviewer for their opinion and we have reviewed the introductory section again. While we made minor edits throughout, we decided not to make substantial modifications to it.

      Reviewer #3 (Recommendations for the authors):

      I only have some minor comments:

      (1) In line 100, the word "that" is repeated.

      We thank the reviewer for spotting this error, which we have corrected.

      (2) Line 433. I believe the word "compromising" should be substituted by "comprising" here.

      We thank the reviewer for spotting this.

      (3) Figure 1 and supplementary: Bothrops asper venom has been very thoroughly studied, and using only one study from Costa Rica might underestimate the venom variation within the species. I suggest looking at the following study: https://doi.org/10.1016/j.toxicon.2022.106983. Maybe it is not necessary to change anything, but worth looking into.

      We appreciate the reviewer flagging this paper, it has been added to the manuscript (reference 48) and has provided additional data for Figure 1 and Supplementary table 1.

      (4) Methods: Given the intraspecies variation described for some of these species, I believe it is relevant to add the locality of origin of the venoms, and not only the country. I, of course, understand this is often unknown for historical samples.

      We have included the following sentence in the methods. Due to the historic nature of the venom samples, the source locality is not available beyond country of origin, with the exception of B. lanceolatus which is endemic to Martinique.

      (5) Figure 3: It is not very accurate to show an SD when the sample number is 2. I suggest, when possible, showing the mean and the two data points in the plots. This also applies to other figures where n=2. Also, in Figure 3D, does Marimastat seem to have an anticoagulant effect, or is this just within normal variation?

      We have removed the statement in the statistics paragraph of the methods Standard deviation (SD) for all kinetic reads and standard error for AUC is reported based on Prism v10 but kept the sentence. The sample sizes for HTS assays including the SVMP, PLA<sub>2</sub> and coagulation experiment are the average of the means from independent assays (n >2 within each independent assay). We understand the reviewer’s opinion on limited meaning of SD as well as SE for Fig 3 A to I, therefore we have changed the error bars to range, as we think that displaying the individual points would result in a lack of visual and analytic clarity.

      In relation to the query about marimastat anticoagulant effect in Fig 4D, as shown in 4B marimastat has no direct anticoagulant effect. The >100% inhibition for marimastat is likely to be normal variation as this is a biological assay which has high variability. However, it could also be that the strong inhibition of the SVMPs in B. asper along with limited SVSP activity has unmasked an anticoagulant effect of the remaining PLA<sub>2</sub> toxin which has high activity in this venom. That being said, as B. asper has a similar profile, we would have expected to see a similar profile in B. atrox in both the plasma and TEG assays. Therefore, assay variation seems the most likely reason for this observation.

    1. Author response:

      The following is the authors’ response to the previous 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 focus on Magude and Matutuine, two districts in south 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 malaria elimination, for example, testing and treating travelers from Matutuine in the dry season.

      Strengths:

      The strength of this study relies in the combination of different sources of data - epidemiological, travel and genetic data - to estimate importation probabilities, 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.

      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.

      Comments on revisions:

      All my questions and concerns were satisfactorily addressed.

      We appreciate the review and comment about the manuscript. In fact, the approach does not pretend to quantify the contribution of each case to overall transmission. In the discussion we state it and refer to future work with this scope.

      Reviewer #3 (Public review):

      This work provides a novel statistical model to identify imported malaria cases, which are an important challenge for elimination, particularly in low-transmission areas. This tool was applied in Plasmodium falciparum populations in Mozambique and determined differences in importation rates in 2 low-transmission districts in the South.

      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 support efforts for malaria elimination.

      Weaknesses:

      The study also has some limitations, although the authors have plans to address them. The sample collection was not representative of some provinces, and not all samples had sufficient metadata for the risk factor analysis. Additionally, the authors used a proxy for transmission intensity and assumed some other conditions to calculate the importation probability for specific scenarios. They plan to conduct a new sample collection and include monthly malaria incidence estimates in the future.

      Comments on revisions:

      Delete "We added this text to the discussion" in line 302 (Discussion)

      I recommend adding the plans to address limitations indicated in the Response to Reviewers document in the Discussion. This would really strengthen the limitation section.

      Thank you for pointing to these aspects. We deleted the sentence mentioned. In the discussion section, we now finish the paragraph on limitations with the proposed future work to address them.

    1. Author response:

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

      Reviewer #1 (Public review):

      (1) The method is an extension of the current state-of-art methods, not a fundamentally new one.

      We respectfully disagree with this characterization. While TopoMetry is inspired by the theory of spectral geometry, it is not a simple extension of existing dimensionality reduction methods such as Diffusion Maps. Instead, TopoMetry introduces a new framework for single-cell analysis that:

      Iteratively approximates manifold geometry by constructing refined diffusion operators on spectral scaffolds (“the geometry of the geometry”), a procedure not present in existing methods.

      Provides a unified workflow for dimensionality estimation, clustering, visualization, imputation, lineage inference, and diagnostics, all within the same geometric framework.

      Introduces operator-native fidelity scores and Riemannian diagnostics to single-cell analysis, enabling researchers to evaluate and trust embeddings—functionality absent in prior methods.

      Thus, TopoMetry represents a new paradigm for geometry-aware single-cell analysis, not merely a reimplementation of existing algorithms.

      (2) The paper contains a lot of jargon.

      We have thoroughly simplified the text throughout the manuscript. We now introduce geometric concepts in accessible terms, avoiding technical details where they are not essential for biological interpretation. For example, references to the Laplace–Beltrami operator and its eigenfunctions have been reduced and reframed in terms of “geometry,” “diffusion,” and “spectral scaffolds,” which are more intuitive for a general audience.

      Reviewer #1 (Recommendations for the authors):

      (1) What happens if the LBO is approximated more than twice? As the main idea of the method is an iterative approach to approximate LBO more precisely, then the authors would have already considered this. If so, this could be additionally discussed in the manuscript.

      We thank the reviewer for this important point. Indeed, TopoMetry’s design naturally supports iterating the Laplace–Beltrami operator (LBO) approximation beyond two steps. However, additional iterations (three or more) lead to only marginal improvements in final results while significantly increasing computational cost. In some tested cases, additional iterations could even over-smooth the data, reducing the resolution of fine-scale structure. The revised manuscript avoids an excessive focus on iterative LBO approximations and instead centers the narrative around representing and evaluating the underlying geometry of single-cell data.

      (2) As the paper describes the method in a very comprehensive way, as a result, it contains a lot of mathematical equations and jargon. This could hinder the visibility of the whole manuscript to biologists who do not have a background in mathematics. Thus, I strongly recommend that the authors consider moving a considerable amount of text to the supplementary material, and the main text should focus on the benchmarking results and the possible applications.

      We appreciate this recommendation and have substantially revised the manuscript to make it more accessible to a broad biological audience. In the revised version:

      We moved detailed mathematical derivations and operator definitions to the Methods section, keeping only the most essential concepts in the main text.

      We reframed technical terms (e.g., Laplace–Beltrami operator, eigenfunctions) in simpler and more intuitive language in the main text. 

      The Results section now emphasizes benchmarking outcomes and biological applications.

      Reviewer #2 (Public review):

      (1) To encourage the single-cell community to adopt this method, the authors should more clearly demonstrate its advantages over existing methods. There are many single cell analysis algorithms that are proposed in each task and some of them are widely used by biologists. However, the comparison in this work is somewhat limited. For example, Even methods mentioned in the relevant work paragraph (2nd paragraph) on page 2 are not all compared, or the reason why they are not included is not discussed. Also, I am curious how PC dimensions are determined. The choice of 300 PCs on page 11 seems arbitrary. Furthermore, the usefulness of dimension-reduced data also depends a lot on the preceding processing steps, such as highly variable gene selection. I understand it is hard to control all those factors, but I think there is room for improvement.

      We have substantially expanded the benchmarking and discussion of competing methods. These additions more clearly demonstrate TopoMetry’s advantages and robustness compared to widely adopted alternatives. In the revised manuscript:

      We now benchmark TopoMetry against 68 diverse single-cell datasets, far exceeding the scope of the original version.

      We explicitly compare TopoMetry with PCA→UMAP, standalone UMAP, and scVI. These workflows represent the de facto current standard in single-cell analysis. While numerous other approaches exist, a comprehensive benchmark of every possible workflow lies beyond the scope of this study and would itself warrant a dedicated report.

      We adopt the exact same preprocessing steps for all evaluated workflows to ensure a fair comparison, except for scVI, which requires gene counts data and performs its own internal preprocessing.

      We adjust the number of PCs used for each dataset based on the currently adopted “elbow point” ad hoc.

      (2) The paper lacks experiments that validate the results. It would be beneficial to see additional evaluation settings with better-established ground truths to more strongly demonstrate the method's effectiveness.

      We agree that validation is crucial and have strengthened this aspect:

      We introduce new geometry-preservation metrics and validate that TopoMetry outperforms current de facto standards.

      We demonstrate that TopoMetry resolves well-established ground-truth structures, such as the cell cycle in pancreas development and T cell proliferation, which PCA→UMAP fails to capture (Suppl. Fig. S3).

      We validate the biological relevance of novel T cell subpopulations by linking them to TCR clonotypes and clonal expansion patterns using datasets with paired VDJ information (ECCITE-TCR, TICA).

      We show that TopoMetry faithfully recovers expected lineage trajectories in atlas-scale datasets (MOCA).

      These analyses demonstrate that TopoMetry not only preserves geometry but also recovers biologically meaningful ground-truth structures. Further experimental investigation of biological insights obtained from the presented examples exceeds the scope of the presented methodological work.

      (3) The effect of various parameters, such as those involved in k-nearest neighbors (KNN) or choosing the appropriate Laplacian operator, is not comprehensively explored. How can we ensure the analysis is not overly sensitive to these parameters?

      We now explicitly address parameter robustness and show that results are stable across a wide range of k values (30–200) in the neighborhood graph (Suppl. Fig. S1e).

      The range of possible Laplacian operators was a design choice aimed at increasing user freedom, but we agree with the reviewer that this option could confuse readers and users. TopoMetry now only uses the appropriate operator (density-normalized graph Laplacian, a.k.a. diffusion operator), reducing variability and improving usability.

      (4) Batch effects are prevalent in single-cell data. The paper does not adequately address this issue.

      Several of the datasets we analyzed include cells from multiple donors and experimental batches, and TopoMetry successfully recovers consistent biological structure across these.

      TopoMetry’s spectral scaffolds can be integrated with data integration methods such as Harmony and Scanorama, which are employed to correct the latent PCA space in current practice.

      Reviewer #2 (Recommendations for the authors):

      (1) The paper introduces technical jargon without sufficient explanation abruptly many times. This makes it difficult for readers from a biological background to follow. Even I, with a more computational background, struggled to grasp some parts.

      We thank the reviewer for this feedback and have streamlined terminology throughout the manuscript, replacing jargon with more intuitive language and providing brief explanations when technical terms are first introduced. This makes the text more accessible to both computational and biological audiences.

      (2) There is no comparison of the computational cost of this method with existing approaches, which is an important factor for practical adoption. Including a benchmarking section on this would be useful.

      We thank the reviewer for this suggestion and have now included a runtime benchmark against PCA→UMAP, PHATE, and scVI (Suppl. Fig. 1f), showing that while TopoMetry is slightly slower than PCA→UMAP, it scales more favorably than alternative geometry-aware methods (PHATE) and neural networks (scVI).

      (3) TopOMetry allows users to obtain and evaluate dozens of possible representations. However, I wonder if this could introduce a user burden, increasing uncertainty and subjectivity, as users should examine them manually. I think this should be clarified.

      We appreciate this concern and have streamlined the workflow to minimize user burden. As shown in the original manuscript, representations learned with different TopoMetry kernels and Laplacian variants converge to highly similar results. Based on this, TopoMetry now defaults to the best-performing kernel and the most appropriate Laplacian operator, yielding only two scaffold representations (fixed-time and multiscale) and corresponding visualizations rather than dozens of alternatives. This removes the need for manual selection while retaining flexibility for advanced users. In addition, we introduced a single-line command that runs the entire analysis and generates a comprehensive PDF report, allowing users to evaluate results in a standardized and user-friendly way. Together, these changes eliminate unnecessary subjectivity and ensure consistent outputs across analyses.

      (4) Formatting. There are errors in figure numbering within the main text. For instance, it should be Figure 4 instead of Figure 3 on page 11. Some figures are not concise. For example, Figure 2 contains too much text, which detracts from its visibility. I recommend trimming the figures to improve clarity. A color map is missing in Figure 2, which could help better interpret the data.

      We have thoroughly adjusted the manuscript and figures for improved visibility and clarity.

      Broader Impact and Reception

      Since our preprint, TopoMetry has been used by Hale et al. (Science, 2024), where it helped reveal morphological T cell subpopulations, and in a recent preprint by Tedeschi et al. (2025). These independent applications highlight the utility and impact of TopoMetry beyond our group, supporting its relevance to diverse biological contexts. In addition, two independent studies performing multimodal integration of RNA and TCR data (Zhang et al., 2023 and Drost et al., 2024) have identified a diversity of T cell subpopulations that resembles the clusters identified by TopoMetry using only RNA data.

    1. Author response:

      eLife Assessment

      This study reports the relative importance of Tie1 and Tie2 signaling for atrial versus ventricular trabeculation. It is an important study and is one of the few works to date that have carefully and simultaneously analyzed these two processes. In line with a previous study in zebrafish, the authors demonstrate key differences between atrial and ventricular trabeculation. While the imaging and quantitative data were conducted with solid and validated methodology throughout the manuscript, the work would benefit from more rigourous approaches where Tie1/2 signaling is disrupted prior to the onset of atrial/ventricular trabeculation, to allow for a more direct comparison.

      We thank the editors for the eLife assessment. We would like to request that the following statement be modified: “…the work would benefit from more rigourous approaches where Tie1/2 signaling is disrupted prior to the onset of atrial/ventricular trabeculation, to allow for a more direct comparison”. We request this change for the following reasons:

      We utilized two distinct genetic mouse models in this study (as summarized in Fig. 7I), comprising conventional knockouts (Tie1<sup>tm1a/tm1a</sup>, Tie1<sup>ΔICD/ΔICD</sup> and Tie1<sup>ΔICD/ΔICD</sup>;Tek<sup>+/-</sup>) and inducible gene deletion models (Tek<sup>iECKO</sup>, Tie1ICD<sup>iECKO</sup>, and Tie1ICD<sup>iECKO</sup>;Tek<sup>+/-</sup>) [1-3]. The Tie1<sup>tm1a/tm1a</sup> line is equivalent to the previously published Tie1<sup>-/-</sup mouse line, as demonstrated in our prior work and by others [1, 2, 4-6]. Therefore, the Tie1 or Tek alleles were inactivated prior to the onset of atrial and ventricular trabeculations, as shown in Fig. 1, Fig. 2, Fig. 3, Fig. 5A-D, and Supplemental Fig. 3. Based on these findings, we propose that TIE1 is differentially required for atria versus ventricle morphogenesis, and acts synergistically with TIE2 during cardiac trabeculation.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Ding et al. use genetic mouse models to demonstrate that atrial trabeculation is more dependent on Tie1/Tie2 signaling than ventricular trabeculation. With additional experimentation that would support the current claims, the results may hold significant value, as atrial trabeculation remains an understudied phenomenon in cardiac biology with potential implications for atrial cardiomyopathy and atrial fibrillation.

      Strengths:

      Detailed characterization of atrial versus ventricular trabeculation across different developmental timepoints, and the use of appropriate animal models to address the scientific question at hand.

      Weaknesses:

      The authors have consistently treated mice with tamoxifen after ventricular, but not atrial, trabeculation has already started. As such, the observed cardiac phenotypes - where predominantly atrial trabeculation is affected - might be a mere consequence of the precise time window in which Tie1/2 signaling was impaired, rather than a direct measurement of its relative importance for atrial versus ventricular trabeculation. The conclusions of the paper may thus be significantly strengthened by depleting Tie1/2 signaling prior to the onset of ventricular trabeculation, as is done for atrial trabeculation.

      We thank the reviewer for the comments.

      Regarding the timeline of gene deletion and tamoxifen treatment, we would like to provide the following clarification.

      Fig. 1-3: As described in the Methods and Materials, Tie1<sup>tm1a/tm1a</sup> is a knockout first mouse model established from EUCOMM embryonic stem cells (EPD0735-3B07) targeting Tie1 gene. Therefore, the Tie1<sup>tm1a/tm1a</sup> line is equivalent to the previously published Tie1 null mice (Tie1<sup>-/-</sup>). The Tie1<sup>Flox/Flox</sup> mouse line (with exon 8 floxed) was generated when the lacZ reporter and neo-cassette were excised using the FLPeR mice.

      Fig. 5A-D: To investigate the synergy of TIE1 and TIE2 in cardiac trabeculation, we utilized the Tek<sup>+/-</sup> and Tie1<sup>ΔICD/+</sup> mouse lines and they were crossbred to generate double mutant mice harboring a homozygous Tie1 mutation and a single null Tek allele (Tie1<sup>ΔICD/ΔICD</sup>;Tek<sup>+/-</sup>). Although no obvious defects were observed in atrial or ventricular structures following Tie1 deficiency alone at E10.5, both atria and ventricle development were disrupted in Tie1<sup>ΔICD/ΔICD</sup>;Tek<sup>+/-</sup> mutants at the same stage (Fig. 5A-D).

      Supplemental Fig. 3: To verify the role of TIE1 in atrial development, we employed alternative knockout mouse line targeting the Tie1 intracellular domain by floxing exons 15 and exon 16 (Tie1ICD<sup>Flox/Flox</sup>). Mutants harboring these null alleles are designated as Tie1<sup>ΔICD/ ΔICD</sup>. As detailed in the previous publication [2], the line is also equivalent to the previously published Tie1 null mice (Tie1<sup>-/-</sup>). The cardiac phenotypes shown in Supplemental Fig. 3 are indeed similar to those of Tie1<sup>tm1a/tm1a</sup> mutant mice.

      For the inducible knockouts targeting Tie1, Tek and both, the results are shown in Fig. 4, Fig. 5E-H, Fig. 6, Fig. 7.

      Fig. 4: As mice homozygous for Tek mutation (Tek<sup>-/-</sup>) die before E10.5 [3, 7], we performed studies using the inducible knockout line targeting Tek (Tek<sup>Flox/-</sup>;Cdh5-Cre<sup>ERT2</sup> named as Tek<sup>iECKO</sup>), as shown in Fig. 4.

      Fig. 5-7: To investigate the synergy of TIE1 and TIE2 in the cardiac trabeculation at the later stages of embryogenesis (Fig. 5E-H, Fig. 6) and the postnatal stage (Fig. 7), we used the inducible knockout models targeting Tie1/Tek, including Tie1ICD<sup>iECKO</sup> (Tie1ICD<sup>Flox/-</sup>;Cdh5-Cre<sup>ERT2</sup>) and Tie1ICD<sup>iECKO</sup>;Tek<sup>+/-</sup> (Tie1ICD<sup>Flox/-</sup>;Cdh5-Cre<sup>ERT2</sup>;Tek<sup>+/-</sup>).

      Reviewer #2 (Public review):

      Summary:

      Ding et al. examine the role of TIE1 in cardiac chamber morphogenesis using genetic mouse models targeting Tie1, Tek, or both, and analyzing endocardial cell-mediated chamber formation across multiple embryonic developmental and postnatal stages, supported by analysis of published single-cell datasets and new bulk RNA seq analyses of murine cardiac tissue. The authors find that Tie1 and Tek expression is higher in atrial than ventricular endocardial cells. Notably, endothelial Tie1 is required for atrial trabeculation at E12.5, but is less critical in ventricular trabeculation. TIE1 also acts synergistically with TIE2 during atrial trabeculation. While Tie1 deficiency alone does not cause defects at E10.5, combined heterozygous deletion of Tek disrupts both atrial and ventricular development at E10.5. This synergy is further supported by analyses at later embryonic stages and in postnatal hearts.

      Strengths:

      The study is well-designed, clearly written, and supported by high-quality figures. The performed experiments demonstrate a previously unrecognized role for Tie1 in cardiac development and identify synergistic control of cardiac morphogenesis by Tie1 and Tie2. This synergy is consistent with the previously identified roles of Tie1 and Tek in venous development and with Tie1 involvement in angiopoietin-dependent postnatal vascular and lymphatic remodeling. Together, these findings support a role for Tie1 as a contributor to Ang1-Tie2 signaling during heart development.

      Weaknesses:

      The manuscript does not include direct mechanistic studies; however, RNA seq analysis of atria and ventricles showed reduced expression of Tek, Dll1, and Notch1 upon Tie1 deficiency in developing hearts. Although previously reported mechanisms, such as TIE1-TIE2 heterodimer formation and effects on endothelial junctions, migration, or survival are discussed, no direct mechanistic experiments are performed. Addressing some of these mechanisms would have clarified the basis of Tie1-Tie2 synergy. As two distinct Tie1 models are used, including one targeting the kinase domain, the authors should state whether phenotypes differed or were similar between models.

      We thank the reviewer for the comments. In this study, we have provided genetic evidence that TIE1 is differentially required for atrial versus ventricular trabeculation. Although the precise molecular mechanisms underlying TIE1 function require further investigation, we have provided compelling genetic evidence of its synergistic role with TIE2 during this process. The two genetic models targeting Tie1 (Tie1<sup>tm1a/tm1a</sup>, Tie1<sup>ΔICD/ΔICD</sup>) produced consistent cardiac and vascular phenotypes as shown in this study and our previous work [1, 2].

      Reviewer #3 (Public review):

      Summary:

      Ding et al. investigate the roles of TIE1 and TEK (Tie2) in mouse cardiac development, with a particular focus on atrial trabeculation. The authors employ multiple genetic models, including Tie1ICDflox/flox (with Cdh5-CreERT2), a knockout-first allele (EUCOMM, Tie1 tm1a/tm1a), and a Tek deletion model.

      Based on the dataset from Feng et al. 2022 Nat Commun, the authors report increased expression of Tie1 and Tek transcripts in atrial endocardial cells compared to ventricular cells at embryonic day (E) 14.5. Loss of Tie1 leads to early atrial trabeculation defects detectable at E12.5, whereas ventricular defects appear later and are less pronounced at E14.5. Chamber-specific RNA sequencing reveals stronger transcriptional changes in atrial tissue.

      Conditional deletion of Tek results in a similar phenotype, with more pronounced atrial defects. Combined deletion of Tie1 and Tek (Tie1 ΔICD/ΔICD; Tek+/-) leads to earlier and more severe defects in both atrial and ventricular trabeculation and results in embryonic lethality around E12.5, suggesting a synergistic interaction between the two genes.

      Conditional endothelial deletion of Tie1 combined with heterozygous global Tek at later embryonic stages allows analysis at later time points and again shows more severe defects in atrial trabeculation. Postnatal analysis of this model reveals reduced heart-to-body weight ratios and potential mild atrial abnormalities.

      Strengths:

      (1) The authors address chamber-specific signaling mechanisms underlying atrial versus ventricular trabeculation, an area of high developmental and clinical relevance.

      (2) The study provides a comprehensive temporal analysis across multiple embryonic stages.

      (3) The use of multiple genetic models strengthens the overall conclusions and allows comparative interpretation.

      (4) While focusing on trabeculation, the authors also include observations on coronary vessel development, increasing the broader relevance of the work. The findings are therefore of interest to the wider cardiovascular research community.

      Weaknesses:

      (1) Timing of recombination vs. trabeculation onset

      Ventricular trabeculation begins earlier than atrial trabeculation. Since tamoxifen (in contrast to 4-hydroxytamoxifen) requires metabolic activation, Cre-mediated recombination will occur with a delay. This suggests that atrial trabeculation may be targeted before its onset, whereas ventricular trabeculation may already be underway for 2-3 days at the time of effective gene deletion.

      How do the authors account for this discrepancy in their interpretation?

      Have earlier induction time points been tested to better capture the onset of ventricular trabeculation? This limitation should be explicitly discussed.

      (2) Clarity of genetic models and experimental design

      The study employs several genetic constructs. It would improve clarity if, for each experiment, the specific genetic model and tamoxifen regimen were clearly described before presenting the results.

      We thank the reviewer for the detailed and constructive comments. For studies employing the inducible gene deletion mouse models, the genetic models and tamoxifen treatment schemes have been provided in the related figures. For the rest of studies, we used the conventional knockouts targeting Tie1 and Tek (Tie1<sup>tm1a/tm1a</sup>, Tie1<sup>ΔICD/ΔICD</sup> and Tie1<sup>ΔICD/ΔICD</sup>;Tek<sup>+/-</sup>), as detailed above.

      (3) Tie1 tm1a/tm1a phenotype vs. known global knockout

      Previous studies (PMID: 8846781, 7596437) show that complete Tie1 loss leads to severe edema, vascular rupture, and embryonic lethality around E13.5-E14.5.

      How does the Tie1 tm1a/tm1a allele differ, given that animals appear to survive longer? Is this allele hypomorphic rather than a full knockout?

      This point requires clarification.

      Tie1<sup>tm1a/tm1a</sup> is equivalent to the full knockout (Tie1<sup>-/-</sup>). As demonstrated in our prior work, the Tie1<sup>ΔICD/ΔICD</sup> model produced lymphatic and blood vascular phenotypes similar to those of Tie1<sup>-/-</sup> mutants [1, 2, 5, 6].

      (4) Limited mechanistic insight

      While the authors aim to investigate underlying mechanisms, the current study is largely descriptive and based on mRNA expression and genetic interaction analyses (Tie1/Tek co-deletion). Direct mechanistic insights into signaling pathways remain limited. However, the dataset provides a valuable foundation for future mechanistic studies, which should be more clearly acknowledged in the discussion.

      We thank the reviewer for the comments. The manuscript will be revised accordingly, and a detailed response will be provided in our final submission.

      Reference

      (1) Cao, X., et al., Endothelial TIE1 Restricts Angiogenic Sprouting to Coordinate Vein Assembly in Synergy With Its Homologue TIE2. Arterioscler Thromb Vasc Biol, 2023. 43(8): p. e323-e338.

      (2) Shen, B., et al., Genetic dissection of tie pathway in mouse lymphatic maturation and valve development. Arterioscler Thromb Vasc Biol, 2014. 34(6): p. 1221-30.

      (3) Chu, M., et al., Angiopoietin receptor Tie2 is required for vein specification and maintenance via regulating COUP-TFII. Elife, 2016. 5:e21032.

      (4) Rodewald, H.R. and T.N. Sato, Tie1, a receptor tyrosine kinase essential for vascular endothelial cell integrity, is not critical for the development of hematopoietic cells. Oncogene, 1996. 12(2): p. 397-404.

      (5) D'Amico, G., et al., Loss of endothelial Tie1 receptor impairs lymphatic vessel development-brief report. Arterioscler Thromb Vasc Biol, 2010. 30(2): p. 207-9.

      (6) Qu, X., et al., Abnormal embryonic lymphatic vessel development in Tie1 hypomorphic mice. Development, 2010. 137(8): p. 1285-95.

      (7) Dumont, D.J., et al., Dominant-negative and targeted null mutations in the endothelial receptor tyrosine kinase, tek, reveal a critical role in vasculogenesis of the embryo. Genes Dev, 1994. 8(16): p. 1897-909.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      In this review paper, the authors describe the concept of neural correlates of consciousness (NCC) and explain how noninvasive neuroimaging methods fall short of being able to properly characterise an unconfounded NCC. They argue that intracranial research is a means to address this gap and provide a review of many intracranial neuroimaging studies that have sought to answer questions regarding the neural basis of perceptual consciousness.

      Strengths

      The authors have provided an in-depth, timely, and scholarly contribution to the study of NCCs. First and foremost, the review surveys a vast array of literature. The authors synthesise findings such that a coherent narrative of what invasive electrophysiology studies have revealed about the neural basis of consciousness can be easily grasped by the reader. The review is also, to the best of my knowledge, the first review to specifically target intracranial approaches to consciousness and to describe their results in a single article. This is a credit to the authors, as it becomes ever harder to apply strict tests to theories of consciousness using methods such as fMRI and M/EEG it is important to have informative resources describing the results of human intracranial research so that theorists will have to constrain their theories further in accordance with such data. As far as the authors were aiming to provide a complete and coherent overview of intracranial approaches to the study of NCCs, I believe they have achieved their aim.

      We appreciate the reviewer's positive feedback on our work.

      Weaknesses

      Overall, I feel positive about this paper. However, there are a couple of aspects to the manuscript that I think could be improved.

      (1) Distinguishing NCCs from their prerequisites or consequences

      This section in the introduction was particularly confusing to me. Namely, in this section, the authors' aim is to explain how intracranial recordings can help distinguish 'pure' NCCs from their antecedents and consequences. However, the authors almost exclusively describe different tasks (e.g., no-report tasks) that have been used to help solve this problem, rather than elaborating on how intracranial recordings may resolve this issue. The authors claim that no-report designs rely on null findings, and invasive recordings can be more sensitive to smaller effects, which can help in such cases. However, this motivation pertains to the previous sub-section (limits of noninvasive methods), since it is primarily concerned with the lack of temporal and spatial resolution of fMRI and M/EEG. It is not, in and of itself, a means to distinguish NCCs from their confounds.

      As such, in its current formulation, I do not find the argument that intracranial recordings are better suited to identifying pure NCCs (i.e. separating them from pre- or post-processing) convincing. To me, this is a problem solved through novel paradigms and better-developed theories. As it stands, the paper justifies my position by highlighting task developments that help to distinguish NCCs from prerequisites and consequences, rather than giving a novel argument as to why intracranial recordings outperform noninvasive methods beyond the reasons they explained in the previous section. Again, this position is justified when, from lines 505-506, the authors describe how none of the reported single-cell studies were able to dissociate NCCs from post-perceptual processing. As such, it seems as if, even with intracranial recording, NCCs and their confounds cannot be disentangled without appropriate tasks.

      The section 'Towards Better Behavioural Paradigms' is a clear attempt to address these issues and, as such, I am sure the authors share the same concerns as I am raising. Still, I remain unconvinced that the distinguishing of NCCs from pre-/post- processing is a fair motivation for using intracranial over noninvasive measures.

      We agree that distinguishing proper NCCs from their prerequisites or consequences is primarily a matter of experimental design and theoretical framework, not merely of recording modality. We did not mean to imply that intracranial recordings inherently solve this dissociation.This is now explicitly stated that at the beginning of this section. Instead, we argued that the high signal-to-noise ratio and spatiotemporal accuracy of sEEG offer a stronger "testing ground" for the null findings often relied on by no-report paradigms. This is now also further clarified in the revised section “Limits of noninvasive measures”.

      We also explicitly acknowledge, as the reviewer noted, that even the most precise recordings require careful task dissociations to distinguish NCCs from their prerequisites and consequences.

      (2) Drawing misleading conclusions from certain studies

      There are passages of the manuscript where the authors draw conclusions from studies that are not necessarily warranted by the studies they cite. For instance:

      Lines 265 - 271: "The results of these two studies revealed a complex pattern: on the one hand, HGA in the lateral occipitotemporal cortex and the ventral visual cortex correlated with stimulus strength. On the other hand, it also correlated with another factor that does not appear to play a role in visibility (repetition suppression), and did not correlate with a non-sensory factor that affects visibility reports (prior exposure). These results suggest that activity in occipitotemporal cortex regions reflecting higher-order visual processing may be a precursor to the NCC but not an NCC proper."

      It's possible to imagine a theory that would predict HGA could correlate with stimulus strength and repetition suppression, or that it would not correlate with prior exposure (e.g. prior exposure could impact response bias without affecting subjective visibility itself). The authors describe this exact ambiguity in interpretation later in the article (line 664), but in its current form, at least in line 270 (when the study is most extensively discussed), the manuscript heavily implies that HGA is not an NCC proper. This generates a false impression that intracranial recordings have conclusively determined that occipitotemporal HGA is not a pure NCC, which is certainly a premature conclusion.

      We agree that our interpretation of these studies (lines 265–271 of the previous version of the manuscript) was presented too definitively. We have modified the text (now lines 314-317) to soften this conclusion and align it with the more nuanced discussion later in the manuscript. Specifically, we now frame this as a "suggested dissociation" rather than a conclusive finding (line 730), and we explicitly acknowledge that alternative interpretations remain viable.

      Line 243: "Altogether, these early human intracranial studies indicate that early-latency visual processing steps, reflected in broadband and low gamma activity, occur irrespective of whether a stimulus is consciously perceived or not. They also identified a candidate NCC: later (>200 ms) activity in the occipitotemporal region responsible for higher-order visual processing."

      The authors claim in this section that later (>200ms) activity in occipitotemporal regions may be a candidate for an NCC. However, the Fisch et al. (2009) study they describe in support of this conclusion found that early (~150ms) activity could dissociate conscious and unconscious processing. This would suggest that it is early processing that lays claim to perceptual consciousness. The authors explicitly describe the Fisch et al results as showing evidence for early markers of consciousness (line 240: '...exhibited an early...response following recognized vs unrecognised stimuli.) Yet only a few lines later they use this to support the conclusion that a candidate NCC is 'later (>200ms) activity in the occipitotemporal region' (line 245). As such, I am not sure what conclusion the authors want me to make from these studies.

      This problem is repeated in lines 386-387: "Altogether, studies that investigated the cortical correlates of visual consciousness point to a role of neural responses starting ~250 ms after stimulus onset in the non-primary visual cortex and prefrontal cortex."

      This seems to be directly in conflict with the Fisch et al results, which show that correlates of consciousness can begin ~100ms earlier than the authors state in this passage.

      We thank the reviewer for pointing out this inconsistency. We agree that stating ">200 ms" conflicts with the findings of Fisch et al. (2009), who observed dissociations as early as ~150 ms. Our goal was to contrast the very early, stimulus-driven responses with the later responses that reflect consciousness. However, as the reviewer correctly notes, the exact "onset" of these signals varies across studies and paradigms. To address this, we have removed the specific ">200 ms" mentioned in line 245 of the previous version of the manuscript and updated the timing in line 284 to "starting 150 ms" to better reflect the results of Fisch et al. We also clarify that while the exact latency depends on the paradigm, a consistent finding is that activity representing conscious contents in higher-order visual cortex follows an initial wave of unconscious processes (lines 809-810).

      (3) Justifying single-neuron cortical correlates of consciousness

      The purpose of the present manuscript is to highlight why and how intracortical measures of neural activity can help reveal the neural correlates of perceptual consciousness. As such, in the section 'Single-neuron cortical correlates of perceptual consciousness', I think the paper is lacking an argument as to why single-neuron research is useful when searching for the NCC. Most theories of consciousness are based around circuit or system-level analyses (e.g., global ignition, recurrent feedback, prefrontal indexing, etc.) and usually do not make predictions about single cells. Without any elaboration or argument as to why single-cell research is necessary for a science of consciousness, the research described in this section, although excellent and valuable in its own right, seems out of place in the broader discussion of NCCs. A particularly strong interpretation here could be that intracranial recordings mislead researchers into studying single cells simply because it is the finest level of analysis, rather than because it offers helpful insight into the NCCs.

      It is true that many prominent theories of consciousness were developed based on macroscopic observations, largely due to the prevalence of non-invasive recordings in humans. However, we argue that recording single-unit activity is important for several reasons, and we made this clearer in the revised version. First, signals like fMRI, EEG (or even LFP) often conflate multiple distinct neural populations. SUA allows us to dissociate neurons representing the percept from neighboring neurons involved in task-related confounds (e.g., motor preparation or arousal) that would otherwise be blurred together. Therefore, some percepts might be represented by sparse coding involving a small, specific population of "concept" or "percept" cells. Electrophysiological studies in animal models reveal that various cognitive processes are encoded within neuronal subspaces that only emerge when single-unit activity is analyzed as lower-dimensional projections of the broader neural activity manifold (Mante et al., 2013; Ebitz & Hayden, 2021; Jayazeri & Afraz, 2017). Importantly, many neural computations are only discernible through the lens of population dynamics (i.e. with single neuron activity) (Vyas et al., 2021). We believe that providing high granularity through SUA recordings prevents over-aggregation of data, ensuring that even system-level theories can build on biologically accurate foundations.

      Moreover, some theories are defined at the cellular level. For instance, the Dendritic Integration Theory (Bachmann et al., 2020) posits that the integration of feedforward and feedback signals occurs at the level of individual pyramidal neurons. Without SUA, these cellular mechanisms remain untestable. Beyond spatial granularity, SUA also provides excellent temporal granularity, which is crucial for testing theories that rely on the precise timing of spikes (e.g., neural synchrony). As LFPs reflect average activity across populations, only SUA can confirm whether individual neurons lock their spikes to a specific phase, a mechanism hypothesized to bind features into a conscious whole.

      We added these points to a new section in the revised manuscript. References:

      Bachmann, T., Suzuki, M., & Aru, J. (2020). Dendritic integration theory: A thalamo-cortical theory of state and content of consciousness. Philosophy and the Mind Sciences, 1(II).

      Ebitz, R. B., & Hayden, B. Y. (2021). The population doctrine in cognitive neuroscience. Neuron, 109(19), 3055-3068.

      Jazayeri, M., & Afraz, A. (2017). Navigating the neural space in search of the neural code. Neuron, 93(5), 1003-1014.

      Mante, V., Sussillo, D., Shenoy, K. V., & Newsome, W. T. (2013). Context-dependent computation by recurrent dynamics in prefrontal cortex. nature, 503(7474), 78-84.

      Vyas, S., Golub, M. D., Sussillo, D., & Shenoy, K. V. (2020). Computation Through Neural Population Dynamics. Annual Review of Neuroscience, 43(1), 249-275.

      (4) No mention of combined fMRI-EEG research

      A minor point, but I was surprised that the authors did not mention any combined fMRI-EEG research when they were discussing the limits of noninvasive recordings. Intracortical recordings are one way to surpass the spatial and temporal resolution limits of M/EEG and fMRI respectively, but studies that combine fMRI and EEG are also an alternative means to solve this problem: by combining the spatial resolution of fMRI with the temporal resolution of EEG, researchers can - in theory - compare when and where certain activity patterns (be they univariate ERPs or multivariate patterns) arise. The authors do cite one paper (Dellert et al., 2021 JNeuro) that used this kind of setup, but they discuss it only with respect to the task and ignore the recording method. The argument for using intracranial recordings is weaker for not mentioning a viable, noninvasive alternative that resolves the same issues.

      We thank the reviewer for this point. We have added a discussion of fMRI-EEG to the "Limits of noninvasive measures" section (lines 167-171). While we acknowledge that fMRI-EEG is a powerful non-invasive tool for bridging spatial and temporal scales, we note that it relies on merging an indirect metabolic signal with a weak electrophysiological one filtered by the skull, which is computationally complex and often noisy. In contrast, intracranial recordings provide direct measures of both local field potentials and spiking activity within the same neural population, offering interpretability and signal-to-noise ratio that non-invasive combinations cannot match. In our view, this is not just an alternative to these methods, but a unique means of accessing the underlying neuronal ground truth.

      Reviewer #2 (Public review):

      Summary:

      In this work, the authors review the study of the neural correlates of consciousness (NCCs). They discuss several of the difficulties that researchers must face when studying NCCs, and argue that several of these difficulties can be alleviated by using intracranial recordings in humans.

      They describe what constitutes an NCC, and the difficulties to distinguish between an NCC proper from the prerequisites and consequences of conscious processing.

      They also describe the two main types of experimental designs used to study NCCs. These are the contrastive approach (with its report and non-report variants), and the supraliminal approach, each with its own merits and pitfalls.

      They discuss the limitations of non-invasive methods, such as fMRI, EEG and MEG, as well as the limitations of the use of invasive recordings in non-human animals.

      After setting the stage in this way, the authors provide an extensive review of the knowledge acquired by using invasive recordings in humans. This included population-level measurements in vision and in other sensory modalities, as well as single-neuron level studies. The authors also discuss studies of subcortical NCCs.

      The second half of this work discusses the theoretical insights gained through the use of intracranial recordings, as well as their limitations, and a perspective for future work.

      Strengths:

      This work offers an impressive review, which will serve as a useful reference document, both for newcomers to the study of NCC and for experienced researchers. The inclusion of non-visual and subcortical NCCs is of particular merit, as these have been understudied.

      Besides serving as a review, this work includes a perspective, exploring several directions to pursue for the progress of the field.

      We thank the reviewer for acknowledging the strength of our work.

      Weaknesses:

      The intention of the authors is to argue how some of the problems faced when studying NCCs are alleviated by the use of intracranial recordings in humans. But in some cases, the link between the problems related to the study of NCCs and the advantages of intracranial recordings over non-invasive methods is not clear.

      For example, the authors explain the difficulties in distinguishing between true NCCs from their prerequisites and consequences. This constitutes a difficult conceptual problems that plague all recording techniques. The authors don't provide a convincing explanation of how intracranial recordings offer advantages over EEG or MEG when dealing with these problems.

      We agree that the distinction between proper NCCs and their prerequisites or consequences is a fundamental challenge that affects all recording modalities. We did not intend to imply that intracranial recordings are a "silver bullet" for solving this conceptual problem in isolation, and we now explicitly state that at the beginning of this section (line 101).

      We have revised the section on "Distinguishing NCCs from their prerequisites or consequences" to clarify that intracranial recordings are a powerful tool when used in conjunction with appropriate experimental designs, rather than a standalone solution to these conceptual difficulties.

      For example, the authors explain how the use of non-report designs to rule out post-perceptual processing relies on null results, which, according to them, are harder to interpret given the low resolution of non-invasive methods. But the interpretation of null results is actually more complicated in the case of intracranial recordings. As the coverage achieved by the electrodes is sparse, if a null result is attested, it remains possible that a true effect was present in a nearby patch of cortex out of coverage.

      It is true that a null result in an intracranial study may simply reflect that the relevant neural population was not sampled by the specific electrode implantation scheme. However, we argue that interpreting null results is equally, if not more, complicated in non-invasive methods, albeit for different reasons. While M/EEG offers broader coverage, it is blind to many cortical sources because of their orientation (radial sources in MEG) or their location in deep sulci and subcortical structures. The signal-to-noise ratio of M/EEG is also much lower than that of intracranial EEG, making it more likely that null results obscure the existence of subtle effects (Parvizi & Kastner, 2018).

      To address this, we revised the manuscript to clarify that intracranial recordings provide high local certainty within the sampled regions (lines 224-227), whereas non-invasive methods provide broader coverage (lines 247-249). We now explicitly emphasize that drawing conclusions from null results based on intracranial recordings requires caution regarding electrode placement. We also point out that these approaches are complementary: M/EEG can identify large regions of interest, while sEEG can then provide high-resolution "ground truth" to confirm whether those regions are part of the NCC.

      Reference: Parvizi, J., & Kastner, S. (2018). Promises and limitations of human intracranial electroencephalography. Nature Neuroscience, 21(4), 474-483. https://doi.org/10.1038/s41593-018-0108-2

      The authors argue that the spatial resolution of intracranial recordings is better than that of EEG and MEG. While this is technically true (especially compared to EEG), the true spatial scale of the NCCs is unknown. If NCCs' span is in the mm range, then the additional spatial resolution of intracranial recordings might not be an advantage.

      We agree with the reviewer that the exact spatial scale of the NCC remains a topic of ongoing debate. However, we believe that the advantage of intracranial recordings holds true whether the NCC spans millimeters or centimeters. The main spatial limitation of non-invasive electrophysiology (M/EEG) is not just its spatial resolution but also the inverse problem. Since scalp sensors detect a mixture of signals from across the brain, different cortical configurations can produce identical scalp patterns. This makes it challenging to precisely locate the NCC or distinguish it from nearby activity (e.g., motor or attentional signals). When recording intracortically, a widespread NCC could be captured across multiple adjacent channels with high accuracy. Conversely, if the NCC is focal, it can be isolated with high spatial resolution. In either case, intracranial recordings eliminate the spatial ambiguity inherent in scalp recordings. We have revised the Introduction (lines 158-164) to clarify that the "spatial advantage" of intracranial recordings also pertains to the inverse problem, not merely to the ability to record from smaller cortical areas.

      Another factor that should be taken into consideration when assessing the spatial resolution of intracranial recordings is that while the listening zone of individual intracranial contacts is small, coverage is sparse and defined by clinical criteria (something that the authors discuss). In practice, the activity recorded by contacts is usually attributed to anatomically defined ROIs with a scale in the cm range. Given the sparse and uneven (across regions and patients) coverage afforded by intracranial recordings, the advantage of intracranial recordings in terms of spatial resolution is overstated.

      We thank the reviewer for raising this point regarding how intracranial data is often aggregated into regions of interest. We agree that if researchers generalize findings to large anatomical regions without accounting for single-channel recordings, some of the spatial benefits of intracranial recordings are indeed mitigated. We toned down some of the original claims accordingly, and acknowledged more clearly that clinical constraints of sEEG lead to sparse coverage (245-249).

      However, we maintain that even when using an ROI-based approach, intracranial recordings offer a clear advantage over non-invasive methods, in that they represent a direct measure from a specific patch of tissue, rather than a statistical estimate that may be contaminated by "leakage" from distant sources. To address the reviewer’s concern, we have updated the manuscript (lines 244-245) to emphasize the importance of relying on MNI coordinates and individual anatomy rather than solely on broad ROI labels.

      Appraisal of whether the authors achieved their aims:

      In this work, the authors have gathered an impressive review and have discussed several important problems in the field of study of NCCs, as well as provided a perspective on how the field could move forward.

      What is less clear is how the use of intracranial recordings per se holds potential to overcome problems such as the distinction between true NCCs and the prerequisites and consequences of conscious processing.

      Discussion of the likely impact of the work on the field:

      This work has the potential of becoming a must-read for anyone working in the field of consciousness research.

      Reviewer #3 (Public review):

      Summary:

      This narrative review provides a clear, well-structured, and comprehensive synthesis of intracerebral recording work on the neural correlates of consciousness. It is written in an accessible manner that will be useful to a broad community of researchers, from those new to iEEG to specialists in the field.

      Strengths:

      The manuscript successfully integrates methodological and theoretical perspectives and offers a balanced overview of current, sometimes contradicting evidence. As such, the manuscript is important as it calls for a concerted and better exploration of NCCs using iEEG in the future.

      We thank the reviewer for stating the importance of our work and its potential contribution to the field.

      Weaknesses:

      The manuscript extensively discusses the use of "report" as a criterion for identifying conscious perception and its limitations for separating between correlates of consciousness and post-consciousness processes, yet the term is not defined at the outset. The authors should specify what they mean by "report" (e.g., verbal report, nonverbal self-report, or any meta-cognitive indication of experience). Importantly, this definition should be explicitly linked to the theoretical landscape: whether the authors adopt an access-consciousness perspective in which (self) reportability is central, or whether the review also aims to address phenomenal consciousness. Making this conceptual grounding explicit at the beginning will help readers interpret the empirical work surveyed throughout the review.

      We agree that a clear definition of report is essential for the reader to interpret the empirical findings presented. We have added a definition to the Introduction (lines 108-111), specifying that we use "report" to refer to any explicit behavioral response (whether verbal, manual, or otherwise) that communicates a subject’s subjective state.

      Regarding the conceptual distinction between Phenomenal and Access consciousness, we refer to recent work from some of the co-authors (Mudrik et al., 2025), which suggests that P and A should not be seen as two types of consciousness, but rather as two necessary conditions for conscious experience. While a full discussion of this distinction is beyond the scope of this review, we now clearly state that our focus is on identifying neural activity that reflects the subjective experience itself, regardless of the downstream requirements of report.

      Reference: Mudrik, L., Faivre, N., Pitts, M., & Schurger, A. (2025). On a confusion about there being two types of consciousness. Trends in Cognitive Sciences. https://doi.org/10.1016/j.tics.2025.11.012

      In addition, the review would benefit from an earlier introduction of the distinction between states and contents of consciousness. This distinction becomes important in the later section on anaesthesia, sleep, and epileptic seizures, where the focus shifts from content-specific NCCs to alterations in global states. Presenting these definitions upfront and briefly explaining how states and contents interact would strengthen the coherence of the manuscript.

      We agree that clarifying the distinction between contents and levels of consciousness early on provides a stronger framework for the paper.

      We have added a brief clarification in the Introduction (lines 63-76): "It is also helpful to distinguish between levels of consciousness, defined as a global level of arousal or wakefulness (e.g., being awake vs. under anesthesia), and the contents of consciousness, defined as the specific subjective experiences one has while conscious (e.g., perceiving a visual stimulus; Bayne et al., 2016; Laureys, 2005). While the majority of this review focuses on 'content-specific' NCCs, the two dimensions are intrinsically linked, as global states typically set the conditions for the occurrence of specific conscious contents."

      Overall, this is an excellent and timely review. With clearer initial theoretical definitions of consciousness, the manuscript will offer an even stronger conceptual framework for interpreting intracerebral studies of consciousness.

      We thank the reviewer again for this highly positive assessment of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I would like to reiterate that I believe this is a very scholarly piece of writing, and I congratulate the authors on producing such a useful and timely manuscript. Below, I suggest just a few ways the authors may resolve some of the issues I raised in the public review. However, I would like to emphasise that these are merely suggestions - the authors may think of different and better ways to address these comments that are more in line with either their thinking or writing style, and I would certainly encourage the authors to follow their own preferences if they feel they are at odds with my suggestions.

      For the longer comment questioning whether intracranial recordings are really a way to isolate NCCs from their pre- and post-processing, there are two ways the authors could resolve this. One is that they collapse the section distinguishing NCCs from their prerequisites and consequences into the previous section regarding limits of noninvasive measures. For instance, they could make the point that null results are easier to interpret with intracranial recordings in this previous section. Then they could discuss how specific intracranial studies have been able to resolve questions of pre-/post- processing confounds when they introduce studies later in the manuscript. At the moment, the Distinguishing NCCs from their prerequisites and consequences section, at least to me, undermines the argument of why intracranial recordings are important because it spends too much time describing how tasks are the core component of isolating pure NCCs, and not the recording method.

      Alternatively, the authors could keep the structure as it is. In this case, I would urge the authors to emphasise the role of intracortical recordings here and to make the argument that this is a problem that intracortical recordings (rather than novel tasks) can solve more convincingly. Citing specific studies that combined intracortical recordings with no-report paradigms and emphasising how the invasive recording allowed the researchers to reach a conclusion that would not have been possible with noninvasive measures would also be helpful.

      We thank the reviewer for these useful suggestions and agree that we would not want readers to take from this paper that design issues can be fixed by using invasive recordings. Because confounding issues are crucial in research on the NCC, we believe it is important to include a section on this topic in the Introduction. However, as we explained in our response to the public review, we revised the section introducing Human intracranial electrophysiology to reflect that intracranial recordings are a complementary tool that improves the interpretability of no-report paradigms, rather than a “silver bullet” solution for confound issues. We also explicitly say now that this problem is relevant to all techniques in the study of consciousness, including intracranial recordings (line 101). Additionally, based on the reviewer’s suggestion, we have added a more detailed explanation of how studies that pair intracranial recordings with no-report paradigms provide a unique insight in the Temporal Insights section (lines 822-823).

      For my comment: Drawing misleading conclusions from certain studies, I think the public review speaks for itself. I would recommend that the authors make sure they are drawing correct conclusions from the studies they cite, and make clear from the outset where there is ambiguity in interpretation.

      We thank the reviewer for bringing these ambiguities to our attention. As explained in the response to the public review, we have modified the text accordingly.

      Finally, with regard to the single-cell analyses, I would imagine that most readers will share at least some scepticism around single neurons being the appropriate level of analysis for revealing the basis of perceptual experience. As such, I think it would strengthen the manuscript greatly if the authors could provide a brief argument as to how such work can either inform theories of consciousness or contribute more generally to the study of NCCs, given that the field and its theories are mostly biased towards studying system-level neural processes. I think single-cell analyses are extremely valuable to NCC research, and the authors have a good opportunity to frame these studies accordingly.

      We agree. As detailed in the response to the public review, we now specify (1) how a higher level of granularity in electrophysiological measurements can distinguish between awareness-related signals and confounds, (2) that these measurements provide an opportunity to study neuronal population dynamics where various cognitive processes have been shown to emerge in animals and (3) that single-neuron measurements are necessary to test predictions of theories that are defined at the cellular level

      Reviewer #2 (Recommendations for the authors):

      Recommendations for improving the writing and presentation:

      My compliments for having written an impressive review. Overall, I think that this is a beautiful piece of work that will be of great use to the community. My only concern is that the advantages of intracranial recordings over non-invasive methods in solving the difficulties faced in the study of NCCs are overstated.

      Here I provide more precise comments for your consideration.

      (1) On page 5, lines 100 to 102, you argue that "Scalp EEG and MEG have limitedanatomical resolution due to the overlap of deep and superficial brain signals at the scalp level and, in the case of EEG, the scattering of the adjacent electrical signals through the scalp". It would be good to provide precise estimates of the spatial resolutions of EEG, MEG and intracranial recordings, with accompanying references. Consider also that MEG is relatively insensitive to deep sources. I recommend this paper: Piastra et al. 2020 https://onlinelibrary.wiley.com/doi/10.1002/hbm.25272

      We thank the reviewer once again for their positive evaluation of our work. As detailed in the response to the public reviews, we now clarify that intracranial recordings provide high local certainty within the sampled regions (lines 224-227), whereas non-invasive methods provide broader coverage (lines 247-249). We thank the reviewer for their additional suggestions and have clarified our concern about the anatomical conclusions that can be drawn from scalp EEG and MEG data (lines 158-164).

      (2) On page 11, you describe work showing that activity in the occipitotemporal cortex mightreflect a precursor to consciousness, but not an NCC proper, except for the case of faces, in which the fusiform seems to behave like a true NCC. Could you discuss how these seemingly contradictory results could be reconciled?

      One possibility is that activity in some parts of the occipitotemporal cortex instantiates content-specific NCCs, i.e., correlates that are only specific to certain stimulus types (in this case: faces), while activity in other parts instantiates precursors of the NCCs. Because faces have been extensively studied, we might have uncovered the content-specific NCCs for these stimuli but not for others. This is now discussed in the text on lines 342-344. Based on reviewer 1’s suggestion, we have also toned down our claim about occipitotemporal activity being a precursor to the NCC.

      (3) From line 322, you start to discuss connectivity analyses. Adding a subheading mightimprove readability.

      We appreciate the suggestion; however, adding a subheading to a single paragraph would require restructuring the entire section, which could disrupt the flow. We believe the current format maintains clarity and cohesion.

      (4) In line 329, you write "It remains unclear to what extent these connectivity patterns reflectpost-perceptual processing and how the signals associated with perceptual consciousness in the occipitotemporal cortex interact with frontoparietal regions." But it's not clear why this is the case.

      We meant to make two separate points: (1) these studies did not control for report-related activity using no-report paradigms and (2) there has been no investigation so far of the interaction between occipitotemporal and frontoparietal signals associated with perceptual consciousness. These two points have been clarified in the text (lines 378-381).

      (5) In line 692, it would be good to clarify that Pereira 2021 is a single-neuron study.

      This has been clarified in the text.

      (6) The phrase "more research/work is needed" is repeated several times.

      Thank you for pointing this out. To avoid redundancy, we have deleted the second mention of this phrase.

    1. Author response:

      The following is the authors’ response to the previous reviews

      eLife Assessment

      This important work begins to understand how BDNF regulates the phosphorylation and activity of LRRK2. The overall strength of evidence has been assessed as compelling, though some claims are only partially supported. The work will be of interest for those that might pursue specific LRRK2 interactions and mutational effects on these pathways as the work continues to develop.

      We thank the editors and reviewers for the constructive feedback. We have revised the manuscript to improve clarity, strengthen statistical analysis and increase the western blot sample size in drebrin KO mice.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      LRRK2 protein is familially linked to Parkinson's disease by the presence of several gene variants that all confer a gain-of-function effect on LRRK2 kinase activity.

      The authors examine the effects of BDNF stimulation in immortalized neuron-like cells, cultured mouse primary neurons, hIPSC-derived neurons, and brain tissue from genetically modified mice. They examine a LRRK2 regulatory phosphorylation residue, LRRK2 binding relationships, and measures of synaptic structure and function.

      Strengths:

      The study addresses an important research question: how does a PD-linked protein interact with other proteins, and contribute to responses to a well-characterized neuronal signalling pathway involved in the regulation of synaptic function and cell health.

      They employ a range of good models and techniques to fairly convincingly demonstrate that BDNF stimulation alters LRRK2 phosphorylation and binding to many proteins. In this revised manuscript, aspects are well validated e.g., drebrin binding, but there is a disconnect between these findings and alterations to LRRK2 substrates. A convincing phosphoproteomic analysis of PD mutant Knock-in mouse brain is included. Overall the links between LRRK2, LRRK2 activity, and the changes to synaptic molecules, structures, and activity are intriguing.

      We thank this Reviewer for appreciating our work including the new experiments performed during the revisions.

      Weaknesses:

      The data sets remain disjointed, conclusions are sweeping, and not always in line with what the data is showing. Validation of 'omics' data is light. Some inconsistencies with the major conclusions are ignored. Several of the assays employed (western blotting especially) are underpowered, findings key to their interpretation are addressed in only one or other of the several models employed, and supporting observations are lacking.

      We understand the Reviewer’s points and agree that it is important to increase the sample size (animals) for western blot. In particular, we acknowledge that the initial experiments with the Dbn1 KO mice included only 3 mice, which was insufficient to draw any definitive conclusion on the effect, especially regarding pRab8 levels. In response to this, we have collected additional animals and repeated the experiment with N=7 wild-type and N=7 KO mice (2 months old). Despite a high degree of interindividual variability, we have confirmed that drebin KO mouse brains have reduced levels of pLRRK2 (Author response image 1). In the new figure 2H we included all the replicates (N=7+3 per genotype) for pLRRK2. However, we removed western blot for pRab8 because a new batch of pRab8 antibody did not yield specific results, making it impossible to reassess.

      Author response image 1.

      Western blot analysis of N=7 WT and N=7 drebrin KO whole brains.

      Main Conclusions of Abstract:

      (1) Increase in pLRRK2 Ser935 and pRAB after BDNF in SH-SY5Y & mouse neurons

      Well supported, but only for pLRRK2 in neurons, why not pERK pAkt & pRab?

      The response of pERK and pAKT in neurons is shown in figure 4C. We have repeatedly tried pRab (both pRab8 and pRab10) in primary neurons but with no success. In support of the difficulty in detecting pRab in primary neurons, we are not aware of studies in the literature of western blot analysis of pRabs in primary neuronal cultures. This is likely due to the high levels of PPM1H in neurons as discussed in Berndsen et at, eLife, 2019 (PMID: 31663853).

      (2) Omics Proteome remodelling of LRRK2 interactome with BDNF & different in G2019S mouse neurons.

      Supports that the phosphoproteome of G2019S is different. Drebrin interaction with LRRK2 very well supported. Link between drebrin and LRRK2 activity somewhat supported (pS935 site), but the consequence (non-specific pRab8) not supported, as there is no evidence of a change in LRRK2 substrate(s).

      As discussed above, we removed the pRab8 western blot in figure 2H as we could not confirm with the new set of mice and a new batch of pRab8 antibody.

      (3) Golgi 1 month LKO mouse altered dendritic spines, transient at 1m not older.

      Supported but very small transient change in spines, disconnected to other results (e.g., drebrin).

      We agree with the Reviewer that the observed effect is modest, still we believe it is important to report. As discussed in the discussion, one plausible explanation for the limited magnitude of the effect is functional compensation by LRRK1.

      (4) iPSC-derived neurons BDNF increases mEPSC frequency (transient at 70 not 50 or 90 days) in WT not KO "which appear to bypass this regulation through developmental compensation"

      Weak, not clear what is being bypassed.

      We reviewed the statistical analysis as described below.

      Main Conclusions Based on Old and New Figure / Data:

      (1) Increase in pLRRK2 Ser935 and pRAB after BDNF in SH-SY5Y & mouse neurons

      Well supported, but only for pLRRK2 in neurons, why not ERK Akt & Rab?

      The response of pERK and pAKT in neurons is shown in figure 4C. We have repeatedly tried pRab (both pRab8 and pRab10) in primary neurons but with no success. In support of the difficulty in detecting pRab in primary neurons, we are not aware of studies in the literature of western blot analysis of pRabs in primary neuronal cultures. This is likely due to the high levels of PPM1H in neurons as discussed in Berndsen et at, eLife, 2019 (PMID: 31663853).

      (2) BDNF promotes LRRK2 interaction with "post-synaptic actin cytoskeleton components"

      Tone down, only one postsynaptic validated - drebrin strong BUT CONTRADICTORY; link between drebrin and LRRK2 activity (pS935 site) supported, consequence (non-specific pRab8) broken, no evidence of change in LRRK2 substrate.

      As suggested we tone down the paragraph title and changed it as follow: “BDNF stimulates LRRK2 interaction with drebrin, an actin cytoskeletal-associated protein enriched at the postsynapse”. As mentioned above, pRab8 has not been incorporated.

      (3) LRRK2 G2019S striatal phosphoproteome is different from WT.

      It is different. Where is link to BDNF or Drebrin?

      We found that debrin S339 phosphorylation is 3.7 fold higher in G2019S KI mice as compared to WT, suggesting a potential functional connection between LRRK2 and drebrin. However, differences in phosphorylation do not necessarily translate into physiological effects so further validation is required. To test if BDNF can induce S339 drebrin phosphorylation in a LRRK2-dependent manner we plan an in vivo experiment where BDNF is acutely administered to WT vs G2019S-KI mice +/- MLi2 to control for LRRK2 dependency. This is an important experiment to establish the mechanistic link, though it will require sufficient time due to the necessary ethical authorization needed to administer BDNF in the mouse brain.

      (4) BDNF signaling is impaired in Lrrk2 knockout neurons

      TrkB changes seem higher in SHSY5Y. pAKT impaired, pERK not convincing. Primary neurons Akt slower but it and Erk mostly intact. MLi-2 did not block pAkt or pErk in WT or KO (higher in latter). Whatever is happening in KO, Mli-2 not really blocking effect in WT. If we are to assume that studying the KO was a means to understand LRRK2 function, the authors data should explain why we care if an effect is absent in LKO, if LRRK2 isn't doing the same job in WT?

      To further support the conclusion that this effect is reproducible and dependent on LRRK2 kinase activity acting upstream of AKT and ERK signaling, we probed the membranes shown in Figure 1H for phosphorylated and total AKT and ERK1/2. Consistent with our hypothesis, the inhibition of LRRK2 with MLi-2 significantly reduced BDNF-induced AKT and ERK1/2 phosphorylation (Author response image 2).

      Author response image 2.

      Western blot (same experiments as in figure 1) was performed using antibodies against phosphoThr202/185 ERK1/2, total ERK1/2 and phospho-Ser473 AKT, total AKT protein levels. Retinoic acid-differentiated SH-SY5Y cells stimulated with 100 ng/mL BDNF for 0, 5, 30, 60 mins. MLi-2 was used at 500 nM for 90 mins to inhibit LRRK2 kinase activity.

      BDNF increases synaptic puncta in WT not LKO (which start higher?). Is this BDNF increase blocked by LRRK2 inhibition?

      This is an important experiment that we plan to investigate in a future study.

      (5) Postsynaptic structural changes in Lrrk2 knockout neurons

      Golgi impregnation shows some very small spine changes at 1m. Not sustained over age. mRNA changes are very small (10% not even a fold... very weak and should be written as so). Derbrin levels reduced clearly at 1m, but probably also at 4 & 18. Underpowered, disconnected time course from the spine changes.

      While differences are small they have been observed in independent sets of mice through qPCR, histology, WB and TEM, supporting the consistency of the effect, although small. For clarity we rescaled the qPCR graphs to 0.

      (6) An effect on "spontaneous electrical activity" at Div70

      Weak. What is so special at 70 days that means we should be confident in the differences, or be satisfied that the other time points are legitimately ignored? These are 10-11 cells from 3 cultures assayed at 3 time points but only one is presented (rest in supplement). This should be a 2 (time) or 3 way (+culture RM) ANOVA. As it stands, in WT there is a little - no activity at 50 days, little to no at 70 days, and variable to lots or none at 90. BDNF did nothing at 50 or 90 but may have at 70. In KO low activity stable at 50 & 70, tanks at 90. BDNF would seem to have a similar effect on KO at 90 as WT at 70, but as there are only 7 cells it remains inconclusive. Thus the conclusion that BDNF signalling is broken in LKO is not well supported by the ephys data, nor is the BDNF effect in WT cells (even at the 70 day time point) shown to be susceptible to LRRK2 inhibition.

      We thank the Reviewer for suggesting a more comprehensive analysis of the data. Following this suggestion, we performed separate two-way ANOVAs (DIV × treatment) for WT and LRRK2 KO neurons. This analysis revealed significant main effects of DIV and BDNF treatment in WT neurons, indicating that synaptic activity increases with neuronal maturation and is globally enhanced by BDNF. In contrast, neither DIV nor BDNF treatment reached statistical significance in LRRK2KO neurons, and no DIV × treatment interaction was observed. These results indicate that BDNFdependent enhancement of synaptic activity is preserved in WT neurons but is lost in the absence of LRRK2. We have now incorporated this analysis into the main figure and removed the individual DIV50 and DIV90 plots from the supplementary material. We also revised the title of the last paragraph to reflect the outcome of this analysis and toned down our interpretation (page 12).

      Furthermore, we have added a paragraph to the Discussion section highlighting the limitations of this study. These include the variability observed in protein content and phosphorylation analyses by western blot, as well as the necessity to confirm the electrophysiological findings in larger datasets, including in dopaminergic neurons.

      Reviewer #2 (Public review):

      The data show that BDNF regulates the PD-associated kinase LRRK2, they place LRRK2 within welldescribed BDNF pathways biochemically, and they show that LRRK2 can play a role mediating BDNFdriven synaptic outcomes at excitatory synapses. The chief strength is that the data provide a potential focal point for multiple observations that have been made across many labs. The findings will be of broad interest because LRRK2 has emerged as a protein that is likely to be part of Parkinson's pathology and its normal and pathological actions remain poorly understood.

      We thank this Reviewer for appreciating our work and acknowledging that our findings will be of broad interest.

      A major strength of the study is the multiple approaches that were used (biochemistry, bioinformatics, light and electron microscopy and electrophysiology) across different experimental models (cells, primary neurons, human neurons, mice) to identify and examine the impact of BDNF on LRRK2 signaling and functions. Noteworthy is also the employment of LRRK2KO preparations to validate outcomes and to place LRRK2 actions up or downstream.

      Thank you to the Reviewer

      The demonstration that LRRK2 and drebrin interact directly is important and suggests that other interacting proteins identified biochemically and bioinformatically in the paper will be important to pursue.

      We agree with this statement

      Some data from different models do not fit well with one another (like mouse and human neurons). This is likely due to inherent differences in the preparations. Since different experiments were carried out on the different preps, however, it is not possible to cross compare. The lack of this information is viewed more as an open question than a cause for concern.

      We thank the Reviewer for raising this point. In response, we have added a new section to the Discussion explicitly addressing the limitations of the study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      MLi2 pretreatment experiment is nice. They state in legends BDNF treatment prior to MLi2, they mean prior MLI2 treatment. Or MLi2 pretreatment, prior to BDNF. However, this experiment is hard to interpret as it has no control (non BDNF treated) time course following MLi2, could this be (at least in part) a rebound effect produced by relief of inhibition? This should be discussed if not addressed directly by experiments.

      The non BDNF treated group represents the 0 time point. We have specified it in the figure legend. We have excluded the rephosphorylation kinetic after MLi-2 relief because pRabs increase significantly at 5 minutes, far exceeding the control levels. This observation gives us feel confidence that the effect if BDNF dependent.

      (1) "As suggested, we performed qPCR and observed that 1 month-old KO midbrain and cortex express lower levels of Dbn1 as compared to WT brains (Figure 5G). This result is in agreement with the western blot data (Figure 5H)."

      There is no Fig 5H? 5F? In 5F effect sizes are exaggerated with axes not crossing zero. There is a 10% reduction in mRNA (normally >1 or 2 fold changes would be considered biologically important?). This isn't much change, and should be presented as such. 1 month old WB in G are much more convincing of a reduction of drebrin levels, but what brain region is this from?

      We apologize for the error in the rebuttal, where we incorrectly referred to figure 5G (the correct is 5F), while what we called 5H is instead 5G. We checked the labeling in the manuscript text and it is correct.

      Following the Reviewer’s important suggestion, we rescaled all plots to start at zero. Although some differences appear relatively modest, they are statistically significant. Importantly, all brains used for qPCR analyses (N = 6 per genotype) were obtained from independent mice. In addition, independent cohorts of mice were used for spine morphology analyses (N = 3 per genotype), TEM analyses (N = 4), and western blot experiments (N = 3). Thus, the overall sample size across approaches is substantial.

      WB are from whole brain, now indicated in the figure legend.

      All blots are underpowered, especially given what appears to be an age dependent loss of drebrin in both genotypes beset by high variability

      (i) Western blots looking at pSer935 and pRab8 (pan Rab) in Dbn1 WT and knockout brains.

      "As reported and quantified in Figure 2I, we observed a significant decrease in pSer935 and a trend decrease in pRab8 in Dbn1 KO brains. This finding supports the notion that Drebrin forms a complex with LRRK2 that is important for its activity, e.g. upon BDNF stimulation."

      Non-sig data in Fig2I/H and especially Fig5G are important data but hard to interpret because the experiment is underpowered. I am surprised the authors designed studies on an n=3 western blot.

      For fig 2 this is a problem if they wish to correlate LRRK2 activity with drebrin. The KO have a clear 50% decrease in LRRK2 pS935 but no change to pRab8(pan).

      As discussed above, we increased the sample size by 7 additional mice per genotype (total of 10 brains analyzed).

      Why not look at Rab10, and certainly redo with a higher n than three. Of special confusion is the observation that the WT with the highest drebrin levels, is the animal with the lowest pS935 & pRab

      As discussed above neither pRab8 nor pRab10 returned convincing results in the new round of western blots. We acknowledge that future experiments should explore the phosphorylation levels of Rab12 which is emerging as a more reliable readout of LRRK2 kinase activity in the brain.

      (ii) "Reverse co-immunoprecipitation of YFP-drebrin full-length, N-terminal domain (1-256 aa) and Cterminal domain (256-649 aa) (plasmids kindly received from Professor Phillip R. Gordon-Weeks, Worth et al., J Cell Biol, 2013) with Flag-LRRK2 co-expressed in HEK293T cells. As shown in supplementary Fig. S2C, we confirm that YFP-drebrin binds LRRK2, with the N terminal region of drebrin appearing to be the major contributor to this interaction"

      CoIP with drebrin (and fragments) is very convincing.

      We thank the Reviewer for his/her comment/feedback

      Ephys data, presentation, and response to review is weak.

      We reanalyzed the data as suggested by the Reviewer and reviewed the text and interpretation.

      Reviewer #2 (Recommendations for the authors):

      p. 12, last paragraph. "sealing" should be "ceiling"

      We corrected the misspelled word

    1. Author response:

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

      eLife Assessment

      This important study sought to investigate the role that early childhood malaria exposure plays in the development of antibody responses to unrelated pathogens and vaccine-derived antigens in Kenyan children. In this natural experiment, the authors compare antibody levels among children who have been exposed to different levels of malaria transmission by using protein microarray technology. Although the findings are of importance, the evidence remains incomplete, and the analysis would benefit from a more in-depth evaluation of potential confounders. With the appropriate analysis, the findings will be of great interest for global health, immunology, and vaccine development.

      We thank the editors for highlighting the need for a more comprehensive evaluation of potential confounding. We agree that this is a critical aspect of the study and have now undertaken additional analyses to address this directly.

      The original longitudinal cohort was designed to investigate the acquisition of naturally acquired immunity to malaria and did not include systematic collection of anthropometric/nutritional, environmental or socioeconomic data, precluding direct adjustment for these factors within the primary dataset. However, to assess whether there were population-level differences in these factors, we leveraged contemporaneous hospital-based surveillance data from the same geographic regions, which includes measurements of anthropometry and nutritional status (muac, weight-for-age, and height-for-age) and detailed infection diagnostics.

      Using this independent dataset, we fitted mixed-effects regression models adjusting for age, calendar year, and concurrent infections (RSV, parainfluenza, influenza A, human metapneumovirus, OC43). For all three anthropometric indices, we found no evidence of systematic differences between children from Junju and Ngerenya. Adjusted differences were small and centred around zero (muac: −0.12, 95% CI −0.38 to 0.15, weight-for-age: −0.05, −0.28 to 0.19, height-for-age: 0.08, −0.17 to 0.33), with no consistent directional effect.

      As the longitudinal cohort was randomly selected from these underlying populations, these findings suggest that the groups were broadly comparable with respect to nutritional status and there were no differences in their exposure to the infections that were included in the analysis. We have incorporated these analyses into the revised manuscript, added a new figure focussed on this analysis -fig. 6, updated the statistical analysis and discussion sections), and believe they substantially strengthen the evidence by addressing a key source of potential confounding.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study shows that childhood malaria can weaken the antibody response to other vaccines and infections. This suggests that early exposure to P. falciparum may have a long-lasting effect on immunity, with implications for vaccine efficacy in endemic areas.

      Strengths:

      This study stands out for its longitudinal design, the use of robust immunological techniques, and the comparison between areas with different levels of malaria exposure. Its findings reveal that early malaria can weaken the response to childhood vaccines, with important implications for public health in endemic regions.

      We thank the reviewer for this comment

      Weaknesses:

      One of the study's main limitations is the lack of functional data confirming the clinical impact of the low antibody levels. Furthermore, although multiple immune responses were measured, other important components, such as cellular immunity, were not assessed. Furthermore, the results may not be generalizable to other regions.

      We thank the reviewer for this important comment and agree that the absence of functional immunological assays is a limitation of the current study. Our analysis was designed to determine whether early-life malaria exposure is associated with durable alterations in antibody responses to unrelated pathogens and vaccine antigens, rather than to establish the downstream functional consequences of these differences. As such, the study is able to demonstrate a broad and persistent attenuation of humoral responses but cannot directly determine whether the lower antibody levels observed translate into reduced neutralising capacity or diminished protection at the individual level.

      We have revised the manuscript to make this distinction more explicit. In the revised discussion, we now state that although reduced antibody titres to vaccine-preventable pathogens may have implications for long-term protection, the clinical significance of these differences remains to be established in future studies incorporating functional assays and clinical outcome data.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated whether early-life malaria exposure has long-term effects on immune responses to unrelated antigens. They leveraged a natural experiment in coastal Kenya where two adjacent communities (Junju and Ngerenya) experienced divergent malaria transmission patterns after 2004. Using 15 years of longitudinal data from 123 children with weekly malaria surveillance and annual serological sampling, they measured antibody responses to multiple pathogens using a protein microarray technology and ELISA.

      Strengths:

      (1) Extensive longitudinal data collection with weekly malaria surveillance, enabling precise exposure classification.

      (2) Use of a natural experiment design that allows for causal inference about malaria's immunological effects.

      (3) Broad panel of antigens tested, demonstrating generalized rather than antigen-specific effects.

      (4) Within-cohort analysis in Ngerenya controls for geographic and environmental factors.

      (5) Validation of key findings using both serologic microarray and ELISA.

      (6) Important public health implications for vaccine strategies in malaria-endemic regions.

      We thank the reviewer for these comments

      Weaknesses:

      (1) Lack of participants' characteristics (socio-economic, nutritional, physical).

      We thank the reviewer for this important comment. We have now included a detailed summary of participant characteristics in Table 1to provide context for the study population. This includes key demographic and longitudinal variables stratified by cohort (Junju and Ngerenya), including sex distribution, age at study entry and exit, duration of follow-up, number of visits per participant, and total serum samples analysed. Detailed data on socio-economic status, nutritional status, and other environmental or physical characteristics were not consistently available across all participants and time points, and therefore could not be included. This has now been explicitly stated as a limitation in the discussion.

      (2) Somewhat limited sample size (longitudinal analysis of 123 children total), with further subdivision reducing statistical power for some analyses.

      We thank the reviewer for this important observation. The study is based on an intensively followed cohort with weekly malaria surveillance and repeated serological measurements throughout childhood, allowing detailed characterisation of early-life exposure and subsequent immune trajectories. This depth of longitudinal sampling provides resolution that is not achievable in larger cross-sectional studies. We acknowledge that subdivision of the cohort reduces statistical power for some analyses. Nevertheless, the key findings were consistent in several independent comparisons, including a reduction in antibody levels for broad panel of antigens in the malaria endemic setting, within-cohort analyses in Ngerenya that replicated this observation, and the confirmation of results generated on the protein microarray on the ELISA platform. The consistency of these findings across analytical approaches and measurement platforms reduces the likelihood that the observed effects are driven by small-sample variability. We have clarified this point in the revised discussion to emphasise that the strength of the study lies in the depth and longitudinal resolution of the data rather than the absolute sample size.

      (3) Potential confounding by unmeasured socioeconomic, nutritional, or environmental factors between communities.

      We thank the reviewer for this important point and agree that residual confounding between communities must be considered. As outlined in reponse to the editorial assesment, we have undertaken additional analyses using contemporaneous population-level data from the same regions and found no evidence of systematic differences in anthropometric indices between children from Junju and Ngerenya after accounting for age, calendar year, and concurrent infections, with effect estimates small and crossing zer. In addition, the within-Ngerenya analysis provides an internal comparison within a shared geographic and environmental setting, reducing the likelihood that unmeasured socioeconomic or environmental differences between communities account for the observed associations. The new analyses suggest that major population-level differences in nutritional status or infection burden are unlikely to explain the observed patterns. We have clarified this point in the revised discussion and explicitly acknowledge the possibility of residual confounding.

      (4) Lack of ability to determine the direction of the associations found between malaria exposure and other IgG levels to unrelated pathogens.

      We agree that, as an observational study, our analysis cannot definitively establish the direction of the association between malaria exposure and antibody responses to unrelated antigens. However, several features of the study design strengthen the inference that early-life malaria exposure contributes to the observed differences. First, malaria exposure was characterised prospectively through intensive weekly surveillance, allowing precise temporal definition of exposure in early childhood. Second, within the Ngerenya cohort, where children were exposed to different levels of malaria due to a rapid decline in transmission, those with even limited early-life exposure exhibited lower antibody responses at 10 years of age than malaria-naïve peers, despite residing in the same geographic and environmental context. In addition, we now show that these differences are not confined to a single timepoint but are evident across the full longitudinal follow-up after adjustment for age and repeated measurements. While we cannot exclude the possibility of residual confounding or bidirectional relationships, the convergence of evidence from the natural experiment design, within-cohort contrasts, and age-adjusted longitudinal analyses supports early-life malaria exposure as a key contributor to long-term differences in antibody responses. We have clarified this in the discussion.

      (5) Despite good longitudinal data, the main analysis was conducted as a cross-sectional analysis at age 10 for many comparisons, which limits the understanding of temporal dynamics.

      We thank the reviewer for highlighting this point. While age 10 was initially used as a standardised reference point for cross-sectional comparisons, the underlying dataset is longitudinal, with repeated antibody measurements across childhood. To address this more directly, we have now complemented these analyses with antigen-specific mixed-effects regression models incorporating all available longitudinal data, with adjustment for age and a random intercept for repeated measurements within individuals. These models demonstrate that the differences between cohorts are not confined to the age-10 cross-section but are evident in an age-adjusted longitudinal framework for multiple antigens. We have retained the age-10 comparisons for reference, but the primary inference is now based on the longitudinal mixed-effects analyses. These changes are reflected in the revised results and statistical analysis sections. We thank the reviewer for this astute point, which we think has substantially improved the manuscript.

      (6) Statistical analysis is limited to univariable comparisons without consideration for confounders or adjusting for multiple comparisons.

      We agree that the original analyses relied primarily on univariable comparisons. In the revised manuscript, we have extended the analytical framework to include mixed-effects regression models that account for age effects and repeated measurements within individuals. These models estimate the average age-adjusted difference in antibody responses between cohorts across the full follow-up period. We have also applied false discovery rate (FDR) correction to account for multiple antigen testing. For multiple antigens, the direction and magnitude of cohort differences remain consistent under this approach, strengthening the robustness of the findings beyond the original univariable comparisons. These analyses have been incorporated into the revised results and statistical analysis sections.

      (7) No mechanistic understanding of how early malaria exposure creates lasting immunosuppression.

      We agree that this study does not directly resolve the mechanistic basis underlying the observed long-term differences in antibody responses. The primary aim of this work was to identify and characterise durable alterations in humoral immune profiles associated with early-life malaria exposure, rather than to define the cellular or molecular pathways involved. However, our findings are consistent with a growing body of experimental and clinical literature suggesting that malaria infection can induce sustained perturbations in B cell and T cell compartments, including the expansion of atypical memory B cells, altered germinal centre responses, and increased regulatory immune activity. These mechanisms have been proposed to impair the generation and maintenance of effective humoral immunity. In the revised discussion, we have clarified that the mechanistic basis of this phenomenon remains to be fully defined and have expanded the discussion of plausible pathways in light of existing literature. We now explicitly position our findings as providing population-level evidence of a durable immunological phenotype that warrants further mechanistic investigation.

      (8) No understanding of the clinical Implications of the reduced IgG levels observed in the area with high malaria exposure.

      We agree that this study does not directly establish the clinical consequences of the reduced antibody levels observed in malaria-exposed children. The primary objective of this study was to characterise long-term differences in humoral immune profiles associated with early-life malaria exposure, rather than to assess downstream clinical outcomes or functional antibody activity. We have clarified this limitation in the revised discussion. Nevertheless, the breadth and consistency of the observed differences for multiple vaccine-preventable and infectious antigens raise the possibility that early-life malaria exposure may have implications for long-term immune protection. We now emphasise in the revised discussion that future studies incorporating functional assays and clinical outcome data will be required to determine whether these serological differences translate into altered susceptibility to infection or reduced vaccine effectiveness.

      Assessment of Claims:

      The data appear to support the authors' primary claims, but the strength of the evidence is limited, and the results should be interpreted with caution. Together with the currently available evidence of P. falciparum's impact on the host's immune function, this natural experiment design provides further evidence for a relationship between early malaria exposure and reduced antibody responses. The within-Ngerenya analysis controls for geographic factors and thus enhances the quality of the evidence, however, it still fails to account for the physical, nutritional, and socio-economic factors that may have driven the observed changes. Additionally, the mechanism underlying this effect remains unclear, and the clinical significance of reduced antibody levels is not established.

      We thank the reviewer for this assessment and for recognising the strengths of the natural experiment design and within-cohort analyses. We agree that, as an observational study, our findings should be interpreted appropriately. In the revised manuscript, we have undertaken additional analyses and clarifications to strengthen the evidential basis of our conclusions and to address the points raised. To address potential confounding by nutritional and related factors, we analysed contemporaneous hospital-based surveillance data from the same geographic populations since nutritional and socioeconomic variables were not consistently collected during the course of longitudinal follow up. For three independent anthropometric indices of nutrition status (muac, weight-for-age, and height-for-age), we found no evidence of systematic differences between children from Junju and Ngerenya after adjustment for age, calendar year, and concurrent infections. As the longitudinal cohort subjects were randomly drawn from these populations, these findings suggest that the two groups were broadly comparable with respect to early-life growth and nutritional status.

      We agree that the mechanistic basis of the observed differences is not resolved in this observational study. We have clarified this point in the revised discussion and expanded our consideration of plausible biological pathways based on existing literature, including perturbations in B cell and T cell compartments. Similarly, we now explicitly state that the clinical implications of reduced antibody levels remain to be determined and will require studies incorporating functional assays and clinical outcomes. We believe these revisions strengthen the manuscript by providing a more comprehensive interpretation of the data.

      Impact and Utility:

      This work has fundamental implications for understanding vaccine effectiveness in malaria-endemic regions and may contribute to informing vaccination strategies. The findings, if strengthened, would suggest that children in areas of high malaria transmission may require modified immunization approaches. The dataset provides a valuable resource for future studies of malaria's immunological legacy.

      We thank the reviewer for this comment

      Context:

      This study builds on prior work showing acute immunosuppressive effects of malaria but uniquely attempts to demonstrate the durability of these effects years after exposure. The natural experiment design addresses limitations of previous observational studies by providing a more controlled comparison.

      We thank the reviewer for this comment

      Recommendations for the authors:

      Reviewing Editor Comments:

      We suggest that further analyses of potential confounders such as anthropometric indices, socioeconomic status, and comorbidities would render the evidence more robust.

      We thank the Reviewing Editor for this important suggestion. We agree that careful consideration of potential confounding factors is critical to the interpretation of these findings, and have undertaken additional analyses to address this.

      Because anthropometric and related socioeconomic measurements were not collected systematically within the original longitudinal malaria cohort, we assessed potential population-level differences using hospital-based surveillance data from the same geographic regions. This dataset includes measurements of anthropometry (mid-upper arm circumference, weight-for-age, and height-for-age) as well as detailed infection diagnostics in childhood. Using these data, we fitted regression models adjusting for age, calendar year, and concurrent, clinically diagnosed infections. For all three anthropometric indices, we found no evidence of systematic differences between children from Junju and Ngerenya, with effect estimates small and crossing zero (fig. 6). As the longitudinal cohorts were randomly selected from these populations, these findings suggest that the groups were broadly comparable with respect to nutritional status and infection exposure. With respect to socioeconomic status and comorbidities, detailed individual-level data were not available within the longitudinal cohort. However, the within-Ngerenya analysis, where children with differing early-life malaria exposure were compared within the same geographic and environmental setting, provides a complementary control for these factors. We have incorporated these additional analyses and clarifications into the revised manuscript statistical analysis, discussion lines and believe they strengthen the robustness of the findings by addressing key sources of potential confounding.

      Reviewer #1 (Recommendations for the authors):

      The manuscript is well written, with clear and informative figures that effectively support the findings.

      We thank the reviewer for this comment

      Suggestions:

      (1) Although the study well controlled for malaria exposure, other environmental or infectious factors that influence immunity could be considered:

      Nutritional status in childhood (malnutrition impacts immune response), co-infections (helminths, respiratory viruses), socioeconomic differences, or differences in access to health services, even minimal, between Junju and Ngerenya.

      We thank the reviewer for highlighting the potential influence of environmental, infectious, and socioeconomic factors on immune responses. We agree that these are important considerations in the interpretation of observational data. To address nutritional status and concurrent infectious exposures, we analysed contemporaneous hospital-based surveillance data from the same geographic populations. This dataset includes measurements of anthropometric indices (mid-upper arm circumference, weight-for-age, and height-for-age) alongside detailed clinical diagnostics for common childhood infections. Using regression models adjusting for age, calendar year, and concurrent infections, we found no evidence of systematic differences in anthropometric profiles between children from Junju and Ngerenya (fig. 6). These findings suggest that the populations from which the longitudinal cohorts were randomly selected were comparable with regard to early-life growth and nutritional status. We agree that we cannot fully exclude the influence of unmeasured factors such as helminth infections, socioeconomic variation, or subtle differences in healthcare access. However, the within-Ngerenya analysis, where children with differing early-life malaria exposure were compared within the same geographic, environmental, and healthcare setting, provides an internal control for many of these factors. The persistence of similar patterns within this setting supports malaria exposure as a key contributor of the observed differences. We have clarified these considerations in the revised discussion and believe that, the additional analyses and within-cohort comparisons strengthen the robustness of our conclusions while acknowledging the limitations inherent to observational studies.

      (2) Measurement of other immunological markers:

      In addition to IgG, include: B cell subpopulations (naive, memory, atypical), cytokine levels (IL-10, IFN-γ) to characterize the immunological microenvironment.

      You could include these recommendations in the text for future studies.

      We thank the reviewer for this thoughtful suggestion. We agree that detailed immunophenotyping, including characterisation of B cell subpopulations and cytokine profiles, would provide important insight into the mechanisms underlying the observed differences in antibody responses. In the revised manuscript, we have expanded the discussion to highlight these important avenues for future work, including the potential role of altered B cell subsets (and regulatory or inflammatory cytokine environments in shaping long-term humoral responses).

      Reviewer #2 (Recommendations for the authors):

      The manuscript is well-written.

      We thank the reviewer for this comment

      (1) Methodological Clarifications:

      Do the authors have any information regarding the characteristics of these children that could be of use in understanding their immune responses better? (e.g., weight, height, BMI, socioeconomic status, HB level, access to health care, etc.).

      We thank the reviewer for highlighting the importance of participant characteristics in interpreting immune responses. Anthropometric and related clinical measures were not collected systematically within the original longitudinal malaria cohort, as the study was designed to investigate the acquisition of naturally acquired immunity to malaria.

      To address this, we analysed contemporaneous hospital-based surveillance data from the same geographic populations, which include measurements of anthropometric indices (mid-upper arm circumference, weight-for-age, and height-for-age) alongside detailed infection diagnostics. Using regression models adjusting for age, calendar year, and concurrent infections, we found no evidence of systematic differences in anthropometric profiles between children from Junju and Ngerenya (fig. 6) Detailed individual-level data on socioeconomic status, haemoglobin levels, and healthcare access were not available within the longitudinal cohort impeding direct adjustment in the longitudinal cohorts. However, the within-Ngerenya analysis, where children with differing early-life malaria exposure were compared within the same geographic and healthcare setting, provides an internal control for many of these factors. These considerations are now clarified in the revised discussion.

      Could the authors provide more detailed statistical analysis, including power calculations and multiple comparison corrections?

      In the revised manuscript, we have extended the statistical analysis and now include antigen-specific mixed-effects regression models incorporating all available longitudinal measurements, which is comprehensively described in the statistical analysis section. We have also applied false discovery rate (FDR) correction to account for multiple testing across antigens, and report both unadjusted and FDR-adjusted significance in the revised results. With respect to power, the sample size was determined by the number of children meeting inclusion criteria within the long-term surveillance cohorts in terms of availability of a sufficient number of longitudinal samples. We have clarified this in the revised manuscript.

      Clarify the criteria for selecting the 123-child subset from the larger surveillance cohorts.

      We thank the reviewer for this comment. The 123 children included in this analysis were selected from the larger surveillance cohorts based on the availability of sufficiently dense longitudinal serum sampling as described above. Specifically, children were required to have at least eight longitudinal samples available in the archive, enabling robust assessment of within-individual antibody trends over time. This criterion was applied to ensure adequate temporal resolution to examine the long-term stability of malaria-associated effects on antibody responses. Children with fewer available samples were therefore excluded, as limited sampling would not allow reliable characterisation of longitudinal patterns. We have clarified these inclusion criteria in the revised manuscript.

      (2) Additional Analyses and Data Presentation:

      The authors could consider dose-response analyses relating malaria episode frequency/timing to degree of immunosuppression or even AMA-1 IgG levels and degree of immunosuppression. How do they associate over time?

      We thank the reviewer for this suggestion. To address this, we examined the relationship between malaria exposure (using cumulative febrile malaria episode count derived from longitudinal surveillance data) and the magnitude of heterologous antibody responses. In mixed-effects models adjusting for age and repeated antibody measurements, higher malaria episode burden was associated with lower antibody responses against multiple antigens (fig 7).

      Analyze whether the effects vary by specific age at malaria exposure.

      We agree that age at exposure is an important consideration. We have now assessed how the relationship between malaria burden and antibody responses varies with age by including age as a non-linear term and modelling interactions between malaria exposure and age as described above. These analyses did not suggest substantial heterogeneity in the association over age, and therefore we have retained the simpler presentation for clarity.

      Provide correlation analyses between different antibody responses to assess whether suppression is generalized.

      We have addressed this by modelling responses jointly across a panel of heterologous antigens and by examining antigen-specific associations. The direction of effect was consistent for the majority of antigens, with no evidence of opposing trends, supporting a broad rather than antigen-specific effect.

      The authors could consider moving Figures 2a and b to the supplementary material.

      We thank the reviewer for this suggestion. We carefully considered whether panels 2a and 2b could be moved to the supplementary material. However, we have retained them in the main text because they provide a simple, intuitive illustration of how AMA1 antibody responses track with malaria exposure at the individual level, complementing the population-level analysis shown in fig. 2c. We feel that this helps establish the biological validity of the microarray platform in a way that is immediately interpretable to the reader, and therefore supports the interpretation of subsequent analyses.

      The authors could consider replacing Figures 3a and b with IgG levels from ALL vaccinated children and ALL non-vaccinated children.

      We thank the reviewer for this suggestion. We would like to retain these figures for the same reasons that have been articulated above for figures 2a and b.

      (3) Discussion Enhancements:

      The authors should consider expanding the discussion to address the limitations of the data more thoroughly, particularly regarding the potential differences between cohorts that could have contributed to the results.

      We have expanded the discussion to more explicitly address potential differences between cohorts that could contribute to the observed findings, including nutritional, socioeconomic, and environmental factors.

      The discussion needs to acknowledge the lack of directionality for the associations observed. As stated above, although I agree in general terms with the observations that the authors have made, it is not possible to distinguish between a suppressive effect of malaria on immune responses to infection-derived pathogens or a protective effect of malaria that leads to less exposure to infection-derived pathogens (and consequently lower IgG levels). The mechanisms behind these could include things like different health-seeking behaviors or social interactions from kids who have malaria versus those who don't, for example.

      We agree that, as an observational study, we cannot definitively establish the direction of the association between malaria exposure and antibody responses to unrelated antigens. We have now clarified this limitation explicitly in the discussion. We acknowledge the alternative interpretations raised by the reviewer, including the possibility that differences in exposure to other pathogens, potentially driven by behavioural, environmental or healthcare-related factors, could contribute to the observed patterns. At the same time, we note that the natural experiment design, prospective malaria exposure classification, and within-Ngerenya comparisons support early-life malaria exposure as a key contributing factor. We have revised the discussion to reflect this balance.

      Extend the discussion of potential biological mechanisms underlying durable immunosuppression.

      We thank the reviewer for this suggestion. We have expanded the discussion to more fully consider potential biological mechanisms that could underlie the observed long-term differences in antibody responses. Specifically, we now discuss evidence from prior studies indicating that malaria infection can induce sustained alterations in B cell and T cell compartments, including expansion of atypical memory B cells, disruption of germinal centre responses, and increased regulatory immune activity. We position our findings as providing population-level evidence of a durable immunological phenotype, while noting that targeted mechanistic studies will be required to define the underlying pathways.

      Extend the discussion around the clinical implications of the observed antibody level differences.

      In the revised discussion, we highlight that studies incorporating functional assays and clinical outcome data will be required to determine whether these serological differences translate into altered susceptibility to infection or reduced vaccine effectiveness.

      (4) Technical Issues:

      Could the authors please:

      (1) Clarify microarray data processing and quality control procedures.

      We thank the reviewer for this request. We have expanded the methods section to provide additional detail on microarray data processing and quality control procedures.

      (2) Provide information on inter-assay variability and batch effects.

      We have expanded the methods section to clarify how these were evaluated and addressed. Inter-assay variability was monitored using pooled adult serum included on every slide as a consistent positive control. This allowed us to assess slide-to-slide consistency in signal detection across the full antigen panel. In addition, fluorophore-conjugated IgG and IgA controls were printed directly onto each miniarray to confirm scanner performance independently of antigen–antibody interactions. At the sample level, each specimen was assayed on two independent miniarrays per slide, generating four spatially separated replicate measurements per antigen. Technical variability was quantified using the coefficient of variation (CV), and measurements with CV >20% were excluded from downstream analyses.

      (3) Include details on how missing data were handled in longitudinal analyses.

      We thank the reviewer for highlighting this point. We have added clarification in the statistical analysis section describing how missing data were handled. Specifically, mixed-effects models were used, which accommodate unbalanced longitudinal data without requiring imputation, allowing all available observations to contribute to the analysis.

      (4) Include details of the parameters of the LOWESS analysis shown in Figure 1.

      We have expanded the figure 1 legend to include the parameters used for the loess smoothing shown, including the smoothing span.

      (5) Include details of the samples used for Figure 3d (Negative and Pooled Adult Serum).

      We have clarified in the methods the nature and purpose of the samples used in Figure 3d. The negative control consisted of phosphate-buffered saline applied to a full miniarray in place of serum, allowing assessment of background and non-specific signal in the absence of antibody binding. The pooled adult serum comprised a composite of sera from multiple healthy adults from the same setting and was included as a positive reference sample, expected to contain a broad repertoire of antigen-specific antibodies. These controls were included on each slide to enable interpretation of assay performance, with the negative control defining baseline signal and the pooled adult serum providing a consistent reference for antigen recognition across the microarray.

    1. Author response:

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

      We sincerely thank the reviewers for their thoughtful and constructive comments. We fully agree that when two independent variables (genotype and age) are being evaluated, the statistical analysis must appropriately account for both factors and their potential interaction. We appreciate the reviewers’ guidance in strengthening the statistical rigor of our study.

      In response to this concern, we have carefully reanalyzed the relevant datasets using two-way ANOVA to properly assess the effects of genotype, age, and their interaction. The manuscript, figures, and figure legends have been revised accordingly. Specifically:

      Figure 1:

      The quantification of p16 expression in Fig. 1F has been reanalyzed using two-way ANOVA. The figure has been replotted, and the corresponding legend has been updated to reflect the revised statistical approach.

      Figure 2:

      The quantification of AUC in Fig. 2F has been reanalyzed using two-way ANOVA. The figure and legend have been updated accordingly.

      Figure 3:

      The quantification of F4/80 in Fig. 3C and 3D has been reanalyzed using two-way ANOVA. The figures and corresponding legends have been revised to reflect this updated analysis.

      Public Reviews:

      Reviewer #1 (Public review):

      Sebag et al. addressed the role of ADH5 in BAT in the development of aging and metabolic disarrangements associated with it. This is a follow-up study after the authors' demonstration of the role of BAT ADH5 in glucose homeostasis, obesity, and cold tolerance. By ablating ADH5 specifically in brown adipocytes or pharmacologically modulating ADH5 through activation of its transcription factor, the authors conclude that preservation of BAT function is crucial for healthy aging and ADH5 is causally involved in this process. The topic is appealing given the rise in the aging population and the unclear role of BAT function in this process. Overall, the study uses several techniques, is easy to follow, and addresses several physiological and molecular manifestations of aging. However, the study lacks an appropriate statistical analysis, which severely affects the conclusions of the work. Therefore, interpretation of the findings is limited and must be done with caution.

      We sincerely thank the reviewer for their thoughtful and constructive comments. We fully agree that when two independent variables (genotype and age) are being evaluated, the statistical analysis must appropriately account for both factors and their potential interaction. We appreciate the reviewers’ guidance in strengthening the statistical rigor of our study.

      Reviewer #2 (Public review):

      Weaknesses:

      (1) Sex needs to be considered as a biological variable, at a minimum in the reporting of the phenotypes observed in this manuscript, but also potentially by further experimentation. The only mention of sex I could find is that the authors reported the general protein SNO status in BAT is increased with age in male C57Bl/6J mice. Is this also true in female mice?

      We thank the reviewer for this insightful comment. In response, we examined whether aging affects Hsf1 and Adh5 transcript levels in wild-type female mice (3 months vs. 19 months). Our analysis did not reveal significant age-associated changes in the expression of either gene. These results have now been incorporated into the revised manuscript and are presented in Figure 4A.

      (2) It would be helpful to know the extent of ADH5 loss in the adipose tissue of knockout mice, either by mRNA or by immunoblotting for ADH5. It could also be helpful to know if ADH5 is deleted from the inguinal adipose tissue of these mice, especially since they seem to accumulate fat mass as they age (Figure 2B).

      We thank the reviewer for this suggestion. Indeed, we have previously measured ADH5 expression in both brown adipose tissue (BAT) and inguinal white adipose tissue (iWAT). These data were published in Cell Reports (PMID: 3478865).

      (3) For Figure 4D, it's not clear how these BAT samples were treated with HSF1A - was this done in vivo or ex vivo?

      We thank the reviewer for their thoughtful comment. We have now provided additional methodological details in the revised manuscript. In Figure 4D (current Figure 4E), BAT was collected from wild-type mice and cultured ex vivo as explants. The BAT explants were treated for 24 hours with HSF1A (an HSF1 activator; 20 µM). Following treatment, mRNA levels of the indicated genes were measured by RT-qPCR.

      (4) I didn't understand what was on the y-axis in Figure 5A, nor how it was measured.

      We apologize for not making these critical points clearer in the initial submission. Figure 5A shows the release profiles of HSF1A from collagen gels with nanoclay (Collagen–NC–HSF1A) and without nanoclay (Collagen–HSF1A), determined using an established standard curve method (Hu et al., PMID: 33225042).

      The concentration of HSF1A was quantified by UV–Vis spectroscopy. Briefly, a standard curve for HSF1A was generated by measuring the UV–Vis spectra of HSF1A at known concentrations (1.25, 2.5, 5, 10, and 20 µM) prepared in phosphate-buffered saline (PBS). Collagen gels with or without nanoclay were then fabricated to evaluate the release profile. At predetermined time points (1, 5, 9, 14, and 21 days), the PBS supernatant from each sample was collected and analyzed by UV–Vis spectroscopy. The amount of released HSF1A was calculated using the previously established standard curves. A brief description has now been included in the figure legend.

      (6) Figure 1B: What is the age of the positive (ADH5BKO) and negative (Adh5 fl) mice?

      We regret that we did not describe our results clearly in the first submission and have included detailed information in the revised manuscript.

      (7) Figure 1F: Can you clarify what I'm looking at in the P16ink4a panels? The red staining? Is the blue staining DAPI? This is also a problem in Figures 3C, 3D and 5G, and 5I. Figure 4B looks great - maybe this could be used as an example?

      We regret that we did not present results clearly in the first submission and have provided detailed information in these figures in the revised manuscript.

      (8) Figure 3B looks a bit odd. Can the approach to measuring IL-1β be clarified, and could the authors explain why they can't show units of mass for IL-1β levels?

      We have provided information in the revised manuscript.

      (9) What are the levels of nitric oxide synthase in the BAT of the aging model? Since protein S-nitrosylation is regulated by a balance of both, the attribution of greater protein S-nitrosylation to ADH5 is incomplete without determining nitric oxide synthase.

      We thank the reviewer for this thoughtful comment. In response, we have now included the analysis of iNOS transcript expression levels in the revised manuscript. These data are presented in Figure 1C.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (2) Presentation of metabolomics is not appropriate. The authors described, using color coding, the metabolites up- or downregulated in the experimental design. However, the current approach does not allow the reader to detect sample size, magnitude of changes, variability of the data, p-values, etc. This approach does not follow the standard practices of scientific rigor and should be modified. Metabolomic data could be uploaded as supplementary data, or a table with all necessary information to allow a full interpretation of the data should be provided.

      We have now provided the the metabolimic data in a table format as Figure 3I.

      (6) What are the levels of nitric oxide synthase in the BAT of the aging model? Since protein S-nitrosylation is regulated by a balance of both, the attribution of greater protein S-nitrosylation to ADH5 is incomplete without determining nitric oxide synthase.

      We thank the reviewer for their thoughtful comment. We have now included iNOS transcript levels expression level in the revised manuscript (Figure 1C).

      Minor Comments:

      (1) The conclusion of the abstract is somewhat vague. I suggest the authors rewrite it to better recapitulate what was found in the study.

      We thank the reviewers for this helpful suggestion. In response, we have revised the Abstract to improve the specificity and clarity of our conclusions.

      (2) In the introduction, the authors mention that an increased level of mitochondrial ROS activates UCP1. Given that the evidence for this statement is circumstantial and not supported by the current state-of-the-art (PMID: 28710335), where it is accepted that UCP1 activation diminishes ROS production, I suggest that the authors tone down this statement or at least acknowledge conflicting findings and interpretations.

      We thank the reviewer’s insight, we have included this important notion in the introduction.

      (3) Figure 2H - It is unclear what this figure (and statistical analysis) represents. Please, improve the description of the experiment and how the data were plotted to reach such a conclusion.

      We regret that we did not present results clearly in the first submission. The trend lines show the relationship between body weight and time on rotarod. The P value is the comparison of the slope of the line between Adh5 BKO mice and Adh5 fl/fl mice. The data implicate that the heavier the BKO mouse, the less time spent on the rotarod.

      (4) Figure 2M - The unit of LV thickness is missing. Please, provide it. In addition, I am missing the other cardiac parameters obtained from the echocardiogram.

      We have included this information in Figure 2M in the revised manuscript.

      (5) Figure 2G - I believe force is not the right unit for the grip strength test. Please, revise accordingly.

      We regret that we did not describe our results clearly in the first submission. We have corrected this unit in the revised figure.

      (6) Figure 3H - What is the unit when reporting mitochondrial area?

      We regret that we did not describe our results clearly in the first submission. We have added this information in the revised figure.

      (7) Is HFS1 also downregulated in iWAT?

      We thank the reviewer for this thoughtful comment. In response, we measured Hsf1 expression in iWAT from young and aged wild-type male mice. Our analysis did not reveal any significant age-associated changes in Hsf1 expression in iWAT. These results have now been included in the revised manuscript (Figure 4C).

      (8) Can the authors explain how HFS1 expression increases upon HSF1 activation? I understand ADH5 is controlled by HSF1, but what would control HSF1 itself? Off targets?

      We thank the reviewer for this insightful comment. At present, we do not have direct mechanistic evidence to definitively support this notion, and we cannot exclude the possibility of off-target effects of HSF1A. However, previous studies have reported that the HSF1 promoter contains heat shock elements (HSEs) in humans and HSE-like domains in mice. Based on this, we speculate that activated HSF1 may enhance its own transcription through an autoregulatory or positive feedback mechanism.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Strengths:

      This work sets a benchmark for integrative 3D genomics in oncology. Its methodological sophistication and conceptual advances establish a new paradigm for studying nuclear architecture in disease.

      We appreciate the very kind words.

      Weaknesses:

      Major Issues

      (1) Functional tests would strengthen the observed links between structure and gene changes. For example, the COL12A1 gene loop formation correlates with its increased expression. Disrupting this loop using CRISPR-dCas9 at chr6 position 75280 kb could prove whether the loop causes COL12A1 activation. Such experiments would turn strong correlations into clear mechanisms.

      We agree that targeted disruption of specific loops such as COL12A1 will be important for functional validation of the causal relationships between enhancer-promoter loop formation/dissipation and changes in gene expression. However, the intent of our current study was to profile changes in genome organization at a global scale to deduce general features of cancer progression-associated changes in genome organization, rather than to explore specific loop interactions. The current findings are a foundation for more targeted functional follow-up studies.

      (2) The H3K27ac looping idea needs deeper validation. Data suggests H3K27ac loss weakens loops without affecting CTCF. Testing how cohesin proteins interact with H3K27acmodified sites would clarify this process. Degron systems could rapidly remove H3K27ac to observe real-time effects. Also, the AP-1 motifs found at dynamic loop sites deserve functional tests. Knocking down AP-1 factors might show if they control loop formation.

      We agree that modulating histone modifications or transcription factors would provide insights into the underlying mechanisms driving the changes we observed. However, such studies utilizing degrons or small molecule inhibitors that globally knock down either H3K27ac or specific transcription factors are often difficult to interpret. For example, assessing the role of AP-1 factors, as suggested, would be complicated by the variety of AP-1 proteins. In addition, H3K27ac reduction could inhibit loop strength either directly (i.e. by reducing cohesin recruitment) or indirectly (i.e. by reducing gene expression which could in turn affect loop strength). Parsing out the exact relationships between these features will require extensive follow-up work and falls outside of the scope of the current study.

      (3) Connecting findings to patient data would boost clinical relevance. The MCF10 model is excellent for controlled studies. Checking if TAD boundary weakening occurs in actual patient metastases would show real-world importance. Comparing primary and metastatic tumor samples from the same patients could reveal new structural biomarkers. If tissue is scarce, testing cancer cells with added stroma cells might mimic tumor environment effects.

      We have leveraged publicly available datasets to link the observations from the progression model to clinical samples. Specifically, we have compared our datasets to chromatin organization data in non-cancerous mammary epithelial cells (HMEC), five cell lines representing distinct cancer subtypes ranging from less (luminal) to more aggressive (triple negative, TNBC), as well as tissue samples from TNBC patients with contralateral normal controls. We explored the conservation of both loops and TADs identified in the MCF10 progression system in each of these maps, paying particular attention to how features that are differential between MCF10 cells differ across other cancer cell types. We observe a high degree of conservation of static loops and TAD boundaries among the cancer samples, as well as some degree of cell-specific changes among loops and boundaries that change during MCF10 progression. These findings are included in Supplemental Figures 3 and 4 and are discussed on page 7.

      Minor Issues

      (1) Adding a clear definition for static loops would help readers. For example, state that static loops show less than 10 percent contact change across replicates.

      Static loops are defined as loops with a fold-change of 1.5 or more between any two MCF10 cell lines and an adjusted p-value of less than 0.025 considering change across biological and technical replicates. This definition is stated on page 6).

      (2) In the ABC model analysis, removing promoter regions from the enhancer list would focus results on true long-range interactions.

      The ABC model already excludes the promoter of each gene. Only self-promoters are excluded, whereas the model allows promoters of other genes to act as potential long-range enhancers of the target gene. We have added text to make this clear (see page 11).

      (3) Briefly noting why this study sees TAD weakening while other cancer types show different patterns would provide useful context.

      The biological reason for TAD weakening in the MCF10 model is not known, but neither the mechanism for boundary weakening nor the reason for apparently different behavior amongst cancers is known. We expanded the text on this discussion slightly, but we refrain from making any definitive claims. We do note that differences in the types of cancer studied or the methods used for detecting changes in TADs (i.e. different sensitivities and thresholds for detecting change) could be responsible (see page 15). We also mention that the loss of insulation at many TAD boundaries detected in our study are subtle changes in intensity that could be potentially missed if using methods tailored to find more drastic changes in TAD architecture.

      Reviewer #2 (Public review):

      While the conclusions are broadly supported, methodological and analytical refinements are required.

      We appreciate these comments.

      (1) Model representativeness. The long-term culture-adapted MCF10 genome harbours extensive aneuploidies and translocations. Validation of key COL12A1/WNT5A loop dynamics in an independent breast-cancer line (e.g., MDA-MB-231, T47D) or in patientderived organoids/PDX models would strengthen generalizability.

      Although the generation of Micro-C datasets in additional cell lines is outside of the scope of this study, we used publicly available Hi-C data from triple negative breast cancer (TNBC) progression and patient samples (Kim, Han & Chun et al. 2022) to assess generalizability of the MCF10 model findings. While these maps are lower resolution than the Micro-C maps used in our study, they are of sufficient depth to detect loops at a similar resolution (10 kb). We report these findings in Supplemental Figures 3 and 4 and discuss them on page 7.

      We find that chromatin loops and TAD boundaries detected across the MCF10 system are highly conserved across all other mammary epithelial lines studied. Chromatin loops that were more prominent in MCF10AT1 and MCF10CA1a lines were also significantly stronger in TNBC cells. Insulation score boundaries that were weakened in MCF10CA1a showed strong insulation across all cell lines in TNBC. These findings highlight that different model systems indeed have distinct profiles of structural change, just as they have distinct gene expression profiles.

      It is worth noting that direct comparison at individual loci is complicated by variations in gene expression profiles between the MCF10 model and the TNBC progression model; for example, COL12A1 is not significantly upregulated between normal and TNBC tissues in this study (unlike in the TCGA-BRCA data) and is downregulated between HMEC and TNBC cell lines. Regardless, our analysis provides some indication of conserved and divergent features in the various model systems.

      (2) The study remains purely correlative; no perturbation experiments are conducted to demonstrate causal roles of chromatin loops on gene expression. CRISPR interference (CRISPR-Cas9-KRAB/HDAC) or enhancer deletion/inversion should be applied to 3-5 pivotal loops (e.g., COL12A1, WNT5A) to test their impact on target-gene expression and cellular phenotypes (e.g., proliferation, migration).

      We agree that targeted disruption of specific loops such as COL12A1 will be important for understanding the causal relationships between enhancer-promoter loop formation/dissipation and changes in gene expression. However, the intent of our current study was to profile changes in genome organization at a global scale to deduce general features of cancer progression-associated changes in genome organization, rather than exploring specific loop interactions. The current findings are a foundation for more targeted follow-up functional studies.

      (3) The manuscript lacks integration with clinical datasets. Integrate TCGA-BRCA data to assess whether elevated COL12A1/WNT5A expression associates with overall survival (OS) or distant metastasis-free survival (DMFS)

      To assess clinical significance of specific loci, we have queried expression of all differentially expressed genes in the MCF10 progression system among TCGA-BRCA expression data. We summarize our findings in Supp. Fig. 5E and discuss them on page 8.

      We found that roughly 25% of genes that change in our model also change significantly in breast cancer, but only roughly half of those genes change in the same direction (i.e. up-regulated in MCF10CA1a vs MCF10A, and up-regulated in tumor vs normal samples). Interestingly, there was a higher degree of directional agreement between latechanging genes (i.e. genes that change in MCF10CA1a compared to MCF10A and MCF10AT1) than early-changing genes (i.e. genes that change in MCF10AT1 and MCF10CA1a compared to MCF10A).

      We have also explored the impact of select highlighted genes on overall survival (OS). We present these data in Supp. Fig. 6 and discuss it on page 8. While not all genes showcased in this study have a significant impact on overall survival, most trend in the same direction as their differential expression would suggest (i.e. genes more highly expressed in cancer vs tumor also have a hazard ratio above 1).

      Reviewer #3 (Public review):

      The differential topology analysis and its integration with transcription is very well done- one of the best versions of this I have read in the 3D genome field!

      We appreciate the reviewers’ endorsement.

      However, the paper is framed largely as a cancer biology study, and it teaches us much less about this. I am worried that some of the trends for each topologic feature are not going to be consistent across the pre-malignant-malignant-metastatic spectrum and would like the authors to soften some of their claims a bit regarding how this clarifies our understanding of cancer evolution.

      We agree that the strength of the study lies in its deep mapping of chromatin architecture and the landscape of enhancers and differentially expressed genes, which we hope to use to better understand the relationship between chromatin structure and gene expression, regardless of their cancer relevance. To better relate the findings in the progression system to cancer, we have added new data from direct comparisons of the MCF10 progression system with multiple patient-derived cancer cell lines and cancer tissues. These data are shown in Supp. Fig. 3 and 4 and discussed on p. 7. Regardless, we have softened the claims regarding cancer progression throughout the manuscript.

      Weaknesses:

      Major Concerns:

      (1) The integration of gene expression and chromatin loops is intriguing. The authors' differential analysis, however, omits consideration of genes that are on and simply further upregulated versus genes that transition on/off or off/on. It would be nice to see the authors break out looping patterns for these two different patterns of regulation, as it may be instructive regarding the rules for how EP loops govern transcription.

      To address different types of gene expression patterns, we analyzed 108 genes that went from an unexpressed or “off” state (2 or fewer read counts) in one cell line to an expressed “on” state (100 or more read counts) in another, and 111 genes that go from “on” to “high” (1000 or more read counts). We present these data in Supp. Fig. 8 and discuss the findings on page 9. While neither of these genes were enriched for differential loops, a large number overlap with loop anchors. We found a relationship between loop strength and gene expression levels; genes that are more strongly expressed are more likely to overlap with the anchor of a chromatin loop. All gene sets show similar strong trends at distal regulatory regions.

      (2) Given the paucity of differential loops at the majority of genes whose expression changes, the authors should examine chromatin subcompartments, as these may associate more with differential transcription.

      We present subcompartment analysis in Supp. Fig. 9. Our CALDER compartment calls are qualitative rather than quantitative, so to explore this we examined how compartments change genome-wide and at specific promoters. We show these data in Supp. Fig. 9 and discuss the findings on page 10-11. We see that between any two cell types, a majority of changes occur between closely related subcompartments, i.e. from A.2.2 to A.2.1 (1 step more A-like) or B.1.1 (1 step more B-like). The promoters of differentially expressed genes have minimal subcompartment changes, but genes that shift from on to off have larger changes. Differentially expressed genes with promoters that shift by multiple subcompartments have significant impacts on fold-change, but smaller shifts have minimal impacts on gene expression. In summary, small changes in subcompartments are very common and have little impact on gene expression, while larger changes are infrequent and correlate more strongly with changes in gene expression.

      (3) The authors could push their TAD analysis further by integrating it with transcription. Can they look at genes and their enhancers that span these altered boundaries to see if these shifts impact transcription?

      We provide this analysis in Supp. Fig. 9. We started, as suggested, by looking at genes with distal enhancers (as determined by the ABC model) that span a single TAD boundary. However, the number of genes that fit this definition was relatively small, so we expanded to look at any genes with promoters in the proximity (50kb) of differential insulation score boundaries, for which we saw the same trends with more robust signal. Our findings are shown in Supp. Fig. 9 and discussed on page 10. We found that genes near weakened boundaries are not enriched for differentially expressed genes, while those near strengthened boundaries are. Comparing the fold-change of genes near strengthened, weakened, and static boundaries showed a significant inverse correlation between boundary strength and gene expression, although effect sizes were small. These results show that changes in TAD boundary insulation have small but noticeable impacts on gene expression.

      (4) The progression of cancer critically goes from a benign -> pre-malignant -> malignant -> metastatic series of steps. The AT1 line is described as 'premalignant' and thus the authors' series omits a malignant line. While I think adding such a sample is an unreasonable request at this point (as it would have had to have been studied in 'batch' with these other samples), the authors should acknowledge that they omit this step and spend some time discussing the genetic, morphologic, and phenotypic features for their 3 conditions. The images in Figure 1S aren't particularly useful- they don't tell the reader that these cells are malignant/benign. The karyotypic data are intriguing but not fully analyzed, so it is hard to know what true phenotype these cells represent. For example, malignant means DCIS/invasive carcinoma - so then what does this pre-malignant cell model represent? The described alteration in the AT1 line is a Ras oncogene, so in some sense, the transition to this line really is just +/- Ras. The authors could spend some time thinking about the effects of Ras specifically on the 3D genome.

      We have expanded our discussion of the relevance of the MCF10 model on page 4, and the limitations of the model on page 17. The MCF10 progression model has been extensively used by many laboratories, and its properties have been discussed in detail (i.e. Polizzotti et al. 2012). Critically, the MCF10AT1 cell line is the product not only of Ras oncogene expression but then derived from a 100-day-old precancerous lesion that formed a squamous carcinoma in a mouse, and over this time it accumulated additional changes. The MCF10AT1 line is considered pre-malignant as it has accrued critical changes that prepare it for the metastatic transition, but it does not immediately form tumors when injected back into mice. Unlike the MCF10DCIS cell line which is malignant but not metastatic, the more aggressive MCF10CA1a is classified as both malignant and highly metastatic, forming tumors that quickly metastasize to the lungs in mouse xenografts. While both MCF10AT1 and MCF10CA1a are tumorigenic, we acknowledge the lack of a nonmetastatic malignant cell line in the discussion on page 17. We have also provided updated karyotype characterization of the cell lines used in this study in Supp. Fig. 1B and now include full composite karyotypes in the Methods section (page 18).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The reviewer’s recommendations are the same as their public review comments. See our response to the review comments above.

      Reviewer #2 (Recommendations for the authors):

      (1) If conditions permit, it is recommended that inclusion of primary human mammary epithelial cells (HMECs) to distinguish immortalisation-specific from malignancy-specific 3D changes.

      Micro-C data of equal resolution is not available for HMECs. We have, however, incorporated analysis of publicly available deeply sequenced Hi-C data of HMECs into several figures that explore the conservation of loops and TADs in these cells (Supp. Fig. 3 and 4).

      We find that chromatin loops and TAD boundaries detected across the MCF10 system are highly conserved across all other mammary epithelial lines studied. Chromatin loops that were more prominent in MCF10AT1 and MCF10CA1a lines were also significantly stronger in TNBC cells. Insulation score boundaries that were weakened in MCF10CA1a showed strong insulation across all cell lines in the TNBC system. These findings highlight that different model systems indeed have distinct profiles of structural change, just as they have distinct gene expression profiles.

      (2) The relationship between loop alterations and copy-number variations (CNVs) is not explored. If conditions permit, it is recommended that overlay differential loops with SNP/Indel/CNV data to exclude spurious differences arising from structural alterations.

      While we have not conducted an in-depth SNP analysis, we have clarified our discussion of the karyotype analysis on pages 21 and 23 and how we mitigated these effects when identifying differential loops between cell lines.

      (3) The horizontal and vertical coordinates of the diagram are difficult to view; it is recommended that the size of the text on the picture be adjusted to ensure that it is clear to read. Some of the text coordinates of the figure are labeled in gray; it is recommended that they be in black.

      The clarity of the figures has been improved.

      Reviewer #3 (Recommendations for the authors):

      I really like this paper. I think if the cancer focus can be down-emphasized (because I'm not fully clear what we've really learned about cancer), then it represents a nice dataset and a thoughtful, comprehensive analysis.

      We greatly appreciate the kind words and helpful feedback. The cancer focus has been toned down throughout the manuscript, as suggested.

      Minor Concerns:

      (1) The authors present a nice summary of the topological changes across samples. However, summary statistics can mask noise/bias and also don't fully convey the effect size of the reported changes. Highlighting individual loci and visualizing these would strengthen the paper and participate in maintaining a high standard for our genomic studies of topology, in which we summarize, but also provide representative examples. I would appreciate seeing more example plots at distinct loci (even if in the supplemental information).

      We have included several more example regions in Supp. Fig. 7 and 12, including four looped genes that change similarly between the MCF10 series and TCGA-BRCA data (2 stably looped genes and 2 differentially looped genes, 2 up-regulated and 2 downregulated), and six differentially looped and differentially expressed genes (3 which change in the same direction as the loops, and 3 which change in the opposite direction).

      (2) "To identify loops that changed significantly during cancer progression, we assessed changes in contact frequency among every loop in each cell type, correcting for karyotypic differences that result in differences in coverage between cell lines (see Methods)." The Methods section is not adequately explained. Also, could you go a bit deeper to define if these large-scale changes shift the 3D genome specifically? This is hard, but there may be some low-hanging fruit given the otherwise fairly isogenic features in your model.

      We have added more detail to the Methods section on pages 21 and 23 on how karyotypic abnormalities were included in our analysis and differential loop calling. A deeper analysis of how large-scale karyotypic changes affect chromatin organization (i.e. through the formation of neoloops and TADs through translocations) is indeed an attractive subject, but due to its complexity requires a separate dedicated study.

      (3) "Approximately half of chromatin loops featured some combination of active gene promoters and enhancers within 10kb of loop anchors". The authors have high-resolution topology data and should be more stringent; these features should have to overlap loop anchors or at least use a distance less than 10kb, which, in some sense, forfeits the advantages of high-resolution topology data.

      The threshold of 10kb was chosen for several specific reasons: First, the loop sizes detected here are large enough that this relatively large region still represents a small fraction of the loop span, and these regions are reasonably considered anchor-proximal. Second, the loops we detect are non-punctate, both in aggregate analysis (Figure 1H, bottom) and at individual loci (see example regions), showing increased contact frequency among several 5kb or 10kb bins. Therefore, adding 10kb to either side (2 pixels on 5kb maps and 1 pixel on 10kb maps) ensures that the full region of increased contact frequency is included. Finally, ultra-resolution Hi-C data has also shown that loops remain diffuse even with 1kb resolution maps (albeit they do get smaller than the 30kb used here) (Harris & Gu 2023). We have added a brief justification of this overlap size to the text on page 24.

      (4) "These results show that not only changes in either contact frequency and enhancer activity correlate with increased gene expression, but they also correlate with each other, suggesting a potentially linked functional role during enhancer-promoter communication." The authors could use this opportunity to disentangle the contributions of loops and chromatin modifications a bit more. The exceptions are of interest - e.g., loop is stable, gene expression changes or loop changes, gene expression does not. Highlighting exemplar cases for these exceptions (rather than just a genomics summary) would be nice to see.

      The additional example regions we have included in Supp. Fig. 7 and 12 now showcase a wider variety of scenarios; in addition to more examples of static loops with gene expression changes (Fig. 2, Supp. Fig. 7E-F) and differential loops with matching gene expression changes (Fig. 4, Supp. Fig. 7C-D, Supp. Fig. 12A-C), we now also feature examples of differential loops where gene expression changes in the opposite direction (i.e. a strengthened loop at a down-regulated gene, Supp. Fig. 12D-F).

    1. Author response:

      eLife Assessment

      This study reports a novel function for syntaxin 11, a specialized SNARE protein critical for the immune system whose mutations cause familial hemophagocytic lymphohistiocytosis type 4. The data convincingly show that depletion of STX11 impairs store-operated calcium entry in Jurkat T cells and that this defect is recapitulated in primary cells from a patient suffering from the disease; the authors further show that the syntaxin interacts with the pore subunit of the ORAI1 channel and propose that it primes the channel by promoting the assembly of multimers before activation by its endogenous ligand, the ER Ca2+ sensing protein STIM1. This is a conceptually important claim that challenges the prevailing view that all structural transitions in ORAI1 are STIM-driven. The data are high-quality and broadly consistent with the interpretation, but alternative mechanisms for the defects are not considered; additional work should rule out vesicular trafficking, discuss other mechanisms, and address methodological issues.

      We thank the editor and reviewers for assessing our work. Although significant amount of data in this paper already rule out any potential defects in the vesicular trafficking of Orai1 in cells lacking STX11, we will still include the additional suggested experiments. In the revised version, we will include the various experiments that we had already performed to measure vesicular trafficking and ER-PM junctions in STX11 depleted cells. We will discuss any remaining alternate explanations, include missing methods, quantifications and calibrations, where applicable, and provide response to each of the reviewer’s comments.

      Public Reviews:

      Reviewer #1 (Public review):

      Weaknesses:

      For readers to appreciate the value of patient experiments derived from a single individual, the authors should quote prior studies showing that STX11 protein levels are abolished in all known human STX11 mutations. The priming model, while functionally well-supported, rests on indirect structural evidence, and the precise conformational transition involved remains to be defined. These are acknowledged limitations, but alternate mechanisms have not been explored and formally excluded. More direct evidence should be provided to exclude the possibility that STX11 could act as a conventional SNARE and sustain calcium fluxes by promoting the delivery of additional ORAI1 channels from vesicles.

      In the revised version, we will include references for the prior STX11 human mutations that have been biochemically characterized till date (Bryceson, Rudd et al. 2007);(Muller, Chiang et al. 2014);(Macartney, Weitzman et al. 2011);(Marsh, Satake et al. 2010). As the reviewer has correctly pointed out, the STX11 protein levels were almost completely abolished in these studies. Therefore, the prior mutations are essentially comparable to the frameshift mutation characterized in this study, in terms of the mechanisms underlying the phenotypic defects reported here versus earlier. From a mechanistic point of view, we believe that our data from even a single FHLH4 patient, where STX11 levels were severely depleted, and additional knockdown studies across three different cell lines, are representative of all STX11 patients that have been reported thus far.

      Regarding the Reviewers’ concern that absence of STX11 as a conventional SNARE could affect Orai1 channel delivery from intracellular vesicles. We would like to point out the following:

      (1) In Miao et al. 2013 (Miao, Miner et al. 2013), Figure 3C-D, we conclusively showed that expression of a dominant negative mutant of NSF, a non-redundant protein in vesicle trafficking, impaired vesicle trafficking but did not impair SOCE. This experiment had essentially ruled out a role for vesicle trafficking in SOCE. In the same paper, we had also shown that Orai1 levels in the PM do not increase post-store depletion (Figure 3, figure supplement 2).

      (2) In this manuscript (Supplementary Figure 3B), we have shown that U2OS cells stably expressing Orai1-BBS-YFP have identical levels of Orai1 in the PM with and without STX11 depletion. This shows that the biosynthesis or delivery of Orai1 to the PM is not affected by STX11 depletion, another broadly classified member of the vesicle trafficking. The levels were also assessed in store-depleted U2OS cells but not included here because in Miao et al. 2013 we had already shown that levels of PM Orai1 are essentially equal in resting and store-depleted cells. In our revised submission, we will include the data from store-depleted cells in U2OS and also repeat this experiment in the other cell types used in this paper. In addition, in our revised submission, we will include three different vesicle trafficking assays performed in STX11 depleted cells.

      (3) Most importantly, in Figure 7I-J of this manuscript, we showed that calcium influx from a constitutively active mutant Orai1 (Orai H134S) is identical between STX11 depleted and scramble control cells. If wildtype Orai1 was indeed stuck in vesicles in STX11 depleted cells, then how would H134S Orai1 be able to rescue the defect in SOCE? In fact, the Orai1 mutant calcium flux assays were done using a 20X water objective, to visualize and confirm whether the expression of mutant and WT Orai1 was comparable in the PM. We will include the quantification of PM levels of Orai1 mutants w.r.t WT Orai1 in the revised paper.

      (4) We have generated and been using HEK293, U2OS and Jurkat cell lines that stably express fluorescently tagged Orai1 for most of our experiments (Miao, Miner et al. 2013); (Li, Miao et al. 2016);(Ramanagoudr-Bhojappa, Miao et al. 2021). In each case, we have never observed Orai1 in intracellular vesicles with or without store depletion. In all cases, it is constitutively and stably expressed in the PM.

      In summary, significant amount of data in this paper already rule out any potential reduction in the PM levels of Orai1 in cells lacking STX11. We will still do the additional experiments suggested by the Reviewer 1.

      Regarding STX11 induced precise conformational transition, we are trying to setup collaborations with scientists who might be able to visualize this in vivo.

      The readers should note that purification of isolated pore subunits of ion channels followed by crystallization or expression in membranes for cryo-EM is currently considered a gold standard in the analysis of ion channel pore subunits. However, we have shown that ion channels are dynamic macromolecular complexes, in vivo (Li, Miao et al. 2016), where synaptic proteins dynamically bind to induce conformational changes and affect their stoichiometry (Li, Miao et al. 2016). Please also see (Chorev, Baker et al. 2018) and (Dorwart, Wray et al. 2010). More advanced in vivo approaches therefore need to be developed to enable visualization of the dynamics of ion channel macromolecular complexes in the native environment. In the absence of such approaches, the structural insights obtained from detergent purified subunits will remain incomplete and biased.

      Reviewer #2 (Public review):

      Weaknesses:

      The authors conclude that Syntaxin 11 directly binds Orai1. This conclusion is well supported by a multifaceted approach, including co-immunoprecipitation (co-IP), molecular dynamics simulations, co-localization/FRET assays, and targeted mutational analysis-all of which are thoroughly executed. While the interaction appears reasonably strong in co-IP experiments, the STX11-Orai1 interaction is comparatively weaker in pull-down assays, which the authors attribute to instability of the purified His-STX11 protein. A remaining gap is direct evidence of interaction in live cells; this is understandably challenging given that fluorescent tagging of STX11 is not feasible. Fully resolving this question lies beyond the scope of the present study and will require more advanced approaches to capture STX11 binding dynamics.

      We thank the reviewer for acknowledging that the above studies will require standardization of advanced techniques which are beyond the scope of the present study. We plan to continue developing methods that will allow us to visualize the binding and unbinding of STX11 to Orai1 in vivo.

      References:

      Bryceson, Y. T., E. Rudd, C. Zheng, J. Edner, D. Ma, S. M. Wood, A. G. Bechensteen, J. J. Boelens, T. Celkan, R. A. Farah, K. Hultenby, J. Winiarski, P. A. Roche, M. Nordenskjold, J. I. Henter, E. O. Long and H. G. Ljunggren (2007). "Defective cytotoxic lymphocyte degranulation in syntaxin-11 deficient familial hemophagocytic lymphohistiocytosis 4 (FHL4) patients." Blood 110(6): 1906-1915.

      Chorev, D. S., L. A. Baker, D. Wu, V. Beilsten-Edmands, S. L. Rouse, T. Zeev-Ben-Mordehai, C. Jiko, F. Samsudin, C. Gerle, S. Khalid, A. G. Stewart, S. J. Matthews, K. Grunewald and C. V. Robinson (2018). "Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry." Science 362(6416): 829-834.

      Dorwart, M. R., R. Wray, C. A. Brautigam, Y. Jiang and P. Blount (2010). "S. aureus MscL is a pentamer in vivo but of variable stoichiometries in vitro: implications for detergent-solubilized membrane proteins." PLoS Biol 8(12): e1000555.

      Li, P., Y. Miao, A. Dani and M. Vig (2016). "alpha-SNAP regulates dynamic, on-site assembly and calcium selectivity of Orai1 channels." Mol Biol Cell 27(16): 2542-2553.

      Macartney, C. A., S. Weitzman, S. M. Wood, D. Bansal, M. Steele, M. Meeths, M. Abdelhaleem and Y. T. Bryceson (2011). "Unusual functional manifestations of a novel STX11 frameshift mutation in two infants with familial hemophagocytic lymphohistiocytosis type 4 (FHL4)." Pediatr Blood Cancer 56(4): 654-657.

      Marsh, R. A., N. Satake, J. Biroschak, T. Jacobs, J. Johnson, M. B. Jordan, J. J. Bleesing, A. H. Filipovich and K. Zhang (2010). "STX11 mutations and clinical phenotypes of familial hemophagocytic lymphohistiocytosis in North America." Pediatr Blood Cancer 55(1): 134-140.

      Miao, Y., C. Miner, L. Zhang, P. I. Hanson, A. Dani and M. Vig (2013). "An essential and NSF independent role for alpha-SNAP in store-operated calcium entry." Elife 2: e00802.

      Muller, M. L., S. C. Chiang, M. Meeths, B. Tesi, M. Entesarian, D. Nilsson, S. M. Wood, M. Nordenskjold, J. I. Henter, A. Naqvi and Y. T. Bryceson (2014). "An N-Terminal Missense Mutation in STX11 Causative of FHL4 Abrogates Syntaxin-11 Binding to Munc18-2." Front Immunol 4: 515.

      Ramanagoudr-Bhojappa, R., Y. Miao and M. Vig (2021). "High affinity associations with alpha-SNAP enable calcium entry via Orai1 channels." PLoS One 16(10): e0258670.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript addresses an important methodological issue-the fragility of meta-analytic findings-by extending fragility concepts beyond trial-level analysis. The proposed EOIMETA framework provides a generalizable and analytically tractable approach that complements existing methods such as the traditional Fragility Index and Atal et al.'s algorithm. The findings are significant in showing that even large meta-analyses can be highly fragile, with results overturned by very small numbers of event recodings or additions. The evidence is clearly presented, supported by applications to vitamin D supplementation trials, and contributes meaningfully to ongoing debates about the robustness of meta-analytic evidence. Overall, the strength of evidence is moderate to strong.

      Strengths:

      (1) The manuscript tackles a highly relevant methodological question on the robustness of meta-analytic evidence.

      (2) EOIMETA represents an innovative extension of fragility concepts from single trials to meta-analyses.

      (3) The applications are clearly presented and highlight the potential importance of fragility considerations for evidence synthesis.

      Reviewer #3 (Public review):

      (1) The manuscript would benefit from a clearer explanation of in what sense EOIMETA is generalizable. The author mentions this several times, but without a clear explanation of what they mean here.

      This is a point I was remiss not to better elucidate. With regards to generalisation, the text has been modified to explicitly state that generalisability in this context means no specific study dependence, just a net number of subjects required to flip a result. The text reads:

      “Atal's method is highly useful, but one possible objection is that it has the downside of non-generalisability, as it finds very specific combinations of trials and patients that would have to be re-coded (events classified as non-events and vice-versa) for results to become insignificant. For example, an Atal meta-analytic fragility of 4 pertains to a specific and often unique circumstance when 4 patients could be recoded from a specific study or combinations thereof to change outputs, but this does not generalise to any 4 patients in that meta-analysis. This makes this definition of meta-analytic fragility useful but not general, and perhaps less intuitive to interpret than a typical RCT fragility metric. In this work, we establish a generalizable meta-analytic fragility metric, based upon Ellipse of Insignificance (EOI) analysis for dichotomous outcome trials. This method creates a pool of events and non-events in both arms, adjusted for weighing, and answers the general question of how many patients would have to be effectively recoded in a meta-analysis for results to flip, without requiring specific study identification.”

      (2) The authors mentioned the proposed tools assume low between-study heterogeneity. Could the author illustrate mathematically in the paper how the between-study heterogeneity would influence the proposed measures? Moreover, the between-study heterogeneity is high in Zhang et al's 2022 study. It would be a good place to comment on the influence of such high heterogeneity on the results, and specifying a practical heterogeneity cutoff would better guide future users.

      This is a very fair observation, and I need to better explain myself here! So there are effectively two measures of heterogeneity considered in this work; the typical value from a meta-analysis and the measure of divergence between the crude and the inverse-variance weighed adjusted – when these differ my small amounts, one could conceivably use either measure. I’ve changed the text to better reflect this, including:

      “This modification in akin to pooled in a meta-analysis, and adjusts for study level heterogeneity. After this modification, a standard EOI analysis can then be applied to the vector . In addition, we can also employ ROAR analysis to the same vector, yielding the raw number of patients in either or both arm who could be added a given direction to change the result, and exact combination of control and experimental group redactions required to change the result from a significant finding to a null one. Caveats for implementation and interpretation are outlined in the discussion section.”

      (3) I think clarifying the concepts of "small effect", "fragile result", and "unreliable result" would be helpful for preventing misinterpretation by future users. I am concerned that the audience may be confusing these concepts. A small effect may be related to a fragile meta-analysis result. A fragile meta-analysis doesn't necessarily mean wrong/untrustworthy results. A fragile but precise estimate can still reflect a true effect, but whether that size of true effect is clinically meaningful is another question. Clarifying the effect magnitude, fragility, and reliability in the discussion would be helpful.

      This is an excellent suggestion – I’ve tried to do it with percentages, as in table 2, but these are minute in the case of the vitamin D trials, partially I suspect because they are extraordinarily weak. The Cohen’s H for these meta-analyses yields tiny values, which I think might be tied to the virtually negligible percentages we obtain for number needed to flip. With stronger data, it might be worth expanding this into a useful heuristic measure for robustness, though I don’t think vitamin D data as in this work is going to help us much. In light of the reviewer’s excellent comment, I added the following:

      In light of the reviewer’s excellent comment, I added lines 230-240 in the revised manuscript.

      (4) Comments on revisions:

      I am unable to find the author's responses to my previous round comments (Reviewer #3) in the revision package, though replies to the other reviewers are present. I will provide my updated feedback once these responses are available for review.

      My sincere apologies, I neglected the specific comments in error – this document should address them now, thank you again for giving this your time and consideration!

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study presents evidence that addition of the two GTPases EngA and ObgE to reactions comprised of rRNAs and total ribosomal proteins purified from native bacterial ribosomes can bypass the requirements for non-physiological temperature shifts and Mg+2 ion concentrations for in vitro reconstitution of functional E. coli ribosomes.

      Strengths:

      This advance allows ribosome reconstitution in a fully reconstituted protein synthesis system containing individually purified recombinant translation factors, with the reconstituted ribosomes substituting for native purified ribosomes to support protein synthesis. This represents a significant development in the long-term effort to produce synthetic cells.

      Weaknesses:

      The authors carried out additional experiments indicating that ~60% of the reconstituted ribosomes are functional and that a significant proportion are capable of synthesizing GFP from the correct initiation codon to the correct stop codon, and also of producing an enzymatically active protein at appreciable levels. Their SDS-PAGE and MS analyses of N-terminally tagged GFP are also quite useful but did not assess the frequency of initiation at the wrong start codon, termination at the incorrect stop codon, or the frequency of frameshifting during elongation. This would require examining additional reporters designed to examine dependence on a Shine-Dalgarno sequence or the impact of an in-frame stop codon to assess the fidelity of initiation and termination events, respectively, and one with a programmed frameshift site to assess the elongation fidelity of their reconstituted ribosomes.

      In response to the reviewer’s comment, we expanded the MS analysis and performed additional analyses against amino acid sequences corresponding to all three reading frames (updated Supplementary Data 2). As a result, only a single peptide fragment likely derived from the +1 frame was detected, but its intensity was approximately 1/1000 of that of peptide fragments detected from the normal frame. No other out-of-frame peptides were detected, and no evidence of stop-codon readthrough was found. We consider that these results suggest that the kind of deterioration in ribosome function is not occurring in the reconstituted ribosomes. Because this analysis cannot completely rule out abnormal translation events such as initiation from internal start codons or termination at internal stop codons, we also added a statement acknowledging that further analyses will be required to examine all aspects of the translation reaction.

      Reconstitution studies in the past have succeeded by using all recombinant, individually purified RPs that, if successful here, would have eliminated the possibility that one or more unknown ribosome assembly factors that co-purify with native ribosomes was added to their reconstitution reactions.

      The issue raised by the reviewer was already added at the end of the Discussion in the previous revision. We fully agree with the reviewer’s point and we are currently continuing research in our laboratory aimed at achieving a more fundamental understanding of ribosome assembly.

      Reviewer #2 (Public review):

      This study has developed a single-step method to assemble active bacterial ribosomes under near-physiological conditions by using the GTPase factors EngA and ObgE. These factors eliminate the need for the traditional, harsh manipulations of temperature and magnesium levels. This integration is an important step toward the bottom-up construction of synthetic cells.

      Comments on revisions:

      The authors have addressed my concerns in the previous round of review.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors are urged to acknowledge that more sophisticated reporter assays would be required to compare the frequencies of errors occurring at each step of translation using their reconstituted versus native ribosomes.

      As described in our response to Reviewer #1, we performed additional MS analyses, updated Supplementary Data 2, and added a statement acknowledging the reviewer’s comment.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      The paper from Hudait and Voth details a number of coarse-grained simulations as well as some experiments focused on the stability of HIV capsids in the presence of the drug lenacapavir. The authors find that LEN hyperstabilizes the capsid, making it fragile and prone to breaking inside the nuclear pore complex.

      I found the paper interesting. I have a few suggestions for clarification and/or improvement.

      (1) How directly comparable are the NPC-capsid and capsid-only simulations? A major result rests on the conclusion that the kinetics of rupture are faster inside the NPC, but are the numbers of LENs bound identical? Is the time really comparable, given that the simulations have different starting points? I'm not really doubting the result, but I think it could be made more rigorous/quantitative.

      (2) Related to the above, it is stated on page 12 that, based on the estimated free-energy barrier, pentamer dissociation should occur in ~10 us of CG time. But certainly, the simulations cover at least this length of time?

      (3) At first, I was surprised that even in a CG simulation, LEN would spontaneously bind to the correct site. But if I read the SI correctly, LEN was parameterized specifically to bind to hexamers and not pentamers. This is fine, but I think it's worth describing in the main text.

      Comments on revisions:

      I found that the authors addressed my concerns satisfactorily. The other reviewer raised a number of important points regarding the nuances of the model and the interpretation of the simulations, which the authors rebutted. I think the paper in its current form now is a worthwhile addition to the literature.

      Reviewer #3 (Public review):

      I have carefully reviewed the manuscript, the two referee reports, and the authors' detailed responses. I appreciate the substantial effort the authors have invested in addressing the reviewers' comments, and I also recognize the strength and ambition of the work. This is a technically sophisticated study that integrates coarse-grained modeling with live-cell imaging to address an important and timely question regarding HIV-1 capsid inhibition by lenacapavir.

      Embedded within Reviewer #2's report are several substantive points that warrant careful consideration, particularly with respect to framing, terminology, and engagement with the broader literature. I view my role here is to distinguish those issues from claims that I do not find to be supported.

      We thank Reviewer 3 for the positive assessment of our work.

      First, I do not agree with Reviewer #2's central assertion that the manuscript lacks novelty or fails to present meaningful new findings. While individual elements of the system studied herecapsid docking at the NPC, lenacapavir-induced capsid hyperstabilization, capsid rupture, and competition with FG- nucleoporins-have been observed previously, this work provides a coherent, mechanistic account of how these elements are coupled. In particular, the proposed sequence linking LEN-induced lattice hyperstabilization, preferential pentamer loss at the narrow end, NPC-induced mechanical stress, and failure of nuclear import represents a nontrivial integration that goes beyond prior phenomenological observations. I therefore do not view this work as redundant with existing literature.

      We thank Reviewer 3 for the positive assessment of our work.

      That said, Reviewer #2 is correct to note that the manuscript would benefit from broader and more explicit engagement with recent independent studies, including computational and hybrid modeling efforts that address capsid mechanics, nuclear entry, and LEN effects using different frameworks. While the authors' bottom-up coarse-grained approach is clearly distinct and, in many respects, more systematically derived, eLife readers would benefit from a clearer discussion of how the present results relate to, complement, or differ from these other approaches. I strongly encourage the authors to add a short discussion paragraph situating their work within this broader context, without disparaging alternative models.

      We have now added several sentences describing papers that use two other CG models that are of some relevance to our work at the beginning of the fourth paragraph of the Introduction, and we have also highlighted the distinguishing features of our work at the end of that paragraph.

      Second, I find that some mechanistic claims in the manuscript would benefit from more careful language distinguishing model-conditioned interpretation from de novo prediction. This applies in particular to discussions of LEN binding heterogeneity and stoichiometry, as well as to conclusions drawn from biased enhanced-sampling simulations. While I agree with the authors that parameterization does not invalidate mechanistic insight, it is important to be precise about what aspects of the behavior emerge from the simulations versus what is constrained by prior experimental knowledge. Modest tightening/revising of language (e.g., "suggests," "is consistent with," "within the model") would address this concern without weakening the scientific conclusions.

      We have revised and softened the language in several places as suggested. However, we do still asert that our overall CG modeling approach is quite rigorous. The use of limited “top down” information on LEN binding is not problematic and in fact warranted in this problem.

      Third, Reviewer #2 raises a legitimate semantic issue regarding the use of the term "elasticity." The manuscript infers changes in capsid mechanical response using heterogeneous elastic network models, which quantify effective stiffness and deformability rather than elasticity in the macroscopic materials sense. I recommend that the authors clarify this definition explicitly in the text to avoid confusion and unnecessary debate.

      We have now added a clarification at the end of the third paragraph of the subsection entitled “LEN binding to the capsid results in hyperstabilized lattice domains”. We have also added text in the second paragraph of the Discussion. Our view is that our perspective is more useful for this problem than a “macroscopic” perspective as the capsid is, in fact, a mesoscopic object and not a macroscopic one.

      Finally, I note that several of Reviewer #2's objections-particularly those asserting circular reasoning, misuse of enhanced sampling methods, or invalidity of coarse-grained predictions reflect a misunderstanding of contemporary bottom-up coarse-grained modeling rather than genuine methodological flaws. I do not believe these points require further rebuttal or revision beyond what the authors have already provided.

      We agree.

      In summary, in my view, the manuscript represents a solid contribution to the field, provided that the authors undertake a limited set of targeted revisions aimed at improving framing, clarity, and engagement with the broader literature. Addressing these points will strengthen the manuscript and ensure that its contributions are clearly and fairly communicated to the community.

      We have done so as suggested by the reviewer.

    1. Author response:

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

      eLife Assessment

      This valuable study examines the cleavage of motor neuron nucleoporins by proteases 2A and 3C of enterovirus D68, a pathogen associated with acute flaccid myelitis. The evidence supporting the effects of EV-D68 proteases on nuclear import and export is solid and confirms previous results on the specific targeting of nucleoporins by proteases from other enteroviruses. However, the claim that cleavage of nucleoporins by EV-D68 2A is neurotoxic, though intriguing, is incomplete, as the evidence is largely indirect.

      We appreciate that the reviewers highlighted multiple strengths of manuscript, including its detailed mechanistic dissection of the disrupted composition and function of the nuclear pore complex during EV-D68 infection, the finding that the viral 2A protease is toxic to motor neurons, and that several novel hypotheses on the pathogenesis of acute flaccid myelitis that are raised by our work.

      It appears that two independent eLife Assessments were made regarding the strength of evidence in our manuscript. The evidence supporting the impact of EV-D68 proteases on the NPC was felt to be solid.

      A second assessment was made as to whether our data support that “the cleavage of nucleoporins by EV-D68 2A is neurotoxic”. We would like to clarify that we did not intend to make this second claim in our manuscript and thought that we had been careful not to do so. In response to reviewer and editorial feedback, we have edited the text to improve the clarity on this issue. Although our data show that 2A<sup>pro</sup> is toxic to motor neurons, it cannot yet be determined whether this toxicity is mediated via 2A<sup>pro</sup>’s effects on the NPC. That is a logical hypothesis that arises from our manuscript, which we are testing through ongoing work that will require a significant volume of experiments that are outside the scope of the present study. We view this manuscript as an important first step towards a comprehensive understanding of the role of the 2A protease in the pathogenesis of AFM. Please see the response to point # 3 of Reviewer 2 below for a more detailed discussion of this issue and the changes we have made to the text in response. We respectfully request that a judgement on the role of nucleoporin cleavage as the mechanism of neurotoxicity not be included in the eLife Assessment.

      Also in response to reviewer feedback that our data was too reliant on the expression of recombinant viral proteins in isolation, we have added additional experiments extending our results into the context of live virus infection of cell lines and motor neurons. We feel that our revised manuscript has been improved as a result of the reviewers’ and editor’s input, and provides strong support for the following claims: (1) NPC composition and function is disrupted during EV-D68 infection, (2) 2A<sup>pro</sup> is primarily responsible for functional disruption, and (3) 2A<sup>pro</sup> is neurotoxic.

      We appreciate your review of this revised manuscript. Detailed responses to each of the reviewers’ comments are provided below.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Zinn and colleagues investigated the role of proteases 2A and 3C of enterovirus D68 (EVD68), an emerging pathogen associated with outbreaks of acute flaccid myelitis (AFM), a polio-like disease, on the nucleocytoplasmic trafficking in different systems, including human neurons derived from pluripotent cells. They found that 2A specifically cleaved Nup98 and POM121. Using reporter proteins and RNA synthesis and trafficking assays in cells expressing viral proteases, they showed that 2A induces broad loss of the nuclear pore barrier function, but, surprisingly, the RNA export appears to be minimally affected. Since nucleocytoplasmic trafficking defects are known to be associated with neuropatologies, they propose a hypothesis that 2A-dependent cleavage of nucleoporins in motoneurons underlies the development of EVD68-induced AFM. They further show that a 2A-specific inhibitor increases the survival of human neurons differentiated from stem cells upon EVD68 infection.

      Strengths:

      Use of multiple methods to investigate the effect of 2A and 3C expression on nucleoporin cleavage and nucleocytoplasmic trafficking.

      We thank the reviewer for detailed and accurate review of our manuscript and recognition of these strengths.

      Weaknesses:

      Overall, the paper follows multiple others that extensively investigated the cleavage of nucleoporins by enterovirus 2As, so the results are of limited novelty. The hypothesis that infection of motoneurons is the cause of EVD68-induced neurological complications so far is supported by only one autopsy report. Other data suggest that infection of other cell types, such as astrocytes, and/or inflammatory cell infiltration in the CNS, are likely to be responsible for the symptoms. In any case, the claim that EVD68 is specifically neurotoxic because of the 2A-dependent cleavage of nucleoporins in neurons is unfounded, as the virus will be just as "toxic" for other infected cell types.

      While we agree that other papers have investigated this pathway in other enteroviruses, we note that our work is the first to do so in Enterovirus D68 and the most comprehensive study, in terms of the number of nucleoporins studied. As we reviewed in paragraph 5 of the introduction section, the activities of enterovirus proteases against specific nucleoporins varies from strain to strain, and is important to understand any strain-specific effects before determining whether this pathway is relevant to toxicity in AFM.

      The infection of motor neurons is strongly supported not only by the aforementioned autopsy data [1], but also by mouse model data demonstrating replication of EV-D68 within motor neurons in the anterior horn of the spinal cord.[2] There are also numerous reports of electromyography and nerve conduction studies from human AFM patients demonstrating that the site of pathology is the spinal motor neuron.[3-10]

      By contrast, infection of astrocytes has been demonstrated only in primary murine astrocyte cultures in which no neurons were present [11]. Therefore, while the available data suggest that EV-D68 infection of astrocytes is possible, in the in vivo context of human and mouse spinal cord, tropism to motor neurons appears to be preferential. The relative toxicity of neuron-autonomous vs non-autonomous processes such as glial dysfunction and inflammatory cell infiltration remain to be elucidated, and are not mutually exclusive.

      The paper also requires a more convincing presentation of the data.

      We are uncertain what other specific changes the reviewer would like to see based on this comment, but feel that the revisions have improved the presentation of the data.

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigates the role of EV-D68 proteases 2A and 3C in nuclear pore complex (NPC) dysfunction and their contribution to motor neuron toxicity. The authors demonstrate that both proteases cleave only a limited number of nucleoporins, with 2A^pro showing the strongest impact by inhibiting nuclear import and export of proteins and disrupting NPC permeability without affecting RNA export. Importantly, treatment with the 2A^pro inhibitor telaprevir reduced neuronal cell death in a dose-dependent manner, achieving neuroprotection at concentrations below those required to inhibit viral replication. The study addresses a relevant mechanism underlying EV-D68-induced neuropathology and explores a potential therapeutic intervention.

      Strengths:

      (1) Provides significant mechanistic insight into how EV-D68 proteases alter NPC function and contribute to neuronal toxicity.

      (2) The use of recombinant 2A and 3C proteins allows clear dissection of the specific contribution of each protease.

      (3) Demonstrates a therapeutic effect of telaprevir, with neuroprotection independent of viral replication inhibition, adding translational value to the findings.

      (4) The topic is highly relevant given the association of EV-D68 with acute flaccid myelitis.

      We thank the reviewer for their insightful comments and recognition of these strengths in our study.

      Weaknesses:

      (1) Most experiments were performed with recombinant proteases, lacking validation in the context of viral infection, where both proteases act simultaneously.

      In response to this concern, we have added additional experiments in the context of viral infection. We show that POM121 and Nup98 are also cleaved in motor neurons infected with EV-D68 and that their cleavage is inhibited by telaprevir (Fig 4A). We also repeated the EU pulse-chase RNA export assay in EV-D68-infected RD cells and again found no effect on RNA export (Fig 3D-E).

      (2) The conclusion that RNA export is unaffected requires confirmation during actual infection.

      As above, we have repeated this experiment in EV-D68 RD cells, showing no effect of EV-D68 infection on RNA export.

      (3) The reduction of neurotoxicity by telaprevir does not fully demonstrate that the protective effect is solely mediated through NPC preservation; additional analyses of eIF4G cleavage, nucleoporin integrity, and stress granules are needed.

      We agree that while the evidence in our manuscript raises the hypothesis that telaprevir-mediated neuroprotection is mediated via NPC preservation, it does not fully demonstrate this to be the case. As discussed above, we have been careful to state only the following conclusions: (1) NPC composition and function is disrupted during EV-D68 infection, (2) 2A<sup>pro</sup> is primarily responsible for functional disruption, and (3) 2A<sup>pro</sup> is neurotoxic.

      Future work will determine the extent to which NPC dysfunction contributes to 2A<sup>pro</sup>-mediated motor neuron toxicity versus other potential targets of 2A<sup>pro</sup>, as suggested by the reviewer. This work is already underway in our lab and it is clear to us the additional experiments required will be extensive, likely 1-2 additional manuscripts. These experiments are therefore beyond the scope of the present study, which represents a key first step in this line of inquiry.

      We specifically acknowledged in the Discussion that “A significant limitation of our study, however, is that we cannot exclude potentially toxic effects of 2A<sup>pro</sup> on aspects of host neuronal biology aside from the NPC.” We have also made the following adjustments to the text to make it more clear that this remains an open question:

      Change the title to more clearly separate the effects of 2Apro on NPC function and motor neuron toxicity as independent events: “Enterovirus D68 2A protease causes nuclear pore complex dysfunction and independently contributes to motor neuron toxicity”

      In the abstract, shortened the following sentence: “We therefore sought to determine the impact of EV-D68 proteases on NPC composition and function” to avoid any implicit connection that a mechanistic link has been established between these two concepts. Neurotoxicity is now introduced later in the abstract by saying “Independently, we show…” instead of “We further show…”

      Removed language in the last paragraph of the Results section that may have been construed to suggest a mechanistic linkage: “Because similar deficits have been reported to contribute to neurotoxicity in neurodegenerative disease…” and simply stated “We next sought to determine the extent to which 2Apro activity independently contributes to motor neuron injury during EV-D68 infection.”

      Edited the opening sentence of the discussion, where it was ambiguous whether the word “their” was referring to the enterovirus protease (which was our intent) or to NPC disruption as the cause of motor neuron toxicity. We removed the discussion of toxicity from this paragraph entirely to remove such confusion.

      Edited the final paragraph of the discussion to include “We have also demonstrated that 2A<sup>pro</sup> activity contributes to nucleocytoplasmic transport dysfunction and separately to cell death in motor neurons infected with EV-D68”. We then go on to discuss the hypothesis that this toxicity might be mediated partially or entirely through NPC dysfunction, and propose that this be a focus of further study.

      (4) The study would be strengthened by including another 2A inhibitor (e.g., boceprevir) to confirm the specificity of telaprevir's protective effects.

      While we would like to be able to include multiple pharmacologic inhibitors of 2A<sup>pro</sup>, unfortunately telaprevir is the only known inhibitor of EV-D68 2A<sup>pro</sup>. The same study that identified telaprevir as an EV-D68 2A<sup>pro</sup> inhibitor also evaluated boceprevir and determined that its inhibitory activity against 2A<sup>pro</sup> is minimal [12].

      Reviewer #3 (Public review):

      Summary:

      The author showed expression of the viral proteases 2Apro and 3Cpro of EV-D68, which cleaved specific components of the nuclear pore complex (Nup98 and POM121 by 2Apro), and 2A but not 3C expression altered nuclear import and export. Similar nucleocytoplasmic transport deficits are observed in EV-D68-infected RD cells and iPSC-derived motor neurons (diMNs). 2A inhibitor telaprevir partially rescued the nucleocytoplasmic transport deficits and suppressed neuronal cell death after infection. While it's clear that 2A can cleave NPC proteins and affect nuclear transport, the link to neurotoxicity after EV-D68 infection is less convincing.

      This study opens up a very intriguing hypothesis: that EV-D68 2Apro could be directly responsible for motor neuron cell death, mediated by POM121 and possibly Nup98 cleavage, that ultimately results in paralysis known as acute flaccid myelitis. This hypothesis notably does run counter to other published data showing that human neuronal organoids derived from iPSCs can support productive EV-D68 infection for weeks without cell death and that EV-D68-infected mice can have paralysis prevented by depletion of CD8 T cells, still with EV-D68 infection of the spinal cord. However, even if 2Apro is not ultimately responsible for motor neurons dying in human infections, that does not exclude the possibility that cleavage of nups could still disrupt motor neuron function. Notably, most children with AFM have some amount of motor function return after their acute period of paralysis, but most still have some residual paralysis for years to life. It is possible that 2A pro could mediate the acute onset of weakness, while T cells killing neurons could determine the amount of long-term, residual paralysis.

      We thank the reviewer for their thoughtful comments. As discussed above, we agree that the present data demonstrate that 2A<sup>pro</sup> causes NPC dysfunction and is toxic in motor neurons, but has not proven that the mechanism of neurotoxicity is via NPC dysfunction.

      We appreciate the commentary on novel hypotheses opened by our work. Our recent thinking on this topic has been similar and we look forward to addressing these ideas further in future studies. Motor neuron dysfunction and motor neuron death may ultimately prove to have separate causes. The infection of motor neurons is likely the initiating event, with multiple downstream consequences which may be neuron-autonomous, or mediated by glial and inflammatory responses, or a mixture thereof.

      Strengths:

      The characterization of nuclear pore complex components that appear to be targets of both poliovirus and EV-D68 proteases is quite thorough and expansive, so this data set alone will be useful for reference to the field. And the process by which the authors narrowed their focus to EV-D68 2Apro reducing Nup98 and POM121 as consequential to both import and export of nuclear cargo but not RNA was technically impressive, thorough, and convincing. As will be detailed below, when the authors move from studying over-expressed proteases in transformed cell lines to studying actual virus infection in both transformed cell lines and iPSC-derived neurons, some of the data only indirectly support their conclusions; however, the quality of the experiments performed is still high. So even if the claim that 2Apro causes neurotoxicity is circumstantial, the data certainly are intriguing and certainly justify further study of the effects of EV-D68 2Apro on the NPC and how this impacts pathogenesis. This is a convincing start to an intriguing line of inquiry.

      We appreciate the reviewer’s recognition of our comprehensive evaluation of NPC disruption and our approach to arriving at a mechanistic understanding of this process. We agree with the reviewer’s viewpoint that the present study represents a beginning, rather than a conclusive end to this line of inquiry. For technical reasons, we were able to achieve more rigorous and mechanistic data in cell lines expressing recombinant proteins than in neurons infected with live virus. In response the reviewers’ comments, as described above, we have added additional experiments in this revision in which we further evaluate nucleoporin cleavage and RNA export during live virus infection, and performed these experiments in iPSC-derived neurons whenever it was technically feasible to do so.

      Weaknesses:

      This study falls a bit shy of actually showing that 2Apro effects are causing motor neuron toxicity because the evidence of this is fairly indirect. At points, the authors do admit these limitations, but at other times, they claim to have shown the link directly. The following are reasons why these claims are only indirectly supported:

      We agree that we have shown direct toxicity of 2A<sup>pro</sup> in motor neurons, but have not shown that the mechanism is via NPC dysfunction. We felt that we were careful to frame our conclusions as such. However, we have revised the text to improve the clarity on this point as described above.

      (1) Cleavage of Nup98 and POM121 after EV-D68 infection in RD cells and diMNs is never demonstrated.

      We have added data showing the cleavage of POM121 and Nup98 in EV-D68 infected diMNs (Figure 4A).

      (2) Telaprevir was able to rescue nucleocytoplasmic transport in RD cells at low concentrations (Figure 4A). It is not shown if this correlates with its antiviral effect in RD cells, or could this correlate with inhibition of 2A cleavage of Nup98 or POM121, which is never measured.

      In the aforementioned new experiment in Figure 4A, we have also included a dose-response curve for telaprevir showing its inhibition of POM121 and Nup98 cleavage.

      (3) Building off of the prior point, the authors' claim that the neuroprotective effect of telaprevir is independent of its antiviral effect is not well-founded. Figure 4E (neuroprotection) was done with MOI 5, and Figure 4G (virus growth) was MOI 0.5. Telaprevir neuroprotection is not shown at MOI 0.5, nor is the neuroprotective effect correlated with inhibition of 2A cleavage of Nup98 or POM121.

      The selection of MOIs for these two experiments was limited by technical considerations. If the viral growth curve were to be performed at MOI 5, it would be confounded by cell death. Further, a low MOI is required in order to allow multiple rounds of infection, and is therefore more sensitive for assaying the effect of telaprevir on viral replication. On the other hand, at MOI 0.5 diMN death is very gradual, and the neuroprotection assay we would have lacked the statistical power to determine whether a rescue of this small magnitude of toxicity is significant. The EC<sub>50</sub> of telaprevir is not expected to vary at different MOIs.

      We have also now correlated the inhibition of 2A<sup>pro</sup> cleavage of Nup98 and POM121 with the neuroprotective effect at comparable concentrations of telaprevir, as described above.

      (4) The use of mixed virus isolates only in the diMNs is problematic because different EV-D68 isolates are known to have drastically different effects on pathogenesis in mice. Since all initial data were generated with the MO isolate, adding the additional MD isolate to the diMN experiments actually adds uncertainty to the conclusions. It is not clear if the authors infected different cultures with the different isolates and combined the data or infected all cultures with a mixture of the two isolates. If the former, then the data should be reported separately to see the effect of each individual strain, which would be interesting to EV-D68 virologists. If the latter, then there is no way to know from these data whether one of the two isolates had increased fitness over the other and exerted a dominant effect. If the MD isolate overtook the MO isolate, from which all other data in this manuscript are derived, then we have much less of an idea how much the data from the first three figures supports the final figure.

      We apologize for the lack of clarity in describing this experiment. The MO/2014 and MD/2018 isolates were not mixed. These were performed in separate experiments, each with four biologically independent replicates. The original figure showed the mean and SEM for these 8 replicates together. To improve clarity, we separated each viral strain into its own panel of the figure. We have also increased the rigor of the statistical analysis in this experiment by using Cox proportional hazard regression instead of ANOVA.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Please consider both public reviews above and recommendations for the authors below. The general consensus among reviewers is that more evidence is needed to support the claim that 2A causes motor neuron toxicity during infection.

      Reviewer #1 (Recommendations for the authors):

      Most of the conclusions are made upon analysis of images, yet the images themselves are seldom shown. It is difficult to evaluate the validity of conclusions without seeing the material that was analyzed.

      (1) Figure 1. Representative Western blots should be shown.

      We considered including representative western blots in this already large figure, however the figure size and complexity became un-manageable because the figure summarizes the quantification of 246 Western blots. In the original submission, we uploaded a supporting data file that included complete un-cropped Western blots for all experiments, including ladders, loading controls, and clear labeling of the samples. We believe these data allow the reader to assess the quality and reliability of our Western blot experiments while maintaining the approachability of the figures and data presentation. We have also included these supporting data again in the revised manuscript.

      (2) Figure 3. Representative images should be shown. This is especially important for the ethynyl-uridine labeling experiment. It would be highly surprising that RNA transcription and processing would proceed normally in 2A-expressing cells on the background of a major redistribution of nuclear proteins. One possible explanation for that would be that cells that can be analyzed express a relatively small amount of 2A, which is known to be toxic, and thus may not fully represent the cellular changes upon infection. The results from bona fide infected cells would be much more convincing.

      Representative images have been added for the ethynyl-uridine pulse-chase experiment, and this experiment has been repeated in RD cells infected with EV-D68. Transfection of proteases or infection of the cells utilized the same protocols and timeframes upon which nucleoporin cleavage and disruption of protein transport were found to be present. The timepoint for all of these experiments was selected to precede the onset of toxicity, and the representative images demonstrate normal cellular morphology. We also selected for analysis only GFP+ cells with normal morphology, ensuring that only viable 2A<sup>pro</sup>-GFP-expressing cells were included in the analysis. The new experiments again showed no effect on RNA export. We were equally surprised as the reviewers by this outcome. However, as we note in the text, disruption of RNA export has not been uniformly present across all enteroviruses previously studied.

      (3) Figure 4 A-D. Similarly, representative images should be shown.

      We have added representative images for these experiments, which are now Fig 4B-E.

      (4) Figure 4G. The demonstration that the "neuroprotective" effect of 2A inhibitor is not related to the inhibition of viral replication requires a control showing that a similar inhibition of viral replication by an inhibitor with another target would not similarly diminish cell toxicity.

      Neuronal survival experiments showed inhibition of toxicity with concentrations of telaprevir as low as 0.3 uM, a concentration at which there was no significant effect on viral replication. Telaprevir had only a marginal inhibitory effect on viral replication at 10uM (achieving statistical significance in only one of two strains), and no consistent effect on replication at lower concentrations. Therefore, the suggested control experiment would not be possible, because the neuroprotective concentration of telaprevir does not inhibit viral replication

      Reviewer #2 (Recommendations for the authors):

      Major concerns:

      (1) Most of the experiments were performed with recombinant 2A and 3C proteins. While these experiments are highly informative for dissecting the role of each protease in NPC dysfunction, it would be important to also perform experiments in the context of infection. How are import and export processes affected when both proteases are present during infection? How is passive transport modified under these conditions?

      Thank you for this important comment. Please see the above discussion of additional experiments that we added utilizing live virus infection to complement the experiments that used recombinant proteins.

      (2) The results regarding RNA export in the presence of recombinant 2A and 3C proteases suggest that RNA export is not altered. It would be important to confirm this finding during infection.

      We agree that this is an important experiment, and have done so as described above.

      (3) While the background information suggests that NPC dysfunction contributes to neurotoxicity, the observed reduction of neurotoxicity by telaprevir does not demonstrate that this effect is solely due to the action of 2A on the NPC. It would be important to evaluate the integrity of eIF4G, nucleoporins, and stress granules during treatment.

      We agree that additional experiments would be required to determine the extent to which the toxicity of 2A<sup>pro</sup> is mediated through its effects on the NPC versus other potential targets. Please see above discussion for more details.

      (4) Including another 2A inhibitor (e.g., boceprevir) would strengthen the conclusions by confirming the results obtained with telaprevir.

      Please see above discussion of boceprevir

      Reviewer #3 (Recommendations for the authors):

      (1) Preferred ICTV nomenclature abbreviates rhinovirus as RV instead of HRV, so the authors should change their abbreviations appropriately. See Simmonds et al.

      Archives of Virology (2020) 165:793-797 https://doi.org/10.1007/s00705-019-04520-6

      We have updated these abbreviations accordingly.

      (2) There is no mention of Figures 1C and 1D in the text.

      These have been added in the appropriate locations.

      (3) In the section "2A protease alters nucleocytoplasmic trafficking of protein substrates" it would be very helpful to just directly state what each construct is meant to demonstrate. Along the lines of "NLS-tdTomato should be located in the nucleus, so seeing more signal in the cytoplasm would indicate a defect in nuclear import." And something equivalent for the other two constructs.

      Thank you for the suggestion. We have added descriptions of the use and interpretation for each construct.

      (4) The following sentence would be more accurate with the addition of "partially" because the effect is not returned to normal levels: "The mislocalization of NLS-tdTomato was partially rescued by 3μM telaprevir."

      We have edited this as recommended.

      (5) SNAP29 is probably a typo and meant to be CREB in the legend of Figure 1B.

      Thank you for catching this. We have corrected this to CREB.

      (6) "Panel A" should likely be "Panel E" in the Figure 4F legend.

      We have corrected this to refer to the appropriate panel, which has also been re-lettered due to the addition of new panels to this figure.

      (7) The authors should at least show representative Western blot data used to determine the data for Figure 1 in a supplemental figure.

      As discussed above, these Western blots were included as supplemental data in the original submission, and have also been included in the revised version.

      (8) As suggested in the public comments, if the diMNs were infected separately with the MO and MD strains of EV-D68, those data should be separated from each other and reported individually. In any case, whatever was done (combined virus inoculum or separate inocula) needs to be clarified.

      These data are now reported separately. Please see above discussion for details.

      References:

      (1) Vogt MR, Wright PF, Hickey WF, De Buysscher T, Boyd KL, Crowe JE, Jr. Enterovirus D68 in the Anterior Horn Cells of a Child with Acute Flaccid Myelitis. N Engl J Med. May 26 2022;386(21):2059-2060. doi:10.1056/NEJMc2118155

      (2) Hixon AM, Yu G, Leser JS, et al. A mouse model of paralytic myelitis caused by enterovirus D68. PLoS Pathog. Feb 2017;13(2):e1006199. doi:10.1371/journal.ppat.1006199

      (3) Andersen EW, Kornberg AJ, Freeman JL, Leventer RJ, Ryan MM. Acute flaccid myelitis in childhood: a retrospective cohort study. Eur J Neurol. Aug 2017;24(8):1077-1083. doi:10.1111/ene.13345

      (4) Elrick MJ, Gordon-Lipkin E, Crawford TO, et al. Clinical Subpopulations in a Sample of North American Children Diagnosed With Acute Flaccid Myelitis, 2012-2016. JAMA Pediatr. Feb 1 2018;173(2):134-139. doi:10.1001/jamapediatrics.2018.4890

      (5) Hovden IA, Pfeiffer HC. Electrodiagnostic findings in acute flaccid myelitis related to enterovirus D68. Muscle Nerve. Nov 2015;52(5):909-10. doi:10.1002/mus.24738

      (6) Knoester M, Helfferich J, Poelman R, et al. Twenty-Nine Cases of Enterovirus-D68 Associated Acute Flaccid Myelitis in Europe 2016; A Case Series and Epidemiologic Overview. Pediatr Infect Dis J. Jan 2018;38(1):16-21. doi:10.1097/INF.0000000000002188

      (7) Martin JA, Messacar K, Yang ML, et al. Outcomes of Colorado children with acute flaccid myelitis at 1 year. Neurology. Jul 11 2017;89(2):129-137. doi:10.1212/WNL.0000000000004081

      (8) Saltzman EB, Rancy SK, Sneag DB, Feinberg Md JH, Lange DJ, Wolfe SW. Nerve Transfers for Enterovirus D68-Associated Acute Flaccid Myelitis: A Case Series. Pediatr Neurol. Nov 2018;88:25-30. doi:10.1016/j.pediatrneurol.2018.07.018

      (9) Van Haren K, Ayscue P, Waubant E, et al. Acute Flaccid Myelitis of Unknown Etiology in California, 2012-2015. JAMA. Dec 22-29 2015;314(24):2663-71. doi:10.1001/jama.2015.17275

      (10) Natera-de Benito D, Berciano J, Garcia A, E MdL, Ortez C, Nascimento A. Acute Flaccid Myelitis With Early, Severe Compound Muscle Action Potential Amplitude Reduction: A 3-Year Follow-up of a Child Patient. J Clin Neuromuscul Dis. Dec 2018;20(2):100-101. doi:10.1097/CND.0000000000000217

      (11) Rosenfeld AB, Warren AL, Racaniello VR. Neurotropism of Enterovirus D68 Isolates Is Independent of Sialic Acid and Is Not a Recently Acquired Phenotype. Mbio. 2019;doi:10.1128/mBio

      (12) Musharrafieh R, Ma C, Zhang J, et al. Validating Enterovirus D68-2A(pro) as an Antiviral Drug Target and the Discovery of Telaprevir as a Potent D68-2A(pro) Inhibitor. J Virol. Jan 23 2019;doi:10.1128/JVI.02221-18

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Fogel & Ujfalussy report an extension of a visualization tool that was originally designed to enable an understanding of detailed biophysical neuron models. Named "extended currentscape", this new iteration enables visual assessment of individual currents across a neuron's spatially extended dendritic arbor with simultaneous readout of somatic currents and voltage. The overall aim was to permit a visually intuitive understanding for how a model neuron's inputs determine its output. This goal was worthwhile and the authors achieved it. Their manuscript makes two additional contributions of note: (1) a clever algorithmic approach to model the axial propagation of ionic currents (recursively traversing acyclic graph subsections) and (2) interesting, albeit not easily testable, insights into important neurophysiological phenomena such as complex spike generation and place field dynamics. Overall, this study provides a valuable and well-characterized biophysical modeling resource to the neuroscience community.

      Strengths:

      The authors significantly extended a previously published open-source biophysical modeling tool. Beyond providing important new capabilities, the potential impact of "extended currentscape" is boosted by its integration with preexisting resources in the field.

      The code is well-documented and freely available via GitHub.

      The author's clever portioning algorithm to relate dendritic/synaptic currents to somatic yielded multiple intriguing observations regarding when and why CA1 pyramidal neurons fire complex spikes versus single action potentials. This topic carries major implications for how the hippocampus represents and stores information about an animal's environment.

      Weaknesses:

      While extended currentscape is clearly a valuable contribution to the neuroscience community, this reviewer would argue that it is framed in a way that oversells its capabilities. The Abstract, Introduction, Results, and Methods all contain phrases implying that extended currentscape infers dendritic/synaptic currents contributing to somatic output., i.e. backwards inference of unknown inputs from a known output. This is not the case; inputs are simulated and then propagated through the model neuron using a clever partitioning algorithm that essentially traverses a biologically undirected graph structure by treating it like a time series of tiny directed graphs. This is an impressive solution, but it does not infer a neuron's input structure.

      We are sorry if our text could be interpreted as if we were inferring unobserved inputs from the known outputs. This was not intentional and we were unaware of the possibility of such interpretation.

      In fact, at the beginning of the Results, we started the description of the extended currentscape method by explicitly stating that we need to measure the input currents: “Our method … requires measuring the membrane and axial currents throughout the dendritic tree of a neuron (in every node of the circuit)”.

      To further clarify that our method starts with measuring the input currents, we made this information explicit already in the abstract (“Our approach relies on the iterative decomposition of the axial current flowing between neighbouring compartments in proportion to the underlying membrane currents measured in the model.”), and in the Introduction (“Even if the membrane currents are known, studying the impact of particular ion channels on the neuronal response in such a dynamical system under in vivo conditions is hindered by two major obstacles”). We also rewrote several parts of the text to remove any phrases that could imply the inference of the inputs (line 568). We believe that after clarifying this at the beginning of the paper, the readers will not misinterpret our descriptions later in the text.

      Because a directed acyclic graph architecture is shown in Figure 2, it is unintuitive that the authors can infer bidirectional current flow, e.g. Figure 3 showing current flowing from basal dendrites and axon to soma, and further towards the apical dendrites. This is explained in Methods, but difficult to parse from Results amidst lots of rather abstract jargon (target, reference, collision, compartment). Figure 2 would have presented an opportunity to clearly illustrate the author's portioning algorithm by (1) rooting it in the exact morphology of one of their multicompartmental model neurons and (2) illustrating that "target" and "reference" have arbitrary morphological meanings; they describe the direction of current flow which is reevaluated at each time step.

      We thank for this comment. We agree that the concepts introduced here to explain our method are rather abstract and could be difficult to understand. To help the reader we followed the instructions of Reviewer and redesigned Fig. 2 to provide a step by step explanation of the extended currentscape method. In particular,

      We used a simpler model where the structure of the graph can be directly related to the morphology of the model.

      We show that the target node can connect multiple subtrees with axial currents flowing in different directions. We explain that in this case the inward and the outward subtrees are pruned and partitioned separately.

      We provide a glossary in Table 1 to ensure that the readers can follow our description and do not get lost amidst lots of rather abstract jargon.

      We also clarified that although the target compartment is chosen arbitrarily by the user, it remains the same for all time points throughout the analysis.

      Analyses in Figure 7, C and D, are insightfully devised and illuminating. However, they could use some reconciliation with Figure 5 regarding initiation of individual APs versus CSBs within place fields.

      We thank the reviewer for the positive comments and also for pointing out the potential source of misunderstanding. We slightly changed the text at Fig 5 to emphasize that this is a single example trial, and we added the following sentence to the paragraph describing Fig 7CD: “Consequently, the somatic current dynamics before the iAP and the CSB presented in Fig 5Cc-Dd can be regarded as illustrative samples from a broad distribution, but the differences observed between them are not representative.}”

      The intriguing observations generated by extended currentscape also point to its main weakness, which the authors openly acknowledge: as of now, no experimental methods exist to conclusively tests its predictions.

      We agree with the Reviewer that not being able to apply our extended currentscape method to reveal the current types driving real neurons recorded in vivo is currently a weakness of our approach. However, we would like to emphasize that it may be feasible to use it to estimate the spatial distribution of the membrane currents driving the cell based on in vivo voltage imaging data, as we briefly outline in the discussion.

      Reviewer #2 (Public review):

      Summary

      The electrical activity of neurons and neuronal circuits is dictated by the concerted activity of multiple ionic currents. Because directly investigating these currents experimentally isn't possible with current methods, researchers rely on biophysical models to develop hypotheses and intuitions about their dynamics. Models of neural activity produce large amounts of data that is hard to visualize and interpret. The currentscape technique helps visualize the contributions of currents to membrane potential activity, but it's limited to model neurons without spatial properties. The extended currentscape technique overcomes this limitation by tracking the contributions of the different currents from distant locations. This extension allows tracking not only the types of currents that contribute to the activity in a given location, but also visualizing the spatial region where the currents originate. The method is applied to study the initiation of complex spike bursts in a model hippocampal place cell.

      Strengths.
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      The visualization method introduced in this work represents a significant improvement over the original currentscape technique. The extended currentscape method enables investigation of the contributions of currents in spatially extended models of neurons and circuits. 
>

      Weaknesses.

      The case study is interesting and highlights the usefulness of the visualization method. A simpler case study may have been sufficient to exemplify the method, while also allowing readers to compare the visualizations against their own intuitions of how currents should flow in a simpler setting. 
>

      We thank the reviewer for this comment. In fact we had been also considering to include a simpler case study to illustrate the extended currentscape method in the original submission. In accordance with the comments from Reviewer 1, we now use a simple model to introduce the concepts in Figure 2 and provide a few examples where the reader can compare the results with their own intuition in simpler cases.

      Recommendations for the authors:

      Reviewing Editor Comments:

      (1) Model complexity vs. intuition/validation. The case study relies on a very complex CA1 model, making it difficult to build intuition about current flow and to validate the visualization. Inclusion of a simpler benchmark (e.g., soma plus a dendrite with two branches, fewer compartments) is recommended to demonstrate how the extended currentscape behaves in a more tractable setting.

      Inspired by the suggestions of the Reviewers, we modified Figure 2 and now first use a simple model with a soma and a dendrite with two branches to introduce the concepts of our analysis. We start with a few examples where the reader can compare the results with their own intuition in simpler cases.

      (2) Rationale and citations for input structure. The in vivo-like input design (untuned inhibition; 12 co-tuned excitatory clusters with large conductances; the goal of generating place fields) would benefit from a more explicit rationale and substantially more literature support. Alternative plausible scenarios (e.g., distributed co-tuned inputs and homosynaptic plasticity) should be articulated, and choices situated within the experimental literature on CA1 excitation/inhibition, including tuning and anti-tuning results.

      We extended the paragraph in the Results describing the input structure and added the most important references there. We added further references to the Methods section where we argue that “Reliable place cell tuning can be achieved by functional synaptic clustering without increased excitatory drive in the place field (Ujfalussy and Makara 2020) or via strong excitatory drive without input clustering (Grienberger et al., 2017, Ujfalussy and Makara, 2020). However, experimental data indicates that both of these mechanisms are present and contribute to the activity of place cells (Adoff et al., 2021,Tasciotti et al., 2025)” and “although interneurons can display spatial tuning, they typically have a broad tuning with low selectivity (Ego-Stengel et al., 2007, Dupret et al., 2013, Geiller et al., 2020). A weak disinhibition within the place field can also contribute to the selective firing of place cells (Geiller et al., 2022, Valero et al., 2022), this was not necessary for place cell activity in novel environments (Geiller et al., 2022) and the overall inhibitory input to place cells is largely untuned (Grienberger et al., 2017).”

      (3) Scope of PCA-based claims. The interpretations derived from the PCA analysis appear broader than warranted, given subcellular heterogeneity and the dominance of somatic action potential variance. These claims should be tempered with more explicit statements about what PCA can and cannot resolve in this context.

      We thank the Reviewer for the opportunity and encouragement to clarify this part of the text. We agree with the Editor and the Reviewers that the results of the PCA analysis can not be used to support claims regarding the presence or the absence of independent dendritic events. In fact, we aimed to use it as an illustration that global activity tends to dominate PCA analysis even when the “neuron is mainly driven by strong, functionally clustered synaptic inputs to a few dendritic branches”. We acknowledge that we did not formulate this point clearly in the original submission. Therefore we substantially rewrote this part of the Results and performed additional analysis to clarify that there is a substantial amount of soma-independent dendritic activity in our model that remains invisible for a PCA based analysis.

      Reviewer #1 (Recommendations for the authors):

      Major concerns:

      (1) Depolarization-inactivated K+ may be an important consideration to model burst-firing.

      Our current model includes 2 kinds of transient K+ channels that show inactivation after depolarization: a proximal and a distal type, as the original model in Jarsky et al., 2005. We now made this explicit in the main text (line 178).

      (2) Description of the in vivo-like model's excitatory and inhibitory input structure needs many more citations of biological studies to communicate rationale for the author's decisions, e.g. untuned inhibitory neurons, organization of a subset of excitatory inputs into 12 function synaptic clusters with co-tuned presynaptic neurons and outsized synaptic conductances. The goal is clearly to create CA1 pyramidal neurons with place fields, which would be helpful to state upfront. But additionally, (a) place fields could arise from homosynaptic potentiation of distributed co-tuned excitatory inputs (e.g., Bittner, et al. 2017 study describing BTSP made no assumptions) and (b) CA1 inhibitory interneurons can be spatially tuned (Ego-Stengel & Wilson, 2006; Wilent & Nitz, 2007; Geiller, et al. 2020) and even anti-tuned (Geiller, et al. 2021).

      We thank the Reviewer for pointing out the lack of appropriate references in this section. We made the following changes in the manuscript:

      (1) Stated explicitly that the goal was to create place cell activity.

      (2) Added references to the main text to justify our choices of the inputs (lines 234-241).

      (3) We included a longer rationale for the choice of synaptic clusters and the lack of inhibitory (anti-)tuning in the Methods section, describing the neuron model. In brief, Adoff et al., 2021 reported more clustering of excitatory inputs within the place field. In our model, the degree of clustering is somewhat larger than the clusters reported. Although inhibitory neurons can be tuned, their tuning is much weaker than that of place cells and seems to play only a minor role in the generation of place fields (Grienberger et al., 2017). The presence of inhibitory anti-tuning is controversial: although Geiller et al., 2021 reported weak (~10%) anti-tuning, they did not find it in novel environments, indicating that it is not needed for spatially selective activity (lines 628-646).

      (3) Interpretation of principal component-based analyses shown in Figure 4 could be toned down. As written in section "CSBs in the CA1 pyramidal neuron", it sounds like CA1 pyramidal neuron dendrites display minimal autonomous activity. However, PCA does not seem well-suited to address the heterogeneity of subcellular voltage dynamics over physiologically relevant timescales. Somatic action potentials, and their backpropagation/modulation of dendritic voltage, would of course explain a very large fraction of variance. However, if local dendritic events summate over fine timescales to initiate somatic firing, it is hard to imagine this important nuance being detected. On the other hand, it is hard to imagine single dendritic branches driving robust somatic firing except in the relatively extreme situation in which large numbers of synapses synchronously drive the same branch to initiate a local Ca2+ spike (Figure 3, A-C).

      We agree with the reviewer that PCA can not reveal the potential dendritic origin of somatic APs, and thus is not suitable to assess the role of local dendritic spikes in shaping the output of the cell. We wanted to highlight here that even in cells with excitable dendrites driven by strong, local input clusters, exhibiting frequent local dendritic spikes, the dendritic membrane potential dynamics will be dominated by global fluctuations with surprisingly little sign of local dynamics in the PCA components. As the reviewer also pointed out, this may not be surprising as local events either remain spatially restricted and thus contribute little to the overall variability of the dendritic Vm or they initiate somatic APs and will thus be counted as global events.

      To demonstrate the high propensity of local dendritic events, we analysed local Vm peaks in dendritic branches and found that ~7.6% of the peaks were not coupled to somatic APs.

      Although this number could seem low, we emphasize that most of the 92.4% of the dendritic peaks coupled to APs potentially reflect the backpropagation of the same somatic events to multiple dendritic sites. To confirm this, we performed an additional analysis measuring the spatial extent (number of branches involved) of the individual dendritic events. We found that 90% of the events remained local, restricted to a few dendritic branches, while 10% of the events were global, associated with BAPs and involving the majority of the dendritic tree. Interestingly, these global events dominate the PCA analysis and are responsible for >90% of the dendritic Vm peaks. These results are included in a new panel in Figure 4H.

      We conclude that, “this way, although only 10% of the dendritic Vm events were associated with bAPs, they were ~60-times larger than local events and they dominated the PCA analysis even in the presence of local regenerative dendritic events driven by strong, functionally clustered synaptic inputs.” We believe that this model and analysis could serve as an important benchmark for future experimental studies investigating the structure of membrane potential correlations in in vivo voltage imaging data (Lee et al., 2026).

      (4) One suggestion would be to display more data as shown in Figure 4F, with a longer X axis to clarify the temporal relationship between local dendritic spikes and the first somatic action potential.

      We added a few more examples including the CSBs presented in Fig8G-I as a new supplementary Figure S4. We also slightly extended the x-axis on this supplementary figure as the reviewer requested.

      If the models indicate that passively filtered EPSPs drive most somatic action potentials, as seems to be the case in Figure 5, then this would also be helpful to show as in Figure 4F.

      In Fig 5 we showed two examples of isolated APs. The first AP was indeed driven by passively filtered EPSPs. The second one was preceded and possibly caused by a dendritic spike, as highlighted by the black arrowhead labelled c in Fig. 5Cc. We further analysed the currents driving iAPs in Fig 7B and C, and found that there is considerable heterogeneity in the magnitude of the dendritic Na currents driving the soma before action potentials. Figure 8 and Figure S3 (now Fig. S5) show further examples for iAPs driven either by passively filtered EPSPs or dendritic spikes. We also included these examples in the new supplementary Figure S4.

      (5) Another suggestion would be to use one-hot vectors containing onset times of different event types, since this would divorce the amplitude/duration of events from their influence over total variance.

      In this paper our goal was to illustrate the ability of the extended currentscape method to reveal the origin of the axial currents driving neuronal activity. In Fig. 4, our primary intention was to characterize the membrane potential response of the model in a way that is easily comparable with experimental data. To further quantify the frequency of local events, we added a new panel showing the spatial extent of dendritic events (Fig. 4H). To make our model more comparable with recent publications, we also calculated two additional metrics used to evaluate the relationship between somatic and dendritic activity (Fig 4I-J). We hope that these additional analyses help the reader to characterize the prevalence and impact of local dendritic events on somatic activity.

      (6) From section "Input conditions for complex spike burst generation", paragraph 2: "Note that synapse density, the ion channel mechanisms and the input statistics are identical for tuft and oblique branches,...". The authors should justify this parameterization given the numerous known differences between tuft and oblique branches in both of these regards and acknowledge accompanying interpretational caveats.

      We agree with the reviewer that experimental data demonstrated several significant differences between the tuft and oblique branches regarding both the inputs they receive and the way they process it. However, in the present paper we chose not to include these differences for several reasons:

      Here we aimed to focus on the abilities of the dendritic currentscape methods and use CSBs as a case study to illustrate how dendritic currentscape can reveal the membrane currents underlying complex neuronal responses.

      Currently there is no CA1PN model that would be able to reproduce all data regarding tuft and oblique integration and would be able to fire calcium spikes. We only wanted to make minimal modifications to the existing CA1PN model to make it capable of generating Ca-spikes and CSBs. We are currently working towards developing and extensively testing a new model, examining the role of these regional differences in CSB generation.

      Although there is information regarding input statistics and dendritic physiology in the literature, many of the relevant parameters are underconstrained. We wanted to avoid overfitting by keeping the model simple.

      By maintaining identical inputs and ion channel distribution we can distinctly highlight the special role of tuft morphology in CSB generation. Altering the inputs or the ion channel density for the tuft would make the interpretation more ambiguous, and elucidating the specific role of the different factors in CSB generation is the subject of future investigations.

      In sum, although we acknowledge that our model does not reflect the full complexity of CA1 PNs and its inputs, we regard this simplicity as a useful feature of the model. We added a section discussing potential future extensions of the model and highlighting interpretational caveats in the discussion (lines 482-490).

      (7) Given the debate in the field regarding the level of functional autonomy present in dendrites, the authors' finding that dendritic voltage largely tracks that of the soma (though see concern above re: PCA), and their access to specific currents, the authors have an important opportunity investigate the divergence between Ca2+ and voltage sensors as reporters of dendritic activity.

      For instance, why have some studies reported relatively common isolated dendritic Ca2+ transients in CA1 pyramidal neurons while other studies, including voltage imaging studies, have reported the opposite?

      We thank the Reviewer for the opportunity to highlight a few important points regarding functional autonomy of dendrites based on the analysis of our model. We would like to first note that only parallel calcium and voltage imaging studies will be able to ultimately resolve this debate. Nevertheless, below we briefly summarize our take on this issue.

      (1) In general, most Ca2+ imaging studies found that soma-independent dendritic events are rare. "Isolated dendritic transients (no coincident somatic event; see fig. S6, C and D, for example) were overall rare. Isolated apical dendritic Ca2+ transients, which have not previously been reported in CA1PNs, were larger and more frequent than those observed in basal dendrites." (O’Hare et al., 2022). "Activity in the ... basal dendrites ... along the track but outside of the place field was rarely observed” (Sheffield and Dombeck, 2014) and “overall, isolated dendritic transients were similar in size but occurred far less frequently than coincident dendrite-soma transients”, or “data indicate that spatially reliable dendritic firing was almost exclusively yoked to somatic tuning, likely reflecting strong backpropagation of burst firing during traversals of the somatic PF” (Rolotti et al., 2022). Consistent with this observation, a dendritic Vm peak chosen randomly from any branch has ~93% probability to be related to a bAP in our model. However, it is also true that ~90% of events in the model are local events, simply because isolated events involve ~60-times fewer branches (1.8 on average) than events associated with bAPs (114 branches) in the model. If the spatial extent of typical local events are also similarly small in real neurons as in the model, then even rare occurrences of dendritic events may reveal substantial dendritic independence. We added a section quantifying the functional autonomy of dendrites in the model in the main text, around Fig 4H.

      (2) Ca2+ indicators are slower and nonlinear and thus they are somewhat unreliable reporters of dendritic voltage events, especially in distal dendrites (Wu et al., 2026; Gonzalez et al., 2026). To illustrate this, we calculated three metrics in our model that were also reported in recent dendritic Ca2+ imaging studies (Rolotti et al., 2022, Sheffield et al., 2014, 2017). First, we calculated the fraction of bAPs detected in a branch (called dendrite-soma coupling in Rolotti et al., 2022, see their Fig. 2C) as a function of the distance of the branch from the soma (our new Fig. 4I). In the Ca2+ imaging data, this was essentially constant ~30% between distances 5-100 µm from the soma. In contrast, the fraction of bAPs detected in the model was 100% in this range as bAPs propagation failures did not occur before µ100 µm. This is also consistent with a recent voltage imaging study showing that even low-transmission bAPs reliably propagate to the proximal dendrites (Lee et al., 2026, Fig 3G). The low and distance independent dendrite-soma coupling reported by Rolotti et al. can only be reconciled with the known biophysics of neurons if the recorded calcium signal is unreliable reporter of the underlying voltage. Indeed, it has been reported that Ca signals associated with bAPs can be absent in some dendritic branches (Landau et al., 2022) or that local, nonlinear Ca signals can appear in the absence of local regenerative voltage response (Weber et al., 2016, Tran-Van-Minh et al., 2016) and that the Ca signals are highly variable across cells (Eltes et al., 2019).

      Second, we calculated the fraction of local events as a function of the distance from the soma (our Fig 4J; see also Fig. 2F in Rolotti et al.). When averaged across all branches, this was somewhat lower in the model (18%) than in the data (38%) which, again, could be explained by the low reliability of detecting global voltage events in all compartments based on the calcium signal.

      Third, the range of branch-spike-prevalence (BSP) values in our model (0.5-0.9; Fig. 4H) seem consistent with that reported (0.4-0.8) at first (Fig 4C of Sheffield et al., 2014; Fig 2 of Sheffield et al., 2017). However, we note that there are several important differences: for technical reasons, Sheffield et al. reported BSP for place field traversals and not for individual events, and they measured Ca2+ dynamics in the basal dendrites. Since bAPs are almost always present in all basal dendrites in the model (basal BSP > 0.9 for all events with somatic spikes) and place field traversals were always accompanied by somatic APs, BSP for basal dendrites would be nearly 1 in the model. Thus, the lower BSP values reported by Sheffield et al. could be explained by the limited reliability of the Ca2+ indicators in reporting regenerative voltage events in neuronal processes.

      We briefly discussed these differences in the Discussion (lines 474-478).

      (3) Finally, to our knowledge, there are 3 relevant in vivo voltage imaging studies in CA1 PNs. Liao et al., 2024 found that in induced place cells the tuning of dendritic events (presumably local or back-propagating Na-spike) was similar to the somatic tuning, which is consistent with our model where dendritic activity and tuning is dominated by bAPs. However, they did not acquire simultaneous signals from the dendrites and the soma so they could not study the independence of the dendritic events. Lee et al. (2026) found that only 10% of the dendritic events are not associated with a somatic spike, which is lower than the number of independent events in the model. However, the events they found were generated in the distal apical trunk (their Fig 3D) and they could not record from the most distal branches where most of the isolated events were generated in our model. Gonzalez et al., 2026 measured voltage and calcium in selected locations within the dendritic tree, and could not reliably estimate the fraction of isolated events throughout the cell. (Gonzalez et al, 2024 measured voltage only in single spines and soma, but did not quantify independent dendritic events; Wong-Campos et al., 2023 measured dendritic integration and bAPs in L23 branches; Wu et al. 2026 recorded in CA2 neurons.)

      We added a paragraph in the discussion comparing the level of functional autonomy present in the model dendrites to recent Ca- and voltage-imaging studies (lines 467-474).

      Minor concerns:

      (1) Abstract:

      There is a need to explain what currentscape is - even at the cost of not invoking its name. To a reader not familiar with currentscape, the abstract is extremely difficult to understand.

      We reworded the title and the abstract to make them more accessible to readers not familiar with the term currentscape.

      (2) "Currentscape analysis of place field dynamics" section:

      It would be helpful to emphasize upfront that dendritic determinants of individual somatic APs versus CSBs will be discussed separately. Since somatic action potentials are discussed before CSBs, I found this section initially confusing as I attributed those findings to CSBs until reading the next paragraph.

      We added a sentence to clarify that we analysed subthreshold responses, APs and CSBs separately.

      (3) Bottom of p2 discussing mixed literature on what drives CSBs in CA1 PCs:

      Overall accurate and useful point, but an important nuance is glossed over which misportrays state of field. References ex vivo studies that fail to drive CSBs with somatic current injection and in vivo study successfully doing so. These aren't really conflicting results. In vivo current injection co-occurs with spontaneous synaptic input, which is high in CA1 and results in PCs that are significantly depolarized at rest relative to those in acute slices. Bittner 2017 ex vivo results are consistent with this: CSBs driven by Cs+-based internal solution to block K+ channels (partially, using strategy of purposefully high series resistance). Similar situation in vivo given that A-type K+ channels are inactivated by depol. Resulting increase in input resistance lowers input threshold to CSB. This is clarified in Results, p.5: "Under in vivo-like synaptic input conditions (see below and Methods), dendritic Ca2+-spikes could also be evoked by somatic current injection (Fig. S1E), as in Bittner et al. (2015).", which makes p. 2 feel especially awkward.

      We agree with the Reviewer that these are not necessarily conflicting results. We rephrased this section, emphasizing that the role of the different input pathways in the initiation of CSBs are not clear.

      (4) Abbreviating "pyramidal neuron" with PC is confusing:

      PC often means place cell. The authors could change this, such that PC refers to "pyramidal cell", or else use PN as an abbreviation. It is important to avoid confusion, especially because place cell dynamics feature prominently in the manuscript.

      Thanks for the suggestion. We replaced PC with PN throughout the manuscript.

      (5) Only apical dendritic parameters are described in section 2 of Results, but the full morphology is shown in Figure 3B with basal currents shown in panels C and F. Some clarification is needed - either what currents were considered for basal dendrites and why, or else why basal dendritic current parameters were not considered for this simulation using apical dendritic current injection but nonetheless examining basal dendritic currents.

      We clarified in the text that the original model contained a standard set of Na and K channels (line 178).

      (6) Clarify "i" and "s" in the Figure 3C legend - "intrinsic" and "synaptic" white letterings are small/hard to see in the bottom subpanels.

      We now spell out intrinsic and synaptic in the Figure and increased the contrast of the letterings.

      (7) Regarding the computational benefit of recursively decomposing axial currents along an adaptively truncated acyclic graph, it would be useful to (a) include a supplemental figure benchmarking this approach to standard approaches to quantify the described gain in computational efficiency and (b) describe computing hardware in the Methods.

      We included an estimated benefit of the pruning process (line 758) as well as the utilised computing hardware and the simulation times in the Methods (line 776).

      Reviewer #2 (Recommendations for the authors):

      The manuscript is in great shape, it is well organized, and the figures are gorgeous. I believe that the extended currentscape is a great extension of the original currentscape method. In particular, the possibility of partitioning currents by the spatial location of their sources is a great addition. 
>

      Recommendations:

      (1) The method is applied in the context of an interesting case study that highlights its usefulness. However, the model in the study is so complex that it is difficult to develop an intuition of how currents should be flowing, and this makes it hard to intuitively validate the visualization method. I think that applying the extended currentscape in a simpler model - maybe a soma with a dendrite with two branches, fewer compartments - would be instrumental in developing this intuition. 
>

      We now first use a simple model with a soma and a dendrite with two branches to introduce the concepts in Figure 2 and provide a few examples where the reader can compare the results with their own intuition in simpler cases. We also added the currentscape analysis of a standard, two-compartmental model from Pinsky and Rinzel, 1994 as Supplementary Figure 1.

      (2) I found a number of typos and minor stylistic details you may want to fix in a revised version of the manuscript.

      (a) Abstractine, line 12. I believe the word "recursive" is a bit technical at this point. It's meaning in this context becomes clear after ones goes through the details of the algorithm (Figure 2). 
>

      We replaced the word “recursive” with “iterative”. We hope that this will make the abstract clearer for the readers. In fact, we realized that the word iterative is a better description of the algorithm, so we replaced the “recursive” with “iterative” consistently throughout the manuscript.

      (b) Figure 1, caption."Since we included the capacitive current, the magnitude of the inward and the outward currents is identical (Kirchhoff's law)."This sentence can be confusing. If the inward and outward currents are the same, the membrane potential doesn't change. I believe that you are including the capacitive current in the inward (or outward) currents.

      Indeed, we included the capacitive current in the inward or outward currents. We changed the text to clarify this.

      (c) Lines 92-93. I do not fully understand this sentence. Are you making an assumption? What does 'continuos flow of axial current' mean?
>

      By ‘continuous flow of axial current’ we meant a spatially continuous stream of axial currents flowing from the reference to the target. To clarify this, we added the explanatory sentence: “i.e., if the axial current is not blocked or reversed between the reference and the target.”

      (d) Equation (1.) Why summing axial currents over j? Is this for the case of a branching point?

      The compartment could be 1) part of a continuous segment of dendritic branch, where axial currents can flow from the distal and the proximal direction (sum over 2); 2) It can be a branch point with 3 axial currents; 3) or it can be a leaf compartment with only one axial current, in which case the summation is not relevant. We clarified this in the text.

      (e) Figure 2, caption. Typo. "When the axial currents flows…" Should it be 'current'? - Figure 3, caption. Typo in (C) "Extended currentscape" 
>

      Corrected.

      (f) Figure 4. I cannot see the grey lines or the dotted lines mentioned in the caption. 
>

      We added an arrow highlighting the gray and the dotted lines in the figure.

      (g) Figure 5, caption. "Red boxes highlight regions analyzed in panels B-D."Because this is a spatially extended model, region may be confused with spatial location, but you are highlighting a temporal interval.
>

      We rephrased the caption referring to temporal intervals now.

      (h) Line 341. This is a numerical experiment, correct? 
>

      We clarified in the text and added that it was indeed a simulation experiment.

      (i) Line 349. Should it be 'distributions'? 
>

      Corrected

      (j) Line 422. Typo. Missing space 'in vivousing'
>

      Corrected

      (k) Line 537. "Preprocessing membrane…" I found this entire subsection a bit confusing and hard to read.

      We rephrased this subsection to clarify it and facilitate reading.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) A few of the claims made are not supported by the references provided. For instance, line 76 states MgIG has hepatoprotective properties and improved liver function, but the reference provided is in the context of myocardial fibrosis.

      Thank you for the correction. We have made the revision on page 4, line74.

      (2) MgIG is clinically used for the treatment of liver inflammatory disease in China and Japan. In the first line of the abstract, the authors noted that MgIG is clinically approved for ALD. In which countries is MgIG approved for clinical utility in this space?

      Thank you for this important comment. MgIG has been recommended for the treatment of alcoholic liver disease (ALD) in Chinese clinical guidelines (2018). We have clarified this point in the manuscript (Page 5, Line 79-80).

      (3) Serum TGs are not an indicator of liver function. Alterations in serum TGs can occur despite changes in liver function.

      Thank you for this important comment. We fully agree that serum triglycerides (TGs) are not a direct indicator of liver function. ALT and AST are more appropriate markers for hepatocellular injury, whereas TG and TC primarily reflect systemic and hepatic lipid metabolism status. We have made the necessary revisions as suggested on page 12, lines 285-288

      (4) There are discrepancies in the results section and the figure legends. For example, line 302 states Idil is upregulated in alcohol fed mice relative to the control group. The figure legend states that the comparison for Figure 2A is that of ALD+MgIG and ALD only.

      We thank the reviewer for the valuable suggestion. Accordingly, we have revised the legend for Figures 2A and 2B as suggested.

      (5) Oil Red O staining provided does not appear to be consistent with the quantification in Figure 1D. ORO is nonspecific and can be highly subjective. The representative image in Figure 1C appears to have a much greater than 30% ORO (+) area.

      Thank you for this insightful comment. We acknowledge that Oil Red O (ORO) staining can be influenced by background signal and may appear subjective in representative images. In our quantification, only well-defined lipid droplets with strong positive staining were included, while diffuse background staining (e.g., light reddish hue) was excluded. This may explain the apparent discrepancy between the representative image and the quantified ORO-positive area. To further strengthen the reliability of our findings, we additionally measured hepatic triglyceride (TG) and total cholesterol (TC) levels. These biochemical assays yielded results consistent with the ORO quantification, thereby supporting our conclusion regarding lipid accumulation. Please refer to page12, lines 285-288. As requested, we have added the required information to Figures 1G.

      (6) The connection between Idil expression in response to EtOH/PA treatment in AML12 cells with viability and apoptosis isn't entirely clear. MgIG treatment completely reduces Idi1 expression in response to EtOH/PA, but only moderate changes, at best, are observed in viability and apoptosis. This suggests the primary mechanism related to MgIG treatment may not be via Idi1.

      Thank you very much. We agree that although MgIG almost completely reverses Idi1 expression induced by EtOH/PA, the improvements in cell viability and apoptosis are only moderate, suggesting a potential discrepancy between these observations. This may indicate that Idi1 functions as a permissive factor, rather than the sole mediator, in this pathological process. In other words, while modulation of Idi1 contributes to the protective effects of MgIG, additional pathways are likely involved in mediating its overall impact on hepatocyte viability and apoptosis. We have clarified this point in the revised manuscript (Page 12, Lines 325–335), stating that MgIG exerts its protective effects against ethanol-induced hepatocellular injury, at least in part, through the regulation of Idi1.

      (7) The nile red stained images also do not appear representative with its quantification. Several claims about more or less lipid accumulation across these studies are not supported by clear differences in nile red.

      Thanks a lot. We acknowledge that Nile Red staining can be influenced by imaging conditions and may appear less distinct in representative images, which could affect visual interpretation. To minimize subjectivity, all images were analyzed using a consistent and standardized thresholding method across groups. We agree that the visual differences in Nile Red staining alone may not be sufficiently pronounced to fully support the quantitative conclusions. Therefore, to strengthen the reliability of our findings, we have included additional biochemical measurements, including serum TG and TC levels, as well as hepatic TG and TC content. These independent assays consistently support the observed changes in lipid accumulation. The corresponding data have been added to the revised manuscript (page 12, lines 285-288)

      (8) The authors make a comment that Hsd11b1 expression is quite low in AML12 cells. So why did the authors choose to knockdown Hsd11b1 in this model?

      Thank you for this important comment. Although the basal expression of Hsd11b1 in untreated AML-12 cells is relatively low, we observed that it is inducible upon EtOH/PA stimulation, indicating its functional relevance under stress conditions. Therefore, knockdown experiments were performed to assess its contribution to EtOH/PA-induced hepatocellular injury. We have clarified this point in the revised manuscript (page 15, lines 281-382).

      (9) Line 380 - the claim that MGIG weakens the interaction between HSD11b1 and SREBP2 cannot be made solely based on one Western blot.

      Thank you for this important comment. We agree that the conclusion that MgIG weakens the interaction between HSD11B1 and SREBP2 should not be based solely on a single co-IP/Western blot experiment. In the revised manuscript, we have therefore toned down this statement to more appropriately reflect the data. Specifically, we now describe this result as a preliminary observation suggesting a potential modulation of the interaction, rather than a definitive conclusion. Please refer to Page 15, line 391.

      (10) It's not clear what the numbers represent on top of the Western blots. Are these averages over the course of three independent experiments?

      Thank you for this helpful comment. We apologize for the lack of clarity in the original figure presentation. The numbers shown above the Western blot bands represent the densitometric quantification of protein expression normalized to GAPDH, calculated from three independent experiments. However, this information was not clearly specified in the original figure, which may have led to confusion. To address this concern, we have now revised the manuscript by explicitly clarifying the meaning of these values in the figure legends. In addition, we have added bar graphs showing the quantified results from three independent experiments for Figures S3A, S4D, S6B, and S8H to improve transparency and data presentation.

      (11) The claim in line 382 that knockdown of Hsd11b1 resulted in accumulation of pSREBP2 is not supported by the data provided in Figure 6D.

      Thank you for pointing out this issue. We sincerely apologize for the incorrect description in the original manuscript. This was a wording error. We have made the revision on page 15, line394-396.

      (12) None of the images provided in Figure 6E support the claims stated in the results. Activation of SREBP2 leads to nuclear translocation and subsequent induction of genes involved in cholesterol biosynthesis and uptake. Manipulation of Hsd11b1 via OE or KD does not show any nuclear localization with DAPI.

      Thank you for this important comment. We agree that the original description was not sufficiently clear, which may have led to misunderstanding of the results. To clarify, Figure 6E includes two experimental contexts. Under basal (physiological) conditions in AML-12 cells, manipulation of Hsd11b1 (overexpression or knockdown) does not significantly affect the subcellular distribution of SREBP2. However, under EtOH/PA-induced stress conditions, Hsd11b1 overexpression promotes both nuclear and cytoplasmic levels of SREBP2, whereas Hsd11b1 knockdown reduces SREBP2 expression in both compartments. We have made the revision on page 16, line399.

      (13) The entire manuscript is focused on this axis of MgIG-Hsd11b1-Srebp2, but no Srebp2 transcriptional targets are ever measured.

      We sincerely appreciate this great suggestion. We have made the necessary revisions as suggested on page 12, lines 285-288, line 292 by adding the mRNA changes of Lcn2 and Ldlr, which are SREBP2 target genes. As requested, we have added the required information to Figures 1F and 1H.

      (14) Acc1 and Scd1 are Srebp1 targets, not Srebp2.

      Thank you for this important comment. We agree that Acc1 and Scd1 are well-established downstream target genes of SREBP1 rather than SREBP2. To better support our proposed SREBP2-related mechanism, we further examined canonical SREBP2 downstream target genes, including Lcn2 and Ldlr. The results are consistent with activation of SREBP2 signaling in our model. These data have now been included in the revised manuscript (Page 12, Lines 285–288 and 292; Figures 1F and 1H).

      (15) A major weakness of this manuscript is the lack of studies providing quantitative assessments of Srebp2 activation and true liver lipid measurements.

      Thank you for this important comment. We acknowledge the concern regarding the lack of direct quantitative assessment of SREBP2 activation in the original version of the manuscript. To address this limitation, we have strengthened the evidence supporting SREBP2 activation using multiple complementary approaches. Specifically, we assessed the expression of canonical SREBP2 downstream target genes (Page 12, Lines 285–288 and 292; Figures 1F and 1H), together with Western blot analysis (Figure 6D) and immunofluorescence staining (Figure 6F), which collectively support activation of SREBP2 signaling in the EtOH/PA-induced ALD model.

      In addition, to provide a more comprehensive evaluation of hepatic lipid accumulation, we measured serum TG and TC levels, as well as hepatic TG and TC content. These biochemical analyses further confirm the presence of significant lipid accumulation in our model. We have made the necessary revisions as suggested on page 12, lines 285-288 (Figure 1G).

      Reviewer #2 (Public review):

      (1) In Supplemental Figure 1A, all the treatment arms (A-control, MgIG-25 mg/kg, MgIG-50 mg/kg) showed body weight loss compared to the untreated controls. However, Figure 1E showed body weight gain in the treatment arms (A-control and MgIG-25 mg/kg), why? In Supplemental Figure 1A, the mice with MgIG (25 mg/kg) showed the lowest body weight, compared to either A-control or MgIG (50 mg/kg) treatment. Can the authors explain why MgIG (25 mg/kg) causes bodyweight loss more than MgIG (50 mg/kg)? What about the other parameters (ALT, ALS, NAS, etc.) for the mice with MgIG (50 mg/kg)?

      We agree that this observation does not strictly follow a dose-dependent pattern. In vivo responses to pharmacological interventions, particularly in metabolic and liver disease models, are not always linear. The relatively greater body weight reduction observed in the 25 mg/kg group may be influenced by inter-individual variability, differences in metabolic adaptation, or sample size–related variation. Importantly, these differences in body weight were not statistically significant. Therefore, we selected the 50 mg/kg dose for subsequent animal experiments, as it demonstrated more consistent and stable improvements across multiple parameters, including body weight, ALT, AST, TG, and TC.

      (2) IL-6 is a key pro-inflammatory cytokine significantly involved in ALD, acting as a marker of ALD severity. Can the authors explain why MgIG 1.0 mg/ml shows higher IL-6 gene expression than MgIG (0.1-0.5 mg/ml)? Same question for the mRNA levels of lipid metabolic enzymes Acc1 and Scd1.

      Thank you for this important comment. We agree that IL-6, as well as lipid metabolism–related genes such as Acc1 and Scd1, are key indicators in ALD. The relatively higher expression observed at 1.0 mg/mL MgIG compared to lower concentrations (0.1–0.5 mg/mL) may be related to experimental constraints associated with the MgIG formulation used in this study.

      Specifically, to maintain consistency with our in vivo experiments, we used a clinically available liquid formulation of MgIG (5 mg/mL), which is approved for intravenous administration in China. Due to its relatively low stock concentration, achieving higher working concentrations (e.g., 1.0 mg/mL) in vitro required a larger volume of the MgIG solution, thereby proportionally reducing the volume of culture medium. This reduction in effective culture conditions may adversely affect hepatocyte viability and function.

      Supporting this, our CCK-8 and LDH assays indicated that higher MgIG concentrations were associated with subtle cytotoxicity or impaired cell status.

      (3) For the qPCR results of Hsd11b1 knockdown (siRNA) and Hsd11b1 overexpression (plasmid) in AML-12 cells (Figure 5B), what is the description for the gene expression level (Y axis)? Fold changes versus GAPDH? Hsd11b1 overexpression showed non-efficiency (20-23, units on Y axis), even lower than the Hsd11b1 knockdown (above 50, units on Y axis). The authors need to explain this. For the plasmid-based Hsd11b1 overexpression, why does the scramble control inhibit Hsd11b1 gene expression (less than 2, units on the Y axis)? Again, this needs to be explained.

      Thank you for this important comment, and we apologize for the lack of clarity in the Y-axis labeling, which may have led to misunderstanding.

      As shown in Figures 5A and 5B, we have revised the Y-axis description to clearly indicate that gene expression levels are presented as relative expression normalized to GAPDH (fold change relative to the control group).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Use terms that show directionality to help the readers comprehend the data. For instance, Line 295 states MgIG treatment also modulated the expression.... In reality, MgIG treatment reduced the expression of those genes relative to ethanol-fed control mice.

      Thank you very much for this precious suggestion. We have thoroughly revised this part as ‘In line with the observed histological and physiological improvements, MgIG treatment also reduced the expression of genes involved in lipid synthesis metabolism (Srebp1, Srebp2, Acc1, and Scd1, Lcn2, and Ldlr), inflammation (Tnf-α and Il-6), and pro-apoptosis (Bax) while restored the level of anti-apoptotic gene (Bcl2) in the liver tissue of EtOH mice (Fig. 1G-1H).’. Please refer to page 12, lines 290-294.

      (2) Oil Red O staining is subjective and nonspecific. The authors make a claim that serum TGs are an indicator of liver function; however, measurement of hepatic TGs would be a better measure here and more consistent with the ORO staining.

      We sincerely appreciate this great suggestion. We have made the necessary revisions as suggested on page 12, lines 285-288 as ‘Notably, significant differences were observed between the EtOH group and the MgIG-treated (EtOH+M) group in serum levels of liver enzymes (ALT and AST), serum lipid parameters (TG and TC), as well as Liver TG and TC contents—-key indicators of liver function and lipid metabolism.’. As requested, we have added the required information to Figures 1G.

      (3) The focus of the paper is on this SREBP2 axis. However, in Figure 1, the authors do not show any SREBP2 target genes. This would be helpful in interpreting SREBP2 activity. Further, hepatic free cholesterol levels would also strengthen these data.

      We sincerely appreciate this great suggestion. We have made the necessary revisions as suggested on page 12, lines 285-288, line 292 by adding the mRNA changes of Lcn2 and Ldlr, which are SREBP2 target genes. As requested, we have added the required information to Figures 1F and 1H.

      (4) Labels showing directionality on the volcano plots in Figures 2A, B would be of great help here. It's unclear which groups are on the left or right.

      Thank you very much! The authors have revised Figures 2A-C as requested. Please refer to the new version of Figures 2A-C.

      (5) Ensure consistency in what is written in the results and the figure legends. See Figure 2 volcano plots for examples. The volcano plot in Figure 2B has no figure legend.

      We thank the reviewer for the valuable suggestion. Accordingly, we have revised the legend for Figures 2B as suggested.

      (6) Ensure consistency in the nomenclature. In some cases, the authors use ALD+MgIG, and in others, they just use MgIG. My recommendation would be to use Ctrl, EtOH, EtOH+M.

      We sincerely appreciate this great suggestion. We have made the necessary revisions as suggested on page 6, lines 111-112, page 11, line 280 and page 12, line 282, 284, 293, 298, 301.

      (7) The gene enrichment analysis in Figure 2C should also include some text about directionality, either in the figure or the figure legend. Upregulated DEGs in the MgIG group? It's unclear.

      We thank the reviewer for the valuable suggestion. Accordingly, we have revised the legend for Figures 2C as suggested.

      (8) The authors should consider shuffling the order of some of the figures for better transitions from one panel to the next. For instance, Figure 3B, C shows cell viability responses before showing the siRNA and OE are effective in knocking down and overexpressing their protein of interest.

      We thank the reviewer for the valuable suggestion. Accordingly, we have revised the legend for Figures 3B and 3C as suggested.

      (9) The authors need to be consistent in the colors that are used in the figures. It's incredibly hard to follow, as presented.

      We appreciate the reviewer's comment regarding color consistency. In response, we have carefully revised all figures to ensure consistent use of colors across the manuscript. The updated versions are shown in Figures 3, 6, and 7.

      (10) For Nile Red staining, multiple images at a lower objective need to be shown and/or cellular triglycerides and cholesterol levels should be quantified.

      We appreciate the reviewer's insightful comment regarding the Nile Red staining. In response, we have quantified triglyceride and total cholesterol levels in the cell supernatant, which are now presented on page 12, line 285-287 and Figures 2F. Furthermore, we have included additional Nile Red staining images at a lower objective in Supplementary Figures 2D, 3B, 4C to better illustrate the lipid droplet distribution.

      (11) Line 362 refers to Figure 4 when it should refer to Figure 5.

      Thank you very much! The authors have revised on page 14, line 364.

      (12) qPCR should be performed on canonical Srebp2 targets throughout the manuscript to tie in the MgG treatment with changes in sterol sensing and Srebp2.

      Thank you for your valuable suggestion. The results are now included on page 12, lines 292 and 311, and the corresponding data in Figures 1H and 2G have been enhanced accordingly.

      Reviewer #2 (Recommendations for the authors):

      (1) The statement, figure labeling, and figure legend for Figure 1A-C are confused. The MgIG dosing on the X-axis for Figure 2D is missing.

      Thank you for the correction. We have revised this problem. Please refer to the new version of Figure 1A-C and Figure 2D.

      (2) Figure 3E is not well described in the main text and figure legend. What are those numbers on top of the blotting bands? It was guessed that the numbers were the mean for each group. But where is the SD or SE for each group? It is hard to tell the statistical significance without showing SD or SE. The same question applies to Figure 5E, Figure 56C-6D, and Figure 7G.

      We sincerely appreciate this great suggestion. We have made the necessary revisions as suggested on page 13, lines 317-322. As suggested, we have added the required information to Figures S3A, S4D, S6B and S8H.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The researchers aimed to identify which neurotransmitter pathways are required for animals to withstand chronic oxidative stress. This work thus has important implications for disease processes that are caused/linked to oxidative stress. This work identified specific neurotransmitters and receptors that coordinate stress resilience, both prior to and during stress exposure. Further, the authors identified specific transcriptional programs coordinated by neurotransmission that may provide stress resistance.

      Strengths:

      The manuscript is very clearly written with a well-formulated rationale. Standard C. elegans genetic analysis and rescue experiments were performed to identify key regulators of the chronic oxidative stress response. These findings were enhanced by transcriptional profiling that identified differentially expressed genes that likely affect survival when animals are exposed to stress.

      Weaknesses:

      Where the gar-3 promoter drives expression was not discussed in the context of the rescue experiments in Fig 7.

      Comments on revisions:

      This issue has now been appropriately addressed in the revision.

      We thank the reviewer for their time and constructive feedback.

      Reviewer #2 (Public review):

      In this paper, Biswas et al. describe the role of acetylcholine (ACh) signaling in protection against chronic oxidative stress in C. elegans. They showed that disruption of ACh signaling in either unc17 mutant or gar-3 mutants led to sensitivity to toxicity caused by chronic paraquat (PQ) treatment. Using RNA seq, they found that approximately 70% of the genes induced by chronic PQ exposure in wild type failed to upregulate in these mutants. The overexpression of gar-3 selectively in cholinergic neurons was sufficient to promote protection against chronic PQ exposure in an AChdependent manner. The study points to a previously undescribed role for ACh signaling in providing organism-wide protection from chronic oxidative stress likely through the transcriptional regulation of numerous oxidative stress-response genes. The paper is well-written, and the data are robust, though some conclusions seem preliminary and are not fully support the current data (see below). While the study identifies the muscarinic ACh receptor gar-3 as an important regulator of the response to PQ, the specific neurons in which gar-3 functions were not unambiguously identified, and the sources of ACh that regulate GAR-3 signaling and the identities of the tissues targeted by gar-3 were not addressed.

      Comments on revisions:

      The authors addressed my comments adequately in their revised submission. Please include representative images to accompany the quantification of the new results presented in Fig S4A.

      We thank the reviewer for their time and constructive feedback. We now include representative images as requested.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      In the manuscript "Conformational Variability of HIV-1 Env Trimer and Viral Vulnerability", the authors study the fully glycosylated HIV-1 Env protein using an all-atom forcefield. It combines long all-atom simulations of Env in a realistic asymmetric bilayer with careful data analysis. This work clarifies how the CT domain modulates the overall conformation of the Env ectodomain and characterizes different MPER-TMD conformations. The authors also carefully analyze the accessibility of different antibodies to the Env protein.

      Strengths:

      This paper is state-of-the-art, given the scale of the system and the sophistication of the methods. The biological question is important, the methodology is rigorous, and the results will interest a broad audience.

      Weaknesses:

      The manuscript lacks a discussion of previous studies. The authors should consider addressing or comparing their work with the following points:

      (1) Tilting of the Env ectodomain has also been reported in previous experimental and theoretical work: https://doi.org/10.1101/2025.03.26.645577

      (2) A previous all-atom simulation study has characterized the conformational heterogeneity of the MPER-TMD domain: https://doi.org/10.1021/jacs.5c15421

      (3) Experimental studies have shown that MPER-directed antibodies recognize the prehairpin intermediate rather than the prefusion state: https://doi.org/10.1073/pnas.1807259115

      (4) How does the CT domain modulate the accessibility of these antibodies studied? The authors are in a strong position to compare their results with the following experimental study: https://doi.org/10.1126/science.aaa9804

      Based on the Reviewer’s comments and suggestions, we have added a discussion related to each previous study mentioned above.

      (1) Tilting of the Env ectodomain has also been reported in previous experimental and theoretical work: https://doi.org/10.1101/2025.03.26.645577

      At the end of the third paragraph (originally the second paragraph) in the Discussion section we added:

      “Shehata et al. also built a model of full-length gp120–gp41 trimer embedded in a lipid bilayer and performed all-atom simulations, in which a tilting motion of the ectodomain was observed. Based on the analysis of accessible surface area using different probe radii, they reported that antibody epitopes on the ectodomain are largely shielded by glycans, while the MPER epitope is mainly occluded by the membrane with tilt angles above 30° required to achieve greater MPER exposure (Shehata et al., 2025).”

      (2) A previous all-atom simulation study has characterized the conformational heterogeneity of the MPER-TMD domain: https://doi.org/10.1021/jacs.5c15421

      In the middle of the first paragraph in the Discussion section we added:

      “This is consistent with the all-atom simulations of MPER–TMD–CT and MPER–TMD in an asymmetric membrane conducted by Majumder et al., which likewise show multiple different conformational states of MPER and TMD (Majumder et al., 2025).”

      (3) Experimental studies have shown that MPER-directed antibodies recognize the prehairpin intermediate rather than the prefusion state: https://doi.org/10.1073/pnas.1807259115

      The paper mentioned by the Reviewer mainly reports the NMR structure of the MPER and TMD. In this study, the authors experimentally examined a series of MPER mutations to assess whether alterations in the MPER affect epitope accessibility in other regions of the Env ectodomain. This study did not investigate whether MPER-directed antibodies recognize the prehairpin intermediate. Instead, it cited prior studies (Frey et al.; 2008, Alam et al., 2009; and Chen et al., 2014) reporting that MPER-directed antibodies target the prehairpin intermediate conformation. We have already cited two of them (Alam et al., 2009 and Chen et al., 2014) in the original preprint, and we have now added the third one (Frey et al., 2008) in the revised manuscript.

      In the middle of the third paragraph (originally the second paragraph) in the Discussion section we added:

      “This is consistent with experiment studies indicating that MPER-targeting antibodies bind effectively only after the gp120–gp41 trimer undergoes major conformational rearrangements toward a fusion-intermediate or post-fusion state (Frey et al., 2008; Alam et al., 2009; Chen et al., 2014; Lee et al., 2016).”

      (4) How does the CT domain modulate the accessibility of these antibodies studied? The authors are in a strong position to compare their results with the following experimental study: https://doi.org/10.1126/science.aaa9804

      At the beginning of the second paragraph in the Discussion section we added:

      “Comparison of the full-length and CT-truncated systems shows that the primary difference arises from changes in the lipid bilayer, particularly in the exoplasmic leaflet, whereas differences in protein conformation and dynamics are less evident. Previous experimental studies have reported that mutations of the TMD residue and CT truncation can substantially affect antigenicity of ectodomain (Edwards et al., 2002; Chen et al., 2015; Dev et al., 2016). However, the ectodomain remains relatively rigid in our simulations for both full-length and CT-truncated systems. It is unclear whether this behavior reflects insufficient conformational sampling or artifacts associated with the model structures. Structural information for the CT is very limited, and the NMR structure (PDB ID: 7LOI) was the only available CT structure at the time the simulation systems were constructed. As a result, the extent to which this structure represents the native CT conformation remains uncertain. Additional experimental structural characterization of the CT will be important for achieving a more complete understanding of its functional role.”

      Reviewer #1 (Recommendations for the authors):

      A minor point: The RMSD values in Figure 3-figure supplement 1, seem a little too small. Please check the units.

      Figure 3-figure supplement 1 shows the RMSD of the ectodomain. Prior to RMSD calculation, the snapshots extracted from each trajectory were aligned to the initial structure using the ectodomain as the reference to avoid falsely high RMSD values arising from different orientations of the ectodomain. The relatively small RMSD values therefore reflect the intrinsic structural stability of the ectodomain, indicating that its internal conformation remains stable even though it undergoes substantial tilting motions.

      Reviewer #2 (Public review):

      Summary:

      In this work, the authors aim to elucidate how a viral surface protein behaves in a membrane environment and how its large-scale motions influence the exposure of antibody-binding sites. Using long-timescale, all-atom molecular dynamics simulations of a fully glycosylated, full-length protein embedded in a virus-like membrane, the study systematically examines the coupling between ectodomain motion, transmembrane orientation, membrane interactions, and epitope accessibility. By comparing multiple model variants that differ in cleavage state, initial transmembrane configuration, and presence of the cytoplasmic tail, the authors aim to identify general features of protein-membrane dynamics relevant to antibody recognition.

      Strengths:

      A major strength of this study is the scope and ambition of the simulations. The authors perform multiple microsecond-scale simulations of a highly complex, biologically realistic system that includes the full ectodomain, transmembrane region, cytoplasmic tail, glycans, and a heterogeneous membrane. Such simulations remain technically challenging, and the work represents a substantial computational and methodological effort.

      The analysis provides a clear and intuitive description of large-scale protein motions relative to the membrane, including ectodomain tilting and transmembrane orientation. The finding that the ectodomain explores a wide range of tilt angles while the transmembrane region remains more constrained, with limited correlation between the two, offers useful conceptual insight into how global motions may be accommodated without large rearrangements at the membrane anchor.

      Another strength is the explicit consideration of membrane and glycan steric effects on antibody accessibility. By evaluating multiple classes of antibodies targeting distinct regions of the protein, the study highlights how membrane proximity and glycan dynamics can differentially influence access to different epitopes. This comparative approach helps place the results in a broader immunological context and may be useful for readers interested in antibody recognition or vaccine design.

      Overall, the results are internally consistent across multiple simulations and model variants, and the conclusions are generally well aligned with the data presented.

      Weaknesses:

      The main limitations of the study relate to sampling and model dependence, which are inherent challenges for simulations of this size and complexity. Although the simulations are long by current standards, individual trajectories explore only portions of the available conformational space, and several conclusions rely on pooling data across a limited number of replicas. This makes it difficult to fully assess the robustness of some quantitative trends, particularly for rare events such as specific epitope accessibility states.

      In addition, several aspects of the model construction, including the treatment of missing regions, loop rebuilding, and initial configuration choices, are necessarily approximate. While these approaches are reasonable and well motivated, the extent to which some conclusions depend on these modeling choices is not always fully clear from the current presentation.

      Finally, the analysis of antibody accessibility is based on geometric and steric criteria, which provide a useful first-order approximation but do not capture potential conformational adaptations of antibodies or membrane remodeling during binding. As a result, the accessibility results should be interpreted primarily as model-based predictions rather than definitive statements about binding competence.

      Despite these limitations, the study provides a valuable and carefully executed contribution, and its datasets and analytical framework are likely to be useful to others interested in protein-membrane interactions and antibody recognition.

      Based on the Reviewer’s comments, we have revised the Discussion section to emphasize the limitation related to model construction and analysis of antibody accessibility.

      In the middle of the second paragraph in the Discussion section we added:

      “Similar limitations apply to other modeled regions where structural information is incomplete, including missing loops in the ectodomain, the cleavage site and heptad repeat 2 where two PDB structures (IDs: 6B0N and 7LOI) were merged. These regions introduce additional uncertainty, and the extent to which they influence the interpretation of our results remains an open question.”

      In the middle of the third paragraph (originally the second paragraph) in the Discussion section we added:

      “In addition, this analysis is based on geometric and steric criteria without accounting for potential conformational adaptations of gp120–gp41, antibodies, or the membrane; therefore, the calculated frequency of antibody accessibility should be interpreted as an approximation rather than a definitive indicator of binding competence.”

      Reviewer #2 (Recommendations for the authors):

      (1) Lines 45-47: The phrase "A major breakthrough was the design of ..." may be confusing. The gp140 trimer refers to a naturally occurring form of the HIV envelope protein rather than a structure designed de novo. If this statement refers to the development of a specific experimental construct or model system, this should be clarified to avoid misunderstanding.

      We have revised the sentence to clarify that the statement refers to soluble gp140 trimer constructs developed to stabilize the prefusion Env ectodomain for structural and immunological studies.

      At the beginning of the second paragraph in the Introduction section, we have modified the following:

      “A major advance was the development of soluble gp140 trimers, composing gp120 and the ectodomain portion of gp41, designed to stabilize the prefusion Env trimer for structural and immunological characterization.”

      (2) Figure 1A: The figure displays a model structure lacking the cytoplasmic tail. Given that the full-length model is central to the study, the authors may wish to explain why the truncated structure is shown here or consider displaying the full-length model to better reflect the complete system analyzed.

      We have combined Figure 1 and Figure 1—figure supplements 1 to show both full-length and CT-truncated models in one figure. We have also added an explanation of why the CT-truncated model was used as the primary system for analysis.

      In the middle of the third paragraph in the Introduction section we added:

      “However, structural information for the CT remains limited, leading to uncertainty in its conformational organization. To reduce potential bias arising from this uncertainty, we also generated a CT-truncated model and used it as the primary system for analysis (Figure 1, Figure 1—figure supplements 1).”

      We have modified Figure 1

      We removed Figure 1—figure supplements 1

      (3) Line 106: The probability distributions of θEC and θTM are cited in support of the statement that the angles "typically range from ... with occasional tilting." Providing explicit quantitative measures (for example, means, percentiles, or fractions of time spent in different angular regimes) would strengthen this claim.

      We have revised the text to explicitly indicate that only 0.7‰ of the sampled θ<sub>EC</sub> values are greater than 40°.

      In the middle of the first paragraph in the subsection “The ectodomain maintains a rigid internal structure and tilts independently of the TMD” we have modified the following:

      “Across trajectories, θ<sub>EC</sub> typically ranges from 0° to 40°, with only 0.7‰ exceeding 40°”.

      (4) Figure 2: The meaning of the contour lines is not clearly explained. If these represent probability density estimates of angular values over the trajectory, this should be stated explicitly. In addition, because the angles may evolve over time, it would be helpful to clarify how temporal drift is accounted for in the contour representation.

      We have clarified in both the main text and the figure caption that the contour lines in Figure 2B represent the joint probability density of the ectodomain and TMD tilt angles. We have also added Figure 2—figure supplements 5–8 showing the temporal evolution of the ectodomain and TMD tilt angles.

      In the middle of the first paragraph in the subsection “The ectodomain maintains a rigid internal structure and tilts independently of the TMD” we have modified the following:

      “The temporal evolution of θ<sub>EC</sub> and θ<sub>TM</sub> is additionally shown in Figure 2—figure supplements 5–8. For the CT-truncated systems, the joint probability densities of θ<sub>EC</sub> and θ<sub>TM</sub> calculated from the final 0.5 µs of each trajectory are shown in Figure 2B, while those for the full-length systems are shown in Figure 2—figure supplement 9.”

      In the caption of Figure 2 we have modified the following:

      “(B) Probability densities of ectodomain and TMD tilt angles, calculated from CT-truncated systems with various initial configurations.”

      We have added Figure 2—figure supplements 5–8.

      We have modified the following:

      “The original Figure 2—figure supplements 5 has been renumbered as Figure 2—figure supplements 9.”

      (5) Figure 2 (supplements): Some datasets are shown using scatter plots, while others are presented as contour plots. Using a consistent visualization style across panels or clearly explaining the rationale for the different representations would improve clarity.

      The contour plots in Figure 2B and Figure 2—figure supplements 9 show the joint distribution of the ectodomain and TMD tilt angles during the final 0.5 µs of each trajectory, whereas the scatter plots in Figure 2—figure supplements 1–4 illustrate the variations of the tilt angles across different time intervals. Each 1-µs trajectory was divided into four 0.25-µs intervals, indicated by light gray, dark gray, black, and red respectively, as shown in the legends of Figure 2—figure supplements 1–4. We have clarified in the main text that the multi-colored scatter plots are intended to demonstrate that large conformational changes predominantly occurred during the first 0.5 µs of each trajectory.

      In the middle of the first paragraph in the subsection “The ectodomain maintains a rigid internal structure and tilts independently of the TMD” we have modified the following:

      “Each 1-µs trajectory is divided into four consecutive 0.25-µs intervals, and data points from each interval are distinguished by four different colors (Figure 2—figure supplements 1–4). The variations of θ<sub>EC</sub> and θ<sub>TM</sub> over time show that large conformational changes predominantly occurred during the first 0.5 µs, followed by convergence of the θ<sub>EC</sub> and θ<sub>TM</sub> distributions during the second 0.5 µs in most trajectories.”

      (6) As noted in Line 97, θEC and θTM tilt independently. In this context, presenting time series plots of θEC and θTM separately would be highly informative. Such plots would help readers distinguish between equilibration behavior, drift from initial conditions, and equilibrium fluctuations.

      We have added Figure 2—figure supplements 5–8 showing the temporal evolution of the ectodomain and TMD tilt angles, as noted in our response to comment (4).

      (7) Figure 3A: It is not immediately clear which panels correspond to top views and which correspond to side views. Explicitly labeling these views in the figure or caption would reduce ambiguity.

      We have added labels in Figure 3A to clearly denote the top-view and side-view panels.

      (8) Figure 3B: The description "...by solid and transparent colors..." is ambiguous, as it is unclear whether this refers to color intensity or transparency. The caption would benefit from explicitly stating the visual encoding used (for example, darker/lighter colors or left/right bars).

      We have revised the figure caption to clarify which boxes correspond to cleaved systems and which correspond to uncleaved systems.

      In the caption of Figure 3 we have modified the following:

      “For each residue, the distribution from cleaved systems is shown in dark color (left), and that from uncleaved systems is shown in light color (right).”

      (9) Figure 4H: The definition of "frequency" expressed as a percentage is unclear. If this represents the fraction of snapshots in which two atoms fall within a specified distance range, this should be stated explicitly. The authors should also clarify whether the reported quantity is a probability or a rate, and ensure that the units and terminology are consistent.

      We have revised the figure caption to clarify that the frequency represents the fraction of snapshots in which the heavy atoms of a TMD residue and the interacting component are within 5 Å.

      In the caption of Figure 4 we have modified the following:

      “For each TMD residue–interacting component pair, the frequency represents the fraction of snapshots in which the heavy atoms of the TMD residue and the corresponding component are within 5 Å. Bar shading reflects this fraction, with fully filled bars indicating 100% and empty bars indicating 0%.”

      (10) Line 170: The manuscript describes a "rapid rearrangement" of the transmembrane domain at early simulation times. It would be helpful to clarify whether this regime is considered equilibration and whether it is excluded from subsequent analyses. Plotting time series of the relevant tilting angles and transmembrane rearrangement metrics could help address this point.

      We have clarified that the TMD underwent conformational changes early in the equilibration stage to enable R696 to interact with lipid headgroups, ions, or CT residues, and these interactions were largely maintained throughout the production stage. The time series of TMD tilting angles are now shown in Figure 2—figure supplements 5–8. Notably, the TMD exhibits heterogeneous conformational changes, including tilting, bending, and partial loss of helical structure. Therefore, no single metric or limited set of metrics can comprehensively capture the full extent of TMD conformational variability.

      In the middle of the first paragraph in the subsection “The energetically unfavorable R696 in the hydrophobic core results in asymmetric, kinked TMD conformations and disrupts membrane integrity” we have modified the following:

      “Early in the equilibration stage, the TMD rapidly rearranged to allow R696 residues to interact with more favorable partners, including negatively charged lipid headgroups from either leaflet, ions and water molecules diffusing into the bilayer center, as well as polar and positively charged groups in the CT when present. Once the interactions between R696 residues and their binding partners (lipid headgroup, ions or CT residues) were established, they remained stable with minimal changes throughout the production stage.”

      (11) Line 213: As with earlier sections, time series plots of θEC and θTM, similar to those shown in Figure 3-figure supplement 1, would greatly aid interpretation by showing whether these angles drift or fluctuate around stable values.

      The time series of θ<sub>EC</sub> and θ<sub>TM</sub> are now shown in Figure 2—figure supplements 5–8. Line 213 refers to the conformational variability of the MPER. For the same reason discussed in our response to comment (10), the MPER exhibits even greater conformational heterogeneity than the TMD, and therefore cannot be adequately described by a single or small set of geometric metrics such as tilt or bending angles.

      (12) Lines 216-222: The term "trajectories" may be misleading in this context. It is unclear whether the differences discussed arise from different trajectories of the same system or from different systems altogether. Clarifying this distinction would improve interoperability.

      In this paragraph, we describe MPER conformational variations observed across all trajectories from all systems. A preceding sentence has been modified to emphasize that all trajectories from all systems are included. In addition, we have clarified which specific trajectory is referred to when discussing each example.

      At the beginning of the first paragraph in the subsection “MPER adopts diverse conformations, and its exposure depends on both MPER and TMD conformations” we have modified the following:

      “…, and a wide variety of conformations were sampled across all trajectories from all systems.”

      “Such conformation and orientation were maintained in some trajectories such as CL<sup>ΔCT</sup>3 (the third trajectory of the cleaved, CT-truncated system with the low TMD position, Figure 4—figure supplement 2C). In other trajectories, such as CL<sup>CT</sup>1, the helix-turn-helix MPER in one protomer shifted into a horizontal orientation parallel to the membrane surface (Figure 4—figure supplement 6A). In UL<sup>ΔCT</sup>1, the entire MPER adopted a more vertical arrangement, with both MPER-N and MPER-C tilted outward (Figure 4E, Figure 4—figure supplement 4A). We also observed in UH<sup>ΔCT</sup>3 and UL<sup>ΔCT</sup>3 that the HR2 helix in the ectodomain, MPER, and TMD merged into a continuous long helix (Figure 4C, F, Figure 4—figure supplement 3C, 4C). In addition, loss of helical structure within the MPER was common, particularly in the MPER-C region, which often transitioned to a random coil.”

      (13) Lines 280 and 287: Similar concerns apply to the use of the term "trajectories." If observations differ primarily between systems rather than between trajectories within a system, revising the wording accordingly would avoid confusion.

      We have revised the text to clarify that all trajectories from all systems are considered collectively.

      In the middle of the second paragraph in the subsection “Ectodomain epitopes are conditionally accessible, whereas MPER epitopes are virtually inaccessible in the closed prefusion state” we have modified the following:

      “When considering all trajectories from all systems collectively, approximately half of them exhibited at least one protomer with >35% accessibility (Supplementary file 1–Supplementary Table 2).”

      (14) Figure 5B: Providing a time series of the distance dF673, at least in the Supporting Information, would help assess sampling and equilibration. Such plots would complement the probability distributions and increase confidence in the reported trends.

      We have added Figure 5—figure supplement 1 showing the time series of the distance d<sub>F673</sub> to complement the probability distribution in Figure 5B.

      In the middle of the second paragraph in the subsection “MPER adopts diverse conformations, and its exposure depends on both MPER and TMD conformations”, we have modified the following:

      “In the initial ‘low’ and ‘high’ TMD configurations, dF673 was 6.1 Å and 9.1 Å, respectively, but across simulations it spanned a wide range from -15 Å to 20 Å (Figure 5A, B, Figure 5—figure supplement 1).”

      We have added Figure 5—figure supplement 1.

      Reviewer #3 (Public review):

      Summary:

      This study uses large-scale all-atom molecular dynamics simulations to examine the conformational plasticity of the HIV-1 envelope glycoprotein (Env) in a membrane context, with particular emphasis on how the transmembrane domain (TMD), cytoplasmic tail (CT), and membrane environment influence ectodomain orientation and antibody epitope exposure. By comparing Env constructs with and without the CT, explicitly modeling glycosylation, and embedding Env in an asymmetric lipid bilayer, the authors aim to provide an integrated view of how membrane-proximal regions and lipid interactions shape Env antigenicity, including epitopes targeted by MPER-directed antibodies.

      Strengths:

      A key strength of this work is the scope and realism of the simulation systems. The authors construct a very large, nearly complete Env-scale model that includes a glycosylated Env trimer embedded in an asymmetric bilayer, enabling analysis of membrane-protein interactions that are difficult to capture experimentally. The inclusion of specific glycans at reported sites, and the focus on constructs with and without the CT, are well motivated by existing biological and structural data.

      The simulations reveal substantial tilting motions of the ectodomain relative to the membrane, with angles spanning roughly 0-30° (and up to ~50° in some analyses), while the ectodomain itself remains relatively rigid. This framing, that much of Env's conformational variability arises from rigid-body tilting rather than large internal rearrangements, is an important conceptual contribution. The authors also provide interesting observations regarding asymmetric bilayer deformations, including localized thinning and altered lipid headgroup interactions near the TMD and CT, which suggest a reciprocal coupling between Env and the surrounding membrane.

      The analysis of antibody-relevant epitopes across the prefusion state, including the V1/V2 and V3 loops, the CD4 binding site, and the MPER, is another strength. The study makes effective use of existing experimental knowledge in this context, for example, by focusing on specific glycans known to occlude antibody binding, to motivate and interpret the simulations.

      Weaknesses:

      While the simulations are technically impressive, the manuscript would benefit from more explicit cross-validation against prior experimental and computational work throughout the Results and Discussion, and better framing in the introduction. Many of the reported behaviors, such as ectodomain tilting, TMD kinking, lipid interactions at helix boundaries, and aspects of membrane deformation, have been described previously in a range of MD studies of HIV Env and related constructs (e.g., PMC2730987, PMC2980712, PMC4254001, PMC4040535, PMC6035291, PMC12665260, PMID: 33882664, PMC11975376). Clearly situating the present results relative to these studies would strengthen the paper by clarifying where the simulations reproduce established behavior and where they extend it to more complete or realistic systems.

      A related limitation is that the work remains largely descriptive with respect to conformational coupling. Numerous experimental studies have demonstrated functional and conformational coupling between the TMD, CT, and the antigenic surface, with effects on Env stability, infectivity, and antibody binding (e.g., PMC4701381, PMC4304640, PMC5085267). In this context, the statement that ectodomain and TMD tilting motions are independent is a strong conclusion that is not fully supported by the analyses presented, particularly given the authors' acknowledgment that multiple independent simulations are required to adequately sample conformational space. More direct analyses of coupling, rather than correlations inferred from individual trajectories, would help align the simulations with the existing experimental literature. Given the scale of these simulations, a more thorough analysis of coupling could be this paper's most seminal contribution to the field.

      The choice of membrane composition also warrants deeper discussion. The manuscript states that it relies on a plasma membrane model derived from a prior simulation-based study, which itself is based on host plasma membrane (PMID: 35167752), but experimental analyses have shown that HIV virions differ substantially from host plasma membranes (e.g., PMC46679, PMC1413831, PMC10663554, PMC5039752, PMC6881329). In particular, virions are depleted in PC, PE, and PI, and enriched in phosphatidylserine, sphingomyelins, and cholesterol. These differences are likely to influence bilayer thickness, rigidity, and lipid-protein interactions and, therefore, may affect the generality of the conclusions regarding Env dynamics and antigenicity. Notably, the citation provided for membrane composition is a laboratory self-citation, a secondary source, rather than a primary experimental study on plasma membrane composition.

      Finally, there are pervasive issues with citation and methodological clarity. Several structural models are referred to only by PDB ID without citation, and in at least one case, a structure described as cryo-EM is in fact an NMR-derived model. Statements regarding residue flexibility, missing regions in structures, and comparisons to prior dynamics studies are often presented without appropriate references. The Methods section also lacks sufficient detail for a system of this size and complexity, limiting readers' ability to assess robustness or reproducibility.

      With stronger integration of prior experimental and computational literature, this work has the potential to serve as a valuable reference for how Env behaves in a realistic, glycosylated, membrane-embedded context. The simulation framework itself is well-suited for future studies incorporating mutations, strain variation, antibodies, inhibitors, or receptor and co-receptor engagement. In its current form, the primary contribution of the study is to consolidate and extend existing observations within a single, large-scale model, providing a useful platform for future mechanistic investigations.

      Following the Reviewer’s comments and suggestions, we have revised the manuscript accordingly.

      While the simulations are technically impressive, the manuscript would benefit from more explicit cross-validation against prior experimental and computational work throughout the Results and Discussion, and better framing in the introduction. Many of the reported behaviors, such as ectodomain tilting, TMD kinking, lipid interactions at helix boundaries, and aspects of membrane deformation, have been described previously in a range of MD studies of HIV Env and related constructs (e.g., PMC2730987, PMC2980712, PMC4254001, PMC4040535, PMC6035291, PMC12665260, PMID: 33882664, PMC11975376). Clearly situating the present results relative to these studies would strengthen the paper by clarifying where the simulations reproduce established behavior and where they extend it to more complete or realistic systems.

      We have added a summary of the prior computational studies in the Introduction section.

      At the beginning of the third paragraph in the Introduction section we added:

      “Molecular dynamics (MD) simulations have been employed to investigate the stability and conformational properties of monomeric and trimeric helical TMD in both aqueous and lipid bilayer environments since late 2000s (Kim et al., 2009; Gangupomu et al., 2010; Baker et al., 2014; Baker et al., 2014; Hollingsworth et al., 2018). Early studies were constrained by limited computational resources and therefore the simulation times are relatively short. Subsequent work employed metadynamics to probe rare events (Gangupomu et al., 2010; Baker et al., 2014), and simulations performed on Anton supercomputers extended sampling to multi-microsecond time scale (Baker et al., 2014). Piai and coworkers determined the NMR structure of a construct comprising the MPER, TMD, and CT, and carried out MD simulations to access the structural stability of the trimeric MPER–TMD–CT complex (Piai et al., 2021). Majumder et al. subsequently simulated the same MPER–TMD–CT complex and applied a machine learning-based approach to classify its conformational ensemble (Majumder et al., 2025). Maillie et al. combined conventional MD, steered MD, and coarse-grained simulations to examine interactions between MPER-targeting antibodies and membrane lipids (Maillie et al., 2025). In addition, MD simulations have been extensively applied to the well-studied ectodomain. Despite these advances, it remains challenging to investigate the gp120–gp41 trimer as an intact entity considering its structural complexity.”

      We have also added a discussion of previous MD simulation studies to the Result section regarding interactions of the TMD residue R696 with ions and lipid headgroups.

      At the end of the first paragraph in the subsection “The energetically unfavorable R696 in the hydrophobic core results in asymmetric, kinked TMD conformations and disrupts membrane integrity”

      “Previously, Kim et al. reported that the inter-chain interactions between protonated R696 gradually diminished over a short simulation time (23 ns), leading to increased crossing angles and reduced bundle length (Kim et al., 2009). Gangupomu et. al and Baker et. al observed that R696 snorkeled toward either exoplasmic or endoplasmic headgroups in simulations of the TMD monomer, resulting in TMD tilting and membrane thinning due to water penetration and lipid headgroups interacting with R696 (Gangupomu et al., 2010; Baker et al., 2014; Baker et al., 2014). These observations are consistent with our finding. Hollingsworth et. al also reported membrane thinning; however, they attributed this effect to interfacial interactions of R683 and R707 with both leaflets and proposed that R696 only interacted with water and ions permeating into the center of the TMD timer (Hollingsworth et al., 2018).”

      A related limitation is that the work remains largely descriptive with respect to conformational coupling. Numerous experimental studies have demonstrated functional and conformational coupling between the TMD, CT, and the antigenic surface, with effects on Env stability, infectivity, and antibody binding (e.g., PMC4701381, PMC4304640, PMC5085267). In this context, the statement that ectodomain and TMD tilting motions are independent is a strong conclusion that is not fully supported by the analyses presented, particularly given the authors' acknowledgment that multiple independent simulations are required to adequately sample conformational space. More direct analyses of coupling, rather than correlations inferred from individual trajectories, would help align the simulations with the existing experimental literature. Given the scale of these simulations, a more thorough analysis of coupling could be this paper's most seminal contribution to the field.

      We have added a discussion of the coupling between TMD, CT and Env antigenicity, and the independent motion of ectodomain and TMD in our simulation.

      In the middle of the second paragraph in the Discussion section

      “Our analysis of the ectodomain and TMD coupling indicates that the motions of these two domains are largely independent. This observation does not contradict experimental studies demonstrating functional coupling between the TMD, CT, and the antigenic profiles of Env (Chen et al., 2015; Dev et al., 2016). Munro et al. proposed that unliganded Env is intrinsically dynamic, transitioning among three distinct prefusion conformations: a closed ground state (predominant), a transient state, and a CD4-/co-receptor-stabilized state. Both laboratory-adapted and clinically isolated strains can spontaneously transition among these three states, although their relative occupancies differ (Munro et al., 2014). It is therefore possible that TMD mutations or CT truncation also alter the equilibrium distribution among three states, thereby affecting the epitope exposure, particularly for epitopes that are occluded in the closed ground state while exposed in the CD4-/co-receptor-stabilized state. However, transition among three states occur on millisecond-to-second timescales. Our simulations on microsecond timescales primarily capture conformational variations within the closed ground state and suggest that the MPER acts as a hinge, providing substantial flexibility that enables the ectodomain and TMD to move independently while Env remains in the closed ground state.”

      We have also calculated the dynamical cross-correlation maps showing very weak correlations between the ectodomain and the TMD.

      At the end of the first paragraph in the subsection “The ectodomain maintains a rigid internal structure and tilts independently of the TMD”

      “We also calculated the dynamical cross-correlation maps (Ichiye et al., 1991) of Cα atoms for all systems using CPPTRAJ (Roe et al., 2013). The results indicate only very weak correlations between the ectodomain and the TMD (Figure 2—figure supplements 10–13).”

      We have added Figure 2—figure supplements 10–13.

      The choice of membrane composition also warrants deeper discussion. The manuscript states that it relies on a plasma membrane model derived from a prior simulation-based study, which itself is based on host plasma membrane (PMID: 35167752), but experimental analyses have shown that HIV virions differ substantially from host plasma membranes (e.g., PMC46679, PMC1413831, PMC10663554, PMC5039752, PMC6881329). In particular, virions are depleted in PC, PE, and PI, and enriched in phosphatidylserine, sphingomyelins, and cholesterol. These differences are likely to influence bilayer thickness, rigidity, and lipid-protein interactions and, therefore, may affect the generality of the conclusions regarding Env dynamics and antigenicity. Notably, the citation provided for membrane composition is a laboratory self-citation, a secondary source, rather than a primary experimental study on plasma membrane composition.

      We have added references to primary experimental studies on plasma membrane composition (van Meer et al., 2008; Sampaio et al., 2011), as well as the prior simulation study proposing the lipid and cholesterol distributions (Ingolfsson et al., 2014).

      At the beginning of the Membrane subsection in the Materials and methods section

      We have modified the following:

      The full-length and CT-truncated gp120–gp41 models were embedded into an asymmetric lipid bilayer with the lipid composition corresponding to a mammalian plasma membrane (van Meer et al., 2008; Sampaio et al., 2011; Ingolfsson et al., 2014; Pogozheva et al., 2022),

      We have also clarified the limitations associated with the choice of lipid composition and emphasized the need to investigate its influence in future studies.

      At the end of the second paragraph in the Discussion section we added:

      “In addition to the limitations inherent to protein structure modeling, the choice of lipid composition remains an open question. In this work, we selected an asymmetric mammalian plasma membrane because it is one of the 18 complex biomembrane systems we previously studied (Pogozheva et al., 2022), and among them, it provides the closest available approximation to the HIV membrane. Nevertheless, experimental studies have reported differences in lipid composition between HIV virions and the host plasma membrane (Aloia et al., 1993; Brugger et al., 2006; Huarte et al., 2016; Mucksch et al., 2019; Tomishige et al., 2023). Although we do not anticipate that our main conclusions regarding Env domain motions and MPER flexibility would change substantially, evaluating the influence of lipid composition represents an important direction for future work.”

      Finally, there are pervasive issues with citation and methodological clarity. Several structural models are referred to only by PDB ID without citation, and in at least one case, a structure described as cryo-EM is in fact an NMR-derived model. Statements regarding residue flexibility, missing regions in structures, and comparisons to prior dynamics studies are often presented without appropriate references. The Methods section also lacks sufficient detail for a system of this size and complexity, limiting readers' ability to assess robustness or reproducibility.

      We have corrected the error in which PDB structure 7LOI was described as a cryo-EM structure; it is in fact an NMR structure. We have also verified that all PDB structures are properly cited at their first occurrence in the manuscript.

      We have clarified that the modeling of palmitoylation sites, glycans and lipid bilayers are done in an automated fashion by different modules in CHARMM-GUI, and added Supplementary file 1–Supplementary Table 8 showing the simulation settings for equilibration and production stages.

      At the end of the subsection “Modeling of full-length gp120–gp41 trimer” we have modified the following:

      “Two mutations (S764C and S837C) were introduced in the CT to restore the palmitoylation sites, and lipid tails oriented towards the hydrophobic core of the bilayer were then attached to the palmitoylation sites using the PDB Manipulation module in CHARMM-GUI (Jo et al., 2008; Jo et al., 2014; Park et al., 2023) (Figure 1D).”

      At the end of the subsection “Glycosylation” we added:

      “The select glycan sequences were represented in the Glycan Reader Sequence format (Jo et al., 2011; Park et al., 2017) and added to the corresponding glycosylation sites using the Glycan Reader & Modeler graphical interface.”

      In the middle of the subsection “Membrane” we added:

      “Membrane systems were constructed using CHARMM-GUI Membrane Builder, which provides a user-friendly graphical interface for selecting lipid types and defining their numbers in each leaflet (Jo et al., 2007; Jo et al., 2009; Wu et al., 2014; Lee et al., 2016; Lee et al., 2019).”

      In the middle of the subsection “Simulation details” we added:

      We have modified the following:

      “Positional and dihedral restraints were applied to proteins, glycans, and lipids, with force constants progressively reduced over successive intervals (Supplementary file 1–Supplementary Table 8).”

      We added Supplementary file 1–Supplementary Table 8.

      Reviewer #3 (Recommendations for the authors):

      Major concerns:

      (1) Strengthen analysis of conformational coupling: Consider analyses that more directly assess coupling between the TMD/CT and ectodomain, such as residue-residue correlation networks, comparisons to smFRET-defined conformational states, or data-driven (e.g., machine learning-based) trajectory analyses. Machine-learning analysis would be particularly helpful in understanding otherwise elusive allosteric networks that could govern large-scale behavior. Discuss how, due to the apparent local minima that occur after ~0.5 us, enhanced sampling methods might be employed to better cover the Env conformational landscape.

      We have calculated the dynamical cross-correlation maps showing very weak correlations between the ectodomain and the TMD.

      At the end of the first paragraph in the subsection “The ectodomain maintains a rigid internal structure and tilts independently of the TMD”

      “We also calculated the dynamical cross-correlation maps (Ichiye et al., 1991) of Cα atoms for all systems using CPPTRAJ (Roe et al., 2013). The results indicate only very weak correlations between the ectodomain and the TMD (Figure 2—figure supplements 10–13).”

      We added Figure 2—figure supplements 10–13.

      We have also noted in the Discussion section that enhanced sampling methods could be employed to better explore the conformational landscape of Env trimer, including fluctuations within the closed state as well as transitions among the closed ground, transient and CD4/co-receptor-stabilized states proposed in the previous experimental study (Munro et al., 2014).

      In the middle of the second paragraph in the Discussion section we added:

      “Enhanced sampling methods could be applied to more thoroughly explore the conformational landscape, including not only variations within the closed ground state but also transitions among the closed ground, transient and CD4-/co-receptor-stabilized states.”

      (2) Qualify strong independence claims: Rephrase or further support statements asserting independence of ectodomain and TMD motions, particularly in light of known experimental evidence for coupling (PMC4701381, PMC4304640, PMC5085267).

      In addition to adding the dynamical cross-correlation maps showing very weak correlations between the ectodomain and the TMD, we have added a discussion of the coupling between TMD, CT, and Env antigenicity, and the independent motion of ectodomain and TMD in our simulation.

      In the middle of the second paragraph in the Discussion section we added:

      “Our analysis of the ectodomain and TMD coupling indicates that the motions of these two domains are largely independent. This observation does not contradict experimental studies demonstrating functional coupling between the TMD, CT, and the antigenic profiles of Env (Chen et al., 2015; Dev et al., 2016). Munro et al. proposed that unliganded Env is intrinsically dynamic, transitioning among three distinct prefusion conformations: a closed ground state (predominant), a transient state, and a CD4-/co-receptor-stabilized state. Both laboratory-adapted and clinically isolated strains can spontaneously transition among these three states, although their relative occupancies differ (Munro et al., 2014). It is therefore possible that TMD mutations or CT truncation also alter the equilibrium distribution among three states, thereby affecting the epitope exposure, particularly for epitopes that are occluded in the closed ground state while exposed in the CD4-/co-receptor-stabilized state. However, transition among three states occur on millisecond-to-second timescales. Our simulations on microsecond timescales primarily capture conformational variations within the closed ground state and suggest that the MPER acts as a hinge, providing substantial flexibility that enables the ectodomain and TMD to move independently while Env remains in the closed ground state.”

      (3) Clarify membrane composition assumptions: Provide a clearer rationale for the chosen lipid composition, and explicitly discuss how differences between host plasma membranes and HIV virions (e.g., PS, sphingomyelin, and cholesterol enrichment) may affect the conclusions.

      We have clarified the limitations associated with the choice of lipid composition and emphasized the need to investigate its influence in future studies.

      At the end of the second paragraph in the Discussion section we added:

      “In addition to the limitations inherent to protein structure modeling, the choice of lipid composition remains an open question. In this work, we selected an asymmetric mammalian plasma membrane because it is one of the 18 complex biomembrane systems we previously studied (Pogozheva et al., 2022), and among them, it provides the closest available approximation to the HIV membrane. Nevertheless, experimental studies have reported differences in lipid composition between HIV virions and the host plasma membrane (Aloia et al., 1993; Brugger et al., 2006; Huarte et al., 2016; Mucksch et al., 2019; Tomishige et al., 2023). Although we do not anticipate that our main conclusions regarding Env domain motions and MPER flexibility would change substantially, evaluating the influence of lipid composition represents an important direction for future work.”

      (4) Address citation and reference issues: Replace PDB-only references with proper citations, correct mischaracterizations of structure determination methods, and ensure all supplementary citations are fully referenced.

      We have corrected the error in which PDB structure 7LOI was described as a cryo-EM structure; it is in fact an NMR structure. We have also verified that all PDB structures are properly cited at their first occurrence in the manuscript.

      (5) Expand the Methods section: Provide additional detail on system construction, glycan modeling, lipid asymmetry, equilibration, sampling, and limitations, including a discussion of potential benefits of enhanced-sampling approaches.

      We have clarified that the modeling of palmitoylation sites, glycans and lipid bilayers are done in an automated fashion by different modules in CHARMM-GUI, and added Supplementary file 1–Supplementary Table 8 showing the simulation settings for equilibration and production stages.

      At the end of the subsection “Modeling of full-length gp120–gp41 trimer” we have modified the following:

      “Two mutations (S764C and S837C) were introduced in the CT to restore the palmitoylation sites, and lipid tails oriented towards the hydrophobic core of the bilayer were then attached to the palmitoylation sites using the PDB Manipulation module in CHARMM-GUI (Jo et al., 2008; Jo et al., 2014; Park et al., 2023) (Figure 1D).”

      At the end of the subsection “Glycosylation” we added:

      “The select glycan sequences were represented in the Glycan Reader Sequence format (Jo et al., 2011; Park et al., 2017) and added to the corresponding glycosylation sites using the Glycan Reader & Modeler graphical interface.”

      In the middle of the subsection “Membrane” we added:

      “Membrane systems were constructed using CHARMM-GUI Membrane Builder, which provides a user-friendly graphical interface for selecting lipid types and defining their numbers in each leaflet (Jo et al., 2007; Jo et al., 2009; Wu et al., 2014; Lee et al., 2016; Lee et al., 2019).”

      In the middle of the subsection “Simulation details” we have modified the following:

      “Positional and dihedral restraints were applied to proteins, glycans, and lipids, with force constants progressively reduced over successive intervals (Supplementary file 1–Supplementary Table 8).”

      We added Supplementary file 1–Supplementary Table 8.

      The discussion of potential benefits of enhanced-sampling approaches is included in our response to major concern (1).

      (6) Data availability: In addition to code, deposit all MD trajectories for re-analysis. The scale of this simulation was likely costly (GPU time), and so data availability is imperative.

      We have deposit MD simulation trajectories to Zenodo.

      At the end of the section “Data availability” we added:

      “The simulation trajectories can be found at https://doi.org/10.5281/zenodo.18853902, https://doi.org/10.5281/zenodo.18854615, and https://doi.org/10.5281/zenodo.18854639.”

      Minor:

      (1) Stylistic: Suggested to revise Figure 1 to provide a clearer overview of all constructs with consistent nomenclature (e.g., "full-length" versus "ΔCT") and explicit domain boundaries. With a better overview figure, the current figures could comprise the Figure 1 associated with Figures 1 and 2.

      We have combined Figure 1 and Figure 1—figure supplement 1 to show both full-length and CT-truncated models in one figure.

      We have modified Figure 1.

      We have removed Figure 1—figure supplements 1.

      (2) Explicitly cross-validate against prior studies: Integrate comparisons to existing MD simulations and experimental studies (e.g., PMC2730987, PMC2980712, PMC4254001, PMC4040535, PMC6035291, PMC4701381, PMC5085267) directly into the Results and Discussion.

      We have added discussion of previous MD simulation studies to the Result section regarding interactions of the TMD residue R696 with ions and lipid headgroups.

      At the end of the first paragraph in the subsection “The energetically unfavorable R696 in the hydrophobic core results in asymmetric, kinked TMD conformations and disrupts membrane integrity” we have modified the following:

      “Previously, Kim et al. reported that the inter-chain interactions between protonated R696 gradually diminished over a short simulation time (23 ns), leading to increased crossing angles and reduced bundle length (Kim et al., 2009). Gangupomu et. al and Baker et. al observed that R696 snorkeled toward either exoplasmic or endoplasmic headgroups in simulations of the TMD monomer, resulting in TMD tilting and membrane thinning due to water penetration and lipid headgroups interacting with R696 (Gangupomu et al., 2010; Baker et al., 2014; Baker et al., 2014). These observations are consistent with our finding. Hollingsworth et. al also reported membrane thinning; however, they attributed this effect to interfacial interactions of R683 and R707 with both leaflets and proposed that R696 only interacted with water and ions permeating into the center of the TMD timer (Hollingsworth et al., 2018).”

      The discussion of PMC4701381 and PMC5085267 is included in our response to major concern (2).

      (3) "In the cryo-EM structure (PDB ID: 7LOI)": This is an NMR model and lacks citation.

      We have corrected this error and added the citation at the first occurrence of PDB ID: 7LOI in the Result section.

      In the middle of the first paragraph in the subsection “The energetically unfavorable R696 in the hydrophobic core results in asymmetric, kinked TMD conformations and disrupts membrane integrity” we have modified the following:

      “In the NMR structure (PDB ID: 7LOI) (Piai et al., 2021),”

      (4) "Higher RMSF values were observed in the residues missing from the cryo-EM structure": This is lacking citation, as there are multiple cryo-EM structures and several dynamics studies using NMR.

      The missing residues here specifically refer to those absent in the cryo-EM structure (PDB ID: 6B0N) used for model building, rather than all cryo-EM structures in the PDB. We have revised the text to clarify this distinction.

      In the middle of the second paragraph in the subsection “The ectodomain maintains a rigid internal structure and tilts independently of the TMD” we have modified th following:

      “Higher RMSF values were observed in the residues missing from the cryo-EM structure (PDB ID: 6B0N) (Sarkar et al., 2018), which was used for the ectodomain in model building (these missing residues are highlighted in red in Figure 1A, B),”

    1. Author response:

      eLife Assessment

      This study provides fundamental insights by demonstrating that the Nanog mRNA coding sequence (CDS) and 3′UTR domains are spatially segregated and functionally distinct in pluripotent stem cells and blastocysts, with 3′UTR-enriched border cells primarily influencing morphogenesis and CDS-enriched inner cells largely regulating transcription and epigenetic programs. The work opens a novel conceptual avenue for understanding how separable mRNA domains can differentially control cell behavior and differentiation. However, the evidence is incomplete, as key aspects of the molecular nature, biogenesis, and precise characterization of the separated 3′UTR and CDS RNA species, as well as causal links between their perturbation and the observed phenotypes (e.g., via rescue and deeper characterization of 3′UTR elements), remain to be fully established.

      We thank the editors and the three reviewers for their careful and constructive engagement with our manuscript. We greatly appreciate the reviewers’ recognition of the conceptual significance of the study and their thoughtful suggestions for strengthening the mechanistic and molecular characterization of the work. We have carefully considered all points raised and outline below the revisions planned for the revised manuscript.

      The phenomenon of differential CDS and 3’UTR expression is not unique to Nanog. Independent 3’UTR and CDS expression and differential CDS/3’UTR usage has been observed across multiple genes, tissues, and developmental contexts, including genome-wide (Mercer et al., 2011) and transcriptome scale studies (Kocabas et al., 2025, Ji et al., 2021). Prior studies have proposed that isolated 3’UTRs may arise through regulated RNA processing pathways coupled to exonucleolytic degradation and, in some cases, recapping mechanisms (Malka et al, 2017, Haberman et al., 2024). While the precise molecular mechanisms underlying isolated Nanog CDS and 3’UTR generation remain unresolved, our observations (contained here) support regulated RNA processing models. Our original submission included a brief discussion of this topic; however the revised manuscript will include substantially expanded analyses and discussion of the generation of isolated Nanog CDS and 3’UTR species.

      The revised manuscript will address the major concerns regarding:

      (1) The molecular nature, biogenesis, and precise characterization of the separated 3′UTR and CDS mRNA species

      (2) The causal relationship between perturbation of these RNA species and the observed phenotypes, including additional rescue experiments and deeper computational characterization of putative, functional 3′UTR elements.

      Specifically:

      (A) New supplementary analyses and schematics designed to further clarify the conceptual and mechanistic framework of the study, including:

      (i) Computational examination of the Nanog 3’UTR across all reading frames for open reading frames (ORFs).

      (ii) As suggested by Reviewers 1 and 3, single cell traces of Nanog mRNA expression from the full-length mESC dataset used in this study, illustrating distinct transcript isoforms and CDS/3’UTR expression patterns across individual cells, complementing the color-coded tSNE analyses currently presented in Fig. 2.

      (iii) Expanded schematic model and analyses addressing possible mechanisms underlying the generation of isolated Nanog CDS and 3’UTR enriched RNA species, including transcript architecture, predicted RNA structural barriers, and exonucleolytic processing models.

      (iv) Expanded discussion of the predominantly nuclear localization of the Nanog 3’UTR signal and its implications for transcript biogenesis, processing, and potential noncoding functions.

      (B) Correction of all minor labeling errors.

      (C) Additional experimental analyses, including:

      - Expansion of Nanog 3’UTR overexpression and rescue experiments to include cell spreading assays.

      - Expanded analysis of the effects of ROCK pathway inhibitors on colony morphology and cytoskeletal organization.

      - Examination of the ability of ROCK inhibition to restore normal embryoid body formation.

      Collectively, these planned revisions are intended to strengthen the mechanistic framing, molecular characterization, and broader significance of the study while clarifying the interpretation and scope of the conclusions.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      There is evidence that some genes encode mRNAs from which separate processed transcripts may arise, separating the coding sequence (CDS) from the 3'-UTR, and with both mRNA elements remaining stable in the cell. However, the functional consequences of these mRNA fragments have not been firmly established. In the manuscript by Yang et al., the authors probe the mRNA domain architecture of Nanog in the context of embryonic stem cell colonies and blastocysts. The authors detect spatial separation of Nanog CDS-containing mRNA from abundant Nanog 3'-UTR RNAs depending on the cell position in 2D embryonic stem cell colonies or in blastocysts.

      Strengths:

      The phenotypic analyses of the Nanog mRNA hold promise for revealing distinct roles for the Nanog encoded protein and a separate RNA encompassing the Nanog 3'-UTR.

      Weaknesses:

      There are a number of questions about the molecular nature of the mRNA species that the authors should address in order for the results to be firmly established, as noted below.

      (1) It is not clear how the authors verified that their probes are specific for Nanog CDS or 3'-UTR regions. Especially for the 3'-UTR probe, it is confusing why colonies show green only regions, suggesting only the CDS is present. I would expect the CDS and 3'-UTR probes to colocalize in the interior cells. Is it possible that the 3'-UTR probe is targeting another RNA?

      We thank the reviewer for raising the important question of probe specificity. We realize that the data that underlying this concern is the absence of colocalizing between CDS and 3’UTR probes in colony border cells.

      The absence of CDS/3’UTR colocalization in colony border cells is not due to probe failure but instead reflects the principal observation underlying the study. If Nanog CDS and 3’UTR sequences were present exclusively as intact full-length transcripts in a strict stoichiometric ratio, Nanog positive cells would be expected to be positive for both probes (appearing yellow). Instead, border cells exhibit strong 3’UTR signal with minimal or absent CDS signal, while adjacent interior cells show the opposite pattern.

      The fact that both probes robustly detect signal within the same sample but in spatially distinct cell populations, argues that both probes are functional and that the observed differential localization reflects genuine biological differences in levels of transcript components.

      The CDS probe targets ~300 bp within the coding region, while the 3’UTR probe targets ~300 bp within the proximal region of the Nanog 3’UTR. Hybridization specificity was validated as described in the Methods and in our previous studies (Kocabas et al 2015; Ji et al 2021), including negative controls. We additionally now provide a supplemental figure (New Figure 1-figure supplement 2A), highlighting that the Nanog 3’UTR and CDS probes label cell populations distinct from each other, further indicating their specificity.

      In addition, full-length scRNA seq datasets from both mouse and human ESCs demonstrate differential CDS/3’UTR expression patterns for Nanog and many other genes. To further clarify this point, the revised manuscript will include single cell transcript traces from mESCs illustrating the distinct Nanog isoforms detected across individual cells (New Figure 2-figure supplement 1A)

      (2) It would help for the authors to include a graphic similar to Figure 3, Figure Supplement 1A, that diagrams the location of the CDS and 3'-UTR probes (this should also be done for Oct4 and Sox2). This graphic could also show all potential polyadenylation signals.

      We agree that additional schematic clarification would improve readability. The revised manuscript will include schematics showing the locations of the CDS and 3’UTR probes for Nanog, Sox2 and Oct4 (New Fig. 1- figure supplement 1A).

      (3) I think, based on the fluorescence patterns, there is evidence that the signal for the Nanog 3'-UTR probe is nuclear (images with DAPI staining), but this is not commented on that I could find. This should be discussed, as nuclear retention has implications for the noncoding function of the 3'-UTR fragment.

      The reviewer is correct that the Nanog 3’UTR signal mostly nuclear. Whie this was noted in (the original) Figure 1-figure supplement 2A, we agree that it is possible that mechanistic and functional implications were not sufficiently discussed in the original manuscript. The revised manuscript will include expanded discussion of the relationship between nuclear localization transcript processing, and potential noncoding functions of isolated Nanog 3’UTR species

      (4) Figure 2, Figure Supplement 1A needs a better explanation. It's not clear how the reads map to the different regions of the Nanog mature mRNA. The authors should show examples at different ratios of CDS to 3'-UTR. Do the reads have a sharp boundary at the junction of where the isolated 3'-UTR is thought to occur?

      We thank the reviewer for this suggestion. The revised manuscript will include new single cell read maps across the Nanog locus from full length mESC scRNA-seq datasets (New Figure 2-figure supplement 1A), illustrating distinct CDS enriched and 3’UTR enriched transcript isoforms across individual cells.

      These analyses indicate that some CDS dominant transcripts contain 3’UTR sequence, while many appear to contain little or no detectable 3’UTR sequence. Conversely, many 3’UTR enriched transcripts contain only minimal or truncated CDS sequence. Importantly full CDS and 3’UTR mRNA components are frequently not present in a strict 1:1 ratio, either within individual cells, or across cell populations.

      The revised manuscript will also include expanded supplementary analyses integrating transcript architecture, predicted RNA structural barriers, polyadenylation analysis, and single cell coverage patterns to further examine possible mechanisms underlying the generation of isolated Nanog CDS and 3’UTR species (New Figure 2-figure supplement 1B,C).

      (5) I looked in the Zenbu browser at human NANOG CAGE mapping in the FANTOM5 dataset. I could not see evidence for substantial capping of a 3'-UTR fragment when filtering for embryonic cell types. Given the strong signal for the 3'-UTR in border cells, I would expect to see evidence for capping if the RNA were indeed capped. This suggests that if it exists, it is likely uncapped and (as noted in point 3) is likely nuclear retained.

      Prior studies have reported isolated uncapped and recapped 3’UTR species in multiple systems (Malka et al, 2017; Haberman et al, 2024). We agree that the predominantly nuclear localization and lack of a strong CAGE signal for Nanog are important observations and will expand discussion of these points in the revised manuscript.

      (6) Are there predicted polyadenylation signals near the end of the CDS that would generate a short 3'-UTR, and are these signals conserved across mammals?

      Computational analysis of the mouse Nanog 3'UTR identifies a single canonical PAS (AATAAA) at position 1074, located at the 3’ end of the annotated 3’UTR and this terminal PAS is conserved across mammals. These analyses will be included as a supplementary figure and discussed further in the revised manuscript section addressing Nanog transcript biogenesis.

      (7) It would help to see a zoomed-in view of the region targeted by one of the guide RNAs in the 3'-UTR, and where that site is relative to the polyadenylation signal. Is the polyadenylation signal upstream, i.e., CDS proximal?

      This will be provided in the revised manuscript (New Figure 2-figure supplement 1C,i) Two guide RNAs were used to generate the Nanog 3’UTR deletions. The downstream guide is upstream of the terminal polyadenylation signal at nt 1074 to preserve polyadenylation of the remaining Nanog CDS containing transcript.

      Consistent with this, all Nanog 3’UTR knockout lines retain normal Nanog protein levels. The revised manuscript will include supplementary schematics showing guide RNA positions relative to the CDS, 3’UTR probes, and terminal PAS.

      (8) A final note, the use of green and red together will be challenging for those who are colorblind. Providing a different false color palette would be helpful. 

      We appreciate this attention to accessibly. The red/green color combination was chosen to provide the highest contrast between CDS and 3’UTR signals in the in situ hybridization experiments, which is important for visualizing their differential spatial localization. We will ensure that figure legends clearly indicate channel assignments throughout the manuscript.

      I am refraining from comments on the cell biology and morphological insights, as they are remote from my core expertise.

      Reviewer #2 (Public review):

      Summary:

      This manuscript shows that the coding sequence (CDS) and 3' untranslated region (3'UTR) of mRNA transcripts from the Nanog gene have distinct expression patterns and functions. In both human and mouse embryonic stem cells colonies and blastocysts, these domains are spatially segregated, with 3'UTR-enriched cells occupying the borders and CDS-enriched cells residing in the interior. CDS mRNA expression is correlated with the expected regulation of transcription and epigenetics associated with the Nanog protein. Interestingly, expression of the 3'UTR appears to play an independent role in cell behavior and colony morphogenesis. Indeed, deletion of the 3'UTR causes specific defects in cell spreading and protrusive activity, with alteration in the localization of adhesion and cytoskeleton-associated proteins. Remarkably, a large proportion of those defects are rescued upon ROCK inhibition. Deletion of either Nanog CDS or 3'UTR leads to distinct modifications in the differentiation competence.

      Strengths:

      The independent role of 3'UTR mRNA domains, although identified in neurosciences a couple of years ago, is a novel and exciting field relatively unexplored in early development.

      The manuscript offers a multilayer series of experiments, in ES cells colony, blastocysts, and embryoid bodies, including imaging, -omics, genetic and pharmacological challenges, and differentiation experiments, thereby unveiling very convincingly the role of Nanog 3'UTR in morphogenesis.

      Weaknesses:

      The pathways leading to the generation of those distinct transcript domains are unknown. Although the functional differential roles are well demonstrated whether the expression patterns are a cause or a consequence of the cells' localization in the embryo remains to be explored.

      We thank the reviewer for these thoughtful comments and for recognizing the potential significance of independent 3’UTR functions in early developmental systems.

      Regarding the mechanisms underlying generation of distinct CDS and 3’UTR transcript domains, the revised manuscript will include new supplementary analyses and schematic models addressing possible Nanog transcript processing pathways, as outlined above.

      We agree that the relation between spatial location and Nanog 3’UTR expression is an important question. Specifically, it remains unclear whether cells first acquire high Nanog 3’UTR expression and subsequently localize to the colony border or whether border position itself promotes high Nanog 3’UTR expression.

      Our current data suggest that both processes may contribute. Deletion of the Nanog 3’UTR does not prevent colonies from establishing border/interior pattern, indicating that high Nanog 3’UTR is not strictly required for border pattern itself. At the same time, Nanog 3’UTR overexpression and rescue experiments increased the likelihood of border localization, suggesting that elevated Nanog 3’UTR expression promotes behaviors associated with border occupancy.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, Yang et al reported distinct functions of the protein-coding sequence (CDS) and the 3' untranslated region (UTR) in the Nanog mRNA in pluripotent stem cells. They first observed different localization patterns for the CDS and 3' UTR in embryonic stem cells and in blastocyst embryos, and this pattern correlates with cell populations in different pluripotent states based on single-cell sequencing data. To characterize the potentially distinct functions of these regions, the authors generated knockout (KO) cell lines in which either the CDS or the 3' UTR was genetically ablated. These deletions led to different phenotypes in multiple assays. These results provided evidence that the CDS and 3' UTR of an mRNA could have distinct functions. Although these results are potentially interesting, several questions need to be addressed before the validity of their conclusion can be confirmed.

      Strengths:

      This study provides evidence for distinct functions of the protein-coding sequence and 3' untranslated region of an mRNA in pluripotent stem cells. The concept could be more broadly applied.

      Weaknesses:

      The initial observation (distinct localization of CDS and 3' UTRs) and the causal relationship between the KO and phenotype need further validation.

      Major points:

      (1) The authors showed distinct localization patterns of the CDS and 3' UTRs in human and mouse ESCs and blastocysts, and the overlap between their signals was minimal (Figure 1). Does this mean that the CDS and 3' UTR RNAs exist separately? For example, in cells that only showed signals for 3' UTRs, do these RNAs only contain 3' UTRs and lack CDS? Was this confirmed by RNA-seq experiments? If so, how are they generated (i.e., by transcription from a novel promoter or partial degradation of the full-length mRNAs)? This is a key question. Without a clear characterization of these RNAs, the rest of the study cannot be substantiated.

      We thank the reviewer for raising this important question, which overlaps substantially with several key points raised by Reviewer #1 concerning the molecular nature and characterization of the Nanog CDS and 3’UTR species.

      Colony border cells exhibit strong Nanog 3’UTR signal with minimal detectable CDS signal, while adjacent interior cells show the reciprocal pattern. These observations strongly suggest the existence of distinct Nanog transcript species rather than exclusively full-length transcripts containing stoichiometric amounts of both CDS and 3’UTR sequence.

      This conclusion is independently supported by full-length Smart-seq2 scRNA seq datasets from both mouse and human ESCs, which provide transcript coverage across both CDS and 3’UTR regions.

      (2) To confirm that the phenotypes of CDS or 3' UTR KO cells were caused by the deleted regions instead of other artifacts, rescue experiments should be performed.

      Rescue experiments were included in the original submission (Fig. 4). The revised manuscript will expand these analyses to include cell spreading. We will also include additional ROCK pathway modulation experiments.

      (3) As over-expression of the 3' UTR showed a phenotype, important regions within it should be identified, and also the possibility that the 3' UTR contains open reading frame(s) and is translated should be tested.

      The revised manuscript will also include supplementary computational analyses of the Nanog 3’UTR, including open reading frame prediction, Kozak scoring, and evolutionary conservation analysis. (New Figure 2-figure supplement 1B). These analyses identify no evidence for strongly supported coding potential within the 3’UTR. Further, isolated Nanog 3’UTR transcripts are largely confined to the nucleus, making active translation unlikely.

      The revised manuscript will include new supplementary analyses addressing Nanog transcript structure and possible biogenesis mechanisms (New Figure 2-figure supplement 1C).

      References:

      ViennaRNA/RNA fold – Lorenz et al 2011 Algorithms Mol Biol 6:26- RNA Secondary Structure stem loop, minimum free energy (MFE) prediction

      NCBI BLASTP- Altschul et al (1990) J Mol Biol 215:403- ORF conservation, protein sequence similarity search

      NCBI Entrez/Biohthon- Cock et al (2009) Bioinformatics 25:1422- sequence retrieval

      PhastCons/UCSC multiz alignments- Siepel et al (2005) Genome Res 15:1034- evolutionary conservation scoring

      UCSC Genome Browser- Kent et al. (2002) Genome Res 12:996-1006- conservation track access

      Eaton et al (2020) Mol Cell 78:439- Stall model

      Brannan et al (2012) Genes Dev 26:2621-Stall model

      Addition to Methods.

      ORFs (≥10 amino acids) were identified in all three forward frames according to Kozak (1987). Evolutionary conservation was assessed by BLASTP (Altschul et al., 1990) against RefSeq proteins. Poly(A) signals were identified by pattern matching for canonical and non-canonical hexamers. Conserved sequence blocks were obtained from UCSC PhastCons tracks (Siepel et al., 2005). RNA secondary structures were predicted using ViennaRNA RNAfold (Lorenz et al., 2011) with a sliding 80-nt window. The stall model for isolated transcript generation follows Eaton et al. (2020).

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Dalben et al. grafted the fusion loop mature (FLM) modification, based on a previously reported D2-FLM, to another serotype DENV4, and adapted them to replicate in Vero cells for live attenuated vaccine (LAV) manufacturing while retaining favorable antigenic profiles, generating two new strains: D2-vFLM and D4-vFLM. Deep sequencing revealed adapted mutations at the junction of envelope domains I and II (EDI and EDII), and both D2-vFLM and D4-vFLM showed no evidence of ADE in the presence of FL-targeting Abs. Sera from D2-vFLM immunized mice displayed strong homotypic and reduced heterotypic neutralization compared to wild-type viruses, with minimal to no ADE potential in vitro. Moreover, D2-vFLM immunization completely protected AG129 mice from lethal challenge with mouse-adapted D220. They demonstrate that the FLM modification platform is transferable across serotypes and yields strains with favorable immunogenicity and reduced ADE risk. The FLM approach provides a promising path toward the development of a safer tetravalent DENV LAV.

      Strengths:

      The authors carried out a series of experiments to generate and characterize two new strains (D2-vFLM and D4-vFLM) of FLM-modified viruses, and showed their antigenic and immunogenic profiles. The observation that the FLM modification platform is transferable across serotypes and yields strains with favorable immunogenicity and reduced ADE risk is interesting.

      We thank reviewer 1 for the encouraging comments for our work.

      Weaknesses:

      However, one concern is the total number of mutations (including originally introduced and compensatory mutations) in this FLM vaccine platform, and it is not clear regarding the future directions for the proof-of-concept vaccine in this study.

      Author response table 1.

      We summarize the mutations in the FLM platform below.

      The maturation mutations are located at the furin cleavage site, which is buried within the membrane or virion. As a result, only five mutations are surface exposed, two of which are in the fusion loop region targeted for removal. Therefore, for a proof-of-concept study, the total number of mutations remains well within the genetic diversity observed among DENV genotypes.

      Compensatory mutations may affect overall DENV antigenicity. Notably, one such mutation, K204R, has been reported to alter antigenicity and could contribute to the improved safety profile of the vaccine. However, we have also shown that multiple adaptive pathways can support Vero cell adaptation, and our data indicate that K204R is not absolutely required for this process.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, YR Dalben et al describe the generation of DENV2 and DENV4 strains with mutations in the fusion loop (FL) of the E protein and pre-membrane (prM) protein to limit potential antibody-dependent enhancement (ADE) resulting from vaccination with live-attenuated vaccines and adapted these strains for growth in Vero cells. They show that the DENV2 version D2-vFLM is immunogenic and generates neutralizing serum against DENV2 and DENV4 after 2 boosts and is protective against lethal challenge. Serum from D2-vFLM also showed no ADE against DENV4.

      Strengths:

      Overall, the paper is well written and presented, and the data presented support most of the conclusions made. Grafting D2-FLM mutations to DENV4 and adapting both to growth in Vero cells is a good step to show that this method could be used to generate production-level LAV. The growth and stability data are clear and well-conducted.

      We thank reviewer 2 for the encouraging comments for our work.

      Weaknesses:

      However, there are several weaknesses, mostly in regard to the immunogenicity data, that limit the overall impact. The FLM mutations were only grafted to DENV4 but not to the other Dengue serotypes. The authors acknowledge that this is a proof-of-concept, but generating mutants of the other serotypes would strengthen the idea that this could be used to develop a tetravalent LAV.

      We selected DENV2 and DENV4 because they are the most genetically divergent. Currently, our data should support the FLM mutations that can be grafted on both DENV2 and DENV4, likely extend to their corresponding genotypes. We agree that the FLM mutations should be evaluated in additional serotypes. We also have promising preliminary data for FLM mutation grafting in DENV1 and are currently applying the same approach to DENV3. We hope to include these results, whether positive or negative, in the revised manuscript.

      Immunizations in mice were only performed for D2-vFLM but not D4-vFLM. Immunogenicity data for D4-vFLM would strengthen this work if it shows that it can be immunogenic, protective, and limit ADE, as is shown for D2-vFLM.

      We are currently immunizing AG129 mice with DV4 and D4-vFLM, followed by heterotypic challenge with D220. Because DENV vaccine-related hospitalization in clinical trials typically occurs 3 - 4 years after vaccination, we are cautious about whether this experimental design will fully capture the added safety benefit of the FLM mutations. We are also developing a passive immunization model in AG129 mice using diluted DENV4 serum to better mimic long-term waning antibody titers. We will include the future findings in the revised manuscript.

      ADE from D2-vFLM was only tested against DENV4; does it also limit ADE from the other serotypes? This would better show that these mutations do limit ADE across serotypes and not just a single one.

      We are trying to keep the scope of the paper within DENV2 and DENV4, however, we will perform ADE and neutralization assays for all four serotypes in the revised manuscript.

      Additionally, some of the immunization data likely need to be repeated:

      The authors should describe why they pooled the sera from the mice and whether they purified total IgG or not (Figure 5).

      We used pooled serum, consisting of equal volumes from each mouse, rather than purified IgG. In Figure 5, our goal was to show the overall increase in serum titer after each immunization using cheek-bleed samples from individual animals. Because the available sample volume was limited, we pooled the sera for this analysis. We also measured end-point serum titers for each individual animal.

      They should also probably repeat the challenge experiment since it was 4 mice (D2) against 5 (D2-vFLM), and it is unclear if there is a statistical difference between the results obtained. It is not even mentioned in the Results section (D2 result vs D2-FLM), and thus unclear if using D2-FLM is an improvement in the way the data is currently presented.

      This experiment was designed to determine whether D2-vFLM protects AG129 mice against homotypic challenge as effectively as DV2-WT. Although the sample size was small, the results support our conclusion. However, we agree with the reviewer that the study should include more animals, and we will increase the group size to n > 8 to 10 in the revised experiment.

    1. Author response:

      We thank the editors and reviewers for their time and feedback. We are encouraged by the feedback that the purpose and abstractions of the model are well articulated and justified, that the explicit control of bursting characteristics is useful, and that the circuit-level validations are convincing.

      Before responding to individual reviewer comments, we would like to address the framing in the current assessment that the model "appears to have limited neurobiological relevance and utility but may be useful as a controller for an artificial system, such as in neuro-robotics applications." We respectfully suggest that this framing understates the model's relevance to neuroscience. Specifically, a growing body of literature aims to understand biological motor control by building embodied simulations. Yet, these simulations either use overly simple artificial neural network (ANN) units without dynamics or computationally intensive biophysical ones that are difficult to train. Our model is not intended as a biophysical account of how individual neurons generate bursts at the level of ionic mechanisms or spikes that goal is already well served by the conductance-based and reduced biophysical models we cite. Rather, its contribution is to make intrinsic bursting dynamics readily incorporable into neural circuit models that can be used in complex settings, with parameters that map directly onto quantities that circuit-level neuroscience most often measures and tunes in models (burst duration, duty cycle, amplitude, shape, input dependence). Indeed, Reviewer #1 notes that: "The purpose of the model and applied abstractions are well articulated and justified [...] This allows modelers to focus on circuit interactions and is especially useful when details of intrinsic currents and bursting mechanisms are unknown. One could even imagine a scenario where this model would help identify predictions on key underlying burst generation mechanisms."

      We see our work as a neuroscience contribution as much as a neuro-robotics one. Bringing tractable, controllable bursting into this regime allows circuit modelers to study how intrinsic bursting interacts with circuit connectivity without committing to specific biophysical mechanisms, and it lets ANN-style models incorporate a class of dynamics that is biologically pervasive but currently underrepresented. We validated the model against two well-studied biological CPGs (the crustacean pyloric circuit and the mammalian locomotor circuit) precisely because the target use case is biological circuit modeling.

      While we remain committed to the belief that bringing bio-inspired neurons with interpretable intrinsic dynamics into ANN-style modeling of biological control systems is a useful contribution as an eLife Methods paper, the reviews have made clear that we have not situated our work clearly enough within the literature. In revision, we will sharpen this positioning in the Introduction and Discussion, and better situate the model relative to both the long tradition of non-spiking relaxation-oscillator and piecewise-linear modeling in neuroscience and also to current trends in simulated control.

      Public Reviews:

      Reviewer #1 (Public review):

      (1) Formal analysis

      The paper heavily relies on numerical demonstrations but does not provide a formal analysis of stability, bifurcations, or entrainment. While appropriate for the intended purposes, a more formal footing could strengthen the model.

      We agree that a formal dynamical-systems treatment would deepen the work, and we appreciate the reviewer's acknowledgment that the numerical-only approach may nevertheless be appropriate for the intended purposes. Because the model is hybrid (continuous dynamics combined with discrete switching rules), a full formal analysis is non-trivial, and we view it as a substantial follow-up rather than something to fold into the present manuscript. In revision, we will discuss more explicitly the opportunities such formal analysis presents.

      (2) Parameter tuning and parameter-space characterization

      It is less clear how model parameterization was chosen, how behavior depends on parameterization, and in what parameter ranges certain behavior can be expected.

      We agree that this would substantially improve usability, and we will expand this aspect of the paper. The revision will include: (a) more details describing how parameters maps onto observable features of the bursting waveform, (b) recommended parameter ranges and the qualitative behaviors expected at their boundaries, and (c) practical guidance for tuning the model to match observations or embed into circuits.

      (3) Locomotor CPG interneuron ablation and noise

      The correspondence of these silencing/ablation of neuron classes has not been shown by the model. Importantly, though, it appears that authors didn't show how the model in general behaves under the influence of noise.

      The reviewer is right that the cited work establishes validity of the circuit model in large part through silencing/ablation experiments, and we did not reproduce those experiments. We understand those gait expression phenomena to be arising from non-bursting interneuron activations and a robust solution found for connection weights between them. The half-center bursting neurons only see a time-varying input signal, and their response is well-characterized by the constant, pulse, and periodic analyses we perform. As such, we chose to reproduce a few key experiments to retain a focus on our simplified neuron model. We will rephrase the relevant passages to make this scope explicit and ensure that our reproduction claims are appropriately stated. We will also expand on how the model interfaces with noise together with the proposed parameter-space characterization.

      Reviewer #2 (Public review):

      (1) Biological relevance

      Central pattern generators and other bursting neurons use specific physical principles to generate their bursts of activity. These principles place constraints on the tuning of these bursts, including relationships between active and silent phase durations and other properties. By discarding these relationships, the proposed model risks losing key constraints that affect performance in biologically relevant scenarios.

      We agree that biophysical models impose constraints that arise from underlying mechanisms. For instance, as input alters the curved shape of nullcline-v in Figure 1, the active/quite phase durations and duty cycle change in constrained ways. The question seems to be if our model is too flexible for instance, making it too easy to achieve desired phase durations, duty cycles, and other input-dependent responses. We see this as a valuable feature of our model, not a bug. Firstly, even if our model may be expressive enough to achieve a variety of response profiles (as in Figure 3—figure supplement 3), the careful modeler will ensure matching to experimental observations. Moreover, in many circuit systems, the relevant biophysical details are often unknown for the specific neurons being modeled as noted by Reviewer #1, and the modelers' primary goal is to reproduce circuit-level activity. Such can be achieved easily with a simplified model, and also with a biophysical model as data becomes available. Finally, we should note that modelers can and do tune the parameters of biophysical models within determined ranges in order to achieve desired phase durations and duty cycles, relaxing constraints somewhat in order to reproduce appropriate activity.

      It is also important to note that spikes within bursts can be important and of interest. [...] The authors' model is specific to square-wave bursting.

      We agree that spikes are important and interesting in many settings, and we believe that biophysical models would be most appropriate in these cases. In many cases, too, some abstraction and simplification is desirable, and this would not necessarily detract from the model's biological relevance. As we discuss in our high-level comments, we aim to bring intrinsic bursting dynamics into the ANN-style modeling regime that typically neglects intrinsic dynamics altogether. While the simplified model may be limited in some ways, it is nevertheless useful for many common biologically relevant scenarios, as validated by our circuit experiments. Finally, we would note that many of the raised limitations (no intra-burst spike structure, restricted bursting class, abstracted constraints) are shared by the relaxation-oscillator and piecewise-linear traditions that the reviewer cites approvingly, which suggests that our model lies along a familiar abstraction continuum rather than outside it. In revision, we will explicitly acknowledge that the model captures a basic/regular form of bursting within a broader taxonomy, and clarify the conditions under which abstracting the biophysical constraints is appropriate.

      (2) Practicality

      The model makes use of various cut-off functions and other aspects that are implemented as rules. Combining rules with differential equations makes for an awkward modeling framework

      On the modeling framework, we would defend the hybrid formulation (rules + ODE) as our aim is to prioritize usability by modelers, not the simplicity or elegance of equations. While a "pure-ODE" Fitzhugh-Nagumo-style polynomial may seem simple and elegant—with dv/dt = av^3 + bv^2 + cv + d and a, b, c, d parameters as the reviewer has pointed out a lot of complexity can arise from this. Tuning these parameters is far from intuitive, as small changes can produce nonlinear effects and qualitative shifts in behavior. Achieving the right phase durations, input-dependent scaling, waveform amplitude and shape, phase delays, and other characteristics simultaneously to match experimental data is quite cumbersome in the elegant models, not to mention the biophysical models. In contrast, these characteristics are easy to control in our model, because we translate complex dynamical behavior from implicit to explicit and surface a set of interpretable and tunable parameters.

      The authors argue for their model based on the idea that more biophysical models are difficult to tune, yet they compare their model to a biophysical one that they were able to tune to achieve the various patterns that they study. They do not give any indication of how easy or hard it was to tune their own model [...] The biophysical model seems to have 22 parameters, whereas the simplified one has 21 in Table 2, which is essentially the same number.

      To clarify, we did not tune the biophysical model, but rather copied its parameters from the cited work. We will make this more explicit in the relevant Methods section.

      We could not simply specify or tune these parameters because they have complex biological priors that must be derived from experimental data for example, the membrane capacitance (20 pF), ionic conductance and reversal potentials (4.5 nS, -62.5 mV), and many gating kinetics parameters (slopes, midpoints, time constants for sigmoid/bell curves).

      It is often the case that such parameters must be estimated in specific preparations then reused and refined over many years. For instance, the biophysical model we compare to borrowed parameters from (Kim et al. 2022), which retuned time constants relative to (Danner et al. 2017), which altered NaP conductance from (Danner et al. 2016), which retuned duty cycles from (Molkov et al. 2015), which adapted from respiratory networks of (Rubin et al. 2008), which used gating kinetics parameters from (Butera et al. 1999). Similarly, the crustacean pyloric circuit model we compare to is from (Alonso and Marder 2020), which augmented the circuit and parameters of (Prinz et al. 2004), which sampled from a database of procedurally generated parameters from (Prinz et al. 2003), which developed parameter priors from the lobster STG experimental work of (Turrigiano et al. 1995). These brief descriptions of the multi-decade lineage of parameter sets omit the substantial parallel and preceding work related their development, but they suffice to demonstrate the incredible science and effort that goes into building biophysical models for particular circuits. Such data is often unavailable and such detail is often undesirable for different research goals, in which case our simplified model is a valuable and practical tool.

      The key parameters of our simplified model are observable quantities like active/quiet durations (in seconds), input-dependent duration scaling (as a fraction of intrinsic durations), input strength that induces tonic firing, etc. As such, tuning the bursting neuron parameters for circuit models was easy, with manual tuning from scratch taking less than 1 day. As Table 3 shows, the resulting parameters are often simple, elegant numbers and can be derived directly from observations. For instance, the pyloric PD active and quiet durations (200 ms and 800 ms, respectively) are set using the exact target values that (Alonso and Marder 2020) encode in their objective for a genetic algorithm to tune their model’s biophysical parameters (or rather, a subset of them for tractability).

      Thus, the 22-vs-21 comparison is not very informative, because the parameters are not comparable in kind. However, to make it easier to tune our model, we will revise the manuscript to include: (a) more details describing how parameters maps onto observable features of the bursting waveform, (b) recommended parameter ranges and the qualitative behaviors expected at their boundaries, and (c) practical guidance for tuning the model to match observations or embed into circuits.

      (3) Originality

      What the authors fail to acknowledge is that Rinzel, Terman, Kopell, and others did seminal work on neuronal activity [...] The authors do not cite the substantial existing work on piecewise linear models [...] I don't see any advantage of the proposed framework over the earlier relaxation oscillator setting, where many important mechanistic principles have already been analyzed, including extensions to networks.

      We thank the reviewer for these pointers and apologize for the gap in our literature coverage. While we had cited McKean, FitzHugh-Nagumo, Izhikevich, et al. as representative examples of different model classes, we agree that the broader relaxation-oscillator and piecewise-linear traditions deserve more comprehensive treatment including Rinzel, Terman, Kopell, et al. on relaxation-oscillators; and Hahnloser, Coombes, Aguirre, et al. on piecewise-linear models. We will expand the related work discussion and clarify how our contribution is novel and valuable.

      To be clear, we do not claim to be the first to use piecewise-linear models for neurons. Our intended contribution is the specific construction a rectangular limit cycle whose horizontal/vertical decoupling permits a closed-form mapping from interpretable parameters to burst features and the demonstration that this construction integrates cleanly into firing-rate circuit models of biological CPGs, which we believe will provide realism for more complex models with learned components.

      Moreover, in contrast to many other relaxation-oscillator models including the elegant Fitzhugh-Nagumo-style model we discussed above, our model is not aimed at establishing mechanistic principles or being simple enough to analyze formally. It is a practical tool that affords precise control of many bursting characteristics, which is important for closer alignment between firing-rate circuit models and biological activity. We will state this contribution more precisely in the revision so it is not conflated with a broader novelty claim.

      Reviewer #3 (Public review):

      (1) Novelty of piecewise-linear approximation

      The use of piecewise linear approximations to explicitly estimate properties of biophysical neurons is a well-known and common technique. This study adds nothing to the technique in terms of novelty.

      We agree that piecewise-linear approximations of neurons are not themselves novel, and we have not intended to claim otherwise: We cite the McKean model as a direct predecessor and, prompted by Reviewer #2, we will substantially expand citations to the relaxation-oscillator and piecewise-linear traditions (Rinzel, Terman, Kopell, Hahnloser, Coombes, Aguirre, et al.). Our intended contribution is not the use of piecewise-linear pieces per se but the specific construction: a rectangular limit cycle whose horizontal/vertical decoupling permits a closed-form, interpretable mapping from burst features (duration, duty cycle, amplitude, shape, input dependence) to dynamics, and clean integration into firing-rate circuit models of biological CPGs. We will revise the relevant passages so this contribution and the boundaries of our novelty claim are stated precisely.

      (2) Dynamical system mechanism

      This is no better than having a look-up table [...] The neuron is restricted to what the user puts in, and therefore, calling it a dynamical system is entirely wrong.

      We would like to take the opportunity to clarify this point, because the model's behavior is much richer than the lookup-table characterization suggests. The model is closed-loop: trajectories evolve through coupled state variables whose response to time-varying input depends on current state, not on a precomputed table of input-to-output values.

      Specifically:

      (a) The input represents the net time-varying synaptic drive, not a clamped voltage level;

      (b) The adaptation and voltage variables evolve according to coupled differential equations both on and off the limit cycle;

      (c) The duration and scale parameters only constrain active/quiet durations at input endpoints (-1, 0, +1), while the response at intermediate inputs is determined by the dynamics and other parameters such as the adaptation time constant, which can qualitatively reshape the constant-input response curve (Figure 3—supplement figure 3);

      (d) The response to a transient input depends on the current state for example, excitatory pulses early in the active phase have little effect, as in the biophysical model.

      This is a direct result of the simplified model using a similar limit cycle and nullcline structure as the biophysical model’s dynamical system (Figure 1).

      (3) PRC usage

      The phase resetting curves are used incorrectly. PRCs are useful when the perturbation is weak (soft) [...] A hard PRC would always reset the cycle to the fixed offset from the perturbation phase and is therefore uninformative in understanding dynamics.

      We appreciate this point and would like to clarify what we show and why. We present finite (non-infinitesimal) PRCs across a range of input strengths and signs, spanning both the "soft" (weak-perturbation) regime as well as the "hard" (strong-perturbation) regime, rather than focusing on the "hard" regime alone. Importantly, even in the strong-perturbation regime we do not see that pulses "always reset the cycle to the fixed offset from the perturbation phase". In Figure 4, we see that the active phase exhibits a non-resetting region whose size and location depend on parameters. This region governs entrainability and phase-locking offset, and is thus a key aspect of the neuron's dynamics. Moreover, the strong-perturbation regime is also biologically relevant in our circuit examples. For instance, the inhibitory connections within the pyloric CPG are strong enough to cause hard resets, and these resets shape the circuit-level dynamics we reproduce. We will revise the pulse-input section to state these points more explicitly so the rationale is clear for showing PRCs across a range of inputs.

      (4) Defining active/quiet phases

      The definition of the active and quiet parts of a burst is often less clear than what the authors suggest. Bursting neurons often do multiple bursts in a cycle, and therefore, substituting the burst envelope is a subjective matter. This is even more problematic in bursting neurons in the brain, where there is often no quiet period.

      We agree that waveform envelope can be subjective in some preparations, and we can add this caveat to the discussion.

      On neurons with no quiet period, we note that this behavior is in fact already supported in our model, as seen in Figure 3: under strong excitatory input, both the biophysical and simplified models enter a regime in which firing rate never reaches zero. As the model can generally be viewed as an abstract limit cycle that maps onto periodic waveforms through the firing function, the quiet phase need not correspond to literal silence.

      On more complex waveforms, we could imagine different firing functions that produce richer burst shapes including multi-peak bursts, but we have not tried this explicitly. Of course, for research questions concerned with irregular bursting or spike-to-burst transitions, a lower-level biophysical model would be more appropriate. In revision, we will expand on how the firing function could produce more complex burst shapes.

    1. Author response:

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

      We sincerely thank the Reviewers for their careful reading and insightful critiques, which have helped make the manuscript clearer and more impactful.

      In response to the Reviewers, we substantially revised the manuscript to improve clarity, framing, and accessibility for readers outside the Drosophila connectomics community, while keeping the core conclusions unchanged. We clarified the study’s scope (defining parallel circuit architecture rather than testing sufficiency for reconstructing grooming sequence order), restructured the last Introduction paragraph, several Results sections, and the Discussion to foreground the main findings and their relevance to the parallel hierarchical-suppression model. We also added key methodological clarifications for non-specialist readers, including how BMN classes were identified in FAFB by a correlative approach (with type-level, not single-bristle, resolution), how FlyWire/Codex synapse counts are defined (contacts vs T-bars), how sensory BMNs can have postsynaptic sites, and what is meant by ascending vs descending neurons in a brain-only dataset. Across the Results, we improved terminology and definitions (e.g., projection zones, hemilineage 23b, BMN nomenclature such as BM-InOm), clarified what derives from prior work (Eichler et al., 2024) versus new analyses, strengthened interpretation of BMN→motor connections as likely modulatory, and expanded explanation of postsynaptic partner categories. We also revised figures and legends to better highlight overlap/segregation and somatotopy, moved the cosine-similarity matrices into the main figures (new Figure 9), added a new graphical summary figure (new Figure 15), and explicitly acknowledged key limitations, including one-hemisphere analysis and lack of VNC coverage in FAFB.

      In addition, in response to the suggestion of a rank-order test relating BMN→second-order wiring to the grooming hierarchy, we clarified throughout the revised manuscript that this study does not aim to test whether connectivity alone is sufficient to reconstruct grooming sequence order, and we removed wording that could imply such a claim. As detailed in our response to that specific critique below, sequence sufficiency is outside the scope of this study, and a simple linear ordering based on aggregate synapse weights is not straightforward to interpret in this system (e.g., BM-Taste vs. BM-InOm output strength does not track grooming order, BMNs likely contribute to multiple behaviors, and head grooming order is not resolved at sufficient granularity). We therefore respectfully request that the sentence in the eLife Assessment suggesting that the paper is weakened by not including this analysis be removed. As currently written, it frames an out-of-scope analysis as a missing test of the manuscript’s main claims and may mislead readers about the paper’s intended contribution: a synaptic-resolution anatomical definition of parallel BMN circuit architecture and motifs consistent with hierarchical suppression.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Calle-Schuler et. al. reconstruct all the pre- and post-synaptic neurons to the bristle mechanosensory neurons on the adult fly head to understand how neural circuits determine the sequential motor patterns during fly grooming. They find that most presynaptic neurons, interneurons, and excitatory postsynaptic neurons are also somatotopically organized, such that each neuron is more connected to bristles mechanosensory neurons that are closer on the head and less connected to bristles mechanosensory neurons that are further away. These include the direct BMN-BMN circuits, excitatory interneurons, as well as the inhibitory networks. They also identify that the entire hemi-lineage 23b forms excitatory postsynaptic circuits with BMNs, highlighting how these circuits and hence their function could be developmentally determined.

      Strengths:

      This is a complete map of all the neurons that make 5 or more pre- and post-synaptic connections of the fly head BMNs. Using this, the authors have identified various trends, such as ascending neurons providing most of the GABAergic inhibitory input, which could provide the presynaptic inhibition essential for the parallel model for sequential grooming generation. Moreover, they identified that the entire cholinergic hemilineage 23b is postsynaptic to BMNs.

      Weaknesses:

      Although the somatotropic organization is an elegant mechanism to generate sequential motor sequences during grooming, none of the analyses in the paper directly demonstrate that this somatotropic connectivity is sufficient to generate hierarchical suppression and reconstruct the grooming sequence. If somatotropic organization is sufficient, then hierarchical clustering should recover the grooming sequence. Their detailed connectome enables the authors to test if some networks are more crucial for grooming sequence than others: to what extent can each network individually (ascending neurons-BMN alone) or a combination (BMN-BMN, ascending-BMN, BMN-descending, etc.) recover the sequence observed during grooming. If all the pre- and post-synaptic neurons put together cannot explain the sequence, then the sequence is probably determined by individual synaptic strengths or other key downstream neurons.

      We appreciate the Reviewer’s interest in how BMN connectivity relates to the grooming sequence, and agree that understanding how mechanosensory circuits contribute to hierarchical action selection is an important direction. In this study, however, our goal was not to test whether connectivity alone is sufficient to reconstruct the full grooming sequence. Rather, we focused on defining the parallel circuit architecture underlying individual grooming movements and on identifying anatomical features—most notably extensive presynaptic inhibition—that are consistent with previously proposed models of hierarchical suppression.

      We recognize that aspects of the Introduction and the references cited there to prior work on the grooming sequence may have led some readers to expect a direct sequence-prediction analysis. To address this, we revised the Introduction and Results to clarify the scope of the study and adjusted language to avoid implying that we aimed to derive the grooming order from connectivity. Consistent with this framing, the Abstract mentions the sequence only in the context of presynaptic inhibition, which provides anatomical support for existing models of hierarchical suppression. We therefore do not draw conclusions about the ordering of grooming movements from the connectome itself. Details of the specific manuscript revisions are provided below in the Recommendations for authors section.

      The Reviewer suggests testing whether somatotopic organization is sufficient to recover the grooming sequence by clustering BMN connectivity or by examining whether specific subnetworks (e.g., BMN → ascending, BMN → descending, or BMN→BMN pathways) reproduce the sequence. We carefully considered these possibilities. However, several factors currently limit the interpretability of such analyses.

      First, synaptic weight alone does not align with known features of the grooming sequence. For example, BM-Taste neurons contribute the majority of BMN synaptic output, yet proboscis grooming is not the first head grooming movement, whereas BM-InOm neurons contribute less than 9% of total output despite eye grooming occurring first. As we now clarify in the Results, global synapse number therefore does not predict the order of grooming movements.

      Second, BMNs likely distribute signals across multiple behavioral pathways beyond grooming, including circuits involved in feeding and escape behaviors. Because the connectome aggregates all postsynaptic targets, analyses based solely on connectivity strength cannot isolate the subset of circuits specifically responsible for grooming-related action selection.

      Third, the head grooming sequence itself has not been resolved at the spatial granularity required for such analyses across head regions. While eye grooming is well characterized as the first head movement, the relative ordering among antennae, proboscis, and other head bristle regions remains less clearly defined, making it difficult to evaluate correspondence between connectivity-derived rankings and behavioral order.

      Because of these limitations, we concluded that clustering or network-based analyses aimed at reconstructing the grooming sequence from connectivity alone would be difficult to interpret and therefore chose not to include them. Accordingly, we have deliberately avoided claiming that the connectome is sufficient to generate the grooming sequence. Instead, we interpret the somatotopic architecture and inhibitory circuitry described here as anatomical features consistent with previously proposed models of hierarchical suppression, while leaving the question of sufficiency for future studies that integrate connectomics with functional and behavioral analyses.

      Given that we do not claim sufficiency of the connectome for producing the grooming sequence, we respectfully request that the eLife Assessment avoid framing the manuscript around this expectation, as wording that implies the manuscript should reconstruct the sequence from connectivity could misrepresent the intended scope of the study and potentially mislead readers about its primary contributions.

      Reviewer #2 (Public review):

      Summary:

      Schuler et al. present an extensive analysis of the synaptic connectivity of mechanosensory head bristles in the brain of Drosophila melanogaster. Based on the previously described set of bristle afferent neurons, (BMNs), located on the head, the study aims to provide a complete, quantitative assessment of all synaptic partners in the ventral brain. Activation of head bristles induces grooming behavior, which is hierarchically organized, and hypothesized to be grounded in a parallel cellular architecture in the central brain. The authors found evidence that, at the synaptic level, neurons downstream of the BMN afferents, namely the postsynaptic LB23 interneurons and recurrent GABAergic neurons (involved in sensory gain control), are organized in parallel, following the somatotopic organization described for the BMN afferents. This study, therefore, represents an important step towards a better understanding of the cellular circuits that govern the hierarchical order of sequentially organized grooming behavior in Drosophila melanogaster.

      The study is well done, the images are well designed and extensive in number, but the account is challenging to read and digest for the reader outside the Drosophila /connectome community. It is amazing what can be done with the connectome nowadays using the up-to-date FAFB dataset, the analytical and visual tools (as in FlyWire), in combination with known anatomy/physiology/behavior in DM. I suggest that the authors provide more detail on hemilineages, their relationship to the FAB connectome, the predicted neurotransmitter identity, and the use of statistical CatMAID tools used in some of the Figures.

      A graphical summary at the end of the study would be very useful to highlight the important findings focusing on neuron populations identified in this study and their position in the hypothesized parallel central circuitry of BMNs.

      We thank the Reviewer for the thoughtful and constructive comments. In response, we substantially revised the manuscript to improve clarity and accessibility, particularly for readers outside the Drosophila connectomics community. We rewrote portions of the Introduction, Results, and Discussion to better foreground the main findings, reduce density, and more clearly distinguish prior work from the new analyses presented here. We also added methodological clarification throughout, including how BMN classes were identified in the FAFB dataset using a correlative, type-level approach, how FlyWire/Codex synapse counts are defined, and clarified terminology related to projection zones, pre- versus postsynaptic structure, and partner classes. To address the Reviewer’s request for more developmental context, we added a more explicit definition of hemilineages at first mention in the Abstract and Results. In addition, we revised figures and legends to make the somatotopic and parallel organization of the circuitry easier to interpret, including moving the cosine-similarity matrices into the main figures. Finally, in direct response to the Reviewer’s suggestion for a higher-level synthesis, we added a new graphical summary figure (Figure 15) at the end of the manuscript to highlight the principal neuron populations identified in the study and their proposed positions within the parallel central BMN circuitry. Together, we believe these revisions have made the manuscript clearer, more accessible, and better framed for a broad readership while preserving its core conclusions. Details of these changes are provided in the Recommendations for the authors section.

      Reviewer #3 (Public review):

      Summary:

      The authors set out to extend their previous mapping of Drosophila head mechanosensory neurons (Eichler et al., 2024) by reconstructing their full second-order connectome. Their aim is to reveal how bristle mechanosensory neurons (BMNs) interface with excitatory and inhibitory partners to generate location-specific grooming movements, and to identify the circuit motifs and developmental lineages that support this transformation.

      Strengths:

      The strengths of this work are clear. The authors present a comprehensive synaptic-resolution connectome for BMNs, identifying nearly all of their pre- and postsynaptic partners. This dataset reveals important circuit motifs:

      (1) BMNs provide feedforward excitation to descending neurons, feedforward inhibition to interneurons, and are themselves strongly regulated by GABAergic presynaptic inhibition.

      (2) These motifs together support the idea that BMN activity is locally gated and hierarchically suppressed, fitting well with known behavioural sequences of grooming.

      (3) The study also shows that connectivity preserves somatotopy, such that BMNs from neighbouring bristle populations converge onto shared partners, while distant BMNs remain segregated.

      (4) A developmental analysis reveals both primary and secondary partners, suggesting a layered scaffold plus adult-specific elaborations.

      (5) Finally, the identification of hemilineage 23b (LB23) as a core postsynaptic pathway - incorporating previously described antennal grooming neurons (aBN2) - provides a striking link between developmental lineage, anatomical connectivity, and behavioral output.

      (6) Together, the dataset represents a valuable resource for the neuroscience community and a foundation for future functional studies.

      Weaknesses:

      There are also some weaknesses that mostly only limit clarity.

      (1) The writing is dense, with results often presented in a cryptic fashion and the functional implications deferred to the discussion. As a result, the significance of circuit motifs such as BMN→motor or reciprocal inhibitory loops is sometimes buried, rather than highlighted when first described.

      We thank the Reviewer for this helpful suggestion. In response, we revised several sections of the Results to improve clarity and more clearly highlight the functional significance of key circuit motifs when they are first introduced. Specifically, we streamlined dense passages and added brief explanatory statements linking motifs such as reciprocal inhibitory loops to their potential roles in the proposed parallel circuit architecture. Additional details of these revisions are provided in the Recommendations for the authors section below.

      (2) Some assumptions require more explanation for non-specialist readers - for example, how bristle identity is inferred in EM in the absence of cuticular structures, or what is meant by "ascending" and "descending" in a dataset that does not include the ventral nerve cord. While some of this comes from the earlier paper, it would help readers of this one to explain this.

      In response, we added clarifying text describing how BMN types were identified in the FAFB dataset using a correlative approach based on stereotyped projection morphologies and prior light-level anatomical data, and we explicitly state the limits of this type-level assignment in the absence of cuticular bristles in the EM volume. We also expanded the explanation of partner categories, including what is meant by “ascending” and “descending” neurons in a brain-only dataset. Additional details of these revisions are provided in the Recommendations for the authors section.

      (3) Visualization choices also sometimes obscure key conclusions: network graphs can be visually appealing but do not clearly convey somatotopy or BMN-type differences; heatmaps or region-level matrices would make the parallel, block-like organization of the circuit more evident.

      We incorporated connectivity matrices (cosine-similarity heatmaps) into the main figures to more clearly illustrate the somatotopic and parallel organization of BMN connectivity, complementing the network graph visualizations (new Figure 9). These matrices make the block-like structure of BMN partner relationships more apparent and help highlight differences among BMN types; additional details are provided in the Recommendations for the authors section.

      (4) The data might also speak to roles beyond grooming (e.g., mechanosensory modulation of posture or feeding), and a brief acknowledgement of this would broaden the impact.

      We added text acknowledging that BMNs contribute to additional behaviors beyond grooming, such as feeding and other mechanosensory-guided actions. These roles are supported by prior studies of bristle function and are also consistent with the diverse downstream circuits revealed in the connectome. This clarification broadens the interpretation of the dataset while maintaining the primary focus of the study on grooming-related circuitry.

      (5) The restriction to one hemisphere should be explicitly acknowledged as a limitation when framing this as a 'comprehensive' connectome.

      We thank the Reviewer for this suggestion. We now explicitly acknowledge this limitation in both the Results and Discussion.

      In the Results section entitled “The BMN connectome” we added a sentence at the end of the paragraph that mentions the limitations. This sentence reads: “In addition, because our analysis was restricted to BMNs entering the left hemisphere, the complete right-side BMN connectome is not included, limiting assessment of bilateral symmetry, inter-hemispheric coordination, and variability across sides.”

      The last paragraph of the first Discussion section describes limitations to our ‘comprehensive’ connectome. The text in this paragraph pertaining to the left/right variability reads: Second, the analysis focuses only on BMNs from the left hemisphere. Although contralateral neurons synapsing with left-side BMNs are included, the absence of the right-side BMN connectome limits assessment of bilateral symmetry, interhemispheric coordination, and side-to-side variability.

      Overall, the authors achieve their main goal: they convincingly show that BMNs connect into parallel, somatotopically organized pathways, with LB23 providing a key lineage-based link from sensory input to grooming output. The dataset is carefully analyzed, and while the presentation could be streamlined, the connectome will be a valuable resource for researchers studying sensory processing, motor control, and the logic of circuit organization.

      Recommendations for the authors:

      Reviewing Editor Comments:

      We enjoyed this work and are enthusiastic about its contribution: the resource is valuable, and the anatomical evidence is solid. Most of our suggestions concern clarity and visualization, detailed below.

      In addition, the editors and reviewers felt one focused analysis would materially strengthen the paper: please use the BMN→second-order synapse weights to produce a similarity-based, one-dimensional order of BMN types and test its agreement with the known grooming sequence (e.g., via a rank correlation). A positive result would support sufficiency of the mapped wiring for the sequence; if not, the claims can be framed as "consistent with" rather than "sufficient for."

      We appreciate the Reviewers’ interest in how BMN connectivity relates to the grooming sequence, and agree that understanding how mechanosensory circuits contribute to hierarchical action selection is an important direction. In this study, however, our goal was not to test whether connectivity alone is sufficient to reconstruct the full grooming sequence. Rather, we focused on defining the parallel circuit architecture underlying individual grooming movements and on identifying anatomical features—most notably extensive presynaptic inhibition—that are consistent with previously proposed models of hierarchical suppression.

      We recognize that references in the Introduction to prior work on the grooming sequence may have led some readers to expect a direct sequence-prediction analysis. To address this, we revised the Introduction and Results to clarify scope and adjusted language to avoid implying that we aimed to derive the grooming order from connectivity. Consistent with this framing, the Abstract mentions the sequence only in the context of presynaptic inhibition, which provides anatomical support for existing models of hierarchical suppression. We do not draw conclusions about the ordering of grooming movements from the connectome itself.

      The Reviewer-suggested analysis—using BMN-to-partner synaptic weights to derive a linear ordering of BMN types—is conceptually reasonable, but its interpretability is limited at present. First, synaptic weight alone does not align with known features of the grooming sequence: BM-Taste neurons contribute the majority of BMN synaptic output, yet proboscis grooming is not the first head movement, whereas BM-InOm neurons contribute less than 9% of output despite eye grooming occurring first. Second, BMNs likely project to multiple pathways supporting distinct behaviors, such as feeding and escape, complicating any attempt to infer a single grooming hierarchy from aggregate connectivity. Third, the head grooming sequence itself has not been resolved at the granularity required for such an analysis, particularly among the antennae, proboscis, and other head bristle regions. Accordingly, we have deliberately refrained from making claims that connectivity is sufficient to generate the grooming order.

      Given that we do not claim sufficiency of the connectome for producing the grooming sequence, we respectfully request that this point be removed from the public eLife Assessment, as its current wording implies an unmet expectation outside the intended scope of the study and could mislead readers about the manuscript’s primary contributions. We appreciate the opportunity to clarify our framing and to ensure that the goals and outcomes of the work are accurately represented.

      Revisions.

      (1) Gave the last paragraph of the Introduction more structure to clearly state the main findings of the study in the context of what we learned about the circuit architecture proposed by the parallel model of hierarchical suppression.

      New paragraph: “Here, we define the synaptic connectivity of head BMNs by mapping nearly all of their pre- and postsynaptic partners—including other BMNs, ascending and descending neurons, interneurons, and motor neurons—within the FAFB dataset. Consistent with a parallel model, we find that both presynaptic and postsynaptic partners are somatotopically organized, preserving the spatial layout of the bristle map and revealing a set of parallel mechanosensory pathways that correspond to distinct head regions. Within the postsynaptic population, we identify the developmentally-related cholinergic hemilineage 23b (LB23), whose members exhibit region-specific BMN connectivity and include neurons previously shown to elicit aimed head grooming movements when activated. This demonstrates how LB23 neurons participate in parallel postsynaptic pathways that may drive discrete components of head grooming. On the input side, BMNs receive substantial presynaptic inhibition from predominantly GABAergic partners, providing strong feedback and feedforward control over mechanosensory signaling. This inhibitory architecture is consistent with hierarchical-suppression models in which inhibition regulates sensory gain and prioritizes competing actions in the grooming sequence. Together, this mechanosensory connectome reveals core organizational principles—parallel somatotopic architecture, region-specific excitatory pathways, and strong inhibitory regulation—that are thought to constitute foundational circuit motifs supporting head grooming.”

      (2) In the Results section entitled “BMN synapses show large quantitative variation across types”, we added text to the third paragraph that makes it clear that raw synapse numbers alone do not predict the sequence, if one just compares the first movement (eye grooming) and a later movement in the sequence (proboscis grooming).

      That text reads: “Notably, if grooming order were driven simply by relative sensory drive—i.e., by BMN types with the strongest synaptic output eliciting cleaning of their corresponding locations first—then synapse number should track the grooming sequence. Instead, differences in synapse number do not align with the order of the grooming sequence: BM-Taste neurons account for the majority of BMN output, yet proboscis grooming is not the first head grooming movement performed, whereas BM-InOm neurons contribute only a small fraction of output despite eye grooming occurring first (Figure 1E, Figure 2A,B). This indicates that global synapse number alone is not a reliable predictor of the grooming sequence.”

      (3) In the results section entitled “BMN postsynaptic partners are excitatory and inhibitory”, we added text to two different sentences to better link the results with what we are trying to test with respect to the parallel model of hierarchical suppression.

      Modified sentence 1: “This excitation is hypothesized in the parallel model to help form BMN feedforward circuits that elicit aimed grooming of specific body locations, while feedforward inhibition could mediate suppression of competing grooming movements (Figure 1 – figure supplement 1A, B).”

      Modified sentence 2: “Taken together, the BMN postsynaptic partners include a diverse set of neurons that mediate both feedforward excitation and inhibition and feedback inhibition, features predicted by the parallel model.”

      (4) In the Results section entitled “BMNs and LB23 neurons form somatotopic pathways that elicit aimed grooming, we added text to the first sentence that better ties the section to the overall goals of the manuscript.

      That text now reads: “In accordance with the parallel model of grooming, we hypothesize that BMNs connect with somatotopically organized excitatory parallel pathways eliciting aimed grooming of specific head locations (Figure 1 – figure supplement 1A, C).”

      Reviewer #1 (Recommendations for the authors):

      (1) The connectivity matrix (like that in Lesser et al., 2024, Nature, and also in Figure 9, Figure Supplement 1 of this paper) is an easier-to-digest representation of the various connections shown in Figure 2.

      We agree that connectivity matrices provide a clearer and more accessible representation of these data. Based on the context of this and other comments, we understand the Reviewer to be referring to Figure 9 rather than Figure 2. In response, we have moved the cosine-similarity connectivity matrices previously shown in Figure 9 – figure supplement 1 into the main manuscript, where they now appear as Figure 9.

      These matrices depict similarity among BMN postsynaptic partners. At present, we are unable to generate equivalent matrices for presynaptic partners due to recent personnel constraints in the lab. For this reason, we have retained the original network-graph representation (now Figure 10) to display the full pre- and postsynaptic connectome structure.

      We hope this compromise addresses the Reviewer’s request while clearly presenting the available analyses.

      (2) Again, "Cosine based clustering is essential to demonstrate the somatotropic organization" the data in Figure 9 - Figure Supplement 1 demonstrates this better than the main Figure 9. This supplementary figure would be a great addition to the main manuscript.

      Please see the preceding response for details on the changes that we made to address this reviewer comment.

      (3) Figure 9 - Figure Supplement 1A: Can the authors explain why the InOm occur in two clusters (red in top and bottom)? Do InOm neurons show two different kinds of connectivity patterns?

      This is a great question! We had written a possible explanation for this in the Discussion section entitled “A synaptic resolution connectome of a head somatotopic map”.

      “One notable exception to this pattern is the BM-InOm population, which occupies a central position in network diagrams and exhibits broad connectivity similarity with BMNs from across the head (Figure 9A, Figure 10A-E). This likely reflects the large surface area of the compound eyes, which span dorsal, ventral, and posterior regions and neighbor multiple bristle populations. Consistent with previous work showing morphological diversity among BM-InOm neurons (Eichler et al., 2024), our output connectivity analysis suggests the presence of multiple BM-InOm subtypes defined by distinct partner profiles (Figure 9A). Future work will be needed to determine how this heterogeneity relates to spatial organization within the eye.”

      Reviewer #2 (Recommendations for the authors):

      All further comments for the authors are aimed at a better understanding of the text and for clarity. The manuscript needs revision.

      (1) Ventral brain:

      Please specify this term. Is it the SEG, or the gnathal ganglion? Throughout the paper, 'ventral brain', or 'brain', is the only anatomical terms you use. Are all pre-/post- partners of BMNs located in this region? I understand that you provide a statistical analysis on a network level, here, but as far as I know, the neuropil regions in Drosophila are reported in more detail on the macroscopic level (see, e.g., Itoh).

      Based on our understanding of the Ito et al reference, SEG was “retired” in that manuscript in favor of gnathal ganglia. We considered using the term subesophageal zone (SEZ) in the manuscript, but ultimately chose not to adopt it. In the Drosophila brain nomenclature (Ito et al., 2014), the SEZ is defined as a region below the esophagus that encompasses multiple neuropils, such as the gnathal ganglia (GNG) and saddle (SAD), rather than a single anatomically discrete structure.

      In our dataset, the GNG are the ventral-most neuropil containing the BMN projections and the highest density of BMN-related synapses, and we therefore refer to this structure explicitly where appropriate. However, BMN pre- and postsynaptic partners are not confined to the GNG or to the SEZ as a whole; some partner neurites extend dorsally into additional neuropils. As a result, the term SEZ does not accurately capture the full spatial extent of the BMN connectome analyzed here.

      For clarity and consistency across analyses that span multiple adjacent neuropils, we therefore use the broader functional descriptor “ventral brain”, while explicitly identifying the gnathal ganglia and other neuropils when discussing neuropil-level synapse distributions. We believe this approach most accurately reflects both the anatomical organization of the circuit and the scope of our analysis.

      Given this Reviewer’s comment, we anticipate that not mentioning the SEZ in this manuscript might result in similar confusion among readers of our manuscript. Therefore, we now mention the SEZ and the supraesophageal zone (SPZ) at the end of the Results section entitled “Synapses of BMN partners are mostly concentrated in the ventral brain”. We also added the SEZ and the SPZ to the new last summary figure (Figure 15) to help clarify the locations of the BMNs and their second order connectome.

      That text reads: “Thus, while most neuropils containing synapses of second-order BMN partners are located below the esophagus (in the subesophageal zone, SEZ), we found more limited involvement of neuropils in the supraesophageal zone (SPZ; above the esophagus), suggesting relatively limited direct top-down control.”

      (2) Please provide greater clarity in your use of the terms synapse-presynapse-pre- and postsynaptic partners:

      In insects, synapses are polyads. It is therefore essential to distinguish whether by presynaptic (pre) you mean 1. the number of T-bars (presynaptic sites) or 2. the number of (outgoing) synaptic contacts made by a single presynaptic T-bar site. For example, a synapse configured as a tetrad (a polyad) consists of one presynaptic T-bar opposed to four postsynaptic profiles and can be counted either as one synapse (one presynaptic site, one T-bar, in CATMAID: a presynaptic connector) OR as four (outgoing) synaptic connections since the single T-bar connects to four different postsynaptic profiles. This distinction is crucial for quantifying synaptic networks in insects. Thus, the "number of synapses" may refer to 1. The number of presynaptic sites = number of T-bars = number of polyads formed by a particular neuron. 2. the number of actually outgoing synaptic contacts, a number that also reflects the degree of polyadicity. 3. number of postsynaptic sites (that is easy).

      This distinction (regarding the counts of presynapses) was reported in previous connectome studies (e.g., Horne, 2018; Gruber, 2025; Schlegel,2023). Schlegel notes: ' Insect synapses are polyadic, i.e., each presynaptic site can be associated with multiple postsynaptic sites. In contrast to the Janelia hemibrain dataset, the synapse predictions used in FlyWire do not have a concept of a unitary presynaptic site associated with a T-bar. Therefore, presynapse counts used in this paper do not represent the number of presynaptic sites but rather the number of outgoing connections.' End of citation from Schlegel.

      We thank the Reviewer for highlighting this important distinction. We now clarify in the Materials and methods that synapse counts are based on Codex/FlyWire annotations, which report individual pre- and postsynaptic contacts rather than unitary presynaptic sites (T-bars), consistent with prior FlyWire-based connectome studies (e.g., Schlegel et al.). We also added a brief clarification in the Results indicating that pre- and postsynaptic numbers refer to incoming and outgoing contacts.

      We added a sentence to the first section of the Materials and methods entitled “Connectome data and neuron meshes”. This text reads: “Synapse counts throughout this study are based on FlyWire/Codex synapse annotations and represent the number of individual pre- to postsynaptic contacts (incoming or outgoing connections), rather than the number of presynaptic active sites (T-bars); thus, presynaptic counts reflect polyadic connectivity as described previously (Schlegel et al., 2023).”

      (3) In your study, a potential misunderstanding of this distinction arises when comparing statements on line 168 versus line 184:

      On line 168, you state: '... each BMN type having .... more postsynaptic than presynaptic sites'. However, on line 184 you state: 'There were significantly more postsynaptic than presynaptic partners, in agreement with the BMNs containing more presynaptic than postsynaptic structures. These are contradictory: the statement on line 168 seems to refer to the number of presynaptic T-bars, while on line 184 you refer to the number of actually outgoing connections (which more accurately reflects the degree of polyadicity). Since BMNs are sensory afferent, they are indeed expected to have more outgoing synapses into the central brain.

      We thank the Reviewer for identifying this mistake. We have revised the sentence at former line 168 to now read: “In addition to differing in total synapse number, BMN types vary in their pre- versus postsynaptic composition: all BMNs contain both (Eichler et al., 2024), with presynaptic sites outnumbering postsynaptic sites by ~2× to ~9× across types (mean ≈5:1 output-to-input ratio, Figure 2 – figure supplement 1A, B, Supplementary file 2, Supplementary file 3).”

      (4) Identification of bristle sensory afferents in the brain:

      This is explained in more detail in the Eichler paper, but not here. I do not understand how you identified these neurons in the FAFB dataset. The number and distribution of the individuum of the FABF EM dataset are not known, and because there is variability in the number of bristles in individual flies, the true number of bristle neurons for synaptic analysis can only be estimated. The correlative approach necessary to find the bristle sensory neurons in the FAFB set is still unclear to me. See also my comments on Figure 1.

      We thank the Reviewer for raising this point. We agree that our original draft did not clearly explain the correlative approach used to identify head BMNs in the FAFB dataset, and we have revised the manuscript to make this workflow explicit.

      In our prior work (Eichler et al., 2024), we quantified the number of bristles in each head bristle population and assessed the extent to which populations are invariant versus variable across individuals. This established an expected range for BMN counts by bristle population and clarified the level of variability that can be expected biologically.

      We then identified BMN types corresponding to specific bristle populations using different techniques, such as dye fills and light microscopy, which allowed us to define the characteristic projection morphologies and CNS entry routes associated with each population. These light-level anatomical signatures provided the basis for locating the corresponding axons in the FAFB EM volume and reconstructing the same neuron classes in EM. Importantly, because bristles themselves are not present in the EM volume, this approach supports type-level assignment (bristle population/BMN class) rather than single-bristle resolution, and we now state this explicitly to avoid overinterpretation.

      To ensure this is clear to readers who have not read Eichler et al., we have added explanatory text in the Results and expanded the Figure 1 legend describing: (i) how BMN types were identified and matched, (ii) what can and cannot be resolved given natural bristle-number variability, and (iii) how this impacts interpretation of “completeness” at the level of BMN types rather than individual bristles.

      In paragraph 1 of the first Results section, entitled “BMN synapses are somatotopically distributed in the ventral brain”, we added text that briefly describes the previous linkage of the head BMNs to the FAFB dataset. That text reads: “In prior work (Eichler et al., 2024), we showed that head bristle populations are innervated by specific BMN types whose axons project to distinct, spatially localized regions (projection zones) in the ventral brain (Figure 1C,D, left, Figure 1 – figure supplement 2A-E). This was determined using dye fills and light-microscopy-based tracing to identify BMN types innervating defined head bristle populations and to establish their characteristic brain projection morphologies. Bristle population counts and their variability across individuals provided expectations for BMN number per type. This quantitative constraint, combined with the highly stereotyped projection morphologies, provided a correlative anatomical framework to locate and reconstruct nearly all BMNs in the FAFB serial-section EM volume and map their projections into the CNS. Because FAFB does not include the head cuticular bristles, individual BMNs could not be linked to single bristles. Therefore, these assignments are necessarily correlative and provide type-level (population) rather than single-bristle resolution. Nevertheless, this level of resolution was sufficient to define somatotopically organized projection zones."

      (5) Results:

      (a) Line 102: explain hemilineage 23 B

      We added text in the manuscript to better define hemilineages.

      In the Abstract, we added to a sentence that highlights that the LB23 neurons are developmentally related. That sentence now reads: “We identified an excitatory cholinergic hemilineage (hemilineage 23b), a developmentally related group of neurons that elicits aimed head grooming and exhibit differential connectivity with BMNs from distinct head locations, revealing a lineage-based somatotopically organized parallel circuit architecture.”

      Results section entitled “The entire cholinergic hemilineage 23b (LB23) is postsynaptic to BMNs”, we added a sentence that defines hemilineage at its first mention in the Results section. We also made slight modifications to the preceding and following sentences. That text reads: “To identify neurons crucial for establishing the BMN-postsynaptic parallel pathways that elicit head grooming movements, we focused on secondary hemilineages. In the Drosophila CNS, a hemilineage refers to the cohort of neurons derived from a single stem cell-like neuroblast that share a common developmental origin, stereotyped morphology, and are thought to have related functional roles within a circuit (Harris et al., 2015; Wreden et al., 2017). This focus was motivated by earlier findings that neurons whose activation elicited head grooming had morphologies consistent with specific hemilineages (Hampel et al., 2015; Seeds et al., 2014).”

      (b) Line 151: - line 171: it is not clear to me what a projection zone is.

      We thank the Reviewer for raising this point. We agree that the term “projection zone” benefits from a brief clarification. We have made minor edits at two locations to explicitly state that projection zones refer to spatially localized regions of BMN axonal arborization and synaptic distribution corresponding to specific head locations.

      Changes made in the manuscript:

      A sentence that first introduces the term in the fourth paragraph of the Introduction now reads: “Indeed, the BMN axon projections in the central nervous system (CNS) show a somatotopic arrangement, where distinct projection zones—spatially localized regions of axonal arborization and synaptic output—correspond to specific head and body locations (Eichler et al., 2024; Johnson and Murphey, 1985; Murphey et al., 1989; Newland, 1991; Newland et al., 2000; Tsubouchi et al., 2017).”

      In a sentence in the first paragraph of the first Results section, we added a brief clarifying definition of “projection zones” at their first mention in the Results. That sentence reads: In prior work (Eichler et al., 2024), we showed that head bristle populations are innervated by specific BMN types whose axons project to distinct, spatially localized regions (projection zones) in the ventral brain (Figure 1C,D, left, Figure 1 – figure supplement 2A-E).

      (c) Input-output versus presynapse-postsynapse?

      A revised sentence in the last sentence of the Results section makes this distinction clear: In addition to differing in total synapse number, BMN types vary in their pre- versus postsynaptic composition: all BMNs contain both (Eichler et al., 2024), with presynaptic sites outnumbering postsynaptic sites by ~2× to ~9× across types (mean ≈5:1 output-to-input ratio, Figure 2 – figure supplement 1A,B, Supplementary file 2, Supplementary file 3).

      (6) Figures:

      For clarity, it would be helpful if you indicated by the arrow the name of the sensory location (antenna, eye, etc.).

      We appreciate this suggestion. Major sensory locations corresponding to different head bristle populations are indicated in Figure 1 – figure supplement 1C. We explored adding these labels directly to Figure 1A, but found that doing so made the panel overly crowded and less clear. To improve visibility while keeping the main figure uncluttered, we now explicitly direct readers to this figure supplement in the Introduction.

      Specifically, we added a reference to Figure 1 – figure supplement 1C in the following sentence in the Introduction: Dust-induced head grooming is performed by the forelegs that start with the eyes and progress to other locations such as the proboscis and antennae (major head locations shown in Figure 1 – figure supplement 1C) (Seeds et al., 2014).

      (a) Figure 1:

      A: the presence of bristle types on the head. Are the JO afferents you mention in the text reported here?

      Figure 1 does not include the JONs, which were described in detail in our previous study (Hampel et al., 2020).

      The JONs are mentioned in the Figure 1 – figure supplement 1. We have added text to this legend to indicate that the JONs are not the subject of this study. This text reads: “(C) Mechanosensory neurons from different head locations project to distinct, somatotopically organized zones in the ventral brain and elicit aimed grooming of those locations, including the antennae (via JONs [Johnston’s organ neurons; not analyzed in this study] and BMNs), eyes (BMNs), and proboscis (BMNs).”

      Are the reconstructions shown 1 B-D also from the Eichler paper?

      We regret that this was not explicitly stated in the figure legend, and have revised the legend to distinguish between what was previously published and what is new to this study.

      In the Figure 1 legend, we revised the following sentence: (C, D) Reconstructed BMN projections in the ventral brain (left, previously described in (Eichler et al., 2024)) and their corresponding pre- and postsynaptic sites (right, this study), colored by type according to the bristles that they innervate.

      To make this clearer in the main text, we have rewritten the first sentence in the first paragraph of the Results: In prior work (Eichler et al., 2024), we showed that head bristle populations are innervated by specific BMN types whose axons project to distinct, spatially localized regions (projection zones) in the ventral brain (Figure 1C,D, left, Figure 1 – figure supplement 2A-E).

      The dots are symbolic, or do they represent the number of bristles? The number of bristles cannot be identified, and thus stems from the FABF dataset.

      The dots are symbolic and do not represent the number of bristles in the FAFB dataset. As noted in response to a related reviewer comment above, the numbers and variability of head bristles were quantified in our prior work (Eichler et al., 2024). We also used dye fills and light-microscopy approaches, which provided the framework for linking BMN types to bristle populations. We have clarified this point in the revised manuscript, as described in the response above.

      Synapse number of bristle afferents: number of all pre-and postsynaptic contacts?

      We have addressed this point above.

      (b) Figure 2:

      Again, the term synapses refers to all pre-and postsynaptic contacts ?

      The Figure 2 legend indicates that synapse numbers include both input and output synapses. Additionally, now the first reference to Figure 2 indicates that numbers refer to both input and output synapses.

      (c) Figure 2:

      Supplement presynaptic/postsynaptic means pre- and post partner?

      Presynaptic: number of BMNs that were connected with at least 5 synapses to any given presynaptic partner (n), the numbers of synaptic inputs to BMNs (inputs), and the number of presynaptic partners (partners). Postsynaptic: number of BMNs that were connected with at least 5 synapses to any given postsynaptic partner, the numbers of synaptic outputs to postsynaptic partners, and the number of postsynaptic partners.

      (d) Figure 3:

      Explain downstream-upstream

      Downstream refers to postsynaptic while upstream refers to presynaptic partners or pathways.

      Comparing the right side of the Sankey d. with your diagram in B, just by judging, I see more partners of descending (post) than interneurons (post) in A. However, in B, there are clearly more postsynaptic interneurons than descending posts? There are no numbers in Figure 3A.

      This is a great point! Figure 3A (the Sankey diagram) summarizes the fraction of BMN synaptic output distributed across partner classes, normalized within each BMN type. In this representation, descending neurons occupy a larger fraction because, across BMN types, they collectively receive a higher proportion of BMN output synapses.

      In contrast, Figure 3B (the sunburst plot) summarizes the number of distinct postsynaptic partner neurons in each category. Here, interneurons are more numerous than descending neurons, even though individual interneurons tend to receive fewer BMN synapses on average.

      Thus, the two plots are consistent: descending neurons are fewer in number but receive more synapses per neuron, whereas interneurons are more numerous but receive fewer synapses per neuron on average. When postsynaptic synapse counts are summed (as in the bottom plots), the totals for descending neurons and interneurons can therefore appear similar, despite their different representations in the Sankey diagram.

      We have added text in the Results section entitled “BMN synaptic partners in the CNS: ascending, descending, and interneurons”. Text was added here because it also nicely responds to another Reviewer comment below for more description of the postsynaptic partners. That added text reads: “Interneurons are more numerous as distinct partner neurons, whereas descending neurons receive a larger fraction of BMN output synapses across BMN types (Figure 3A,B). Thus, descending neurons are fewer in number but tend to receive more BMN synapses per neuron on average, while interneurons are more numerous but often receive fewer synapses per neuron.”

      (e) Figure 10: I cannot see colored circles. I found Figure 10 very hard to understand. Is this a visualization created in CATMAID? As I mentioned before, a graphical summary highlighting the information flow and architecture of the circuits analyzed in this study would be useful. In such a diagram, you could combine the findings of your study, the open question, and the undeciphered pathways. In short, a schematic of the current knowledge of the potentially parallel and recurrent architecture of the BMN circuitry.

      Figure 10 (now Figure 11) is intended to specifically examine neurons that are both pre- and postsynaptic to BMNs, rather than to summarize the full connectome. The goal of this figure is to highlight two features of pre/post neurons: their somatotopic connectivity with BMN types and the presence of bilaterally symmetric neuron pairs that connect to common BMN populations.

      This visualization was generated from connectome-derived connectivity data and not from CATMAID, although it uses neuron reconstructions and synapse annotations from the FAFB dataset. The colored nodes represent BMN types and are now consistently referred to as “dots” rather than “circles” to better match their appearance. We have simplified the figure legend to clarify these points.

      In response to this and related comments, we also added a new graphical summary figure (Figure 15) at the end of the manuscript that schematically summarizes the information flow and parallel, recurrent architecture of the BMN circuitry at a higher level.

      (7) Discussion:

      I found the first part of your discussion hard to read; the second part is better. You can condense the discussion by mentioning the results/hypothesis of previous work once, and avoiding repetitions, such as the uniqueness of the BMN connectome/FAB dataset.

      In response to this comment, we condensed the opening portion of the Discussion by reducing repetition of background and prior findings, particularly references to earlier BMN work and the uniqueness of the FAFB dataset. We streamlined overlapping sections, mentioned prior hypotheses and results only once, and focused the revised text more directly on the new contributions of this study—namely, the synaptic-resolution organization, somatotopic connectivity, and circuit principles revealed by the BMN connectome.

      There are several cases of vague sentences, e.g.: a) Line 827: 'Head BMNs project from bristles to somatotopically organized zones in the brain (? ventral brain ?), with those innervating neighboring populations (? of bristles ?) occupying overlapping zones (Figure 1A-D)'.

      We made this suggested change: Head BMNs project from bristles to somatotopically organized zones in the ventral brain, with those innervating neighboring bristle populations occupying overlapping zones (Figure 1A-D).

      A remark: maybe you should indicate in Figure 1D the overlapping and segregated zones. The resolution is very low in these images.

      We thank the Reviewer for this comment and agree that overlap versus segregation of projection zones was not sufficiently guided in the original presentation. Rather than adding arrows to Figure 1C,D, which we felt would reduce clarity, we now explicitly describe how overlap and segregation can be identified based on color mixing of BMN synapses in the text and figure legend. In addition, we highlight these features more clearly in Figure 1 – figure supplement 3, which provides higher-resolution, multi-view visualizations of BMN synapses where overlap and non-overlap are most evident.

      Results:

      Segregation between projection zones is apparent where synapses of distinct BMN types occupy non-overlapping regions with little or no color mixing, whereas overlap between projection zones is visible as spatial intermixing of differently colored synapses from neighboring BMN types (Figure 1C, D, right, Figure 1 – figure supplement 3A-E).

      Figure 1 legend:

      Overlapping projection zones are evident where synapses of different BMN types spatially intermingle, whereas segregated zones show little or no color mixing.

      Figure 1 – figure supplement 3 legend:

      These views highlight both overlapping projection zones, visible as intermingled synapses of different colors from neighboring BMN types, and segregated zones, where synapses from distinct BMN types remain spatially separated with minimal color mixing.

      (b) Line 860: What is: 'location groomed'?

      Added a clarification to this sentence: Thus, the location groomed (i.e. antennae) corresponds to the location of the majority of BMN inputs.

      (c) Line 944: 'The sensory to motor resolution' What do you mean, here?

      We have revised this sentence to “The spatial resolution of the sensory-to-motor transformation in this parallel circuit architecture remains to be tested.”

      (d) The term: 'neighboring bristles' is unclear. Does it mean 'neighbor relates to members within he same bristle type (antennae)', or 'bristles of different types', e.g. antennae and eye bristles.

      We thank the Reviewer for raising this point. Throughout the manuscript, the term “neighboring bristles” is used primarily to refer to neighboring bristle populations (i.e., bristles from different anatomical groups that are spatially adjacent on the head). In some contexts, the term is also used more generally to describe spatial proximity, regardless of whether the bristles belong to the same or different populations. Importantly, in both cases, the usage reflects the same underlying observation: BMNs innervating bristles that are spatially closer—whether within or between populations—show greater similarity in their postsynaptic connectivity than BMNs innervating more distant bristles.

      (e) Avoid abbreviations, or explain shortly, the term under discuss: line 725: BMlnOm?

      We thank the Reviewer for pointing out that the BMN nomenclature was not sufficiently clear. BMNs are named according to the bristle population they innervate (e.g., BM-Ant neurons innervate antennal bristles; BM-InOm neurons innervate interommatidial eye bristles), as defined in the Figure 1 legend. To improve clarity, we ensured that the first occurrences of these terms in the Results explicitly include the corresponding head location (e.g., “eye BM-InOm neurons”), and we added brief contextual reminders at later points where this abbreviation appears. These changes clarify the meaning of BM-InOm and related abbreviations without introducing additional terminology.

      Changes made:

      Figure 1 legend: clarified that BMNs are named according to the bristle population they innervate (e.g., BM-Taste neurons innervate Taste bristles).

      Results, early first section (second paragraph): added head-location qualifiers at first mention (e.g., “eye BM-InOm neurons,” “proboscis BM-Taste neurons”) in sentences such as: “35 BM-Taste neurons innervating Taste bristles on the proboscis…” and “405 eye BM-InOm neurons innervating the interommatidial bristles on the eyes…”.

      Later Results text where the abbreviation appears (including the sentence addressing the 5-synapse cutoff): added “eye” before BM-InOm for context (e.g., “although 555 eye BM-InOm neurons are present… only 405 meet the five-synapse threshold”).

      (f) LB23 hemilineage: what was that again?

      We added text in the manuscript to better define hemilineages. This is described above in response to another Reviewer suggestion.

      (g) Line 732: What are ascending neurons?

      We had already included a definition of ascending neurons in the second Results section entitled “The BMN connectome”. Since this was not clear to the Reviewers, we expanded on this section. There is now a new paragraph in this same section. This paragraph reads:

      “Partners were grouped into five morphological categories—interneurons, descending neurons, ascending neurons, BMNs, and motor neurons—following FlyWire annotations (Dorkenwald et al., 2024). Interneurons were defined as neurons whose soma and all neurites were confined to the brain. Descending neurons were defined as neurons whose somata are located in the CNS and whose neurites extend into the descending tracts toward the ventral nerve cord (VNC). Conversely, ascending neurons were identified as neurons whose neurites enter the brain through the cervical connective and whose somata lie outside the FAFB imaged volume, resulting in only their neurites being visible in the dataset.”

      (h) Line 896: What is lineage matching?

      We thank the Reviewer for pointing this out. We realized that this sentence did not add clarity and contributed little to the manuscript, so we removed the sentence that used “lineage matching” from the manuscript.

      (i) Line 926: The Previous work ... sentence makes no sense to me.

      The sentence was reworked and now reads: “The mechanosensory neurons hypothesized from the parallel model that elicit the Drosophila grooming sequence were identified in previous work (Eichler et al., 2024; Hampel et al., 2020a, 2017, 2015; Mueller et al., 2019; Seeds et al., 2014; Zhang et al., 2020).”

      (j) The FAB-dataset is indeed unique, but the fact that it is repeated several times in your discussion does not ensure understanding of the obviously complex circuit architecture potentially underlying behavior. Please, focus on your discussion strictly and condense your arguments to the specific contribution and outcome of the data in the current manuscript.

      In response to this comment, we condensed the opening portion of the Discussion by reducing repetition of background and prior findings, particularly references to earlier BMN work and the uniqueness of the FAFB dataset. We streamlined overlapping sections, mentioned prior hypotheses and results only once, and focused the revised text more directly on the new contributions of this study—namely, the synaptic-resolution organization, somatotopic connectivity, and circuit principles revealed by the BMN connectome.

      (k) At some parts of the discussion, it is not clear to me, if you refer to results of the actual study or refer to previous studies (Hampel, Eichler) e.g., 'Our work has shown ...' on line 872.or '...we find ... LB23 neuron elicit antennal grooming....'. or line 909: Our work reveals ......

      Sentence a former line 872 was revised and now reads: “While our past and present work together reveal that a subpopulation of LB23 neurons elicits antennal grooming, we also find evidence that other LB23 neurons in the hemilineage elicit additional head grooming movements.”

      Sentence at former line 909 was revised and now reads: “Our previous work and the present study reveal that the antennal grooming circuit receives inputs from two different classes of antennal mechanosensory neurons, the BMNs and JONs.”

      Reviewer #3 (Recommendations for the authors):

      All my comments are mostly only for clarity.

      (1) It would help readers if the manuscript explicitly stated how a sensory neuron can be postsynaptic - i.e., that BMN axons receive inhibitory inputs in the CNS - since this may not be intuitive to a broader audience.

      We appreciate this comment and added the following text to the last paragraph of the first Results section: As expected for sensory afferents, BMNs provide synaptic output to downstream circuits; however, the presence of postsynaptic sites may be less intuitive, and reflects that BMNs can also receive synaptic input onto their central axons within the CNS.

      (2) Figure 1 is a helpful context, but since much of it is directly reused from Eichler et al., 2024, it would strengthen the presentation if you clarified what is new here (e.g., the synapse quantification) versus what is recap. In addition, for readers less familiar with EM connectomics, it would be valuable to spell out how bristle neurons are assigned to classes in the absence of bristles themselves in the volume - i.e., that classification rests on stereotyped nerve entry and projection zones, which allow type-level but not single-bristle resolution. Explicitly flagging these methodological boundaries up front would make it clearer what information comes from the current work, what derives from previous reconstructions, and what the limits of resolution are.

      We have addressed this recommendation above for a similar suggestion by Reviewer 2 (see above for details). In brief, we inserted an overview of the methodology used to identify BMN types in the FAFB dataset, and we now explicitly state the limitations of this correlative approach. We added a sentence in the first paragraph of the Results section that states, “Because FAFB does not include the head cuticular bristles, individual BMNs could not be linked to single bristles. Therefore, these assignments are necessarily correlative and provide type-level (population) rather than single-bristle resolution.” In addition, we revised the Figure 1 legend to more clearly distinguish panels and reconstructions that were previously reported in Eichler et al. (2024) from synapse quantification and analyses that are new to the present study.

      (3) BMNs from neighboring bristle populations converge onto shared partners, while distant BMNs remain segregated - while the overlap was clear, the segregation was not visually clear in the first figure.

      We thank the Reviewer for this suggestion. We have addressed this point in our response to a similar comment from Reviewer 2 (see above), where we clarified how overlap versus segregation can be identified in Figure 1 and strengthened the text and figure legends to guide readers to these features without adding clutter to the figure.

      (4) The identification of direct BMN → motor neuron synapses is intriguing, but since these inputs make up only a small fraction of motor neuron synapses, it would help if the authors explicitly cautioned readers that these are likely modulatory contributions rather than stand-alone reflex arcs. This would prevent over-interpretation of the sensory-motor link. Similarly with the BMN>BMN connections.

      We thank the Reviewer for this suggestion. We revised the Results section “BMN postsynaptic motor neurons” to more explicitly caution that the direct BMN → motor neuron connections are likely modulatory rather than stand-alone reflex arcs, consistent with their small contribution to total motor neuron input. The revised text reads: “However, BMN inputs accounted for only a small fraction of total synapses onto each motor neuron (≦6.28% of total inputs/BMN type, Figure 4 – figure supplement 1, Supplementary file 7), suggesting a modulatory contribution rather than direct sensory-driven motor activation.”

      (5) Since the FAFB dataset only includes the brain, it would be helpful to clarify what is meant by "ascending" and "descending" partners in this context - namely that ascending neurons are VNC-derived axons entering the brain, while descending neurons are brain-derived neurons projecting out toward the VNC. Explicitly stating this will prevent confusion, given that all BMNs themselves terminate in the SEZ.

      We had already included definitions in the second Results section entitled “The BMN connectome”. Since this was not clear to the Reviewers, we expanded on this section. There is now a new paragraph in this same section. This paragraph reads: Partners were grouped into five morphological categories—interneurons, descending neurons, ascending neurons, BMNs, and motor neurons—following FlyWire annotations (Dorkenwald et al., 2024). Interneurons were defined as neurons whose soma and all neurites were confined to the brain. Descending neurons were defined as neurons whose somata are located in the CNS and whose neurites extend into the descending tracts toward the ventral nerve cord (VNC). Conversely, ascending neurons were identified as neurons whose neurites enter the brain through the cervical connective and whose somata lie outside the FAFB imaged volume, resulting in only their neurites being visible in the dataset.

      (6) In the section titled "BMN synaptic partners in the CNS: ascending, descending, and interneurons", the balance of explanation is skewed toward presynaptic input to BMNs. It would strengthen clarity if you expanded equally on the postsynaptic side (i.e., BMN outputs) or explicitly signposted why the focus here is on inputs. That way, readers won't be left wondering whether outputs are less important or just deferred to later figures.

      We have revised the section that was previously skewed toward presynaptic BMNs. This section also addresses some confusion about interpreting Figure 3, from a critique from Reviewer 2. The section now reads: “Postsynaptic connections were predominantly interneurons (56%), with significant contributions from descending (28%) and ascending (16%) neurons (Figure 5D, F,H,J). Interneurons are more numerous as distinct partner neurons, whereas descending neurons receive a larger fraction of BMN output synapses across BMN types (Figure 3A, B). Thus, descending neurons are fewer in number but tend to receive more BMN synapses per neuron on average, while interneurons are more numerous but often receive fewer synapses per neuron. Together, these partner categories underscore the strong integration of BMNs with local brain circuitry (interneurons), and with pathways linking the brain and ventral nerve cord (VNC), through ascending neurons that provide VNC-derived synaptic input and descending neurons that carry BMN output toward the VNC.”

      (7) The network diagrams in Figure 9 convey clustering, but a complementary heatmap of BMN type × partner connectivity could highlight the parallel organization more clearly. This would make the block-like separation of dorsal, ventral, and posterior subnetworks more immediately apparent, reinforcing the conclusion of parallel somatotopy-based processing. This section would also benefit from drawing the functional message more explicitly: that BMNs form largely independent, somatotopically aligned pathways with regional overlap, supporting the idea of parallel grooming circuits. Right now, the text reads as a connectivity catalog, and the key concept of parallel regional architecture risks being underemphasized.

      We agree that connectivity matrices provide a clear and accessible representation of these data. We have moved the cosine-similarity connectivity matrices previously shown in Figure 9 – figure supplement 1 into the main manuscript, where they now appear as Figure 9. These matrices depict similarity among BMN postsynaptic partners. For this reason, we have retained the original network-graph representation (now Figure 10) to display the full pre- and postsynaptic connectome structure.

      Based on the Reviewer’s suggestion to clearly state the key concepts of the parallel architecture, we added a sentence to the end of the Results section entitled: Somatotopy-based connectivity among BMN synaptic partners in the CNS. That text reads: “Thus, the BMNs form largely independent, somatotopically aligned pathways with regional overlap, supporting the idea of parallel grooming circuits.”

      (8) It would help if the manuscript if the authors explained more explicitly the somatotopy logic (that reciprocal inhibition preserves local head regions, ensuring that suppression and gain control act locally) more clearly. At present, the narrative is buried in network-graph detail - a heatmap or simple region-level summary would make this organizational principle much clearer to readers.

      We thank the Reviewer for this suggestion. To make the somatotopy logic of pre/post feedback inhibition clearer and less buried in network-graph detail, we revised the text in this Results section to more explicitly distinguish (i) reciprocal, head-region–localized inhibitory loops that could support local gain control from (ii) non-reciprocal cross-type inhibitory pathways that could contribute to heterotypic suppression between head regions. In addition, we modified the figure to more clearly convey somatotopy by adding text on the plot and updating the legend to state: “Bold text indicates the general head location of BMNs on the plot, revealing somatotopy-based connectivity with pre/post neurons (i.e. ventral, dorsal, posterior, and the ventral/dorsal transition).”

      (9) Please adjust the section title, "LB23 hemilineage member neurons elicit aimed head grooming movements" to avoid implying new functional experiments. For example:

      (a) "LB23 neurons include previously defined antennal grooming command neurons" or

      (b) "LB23 hemilineage anatomically corresponds to grooming-related neurons".

      This would make it clear that the contribution here is anatomical linkage, not fresh functional data.

      We changed the section title to the Reviewer-suggested title b: LB23 hemilineage anatomically corresponds to grooming-related neurons

      (10) The current network graphs in Figure 13B are not very intuitive - it is hard to visually extract the somatotopy. A connectivity heatmap or matrix (BMN types on one axis, LB23 neurons or subgroups on the other, with synapse strength as colour) would make the block-like, region-specific mapping immediately clear. A coarse-grained version (e.g., dorsal/ventral/posterior BMNs vs LB23 subgroups) could further highlight the parallel, somatotopically organized pathways. This would better support the central claim of Figure 13 than the current spring-layout graphs. Figure 13F does this for BMN inputs onto aBN2 neurons. (But it is presented only in binary form; could the authors not add a graded colour scale proportional to synapse number?)

      The binary form was necessary because the results are from different sources (i.e. Catmaid versus flywire synapse counts) with different synapse numbers.

      We modified the Figure 13B to more clearly convey somatotopy by adding text on the plot and updating the legend to state: “Bold text indicates the general head location of BMNs on the plot, revealing

      somatotopy-based connectivity with LB23 neurons (i.e. ventral, dorsal, and posterior head).” We hope that this modification satisfies the Reviewer.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      The strength of this manuscript lies in the behavior: mice use a continuous auditory background (pink vs brown noise) to set a rule for interpreting an identical single-whisker deflection (lick in W+ and withhold in W− contexts) while always licking to a brief 10 kHz tone. Behaviorally, animals acquire the rule and switch rapidly at block transitions and take a few trials to fully integrate the context cue. What's nice about this behavior is the separate auditory cue, which shows the animals remain engaged in the task, so it's not just that the mice check out (i.e., become disengaged in the W- context). The authors then use optical tools, combining cortexwide optogenetic inactivation (using localized inhibition in a grid-like fashion) with widefield calcium imaging to map what regions are necessary for the task and what the local and global dynamics are. Classic whisker sensorimotor nodes (wS1/wS2/wM/ALM) behave as expected with silencing reducing whisker-evoked licking. Retrosplenial cortex (RSC) emerges as a somewhat unexpected, context-specific node: silencing RSC (and tjS1) increases licking selectively in W−, arguing that these regions contribute to applying the "don't lick" policy in that context. I say somewhat because work from the Delamater group points to this possibility, albeit in a Pavlovian conditioning task and without neural data. I would still recommend the authors of the current manuscript review that work to see whether there is a relevant framework or concept (Castiello, Zhang, Delamater, 'The retrosplenial cortex as a possible 'sensory integration' area: a neural network modeling approach of the differential outcomes effect of negative patterning', 2021, Neurobiology of Learning and Memory).

      The widefield imaging shows that RSC is the earliest dorsal cortical area to show W+ vs W− divergence after the whisker stimulus, preceding whisker motor cortex, consistent with RSC injecting context into the sensorimotor flow. A "Context Off" control (continuous white noise; same block structure) impairs context discrimination, indicating the continuous background is actually used to set the rule (an important addition!) Pre-stimulus functional-connectivity analyses suggest that there is some activity correlation that maps to the context presumably due to the continuous background auditory context. Simultaneous opto+imaging projects perturbations into a low-dimensional subspace that separates lick vs no-lick trajectories in an interpretable way.

      In my view, this is a clear, rigorous systems-level study that identifies an important role for RSC in context-dependent sensorimotor transformation, thereby expanding RSC's involvement beyond navigation/memory into active sensing and action selection. The behavioral paradigm is thoughtfully designed, the claims related to the imaging are well defended, and the causal mapping is strong. I have a few suggestions for clarity that may require a bit of data analysis. I also outline one key limitation that should be discussed, but is likely beyond the scope of this manuscript.

      Major strengths

      (1) The task is a major strength. It asks the animal to generate differential motor output to the same sensory stimulus, does so in a block-based manner, and the Context-Off condition convincingly shows that the continuous contextual cue is necessary. The auditory tone control ensures this is more than a 'motivational' context but is decision-related. In fact, the slightly higher bias to lick on the catch trials in the W+ context is further evidence for this.

      (2) The dorsal-cortex optogenetic grid avoids a 'look-where-we-expect' approach and lets RSC fall out as a key node. The authors then follow this up with pharmacology and latency analyses to rule out simple motor confounds. Overall, this is rigorous and thoughtfully done.

      (3) While the mesoscale imaging doesn't allow for cellular resolution, it allows for mapping of the flow of information. It places RSC early in the context-specific divergence after whisker onset, a valuable piece that complements prior work.

      (4) The baseline (pre-stim) functional connectivity and the opto-perturbation projections into a task subspace increase the significance of the work by moving beyond local correlates.

      Key limitation

      The current optogenetic window begins ~10 ms before the sensory cue and extends 1s after, which is ideal for perturbing within-trial dynamics but cannot isolate whether RSC is required to maintain the context-specific rule during the baseline. Because context is continuously available, it makes me wonder whether RSC is the locus maintaining or, instead, gating the context signal. The paper's results are fully consistent with that possibility, but causality in the pre-stimulus window remains an open question. (As a pointer for future work, pre-stimulusonly inactivation, silencing around block switches, or context-omission probe trials (e.g., removing the background noise unexpectedly within a W+ or W- context block), could help separate 'holding' from 'gating' of the rule. But I'm not suggesting these are needed for this manuscript, but would be interesting for future studies.)

      We thank the reviewer for the comprehensive summary of our work.

      We also thank the reviewer for highlighting the work from the Delamater group (Castiello et al., 2021), and we now briefly discuss this paper on P. 14 Lines 434-437 writing: “RSC was shown to contribute to negative patterning in behavioral tasks requiring rats to learn that the simultaneous presentation of two stimuli lead to an opposite outcome than each individual stimulus (Castiello et al., 2021).”

      We also agree with the reviewer’s noted ‘Key limitation’ regarding the role of RSC as either maintaining context representation or serving a gating function. The reviewer proposes an exciting set of further experiments inactivating RSC at different time points to investigate when RSC activity is needed. We hope to carry out such experiments in the future. We now include a brief discussion of this interesting point on P. 14-15 Lines 455-459 writing: “First, further inactivation experiments would shed light on the timing at which RSC activity is necessary for the integration of contextual information. Specifically, it would be of great interest to inactivate RSC at different time points such as during the intertrial interval or at the transition between contexts.”

      We have of course also addressed each of the more detailed comments from the “Recommendations for the authors” section, please see below.

      Reviewer #2 (Public review):

      Summary:

      The authors aim to understand the neural basis of context-dependent sensory processing and decision-making.

      Strengths:

      They used an innovative behavioral paradigm where the action-outcome association changes independent of the sensory stimulus. This theoretically allows the authors to disentangle the effect of behavioral context on sensory processing. Using this approach combined with optogenetic silencing, they discover that RSC activity is necessary for suppressing a lick response when the stimulus switches to the unrewarded context.

      Weaknesses:

      Sensory processing appears to be entangled with jaw/tongue movement initiation. Activity in M1 and RSC during auditory-evoked lick responses appears to be identical to activity during whisker-evoked lick responses, indicating that movement initiation is the main driver of M1/RSC activity, rather than changes in the flow of sensory information. If sensory information were the main driver of the initial M1/RSC response, then auditory evoked responses should have a longer latency. Perhaps this is beyond the resolution of the calcium indicator or imaging frame rate. It is not clear from the data shown if differences in S1 activity when comparing W+ and W- stimulation are caused by context-sensitive sensory processing or whisker movement following whisker deflection.

      We thank the reviewer for the comments on our work and we agree that separating sensory processing and movement initiation is very important. In the revised manuscript, we have carried out several new analyses to specifically address the points of the reviewer. The most important point is that context-dependent activity in RSC emerges at ~50 ms after the whisker stimulus, which precedes any differences in movements of the jaw or whisker. Although sensory and motor representations become increasingly entangled after stimulus delivery, we think that the first ~100 ms after the whisker stimulus is a relatively safe period for analysing sensory processing and decision making before overt context-dependent differences in movements.

      Addressing the specific point “Activity in M1 and RSC during auditory-evoked lick responses appears to be identical to activity during whisker-evoked lick responses, indicating that movement initiation is the main driver of M1/RSC activity, rather than changes in the flow of sensory information.” - We have now directly compared the pattern of cortical activity evoked by whisker and auditory stimuli in correct trials in the W+ context (new Figure 3 – figure supplement 2). As expected, activity in wS1/wS2 and A1 is stronger in whisker and auditory trials respectively, following their sensory modalities. However, we also evidence a stronger response of wM1/wM2 in whisker trials as early as 40 to 60 ms following the stimulus, showing the specificity to the whisker system. We also observe a stronger response of RSC to whisker than to auditory stimulus. The auditory and whisker evoked responses are therefore different.

      Addressing the specific point “If sensory information were the main driver of the initial M1/RSC response, then auditory evoked responses should have a longer latency. Perhaps this is beyond the resolution of the calcium indicator or imaging frame rate.” – As stated above, the responses to auditory and whisker stimuli are different.

      Addressing the specific point “It is not clear from the data shown if differences in S1 activity when comparing W+ and W- stimulation are caused by context-sensitive sensory processing or whisker movement following whisker deflection.” - We think that the data shown in Figure 3F-H indicate that differences in S1 activity when comparing W+ and W- stimulation are not directly caused by context-sensitive sensory processing. On P. 9 Lines 270273 we write: “Early after stimulus onset, whisker deflection evoked similar activation of primary and secondary whisker somatosensory cortices (wS1 and wS2) in both W+ and W− contexts.” Indeed, context separation in wS1/wS2 only emerged later than 100 ms, which is indeed confounded by the difference in movement evoked by the sensory stimulus (now quantified in new Figure 3 – figure supplement 4). On the contrary RSC and wM1/2 responses to the whisker stimulus were different in W+ and W- at early time points (~50 ms for RSC and ~80 ms for wM1/2) which is consistent with context dependent sensory processing. At least 2 hypotheses could explain the absence of early difference in whisker evoked activity in wS1/wS2 between W+ and W-. The first one is that sensory activity in wS1/wS2 is not modulated by contextual information at all, while the alternative option would imply that sensory activity is mediated by different neuronal populations depending on context with an overall similar average response. We think this is an interesting question which we hope to address in future experiments using Neuropixels recordings and multiphoton cellular imaging to address the single neuron representation of whisker stimulus in wS1/wS2 according to context in the task presented here.

      We have of course also addressed each of the more detailed comments from the“Recommendations for the authors” section, please see below.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Suggestions to strengthen the manuscript (no new data collection)

      (1) The block-switch dynamics were clearly demonstrated behaviorally. It would be very powerful to mirror this with an analysis of neural data around the block-switch: how do the various areas adjust immediately after a shift in the continuous contextual sound? Does the RSC show any evidence of changing activity patterns? How does the within-trial activity dynamic look as a function of the number of trials from the context switch? This could be done with the data collected for Figure 3 (for within-trial dynamics), but also for the pre-stimulus baseline activity data (Figure 4A-B).

      We thank the reviewer for raising this interesting point. We have now investigated the change of cortical activity at the transition between contexts (new Figure 3 – figure supplement 5). At the context transition, both to W+ and to W- contexts, we observed a rapid activation of the auditory cortex (new Figure 3 – figure supplement 5A). In addition, there appeared to be a slightly higher activation of RSC when transitioning to W- rather than to W+ (new Figure 3 – figure supplement 5A). In the future, it will be of great interest to further investigate this phenomenon.

      We also evaluated the whisker deflection-evoked responses of the different cortical regions according to the number of whisker trials from context switch (new Figure 3 – figure supplement 5B&C). This analysis revealed that while the sensory response in wS1 and wS2 were constant over the time course of a context block, the response of wM1/2 and especially RSC became progressively lower in the W- context, consistent with the behavioral results in Figure 1 supporting time-dependent contextual integration.

      Overall, these results strengthen the role of RSC and wM1/2 in integrating contextual information to guide the response to the whisker stimulus, and we thank the reviewer for raising this important point.

      (2) It might be useful to state 'earliest among the imaged dorsal cortical areas,' and briefly acknowledge potential subcortical contributors (since those were not explored and could be earlier than cortical areas).

      We agree with the reviewer. In the Summary, on P. 2 Line 39-40 we now write: “Widefield calcium imaging revealed that retrosplenial cortex was the first dorsal cortical area to show context discrimination in response to whisker stimulation”. On P. 8 Lines 257-258, we now write: “To investigate the spatiotemporal neural dynamics underlying task execution, we recorded calcium activity across the dorsal cortex in transgenic mice”. On P. 13 Lines 416-420 we now write: “Functional imaging of cortical activity with two different genetically-encoded calcium indicators each showed similar spatiotemporal dynamics of whisker sensory processing with the earliest contextdependent divergence in signalling being detected in RSC, out of the imaged dorsal cortical areas (Figure 3).” On P. 15 Lines 470-473, we now write: “Finally, it is of course important to note that many subcortical regions (as well as non-dorsal cortical regions, which were not imaged) are likely to contribute importantly to context-dependent task performance.”

      (3) Fit a simple exponential/logistic to lick probability vs time-since-switch (your Figure 1Hstyle analysis) to report a time constant with CIs; it will help quantify the integration of the continuous cue.

      We thank the reviewer for this suggestion. We have fitted an exponential to the grand average data to quantify the time constants for integration of contextual information before the presentation of the first whisker stimulus of the block (see new Figure 1H). On P. 6 Lines 170-173 we now write: “To assess whether this temporal integration would differ between contexts we fitted an exponential to the time evolution of the lick probability. This suggested a faster transition to the W+ context than to the W- context (W+ time constant: 9.4 s, W- time constant: 15.5 s) (Figure 1H).”

      (4) Because catch-trial false alarms are higher in W+ than W−, report per-context d′ and criterion for whisker trials (using signal detection theory); this separates sensitivity from bias and makes the behavioral shift more interpretable. It is also further proof that the behavior is contextual (versus a compound stimulus, for example).

      We have computed the d’ and criterion for the whisker trials in the W- and W+ contexts. (see new Figure 1 - figure supplementary 1D). As suggested by the reviewer, this further supports that the behavior is driven by contextual information.

      (5) For the pre-stimulus seed-correlation analysis, can you regress out the pupil/jaw/whisker activity to confirm whether the context modulation is (or is not) movement-driven? It would be helpful to better understand whether the baseline correlation is driven by differences in lowlevel factors between the contexts, versus the higher-level decision rule/context.

      The reviewer raises an interesting point. However, we did not find a straightforward way to regress out movements, and thus we leave this point for future in-depth analysis. On P. 11 Lines 354-357 we now write: “It is important to note that these context-dependent changes in resting-state functional connectivity could relate to the overt context-dependent movements in the prestimulus baseline (Figure 1I&J) and/or a manifestation of higher-level internal rule representations.”

      (6) For the earliest divergence analysis, is this consistent across animals and across sessions within animals? Can you show per-mouse distributions of first-crossing times (d′>2) for RSC vs wM1/2/wS2? This would help provide confidence in this key finding.

      The d’ presented in Figure 3H is computed as the discriminability between contexts at the population level, meaning that at each timepoint (from Figure 3F) we compared the 2 distributions built on N=6 mice. As such if the divergence between context was not consistent across animals this d’ would be low. That said, as suggested by the reviewer, we further investigated this context divergence at single mouse level and single session level. Our analysis supporting the main finding (Figure 3F-H) is shown in new Figure 3 – figure supplement 3.

      First, we show the results for a single mouse across sessions in Figure 3 – figure supplement 3A. We show the stimulus aligned activity in correct whisker trials in both contexts for the 3 recording sessions. For each session we quantified the main effect size defined as the difference of the trial average between contexts. Plotting the difference of mean response, we consistently observed that RSC ramps-up before wM1/2 for the 3 sessions.

      Second, across all individual mice: we further aggregated the session average responses to show discriminability between context for each region at the single mouse level (Figure 3 – figure supplement 3B). We show that RSC is the first region to exhibit context separation in 4 out of the 6 mice that we recorded. In 2 other mice all regions seemed to show context separation but without clear temporal ordering.

      Finally, when averaging across mice, we observed a clear separation and first discrimination in RSC (Figure 3F-H and Figure 3 – figure supplement 3C).

      Overall, these further analyses suggest that the early divergence of RSC activity appears to be robust with a consistent mean difference in single sessions and single mice, as well as across the population of mice. We think this analysis has strengthened our manuscript and we thank the reviewer for the valuable suggestion.

      (7) For the opto mapping data, could you provide P(lick) effect sizes with CIs per grid site? It would also be nice to summarize the qualitative dichotomy: RSC/tjS1 increases licking in W−; canonical wS1/wS2/wM/ALM decreases licking across contexts (to my understanding).

      We now provide the P(lick) effect sizes for the main cortical areas studied in the paper in Figure 2 – figure supplement 1C. This shows the relative change in lick probability in optogenetic trials compare to control trials for each mouse.

      Reviewer #2 (Recommendations for the authors):

      (1) Do mice move their whiskers after stimulus onset? If so, are these movements dependent on behavioral context? What causes the increase in S1 activity during auditory-evoked response trials?

      To answer the reviewer’s questions we have further investigated whisker movements following the sensory stimuli (whisker and auditory correct trials) in both contexts. The results of this analysis are presented in new Figure 3 – figure supplement 4.

      We find that mice move their whiskers shortly after the whisker stimulus in both contexts. The time course of whisker angle in correct whisker trials is similar in both contexts with a discriminability index (d’) consistently below 1. The whisker speed in response to stimulus is slightly higher in the W+ context compared to W- with a d’ slightly above 1 after ~100 ms. We also observed evoked whisker movements in auditory trials independent of context. Thus, whisker movements are indeed evoked by the sensory stimuli, but the overall context-dependent modulation of whisker movements is weak. The early differences in whisker-evoked cortical activity in W+ compared to W- contexts are therefore more likely related to the integration of contextual information than to differences in evoked movements.

      The reviewer is correct to point out that wS1 activity increases in auditory trials (Figure 3E). The response is initially very weak, but becomes more prominent after ~100 ms following the auditory tone. We do not know the underlying mechanisms, but there are several likely explanations. First, as discussed above, there are indeed some whisker movements evoked in response to the auditory stimulus (Figure 3 – figure supplement 4), which could result in sensory input to wS1. Equally, the increase could relate to licking, given the broad representation of movements in cortex and an appropriate reaction time in auditory trials (Figure 3C). Alternatively, wS1 activity in auditory trials could also be related to input connectivity from auditory cortex, top-down input from frontal cortex or subcortical regions such as high-order POm.

      (2) What do the authors think is causing the W+ vs W- difference in S1/S2 activity approximately 100ms after whisker deflection?

      The late W+ vs W- difference in wS1/wS2 activity could be explained by several factors. First this could be due to the difference in whisker movements after ~100 ms as shown in Figure 3 – figure supplement 4. Second this could be driven by the lick vs no lick activity (see reaction time in Figure 3C for whisker trials ~110 ms). Finally, this could be partly due to some movement independent top-down contextual information reaching wS1/wS2 at late time points. Overall, our claim in the paper is that there was no contextual difference in whisker primary and secondary cortices at early time points (before movement). On P. 9 Lines 270-273 we explicitly write: “Early after stimulus onset, whisker deflection evoked similar activation of primary and secondary whisker somatosensory cortices (wS1 and wS2) in both W+ and W− contexts.” In contrast, our main findings are grounded in the divergence of cortical activity in RSC and wM1/2 at early time points (<100 ms).

      (3) The choice of PC3 seems arbitrary. Is there no task-relevant information in PC1 and PC2?

      We appreciate the point raised by the reviewer and have clarified the reasoning leading to PC3 selection in the main text, where on P. 12-13 Lines 384-391 we now write: “The loadings of the first principal components were uniformly distributed and could reflect a late movement driven activation distributed across all cortical areas (Figure 4 – figure supplement 2C&D). PC2 loadings show variation along the anteroposterior axis that could reflect differences between sensory and motor regions but its time course does not separate between lick and no lick in control conditions (Figure 4 – figure supplement 2C&D). The loadings of PC3 highlighted task-related cortical regions and its time course exhibited clear differences comparing lick and no-lick trials.” In addition, we now also show the time courses for PC1 and PC2 in Figure 4 – figure supplementary 2D.

      Overall, the reasoning is the following:

      PC1 has spatially-homogeneous positive loadings (Figure 4 – figure supplementary 2C) and activity along PC1 gradually ramps up following sensory stimulation (Figure 4 – figure supplementary 2D). It is likely driven by widespread activation of the cortex following the whisker stimulus and the lick response. As such we believe that the taskrelated information captured by PC1 is movement related and not necessarily informative about processing of whisker and context.

      PC 2 has loadings varying along the antero-posterior axis (Figure 4 – figure supplementary 2C), which could be relevant for the task, but its time-course does not discriminate between lick and no lick neither in W+ nor W- (Figure 4 – figure supplementary 2D).

      PC3 has both loadings that vary between several cortical regions involved in the task (Figure 4 – figure supplementary 2C) and a time course that separates between lick and no lick in both contexts (Figure 4 – figure supplementary 2D). We thus focus on PC3 to investigate the effect of optogenetic inactivation on whisker stimulus evoked activity.

      The remaining components beyond PC3 contain a very small fraction of variance and were thus not considered.

      (4) Figure 3 - Supplement 1: What explains the change in fluorescence in GFP/tdT mice during W+ stimulation? Is it brain movement on the z-dimension? Could this explain differences in calcium imaging results?

      We thank the reviewer for this question. The nature of intrinsic signals is a complex topic, but brain movement is unlikely to contribute importantly, because under similar behavioral conditions we (and others) typically find brain movements to be on the scale of a few microns. The three most widely-reported contributions to intrinsic optical changes in cortex relate to:

      (i) Light scattering – as neurons integrate synaptic inputs and fire action potentials, the neuronal elements swell slightly due to the ionic and water fluxes (see for example Vincis et al. Cell Reports 2015, doi: 10.1016/j.celrep.2015.06.016). This reduces the refractive index mismatch between the intracellular and extracellular space. This in turn reduces light scattering, which could result in fluorescence increases.

      (ii) Hemodynamics – changes in blood volume and changes in oxygenation/deoxygenation will change the absorption of light at different wavelengths, in an activity-dependent manner (also forming the basis of BOLD fMRI signals).

      (iii) Flavoproteins – endogenous fluorescent proteins, such as flavoproteins present at high levels in mitochondria, have been reported to change their fluorescence depending upon neuronal activity, presumably in relationship to increased mitochondrial activity.

      We therefore think it is very important to image GFP/tdTomato-expressing mice as controls, and we would suggest that this should be carried out more commonly in the field. Indeed, similar to our results, another study (Yogesh et al., eLife 2025, doi: 10.7554/eLife.104914) recently reported upon the importance of carefully examining intrinsic fluorescence changes, which were found to be present in both wide-field and two-photon imaging of GFP expressing mice.

      Our results reported in Figure 3 – figure supplement 1, show that GFP/tdTomato signals over the first ~120 ms following whisker stimulation were much smaller that the equivalent changes in GCaMP6f/jRGECO1a-expressing mice, and therefore would only have a minor contribution to our analyses. However, we refrained from analysing fluorescence changes at later post-stimulus times, because the intrinsic signals indeed become increasingly prominent as the mice initiate licking.

    1. Author response:

      The following is the authors’ response to the original reviews

      General note

      We have issued a new release of the general Peekbank database, 2026.1, which includes more data integrity checks and several more datasets. As a result of this release, the underlying dataset we use in our paper has shifted slightly. The shifts represent a relatively small proportion of the total data and thus these changes have caused only relatively minor changes to our numerical results. We also highlight that we now include a small amount of data regarding children younger than 12 months, increasing the developmental range of our analysis (see Figure 1).

      Reviewer 1 (Public review):

      The limitations of the study are acknowledged to some extent, but need to be improved and ensured that they run throughout the manuscript. Thus, in the discussion, the authors note that the approach is observational and exploratory, and highlight for me a key alternative explanation of the findings, namely that faster children could be faster due to their larger vocabulary, rather than faster children learning more words. Indeed, the latter explanation for the relationship is called into question, given that growth in speed was not related to growth in vocabulary. Here, the authors note that the null result may be related to the fact that they do not sufficiently precise estimates of growth slopes, rather than taking the alternative explanation seriously that there may not be as causal a link between being a faster word learner and a better word learner (learn more words).

      Thank you very much for your challenging and thoughtful comments. In hindsight we did not realize that the way we were writing about our results was ambiguous between several interpretations (one of which we endorse and one of which we do not).

      We respond below to the specific suggestions about causal directionality in the longitudinal analysis, but we certainly believe that we cannot draw strong conclusions about causality from our dataset and have attempted throughout the paper to remove causal language that might have crept into our interpretation.

      In response to your comments, we have made a number of key revisions aimed at qualifying and clarifying our points:

      • The abstract now prominently notes that our design is observational: “In an observational study…”

      • The abstract notes a positive and a negative result in the relationship between word recognition and vocabulary: “Further, across a range of longitudinal models, speed, accuracy, and vocabulary were coupled. Children with overall faster word recognition tended to show faster vocabulary growth, though developmental growth in word recognition skill was not specifically associated with growth in vocabulary.”

      • The abstract removes potential casual language in the final sentence: “... these findings support the view that word recognition is a skill that develops gradually across early childhood and that this skill is deeply intertwined with early language learning.”

      • A new paragraph in the Results introduces the potential hypotheses investigated via the longitudinal models.

      • The final paragraph of the Results section sharpens the contrast between two possible growth hypotheses: “However, we did not find evidence for the stronger version of this claim: in neither the non-linear growth model nor the linear SEM did we find evidence that increases in speed were related to increases in vocabulary size. Thus, our findings do not support a ‘virtuous cycle’ model in which increases in recognition specifically lead to increases in vocabulary size.”

      We hope these changes lead to a manuscript that better aligns with the limitations of the study.

      This is especially since, but correct me if I’m wrong here, the current vocabulary size is not taken into consideration in the model examining vocabulary growth. Given the increasing number of studies showing that current vocabulary knowledge predicts vocabulary growth (Laing, Kalinowski et al, Siew & Vitevitch), one simple alternative explanation is that current vocabulary knowledge predicts both current word recognition skill and later vocabulary knowledge. Is there anything in the data speaking against this hypothesis?

      We think the reviewer’s overall point is generally correct, as we described above, but we want to clarify a specific statistical point. The non-linear longitudinal model of vocabulary growth does in fact take into account a child’s average vocabulary size. (This point feels tricky in a non-linear model but it’s actually quite similar to a linear model for the purposes of this discussion). Basically, vocabulary (at all timepoints) is modeled as a function of age, with both main effects and interactions with age. Critically, each participant is also modeled as having a random intercept capturing their deviation from the average growth pattern across ages (as expressed by the fixed effects). In this model, the “main effect” (here captured by the intercept for the logistic curve in the model) that we observe for speed indicates that vocabulary growth for individuals is predicted to be faster (their curve is shifted left) if their RTs are fast. The presence of the random effects in this model thus “controls” for the fact that some participants have overall higher vocabularies (and are shifted up relative to the average growth curve).

      But, we note that this model does not show an “interaction effect” (here captured by the null effect of RT on the slope parameter in the logistic model). That’s one of the null effects that we now call out much more prominently in the abstract and end of the results (per our response above).

      Equally, while the SEM examines vocabulary growth controlling for age, I wonder about the other way around. What would happen to the effect of age on word recognition skill (in the LME model, S8) if one were to add concurrent vocabulary size? So does chronological age explain word recognition skill or vocabulary knowledge? Right now, the manuscript describes this effect purely related to chronological age, but is it age per se or other cognitive abilities, including a key change across development, namely, vocabulary size? Thus, the presentation of the skill learning hypothesis suggests that age is a proxy for experience, while you actually have here a very nice proxy for experience in terms of children’s vocabulary size.

      Again, thank you for engaging with this tricky set of issues. Overall, our goal is to adjust the manuscript to reflect points of agreement; in particular, we agree that age is a proxy for language experience, vocabulary, and other cognitive changes, and we have stated this explicitly now in the intro to the factor analyses: “In our prior analyses, chronological age acts as a proxy for greater language experience and larger vocabulary as well as a host of other correlated developmental changes in cognition. Now we explicitly explore relations to vocabulary growth and the triadic relationship between age, word recognition, and vocabulary.”

      On the statistical side, we do think that the NLME (non-linear mixed effects; the logistic growth mode) effectively controls for average vocabulary size, as described above. The longitudinal SEM also relates vocabulary growth to growth in word recognition skill. In both models, we find no evidence for coupled growth; instead the evidence points to children with higher baseline word recognition skill showing faster growth in vocabulary (speed intercept significantly related to vocabulary slope, -.14, p < .01) but not the reverse (vocabulary intercept not strongly related to speed slope; -.01, ns).

      More generally, we hope our edits to the paper, detailed above, both clarify this tricky set of issues and also remove inappropriate casual language throughout.

      Critically, while the discussion is more nuanced, the way the abstract is concluded and the way the Introduction is phrased suggest that the study is able to answer a causal question, which, as the authors themselves note, is not possible. The abstract, for instance, states that word recognition becomes faster, more accurate and less variable...consistent with a process of skill learning. And also that this skill plays a role in supporting early language learning, which is very causal language. I don’t think you can really claim that you are testing the two hypotheses you suggest here. The work is definitely embedded in the context of these hypotheses, but are you really able to test them? My worry is that while the discussion is more nuanced, the extent to which this study will then be cited down the line as showing that children learn more words down the line because they are faster at recognizing words, and anything that you can do to tamper with such interpretations would be good for the literature. For me, this should not just be relegated to the discussion but should be touched upon in the abstract and Introduction.

      Thanks for pushing us to be more precise with how we frame and describe our findings. We agree with the reviewer that our findings do not warrant strong conclusions about the causal role of word recognition skill in vocabulary growth. Per our response above, we have now tried to carefully revise our language throughout the paper (in particular, in the abstract and introduction, as noted by the reviewer).

      Finally, it would help to talk more about the mechanisms at work in any relationship between word recognition and language learning. It seems to me that this would rely on some predictive processing framework, given the description on page 4, and it would be good to make this clear (faster and more accurately you can recognize a ball, better use this evidence to infer the speaker’s intended meaning).

      Thanks, this is a great point. We’ve revised this text and added references to predictive processing, unpacking a problematic paragraph into two:

      “Familiar word recognition -- as measured by LWL -- is hypothesized to play a key role in language learning (19). The idea, in a nutshell, is that the faster and more accurately a child can process incoming words, the more opportunities they have for learning. Consider a child hearing the utterance "Can you put the ball in the crate?" The better the child can recognize the word "ball", the better they can use this evidence to help infer the speaker's intended meaning, allowing possible inferences about the meaning of the less familiar word, "crate" (20).

      “Real time language processing, including word recognition, relies heavily on predictive processing, in which comprehenders integrate expectations from prior linguistic context with noisy and ephemeral incoming signals (21, 22). The more input a child receives, the better their predictions are likely to be, and hence the more they can learn (19, 23). Indeed, measurements of children's language input at home are consistently associated with their vocabulary size (24, 25). And, in line with this predictive processing framework, one important study found that children's word recognition speed mediated the longitudinal relationship between home language input and vocabulary growth (26). Thus, word recognition is thought to be a key support for ongoing word learning.”

      Equally, when referring to word recognition, it would be good to clarify what this refers to - how well a child knows what a word refers to (and in the context of LWL, what it does not refer to) or how quickly it directs attention to what is referred to.

      Thanks, we’ve added a capsule definition in the second paragraph, and added the sentence “This procedure [LWL] measures the general construct of word recognition by operationalizing knowledge of a meaning as visual attention to a specific named referent.” We hope this clarifies the relationship between LWL and word recognition.

      With regards to the data, I wonder if there is a clustering of kids past 24 months that is happening here, looking at Figures 1 and 2, where it seems like there is less change past the 24-month point. Is there any way to look at whether the effect of age or vocabulary on word recognition is not linear but asymptotic?

      Thanks for pointing this out; we do see what you are talking about but think it’s being handled appropriately in the analysis. In Figure 1 it clearly looks like changes to RT are asymptotic – this is why we analyze the logarithm of RT throughout the paper. In Supplement S6 we show that reaction time is indeed best fit by a log-log function. Your question about Figure 2 asks whether there is further structure beyond the log-log fit; in Supplement S7 we show some analyses that suggest a polynomial fit is not better than the log-log fit; there is some small additional linear effect of age over and above the log-log fit, but it’s minor and pretty hard to interpret in our view.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Page 3. Word production may manifest in overt behaviour but need not reflect complete knowledge. A child can say the word dog and use it to refer to a cat.

      This is a good point. Since we are not able to speak to the precision of meaning representations (an important issue in its own right), we have omitted the phrase “with incomplete knowledge.”

      Page 4. The first two sentences of the paragraph beginning with word recognition ability... don’t go together. The second sentence does not support the claim that word recognition plays a role in language learning.

      Thanks, we’ve tried to smooth out this transition as part of unpacking the role of predictive processes.

      Page 4. “predicts children’s standardized test scores years later” - make clear what test scores are here.

      We added some additional details. The specific tests were the CELF (expressive language) and the KABC (IQ), but we thought too much detail might be distracting.

      Page 5. I love Table 1, but would like for the data to be weighted somehow. So, given that some studies had a lot more trials and more children, what percentage of the data did this study contribute? That allows a clearer view of how biased the sample is in certain studies. The x in CDIS and longitudinal could be aligned to the right. I kept wondering why there was an x near some trials.

      Thanks, we’ve adjusted the table to add the percentage of the total dataset (in trials) due to each study and fixed the alignment issue.

      Page 6. 12 million individual samples: what samples are these? Individual data points per trial per time point. Making this clear would be great.

      Clarified, thanks.

      Page 9. Your accuracy measures only seem to consider the target. From what I remember of my preferential looking days, this measure usually also includes the distractor. Why do you not do this? This is especially since you have such a wide age range, so if a 12-month-old only looks for about 50 per cent of the trial and spends that time looking at the target, that is very different from a child who looks at the screen all of the trial and spends less time looking at the target here.

      Sorry for any lack of clarity: we do in fact compute accuracy as the ratio of looking to target over looking to target plus looking to distractor. We have added this information to the parenthetical referenced above: “... accuracy (more target looking; computed as the ratio of target to target plus distractor looking)”.

      Page 12. I only found out that age was in this model by looking at S9.

      Thanks for mentioning this omission, we’ve clarified in the text: “We initially add age as an additional variable to our models to explore whether this factor structure relates to age; later we treat age as a predictor of latent factors.”

      Page 12. Isn’t it trivial that speed and accuracy show negative covariance, especially given how you measure accuracy? Thus, if I take longer to fixate the target, I have less time to look at the target during the trial. If, however, I included the distractor in my accuracy measure, then I could still take longer to look at the target, but still look more at the target than the distractor.

      Thanks for mentioning that this covariance is not the key result of interest; that observation didn’t come out in the text. Now we note that this covariation is “... as expected since they [speed and accuracy] are derived from the same data.” Note per above that accuracy is computed as target / target + distractor looking; even so, your observation is correct: slower looking at the target means lower accuracy at least to some degree.

      Page 19. If you excluded data from trials with less than 50% of timepoints, how did this vary across age? Arguably, your study has to worry less about this, given your sample size, but it would be nice to know, which you could include in the percentage of data that each study contributed to the final sample.

      Thanks, we’ve added this information to a new table in S1.

      Reviewer #2 (Public review):

      First, I wasn’t entirely clear about what the authors meant by “word recognition ability”. For much of the manuscript (including the use of the term “word recognition ability” itself), this comes across as an intrinsic ability or skill that improves with development. Alternatively, the speed and accuracy metrics taken from studies in Peekbank might capture children’s increasing knowledge of the common, concrete words typically used in these studies. To me, this is a somewhat different construct from a general skill at recognizing words. It would be helpful if the authors could clarify which construct they intend to capture, or if it is not possible to distinguish between these constructs from the Peekbank data.

      In response to this comment and related comments above, we’ve added text to the first two paragraphs trying to clarify the general construct that we’re talking about – recognizing the meaning of a word in real-time language comprehension. We’ve also clarified several times throughout the introduction that we’re talking about familiar word recognition, that is, the ability to recognize specific known words. Further, we directly acknowledge the issue above in the introduction:

      “Critically, most word recognition paradigms use words that children at the target age are reported to understand and produce. They are thus not indices of vocabulary size but rather measures of how quickly and accurately the child can recognize a familiar spoken word and use it to guide their visual attention to a referent. However, it is unknown the extent to which specific responses reflect an individual child's general speed of language processing versus their familiarity of specific words.”

      Second, and relatedly, if the source of the age-related improvements is increasing experience with the common concrete words used in the Peekbank studies, then one might expect word recognition and improvements with age to be related to word frequency, given that more frequent words are experienced more often. Word frequency predicts word knowledge when assessed using CDI data. Can effects of frequency be detected in Peekbank word recognition metrics? If not, why? Similarly, is the speed and accuracy of word recognition in Peekbank data related to CDI-derived word age of acquisition, and again, if not, why?

      This is a fascinating set of ideas, and one that we’ve pursued extensively using the Peekbank data. Unfortunately, we think it is out of scope for the current paper, which focuses on child-level metrics (including vocabulary and processing measures). Right now the current paper doesn’t include any analysis of individual words.

      Just to expand a bit on the problem here: unfortunately, modeling word recognition as a simple linear function of (log) word frequency is only possible in the case that distractors are held constant (e.g., “ball” always has “book” as its distractor), because distractor frequency plays an important role in the recognition process. However, in our dataset, words are paired with many different distractors across studies. This property means a fairly complex model of the LWL decision process would be necessary for a model to successfully predict effects for individual words. While such a model is an exciting research goal, it’s not something we can include in the current manuscript.

      Finally, there is a bit of a risk of the main findings of this paper coming across as a foregone conclusion. I.e., how could it be otherwise that word recognition improves with development?

      Reviewer #2 (Recommendations for the authors):

      Regarding the feedback about the risk of the findings coming across as a foregone conclusion - perhaps a primary place in the paper where it would be useful to clarify this point is on page 6, in the paragraph beginning, “We investigate two specific hypotheses here. First, one influential theory...”. Here, it might be worth clarifying whether there are alternative ideas about the emergence of word recognition in childhood that predict different patterns, so that the findings of the current paper can be framed as shedding new light on word recognition in development, rather than a confirmation of the common-sense idea that word recognition must improve over development.

      Thanks, we appreciate this feedback and it’s something we’ve struggled with in this project. Our conclusion is that this paper does not constitute a binary hypothesis test of e.g., whether word recognition is linked to vocabulary development. Instead, we lean into the idea that there are empirical issues (rather than hypotheses) that have not been quantified sufficiently. Thus, we end the revised introduction with the following paragraph:

      “Across both of these issues, the contribution of our work here lies in the detailed quantitative description of development. Nearly every theory of language learning assumes some role for continuous developmental change in word recognition, but these assumptions have not previously been anchored to specific measurements. Hence neither the functional form of the assumed changes nor their concurrent and predictive relationships to vocabulary have been quantified. We leverage the Peekbank dataset to accomplish these goals.”

    1. Author response:

      The following is the authors’ response to the original reviews

      The following revisions have been made to address most of the publicly available suggestions made by the Reviewers.

      We have also corrected formatting issues in two figure panels:

      Fig.1B: embryo ages added over placenta images.

      Fig. 4D: fixed a truncated label.

      Reviewer #1 (Public review):

      The study would benefit from clearer evidence and additional experiments that would help to establish the molecular and cellular mechanisms underlying the brain phenotype, the central topic of the work.

      We agree that additional experiments are necessary to elucidate the mechanism(s) by which EML3 deficiency causes the observed developmental phenotypes. However, as no further experimentation is possible due to the closure of our laboratory, we are committed to sharing available materials including custom antibodies and cryopreserved sperm from our mouse lines. We include previously generated experimental data not presented in the original submission. While these additional data do not reveal the mechanisms, we believe that sharing hypotheses that were experimentally ruled out will benefit the scientific community.

      M&M: we have added a section listing several tissue-specific Eml3 KOs generated. All of the generated cKO mice were indistinguishable from Eml3<sup>wt</sup> controls.

      Supp. Fig. 2 with staining for major PBM components has been added. We have included antibody information to M&M.

      Reviewer #2 (Public review):

      (1) While the manuscript presents valuable data, there are also several weaknesses that limit the overall impact of the study. Most notably, there is no clear mechanistic link established between the loss of Eml3 function and the observed phenotype, leaving the biological significance of the findings somewhat speculative, as it is not straightforward how a microtubule-associated protein can have an impact on the stability of the pial basement membrane. In this respect, but also in general for the whole manuscript, there seems to be a considerable amount of experimental work that has been conducted but is not presented, possibly due to the negative nature of the results. At least some of those results could be shown, particularly (but not only) the stainings for the composition of the ECM components.

      We agree that additional experiments are necessary to elucidate the mechanisms at play. While we cannot conduct further experiments, we provide additional existing data, including a new Supp. Fig. 2 showing ECM component staining. As this reviewer rightly anticipated, these results might not clarify the mechanism but sharing the hypotheses that were already experimentally tested will be helpful.

      (2) Additionally, the phenotype reported appears to be dependent on the genetic background, as it is absent in the CD1 strain. This observation raises concerns as to how robust the results are and how much they can be generalized to other mouse strains, but, more importantly, to humans.

      Indeed, we have determined that genetic background greatly influences the manifestation of developmental defects caused by absence or mutation of the EML3 protein in mice. Modifier genes appear to play a significant role in phenotypic expression. In humans, the presence or absence of such modifiers may result in a broad spectrum of outcomes from no clinical relevance, as seen in CD1 mice, to potential intrauterine mortality. We agree that this underscores the challenge of translating mouse model findings to human implications. Future studies could include a search for EML3 non-coding regulatory mutations and expanded analysis of neuronal development defects, such as COB, as well as cases of intrauterine growth restriction (IUGR).

      (3) There is no data included in the manuscript about the generation and analysis of the Eml3AAA/AAA mouse line. This is an important omission, especially as no details on the validation or phenotypic characterization of this additional mouse line are provided. Including these elements would greatly strengthen the rigor and interpretability of the work, especially if that mouse line is to be shared with the scientific community.

      We acknowledge this oversight and have added a Materials and Methods section describing the generation of Eml3 TQT86AAA mice. Validation of the Eml3 TQT86AAA mice included showing absence of EML3-DYNLL binding in our co-IP MS data in Table 3. We state that the validated Eml3 TQT86AAA mice were phenotypically indistinguishable from Eml3<sup>wt</sup> control mice.

      Reviewer #3 (Public review):

      (1) Besides the data provided in the figures, the authors report a significant amount of experiments/results as "Data not shown". Negative data is still important data to report, and the authors may want to choose some crucial "not shown data" to report in the manuscript.

      We have incorporated key datasets previously omitted, with priority given to those specifically requested by Reviewer #2.

      (2) Results in Figure 3A apparently contradict results in 3B. A better explanation of the results should improve understanding of the data. Even though the conclusion that the "onset and progression of neurogenesis is normal in Eml3 null mice" seems logical based on the data, the final numbers are not (Figure 3A) and this should be acknowledged, as well.

      We provide further explanations for the data presented in figures 3A and 3B to better convey the fact that the two datasets are not contradicting. In essence, since Eml3 null mice are developmentally delayed (as determined by the number of somites at a specific age, Fig. 1C), the milestones in neurogenesis are reached at a later age in Eml3 null mice, thus at embryonic age E11.5 Eml3 null mice have fewer TBR2-positive cells (Fig. 3A). However, Eml3 null mice have reached the same neurogenesis milestones as their WT counterparts when they have the same number of somites (Fig. 3B).

      Results section for Fig. 3: we provide additional explanations that reconcile the results shown in Fig. 3A and Fig. 3B.

      (3) The authors should define which cell types are identified by SOX1 and PAX6.

      We have defined the expression timing and cell identity marked by SOX1 and PAX6 in neural progenitors during cortical development.

    1. Author response:

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

      We would like to express our deep appreciation to the editor and reviewers for their constructive comments and suggestions, which have significantly improved the quality of our manuscript. In response, we have carefully revised the manuscript, addressed all comments, and performed additional experiments and analyses to strengthen our findings.

      (1) We repeated retrograde tracing using CTB-647 to verify precise targeting of SPN and DGC neurons, as shown in the new Figure 7.

      (2) We performed dual retrograde tracing combined with fiber photometry or optogenetic activation to investigate the role of PMC dual-projecting neurons in the control of urination, as shown in Figure supplements 11 and 12.

      (3) We conducted new experiments activating PMC<sup>ESR1+</sup> neurons after PDNx to assess their role in urination, as shown in new Figure 6.

      (4) We added a more detailed analysis of the dynamics of neural responses in PMC<sup>ESR1+</sup> neurons in Figure supplements 3F-3G.

      (5) We analyzed peak Ca<sup>2+</sup> signals in the PMC during and after the onset of EMG bursting, as shown in Figure supplement 4F.

      (6) We added a comparison of spontaneous and light-induced spikes in PMC<sup>ESR1+</sup> neurons, as shown in Figure supplements 3B–3C.

      (7) We expanded the Discussion to address how PMC<sup>ESR1+</sup> neurons coordinate bladder contraction and sphincter relaxation to control both the initiation and suspension of urination.

      We hope these revisions meet the reviewers' expectations and contribute to the improvement of our manuscript.

      Reviewer #1 (Public review):

      Summary:

      Urination requires precise coordination between the bladder and external urethral sphincter (EUS), while the neural substrates controlling this coordination remain poorly understood. In this study, Li et al. identify estrogen receptor 1-expressing neurons (ESR1+) in Barrington's nucleus as key regulators that faithfully initiate or suspend urination. Results from peripheral nerve lesions suggest that BarEsr1 neurons play independent roles in controlling bladder contraction and relaxation of the EUS. Finally, the authors performed region-specific retrograde tracing, claiming that distinct populations of BarEsr1 neurons target specific spinal nuclei involved in regulating the bladder and EUS, respectively.

      Strengths:

      Overall, the work is of high quality. The authors integrate several cutting-edge technologies and sophisticated, thorough analyses, including opto-tagged single unit recordings, combined optogenetics, and urodynamics, particularly those following distinct peripheral nerve lesions.

      We are grateful for your insightful and constructive comments, which affirmed the importance and technical depth of our work. Thank you for dedicating your expertise and time to reviewing our manuscript. Guided by your suggestions, we have revised the paper as detailed below.

      Weaknesses:

      (1) My major concern is the novelty of this study. Keller et al. 2018 have shown that BarEsr1 neurons are active during urination and play an essential role in relaxing the external urethral sphincter (EUS). Minimally, substantial content that merely confirms previous findings (e.g. Figures 1A-E; Figures 3A-E) should be move to the supplementary datasets.

      Thank you for this valuable and constructive comment. We fully agree that the novelty of our study relative to Keller et al., 2018 must be made explicit. Keller et al. established that PMC<sup>ESR1+</sup> neurons are active during socially evoked urine-marking behavior (voluntary urination) and demonstrated their essential role in relaxing the EUS. Their study mainly focused on behavioral context and EUS relaxation. In contrast, our work addresses a distinct, mechanistic question: how these same neurons participate in reflexive, physiological urination and coordinate both bladder detrusor contraction and EUS relaxation.

      Novel aspects of the present study:

      (1) Temporal dynamics of PMC<sup>ESR1+</sup> neurons during reflexive micturition.

      Using opto-tagging and single-unit recordings, we reveal the precise firing pattern of PMC<sup>ESR1+</sup> neurons during reflexive voiding. Simultaneous fiber photometry, cystometry, and EUS-EMG recordings demonstrate that population-level activity of PMC<sup>ESR1+</sup> neurons precedes and tightly correlates with both bladder contraction and EUS relaxation a coordination not previously demonstrated.

      (2) Causal role in reflexive urination.

      Manual closed-loop optogenetic inhibition at the onset of reflexive voiding acutely terminates EUS bursting and bladder contraction, immediately halting urine release.

      (3) Dual control of bladder and EUS.

      Optogenetic activation combined with selective pelvic or pudendal nerve transection shows that PMC<sup>ESR1+</sup> neurons drive both bladder contraction and EUS relaxation, revealing a coordinating role beyond EUS relaxation alone.

      (4) Anatomical substrate for coordinated control of bladder contraction and EUS relaxation in reflexive urination.

      Retrograde tracing identifies three spinal-projecting sub-populations: SPN-only, DGC-only, and dual-targeting neurons, providing a circuit-level explanation for the simultaneous control of bladder and EUS.

      Following your suggestion, panels that merely replicate Keller et al. (former Figures 1A–1E and Figures 3A–3E) have been moved to new Figure Supplements 1 and 7, respectively, so that the main figures now emphasize the new mechanistic findings.

      (2) I also have concerns regarding the results showing that the inactivation of BarEsr1 neurons led to the cessation of EUS muscle firing (Figures 2G and S5C). As shown in the cartoon illustration of Figure 8, spinal projections of BarEsr1 neurons contact interneurons (presumably inhibitory) that innervate motor neurons, which in turn excite the EUS. I would therefore expect that the inactivation of BarEsr1 should shift the EUS firing pattern from phasic (as relaxation) to tonic (removal of relaxation), rather than stopping their firing entirely. Could the authors comment on this and provide potential reasons or mechanisms for this finding?

      Thank you for this crucial comment. We apologize that the representative EUS-EMG traces in Figures 2G and S5C were too small to be clearly seen and that the corresponding results description was not sufficiently accurate. We have now replaced these EMG traces with enlarged versions (revised Figures 2G and S5C) and revised the corresponding Results section (lines 184, 197, 340-341). Based on the enlarged traces, we found that acute photoinhibition of PMC<sup>ESR1+</sup> neurons at the onset of phasic EUS-EMG bursting shifted the EUS firing pattern from large-amplitude phasic bursts to low-amplitude tonic firing. This suggests that ongoing activity of PMC<sup>ESR1+</sup> neurons is required to maintain phasic EUS bursting. A similar shift from phasic to tonic EUS-EMG activity during optogenetic silencing of PMC<sup>ESR1+</sup> neurons was reported by Keller et al., 2018 (Figure supplement 8C), confirming the reproducibility of the phenotype. We propose that the potential mechanism of this low-amplitude tonic activity may be mediated in part by a spinal reflex pathway (the guarding reflex) for preventing urination, whereby the loss of PMC<sup>ESR1+</sup> neurons-mediated supraspinal facilitation reduces inhibition of spinal interneurons, leading to enhanced baseline excitability of EUS motor neurons in response to bladder afferent input during bladder distension (William C. de Groat et al., Comprehensive Physiology. 2015, PMID: 25589273).

      (3) Current evidence is insufficient to support the claim that the majority of BarEsr1 neurons innervate the SPN but not DGC. The current spinal images are uninformative, as the fluorescence reflects the distribution of Esr1- or Crh-expressing neurons in the spinal cord, along with descending BarEsr1 or BarCrh axons. Given the close anatomical proximity of these two nuclei, a more thorough histological analysis is required to demonstrate that the spinal injections were accurately confined to either the SPN or the DGC.

      Thank you for raising this important concern. To rigorously verify that our spinal injections were confined to either the SPN or the DGC, we performed new retrograde-tracing experiments in ESR1-Cre and CRH-Cre mice. We injected a mixture of AAV-Retro-DIO-mCherry or AAV-Retro-DIO-EGFP with the retrograde tracer CTB-647 specifically into the SPN or DGC (Methods, lines 465-466). Only animals in which CTB-647 fluorescence was strictly limited to the target nucleus, without detectable spread to the adjacent region, were included in the analysis (new Figures 7A and 7E). These results confirm our original observation that PMC<sup>ESR1+</sup> neurons comprise three distinct spinal-projection subpopulations: one (19.0%) targeting the SPN, one (52.2%) innervating the DGC, and a third (28.8%) projecting to both regions (Results, lines 304–306; new Figures 7F–7H). In addition, the majority of PMC<sup>CRH+</sup> neurons project to the SPN but not the DGC (new Figures 7B–7D; Results, lines 297–301). We have assembled new Figure 7 using the newly acquired spinal images and the validated data.

      Reviewer #1 (Recommendations for the authors):

      From the abstract: "Anatomically, PMCESR1+ cells possess two subpopulations projecting to either the pelvic or pudendal nerve". I don't think these neurons directly project to either nerve.

      Thank you for this precise comment. We apologize for incorrectly stating that PMC<sup>ESR1+</sup> cells project directly to the pelvic or pudendal nerves. In the revised Abstract (lines 32–36) we have rephrased the sentence to clarify the actual anatomy: “Anatomically, PMC<sup>ESR1+</sup> neurons consist of three distinct spinal-projection-based subpopulations: one targeting the sacral parasympathetic nucleus (SPN), one innervating the dorsal gray commissure (DGC), and a third that projects to both regions, thereby enforcing the coordination of bladder contraction and sphincter relaxation in a rigid temporal sequence.”. We trust this revision now accurately reflects the anatomical findings.

      Reviewer #2 (Public review):

      Summary:

      The authors have performed a rigorous study to assess the role of ESR1+ neurons in the PMC to control the coordination of bladder and sphincter muscles during urination. This is an important extension of previous work defining the role of these brainstem neurons, and convincingly adds to the understanding of their role as master regulators of urination. This is a thorough, well-done study that clarifies how the Pontine micturition center coordinates different muscle groups for efficient urination, but there are some questions and considerations that remain.

      Strengths:

      These data are thorough and convincing in showing that ESR1+PMC neurons exert coordinated control over both the bladder and sphincter activity, which is essential for efficient urination. The anatomical distinctions in pelvic versus pudendal control are clear, and it's an advance to understand how this coordination occurs. This work offers a clearer picture of how micturition is driven.

      We sincerely thank you for highlighting the rigor of our study and for recognizing the advance in understanding how PMC<sup>ESR1+</sup> neurons exert coordinated, anatomically segregated control over bladder and sphincter. We also appreciate the constructive suggestions that helped us further improve clarity, which we address point-by-point below.

      Weaknesses:

      The dynamics of how this population of ESR1+ neurons is engaged in natural urination events remains unclear. Not all ESR1+ neurons are always engaged, and it is not measured whether this is simply variation in population activity, or if more neurons are engaged during more intense starting bladder pressures, for instance. In particular, the response dynamics of single and doubly-projecting neurons are not defined. Additionally, the model for how these neurons coordinate with CRH+ neuron activity in the PMC is not addressed, although these cell types seem to be engaged at the same time. Lastly, it would be interesting to know how sensory input can likely modulate the activity of these neurons, but this is perhaps a future direction.

      Thank you for this insightful comment. First, we agree that not all ESR1+ neurons are consistently engaged during urination (Figure 1B). Because bladder pressure was not measured during the opto-tagging experiments, we cannot determine whether this reflects trial-to-trial variability in population activity or pressure-dependent recruitment of additional neurons. We speculate that stronger starting bladder pressures may recruit a larger subset of ESR1+ neurons, analogous to graded, pressure-dependent recruitment observed in peripheral sensory neurons (Bruns et al., J Neural Eng. 2011, PMID: 21878706; Marshall et al., Nature. 2020, PMID: 33057202).

      Second, using fiber photometry recording and optogenetic activation, we examined the dynamics of dual-projecting neurons in the PMC that were retrogradely labeled from the SPN and DGC. Their activity correlated with bladder contraction and sphincter relaxation, and optogenetic activation sequentially induced these events to trigger urination (see Recommendation #8). Although retrograde labeling captured only a subset of dual-projecting neurons, the results indicate that they coordinate bladder and sphincter activity.

      Third, previous studies suggest that PMC<sup>CRH+</sup> cells are associated with bladder contraction and likely serve as an integration center for context-dependent micturition behavior (Hou et al., Cell. 2016, PMID: 27662084; Ito et al., Elife. 2020, PMID: 32347794). We therefore propose that PMC<sup>CRH+</sup> cells establish the baseline conditions and contextual readiness for voiding, whereas PMC<sup>ESR1+</sup> cells act as the executive command to reliably initiate and execute the event.

      Finally, we agree that sensory inputs likely modulate PMC<sup>ESR1+</sup> neuron activity. Although this falls beyond the scope of the present study, it represents an important avenue for future investigation.

      Reviewer #2 (Recommendations for the authors):

      (1) In the introduction, the authors write that Keller 2018 only showed this ESR1 population to induce EUS relaxation, but those results also do show bladder contraction with photostimulation of this population. While the authors' work extends this finding in important ways, this should be acknowledged (line 60).

      Thank you for this important correction. We have now revised the Introduction to explicitly acknowledge that stimulation of neurons expressing estrogen receptor 1 (ESR1) in the PMC (PMC<sup>ESR1+</sup>) contributes to sphincter relaxation and increased bladder pressure (Introduction, lines 60-62), as originally reported by Keller et al., 2018.

      (2) I think a more detailed analysis of the dynamics of neural responses in the PMC ESR1 neurons would be valuable. For example: are the same cells always engaged before micturition, or do different populations activate on different trials? Can the authors comment on the half of the opto-tagged ESR1 population that is not firing during urination? Do they ever fire? A cell-by-cell analysis of which neurons are engaged over multiple trials would be very valuable to understand the dynamics of population activity. Figure 1H shows cumulative sessions, but what do single sessions look like?

      Thank you for these valuable comments. In response, we have performed refined single-trial analyses of neuronal activity, as detailed in the point-by-point replies below.

      For example: are the same cells always engaged before micturition, or do different populations activate on different trials?

      Among 11 PMC<sup>ESR1+</sup> units that showed urination-related excitation, 8 units exhibited a consistent firing increase in every voiding trial, whereas the remaining 3 increased their discharge in >78 % of trials (Figure 1B; new Figure supplement 3F). Thus, the same PMC<sup>ESR1+</sup> cells are recruited repeatedly, rather than distinct populations being activated on different trials. We have added this clarification to Results (lines 106–108).

      Can the authors comment on the half of the opto-tagged ESR1 population that is not firing during urination? Do they ever fire? A cell-by-cell analysis of which neurons are engaged over multiple trials would be very valuable to understand the dynamics of population activity.

      Approximately half of the opto-tagged PMC<sup>ESR1+</sup> cells showed no increase in firing rate during urination, yet exhibited spontaneous spikes at other times (new Figure supplement 3G), confirming their electrical competence. Because the PMC also participates in defecation, uterine activity, and other pelvic functions (Rouzade-Dominguez et al., Eur J Neurosci. 2003, PMID: 14686905; Schellino et al., Frontiers in Neuroanatomy. 2020, PMID: 33013330; Quaghebeur et al., Auton Neurosci. 2021, PMID: 34391125), these ESR1+ neurons may serve functions other than urination. We have now added this cell-by-cell analysis and discussion to the manuscript (Results, lines 108-112).

      Figure 1 H shows cumulative sessions, but what do single sessions look like?

      As shown in new Figure supplements 3F–3G, single-session raster plots reveal that PMC<sup>ESR1+</sup> neurons display consistent firing patterns across individual trials. Neurons whose firing rate increased during urination did so in most trials (Figure supplement 3F), whereas neurons unrelated to voiding remained silent or showed no discernible rate change during voiding across trials (Figure supplement 3G). These single-session observations are consistent with the cumulative population analysis shown in Figure 1H (new Figure 1B).

      (3) Supplemental Figure 4: It seems clear from this figure that NVCs are only occurring when the sphincter fails to engage. Can the authors quantify how often this is the case?

      Thank you for this important point. We have now quantified the occurrence of non-voiding contractions (NVCs) across all 229 bladder contraction events from 3 mice shown in Supplemental Figure 4. NVCs were observed exclusively when the external urethral sphincter failed to relax, accounting for 62/229 events (27.1 %), whereas coordinated voiding contractions (VCs) occurred in the remaining 167 events (72.9 %). These new data are presented in Figure supplement 4C.

      (4) Continuing from the above point: the authors say that the insufficient top-down drive or strength of activity from PMC ESR1 neurons is why NVCs occur. In looking closely, it also seems there is a small hump and subsequent increase in the calcium signal when the EUS bursting begins (particularly clear in Supplementary Figure 4). Could this instead mean that the bursting/urethral activity itself is feeding back onto the PMC to continue/enhance its activity, and it is instead the lack of sphincter bursting that results in the NVC? Could the authors analyze the signal during and after bursting starts? This model is consistent with one of the classic reflexes defined by Barrington, in which urethral fluid flow/activation enhances bladder contraction. The Figure 4 transection experiments do not fully answer this, as the authors are driving activity in the PMC at this time, but they could test this using PDN transection with fiber photometry recording.

      Thank you for this important point. We fully agree that EUS bursting may provide excitatory feedback to the PMC that sustains or even amplifies its activity, and that the absence of such feedback could underlie NVCs. To test this possibility, we re-analyzed the fiber-photometry traces aligned to the onset and offset of each EUS bursting (new Figure supplement 4). A small but consistent hump in the Ca<sup>2+</sup> signal appeared before bursting onset and the Ca<sup>2+</sup> signal continued to rise throughout the bursting (Figure supplement 4B, yellow arrow). The amplitude at bursting offset was significantly higher than both the NVC peak and the level recorded at bursting onset. These observations support the interpretation that urethral fluid flow/activation supplies excitatory feedback that reinforces PMC activity and bladder contraction, consistent with Barrington’s classic reflex. We have incorporated these new analyses into the revised manuscript (lines 145–155 and Figure supplement 4F).

      We agree that the positive-feedback loop described by Barrington’s classic urethra-to-bladder reflex is an intriguing mechanism. However, the PDN-transection experiment in Figure 4 was designed to determine if bladder contractions triggered by PMC<sup>ESR1+</sup> cells can proceed in the absence of sphincter bursting, not to evaluate this reflex. Incorporating simultaneous fiber-photometry recording into the PDN-transection experiment would therefore go beyond the scope of the present study. In future work we are keen to combine PDN transection with fiber photometry to further determine whether the urethra-to-bladder reflex contributes to the sustained PMC activity observed in our paradigm.

      (5) In Figure 4, is the timing of sphincter engagement different with ChR2 stimulation from what normally occurs? It appears that the bursting happens immediately upon activation whereas bladder contraction is a bit delayed.

      Thank you for this important observation. We have carefully re-examined the EMG traces from all animals shown in Figure 4. We confirm that the onset of sphincter bursting activity during ChR2 stimulation is indeed more rapid than during natural reflex voiding; nevertheless, the onset of phasic sphincter bursting during ChR2 stimulation remained delayed relative to the intravesical pressure rise (see Figure 8B).

      The immediate sphincter discharge visible in some trials was tonic EUS discharge or rare irregular bursting, not the typical EUS bursting. This tonic pattern corresponds to the spinal guarding reflex that suppresses urine leakage (Fowler et al., Nature Reviews Neuroscience. 2008, PMID: 18490916; Keller et al., Nature Neuroscience. 2018, PMID: 30104734). These segments were identified by their amplitude and spectral content and excluded from burst-onset analysis. Our analysis protocol therefore distinguishes tonic guarding activity from true phasic bursting, ensuring that only the latter was used to determine burst timing.

      (6) The explanation on line 299 about how spinal reflexes are impinging on this circuit is confusing. I agree that the bladder contraction stopping later than the EUS signal likely has something to do with spinal reflexes, but it seems this could instead be feedback from the urethral fluid flow, which continues bladder contractions (urethra-destrusor facilitative reflex). Could the authors clarify their thoughts here?

      Thank you for highlighting this ambiguity. We agree that the delayed cessation of bladder contraction could equally reflect either (1) the urethra-to-bladder facilitative reflex driven by ongoing urethral fluid flow or (2) spinal reflexes that we described. In the revised manuscript (Results, lines 343–349), we have re-worded the paragraph to make this dual possibility explicit, thereby avoiding an overly strong emphasis on spinal mechanisms alone.

      (7) A note on phrasing: the authors frequently say PMCESR1 cells drive sphincter relaxation, but then show an effect on sphincter bursting. Experienced readers might realize that relaxation and bursting are connected, but this might be confusing for readers and should be clarified in the text.

      Thank you for highlighting the potential ambiguity. We agree that the sentence “PMC<sup>ESR1</sup> cells drive sphincter relaxation” can seem paradoxical when our data show increased EUS bursting. In adult mice, the EUS does not remain continuously relaxed during voiding; instead, it generates rhythmic bursting composed of high-frequency spike clusters (active periods) alternating with low tonic activity (silent periods), resulting in rhythmic contractions and relaxations of EUS. This phasic activity acts as a pump that facilitates urine flow through the narrow rodent urethra (Kadekawa et al., Am J Physiol Regul Integr Comp Physiol, 2016, PMID: 26818058). The EUS bursting activity we recorded is consistent with the results reported in previous studies (Keller et al., Nat Neurosci, 2018, PMID:30104734; Ito et al., Elife, 2020, PMID:32347794).

      Consequently, when PMC<sup>ESR1</sup> neurons initiate bursting, they simultaneously generate the relaxation phases that separate the spikes. To make this explicit we have replaced the phrase “PMC<sup>ESR1+</sup> cells drive sphincter relaxation” with “PMC<sup>ESR1</sup> neurons trigger EUS bursting, which generates rhythmic sphincter contractions and relaxations.” (Results, page 7, lines 219-221). We have applied similar clarifications throughout the revised manuscript (Results, lines 125-129). We hope this revision eliminates any apparent contradiction.

      (8) The question remains as to which neurons (dual projecting, single projecting, or all?) are active in natural urination. This is possible to do through dual injection of retrograde virus in SPN and DGC that could coordinately turn on Gcamp, but this challenging experiment is perhaps beyond the scope of this paper. Even still, the authors could discuss their model for whether the dual- and single-projecting neurons are all engaged at once in a natural urination event. Do the authors have any data that could provide insight as to when these sub-populations are active? Results from the opto-tagging in Figure 1 (and comment #2 about single neuron firing properties) might provide a foundation for hypotheses or insights.

      Thank you for this valuable suggestion. We have now performed the experiment you proposed: dual injection of retrograde virus (AAV-Retro-Cre and AAV-Retro-DIO-GCaMP6s) in SPN and DGC were used to selectively label PMC dual-projecting neurons, and a 200-µm optic fiber was implanted above the PMC to record their Ca<sup>2+</sup> dynamics during natural urination (Figure supplement 11A and Methods, lines 470–474, 652-655). Dual-projecting neurons exhibited robust activation throughout the entire voiding phase that was tightly correlated with intravesical pressure rise and EUS bursting (Figure supplements 11A–11H). However, technical limits of current retrograde tools preclude selective isolation of single-projecting (SPN-only or DGC-only) subsets for independent fiber-photometry recordings and injection restricted to one target unavoidably labels both single- and dual-projecting cells. We now state this technical limitation explicitly (Discussion, lines 426-430).

      Accordingly, in the revised Discussion (lines 389-406), we integrate fiber-photometry Ca<sup>2+</sup> signals with single-unit data from opto-tagged recordings to propose several testable, non-mutually-exclusive models for how dual- and single-projecting PMC<sup>ESR1+</sup> neurons are engaged during natural urination: “Based on population dynamics obtained by fiber photometry (Figures 1D-1H, Figure supplements 1A-1F, and Figure supplements 11A-11H) and single-neuron firing properties recorded via optrode (Figures 1A-1C), we propose several mechanistic models for the engagement of dual- and single-projecting PMC<sup>ESR1+</sup> neurons during natural micturition. One possibility is that all three populations (dual-projecting, SPN-projecting and DGC-projecting neurons) are co-activated, with the dual-projecting subset acting as a “bridging amplifier” that sustains rising bladder pressure while coordinating EUS relaxation. Alternatively, SPN-projecting neurons may be recruited first to initiate bladder contraction, followed by DGC-projecting neurons that evoke EUS bursting and facilitate urine entry into the urethra; once flow begins, the urethro-detrusor facilitative reflex could recruit dual-projecting neurons to further enhance voiding efficiency. In addition, contextual or state-dependent urination—such as scent-marking behavior characterized by multiple voiding events with smaller volumes than reflexive urination—may predominantly rely on sequential and cooperative activation of single-projecting neurons. Other recruitment sequences remain conceivable. Future studies combining diverse urination-related behavioral paradigms with simultaneous recordings from projection-specifically labeled PMC neurons will be required to validate and refine these models.”

      Reviewer #3 (Public review):

      Summary:

      The paper by Li et al explored the role of Estrogen receptor 1 (Esr1) expressing neurons in the pontine micturition center (PMC), a brainstem region also known as Barrington's nucleus (Hou et al 2016, Keller et al 2018). First, the author conducted bulk Ca2+ imaging/unit recording from PMCESR1 to investigate the correlations of PMCESR1 neural activity to voiding behavior in conscious mice and bladder pressure/external urethral muscle activity in urethane anesthetized mice. Next, the authors conducted optogenetics inactivation/activation of PMCESR1 to confirm the contribution to the voiding behavior also conducted peripheral nerve transection together with optogenetics activation to confirm the independent control of bladder pressure and urethral sphincter muscle.

      We sincerely thank you for providing a thoughtful summary and insightful comments on our study.

      Weaknesses:

      (1) The study demonstrates that pelvic nerve transection reduces urinary volume triggered by PMC ESR1+ cell photoactivation in freely moving mice. Could the role of pudendal nerve transection also be examined in awake mice to provide a more comprehensive understanding of neural involvement?

      Thank you for this valuable suggestion. We conducted an additional experiment to determine the contribution of the pudendal nerve to PMC<sup>ESR1+</sup> neuron-driven voiding in awake mice. Bilateral pudendal nerve transection (PDNx) reduced the optogenetically evoked urine volume compared with sham-operated controls, yet photoactivation of PMC<sup>ESR1+</sup> neurons still reliably induced urination after PDNx (new Figure 6). Thus, bilateral integrity of the pudendal nerve is required for efficient PMC<sup>ESR1+</sup> neuron-driven voiding, most likely by transmitting the signals that entrain rhythmic EUS bursting. These data and experimental details have been incorporated into Figure 6, Results (lines 272–276), and Methods (lines 542–545).

      (2) While the paper primarily focuses on PMCESR1+ cells in bladder-sphincter coordination, the analysis of PMCESR1+-DGC/SPN neural circuits - given their distinct anatomical projections in the sacral spinal cord - feels underexplored. How do these circuits influence bladder and sphincter function when activated or inhibited? Also, do you have any tracing data to confirm whether bladder-sphincter innervation comes from distinct spinal nuclei?

      Thank you for this critical comment. To determine how PMC<sup>ESR1+</sup> neurons that target distinct sacral nuclei influence bladder–sphincter coordination, we first focused on the dual-projecting subset in a new experiment (Figures supplement 11 and Methods, lines 470–477, 652-655, 669-673). Dual retrograde virus injections into SPN and DGC selectively labelled PMC dual-projecting neurons, a subset of which are ESR1+. Fiber-photometry recordings showed that these cells were active during bladder contraction and sphincter relaxation (Figure supplements 11E-11H), whereas optogenetic activation reliably initiated urination: bladder pressure rose immediately and was followed by rhythmic EUS bursting (Figure supplements 11I-11N and 12B; Results, lines 309-313, 332-335). Thus, the dual-projecting sub-population is sufficient to coordinate bladder contraction with sphincter relaxation. Current retrograde tools do not allow selective isolation of single-projecting (SPN-only or DGC-only) subsets; injecting only one target unavoidably labels both single- and dual-projecting cells. Consequently, we cannot yet compare the functional impact of pure SPN-only versus DGC-only PMC populations. This limitation is now stated explicitly in the revised Discussion (lines 426–430).

      In our 2025 paper (Yan et al., Commun Biol, 2025, PMID: 40259086), we used PRV-based retrograde tracing to show that SPN and DGC constitute two separate spinal nuclei controlling the bladder and the EUS, respectively. Classic studies have reached the same conclusion (Yao et al., Nat Neurosci, 2018, PMID: 30361547; Karnup & De Groat, IBRO Reports, 2020, PMID: 32775758; Karnup, Auton Neurosci, 2021, PMID: 34391124). These citations and a concise summary have been added to the Results (lines 289–294).

      (3) Although the paper successfully identifies the physiological role of PMCESR1+ cells in bladder-sphincter coordination, the study falls short in examining the electrophysiological properties of PMC ESR1+-DGC/SPN cells. A deeper investigation here would strengthen the findings.

      Thank you for this thoughtful suggestion. While a detailed electrophysiological characterization of PMC<sup>ESR1+-DGC/SPN</sup> neurons would provide complementary information, the primary goal of the present study was to define the in vivo functional dynamics and behavioral role of these neurons during natural urination. As you suggested, further electrophysiological analysis of PMC<sup>ESR1+-DGC/SPN</sup> neurons will be an important direction for our future work.

      (4) The parameters for photoactivation (blue light pulses delivered at 25 Hz for 15 ms, every 30 s) and photoinhibition (pulses at 50 Hz for 20 ms) vary. What drove the selection of these specific parameters? Moreover, for photoactivation experiments, the change in pressure (ΔP = P5 sec - P0 sec) is calculated differently from photoinhibition (Δpressure = Ppeak - Pmin). Can you clarify the reasoning behind these differing approaches?

      Thank you for this opportunity to clarify our experimental design. The photoactivation protocol (25 Hz, 15 ms pulses) was chosen because PMC<sup>ESR1+</sup> neurons faithfully follow this frequency without depolarisation block and it reliably triggers voiding (Keller et al., Nat Neurosci, 2018, PMID:30104734). For photoinhibition we originally stated “50 Hz, 20 ms pulses”, but this was an error. Consistent with the same study (Keller et al., Nat Neurosci, 2018, PMID:30104734), we used continuous light (constant illumination) to maintain sustained suppression. The Methods section has been corrected (lines 659-661, 690-691).

      The ΔP formula was tailored to the temporal profile of each manipulation. For activation, ΔP (P<sub>5 sec</sub> - P<sub>0 sec</sub>) captures the rapid pressure rise after light onset; the same window was used in (Hou et al., Cell. 2016, PMID: 27662084). For inhibition, because saline infusion produces rhythmic reflex voiding, we delivered light at the onset of EUS bursting (i.e. when pressure was already at ~peak). Inhibition abruptly stops the bladder contraction, so the bladder cannot return to its pre-void baseline. The Δpressure (P<sub>peak</sub> – P<sub>min</sub>) was therefore used to quantify the extent to which the ongoing pressure wave was aborted by photoinhibition. P<sub>min</sub> is the lowest value reached before the next infusion-driven upswing, making the metric insensitive to the slow baseline drift produced by continuous infusion. These clarifications have been added to the Methods (Methods, lines 676-677, 679-680, 692-693).

      (5) The discussion could further emphasize how PMCESR1+ cells coordinate bladder contraction and sphincter relaxation to control urination, highlighting their central role in the initiation and suspension of this process.

      Thank you for this valuable comment. We have revised the Discussion to emphasize that PMC<sup>ESR1+</sup> neurons coordinate urination by sequentially driving bladder contraction followed by sphincter relaxation through their dual projections to the SPN and DGC. We also emphasized that this coordination is essential for the initiation and effective execution of voiding (Discussion, lines 369-388). In addition, in the revised Discussion (Discussion, lines 389-406), we integrate fiber-photometry Ca<sup>2+</sup> signals with single-unit data from opto-tagged recordings to propose several testable, non-mutually-exclusive models for how PMC<sup>ESR1+</sup> cells are engaged during natural urination.

      (6) In Figure 8, The authors analyze the temporal sequence of bladder pressure and EUS bursting during natural voiding and PMC activation-induced voiding. It would be acceptable to consider the existence of a lower spinal reflex circuit, however, the interpretation of the data contains speculation. Bladder pressure measurement is hard to say reflecting efferent pelvic nerve activity in real time. (As a biological system, bladder contraction is mediated by smooth muscle, and does not reflect real-time efferent pelvic nerve activity. As an experimental set-up, bladder pressure measurement has some delays to reflect bladder pressure because of tubing, but EUS bursting has no delay.) Especially for the inactivation experiment, these factors would contribute to the interpretation of data. This reviewer recommends a rewrite of the section considering these limitations. Most of the section is suitable for the results.

      We agree with the reviewer that bladder pressure, mediated by smooth muscle contraction, provides an indirect measure of efferent pelvic nerve activity and is subject to both physiological and experimental delays. Regarding potential delay from the tubing system, pressure propagates in fluid at approximately 1000 m/s (Kela & Pekka, Proceedings of World Academy of Science Engineering & Technology, 2009, DOI: 10.5281/zenodo.1080526). Given that the total tubing length in our setup is 0.5-1 meter, this gives an estimated transmission delay of only 0.5-1 ms. However, this delay is negligible compared with the observed time difference (~700 ms) between the cessation of EUS bursting and the termination of bladder contraction. Theoretically, pressure transmission is not expected to introduce a temporal delay. However, we cannot exclude the possibility that the pressure measurement itself may impose such a delay, because bladder pressure does not necessarily reflect efferent pelvic nerve activity in real time. Future studies using simultaneous recordings of bladder pressure and pelvic nerve discharges will help clarify whether a true temporal delay exists. Nevertheless, we agree that additional physiological or peripheral factors may also contribute to this difference in timing. As suggested by the reviewer, we have revised the discussion to consider the potential influence of other factors, such as urethra-detrusor facilitative reflex (Results, lines 343-349).

      Reviewer #3 (Recommendations for the authors):

      (1) In opto-tag experiments, a comparison of average AP waveform during behavior and during light stimulation should be included as criteria. It should be mostly the same waveform.

      Thank you for bringing this to our attention. We have now added this comparison as an inclusion criterion in the revised manuscript. Figure supplement 3B shows representative examples of the average waveforms, and Figure supplement 3C displays the distribution of correlation coefficients between spontaneous and light-evoked spikes for all recorded PMC<sup>ESR1+</sup> units, all of which exhibited r > 0.8.

      (2) Optical fiber implantation seems to be done in two different methods. In Figure 1 and Figure 2, the fiber tip is positioned just above PMC but in Figure 3 it seems to be angled. The information should be included in the Methods section.

      Thank you for this important comment. We have now clarified in the Methods that for Figures 1 and 2, the optical fibers were implanted vertically above the PMC, whereas for Figure 3, the left optical fiber was implanted at a 33° lateral angle targeting the PMC (Methods, lines 499-503).

      (3) In the closed-loop inhibition experiments of Figure 2, the parameters to start closed-loop photo-inactivation were not described in the method. If it is a manual closed loop, it should be described clearly.

      Thank you for raising this important point. We apologize for omitting these details in the original Methods. We have now added a complete description of the manual closed-loop photo-inhibition protocol, including the triggering criteria and operator-controlled timing, in the revised Methods section (lines 602–605).

      (4) In Figure 7A/E the authors provide a spinal cord image to show the injection site, but the image is misleading. The figure only shows AAV-infected CRH/ESR1 neurons in the spinal cord section. It does not indicate the AAV injection site or the terminal distribution.

      Thank you for your important comment. We apologize for providing a spinal cord image that did not accurately depict the injection site. To rigorously verify that our spinal injections were confined to SPN or DGC, we performed new retrograde-tracing experiments in ESR1-Cre and CRH-Cre mice. A mixture of AAV-Retro-DIO-mCherry or AAV-Retro-DIO-EGFP with the retrograde tracer CTB-647 was injected specifically into SPN or DGC. Only animals in which CTB-647 fluorescence was strictly limited to the target nucleus, without spread to the adjacent region, were included (new Figures 7A and 7E). These data confirmed our original observations and have been pooled in Figure 7. The manuscript and figure have been updated accordingly (Results, lines 297-301, 304-306; Methods, lines 465–466).

    1. Author response:

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

      We thank both editors and the three reviewers for their constructive criticism of our work. As a result of these comments, we have made several significant revisions to the paper that we believe strengthen and clarify our major results:

      (1) Following suggestions from Reviewers #1 and #3, we have have improved our introduction to the different fitness concepts (lines 105–148) and streamlined the discussion of the logit encoding (lines 175–190). In particular, we have moved the most technical points to the SI (Sec. S3).

      (2) Based on criticisms of our usage of the population dynamics model from Reviewers #1 and #3, we significantly revised our explanation of the motivation and interpretation of this model (lines 284–310 and 323–336) and our discussion of the generalizability of these results (lines 678–728), including the possible effects of interactions besides resource competition.

      (3) Following a request from Reviewer #3, we have expanded our analysis of epistasis to systematically test all possible double mutants between qualitative types of trait perturbations in the model. We have added a new main text figure (Fig. 3), new SI figures (Figs. S9–S15), a new subsection in the Results (lines 344–395), and corresponding new sections in the Methods (lines 864–892) and SI (Sec. S8).

      (4) Following concerns from Reviewers #2 and #3 about the limited empirical data, we have expanded our analysis of the LTEE data (new main text Fig. 4, revised text on lines 416–439, and revised SI Figs. S16–S18) and have analyzed two new benchmarking datasets for bulk fitness to test our predictions (new main text Fig. 6, new Results subsection on lines 561–590, and new SI Figs. S24 and S25).

      (5) Following the criticism of Reviewer #3 about the lack of a clear recommendation on fitness quantification that provides the greatest value for a given scientific question, we have better explained what we think the scientific consequences of fitness are as a motivation for our analysis (lines 82–88, 319–322, and 615–630) and replaced the final flowchart figure with a step-by-step guide in the Methods to implement our recommendations in practice (lines 964–982).

      Reviewer #1 (Public review):

      The authors point out that the fitness estimates obtained from different experimental assays (monoculture, pairwise competition, or bulk competition) are not generally equivalent, not even with regard to the fitness ranking of different genotypes. Using a computational model based on experimentally measured growth phenotypes for knockout strains in yeast, as well as data from Lenski’s Long Term Evolution Experiment (LTEE), they derive a set of best practice rules aimed at extracting the optimal amount of information from such experiments.

      The study is very complete on a technical level and I have no suggestions for further analyses. However, I feel the readability and the conceptual focus of the manuscript could be significantly improved by rearranging the material with regard to the contents of the main text vs. the Methods and the Supplement. Detailed recommendations:

      (1) Regarding readability, the large number of references to material in the Methods and Supplement fragment the main text and make it difficult to follow.

      We understand the challenges these references pose to the flow of the main text; we have attempted to keep those references to a minimum, while ensuring that technical details of the work are fully documented and referenced for completeness.

      (2) Conceptually, it seems to me that the current presentation obscures the reasons why we should care about fitness in the first place. In the first paragraph of Results, the authors define fitness “as any number that is sufficient to predict the genotype’s relative abundance x(t) over a short-time horizon”. To me, this seems like an extremely narrow and not very interesting definition. Instead, I view fitness as an intrinsic property of a genotype that allows us to predict its performance under a range of conditions, including in particular conditions that are different from the experimental setup that was used to obtain the fitness estimates. The latter viewpoint is well expressed in Supplementary Section S1, where the authors discuss the notion of fitness potential. I would recommend to move at least part of this discussion to the main text.

      We appreciate the reviewer’s viewpoint and have moved that conceptual discussion from the SI to the beginning of the Results section to give readers a broader perspective on fitness (lines 105–148). We use “potential” in analogy with potential energy in physics and have clarified this on lines 126–135.

      What we call fitness potential, like the other notions of fitness we discuss in this paper (relative and absolute fitness), is still specific to an environmental condition. Fitness as a property intrinsic to a genotype and independent of any environment, as the reviewer mentions, is an interesting concept but beyond the scope of this paper, which is focused on analyzing fitness measurements that are inevitably environment-specific and we have clarified this on lines 142–148. While it is true that this definition of fitness is narrow, it is what can be empirically measured directly, and thus we believe it is crucial to understand how to best interpret that data.

      By comparison, the arguments in favor of the logit encoding that currently opens the Results session are rather straightforward and could be shortened significantly.

      We agree and have condensed this section (lines 175–192).

      (3) Similarly, the modeling strategy used in this work is quite subtle and needs to be explained more fully in the main text. The authors use growth traits (lag time, growth rate, and yield) extracted from monoculture experiments on a yeast knockout collection and feed them into a specific mathematical model to simulate pairwise and bulk competition scenarios. Since a key claim of the work is that monoculture experiments are generally poor predictors of competitive fitness, the basis for this conclusion and the assumptions on which it is based need to be described clearly in the main text. In the current version of the manuscript, this information has been largely relegated to the Methods section.

      We agree that our motivation for the population dynamics model and growth curve data was not clearly explained. We have significantly revised this section of the Results in the main text (lines 284–310).

      In particular, we recognize the potential for misunderstanding this material we do not intend the relative fitness values calculated from this model to be interpreted as predictions of the true relative fitness between yeast deletion strains. Rather, we use the population dynamics model for our proof of principle: that the most basic features of microbial population dynamics in laboratory experiments, as captured by this model (resource competition, lag phase, growth phase, saturation), are sufficient to create discrepancies between common fitness statistics used in these experiments (different encodings, time scales, choices of reference subpopulations). We have added a statement to highlight existing work on monoculture predictors for competition outcomes [32, 34, 36, 37] on lines 453–459.

      Reviewer #1 (Recommendations for the authors):

      In the discussion of the LTEE in Section S8, the authors write on page 8 that “we couldn’t fit the fitted values a,b in ref. 29 so we were unable to check it”. I don’t understand this sentence - is the claim that the fit in ref. 29 was incorrect?

      We have clarified this point in the SI (now Sec. S9). Our point was not that the fit in Wiser et al. 2013 is incorrect, but merely that we could not find the exact values of the fitted parameters they obtained documented in their paper, so we could not compare our own fitted parameters directly to theirs.

      Also, at the end of the section, the authors refer to theory work on the long-term fitness trend in the LTEE. Here, two early references arguing for a logarithmic increase in fitness could be mentioned as well:

      International Journal of Modern Physics B 12,:361-391 (1998) Evolution and Extinction Dynamics in Rugged Fitness Landscapes Paolo Sibani, Michael Brandt, and Preben Alstrøm

      J. Stat. Mech. (2008) P04014 Evolution in random fitness landscapes: the infinite sites model Su-Chan Park and Joachim Krug

      We thank the reviewer for providing these two references and have added them to the list of previous works on long-term fitness trends at the end of the section (now Sec. S9).

      Reviewer #2 (Public review):

      Summary:

      The manuscript “Quantifying microbial fitness in high-throughput experiments” provides a comprehensive analysis of the various approaches to quantifying fitness in microbial evolution, focusing on three primary factors: encoding of relative abundance, time scale of measurement, and the choice of reference subpopulation. The authors systematically explore how these choices impact fitness statistics and provide recommendations aimed at standardizing practices in the field. This manuscript aims to highlight the impact of differing fitness definitions and the methodologies utilized for analysis and how that can significantly alter interpretations of mutant fitness, affecting evolutionary predictions and the overall understanding of genetic interactions in the experiments. Although this manuscript focuses on a critical issue in the quantification of fitness in high throughput experiments, it heavily relies on only one experimental dataset (Warringer et al 2003) and one organism i.e, Yeast (Saccharomyces cerevisiae) grown in a defined medium, the environmental influence is not completely captured. While the theoretical framework is strong, more experimental examples with more organisms (i.e., more datasets) in their analysis and comparison would enhance the manuscript, especially its conclusion.

      We have expanded our analysis of competition data from the Long-Term Evolution Experiment in E. coli (lines 416– 439), including adding a main text figure (Fig. 4) along with the three SI figures (Figs. S16–S18). We have also added two completely different data sets that directly test our predicted discrepancies in fitness estimates from bulk competition experiments. From this data we have added a new main text figure (Fig. 6), two new SI figures (Figs. S24 and S25), and a new section at the end of the Results (lines 563–590).

      We wish to clarify, though, that the aim of this study is to develop theory on fitness quantification choices and minimal examples to demonstrate the potential for discrepancies between these choices. While we appreciate the reviewer’s interest in understanding how discrepancies in fitness statistics vary across organisms and environments, that is an empirical question beyond the scope of this paper.

      Strengths:

      The choices for quantifying fitness in evolution experiments are critical and highly relevant given the increasing prevalence of high-throughput experiments in evolutionary biology. The authors methodically categorize fitness statistics and their implications, providing clarity on a complex subject. This structured approach aids in understanding the nuances of fitness measurement. The manuscript effectively highlights how different choices in fitness measurement can influence fitness rankings and the understanding of epistasis, which is important for modeling evolutionary dynamics.

      Weaknesses:

      The theoretical framework is robust, but the manuscript could benefit from more empirical examples to illustrate how different fitness quantification methods lead to varied conclusions in experiments.

      Please see our response to the previous comment on this point.

      The discussion on the choice of reference subpopulation could be expanded with the influence of the environment or the condition. Different types of reference groups might yield different implications for fitness calculations, and further elaboration would enhance this section.

      While we agree that studying how environmental conditions affect fitness is an important and interesting problem, it goes beyond the scope of this paper, which focuses on the basic theory of quantifying microbial fitness from highthroughput experiments. Applications of this theory to empirical questions about environmental variation would be best served by their own studies. We have added a statement clarifying this goal (lines 144–148).

      We are unsure how the choice of reference subpopulation is related to this issue. In our view, if the goal of a mutant fitness measurement is to predict how that mutant would behave when arising spontaneously and competing against its immediate ancestor, the gold-standard reference subpopulation must always be the mutant’s immmediate ancestor, or another mutant that is known to be phenotypically equivalent to the ancestor (e.g., neutral mutants in the case of a large mutant library). Other choices of reference subpopulations would not provide directly meaningful information in this regard.

      The authors overgeneralize some findings; for instance, the implications of fitness measurement choices could vary significantly across different microbes or experimental conditions. A more detailed discussion would strengthen the conclusion.

      We certainly agree that the consequences of fitness quantification choices could vary significantly across organisms and environments; our goal for this paper is to demonstrate what discrepancies are possible in principle and in particular how they depend on basic features of microbial population dynamics (e.g., variation in yield). We have added two separate paragraphs in the Discussion section to address the generalizability of our results in the context of pairwise (lines 678–710) and bulk fitness measurements (lines 711–728).

      Overall, this manuscript is a significant contribution to the field of evolutionary biology, addressing a critical issue in the quantification of fitness but lacks more experimental support to make it a wider claim. By systematically exploring the factors that influence fitness measurements, the authors provide valuable insights that can guide future research - the framework is computationally thorough but needs a more detailed explanation of concepts instead of generalizing.

      We have improved our explanation of several of the important concepts. In particular, we have significantly revised our explanation of the population dynamics model (lines 284–310) to emphasize its role as a null model to demonstrate how fundamental aspects of microbial growth are sufficient to cause discrepancies between fitness statistics. We have also revised two paragraphs on the generalizability of our results in the Discussion section (lines 678–728).

      Further work is needed, particularly to incorporate empirical examples and expand certain discussions to include environmental variation and their impact, which would improve clarity and applicability.

      We have added a sentence at the beginning of the Results section to acknowledge the environmental dependence of fitness (lines 142–148). We believe further discussion of that issue is beyond the scope of this paper, as it would require a significant amount of additional data and/or environmental modeling.

      Reviewer #2 (Recommendations for the authors):

      In addition to the comments from the previous sections, other specific comments:

      (1) Figure 5 needs to be populated with additional parameter details. For example, include brief descriptions of each parameter involved in the encoding, time scale, and reference choices. This will help users understand the implications of each choice. Adding these details will make the flow diagram more comprehensive, aiding researchers in implementing these steps more clearly.

      Following this comment and another comment about this figure from Reviewer #3, we decided to replace this figure with a new Methods section with step-by-step instructions (lines 964–982).

      (2) Duplication in Line 620: “Nevertheless, the fact that we see the fact that we see...” This redundancy needs to be corrected.

      We thank the reviewer for pointing this out; we have rewritten this paragraph.

      (3) More experimental data comparisons and their assessment concerning various microbial systems and multiple environmental conditions are recommended to support the claim.

      Please see our responses to the related public comments.

      Reviewer #3 (Public review):

      Summary:

      The authors present analyses of different fitness measures derived from empirical data from yeast knockout mutants and the long-term evolution experiment (LTEE) with Escherichia coli to explore discrepancies and identify preferred methods to estimate relative fitness in high-throughput experiments. Their work has three components. They first discuss the different “encodings” of relative abundance data and conclude that logit transformations are preferred because they transform nonlinear abundance trajectories into linear trajectories with greater predictive power. Next, they compare per-generation with per-growth cycle relative fitness estimates inferred from simulations of pairwise competitions based on published growth traits for the yeast strains and on published pairwise competition measurements for the LTEE data. Both data sets show quantitative and qualitative (i.e. rank order) discrepancies of estimates across different time scales, which are highlighted by considering possible underlying causes (i.e. trade-offs between growth traits) and consequences (i.e. epistasis among mutations affecting different growth traits). Finally, the authors compare simulated pairwise and bulk (i.e. where many mutants compete during a growth cycle in a single environment) competition assays based on the yeast knock-out mutants and demonstrate an optimal ratio of collective mutants to wild-type strains that minimizes both sampling error and overestimation of fitness estimates when compared with pairwise competitions.

      Strengths:

      The study deals with a highly relevant topic. Fitness is central to general evolutionary theory, but also poorly defined and implies different traits for different organisms and conditions. For microbes, which are often used in evolution experiments, high-throughput experiments may yield different measures to quantify abundance over time, from individual growth traits to bulk competition experiments. Hence, it is relevant to consider discrepancies among those measures and identify preferred measures with respect to predicting population dynamics and evolutionary processes. The present study contributes to this aim by (i) making readers aware of differences among commonly used fitness estimates, (ii) showing that simulated (yeast) and calculated (E. coli) competitive fitness may differ across time scales, and (iii) showing that bulk competitions may yield relative fitness estimates that are systematically higher than pairwise competitions. The study is rather thorough on the theory side, with extensive derivations and analyses of various fitness measures using their resource competition model in the Supplementary Information. The study ends with a few practical recommendations for preferred methods to infer relative fitness estimates, that may be useful for experimentalists and stimulate further investigations.

      Weaknesses:

      The study has several limitations. Perhaps the most apparent limitation is the lack of a clear answer to the question of which fitness measure is best “in the light of first principles”. The authors show clear discrepancies between fitness estimates across different time scales or using different reference genotypes in bulk competition and provide useful recommendations based on practical considerations (e.g. using pairwise competitions as the “golden standard”), but it remains unclear whether these measures provide the greatest value for the questions researchers may want to answer with them (e.g. predict shifts in genotype frequencies).

      We agree on the importance of considering the scientific questions researchers want to answer in determining the best way to quantify fitness. We have revised both the Introduction (lines 82–88) and the Discussion (lines 615–630) to more clearly explain possible downstream questions researchers may wish to answer with fitness data, and thus why discrepancies in that data based on analysis choices may be important.

      We believe that the text does provide a specific recommendation (second subsection of the Discussion, lines 635– 658) for how to quantify relative fitness: using the logit encoding (rather than other encodings), measuring fitness per-cycle (rather than per-generation), and using the wild-type or a phenotypically-equivalent proxy as reference subpopulation to calculate pairwise fitness in a bulk competition (rather than using the mutant library as a whole). This recommendation is based on first principles: the logit encoding is based on the principle of the logistic equation as the null model of relative abundance dynamics (lines 635–637), the choice of the per-cycle timescale is based on the principle that in non-steady state environments the time scale for measuring selection should not depend on the wild-type growth (lines 640–645), and the choice of reference population is based on the principle that a mutant’s fitness should serve as a predictor of its dynamics when arising de novo at low frequency and competing against its wild-type (lines 648–653).

      A second limitation is that the authors analyse fitness differences arising solely from resource competition, whereas microbes often interact via other mechanisms, e.g. the production of anticompetitor toxins, cross-feeding of metabolites, or lack of growth to enhance their persistence in stress conditions. Without simulations of these processes, understanding discrepancies among fitness measures is necessarily limited.

      We agree that other interactions are important in many microbial ecosystems and could affect measurements of fitness. We discuss the possibility of these other interactions and their potential consequences for fitness on lines 697– 710.

      We focus on resource competition in this paper, however, for two reasons. One is that we are using it as a null model: resource competition is always present, and thus it provides an important baseline for discrepancies in fitness statistics in the absence of any other assumptions. Indeed, our results are that this minimal assumption alone is sufficient to produce a wide range of significant discrepancies, which provides the proof of principle that choices of fitness quantification matter. We have clarified this in a revised explanation of the population dynamics model on lines 294–304.

      The second reason is that fitness measurements of the type discussed in this paper are typically performed on mutants that have only small genetic differences with their ancestor (e.g., a point mutation or gene deletion). While more complex interactions between such similar genotypes are not impossible, we expect them to be rare, in which case resource competition is the only interaction. Explicit modeling of other interactions is an important question for future work, but would require more detailed models and data of those phenomena, and thus would go beyond the scope of the present study. We have added a sentence to explain our emphasis on resource competition on lines 298–301 and 690–697.

      In addition, the analysis of trade-offs between growth traits causing these discrepancies during resource competition seems confounded by biases in measurement error or parameter estimation, at least for growth rate and lag time (Figure 2B), where the replicate estimates for the wildtype show a similar negative correlation.

      The tradeoff between growth traits was only an incidental observation and is not necessary for the fitness statistic discrepancies we analyze in this paper; the only important pattern in the growth traits is the existence of mutants with reduced yields (so as to reduce the wild-type log fold-change in a competition) as well as variation in one other trait under selection (lag time or growth rate in this model). We have clarified this mechanism on lines 328–336, which is demonstrated by Fig. S7. Since these tradeoffs are not relevant to the results and we agree that their significance may be unreliable due to the noisiness of the data, we have removed mention of them.

      Third, the study does not validate relative fitness predictions from growth traits (as is done for the yeast mutants) with measured relative fitness estimates using competition assays, while such data are available, e.g. for the LTEE. This would strengthen their inferences about preferred fitness measures.

      The goal of our modeling with the yeast growth trait data is not to test the ability to predict competition experiments from monoculture data; that has been the focus of previous studies [32, 34, 36, 37]. Rather, we use the population dynamics model for a proof of principle: that the most basic features of microbial population dynamics in laboratory experiments, as captured by this model (resource competition, lag phase, growth phase, saturation), are sufficient to create discrepancies between common fitness statistics used in these experiments (different encodings, time scales, choices of reference subpopulations). The yeast growth curve data merely provides realistic parameters for this model, to ensure we are studying a biologically relevant regime of the dynamics. To avoid this misconception, we have revised our explanation of this model and the data on lines 284–310.

      Fourth, the analysis of epistasis between mutations affecting different growth traits (shown in Figure 3) based on the LTEE data could be better introduced and analysed more comprehensively. Now, the examples given in panels C-F seem rather idiosyncratic and readers may wonder how general these consequences of using fitness estimates based on different time scales are.

      We agree that this analysis was incomplete and missed an opportunity to emphasize this important consequence of fitness quantification. We have thus expanded this analysis into a systematic test of all possible double mutants between qualitative types of trait perturbations in the model. We have added a new main text figure (Fig. 3), new SI figures (Figs. S9–S15), a new subsection in the Results (lines 346–395), and corresponding new sections in the Methods (lines 864–892) and SI (Sec. S8).

      Finally, the study is generally less accessible to experimentalists due to the extensive and principled treatment of specific population dynamic models and fitness inferences. This may distract from the overarching aim to identify fitness measures that are most accurate and useful for predictions of population dynamics and evolutionary processes.

      We appreciate this concern as we do hope to make the paper as broadly accessible as possible, especially to experimentalists who measure microbial fitness. To this end, we have reduced the technical discussion of encodings in the first section of the Results (lines 164–187); revised explanations of the population dynamics model (lines 284–310), importance of growth trait variation (lines 328–336), and epistasis (lines 346–395) to better emphasize the conceptual intuition of these parts; and added a step-by-step guide for our recommended best practices of quantifying fitness in bulk competition experiments (lines 964–982).

      In this light, the motivation for the initial discussion of the importance of how to best encode relative abundance (Figure 1) is unclear. Also, the conclusion, that logit encoding is preferred, because it linearizes logistic growth dynamics and “improves the quality of predictions”, is not further motivated. Experimentalists using non-linear models to infer fitness from growth curves or competition assays may miss the relevance of this discussion.

      The motivation for the discussion of encodings is that it is one of the choices made differently by researchers, mainly using either the logit (more common in experimental evolution and population genetics studies) or log encoding (more common in TnSeq analyses). As such we believe it is important to explain where this choice comes from (a transformation of relative abundance data to make it approximately linear in time, and thus amenable to characterization by a single slope parameter) and why we believe the logit encoding is more logical in most cases. We have streamlined and revised this subsection to make it clearer (lines 164–187).

      Our argument for favoring the logit encoding in most cases is based on the logistic model being a null model for relative abundance dynamics (Sec. S3). In light of the reviewer’s comments, we have realized this may be confusing because there are two common usages of logistic dynamics that are biologically distinct. What we mean by logistic model is the dynamics of relative abundance x of a mutant in competition with other genotypes:

      Here s turns out to be the relative fitness under the logit encoding. On the other hand, researchers also use a logistic ODE to describe the dynamics of absolute abundance N of a single strain in monoculture (e.g., as in a growth curve):

      We believe the reviewer’s last point refers to Eq. (2), whereas our argument about the logit encoding is based on Eq. (1). We have added a note to clarify this distinction for the reader (lines 192–196).

      Reviewer #3 (Recommendations for the authors):

      In addition to my general comments in the public review, I have several more specific recommendations:

      (1) Line 183-189: unclear why logit-based relative fitness is preferred. Abundance data are not typically binomial.

      We agree this claim about abundance data was incorrect and have removed it. We have revised the section to focus on motivating the logit encoding from logistic dynamics of relative abundance as a null model for most systems (main text lines 175–187 and Sec. S3).

      (2) Line 205: it may be mentioned that s(logit) is the same as the “selection rate constant” often used in microbial studies.

      We have added a sentence clarifying the equivalence of the logit-encoded relative fitness to the selection coefficient in population genetics (lines 188–190).

      (3) Line 368: why do mutations that increase biomass yield also increase WT LFC? Is this, because they grow slower and hence allow the WT more time to grow?

      Mutants with higher yield allow the wild-type to achieve higher log fold-change because those mutants consume fewer resources per cell, which frees up more resources for the wild-type to consume and increase its overall growth. It’s not about growth rate or time, as this would occur even for mutants whose growth rates are identical to the wild-type’s. We have revised our explanation of how variation in growth traits differentially affects fitness statistics (lines 323–340) and epistasis (lines 361–378).

      (4) Line 382-386: you may want to cite Ram et al. (2019, 10.1073/pnas.1902217116), who also did such analyses for experimental data from E. coli.

      We have cited this work as Ref. [34].

      (5) Line 415: perhaps use “bulk relative fitness” instead of “total relative fitness”, to contrast with “pairwise relative fitness”.

      We acknowledge the language in this section can be subtle. However, “bulk” is not a sufficient identifier for the concept of total relative fitness as bulk competition experiments (with many genotypes competing simultaneously) can be used to measure either total relative fitness or pairwise relative fitness. (In pairwise competition experiments with only two genotypes, these two types of fitness are identical.) As such we adhere to our original language but have added words to clarify which type of experiment (bulk or pairwise) we are talking about in a given context (e.g., on lines 495–504).

      (6) Line 451-453: why does a population in bulk competition consume resources more slowly than in pairwise competitions?

      Mutant libraries used in bulk competition experiments usually include a large number of deleterious mutants, which grow more slowly than the wild-type. Thus these populations typically consume resources more slowly than a population in a pairwise competition would, where a large part of the population is the wild-type.

      (7) Line 565: I don’t understand how one can compare relative fitness to other timescales.

      Relative fitness, as we’ve defined it, has units of rate, since it describes the rate of change of relative abundance (or an encoding of it) over some time scale (e.g., a batch growth cycle or a generation). Therefore it can be compared to other times scales of the system, such the rate of new mutations arising or the rate of genetic drift fluctuations, as long as they are measured in the same units. This comparison is important to population genetics analyses, such as determining whether the population is in the strong selection-weak mutation limit or the clonal interference regime.

      (8) Line 620 repeats text.

      Thank you, we have revised this paragraph and removed the typo.

      (9) Figure 1C+D: the link between the scenarios on the left and the graphs on the right may be better explained. For example, it may help to make explicit that the 4 scenarios in panel C show the same relative fitness per cycle and that mutant and wildtype have the same growth rate, but different growth periods in both scenarios in panel D. It is also unclear whether the grey dot links to the upper scenario in D.

      We have clarified this issue in the caption and changed the colors to avoid this confusion.

      (10) Figure 2E: it is unclear why “mutants with equal fitness are assigned the lowest rank”.

      This was a technical comment about how to handle ties in our analysis of mutant rankings, but it is moot since no exact ties actually occur in our simulations. We have removed this remark to avoid confusion.

      (11) Figure 2F: the axis labels are confusing, as for the WT estimates no LFC mutant exists. It would also help to make explicit in the legend against which WT replicate/reference strain each strain has competed.

      We agree the inclusion of wild-type replicates in this plot was confusing and unnecessary, so we have removed them. The mutants compete against a wild-type with traits defined by their median values across all wild-type replicates; this is noted in Fig. 2A and the Methods section on our analysis of this data (lines 809–813).

      (12) Figure 5: I am not sure this is needed, as its information is rather limited.

      We agree and have removed this figure.

    1. Author response:

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

      eLife Assessment

      This is a useful study presenting solid data indicating that the bacterial GTPases EngA and ObgE enable single-step reconstitution of functional 50S ribosomal subunits under near-physiological conditions. The study elegantly bridges the gap between the non-physiological aspects of the previous two-step reconstitution method and the extract-dependent iSAT system to enable ribosome assembly under translation-compatible conditions; however, it is limited by reliance on rRNA and proteins extracted from native ribosomes and does not achieve a true bottom-up reconstruction from all synthetic components. The evidence is incomplete in not characterizing the spectrum of reporter polypeptides produced and not comparing their rate and yield of synthesis from reconstituted ribosomes to that obtained with pure native ribosomes; and the impact of the study is limited by not including reporters to examine the fidelity of initiation, elongation or termination achieved with the reconstituted ribosomes.

      As described below, based on the comments from the public reviewers, we have summarized at the end of the Discussion how this study contributes toward true bottom-up reconstruction from fully synthetic components, as well as the aspects that will require further development. In addition, we have newly provided data characterizing the reporter polypeptides from multiple perspectives, demonstrating that the assembled ribosomes do not exhibit issues such as reduced fidelity (Fig. 6, 7, Supplementary Data 2, 3). We believe that these data adequately address the limitations that were pointed out in the eLife Assessment.

      Public Reviews:

      Reviewer #1 (Public review):

      This study presents evidence that the addition of the two GTPases EngA and ObgE to reactions comprised of rRNAs and total ribosomal proteins purified from native bacterial ribosomes can bypass the requirements for non-physiological temperature shifts and Mg+2 ion concentrations for in vitro reconstitution of functional E. coli ribosomes.

      Strengths:

      This advance allows ribosome reconstitution in a fully reconstituted protein synthesis system containing individually purified recombinant translation factors, with the reconstituted ribosomes substituting for native purified ribosomes to support protein synthesis. This work potentially represents an important development in the long-term effort to produce synthetic cells.

      Weaknesses:

      While much of the evidence is solid, the analysis is incomplete in certain respects that detract from the scientific quality and significance of the findings:

      (1) The authors do not describe how the native ribosomal proteins (RPs) were purified, and it is unclear whether all subassemblies of RPs have been disrupted in the purification procedure. If not, additional chaperones might be required beyond the two GTPases described here for functional ribosome assembly from individual RPs.

      Native ribosomal proteins (RPs) were prepared from native ribosomes, according to the well-established protocol described by Dr. Knud H. Nierhaus [Nierhaus, K. H. Reconstitution of ribosomes in Ribosomes and protein synthesis: A Practical Approach (Spedding G. eds.) 161-189, IRL Press at Oxford University Press, New York (1990)]. In this method, ribosome proteins are subjected to dialysis in 6 M urea buffer, a strong denaturing condition that may completely disrupt ribosomal structure and dissociate all ribosomal protein subassemblies. To make this point clear, we described the detailed ribosomal protein (RP) preparation procedure in the manuscript, rather than merely referring to the book.

      In addition, we would like to clarify one point related to this comment. The focus of the present study is to show that the presence of two factors is required for single-step ribosome reconstitution under translation-compatible, cell-free conditions. We do not intend to claim that these two factors are absolutely sufficient for ribosome reconstitution. Hence, we have revised the manuscript to more explicitly state what this work does and does not conclude.

      (2) Reconstitution studies in the past have succeeded by using all recombinant, individually purified RPs, which would clearly address the issue in the preceding comment and also eliminate the possibility that an unknown ribosome assembly factor that co-purifies with native ribosomes has been added to the reconstitution reactions along with the RPs.

      As noted in the response to the Comment (1), the focus of the present study is the requirement of the two factors for functional ribosome assembly. Therefore, we consider that it is not necessary to completely exclude the possibility that unknown ribosome assembly factors are present in the RP preparation. Nevertheless, we agree that it is important to clarify what factors, if any, are co-present in the RP fraction. To address this, we performed proteomic analysis of the TP70 preparation (Supplementary Data 3) and stated the possibility of other factors’ inclusion.

      We also agree that additional, as-yet-unidentified components, including factors involved in rRNA modification, could plausibly further improve assembly efficiency. We also consider that such studies may contribute to extending the system to the use of in vitro-transcribed rRNA and fully recombinant ribosomal proteins, which could be essentially a next step of this study. We noted the possibility of as-yet-unidentified components and the future perspectives in the Discussion.

      (3) They never compared the efficiency of the reconstituted ribosomes to native ribosomes added to the "PURE" in vitro protein synthesis system, making it unclear what proportion of the reconstituted ribosomes are functional, and how protein yield per mRNA molecule compares to that given by the PURE system programmed with purified native ribosomes.

      According to this suggestion, we measured the sfGFP synthesis rate from the increase in fluorescence over time under conditions where the template mRNA is in excess, and compared this rate directly between reconstituted and native ribosomes. We consider that this comparison provides insight into what fraction of ribosomes reconstituted in our system are functionally active (Fig. 6).

      As noted in the provisional responses, quantifying protein yield per mRNA molecule is substantially more challenging. The translation system is complex, and the apparent yield per mRNA can vary depending on factors such as differences in polysome formation efficiency. In addition, the PURE system is a coupled transcription–translation setup that starts from DNA templates, which further complicates rigorous normalization on a per-mRNA basis. Because the main focus of this study is to determine how many functionally active ribosomes can be reconstituted under translation-compatible conditions, we addressed this comment by just carrying out the experiment comparing sfGFP synthesis rate.

      (4) They also have not examined the synthesized GFP protein by SDS-PAGE to determine what proportion is full-length.

      We have added an affinity tag to the sfGFP reporter, and then, purified the synthesized products from the reaction mixture and analyzed it by SDS–PAGE (Fig. 7a).

      (5) The previous development of the PURE system included examinations of the synthesis of multiple proteins, one of which was an enzyme whose specific activity could be compared to that of the native enzyme. This would be a significant improvement to the current study. They could also have programmed the translation reactions containing reconstituted ribosomes with (i) total native mRNA and compared the products in SDS-PAGE to those obtained with the control PURE system containing native ribosomes; (ii) with specifc reporter mRNAs designed to examine dependence on a Shine-Dalgarno sequence and the impact of an in-frame stop codon in prematurely terminating translation to assess the fidelity of initiation and termination events; and (iii) an mRNA with a programmed frameshift site to assess elongation fidelity displayed by their reconstituted ribosomes.

      Following the recommendation, we selected DHFR as an enzymatically active protein and used it as a reporter, confirming that it exhibited enzymatic activity comparable to that observed when synthesized by native ribosomes (Fig. 7c). In addition, MS analysis of the purified sfGFP used for SDS-PAGE analysis showed that nearly all peptide fragments were detected, covering almost the entire sequence from the initiator amino acid to the amino acid immediately preceding the stop codon (Fig. 7b, Supplementary Data 2. These results suggest that protein synthesis by the newly assembled ribosomes proceeds smoothly from initiation to termination, with no apparent problem in fidelity, and therefore indicate that functional ribosomes were successfully reconstituted.

      Reviewer #2 (Public review):

      This study presents a significant advance in the field of in vitro ribosome assembly by demonstrating that the bacterial GTPases EngA and ObgE enable single-step reconstitution of functional 50S ribosomal subunits under near-physiological conditions-specifically at 37 {degree sign}C and with total Mg<sup>2+</sup> concentrations below 10 mM.

      This achievement directly addresses a long-standing limitation of the traditional two-step in vitro assembly protocol (Nierhaus & Dohme, PNAS 1974), which requires non-physiological temperatures (44-50 {degree sign}C), and high Mg<sup>2+</sup> concentrations (~20 mM). Inspired by the integrated Synthesis, Assembly, and Translation (iSAT) platform (Jewett et al., Mol Syst Biol 2013), leveraging E. coli S150 crude extract, which supplies essential assembly factors, the authors hypothesize that specific ribosome biogenesis factors-particularly GTPases present in such extracts-may be responsible for enabling assembly under mild conditions. Through systematic screening, they identify EngA and ObgE as the minimal pair sufficient to replace the need for temperature and Mg<sup>2+</sup> shifts when using phenol-extracted (i.e., mature, modified) rRNA and purified TP70 proteins.

      However, several important concerns remain:

      (1) Dependence on Native rRNA Limits Generalizability

      The current system relies on rRNA extracted from native ribosomes via phenol, which retains natural post-transcriptional modifications. As the authors note (lines 302-304), attempts to assemble active 50S subunits using in vitro transcribed rRNA, even in the presence of EngA and ObgE, failed. This contrasts with iSAT, where in vitro transcribed rRNA can yield functional (though reduced-activity, ~20% of native) ribosomes, presumably due to the presence of rRNA modification enzymes and additional chaperones in the S150 extract. Thus, while this study successfully isolates two key GTPase factors that mimic part of iSAT's functionality, it does not fully recapitulate iSAT's capacity for de novo assembly from unmodified RNA. The manuscript should clarify that the in vitro assembly demonstrated here is contingent on using native rRNA and does not yet achieve true bottom-up reconstruction from synthetic parts. Moreover, given iSAT's success with transcribed rRNA, could a similar systematic omission approach (e.g., adding individual factors) help identify the additional components required to support unmodified rRNA folding?

      We fully recognize the reviewer’s point that our current system has not yet achieved a true bottom-up reconstruction. Although we intended to state this clearly in the manuscript, the fact that this concern remains indicates that our description was not sufficiently explicit. We therefore added the paragraph to ensure that this limitation is clearly communicated to readers.

      (2) Imprecise Use of "Physiological Mg<sup>2+</sup> Concentration"

      The abstract states that assembly occurs at "physiological Mg<sup>2+</sup> concentration" (<10 mM). However, while this total Mg<sup>2+</sup> level aligns with optimized in vitro translation buffers (e.g., in PURE or iSAT systems), it exceeds estimates of free cytosolic [Mg<sup>2+</sup>] in E. coli (~1-2 mM). The authors should clarify that they refer to total Mg<sup>2+</sup> concentrations compatible with cell-free protein synthesis, not necessarily intracellular free ion levels, to avoid misleading readers about true physiological relevance.

      We agree that this is a very reasonable point and revised the manuscript to clarify that we are referring to the total Mg<sup>2+</sup> concentration compatible with cell-free protein synthesis, rather than the intracellular free Mg<sup>2+</sup> level under physiological conditions. We also changed the term “physiological” to “near-physiological” to avoid the misunderstanding.

      In summary, this work elegantly bridges the gap between the two-step method and the extract-dependent iSAT system by identifying two defined GTPases that capture a core functionality of cellular extracts: enabling ribosome assembly under translation-compatible conditions. However, the reliance on native rRNA underscores that additional factors - likely present in iSAT's S150 extract - are still needed for full de novo reconstitution from unmodified transcripts. Future work combining the precision of this defined system with the completeness of iSAT may ultimately realize truly autonomous synthetic ribosome biogenesis.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Recommendations for improvement:

      (1) Assess the length distribution of GFP polypeptides being produced using SDS-PAGE.

      SDS-PAGE was performed according to the comment 4 of the Reviewer #1 (Fig. 7b). Please refer to our response addressing the comment.

      (2) Compare the rate and yield of GFP synthesized per mRNA using their reconstituted ribosomes to that obtained with pure native ribosomes.

      The efficiency of the reconstituted ribosomes was compared to native ribosomes according to the comment 3 of the Reviewer #1 (Fig. 6). Please refer to our response addressing the comment.

      (3) Expand the panel of reporter mRNAs being examined to compare the fidelity of initiation, elongation or termination achieved with reconstituted ribosomes to that obtained using native ribosomes.

      DHFR synthesis was addressed and also MS analysis of synthesized sfGFP was performed according to the comment 5 of the Reviewer #1 (Fig. 7b, c). Please refer to our response addressing the comment.

      (4) Revise the manuscript to clarify that the in vitro assembly demonstrated here is contingent on using native rRNA and thus does not achieve a true bottom-up reconstruction from synthetic parts.

      We added to the Discussion a paragraph summarizing the findings of this study, limitations, and future perspectives according to the comment 1 and 2 of the Reviewer #1 and the comment 1 of the Reviewer #2. Please refer to our responses addressing these comments.

      (5) Revise the manuscript to clarify that they are referring to total Mg2+ concentrations compatible with cell-free protein synthesis, not necessarily intracellular free ion levels, to avoid misleading readers about the physiological relevance of the reconstitution.

      We revised the manuscript to clarify this point according to the comment 2 of the Reviewer #2. Please refer to our response addressing the comment.

      (6) Revise the text to fully describe how the native ribosomal proteins (RPs) were purified and indicate whether all subassemblies of RPs were disrupted in the purification procedure.

      We revised the Methods section to clarify how the native RPs were purified and that all subassemblies of RPs were disrupted according to the comment 1 of the Reviewer #1.

      (7) Revise the text to indicate that achieving ribosome reconstitutions using all recombinant, individually purified RPs is required to achieve a true bottom-up reconstruction from all synthetic components.

      As with our response to the comment 4, we have added the point at the end of the Discussion as a future perspective toward true bottom-up reconstruction from all synthetic components.

      (8) Consider conducting a similar systematic omission approach (e.g., adding individual factors) to help identify the additional components required to support unmodified rRNA folding.

      As with our response to the comment 4 and 7, we have added the point at the end of the Discussion as a future perspective toward identification of additional essential factors for true bottom-up reconstruction.

      Reviewer #1 (Recommendations for the authors):

      (1) Assessing the spectrum of GFP polypeptides being produced by SDS-PAGE and comparing the rate and yield of GFP produced to that obtained with pure native ribosomes would seem to be essential additional measurements needed to bolster the evidence supporting the main conclusions of the work.

      SDS-PAGE and MS analysis of the synthesized sfGFP were performed (Fig. 7a, b). Comparison of the assembled ribosomes and native ones were also performed (Fig. 6).

      (2) Examining translation of other reporter mRNAs designed to compare the fidelity of initiation, elongation or termination achieved with reconstituted ribosomes to that produced by native ribosomes in the PURE system would be required to elevate the scientific quality of the work and its significance to the field.

      DHFR synthesis and its activity measurement were performed (Fig. 7c). Also, MS analysis of the purified sfGFP showed that nearly all peptide fragments were detected, covering almost the entire sequence from the initiator amino acid to the amino acid immediately preceding the stop codon (Fig. 7b). We consider that these findings indicate that there is no apparent problem with fidelity.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This is an important study that describes the consequences of the DNMT3A mutation in human neuronal development for the first time. The selective impact of DNMT3A function on GABAergic interneurons is interesting and an important feature of future therapeutics. The claims made in that manuscript are supported by strong evidence for the most part. And the data are of high quality in general and presented well.

      Strengths:

      The strengths of the work include: Characterization of multiple DNMT3A loss-of-function alleles, including two misense variants, R882H, P904L, and a deletion allele. The missense mutation lines both include an ideal control with the same genetic background. The CRISPRi-mediated DNMT3A knockdown has also been included. The study identifies the mTOR-PI3K pathway as a factor of overgrowth issues found in the mutant organoid. In bulk mRNA sequencing and whole-genome bisulfite sequencing, identify hypomethylated genomic regions associated with gene expression repression. Again, this is more pronounced in the ventral organoid compared to the dorsal organoid. In addition, the extensive electrophysiological characterizations with a high-density microelectrode array support the more mature status of mutant interneurons.

      Weaknesses:

      Although a strong study overall, some weaknesses are noted. These include:

      (1) The lack of validation data for the generated iPSCs and hESCs, such as the chromosomal contents, ploidy, and pluripotency states.

      We thank the reviewer for their constructive feedback. We previously validated our 882 models with whole genome sequencing and teratoma formation upon mouse fat pad injection, while the parental human embryonic stem cell line (WA01 hESCs) used for P904L variant knock-in was validated by our Genome Engineering Stem Cell (GESC) core upon derivation of that variant knock-in model. We have now added both karyotyping and pluripotency staining (SOX2/OCT4) for all other hPSC lines as (new) Supplementary Figure S17 and included further description in our Methods section under “hPSC Model Generation and Culture”.

      New Data: Supplemental Figure S17 (SOX2/OCT4 staining in hPSCs and karyotyping of all lines used)

      Text edits: Additional language confirming hPSC line validation will be added to the Methods section under “hPSC Model Generation and Culture” on page 18.

      (2) Other weaknesses relate to data interpretation and insufficient discussion of related matters, as detailed in the recommendations to the authors.

      We thank the reviewer for their insightful suggestions and have detailed our responses in the “recommendations to the authors” section.

      (3) Also, some errors are noted and detailed in the recommendation section.

      We thank the reviewer for catching these errors and have since corrected them, with detailed responses below.

      Reviewer #2 (Public review):

      Summary:

      Chapman, Determan et al. investigate how pathogenic mutations in DNMT3A, which cause Tatton-Brown-Rahman Syndrome (TBRS), disrupt human cortical developmental processes using a comprehensive panel of human pluripotent stem cell models spanning DNMT3A loss-of-function severity. The authors aim to identify the cellular and molecular mechanisms underlying TBRS-associated brain overgrowth and intellectual disability, and to test whether mechanistic convergence exists between TBRS and other overgrowth-intellectual disability disorders (OGIDs) caused by mutations in EZH2 (Weaver syndrome) or PIK3CA pathway components. Their central conclusion is that GABAergic interneuron development is selectively vulnerable to DNMT3A mutation, where reduced DNA methylation causes premature de-repression of neuronal and synaptic genes, driving precocious neuronal maturation and hyperactivity sufficient to disrupt neuronal network synchrony. This report adds to a growing literature supporting the vulnerability of GABAergic interneurons in NDDs and further provides a mechanistic view of this vulnerability, potentially convergent across OGIDs. The mechanistic claims around H3K27me3 compensation and mTOR-based therapeutic convergence, while promising, rest on more preliminary evidence and would benefit from the distinction between correlation and mechanism being made more explicit in the text. Overall, this is a compelling study with a rigorous experimental design and novel findings with a potential impact on a better understanding of the OGID pathophysiology.

      Strengths:

      (1) A major strength of this work is the breadth and rigor of the disease modeling approach. Four independent TBRS model systems are used in tandem: a patient-derived iPSC line with isogenic CRISPR-corrected control (R882H), a knock-in hESC model (P904L) with its wild-type isogenic, patient deletion iPSC lines (Del1/2), and CRISPRi knockdown models (G1/G2), collectively spanning a range of DNMT3A loss-of-function that correlates with phenotypic severity. This allelic series design substantially strengthens causal inference beyond what any single isogenic pair could provide.

      (2) The multi-omic integration across matched developmental stages provides a strong mechanistic foundation for the cellular phenotyping and provides significantly enhanced novelty. RNA-seq, whole-genome bisulfite sequencing, and H3K27me3 CUT&Tag are combined in the same cell types, and timepoints show that DNMT3A loss reduces CG methylation at neuronal and synaptic gene loci, leading to premature transcriptional activation.

      (3) The selective vulnerability of ventral (GABAergic) versus dorsal (glutamatergic) progenitors is one of the study's most important findings. This lineage specificity is consistently observed across all model systems and in both 2D and organoid formats, where ventral NPCs show increased proliferation, premature neuronal gene expression, and increased neurogenesis, while dorsal NPCs are largely unaffected at the transcriptomic and cellular level despite exhibiting comparable DNA methylation changes. This adds to a body of emerging work showing GABAergic interneuron vulnerability in NDDs where ubiquitously expressed genes such as chromatin modifiers are perturbed, and provides additional molecular insights into potential mechanisms of "resilience" of dorsal populations.

      (4) The functional characterization follows a logical progression from single-neuron electrophysiology (demonstrating GABAergic hyperactivity with increased action potential amplitude and firing rate) to network-level analysis using high-density multi-electrode arrays. The HD-MEA experimental design - pairing TBRS or control GABAergic neurons with a constant background of control iGlut neurons - cleanly isolates GABAergic dysfunction as the driver of network hypersynchrony.

      Weaknesses:

      (1) The concomitant induction of proliferation and differentiation in TBRS V-NPCs is conceptually striking, since these are generally considered antagonistic developmental programs. The authors partially address this tension by noting that DNMT3A LOF alone is insufficient to initiate neuronal differentiation, i.e., V-NPCs upregulate neuronal and synaptic genes while retaining progenitor identity, implying that transcriptomic priming and commitment to differentiation are decoupled. However, the relationship between the proliferative phenotype and the epigenetic priming phenotype remains mechanistically unresolved. The manuscript documents mTOR pathway upregulation at the protein level and identifies shared DEGs that include proliferative regulators, but it does not establish whether mTOR-driven proliferation and mCG-loss-driven neuronal gene de-repression/enhanced differentiation are causally linked or represent two independent consequences of DNMT3A LOF.

      We thank the reviewer for their comment and agree that this phenotype, whereby progenitors exhibited both increased proliferation and hallmarks of gene expression associated with neuronal differentiation is striking and interesting, given that these are typically antagonistic paradigms during normal development.

      We documented that these phenotypes involve upregulated expression of both neuronal/synaptic and proliferative genes in V-NPCs (Figure 2d), with concomitant loss of repressive DNA methylation at regulatory elements associated with these genes (Figure 2f, Supplemental Data 5). In this work, DNMT3A mutation had a more prominent role in de-repressing neuronal and synaptic gene expression to promote hallmarks of neuron differentiation, while playing a relatively less central role in direct regulation of proliferation genes, as seen from the relative prominence of neuronal/synaptic- versus proliferation-related GO terms in our Supplemental Data 5 table.

      To examine the mechanisms underlying increased V-NPC proliferation in our TBRS models, we assessed a potential relationship with the PIK3/AKT/mTOR pathway, as this is implicated in increased proliferation resulting from DNMT3A-associated mutation in myeloid leukemia (Dai et al., 2017, PMID: 28461508). In our work, DNMT3A mutation increased the expression and/or phosphorylation of mTOR signaling pathway targets specifically in V-NPCs (Figure 1q-r, Supplemental Figure S3a-d). However, while TBRS mutation directly affected repressive DNA methylation at a suite of cell proliferation-related genes, these did not include the PIK3/AKT/mTOR pathway genes themselves, suggesting an indirect relationship between altered DNA methylation and increased mTOR signaling.

      Text Edits: We will incorporate further discussion of how DNMT3A-mediated gene repression and levels of PIK3/AKT/mTOR pathway signaling may be interacting, providing a framework for future studies to identify how these related OGID gene mutations may converge mechanistically.

      (2) Relatedly, the rapamycin rescue experiment is a valuable proof-of-concept for the PIK3/AKT/mTOR convergence but is limited to a single dose in a single model (882) with a single readout (Ki67+ proliferation). Given the prominence of mTOR pathway convergence in the manuscript as a potential shared therapeutic avenue across OGIDs, the data supporting this claim are somewhat preliminary. It remains unknown whether mTOR inhibition rescues downstream phenotypes (neurogenesis, gene expression, neuronal maturation) or whether less severe TBRS models respond similarly. This might also help tackle the first comment above. e.g., if mTOR inhibition rescued proliferation but not the transcriptomic priming, that would support two independent mechanisms.

      We thank the reviewer for their comment. We explored both the overall levels and phosphorylation of proteins involved in PIK3/AKT/mTOR signaling in the 882, 904, Del1, Del2, and KO V-NPC models (Figure 1q-r, Supplementary Figure S3a-d), finding specific increases of all proteins. We showed that rapamycin addition reversed the increased proportion of KI67+ proliferating cell nuclei resulting from 882 mutation in V-NPCs in main Figure 1s, while demonstrating that rapamycin also reduced the proportion of KI67+ nuclei observed in both less severe 904 and Del1 V-NPC models (Supplementary Figure S3e-f).

      We agree that understanding whether rapamycin treatment can rescue TBRS neuronal phenotypes would be very interesting, as previous work on Tuberous Sclerosis Complex has utilized rapamycin and other mTOR inhibitors to effectively reverse TSC-related alterations of neuronal morphology and neuronal hyperexcitability (Buttermore et al., 2025, PMID: 40792287). Future studies examining convergent mechanisms and therapeutics for OGIDs should examine how similarly targeting this and related pathways rescues altered neuronal morphology, maturation, and function, as we have demonstrated that TBRS mutation has subsequent consequences for V-IN differentiation, maturation, and function. This point has been detailed in the discussion section on pages 15-16.

      (3) The claim that H3K27me3 compensates for mCG loss is an important mechanistic point, but the current data do not distinguish between active compensation, in which EZH2 is recruited in response to methylation loss, and functional redundancy, in which H3K27me3 is independently established and becomes the dominant repressive mark once DNA methylation is reduced. The EZH2 knockdown/inhibition experiments show that H3K27me3 is sufficient to maintain repression at hypo-DMR sites, but they do not establish that H3K27me3 gain is itself a response to methylation loss. Because H3K27me3 profiling was performed only in the severe 882 model, it is also unclear whether H3K27me3 gain scales with DNMT3A LOF severity, as a compensatory model would predict. Finally, the EZH2 overexpression rescue is performed in V-NPCs, whereas the compensation model is developed primarily in D-NPCs, making it difficult to assess whether the same mechanism operates in the lineage where it was originally inferred.

      We thank the reviewer for the opportunity to clarify our findings and experimental reasoning. A previous study using a conditional Dnmt3a knockout mouse model (Li et al., 2022, PMID: 35604009) demonstrated increased expression of multiple PRC2 components following the loss of Dnmt3a. This study demonstrated that sites which lost DNA methylation gained H3K27me3 in postnatal neurons upon Dnmt3a loss. Therefore, we hypothesize that the gain of H3K27me3 likely occurs in response to loss of DNMT3A methylation.

      While we did not perform CUT&Tag for H3K27me3 in our less severe models, we did validate gene expression changes following EZH2 knockdown and inhibition in both the R882H (Figure 4g-h) and P904L (Supplementary Figure S8b) models, finding that gene expression was unchanged in the model with the less severe DNMT3A mutation (P904L). Based upon these findings, we hypothesized that compensatory H3K27me3 may occur only upon severe DNMT3A loss, as seen in the dominant-negative R882H model. Furthermore, as H3K27me3 compensation was more prominent in D-NPCs, we hypothesized that this might be sufficient to prevent de-repression and aberrant neuronal gene repression upon loss of DNMT3A-mediated repression in D-NPCs. However, since TBRS mutation caused the most prominent de-repression of neuronal gene expression in V-NPCs, we also tested whether EZH2 overexpression could reverse this, finding that it partially suppressed this dysregulated neuronal gene expression. To better clarify this logic and the findings, we will make text edits to this results section.

      Text edits: We will clarify the reasoning for performing the EZH2 overexpression experiments in V-NPCs and reference Li et al., 2022 in both the results (pg. 9-10) and discussion.

      (4) The narrative framing of dorsal neuron development as unaffected by DNMT3A LOF is somewhat at odds with the data presented. The 882 D-NPCs show substantial DNA methylation changes, and TBRS D-INs exhibit what the authors describe as "substantive transcriptomic differences" involving persistent expression of pluripotency and progenitor genes, which seems to be a distinct but potentially significant phenotype. The impact of DNMT3A loss between ventral and dorsal lineages might be more accurately framed as divergent in nature rather than specific to a certain population.

      We thank the reviewer for their comment. While TBRS mutations appear to have a significantly stronger effect on V-NPCs and subsequently V-INs, both transcriptomic and methylation alterations do also occur upon TBRS mutation in D-NPCs and D-INs, as noted in Supplemental Figure S4d, S11, and Supplemental Data 2. However, we observed substantially greater molecular alterations in V-NPCs/V-INs, a lack of overt cellular phenotypes in D-NPCs where assayed, and a lack of functional consequences in matured D-INs, suggesting a more significant requirement for DNMT3A in regulating the differentiation and subsequent maturation of cortical inhibitory interneurons during embryonic and early pre-natal development, the developmental periods that we can readily model in hPSC-derived neurons.

      It should also be noted that these hPSC differentiation models do not recapitulate post-natal deposition of non-CpG (mCA) DNA methylation, a mechanism disrupted postnatally by TBRS-associated mutations in our prior work in murine models (Harrison Gabel; e.g. Beard et al., 2023, PMID: 37952155). Therefore, we hypothesize that if we could sufficiently mature D-INs to a state that modeled postnatal development and recapitulated this non-CpG methylation, we might be able to detect cellular and functional phenotypes in later stage D-INs. To avoid misinterpretation, we will alter the language in the results section to confirm that there are both transcriptomic and methylation changes in our D-NPCs/D-INs, but that these are not accompanied by cellular phenotypes or neuronal dysfunction.

      Text edits: We will better clarify that there are transcriptomic and methylation changes in D-NPCs/D-INs, but that these changes are minimal compared to those in V-NPCs/V-INs, as supported by the lack of cellular and functional phenotypes seen in D-NPCs/D-INs.

      (5) SST stainings are not entirely convincing. They appear mostly nuclear, and some instances localized to rosettes in organoids, whereas the protein is largely confined to processes and is expected to be found outside progenitor-rich zones like rosettes.

      We agree that the perinuclear SST staining detected in these young ventral telencephalic-patterned organoids at day 30 differs somewhat from the more process-localized and cytosolic signal seen in later stage organoids in other studies. This may be related to the use of different commercial SST antibodies across studies but also likely reflects SST immunoreactivity in newborn neurons near the onset of SST expression. For example, immature SST-immunoreactive neurons in the early postnatal rat cortex exhibit predominant SST staining in perinuclear cytoplasm and short processes (e.g. Fig. 3 in Lee et al, PMID: 9664223) while acquiring more cytosolic and process-localized staining as postnatal neuron maturation occurs. Evaluation of immunopositivity for other markers of neurogenesis (ASCL1) and immature neurons (TUJ1) is also congruent with these findings for SST, with TBRS-associated mutations increasing in the fraction of cells in V-NPCs/V-ORGs that express these three markers.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, the authors investigated TBRS etiology by using new human pluripotent stem cell models, modeling varying levels of TBRS-associated loss of DNMT3A function. They identified increased lineage-specific proliferation of precursors in TBRS ventral MGE-like progenitors, which they propose was related to increased signaling through the PIK3/AKT/mTOR pathway. Furthermore, they show that reduced DNA methylation during MGE-like progenitor differentiation into GABAergic interneurons can cause a premature expression of neuronal and synaptic genes, triggering precocious neuronal maturation. In conclusion, they propose that TBRS-derived GABAergic neurons exhibit hyperactivity that can alters the development and structure of neuronal networks.

      Strengths:

      Overall, the data presented is convincing, from an early developmental point of view, given that the iPSC-derived 2D cultures or organoids used do not get to reach a mature state. Nonetheless, the data clearly show the effects that deleterious mutations in TBRS can cause during the period of neurogenesis, which was missing in the field.

      Weaknesses:

      (1) Li et al., 2022 (referred to in the manuscript) seems to already show the interplay between H3K27me3 and Dnmt3a discussed in this study i.e., that in the absence of DNA methylation, there is an expansion of polycomb-like repression. These data should be better acknowledged in the paragraph 'Repressive H3K27me3 compensates for severe loss of DNA methylation' (page 9), given it supports the data presented in this manuscript and suggests this as a common mechanism in the interplay between these two repressive marks, as it is well established in the literature.

      We thank the reviewer for this suggestion and will incorporate this reference into both the results and the discussion when discussing the respective roles of DNMT3A and PCR2-mediated repression.

      Text edits: We will add Li et al., 2022 to both the results section (pg. 9-10) and our discussion section.

      (2) The authors should acknowledge that the omics data come from a mixed population of cells.

      We thank the reviewer for their comment. We have validated that the established 2-D differentiation methods we used in this study generate cell populations with >85-90% enrichment for the desired progenitor and neuronal cell type, based upon marker expression, but acknowledge that these are bulk -omics data obtained from cells that may represent a mixed population and have now detailed this in the methods section under “Sequencing”.

      Text edits: we will add language acknowledging that our omics data (bulk) was generated from mixed populations of cells.

      (3) The authors are encouraged to further discuss whether the overgrowth observed in ventral GABAergic cultures or organoids compares to the overgrowth observed in diseased patients. One expects MRIs to have been performed in patients and that these could be harnessed to discern if overgrowth occurs in the cortex or ventral regions of the brain.

      We thank the reviewer for their suggestion and do note that at least one published study documents increased cortical thickness in the MRIs of TBRS patients (Jiménez de la Peña et al., 2024, PMID: 37795572); however, to our knowledge studies have not examined regional or cell type-selective overgrowth of cortical tissue in TBRS patients. Future clinical studies examining the nature of the neuronal progenitor overgrowth and resulting consequences for patient brain imaging would be of interest to better understand TBRS-associated etiology of brain overgrowth and its manifestations.

    1. Author response:

      We sincerely appreciate the efforts of the Senior and Reviewing Editors, as well as the three reviewers, for their careful evaluation of our manuscript and their insightful comments. Previous studies have suggested that smooth muscle activity contributes to gut elongation; however, these studies do not directly demonstrate that peristaltic movements per se drive elongation. For example, studies in mouse have primarily focused on residual stress of smooth muscle (Yang et al., 2021), rather than the dynamic spatiotemporal nature of peristalsis. In chickens, inhibition of peristalsis by nifedipine has been interpreted as evidence for a role of peristalsis in gut elongation (Khalipina et al., 2019). However, because nifedipine broadly affects calcium-dependent cellular processes, these experiments cannot distinguish whether the observed effects arise specifically from loss of peristalsis or from other cellular perturbations. In our current study, we aimed to challenge this limitation by combining pharmacological inhibition with optogenetic reactivation. This approach allows us to selectively restore peristaltic movements under conditions in which endogenous peristalsis are suppressed. Based on these experiments, we provide evidence supporting a causal contribution of peristalsis to the anisotropic gut growth. We agree with the reviewers that the positioning of our study relative to previous work should be clarified. In a revised manuscript, we will more clearly distinguish between static mechanical tension and endogenous peristaltic movements, and better define the conceptual advance of our study. In addition to macroscopic growth analysis, we identified cellular dynamics associated with elongation, including circumferentially oriented cell division and peristalsis-dependent longitudinal cell rearrangement. We agree that the mechanistic link between peristalsis and downstream cellular behaviors remains incompletely understood. In the revised manuscript, we will clarify this limitation and outline future directions, including experiments to test the role of mechanical cues (e.g., mechanical perturbation and pharmacological manipulation of mechanotransduction pathways).

      Public Reviews:

      Reviewer #1 (Public review):

      The mechanism by which peristalsis and the cell rearrangement are mediated

      We appreciate this important point. As suggested, the possibility that mechanical aspects of peristalsis contribute to the gut elongation is highly plausible. To address this, we plan to perform additional experiments aimed at isolating the mechanical component of peristalsis. Furthermore, we will investigate the involvement of mechanotransduction pathways, including Piezo-mediated pathway, using pharmacological approaches. We will revise the manuscript to better discuss these possibilities and clarify the current limitations of our study.

      The novelty and positioning of our study

      We appreciate this comment and have addressed this point in the General response above. In the revised manuscript, we will more clearly position our study relative to the previous studies.

      Reviewer #2 (Public review):

      Longitudinal separation of daughter cells even without peristalsis

      We appreciate this insightful and important comment. As noted, daughter cells can exhibit longitudinal separation even under nifedipine treatment, whereas the divergence index (DI) shows a clear increase only in the control (with peristalsis) condition. We interpret this as follows; immediately after cell division, two daughter cells occupy nearly identical positions along the longitudinal axis, and stochastic fluctuations may cause them to separate each other. Such local separation does not necessarily reflect population-level cell rearrangement. In contrast, DI captures collective dispersion of a cell population, which reflects organized tissue-level rearrangement associated with elongation. We will revise the manuscript to clarify this distinction between local cell behavior and population-level dynamics, and to better explain how DI reflects elongation-related processes.

      Contributions from other gut layers and ECMs

      We agree that contributions from other tissue layers and extracellular matrix (ECM) components might be important. To address this, we plan additional experiments including targeted ablation of specific tissue layers and pharmacological manipulation of ECM remodeling (e.g., using MMP modulators). We will also expand the Discussion to better acknowledge these factors.

      Reviewer #3 (Public review):

      (1) We agree that experiments based solely on nifedipine treatment cannot fully exclude potential off-target effects. To address this limitation, we plan to perform additional experiments that rescue the mis-rearrangement of cells by applying mechanical forces.

      (2) We agree that more elaborate analyses of cell proliferation and apoptosis are needed. In the revised manuscript, we will incorporate additional analyses using appropriate markers and methods suitable for developing gut tissue.

      (3) In Figure 2, we had already shown an increased the frequency of peristaltic contractions (30 s intervals, Fig. 2i, j, k, n). This did not result in a significant increase in elongation or widening compared to the control condition (120 s intervals). This suggests that the effect of peristalsis on elongation may reach a plateau at a certain frequency. We will revise the manuscript to clarify this interpretation and discuss its implications.

      (4) We appreciate this important comment and have addressed the issue of novelty and positioning in the General response shown above.

      Reference

      Yang, Y. et al. Ciliary Hedgehog signaling patterns the digestive system to generate mechanical forces driving elongation. Nat. Commun. 12, 7186 (2021).

      Khalipina, D., Kaga, Y., Dacher, N. & Chevalier, N. R. Smooth muscle contractility causes the gut to grow anisotropically. J. R. Soc. Interface 16, 20190484 (2019).

    1. Author response:

      [Editors' note: The authors included an author response to reviews from another journal]

      Reviewer #1 (Comments to the Authors):

      In this manuscript the authors describe that cells in collective movements adopt a superdiffusive behavior to out pace individual cells. This behavior is regulated by cell-cell junctional stability and force transmission. The authors state that speed is regulated by vinculin through mechanosensitivity.

      While is makes intuitive sense that cells may move more efficiently collectively as it reduces their exploratory space and therefore increases their efficiency of movement,

      We agree that this is an intuitive explanation. However, previous literature had shown that confluent cells may or may not migrate depending on conditions that do not solely depend on the space available per cell, but also involve the intrinsic activity of the cell, its cortical tension, and its adhesion with its neighbors, with sometimes counterintuitive effects (doi: 10.1016/J.CEB.2021.07.011). This was the reason that motivated us to investigate how these various ingredients affected space exploration efficiency on different time scales.

      Our results indeed refute the intuition that cells move more efficiently when their exploratory space is reduced by showing that the outcome depends on the time scale considered (Fig. S3B). Specifically, on short time scales (less than 3 hours), the area explored by individual MDCK cells is larger than that explored by MDCK cells at confluence. On a longer time scale (greater than 3 hours), however, the area explored by confluent MDCK cells is larger. This switch is a direct consequence of the change in migratory behavior from persistent random walk to superdiffusion, Moreover, its position in time depends on the cell line: extrapolation of our results on RPE-1 cells suggests that it should theoretically occur after approximately 300hrs, if this time scale was experimentally accessible (Fig. S3F).

      …the role of junctions specifically is less clear.

      We are sorry that we were not able to clearly convey the roles of junctions. We have substantially rewritten our text to address this and all the changes are highlighted in orange. As summarized in Fig. 6F, junctions have three roles. The first role is on persistence, through velocity coordination between neighbors, the second is on speed, through the stability of junctions, and the third role is on directionality, through the sensitivity of the monolayer to the wound edge.

      The first role is evidenced thanks to the comparison of the MSD between single cell and confluent migration assays and the use of the alpha-catenin KD cell line. Alpha-catenin depletion is known to be the most potent disruptor of adherens junctions (DOI:10.1091/mbc.e06-05-0471, , DOI:10.1126/science.aaf7119, (DOI:10.1073/pnas.1002662107, DOI:10.1073/pnas.1119313109), and we show that it significantly alters the superdiffusive behavior that emerges in the confluent migration assay (Fig. 3E,F, 5C). Therefore, junction integrity is critical for the control of cell persistence.

      Moreover, alpha-catenin depletion induces a loss of velocity coordination between neighbors (Fig. S3E), which we show through numerical simulations to induce superdiffusion (Fig. 3G). By contrast, E-cadherin KO and vinculin mutants have no effect on the superdiffusion of confluent cells (Fig. 3E, 4A). Therefore, the critical molecular ingredient is the link provided by alpha-catenin to the cytoskeleton that provides junction integrity.

      The second role of junctions is evidenced thanks to the comparison of cell speeds between single and confluent migration assays with the vinculin mutants (Fig. S4A). Results show that cell speed is reduced of about 10µm/h by confluence, regardless of the mutant except for YE, whose only difference with other mutants is its lower stability (Fig. 4F). This supports that junction stability, and not the other effects of mutants, controls cell speed (we provide a detailed demonstration in the response to the following question). As expected, junction integrity is required as well, as seen from the higher cell speed of the alpha-catenin KD cell line compared to WT (first MSD point in Fig. 3B, E).

      The third role of junctions is evidenced thanks to the comparison between confluent and directed migration assays (Fig. 6A). Results show that the wound healing rate is proportional to cell speed at confluence, regardless of the mutant except for YE, which displays no tension gradient in junctions from front to back cells (Fig. 6C). This supports that such gradient is required for cells to identify on which side is the wound edge. As expected, junction integrity is required as well, as seen from the loss of directional bias of the alpha-catenin KD cell line (Fig. 5F).

      The authors chose vinculin as the basis by which to manipulate tensions at cell-cell junctions, but this comes with considerable drawbacks. Namely, since vinculin appears at both cell-cell and cell-matrix junctions, its role and the role of its mutations is not clear here. The authors state that the collective migration speed is related to junctional stability, but because vinculin is also at FA, how can this be concluded?

      We apologize for the lack of clarity. We hope that the highlighted changes in the revised manuscript will improve this point. As exemplified above, comparing cell migration between isolated cells and confluent cells is essential to enable us to distinguish between the contributions of AJs and FAs. Indeed, since isolated cells lack AJs, the impact of vinculin mutants on single cell migration can only be explained by their effects on FAs. This is how we first determine the effects of vinculin mutants on migration that depend on FAs. Because confluent cells also have FAs, we expect that the effects of vinculin mutants on the migration of isolated cells will still be present in confluent cells, to which will be added the effects of these mutants on AJs and their consequences on migration, if any.

      Therefore, when compared to WT cells, if a given mutant decreases or increases migration speed in individual cells, and does so in confluent cells in the same proportion, then its effects at confluence can be entirely explained by its effects in individual cells, and there are no additional effects of that mutant from AJs. This is indeed what we observe for all mutants except the YE mutant (Fig. S4C), leading us to conclude that none of the vinculin mutants, except the YE mutant, have an effect on migration at confluence that results from AJs. In contrast, the YE mutant has effects on migration at confluence that cannot be explained by its effect on individual cell migration. Therefore, the effects of YE at confluence depend on AJs, whether they result from alterations in AJs, FAs, or both. To distinguish between these scenarios, we proceed by elimination, comparing the effects of YE to those of other mutants on force transmission and adhesion stability, and how these two factors associate with migration speed, as explained below. In FAs, YE alters force transmission differently in individual cells and at confluence, but we already know from Fig. 2 that force transmission in FAs cannot alone explain the speed of migration. This result rules out an indirect effect of AJs on cell migration at confluence through FAs. Furthermore, in AJs, YE affects stability and force transmission, but TL has the same effect on force transmission as YE and we already know that none of the effects of TL on migration depend on AJs (Fig. 3, S4C). This result rules out an effect of force transmission in AJs on migration speed at confluence. We conclude that stability at the AJ level, which is the remaining property specifically impaired by YE, is what regulates migration speed at confluence.

      The manuscript's logic and flow are not clear in some places, making the story hard to follow. As one example, the FRAP data, which the authors suggest is used to investigate vinculin's combined role does not help in this capacity as the interpretation and its connection to the bigger story are not clear.

      We are sorry again for the lack of clarity. We used FRAP data to evaluate the effects of vinculin mutants on adhesion stability. Indeed, mutants have different effects on adhesion stability (Fig. 2E, 4F). In addition, they also have different effects on force transmission (Fig. 2D, 4D,E). The partial overlap in functional alterations caused by the mutants allows us to test the involvement of the overlapping function (here stability) in the overall migration outcome. For example, if two mutants have a similar effect on adhesion stability but different effects on migration speed (such as TL and T12), we can then rule out that speed results from adhesion stability. Similarly, if two mutants have different effects on stability but a similar effect on speed (such as TL and YE), we can also rule out that speed results from stability. We applied the same reasoning to force transmission to conclude that neither adhesion stability nor force transmission alone is sufficient for cells to migrate rapidly. However, the combination of the two enables rapid migration.

      As another example, the information derived from the use of the mutants is not clear in the context of the message in the manuscript since they affect cell-cell and cell-matrix junctions and in some places show results that are counter intuitive and not well-explained, to which the authors admit they are surprising but then do not explain their meaning.

      As such, it is very hard to follow the logic with regard to the information resulting from the mutant experiments.

      We provide above a detailed break-down of our strategy to analyze the results. We regret that our manuscript did not adequately convey our conclusions and we hope that the new version of the manuscript improves this point.

      Proliferation has been shown to play a role in wound healing. Does proliferation change in the various conditions?

      This is an important point. The average speed of cells at confluence is approximately 20 µm/h (Fig. 4B), which means that each cell moves approximately its own size in one hour. During this time, assuming a 16-hour cell cycle, 6% of the cells would have divided, each of them likely pushing one of its neighbors a distance equivalent to the size of a cell. Therefore, cell proliferation accounts for at most a few percent of the total cell movement. For this reason, we can assume that growth does not account for a large part of the movement we observe. This is consistent with previous work showing that proliferation does not contribute significantly to wound healing (DOI: 10.1073/pnas.0705062104, DOI: 10.1083/jcb.201207148).

      Minor comments:

      The authors should provide a better description of the mutants: what does a tailless mutant not bind, or bind differently? More context is needed to help interpret the results. While the mutants have all been published on before, it would be helpful to have more information here so that the manuscript is easier to follow.

      We are sorry that the information we provided was insufficient. We have now detailed the mutations to help the reader understand how interactions are altered.

      Figure 1A is not necessary. Figure 1 overall is fairly predictable as there have been many papers using the persistent random walk as the best model to single cell migration (dating back to the early 1990's). The authors define a new term, angular memory, which they show decreases with increasing delta t as one would predict.

      We acknowledge that persistent random walks have already been observed for individual cells, as in references 3-4 cited in the introduction. Nevertheless, we believe that Figure 1 is important because not all cells migrate as persistent random walkers when isolated. Some migrate in a more exotic manner, resulting in superdiffusive behavior, as in references 5-8 cited in the introduction. Since we observe superdiffusive behavior at confluence (Figure 2), it was therefore necessary to show whether or not single cells were superdiffusive too. We also use this figure to introduce angular memory, a measure that, to our knowledge, has never been used before. According to intuition, it decreases to 0 for persistent random walkers, just as another resembling measure, velocity autocorrelation, would do. However, the angular memory of fractional Brownian walkers does not vanish with increasing delta t (Fig. 3D), while velocity correlation would, just as that of persistent random walkers. This difference makes angular memory much more appropriate for distinguishing between the two migration behaviors, and prompted us to introduce it in the first figure as a reference.

      In the wound healing assay, which cells were measured? Leading edge or interior, and does it matter?

      Figure 5A shows that cells behave differently depending on their distance from the wound. This is because the traces shown correspond to the first few hours of the movie, during which the cells at the front begin to move first. Figure S5A shows the speed of the cells over time after the wound and indicates that the cells reach a stable speed after approximately 3 to 4 hours. Figure S5B shows the speed of the cells as a function of distance from the wound at steady state. These results show that the speed of the cells no longer depends on the distance from the wound at this stage. As indicated in the “Materials and Methods” section, we only considered time points beyond this stage for subsequent analyses of population-averaged MSD and velocity presented in Figure 5, so the location of cells at the front or rear was irrelevant.

      Reviewer #2 (Comments to the Authors):

      To migrate cells must spatially explore their environments, a process that is guided by intrinsic signals (adhesive and mechanical properties, etc) and extrinsic (gradient cues) signals. This exploration can occur on the single or multicellular level. In this study, the authors examine the effect of cell-cell interactions, guidance cues, and cell mechanics in the exploratory capacity of MDCK cells. The authors show that cell-cell adhesion provides a "infinite directional memory for migration" and cell speed is dependent upon the focal adhesion stability, cell mechanics, and the mobility of adherens junctions-these processes are modulated by vinculin.

      My three major concerns with the manuscript are as follows:

      (1) While there is potential new information about the role cell-cell junctions and guidance cues play in cell migration, there is not enough NEW insight presented. Rather the role of vinculin in these processes is expected given what is already known about its ability to control focal adhesion stability, mechanics, and adherens junctions.

      We agree that our cell migration results make sense based on the effects of vinculin mutants on the stability and force transmission of adhesions. Nevertheless, we argue that this was not the only possible scenario. Indeed, we find that none of the effects of vinculin mutants on AJs (except YE) have an impact on cell migration (Fig. S4C). One might have expected that the increased stability provided by the TL and T12 mutants would reduce the speed of collective cell migration, just as the YE mutant increased cell speed due to its altered stability. This is not what we found, and this reveals a nonlinear relationship between AJ stability and migration speed that could be investigated more thoroughly in future studies. Another example is that the effects of the mutants on force transmission in AJs do not impact migration speed at confluence but do impact directed collective migration (Fig. 6). One might have expected that vinculin-mediated force transmission in AJs would impact collective migration, whether directed or not.

      More importantly, we show that the role of intercellular adhesion in cell migration is more complex than expected. Indeed, it depends on the timescale considered: intercellular adhesion is detrimental to short-term spatial exploration and beneficial in the long term (Fig. S3B). Such a timescale-dependent behavior is impossible to predict from previously known effects of the mutants or other molecular considerations. Furthermore, we show that this behavior can be fully explained by the coordination of velocities between neighbors, which depends on intact connections between AJs and the cytoskeleton via alpha-catenin, but is independent of vinculin mutants that connect AJs to the cytoskeleton in parallel with alpha-catenin. One might have expected these connections to also have an impact on velocity coordination, and thus on spatial exploration, but we show that this is not the case (Fig. 3). Finally, we show that directed collective migration has a negligible impact on cell exploration at our experimental timescale (Fig. 5), whereas we initially expected the wound to make migration more ballistic. This reveals that such a directional signal affects spatial exploration at much longer timescales than expected.

      Overall, our results quantify the outcome of competing effects and provide timescales at which one effect outweighs the other in influencing cell migration. We believe this is an original approach that provides substantial new insights into collective cell migration.

      (2) The phenotypes of the cells expressing the mutant vinculins varying greatly. These phenotypes are not addressed despite the fact that they could potentially complicate the analyses. For example, there are dramatic differences between focal adhesion numbers and sizes in the cells expressing the different vinculin mutants; cell spreading is also dramatically altered. Likewise, the T12 mutant vinculin has previously been reported to have increased adhesive strength, increased traction forces, and cell spreading. How does this knowledge change the interpretation?

      We agree that vinculin mutants may have effects on the size and number of FAs, cell spreading, and traction forces that we do not examine here. These consequences can be explained by the effects of these mutants on force transmission in FAs and on their stability, which we report in our work. They do not affect our interpretations. Here, we provide a predictive model of migration speed based on the combination of two consequences of vinculin function, namely stability and force transmission. An interesting avenue for future research would be to assess whether these combinations can be reduced to a single higherlevel effect of vinculin on the cellular phenotype that would be sufficient to predict migration speed. This work remains to be done, as neither FA size and number, cell spreading, adhesion force, nor traction forces alone are sufficient to predict migration speed.

      Along the same lines, it has previously been established that tagged version of vinculin do not efficiently integrate into adherens junctions. Published work from the Nelson laboratory suggests that GFP-vinculins do not localize to cell-cell junctions and work from other laboratories suggests localization occurs only when the endogenous vinculin is silenced.

      We are aware that some GFP-vinculin constructs may not localize as well as the endogenous protein at AJs. This is due to the localization of the GFP tag on the head of vinculin and depends on the length of the linker between GFP and the head of vinculin. The longer the linker, the easier the interaction with AJ partners. Unlike these constructs, the vinculinTSMod sensors we use in our work do not carry a GFP on the head and do not suffer from the same limitations.

      Furthermore, vinculin recruitment to AJs depends on force, with little or no recruitment when tension on the AJs is relaxed (DOI: 10.1038/ncb2055). Vinculin recruitment has in fact already been used as an indicator of AJ tension in Drosophila (DOI: 10.1038/s41467-01807448-8). Consequently, the amount of vinculin visible at the AJs varies depending on the tension exerted on the AJs, which our results confirm: vinculin is more difficult to detect at the AJs in cells located at the front of a wound than in those located at the back (Fig. 6B), which is consistent with the difference in vinculin tension between front and back cells (Fig. 6C) and to the E-cadherin tension gradient between front and back cells (DOI: 10.1083/jcb.201706013). Overall, these results show that vinculin is not always easy to detect at AJs, but this is due to the properties of vinculin, which the constructs we use reproduce better than previous constructs (see also below).

      The images in figure S2 and the prebleach images in figure S4 do not show convincing localization of the mutant vinculins to cell-cell adhesions. This is of special concern given that YE mutant protein hardly has any discernable localization to cell-cell junctions; additionally, none of the mutant proteins were tested for their ability to co-localize with adherens junction components. This raises the question if the parameters being examined and the conclusions drawn from them are affected by a difference in localization.

      We agree that the recruitment of vinculin at intercellular contacts may be difficult to see.

      Besides force-dependent effects mentioned above, other factors are involved. The images shown in Figures S2 and S4 are from live cells in which cytoplasmic vinculin is still present, and its level proportional to the mobility of vinculin. Indeed, the TL and T12 mutants show a more marked contrast between intercellular contacts and the cytoplasm, which is consistent with their greater stability at AJs (Fig. 4F). Conversely, YE shows lower contrast, which is consistent with the lower stability of this construct at AJs (Fig. 4F). The FL construct lies between the two. As a result, the cytoplasmic content can variably mask vinculin recruitment at the AJs depending on the mutant.

      We have now performed additional quantifications of mutant recruitment at intercellular contacts as a function of distance from the basal surface of the cells and relative to their recruitment in FAs, in live cells. Results are shown in the new Fig. S4F. We find that all the constructs are recruited to intercellular contacts with a density that is at most half of that in FAs and that varies along the height. FL shows the highest density, localized more apically, consistent with the localization of an AJ-bound actin belt. The mutants appear to be more homogenously distributed along the height of the lateral surface, which may be explained by their impaired autoinhibition (TL, T12), or mechanosensitivity (YE). This variability also contributes to the difficulty in seeing vinculin recruitment in all cells in a single z-slice.

      To confirm the proper recruitment of vinculin constructs to AJs we have performed immunofluorescence against alpha-catenin and phalloidin on each of the stable cell lines. Results are shown in the new Fig. S4D and E. In these experiments, cell permeabilization allows for the release of some of the cytoplasmic pool of vinculin, which highlights the recruitment of all vinculin constructs to intercellular contacts. There, all vinculin constructs colocalize with alpha-catenin and F-actin, as expected. Additionally, images displayed are maximum intensity projections to mitigate recruitment variability along the height.

      Overall, our results clearly support the localization of vinculin at intercellular contacts, and the differences between the constructs are consistent with the effects of their mutations.

      (3) There is a lack of new mechanistic insight. Conclusions are made about a role of vinculin dimerization. This conclusion appears to be based upon the usage of the mutant version of vinculin Y1065. Did the authors directly measure the ability of this mutant protein to dimerize? Is actin binding also affected.

      The binding properties of the Y1065E mutant, including its dimerization and binding to actin, have already been characterized by other researchers (ref. 40 in our manuscript, as well as DOI:10.1111/j.1432-1033. 1997.01136.x or DOI: 10.1016/j.febslet.2013.02.042). We assumed that these properties are now well established and can be used to explain higher-level phenotypes that we show for the first time, to our knowledge.

      Reviewer #3 (Comments to the Authors):

      Canever et al. tracked two epithelial cell lines on collagen coated glass and showed that isolated cells (non confluent) move as persistent random walkers, whereas confluent monolayers migrate super diffusive, with long range directional memory. By systematically perturbing adhesion machinery they found that focal adhesion mutations mainly tune the speed of single cell tracks, but cannot create long range memory, while force bearing adherens junctions are essential for the super diffusive regime-genetically perturbing them collapses collective memory. These interesting results identify junctional tension as important to switch epithelial cells/sheets between individual and collective search modes - an important quantitative insight that is of clear relevance to cell biologists.

      - The presented data is nicely quantitative and convincing, but I have subtle concerns about the generality of the findings. While the authors show that the differential behavior, they describe is not cell-line specific (MDCK, RPE), there are no experiments evaluating the generality of their conclusions across different matrix conditions. How are the measured migration parameters affected by matrix stiffness? Cell migration on collagen coated glass coverslips is a relatively narrow and artificial condition. How is the collective directional memory expected to behave on softer substrates? The generality of the conclusions could be strengthened by repeating measurements using hydrogels of varying stiffness. Further, it should be discussed to which tissues in the body the selected matrix conditions and migration modes plausibly apply.

      We agree that the generality of our results and the relevance of glass-rigid substrates is an important point. In vivo, epithelial cells rest on a basement membrane with a typical stiffness of approximately 10 MPa, as demonstrated by experimental evaluations on various tissue explants, including renal glomeruli and Bruch's membrane, which are relevant to MDCK and RPE-1 cells (DOI: 10.1111/j.1742-4658.2007.05823.x, DOI: 10.1172/JCI106898, DOI:10.1038/eye.1987.35), we have added these references in the manuscript to support our experimental strategy. In vitro, the most significant effects of substrate stiffness on FAs and cell migration generally occur at much lower stiffnesses, between 0.2 and 100 kPa, and cell phenotypes generally plateau at levels comparable to those observed on glass, even below 100 kPa (DOI: 10.1242/jcs.133645, DOI: 10.1038/ncb3268, DOI:10.1039/c5ib00307e, DOI: 10.1039/c9sm01893j). Furthermore, substrate stiffness has much more moderate effects on confluent cells than on isolated cells. For example, it has been previously demonstrated that confluent layers of MCF10A epithelium showed no change in velocity coordination in the range of 3 to 65 kPa (DOI: 10.1083/jcb.201207148). Therefore, collagen-coated glass appears to be a reasonable model for the basement membrane. Overall, we believe that we have conducted our experiments under physiological conditions, and that our results apply to a wide range of substrate stiffnesses.

      - It would be nice to see how long it takes confluent cell layers to close rectangular wounds of defined size when cells migrate as individual (adherens junctions perturbation) versus collective (wt) (on substrates of different stiffness). Presumably, there should be faster wound closure under the collective regime, at least for simple shaped wounds.

      This is an interesting question, which our results indirectly address. In our study, we measured the wound healing speed of the WT MDCK cell line as well as lines expressing mutant vinculin constructs (Fig. 6A). These results show that this speed ranges from 5 to 15 µm/h depending on the construct expressed (and for reasons that we explain in the manuscript). These values make it easy to estimate the time required to close a wound based on its width. For example, it would take 5 hours to close a 100 µm wide wound for the WT cell line, which has a rate of 10 µm/h (on both sides of the wound).

      Wound closure for cells with disrupted adhesive junctions has already been documented (DOI: 10.1083/jcb.200910041). The results show that wound closure is indeed slower than with WT cells. Although this previous study does not reveal the underlying causes, our work now shows that there are two factors: weaker directional memory due to impaired intercellular coordination and, in the longer term, an additional lack of sensitivity to the guidance signal provided by the wound.

      - Akin to substrate stiffness variation, I am missing experiments that test the effect of cytoskeletal tension on these migration modes. Experiments with Rho kinase or myosin inhibitors could meaningfully broaden the scope of this study.

      Rho kinase or myosin inhibitors applied to cells during the time required to assess migration patterns (a movie recorded overnight is necessary to obtain a statistically reliable calculation of MSD over 3 to 4 hours) are likely to affect many other cellular processes in addition to the cytoskeletal tension directly involved in migration. We believe that the accumulation of these effects will make interpretation of the results very difficult. For example, it has been shown that inhibition of ROCK by Y27 promotes healing of corneal endothelial lesions by affecting proliferation through cyclin D and p27 (DOI: 10.1167/iovs.13-12225), or by improving respiration, which would provide the energy necessary for migration (DOI: 10.1096/fj.202101442RR). Consistently, another study on HaCaT epidermal cells confirms that myosin phosphatase accelerates wound healing through proliferation (DOI: 10.1016/j.bbadis.2018.07.013). In contrast, in HUVEC cells, ROCK inhibition significantly impaired the proliferation and migration of vascular endothelial cells in vitro in a dose-dependent manner (DOI: 10.1097/ICO.0000000000000493).

      Furthermore, previous studies have highlighted that differential contractility at the subcellular level is important for collective migration (DOI: 10.1038/ncb2133, DOI: 10.1083/jcb.201706013), which is not possible to examine with global activation or inhibition of contractility. This prompts the development of more refined and specific measurement and disruption strategies to assess the respective impact of cytoskeletal tension on cell-cell and cell-matrix adhesion mechanisms. Our work, which uses biosensors to assess how this tension differentially affects cell-cell and cell-matrix adhesions, is a step in this direction. The localized spatio-temporal activation or inhibition of myosin subtypes or Rho GTPase regulators specific to these adhesion structures will likely answer these questions in the future, but we believe that the development and application of these approaches will require a substantial amount of work that goes beyond the scope of our study.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      Summary:

      This study uses dental traits of a large sample of Chinese mammals to tract 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:

      For the original draft of the manuscript, I had four major concerns with the study, especially related to the sampling, diet, and evidence for the 'brawn before bite' hypothesis. I still believe that the original issues that I raised may be weaknesses of the study. For example, there is still limited discussion on diets (even though the dental topographic analyses used in the study are designed for inferring diets). And I find the results a little challenging to interpret because teeth of multiple positions are included in the same samples, which seems problematic. That said, the authors have addressed each of my previous concerns and have made major revisions, including running new analyses, and thus I support the paper.

      This revised submission includes only minor changes aimed at clarifying the main text.

      Reviewer #2 (Recommendations for the authors):

      I appreciate that the authors made many improvements to their study based on reviewers' comments. I don't have any remaining major issues with the paper, but I do have several minor comments.

      Thank you for taking the time to provide additional helpful feedback on our study. We have made minor revisions to the manuscript based on your suggestions. Please see our point-by-point response below.

      Lines 48-50. I reiterate my suggestion in my previous review to explicitly state which clade is being discussed, which is important because several major mammal groups beyond placentals (metatherians, multituberculates, dryolestoids, gondwanatherians) survived the K-Pg and had very different diversification patterns. You mention "mammal taxonomic diversity" but in the next sentence say "This initial placental mammals diversification ..." and later mention "stem placental/eutherian lineages." To stay consistent, you might replace "mammal" (L48) and "placental mammals" (L50) with "eutherian(s)" (usually defined as stem + crown placentals). If you follow this suggestion, then elsewhere in the paper I recommend replacing "mammals" with "eutherians" for consistency.

      Thank you for this suggestion. We modified the use of “mammals” throughout the text to general reference to the group only; specific mentions of the dataset analyzed are revised to “eutherians.”

      Lines 75-83. I respect the authors' hesitancy to reconstruct specific diets for the fossil taxa (L75-83), especially considering that dental topographic analyses (DTAs) often struggle to differentiate diets in extant taxa (e.g., Pineda-Munoz et al. 2016 Methods Ecol Evol). I still think that the authors might be able to interpret dietary trends from their results (e.g., an increase in average OPCR values indicating a shift toward more herbivorous diets) - I think discussing dietary trends would be an interesting discussion topic later in the paper. That said, I also recognize that different DTA results seem to show conflicting dietary trends (based on my limited knowledge of those metrics) so maybe that complicates things too much.

      We concur with Reviewer 2 that dietary inferences of DTA data are premature, especially given the ongoing controversies of its use in studies of extant mammal teeth. We kept our current scope of discussion unchanged.

      Lines 75-77. "early mammals ... are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction." But your fossils (eutherians) are certainly within 'phylogenetic brackets' of modern clades (therians, i.e. Eutheria + Metatheria). Maybe you're alluding to the fossils being stem lineages of extant subgroups like Ungulata, which means we can't bracket them specifically within those eutherian subgroups? So, I recommend revising or expanding your statement for clarity. Also, the considerable phylogenetic uncertainty for Paleocene groups (e.g., Halliday et al. 2015) complicates this issue, which you could mention.

      We modified the sentence to now say “Additional complications with ecomorphological analysis of these stem eutherians include the uncertainty in their dietary ecology, having diverged prior to the crown radiation, and uncertainty in phylogenetic positions of Paleocene taxa [7]; thus, they are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction.”

      Line 84. "We investigated dental topography-performance shifts ...". You haven't introduced dental topography or even mentioned teeth yet, and "performance shifts" is vague. So, this phrase might confuse readers. Maybe you can just erase it and start the sentence with "We investigated the timing of ecomorphological ..."?

      We made the recommended revision.

      Lines 104-105 (and elsewhere). "Dental traits paralleled Paleocene global and regional environmental conditions" and "We found that dental topographic trait variability in Paleocene mammals in south China tracked global and regional climatic changes". These conclusions seem a little too assertive to me. Your sample is grouped into 3 rough time bins (of somewhat uncertain ages) and is from a relatively small geographic range - that seems like very limited information for inferring links between dental patterns and climatic changes, especially global patterns. I think it's worth HYPOTHESIZING that dental traits are linked to environmental/climatic changes (with results like those in Figure 2A & B as evidence to support that hypothesis), but I wouldn't make that claim with any confidence. So, I recommend that you temper your relevant conclusion statements. For example, for Line 105, you could replace "We found ..." with "We posit ..." (L105). I would make similar changes to similar statements throughout the paper (e.g., L243).

      Thank you for this suggestion to temper our phrasing. We edited throughout the text to make our interpretations less assertive.

      Figure 1 (and your response to reviewers). Why was the timescale changed to 65.5 Ma for the K-Pg boundary? The K-Pg is 66 Ma (not 65.5), which is the age you mention in the text (e.g. Pg 3 L39) and is well established in the literature - see recent papers from the Paul Renne lab for a more exact age.

      We revised the figure to have the K-Pg at 66 Ma.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Meiotic recombination at chromosome ends can be deleterious, and its initiation-the programmed formation of DSBs-has long been known to be suppressed. However, the underlying mechanisms of this suppression remained unclear. A bottleneck has been the repetitive sequences embedded within chromosome ends, which make them challenging to analyze using genomic approaches. The authors addressed this issue by developing a new computational pipeline that reliably maps ChIP-seq reads and other genomic data, enabling exploration of previously inaccessible yet biologically important regions of the genome.

      In budding yeast, chromosome ends (~20 kb) show depletion of axis proteins (Red1 and Hop1) important for recruiting DSB-forming proteins. Using their newly developed pipeline, the authors reanalyzed previously published datasets and data generated in this study, revealing heretofore unseen details at chromosome ends. While axis proteins are depleted at chromosome ends, the meiotic cohesin component Rec8 is not. Y' elements play a crucial role in this suppression. The suppression does not depend on the physical chromosome ends but on cis-acting elements. Dot1 suppresses Red1 recruitment at chromosome ends but promotes it in interior regions. Sir complex renders subtelomeric chromatin inaccessible to the DSB-forming machinery.

      The high-quality data and extensive analyses provide important insights into the mechanisms that suppress meiotic DSB formation at chromosome ends. To fully realise this value, several aspects of data presentation and interpretation should be clarified to ensure that the conclusions are stated with appropriate precision and that remaining future issues are clearly articulated.

      (1) To assess the chromosome fusion effects on overall subtelomeric suppression, authors should guide how to look at the data presented in Figure 2b-c. Based on the authors' definition of the terminal 20 kb as the suppressed region, SK1 chrIV-R and S288c chrI-L would be affected by the chromosome fusion, if any. In addition, I find it somewhat challenging to draw clear conclusions from inspecting profiles to compare subtelomeric and internal regions. Perhaps, applying a quantitative approach - such as a bootstrap-based analysis similar to those presented earlier-would be easier to interpret.

      The reviewer is correct that we could not simply fuse two ends but had to create translocations that also removed variable amounts of subtelomeric sequence. Targeted translocations require unique sequences, and thus the extent to which telomeric sequences were deleted varied based on the availability of such sequences. As noted by the reviewer this necessarily limits the conclusions that can be drawn. We have expanded the description of this experiment and also explicitly state the limitations of this assay. To improve clarity, we have also included a schematic to better highlight which chromosomal sequences were removed.

      To further probe our finding that subtelomeric axis protein enrichment may largely be encoded in cis, we now compared axis protein enrichment between S288c and SK1, as suggested by reviewer 2. For this analysis, we took advantage of a dataset we had produced previously that measures Red1 enrichment in SK1/S288c hybrid strains, which provide a powerful internally controlled setup that eliminates effects caused by differential timing and synchrony between samples. As now shown in Supplementary Fig. 5, SK1 and S288c differ substantially in their subtelomeric architecture at many ends, including extensive differences in the number and distribution of Y’ elements. Importantly, axis protein distribution was very consistent between SK1 and S288c when correcting for the differences in length of individual chromosome ends, supporting the conclusion that axis protein enrichment levels are primarily encoded in cis. This analysis is now shown in Fig. 2c. These data also indicate that the presence of a Y’ element does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior.

      (2) The relationship between coding density and Red1 signal needs clarification. An important conclusion from Figure 3 is that the subtelomeric depletion of Red1 primarily reflects suppression of the Rec8-dependent recruitment pathway, whereas Rec8-independent recruitment appears similar between ends and internal regions. Based on the authors' previous papers (referencess 13, 16), I thought coding (or nucleosome) density primarily influences the Rec8-independent pathway. However, the correlations presented in Figure 2d-e (also implied in Figure 3a) appear opposite to my expectation. Specifically, differences in axis protein binding between chromosome ends and internal regions (or within chromosome ends), where the Rec8-dependent pathway dominates, correlate with coding density. In contrast, no such correlation is evident in rec8Δ cells, where only the Rec8-independent pathway is active and end-specific depletion is absent. One possibility is that masking coding regions within Y' elements influences the correlation analysis. Additional analysis and a clearer explanation would be highly appreciated.

      Thank you for pointing this out. We now also included Y’ elements in the analysis in Fig 2d. Including the Y’ elements yielded an increase in average coding density near the very ends of the chromosomes. This increase matches the higher level of axis protein binding seen in rec8 mutants in Fig. 3a and is consistent with the previously noted link between coding density and axis protein deposition. We now provide further description in the text and the figure legends.

      We do not have an explanation for why there is no correlation with coding density in the EARs but assume that this reflects the unique regulation of this region (as also implied by Supplementary Fig. 4d). At present, the signals that establish the EARs remain unknown although our data indicate that the Hop1-CBR as well as Dot1 are important for axis protein enrichment in the EARs.

      (3) The Dot1-Sir3 section staring from L266 should be clarified. I found this section particularly difficult to follow. It begins by stating that dot1∆ leads to Sir complex spreading, but then moves directly to an analysis of Red1 ChIP in sir3∆ without clearly articulating the underlying hypothesis. I wonder if this analysis is intended to explain the differences observed between dot1∆ and H3K79R mutants in the previous section. I also did not get the concluding statement - Dot1 counteracts Sir3 activity. As sir3Δ alone does not affect subtelomeric suppression, it is unclear what Dot1 counteracts. Perhaps, explicitly stating the authors' working model at the outset of this section would greatly clarify the rationale, results, and conclusions.

      Thank you for this comment. We reworked the introduction to this paragraph to be more focused on Sir3 rather than Dot1. We hope that this introduction is less confusing and more in line with the data presented in this paragraph. We also expanded the conclusion to suggest the alternative possibility that the Sir complex only becomes a regulator of axis proteins in the absence of Dot1.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Raghavan and his colleagues sought to identify cis-acting elements and/or protein factors that limit meiotic crossover at chromosome ends. This is important for avoiding chromosome rearrangements and preventing chromosome missegregation.

      By reanalyzing published ChIP datasets, the researchers identified a correlation between low levels of protein axis binding - which are known to modulate homologous recombination - and the presence of cis-acting elements such as the subtelomeric element Y' and low gene density. Genetic analyses coupled with ChIP experiments revealed that the differential binding of the Red1 protein in subtelomeric regions requires the methyltransferase Dot1. Interestingly, Red1 depletion in subtelomeric regions does not impact DSB formation. Another surprising finding is that deleting DOT1 has no effect on Red1 loading in the absence of the silencing factor Sir3. Unlike Dot1, Sir3 directly impacts DSB formation, probably by limiting promoter access to Spo11. However, this explains only a small part of the low levels of DSBs forming in subtelomeric regions.

      Strengths:

      (1) This work provides intriguing observations, such as the impact of Dot1 and Sir3 on Red1 loading and the uncoupling of Red1 loading and DSB induction in subtelomeric regions.

      (2) The separation of axis protein deposition and DSB induction observed in the absence of Dot1 is interesting because it rules out the possibility that the binding pattern of these proteins is sufficient to explain the low level of DSB in subtelomeric regions.

      (3) The demonstration that Sir3 suppresses the induction of DSBs by limiting the openness of promoters in subtelomeric regions is convincing.

      Weaknesses:

      (1) The impact of the cis-encoded signal is not demonstrated. Y' containing subtelomeres behave differently from X-only, but this is only correlative. No compelling manipulation has been performed to test the impact of these elements on protein axis recruitment or DSB formation.

      Thank you for this comment. Our data indeed appeared contradictory because XY’ ends showed overall lower axis protein enrichment, yet our analysis of chromosome fusions, which also eliminated Y’ elements at some the fused ends, provided no evidence for an effect of Y’ elements at those ends. As also noted in the response to reviewer 1, we now compared axis protein enrichment between S288c and SK1, which differ substantially in their number and distribution of Y’ elements (Supplementary Fig. 5). We found that axis protein distribution and enrichment was very consistent between SK1 and S288c when correcting for the displacement caused by the presence of Y' elements and other subtelomeric sequences (now shown in Fig. 2d). These data support the conclusion that axis protein enrichment levels are primarily encoded in cis and indicate that the presence of Y’ elements does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior (giving rise to the apparently lower axis protein enrichment on XY’ ends).

      (2) The mechanism by which Dot1 and Sir3 impact Red1 loading is missing.

      Although we do not yet understand the precise molecular details of these effects, we nevertheless believe we have obtained several important insights into this mechanism. First, our data indicate that the suppressive effect of the ends primarily impacts the Rec8-dependent loading of Red1, whereas loading via the Hop1-CBR is largely unaffected. The effect of Dot1 thus likely occurs via the Rec8-Red1 interaction. Second, the increase in Red1 recruitment is fully rescued by deletion of Sir3, suggesting that Sir3 becomes a promoter of axis protein recruitment in the absence of Dot1. These dependencies are now outlined in the model in Fig. 9. We would also like to note that the Sir complex was previously shown to impact cohesin in mitotic cells. Thus, a connection between the Sir complex and cohesin is not without precedent.

      (3) Sir3's impact on DSB induction is compelling, yet it only accounts for a small proportion of DSB depletion in subtelomeric regions. Thus, the main mechanisms suppressing crossover close to the ends of chromosomes remain to be deciphered.

      Thank you, we absolutely agree. We had discussed this point in the discussion but now also explicitly state this point in the abstract and expanded the discussion of these findings in the results and discussion.

      Reviewer #3 (Public review):

      Summary:

      The paper by Raghavan et. al. describes pathways that suppress the formation of meiotic DNA double-strand breaks (DSBs) for interhomolog recombination at the end of chromosomes. Previously, the authors' group showed that meiotic DSB formation is suppressed in a ~20kb region of the telomeres in S. cerevisiae by suppressing the binding of meiosis-specific axis proteins such as Red1 and Hop1. In this study, by precise genome-wide analysis of binding sites of axis proteins, the authors showed that the binding of Red1 and Hop1 to sub-telomeric regions with X and Y' elements is dependent on Rec8 (cohesin) and/or Hop1's chromatin-binding region (CBR). Furthermore, Dot1 functions in a histone H3K79 trimethylation-independent manner, and the silencing proteins Sir2/3 also regulate the binding of Red1 and Hop1 and also the distribution of DSBs in sub-telomeres.

      Strengths:

      The experiments were conducted with high quality and included nice bioinformatic analyses, and the results were mostly convincing. The text is easy to read.

      Weaknesses:

      The paper did not provide any new mechanistic insights into how DSB formation is suppressed at sub-telomeres.

      We respectfully disagree with this assessment. We show that the Sir complex suppresses DSB formation at a number of cryptic hotspots in the X elements and the adjacent subtelomeric sequences by causing chromatin compaction. The role of the Sir complex in transcriptional silencing, chromatin accessibility, and DSB formation had not previously been analyzed in the meiotic subtelomeres. That being said, Sir-dependent suppression is clearly not the only mechanism that suppresses DSBs in the subtelomeres, as we only observed DSB formation at a small number of hotspots. This was in and of itself a surprise, in particular given the large scale effect on chromatin compaction. We made an effort to more strongly emphasize the fact that additional layers of regulation must exist in the abstract and in the discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Evidence for cis-acting suppression by Y' elements requires further support. The authors propose that Y' elements act in cis to suppress axis protein association at chromosome ends. While this is an attractive model, the current analyses do not yet provide sufficient support for it.

      Thank you for this comment. Our data indeed appeared contradictory, because XY’ ends showed overall lower axis protein enrichment, yet our analysis of chromosome fusions, which also eliminated Y’ elements at some the fused ends provided no evidence for an effect of Y’ elements at those ends. As noted above, we now compared axis protein enrichment between S288c and SK1, which differ substantially in their number and distribution of Y’ elements (Supplementary Fig. 5). We found that axis protein distribution and enrichment was very consistent between SK1 and S288c when correcting for the displacement caused by the presence of Y' elements and other subtelomeric sequences. These data support the conclusion that axis protein enrichment levels are primarily encoded in cis and indicate that the presence of Y’ elements does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior (giving rise to the apparently lower axis protein enrichment on XY’ ends).

      (1a) In Figure S4c, the authors masked Y' elements to rule out the possibility that reduced binding within Y' elements themselves accounts for the overall underrepresentation in subtelomeric regions. However, since the authors propose that Y' elements suppress axis protein binding in surrounding regions in cis, it is appropriate to perform this analysis specifically on chromosome ends containing XY'.

      Thank you for this suggestion. We agree that this would specifically affect the XY’ ends. However, given that we did not see a change even with all the ends, we do not expect a change with just the XY’ ends.

      (1b) In Figure 2b-c, the authors conclude that removal of Y' elements by chromosome fusion does not reveal a long-range suppressive effect. However, the spatial extent of Y'-mediated suppression is not defined, making it unclear whether this experiment can test the proposed model. Perhaps plotting the averaged axis protein profile as a function of distance from Y' elements could help define the effective range of suppression and clarify whether the fusion experiment is informative in this context.

      Thank you. As noted above we now compared SK1 and S288c ends, which provided further evidence that Y’ elements do not affect axis protein enrichment beyond displacing binding sites further into the chromosome interior. In addition, we substantially expanded the description of the chromosome fusion experiment to more clearly outline the setup and the limitations of this experiment.

      (2) L402: "one of the first pieces of direct evidence that nucleosomes block meiotic DSB formation in vivo" sounds overstated, considering past publications (e.g., ref 45 and S. pombe ade6-M26 papers).

      We toned this down and added the references.

      (3) Figure 2e and other scatter plots: Correlation coefficients are reported without p-values. If the authors prefer to use confidence intervals from linear regression instead, they should justify this approach.

      We added p-values to all scatter plots.

      (4) Figure 7f. Explain blue dots.

      We apologize for this oversight (also applies to Supplementary Fig. 10). The blue dots are measurements within 5 kb of an X element. The red dots are the rest of the genome. We now included a legend in the panel to clarify this notation.

      (5) Figure 8d. To assess whether the conclusion can be generalized, the authors could plot the MNase and TrAEL-seq signal fold changes (sir3Δ/SIR3) for hotspots within 5 kb of X elements.

      We attempted various analyses in this direction. However, the range of the MNase-seq effect in sir3 mutants is much greater than the effect on DSBs, making it difficult to make any correlative statements. There are clearly additional layers of DSB suppression in the telomeric regions, and loss/gain of nucleosomes is not sufficient to switch hotspots on/off at most hotspots. We now included a statement to this end in the abstract and also further discuss this notion in the discussion.

      (6) Figure S1c. The apparent difference in X-element distribution may be influenced by bin size. This could be tested by repeating the analysis using smaller bins, comparable in size to the X elements, for all regions.

      We thank the reviewer for this thoughtful suggestion. To address this concern, we repeated the analysis using smaller bins comparable in size to X elements (450 bp) across all region types. Specifically, X elements were analyzed per annotated element, while Y′ elements, subtelomeric 20 kb regions, and internal regions were subdivided into fixed 450 bp windows, and mean input coverage was calculated for each window using the same width-weighted approach.

      This reanalysis did not materially alter the overall distribution patterns observed in Figure S1c. We observed only minor shifts in absolute values, which are expected when changing bin granularity.

      Any residual differences likely reflect underlying copy number of X elements at chromosome ends. Importantly, all ChIP signals in the manuscript are normalized to their corresponding input (ChIP/Input), which mitigates potential biases arising from local copy number variation.

      (7) Figure S2. X elements are difficult to find (e.g., chrVII-L).

      We now included arrowheads at locations with full-length X elements. Partial X elements are marked with stars.

      (8) Figure S7. Please indicate the endpoints of spreading.

      As apparent in this figure and also indicated in the quantification in Supplementary Fig. 9a, spreading of the Sir complex is in most cases quite limited. The example in Supplementary Fig. 9b is one of the largest spreads we observed. The scale of the spreading is hard to meaningfully visualize in Supplementary Fig. 8 given the relatively large genomic distances shown in these profiles. We therefore refer the reader to the analyses shown in Supplementary Fig. 9a, which shows chromosome-resolved extent of spreading.

      Reviewer #2 (Recommendations for the authors):

      To go beyond the correlation between the presence of Y' elements and low levels of protein axis binding, subtelomeres could be easily truncated. Analyzing strains with different distributions of Y' elements would also be informative. The correlative analysis could also be expanded to compare how far the influence of Y' elements goes and whether the number of Y' impacts the extent of protein axis depletion.

      We respectfully disagree with the assertion that subtelomeres could easily be truncated. The high repetitiveness of these sequences makes targeted manipulations of the extreme ends where the Y’ elements are located essentially impossible and is the main reasons for the limitations associated with the analysis of the chromosome fusions as outlined in the response to reviewer 1.

      However, we would like to thank the reviewer for their suggestion to analyze different strain backgrounds. We now compared axis protein enrichment between S288c and SK1. For this analysis, we took advantage of a dataset we had produced previously that measures Red1 enrichment in SK1/S288c hybrid strains, which provide a powerful internally controlled setup that eliminates effects caused by differential timing and synchrony between samples. As now shown in Supplementary Fig. 5, SK1 and S288c differ substantially in their subtelomeric architecture at many ends, including extensive differences in the number and distribution of Y’ elements. Importantly, axis protein distribution was very consistent between SK1 and S288c when correcting for the differences in length of individual chromosome ends, supporting the conclusion that axis protein enrichment levels are primarily encoded in cis. This analysis is now shown in Fig. 2c. These data also indicate that the presence of Y’ elements does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior.

      Given the separation between protein axis loading and DSB induction, it would be interesting to test whether the presence of Y' elements influences the frequency and position of DSB induction.

      We agree that this experiment would be very interesting. However, given the experimental challenges associated with targeted manipulation of Y’ elements as outlined above, we believe that this experiment lies outside the scope of this study. Our observations that Y’ elements do not grossly influence axis protein enrichment in their vicinity may also make an effect on DSB formation less likely.

      The effect of Dot1 on Red1 loading is intriguing because it is at least partially independent of its main known target H3K79, yet fully dependent on Sir3. However, this effect extends far beyond Sir3 binding as detected by ChIP. This is surprising because Dot1 has a limited effect on Sir3 binding as detected by ChIP, and SIR3 deletion has no impact on Red1 binding. However, Dot1 was shown to limit Sir3 spreading to 20 kb on average when overexpressed (Katan-Khaykovich and Struhl 2005; Hocher et al, 2018). It would be interesting to test whether the regions affected by DOT1 deletion coincide with the zone covered by Sir3 upon overexpression (Extended Silent Domains: ESDs, Hocher et al., 2018).

      We agree that this would be an interesting analysis. Unfortunately, the available data on the extended silent domains were not obtained in SK1 and, as noted above, the chromosome end structure differs substantially between the strains, preventing direct comparisons without repeating all the relevant analyses in S288c. In addition, the available data was collected in vegetative cells, although this may be less of an issue given that our analyses show similar spreading in vegetative and meiotic cells. However, short of repeating SIR3 overexpression in meiosis (which also would require a different overexpression regimen as galactose interferes with meiosis), we are not in a position to do this analysis.

      As mentioned in the manuscript, the interplay between the Sir complex and Dot1 has been shown to affect checkpoint regulation during meiotic recombination. However, a discussion on how this relates to the observations reported here is missing.

      Thank you. We included a discussion of this role and its relation to our observations.

      Also, it is unclear why the authors did not investigate the impact of Dot1 and Sir3 impact on the binding of Hop1 rather than Red1, given that Hop1 is currently « the most upstream regulator of recombination known to be depleted about 20 kb from chromosome ends. »

      We changed this statement in the introduction to avoid confusion and also included a model figure that specifically highlights the Rec8-dependent recruitment as a regulatory target.

      Our data show that most of the telomere-proximal effects seem to act through the Rec8-dependent recruitment pathway for which Red1 is the most upstream regulator known. So, although the most upstream factor known before this study was Hop1, our data now identify the interaction between Red1 and Rec8 as the most upstream regulatory node.

      Sir3's impact on DSB induction is compelling, yet it only accounts for a small proportion of DSB depletion in subtelomeric regions. Thus, the main mechanisms suppressing crossover close to the ends of chromosomes remain to be deciphered. This should be acknowledged and discussed.

      In addition to the explicit statement of this conclusion in the results, we now added another statement in the abstract and also expanded the discussion of the fact that there are clearly additional levels of regulation that remain to be discovered.

      Reviewer #3 (Recommendations for the authors):

      Major points:

      It would be nice to show a schematic summary of the authors' main conclusion.

      Thank you, we now included a model schematic as Fig. 9.

      Minor points:

      (1) Supplemental Figure 2: A small box for the X element is marked with the same color as the Y' element, and so it is very hard to find the X element. Please use the clearer color, and it would be nice to show the chromosome ends without the X element (lines 129-130).

      We now included arrowheads at locations with full-length X elements. Partial X elements are marked with stars. This notation also makes it obvious which ends lack annotated X elements.

      (2) Line 156-163, Figure 2b: In the main text, "chromosome fusion between chromosome IV right arm and chromosome I left arm" should be mentioned. Moreover, it isn't very clear to have the data in the S288C background. The fusion points are different between S288C and SK1 (the structures of these ends are quite different). Please explain the authors' logic in the text. 

      To improve clarity, we have included a schematic to better highlight which chromosomal sequences were removed. We have also substantially expanded the description of this experiment and explicitly state the limitations of this assay.

      (3) Supplemental Figure 6: Since the sir3 mutation affects the binding of Red1 EARs (and centromeres). It would be nice to show the similar sets for the HML, MAT, and HMR loci (and intergenic regions as a control).

      We are unfortunately statistically underpowered to perform a meta-analysis of just HML, HMR and MAT. However, we now indicated the positions of HML and HMR in Supplementary Fig. 2 and 8, so the binding of the axis proteins and Sir3 can be inspected directly. MAT is not within 50 kb of a chromosome end and thus was not captured in these analyses.

      (4) Line 322-, the section: From here, the authors switched their story from the sir3 to the sir2. It would be nice to provide the logic with a small introduction on the relationship between Sir2 and Sir3.

      We apologize for this confusion. We are not switching our story to Sir2 but rather are taking advantage of an available dataset that analyzed DSBs in sir2 mutants. We then return to Sir3 to also analyze DSBs in the sir3 mutant and analyze its interaction with a dot1 mutation. To better support the logic, we now briefly reiterate that Sir2 and Sir3 are part of the same complex at the beginning of this section.

      (5) Line 330-331, Figure 8a (and also Supplemental Fig. 8c): Would you explain a bit more about matched strain in the text or figure legend? Each dot represents a strain. If so, please show the strains used here.

      Each dot refers to an individual X or Y’ element that is shown matched in WT and mutant to highlight the trends at the level of individual elements. This is noted in the figure legend.

      (6) Supplemental Figure 7 (and 2): It would be nice to show the position of the HML, MAT, and HMR loci as well as the centromeres in the Figure.

      We now indicated the positions of HML and HMR in Supplementary Fig. 2 and 8. MAT and the centromeres are not located within 50 kb from chromosome ends.

    1. Author response:

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

      We thank you for the time you took to review our work and for your feedback! The main changes to the manuscript are:

      (1) We have performed additional experiments to increase the number of recordings from frontal and occipital electrodes (previously 51 (occipital: O1+O2) and 26 (frontal: Fp1+Fp2), now 133 and 102). The additional data have strengthened many of our results, including for example the trend for a latency difference between occipital and frontal electrodes that was likely underpowered and is now significant (Figure 3E). We have updated all relevant figures to include the additional data (Figures 2–6, Figure S4, Figure S5). None of the main conclusions have changed.

      (2) As suggested by reviewer 1, we have conducted additional experiments to rule out the possibility that the observed effects were driven by the temporal order of open and closed loop sessions (new Figure S6). We also found another 9 participants who were willing to go on the ‘vomit comet’ of six degrees of freedom (6DOF) playback (previously 5, now 14). These data have further strengthened our conclusion that playback halt responses in 4DOF and 6DOF playback are not substantially different (Figure S4).

      (3) To address the point of reviewers 2 and 3, that mismatch negativity (MMN) responses would be larger on temporal electrodes, we conducted additional experiments in which we also recorded from temporal electrodes T3–T6. We have now added a comparison of visuomotor mismatch and MMN responses on T3–T6 electrodes as Figures S8–S9. On all electrodes, visuomotor mismatch responses were larger than MMN responses.

      (4) As suggested by reviewer 1, we have added an analysis of the experience-dependent changes in mismatch responses comparing frontal and occipital responses early and late in the session (new Figure 4).

      (5) As suggested by reviewer 2, we conducted additional experiments in an independent cohort of participants (note, without concurrent EEG) to measure eye movements triggered by visuomotor mismatches. We found eye-movement speed and blink/eye-closure changes, but these had longer latency than visuomotor mismatch responses (Figure S7).

      (6) Finally, as suggested by reviewers 2 and 3, we applied independent component (ICA) and time–frequency analyses to the EEG data. We show these results and explain why they are not applicable or useful in our case in the responses below.

      Please note, during the revision, we found that a part of our analysis used a bandpass of 0.2-100 Hz while a 1-100 Hz bandpass filter was used elsewhere. This has now been standardized to a 1-100 Hz bandpass filter, and the corresponding methods were updated. This resulted in no relevant changes to the figures. Additionally, the 50 Hz band-stop filter was erroneously described in the methods as 49-51 Hz. The filter used was 40-60 Hz, and the methods have been updated to reflect this.

      Reviewer #1 (Public review):

      In this paper, the authors wished to determine human visuomotor mismatch responses in EEG in a VR setting. Participants were required to walk around a virtual corridor, where a mismatch was created by halting the display for 0.5s. This occurred every 10-15 seconds. They observe an occipital mismatch signal at 180 ms. They determine the specificity of this signal to visuomotor mismatch by subsequently playing back the same recording passively. They also show qualitatively that the mismatch response is larger than one generated in a standard auditory oddball paradigm. They conclude that humans therefore exhibit visuomotor mismatch responses like mice, and that this may provide an especially powerful paradigm for studying prediction error more generally.

      Asking about the role of visuomotor prediction in sensory processing is of fundamental importance to understanding perception and action control, but I wasn't entirely sure what to conclude from the present paradigm or findings. Visuomotor prediction did not appear to have been functionally isolated. I hope the comments below are helpful.

      (1) First, isolating visuomotor prediction by contrasting against a condition where the same video stream is played back subsequently does not seem to isolate visuomotor prediction. This condition always comes second, and therefore, predictability (rather than specifically visuomotor predictability) differs. Participants can learn to expect these screen freezes every 10-15 s, even precisely where they are in the session, and this will reduce the prediction error across time. Therefore, the smaller response in the passive condition may be partly explained by such learning. It's impossible to fully remove this confound, because the authors currently play back the visual specifics from the visuomotor condition, but given that the visuomotor correspondences are otherwise pretty stable, they could have an additional control condition where someone else's visual trace is played back instead of their own, and order counterbalanced. Learning that the freezes occur every 10-15 s, or even precisely where they occur, therefore, could not explain condition differences. At a minimum, it would be nice to see the traces for the first and second half of each session to see the extent to which the mismatch response gets smaller. This won't control for learning about the specific separations of the freezes, but it's a step up from the current information.

      In theory, it is correct that the open loop (playback) session is predictable. However, this is relatively unrealistic. The open loop session is a 5-minute sequence that participants have only experienced once before, when they were generating it in the closed loop session a couple of minutes earlier. It is unlikely that participants would remember the entire sequence to a precision of less than a second, which is what they would need to predict the mismatch event. However, the reviewer is correct that it is possible that the mismatch events lose salience with time, for example as a consequence of participants losing interest in the task with time, or by undergoing some form of adaptation. To address this, we repeated the experiments with the sequence of closed and open loop sessions reversed (Figures S6A-S6C), and we analyzed the responses as a function of time within the session (Figures S6D and S6E), as suggested.

      The reversed-order design consisted of (1) open loop session: a playback, in which participants viewed the recorded closed loop session of a previous participant. This was followed by (2) a closed loop session, in which participants actively walked through the tunnel and experienced visuomotor mismatch events. Using this design, we again found that responses in the closed loop session were significantly larger than in the open loop session (Figures S6A-S6C).

      In addition, we analyzed both new and previously collected data as a function of time in the session. We computed moving average responses across 10 mismatch or playback halt trials at different percentages of progress through the paradigm (Figures S6D and S6E). This analysis revealed no consistent experience-dependent changes that could account for the observed differences between closed and open loop session. While there was indeed some form of experience dependent attenuation of visuomotor mismatch responses (see new Figure 4), the difference at the transition from mismatch to playback halt (and vice versa) far exceeded these adaptation effects (Figures S6D and S6E). This analysis was performed only on data from participants for whom we had both closed and open loop sessions and met our inclusion criteria.

      We used a similar analysis to test whether early and late responses within a session systematically differed (new Figure 4). Here, to maximize the chance of finding a difference, we compared early (first five) and late (last five) trials. Behaviorally, participants reduced their walking speed following mismatch events, with a significantly larger reduction during early trials (14.3%) than during late trials (5.7%) (Figure 4A). Neural responses mirrored this pattern primarily on frontal electrodes: frontal activity showed a clear attenuation from early to late trials (Figure 4B), consistent with the reduction in behavioral responses. In contrast, changes on occipital electrodes were much smaller between early and late trials (Figure 4C-4D). Thus, experience-related modulation is substantially stronger in frontal compared to occipital regions.

      In sum, we do not believe that the difference between visuomotor mismatch responses and playback halt responses can be explained by differences in the predictability of mismatch and playback halt events.

      (2) Second, the authors admirably modified their visual-only condition to remove nausea from 6 df of movement (3D position, pitch, yaw, and roll). However, despite the fact it's far from ideal to have nauseous participants, it would appear from the figures that these modifications may have changed the responses (despite some pairwise lack of significance with small N). Specifically, the trace in S3 (6DOF) and 2E look similar - i.e., comparing the visuomotor condition to the visual condition that matches. Mismatch at 4/5 microvolts in both. Do these significantly differ from each other?

      Yes, the 6DOF playback halt response shown in the previous Figure S3 and the mismatch response shown in previous Figure 2E are significantly different (Author response image 1).

      Author response image 1.

      Comparison of visuomotor mismatch response (A) and 6DOF playback halt response (B) from the original submission with statistics of the comparison (C).

      Nevertheless, to strengthen this conclusion, we collected additional data in the 6DOF condition. We show the comparison for participants for whom both closed loop (active) and open loop sessions (6DOF) were recorded within the same recording session (14 participants) in Figure S4. Consistent with our previous findings, visuomotor mismatch responses were significantly larger than 6DOF playback halt responses (Figures S4A-S4C). And we found no evidence of a difference between 6DOF and 4DOF playback halt responses (Figures S4D and S4E).

      (3) It generally seems that if the authors wish to suggest that this paradigm can be used to study prediction error responses, they need to have controlled for the actions performed and the visual events. This logic is outlined in Press, Thomas, and Yon (2023), Neurosci Biobehav Rev, and Press, Kok, and Yon (2020) Trends Cogn Sci ('learning to perceive and perceiving to learn'). For example, always requiring Ps to walk and always concurrently playing similar visual events, but modifying the extent to which the visual events can be anticipated based on action. Otherwise, it seems more accurately described as a paradigm to study the influence of action on perception, which will be generated by a number of intertwined underlying mechanisms.

      We are not entirely sure we understand the point here correctly. If the reviewer is suggesting that visuomotor coupling is not describable by the ideas of predictive processing, we disagree. However, given that the papers the reviewer is pointing to are premised on what seems to be a somewhat unorthodox interpretation of predictive processing when it comes to cortical circuits, we suspect this is contributing to the misunderstanding here. Let us briefly explain. In the two papers, Press and colleagues argue that most experiments cannot distinguish between “predictive cancellation” and “gated suppression”. This is indeed relatively tricky, even when one has single neuron data. The question is, does movement simply suppress sensory feedback (as is likely the case e.g. in the famous example of the cricket), or does movement result in a precise removal of only the self-generated sensory reafference? The first good evidence of the latter happening in any system is quite recent (Keller and Hahnloser, 2009). The premise the authors build their argument on is that the theory posits that “the brain predictively ‘cancels’ expected action outcomes from perception” (from the abstract of one of the papers). This is incomplete. The minimum circuit for predictive processing is composed of 3 neuron types: positive prediction error neurons, negative prediction error neurons, and internal representation neurons. Only the positive prediction error neurons have the predictive cancellation property the authors discuss. This is not the case for either negative prediction error neurons, or for the internal representation neurons. Negative prediction error neurons are excited by predictions and suppressed by sensory input (i.e. if anything, they are “predictively amplified”). This circuit is relatively well characterized in mouse cortex – for a brief summary see (Keller and Mrsic-Flogel, 2018). Note, this is not our idea of course – the original formulation of predictive processing (Rao and Ballard, 1999) was built to explain end-stopping. These are responses to the absence of an expected line that were stronger than would be expected from classical theories (i.e. negative prediction error responses). In mouse visual cortex, we know that a sudden break in the coupling between locomotion and visual flow selectively activates layer 2/3 negative prediction error neurons. Thus, if human cortex also implements a predictive processing like circuit with positive and negative prediction error neurons, we would expect a break in visuomotor coupling to drive a measurable response in visual cortex (by exciting the population of negative prediction error neurons – this is also why we are quite excited by the phase reversal of visual and mismatch responses as this could indicate that mismatch activates negative prediction error neurons first and positive prediction error neurons later, and vice versa for visual stimulation – negative prediction error neurons are more superficial in cortex (O’Toole et al., 2023)). We do indeed find a response over occipital cortex consistent with the negative prediction error response we observe in mouse cortex. The difficulty in distinguishing “predictive cancellation” and “movement driven suppression” comes only when looking at positive prediction error type responses (that are suppressed by predictive inputs) but does not apply to negative prediction error responses. The predictive processing circuit we are testing is the one described by (Keller and Mrsic-Flogel, 2018; Rao and Ballard, 1999), and here the break in visuomotor coupling is a stimulus that drives negative prediction error responses. Note, other authors who have thought about cortical implementations of predictive processing (e.g. (Bastos et al., 2012)) have glossed over the problem that individual neurons cannot trivially encode both positive and negative errors. Prediction errors are a signed quantity. If neurons signal prediction errors in firing rates and are close to zero firing rate at baseline (as is the case in layer 2/3 of cortex), they cannot (short of rather exotic ideas) encode a signed prediction error. Hence such proposals are not very useful for thinking about prediction error responses in cortex. For these reasons, we see no problem with referring to the response as a prediction error response. This is in line with a large body of mouse research (using a nearly identical paradigm) on the topic.

      One could of course argue that gated suppression could also mean that movement relieves suppression. Thus, one could assume that some neurons are suppressed by movement while others are enhanced. If one allows for enough neuron and stimulus specificity in the precision of the movement related suppression and enhancement of responses, the two models (predictive processing and gated suppression) become equivalent, and the discussion becomes semantic. See (Vasilevskaya et al., 2023) for an extended discussion on this point, and the reasons why we think predictive processing is a more useful model than gated suppression (keep in mind, gated suppression only explains the data if we allow for stimulus/neuron specific gain factors of the suppression, in which case the two models are equivalent).

      More minor points:

      (1) I was also wondering whether the authors may consider the findings in frontal electrodes more closely. Within the statistical tests of the frontal electrodes against 0, as displayed in Figure 3c, the insignificance of the effect of Fp2 seems attributable to the small included sample size of just 13 participants for this electrode, as listed in Table S1, in combination with a single outlier skewing the result. The small sample size stands out especially in comparison to the sample size at occipital electrodes, which is double and therefore enjoys far more statistical power. It looks like the selected time window is not perfectly aligned for determining a frontal effect, and also the distribution in 3B looks like responses are absent in more central electrodes but present in occipital and frontal ones. I realise the focus of analysis is on visual processing, but there are likely to be researchers who find the frontal effect just as interesting.

      That is correct; our data in frontal electrodes was likely underpowered. The reason we have fewer data in frontal electrodes is that eye-blink artifacts are particularly strong in frontal channels, resulting in a larger proportion of trials failing to meet our data inclusion criteria. We have now added more data from frontal and occipital electrodes by including additional experimental sessions. In addition, we applied less stringent trial-exclusion criteria, requiring that no artifacts occur within the time window −0.5 to 1 s relative to the event trigger (instead of −0.5 to 2 s). This adjustment allowed us to retain a larger number of trials. As anticipated by the reviewer, this increase in data was sufficient to confirm a significant response to the visuomotor mismatch event at both frontal electrodes (Figure 3C). The expanded dataset also revealed a significant difference in response onset times between occipital and frontal electrodes (Figure 3E), an effect that was not significant previously. In addition, we have included analysis comparing early and late mismatch responses in frontal and occipital electrodes (Figure 4).

      (2) It is claimed throughout the manuscript that the 'strongest predictor (of sensory input) - by consistency of coupling - is self-generated movement'. This claim is going to be hard to validate, and I wonder whether it might be received better by the community to be framed as an especially strong predictor rather than necessarily the strongest. If I hear an ambulance siren, this is an especially strong predictor of subsequent visual events. If I see a traffic light turn red, then yellow, I can be pretty certain what will happen next. Etc.

      This is a statistical argument. Every movement – throughout life – is directly and immediately coupled to sensory feedback and has been throughout evolutionary history. The vast majority of visual input you receive (we estimate, well above 99%) is the consequence of your own movements (e.g. every few 100 ms your eye movements cause a full field change in your visual input). The same is likely true of proprioceptive and somatosensory input – the vast majority is the direct consequence of your own movements (not other people poking you). This is likely different in the auditory system where a much larger fraction of the input is externally driven (depending a bit on how much one likes to talk). But even here the best predictor is self-motion (most non-self-generated sounds one experiences in life are very difficult to predict with millisecond precision). The example the reviewer gives is a good illustration of this. Take the siren that hails the appearance of an ambulance. The siren tells us that an ambulance will appear, but not how it will look, not when exactly it will appear, and with only very low resolution as to where it will appear. Incidentally, if you ask people to draw an ambulance they tend to draw a WWII style white square vehicle with a red cross on the side – a style of ambulance they likely have not ever seen in life. Their visual predictions of what they are about to see are very low resolution. We catastrophically fail at making pixel perfect predictions from learned stimulus associations of this nature. The traffic light example is difficult to compare to visual feedback control of movement as it is a much simpler prediction of a single bit in the form of a change in color of an existing object.

      In addition, consider how often (in life) you have seen an ambulance after hearing it? 100 times maybe? Maybe less. How often have you seen traffic lights change - 10 000 times? 100 000 times? Now consider, how often you have experienced the visual consequences of moving your head or eyes to the left (keep in mind this includes micro saccades) – at a conservative, once per second, that is somewhere on the order of 1 000 000 000. This is not even in the same ballpark. Our brains can certainly learn to make the ambulance and traffic light type predictions - to some extent - but by far the best predictor of sensory feedback (simply by virtue of the physics of how our body interacts with the world) is self-motion.

      We think this is an argument we can make based on first principles, and one that is frequently overlooked in the field, as experiments often focus on training people or animals to learn novel associations that, especially in the case of mice, we often have no idea whether cortical circuits can even learn. We should focus experiments on the predictive systems our brains have evolved since long before the evolutionary appearance of ambulances and traffic lights. We understand that the reviewer may disagree with this, but unless the reviewer has a concrete example of an even stronger predictor (as measured by frequency of experience, consistency in coupling, and precision in timing – we can’t think of one), it is a point we will make.

      (3) The checkerboard inversion response at 48 ms is incredibly rapid. Can the authors comment more on what may drive this exceptionally fast response? It was my understanding that responses in this time window can only be isolated with human EEG by presenting spatially polarized events (cf. c1, e.g., Alilovic, Timmermans, Reteig, van Gaal, Slagter, 2019, Cerebral Cortex).

      We don’t know, but it is not inconsistent with previous reports. For example, compare the “standing” and “fast walking” target ERP responses in Figure 5 of (Gramann et al., 2010). Both here and in our data, the fast response peak is only really apparent in the direct comparison of visual responses recorded while participants were walking to those when they were stationary.

      While we have taken great care to calibrate the timing of the visual display with the EEG recording, one could be worried that the alignment is off by as much as tens of milliseconds. However, even if this were so, one could use P1 as a reference and determine that the fast peak roughly precedes P1 by about 40 ms. Which again would result in a latency of about 50 ms of the fast walking peak (assuming P1 peaks at about 90 ms). In sum, we have added a reference to the previous work (that we found thanks to the reviewer’s comment) but fear we have nothing intelligent to say beyond that.

      Reviewer #2 (Public review):

      Summary:

      This study investigates whether visuomotor mismatch responses can be detected in humans. By adapting paradigms from rodent studies, the authors report EEG evidence of mismatch responses during visuomotor conditions and compare them to visual-only stimulation and mismatch responses in other modalities.

      Strengths:

      (1) The authors use a creative experimental design to elicit visuomotor mismatch responses in humans.

      (2) The study provides an initial dataset and analytical framework that could support future research on human visuomotor prediction errors.

      Weaknesses:

      (1) Methodological issues (e.g., volume conduction, channel selection, lack of control for eye movements) make it difficult to confidently attribute the observed mismatch responses to activity in visual cortical regions.

      (2) A very large portion of the data was excluded due to motion artefacts, raising concerns about statistical power and representativeness. The criteria for trial inclusion and the number of accepted trials per participant appear arbitrary and not justified with reference to EEG reliability standards.

      (3) The comparison across sensory modalities (e.g., auditory vs. visual mismatch responses) is conceptually interesting, but due to the choice of analyzing auditory mismatch responses over occipital channels, it has limited interpretability.

      We have responded to these points in the more detailed itemization below.

      The authors successfully demonstrate that visuomotor mismatch paradigms can, in principle, be applied in human EEG. However, due to the issues outlined above, the current findings are relatively preliminary. If validated with improved methodology, this approach could significantly advance our understanding of predictive processing in the human visual system and provide a translational bridge between rodent and human work.

      Reviewer #2 (Recommendations for the authors):

      Overall, the study addresses an interesting and underexplored question (translation of the visuomotor mismatch responses observed in rodents to humans). Below, please find a list of specific suggestions for improvement

      Introduction:

      (1) "updating internal representations and internal models" - what is the difference between the two, and why is it relevant to this study?

      In a nutshell, an internal model is the synaptic weight matrix that transforms between coding spaces. An internal representation is the activity pattern coding for the current representation. See (Aizenbud et al., 2025; Keller and Mrsic-Flogel, 2018) for more lengthy elaborations. The fact that the mechanism used for representation update can also be used to update internal models (i.e. solve the credit assignment problem) is likely the prime advantage of predictive processing (see work from the Bogacz lab). The relevance to the current study is justifying why predictive processing is a reasonable hypothesis for the function of cortex.

      (2) "Certain stimuli can be predicted from the preceding sensory input" vs. "Predictions can also be based on memory" - how are these two different? Do you mean specific (e.g., long-term associative or episodic) memory types in the latter?

      Correct, this is an arbitrary distinction that primarily makes sense in the light of experimental approaches. In this particular case, we were talking about spatial memory. We made this explicit to increase clarity.

      (3) "the strongest predictor - by consistency of coupling - is self-generated movement"

      (a) Externally induced movement, while not self-generated and therefore not predicted, will also generate sensory coupling, so is it really only about consistency?

      Externally induced movement (as in somebody else moving one’s arm we are not sure this is what the reviewer means) will induce sensory-sensory coupling but not sensorimotor coupling. We might be misunderstanding the point. In case the reviewer means stimuli that trigger movement as in us asking participants to walk, or a sudden startle stimulus that makes them jump in all such cases there are of course sensorimotor predictions. Sensorimotor predictions are driven by efference copies of the motor command thus all movements whether ‘voluntarily’ executed or triggered by an external stimulus will drive sensorimotor predictions. (All of this of course assumes that the predictive processing theory is correct.)

      (b) Do you mean temporal consistency (minimal lags), statistical contingencies (same movements linked to the same sensory inputs), or both? How does it differentiate sensorimotor/visuomotor mismatch responses from responses to incongruent stimuli in sensory modalities (e.g. audiovisual)?

      Both. We have rephrased the sentence to try to make this clearer. See also response to reviewer 1 minor point 2 above.

      How does it differentiate sensorimotor/visuomotor mismatch responses from responses to incongruent stimuli in sensory modalities (e.g. audiovisual)?

      Most cross-modal associations are much less consistent (the exact sound of a glass shattering is always slightly different and impossible for us to predict), and orders of magnitude less frequently experienced, than sensorimotor associations. Again, see also response to reviewer 1 minor point 2 above.

      (4) "Every movement is directly coupled to sensory feedback throughout life"

      This may be the case for proprioceptive and/or somatosensory feedback, but not necessarily for visual feedback (e.g., a mouse moving its tail), which is the topic of the study.

      Correct, there are movements that can be disconnected from visual feedback. Most of the time, most movements however are not, and we are studying one of the more prominent ones that is clearly not decoupled locomotion. The contrast we aim to highlight here very prominently is that there is still this vague idea in the field that you can take a participant, or a mouse, and expose them/it to a few tens or hundreds of trials of some sensory stimulus contingency and then probe for prediction error responses to a pattern only recently if at all learned. Given the life-long experience of subjects and mice, is it really surprising that oddball responses are less strong than a sensorimotor mismatch?

      (5) "However, the overall level of this motor-related activity is much higher than one would expect simply from predictions of visual feedback that are compared against visual input."

      Could you please clarify what one would expect in this case, and/or back it up with citations?

      This is in reference to the fact that there are very strong movement related signals in the mouse visual cortex that persist even when the mouse is in complete darkness. In darkness, movements should not trigger any visual feedback change hence the activity is difficult to explain as a movement related prediction of visual flow. We have rephrased this section of the introduction to make this clearer.

      (6) "The more precise the prediction and comparison, the less motor-related activity should be detectable in visual cortex."

      I think this conflates two issues. A good match between prediction and input would indeed result in sensory attenuation. However, sensory precision, at least in active inference, can upregulate prediction error responses. Since predictions cannot be assumed to be perfect (due to external or internal noise), increased precision may therefore augment activity. See e.g. https://doi.org/10.1007/s10339-013-0571-3

      We agree with the reviewer – the phrasing here was misleading. We do not mean precision in the predictive processing sense, but the precision of sensorimotor control necessary for the behavior. We have rephrased the corresponding section of the manuscript.

      (7) Neither the introduction nor the discussion refers to previous human EEG studies on sensorimotor mismatch responses, where sensory feedback doesn't match motor actions (e.g. https://doi.org/10.3758/s13423-021-01992-z ; https://www.sciencedirect.com/science/article/pii/S0028393214003777 ; https://www.sciencedirect.com/science/article/pii/S0028393219301265).

      The studies cited by the reviewer primarily test how discrete violations of learned action–outcome associations are represented in the brain, whereas our visuomotor mismatch paradigm probes violations of continuous sensorimotor coupling during ongoing action. The paradigms are conceptually different both in how strong the coupling is (lifelong vs. learned in the experiment), and in how prediction errors are likely used (visuomotor control vs. stimulus detection). We have added a brief part to our introduction discussing this.

      Results:

      (1) A very large proportion of the dataset was excluded due to movement artefacts. This is rather problematic as

      (a) the rationale behind finding mismatch responses is that motion-related (neural) signals should affect visual cortical activity, so it's essential to disentangle these neural signals from artefacts;

      Correct, we excluded 21.7% of the total data for visuomotor mismatch paradigm. Note, this percentage compares to other similar studies of EEG recordings during movement (Oliveira et al., 2016). By “problematic”, we assume the reviewer means the fact that we have artefacts, not that we exclude trials with artefacts. The movement artefacts are typically caused by the acceleration during stepping in participants with a heavy gait. None of these movement artefacts are time locked to any of the responses we investigate. Thus, they should just appear as increased levels of noise if not excluded. We don’t understand why the reviewer thinks this is particularly problematic for our analysis/conclusions (beyond the trivial consequence of increasing noise levels that would only cause us to underestimate the strength of the mismatch signals we report).

      (b) the criterion for the number of trials of 15 triggers (per condition?) is arbitrary and lower than widely used in the literature, so authors should demonstrate that this is a sufficient number to observe a measurable ERP even for those participants with 15 triggers;

      We have between 16 and 25 visuomotor mismatch events per participant. Author response image 2 is a selection of single participant examples with different number of trials. The number of mismatch events is limited by the fact that we introduce them approximately every 10 - 15 s and have a total duration of the closed loop session of 5 minutes. Thus, on average, we expect to have 24 mismatch events. But we are not sure we understand the logic of the comment, if we set exclusion too low, we just risk losing a response in the noise. And we clearly have stronger and higher signal to noise mismatch responses with an average of 20 trials compared to visual responses during movement with an average of 40 trials or MMN responses with an average of 28 trials.

      Author response image 2.

      Reliable ERPs can be observed with as few as 16 trials across EEG channels. (A) Histograms showing the distribution of the number of valid mismatch trials per participant for each electrode pair (Fp1–2, C3–4, P3–4, O1–2). (B) Representative EEG responses to visuomotor mismatch events from a single participant, recorded at electrode pairs Fp1–2, C3–4, P3–4, and O1–2. Waveforms were computed using the indicated number of trials (shown above each trace). Dashed vertical red lines are onset and offset of the visuomotor mismatch.

      (c) it seems that the seemingly static "visual" condition resulted in a larger proportion of data rejected due to movement (or, as later mentioned, nausea) than the "visuomotor" condition, which is counterintuitive and needs further explanation;

      This is a misunderstanding the ‘visual paradigm’ the reviewer is referring to are the experiments shown in Figure 1. Here we record visual responses in both sitting and walking participants. In this experiment, as in others, exclusion was primarily driven by part of the paradigm where the subjects were moving. To make this clearer we have added Table S2 to the manuscript that provides an overview of trials excluded by paradigm and session.

      (d) authors mention eye movements as a potential issue, which should be possible to detect from frontal channels. Additionally, it's not entirely clear how many datasets were discarded (the results section mentions 19/48 in the visual condition, then 4+11 in the playback condition - isn't this the same condition?)

      The visual paradigm corresponds to the data shown in Figure 1, in which participants viewed a flipping checkerboard in both a walking and a stationary session. The open loop session is part of the visuomotor paradigm shown in Figure 2, where participants were exposed to a replay of the visual flow that had been self-generated during the preceding closed loop session, including the visual flow halts that constituted visuomotor mismatches in the closed loop session. Please note, to avoid such confusion, we have attempted to standardize the usage of paradigm (visual vs. visuomotor) and session (sitting vs. walking, and closed loop vs. open loop) throughout. In addition, we have added a table to summarize the number of excluded trials by paradigm and session as Table S2 to the manuscript.

      In comments 1 and 2 of the public review, the reviewer also points out that we did not control for eye movements and we presume relatedly claims that we did not use common EEG reliability standards. Regarding the first point, we performed additional experiments in an independent cohort of participants to test whether eye movements could account for the visuomotor mismatch responses. We recorded eye movements during closed loop sessions and found that changes in eye speed (Figure S7A) or blink rate (Figure S7B) following the mismatch stimulus had a longer latency than visuomotor mismatch responses in EEG. This suggests that the visuomotor mismatch response cannot be explained by eye blinks or changes in eye movement speed. Regarding the second point, we are not sure we understand. Trial exclusion based on a fixed voltage threshold of 100 µV is relatively common, and our rejection rates are on par, and particularly on occipital electrodes even lower, with other work in EEG recordings during locomotion or movement (see e.g. (Oliveira et al., 2016)).

      Nevertheless, we did attempt to apply independent component analysis (ICA) based filtering to the EEG data (Delorme and Makeig, 2004). However, these methods were designed for high channel density recordings. With only 8 channels, ICA is unable to reliably isolate eye movement or motion artefact components of the EEG. To illustrate this, we tested two artifact-rejection strategies. In the first approach, components associated with non-neural artifacts (e.g., muscle activity, line noise, eye movements) were removed only if at least 90% of the component’s variance was assigned to a single artifact class (Author response image 3A). In the second, more permissive approach aimed specifically at reducing eye movement artifacts, components were removed if artifact-related activity exceeded 90% for non-eye artifacts, while the threshold for eye-related components was lowered to 60% (Author response image 3C). We lowered the threshold for excluding eye-related components to ensure that EEG signals influenced by eye movements were effectively removed. In both cases - whether the eye-component threshold was set to 90% or 60% - the averaged responses to visuomotor mismatch trials remained largely similar to the previously reported data, despite higher noise in some traces. Interestingly, when we then followed the ICA filtering by our voltage threshold based exclusion with a threshold of 100 µV, the resulting traces closely resembled the patterns described in the paper (Author response image 3B and 3D). Thus, we conclude the nonICA filtered responses are easier to interpret, free of any potential ICA filtering artifacts, and far less parameter choice (of the ICA filtering) dependent.

      Author response image 3.

      Removal of artifacts identified with ICA does not change the visuomotor mismatch responses. (A) Visuomotor mismatch responses recorded from occipital electrodes after artifact correction. Components associated with non-neural artifacts (e.g., muscle activity, line noise, eye movements) were removed only if ≥90% of the component’s variance was attributed to a single artifact class. Solid black line represents the mean, and shading indicates the SEM across participants. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but excluding trials with amplitudes exceeding 100 µV. (C) As in A, but components were removed if artifact-related activity exceeded 90% for non-ocular artifacts, while the threshold for eye-related components was lowered to 60%. (D) As in C, but excluding trials with amplitudes exceeding 100 µV.

      (2) The finding that mismatch responses are observed at all channels, with differences in amplitudes but not latencies, indicates that volume conduction may affect the results. I would strongly suggest accounting for this using a method appropriate for the very small number of channels, e.g., phase lag index.

      We are not sure we understand. The phase lag index is a method to estimate functional connectivity in a way that corrects for volume conduction (using phase lag). We make no claims about functional connectivity; thus, we are not sure what the reviewer is suggesting we do. The fact that the visual and visuomotor mismatch responses were measurable on all electrodes could indeed be in part explained by volume conduction, but we see no way to estimate the volume conduction contribution. From mouse calcium imaging data, we know that both visual and visuomotor mismatch responses spread across large parts of dorsal cortex (including frontal regions like the ACC).

      With the addition of new data, the latency difference between occipital and frontal electrodes - previously observed only as a trend - is now statistically significant (Figure 3E). Occipital responses emerge earlier than frontal responses, suggesting that mismatch-related activity likely originates in sensory visual regions and subsequently propagates to more frontal areas, as similar to what had been reported in mouse cortex (Heindorf and Keller, 2024).

      (3) The authors compare different types of mismatch responses (including auditory oddballs) in the same set of (occipital) channels, but doesn't this undermine the spatial specificity of the results? Classical auditory mismatch negativity is typically observed over central channels, so weaker amplitudes of auditory mismatch responses in occipital channels are likely trivially explained by modality differences. As such, I'm not convinced that this comparison is informative even in a qualitative manner.

      To address this point, we conducted additional auditory oddball experiments with recordings over the auditory cortex (channels T3, T4, T5, and T6). Given our central reference, these channels should capture the strongest mismatch negativity. The amplitude of the visuomotor mismatch response exceeded that of mismatch negativity on all tested channels (new Figures S8 and S9).

      (4) On a similar note, is the polarity reversal found for visual vs. mismatch responses specific to occipital channels?

      Thank you for this interesting question. In fact, polarity reversal was consistently observed across all recorded channels; this has now been added as a main figure to the manuscript (Figure 5).

      (5) Figure S4C seems to cut off one outlier, and I don't see this outlier included in the boxplot.

      Correct, that is why we describe the boxplots in the figure legend as: “Boxes mark median, quartiles, and range of data not considered outliers.” The axes were now adjusted to include all data points.

      Discussion:

      "A central tenet of the cortical circuit for predictive processing is the split into separate populations of neurons that compute positive and negative prediction errors (Keller and Mrsic-Flogel, 2018; Rao and Ballard, 1999)" - this may be the case for visuomotor mismatch signals or reward prediction errors, but signed PEs do not play a central role in other proposed microcircuits for predictive processing in the perceptual domain (e.g. Bastos)

      Signed prediction errors do not play a central role in proposed cortical microcircuits for predictive processing that do not burden themselves with making a concrete proposal for the implementation of the prediction error computation. The (Bastos et al., 2012) work is a good example of this. The equation for the error term provided in that paper is clearly signed (nothing stops the error from going negative), but no proposal is made for how layer 2/3 excitatory neurons are supposed to signal this quantity. With baseline activity levels close to zero in layer 2/3, there really is only one way to do this, and that is separate populations of negative and positive prediction error neurons. With non-zero baseline firing rate, one could do this bidirectionally around a mean firing rate (as is typically thought of dopaminergic RPE neurons). There are more abstract Bayesian implementations that assume logarithmic transformations that could also implement a prediction error-like system without negative firing rates. But given the absence of any physiological evidence, we will refrain from discussing these. However, most importantly, there is now considerable evidence for the existence of both negative and positive prediction error neurons in layer 2/3 of mouse visual cortex. Thus, by “cortical circuit for predictive processing” we here mean those that make biologically plausible proposals for prediction error computations. Also note, the (Rao and Ballard, 1999) model is probably the prime example for what the reviewer calls a proposed microcircuit for predictive processing in the “perceptual domain”.

      Reviewer #3 (Public review):

      Summary:

      Solyga, Zelechowski, and Keller present a concise report of an innovative study demonstrating clear visuomotor mismatch responses in ambulating humans, using a mobile EEG setup and virtual reality. Human subjects walked around a virtual corridor while EEGs were recorded. Occasionally, motion and visual flow were uncoupled, and this evoked a mismatch response that was strongest in occipitally placed electrodes and had a considerable signal-to-noise ratio. It was robust across participants and could not be explained by the visual stimulus alone.

      Strengths:

      This is an important extension of their prior work in mice, and represents an elegant translation of those previous findings to humans, where future work can inform theories of e.g., psychiatric diseases that are believed to involve disordered predictive processing. For the most part, the authors are appropriately circumspect in their interpretations and discussions of the implications. I found the discussion of the polarity differences they found in light of separate positive and negative prediction errors, intriguing.

      Weaknesses:

      The primary weaknesses rest in how the results are sold and interpreted.

      Most notably, the interpretation of the results of the comparison of visuomotor mismatches to the passive auditory oddball induced mismatch responses is inappropriate, as suboptimal electrode choices, unclear matching of trial numbers, and other factors. To clarify, regarding the auditory oddball portion in Figure 5, the data quality is a concern for the auditory ERPs, and the choice of Occipital electrodes is a likely culprit. Typically, auditory evoked responses are maximal at Cz or FCz, although these contacts don't seem to be available with this setup. In general, caution is warranted in comparing ERP peaks between two different sensory modalities - especially if attention is directed elsewhere (to a silent movie) during one recording and not during the other. The authors discuss this as a purely "qualitative" comparison in the text, which is appreciated, and do acknowledge the limitations within the results section, but the figure title and, importantly, the abstract set a different tone. At least, for comparisons between auditory mismatch and visuomotor mismatch, trial numbers need to be equated, as ERP magnitude can be augmented by noise (which reduces with increased numbers of trials in the average).

      To address this point, we conducted additional auditory oddball experiments with recordings over the auditory cortex (channels T3, T4, T5, and T6). Given our central reference, these channels should capture the strongest mismatch negativity. Nevertheless, the amplitude of the visuomotor mismatch response exceeded that of mismatch negativity on all tested channels (these results are now shown in the new Figures S8 and S9), and the response power was significantly greater for the visuomotor mismatch than for mismatch negativity. Independent of electrode we test, the visuomotor mismatch response has a power 5 to 10 times higher than that of the MMN response. And the number of trials per participant that met quality criteria was comparable between the visuomotor mismatch paradigm (mean = 23 trials) and the auditory mismatch paradigm (mean = 28 trials) (Author response image 4).

      Author response image 4.

      Number of trials included for analysis is comparable between visuomotor and oddball paradigm. (A) Histogram showing the distribution of the number of valid trials per participant for O1-2 electrode pair in visuomotor mismatch paradigm. (B) Same as in A but for deviant stimulus presentations in the oddball paradigm.

      And more generally, the size of the mismatch event at the scalp does not scale one-to-one with the size at the level of the neural tissue. One can imagine a number of variables that impact scalp level magnitudes, which are orthogonal to actual cortex-level activation - the size, spread, and polarity variance of the activated source (which all would diminish amplitude at the scalp due to polyphasic summation/cancelation). The variance of phase to a stimulus across trials (cross trial phase locking) vs magnitude of underlying power - the former, in theory, relates to bottom-up activity and the latter can reflect feedback (which has more variability in time across trials; the distance of the scalp electrode from the activated tissue (which, for the auditory system, would be larger (FCz to superior temporal gyrus) than for the visual system (O1 to V1/2)). None of this precludes the inclusion of the auditory mismatch, which is a strength of the study, but interpretations about this supporting a supremacy of sensory-motor mismatch - regardless of validity - are not warranted. I would recommend changing the way this is presented in the abstract.

      We agree with the point that the EEG response does not need to reflect the total cortical activation. However, the discussion in the abstract (and elsewhere) is in the context of clinical experiments where the underlying cortical activity pattern is irrelevant if it does not trigger a clinically measurable (by EEG in this case) response. The abstract only makes a comparison to MMN implicitly in this sentence “Second, a paradigm that can trigger strong prediction error responses and consequently requires shorter recording times could simplify experiments in a clinical setting.” We are not sure how to phrase this even more carefully – the statement at face value is a truism. The reviewer, we assume, takes exception to the unstated implication that visuomotor prediction errors trigger stronger responses than MMN. Given the data we have, we assume most authors would not consider it an overstatement to make that claim outright.

      Otherwise, the data are of adequate quality to derive most of their conclusions.

      The authors claim that the mismatch responses emanate from within the occipital cortex, but I would require denser scalp coverage or a demonstration of consistent impedances across electrodes and across subjects to make conclusions about the underlying cortical sources (especially given the latencies of their peaks). In EEG, the distribution of voltage on the scalp is, of course, related to but not directly reflective of the distribution of the underlying sources. The authors are mostly careful in their discussion of this, but I would strongly recommend changing the work choice of "in occipital cortex" to "over occipital cortex" or even "posteriorly distributed". Even with very dense electrode coverage and co-registration to MRIs for the generation of forward models that constrain solutions, source localization of EEG signals is very challenging and not a simple problem. Given the convoluted and interior nature of human V1, the ability to reliably detect early evoked responses (which show the mismatch in mouse models) at the scalp in ERP peaks is challenging - especially if one is collapsing ERPs across subjects. And - given the latency of the mismatch responses, I'd imagine that many distributed cortical regions contribute to the responses seen at the scalp.

      This is an excellent point we have rephrased throughout to “over occipital cortex” instead of “in occipital cortex”.

      I think that Figure 3C, but as a difference of visual mismatch vs halting flow alone (in the open loop) might be additionally informative, as it clarifies exactly where the pure "mismatch" or prediction error is represented.

      We performed the analysis as suggested (Author response image 5). Visuomotor mismatch responses are stronger on all electrodes compared to playback halt responses. This difference is also larger in data recorded on occipital electrodes.

      Author response image 5.

      Comparison of the difference between visuomotor mismatch and playback halt on all electrodes. Average response strength was calculated within a 100 ms window centered on the peak of the average visuomotor mismatch response across all electrodes. Boxes mark median, quartiles, and range of data not considered outliers. Each circle represents data from one participant. **: p<0.01, *: p<0.05, Fp1-2: 20 participants, C3-4: 31 participants, P3-4: 35 participants, O1-2: 32 participants.

      As a suggestion, the authors are encouraged to analyse time-frequency power and phase locking for these mismatch responses, as is common in much of the literature (see Roach et al 2008, Schizophrenia Bulletin). This is not to say that doing so will yield insights into oscillations per se, but converting the data to the time-frequency domain provides another perspective that has some advantages. It fosters translations to rodent models, as ERP peaks do not map well between species, but e.g., delta-theta power does (see Lee et al 2018, Neuropsychopharmacology; Javitt et al 2018, Schizophrenia research; Gallimore et al 2023, Cereb Ctx). Further, ERP peaks can be influenced by the actual neuroanatomy of an individual (especially for quantifying V1 responses). Time frequency analyses may aid in interpreting the "early negative deflection with a peak latency of 48 ms " finding as well.

      We have performed time–frequency power and phase-locking analyses for both visual responses (Author response image 6 and Author response image 7) and visuomotor mismatch and playback halt responses (Author response image 8 and Author response image 9), as suggested. We have added the results of these analyses here, as these are not fully developed yet. We may add these to a future publication, for which we would properly want to quantify stability of these effects.

      In brief, time–frequency representations of power did identify potentially interesting differences between walking and sitting sessions in the visual paradigm. Inter-trial phase coherence (ITPC) revealed an early increase in alpha-band synchronization suggesting that phase alignment of alpha oscillations may contribute to the early differences in visual responses between walking and sitting. The same analyses were applied to visuomotor mismatch and playback halt responses. Time–frequency power analysis revealed an increase in delta-band power during visuomotor mismatch, consistent with previous reports linking delta activity to prediction error processing, including reward prediction errors (Cavanagh, 2015), unexpected final words (Webb and Sohoglu, 2025), and visual deviance detection (West et al., 2024). Notably, it appears as if the increase in delta power emerged first over occipital electrodes and appeared later over more frontal electrodes, forming a spatiotemporal gradient of onset across the scalp.

      Delta power changes were markedly reduced in the playback halt responses at the time of visual flow cessation. While some power changes were observed, they occurred primarily at visual flow onset rather than at flow offset. Inter-trial phase coherence analysis further revealed delta-band synchronization over occipital electrodes following visuomotor mismatch, whereas the playback halt response showed strong phase synchronization in both delta and theta bands following visual flow onset.

      Author response image 6.

      Time–frequency representations of EEG power changes during the visual paradigm. (A) Time–frequency maps showing changes in spectral power relative to baseline for electrodes Fp1–2, C3–4, P3–4, and O1–2 following checkerboard reversal in the sitting session. The dashed red vertical line indicates the time of the checkerboard reversal (0 s). (B) As in A, but recorded while participants were walking.

      Author response image 7.

      Inter-trial phase coherence (ITPC) for visual trials during sitting and walking. (A) ITPC across trials for electrode pairs Fp1–2, C3–4, P3–4, and O1–2 following checkerboard reversal in the sitting session. The dashed red vertical line marks the time of the checkerboard reversal (0 s). (B) As in A, but recorded during walking.

      Author response image 8.

      Time–frequency representations of EEG power changes during visuomotor mismatch and playback halt responses. (A) Time–frequency maps showing changes in spectral power relative to baseline for electrodes Fp1–2, C3–4, P3–4, and O1–2 following visuomotor mismatch presentation. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but for playback halts.

      Author response image 9.

      Inter-trial phase coherence (ITPC) for the visuomotor mismatch and playback halt responses. (A) ITPC across trials for electrode pairs Fp1–2, C3–4, P3–4, and O1–2 following visuomotor mismatch presentation. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but for playback halts.

      Finally, the sentence in the abstract that this paradigm " can trigger strong prediction error responses and consequently requires shorter recording times would simplify experiments in a clinical setting" is a nice setup to the paper, but the very fact that one third of recordings had to be removed due to movement artifact, and that hairstyle modulates the recording SnR, is reason that this paradigm, using the reported equipment, may have limited clinical utility in its current form. Further, auditory oddball paradigms are of great clinical utility because they do not require explicit attention and can be recorded very quickly with no behavioral involvement of a hospitalized patient. This should be discussed, although it does not detract from the overall scientific importance of the study. The authors should reconsider putting this statement in the abstract.

      We have added a paragraph to the discussion to address these points. Note, we get robust and strong responses with very few trials (Author response image 2). The fact that we need to discard up to 21.7 % of trials due to movement/eye blink artefacts, does little to change the fact that we need much fewer trials and have larger and more robust responses compared to other EEG paradigms. Finally, we understand that sometimes not needing participants to pay attention to the task is useful. However, having a paradigm that is engaging and fun for participants and takes 5 minutes of recording time is probably equally often of advantage.

      Reviewer #3 (Recommendations for the authors):

      Minor points:

      (1) In the Introduction, I'm not sure that the logic comes through as to what the authors aim to illustrate by comparing mice to humans, in terms of precision and "movement modulation". In some cases, the precision of the comparison is referred to, and in others, the precision of the prediction (I think?). I'm not sure if they mean for this to be different or not. Simlarly, on line 81, "If indeed the precision of visuomotor coupling determines the amount of motor modulation of visual responses" - here I'm a little confused, as "amount of motor modulation" to me, the term "modulation" refers to a conditional modifier (if moving, than suppress visual movement resposnes. if not moving, then amplify visual movement repssones) rather than movement driven activity. The way I'm reading it, the authors mean the latter, but I could be misunderstanding.

      We have rephrased this section of the introduction.

      (2) I think it could be helpful, in the sentence starting on line 65, to reiterate that this observation of higher-than-expected motor activity in V1 is in mice (if I'm understanding it correctly). I also found myself tangled up in the difference between motor-related activity in V1 and motor-modulation in V1 in this paragraph.

      We have rephrased this section of the introduction.

      (3) For signal power, was the amplitude squared on individual trials prior to averaging, or after averaging? If prior, it would help with separating amplitude modulations from phase variance.

      In our previous analysis, power was computed by squaring the amplitude after trial averaging (Author response image 10A). We repeated the analysis using the alternative approach in which power was calculated for individual trials and then averaged (Author response image 10B). Although this method yields substantially higher absolute power values, the overall pattern of results remains unchanged: visuomotor mismatch responses continue to show significantly higher power than visual responses. To look at the phase variance we additionally analyze inter-trial phase coherence (Author response image 7 and Author response image 9).

      Author response image 10.

      Visuomotor mismatch responses have more power compared to visual responses. (A) Comparison of power between visuomotor mismatch and visual responses, calculated within a 0 - 0.5 s time window following stimulus onset. Power was computed by squaring the amplitude after trial averaging. Boxes indicate the median and interquartile range, with whiskers showing the range excluding outliers; circles represent data from individual participants. ***p < 0.001. (B) Same comparison as in (A), but with power calculated by squaring the amplitude of individual trials prior to averaging.

      (4) The "the world suddenly flew forward!" response from the participant, I understand, and I believe that it is useful to illustrate a point. I do not understand the "Are you printing this? - Hi Mom! " part of the participant response, and I'm not sure it adds to the paper, beyond amusement, which seems inappropriate.

      One of the authors (the one who did none of the experiments) finds this endlessly hilarious and as the reviewer notes, it might add amusement more generally. “Inappropriate” might be a bit harsh – according to our favorite AI chatbot: “Amusement provides significant mental, physical, and social value by offering a necessary escape from routine, reducing stress, and fostering a connection. It enhances well-being through endorphin-releasing experiences and encourages social bonding, learning, and joy.” Nevertheless, we have censored the offending passage.

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