it is unclear if these morphological changes are representative of a “stable” state of a lysosome or if the morphological shifts represent a “transient” stage.
I think this will definitely be an interesting future area of study, and would potentially benefit from examining the expression, localization, and activity of enzymes like superoxide dismutases, which are essential for copper, zinc, and manganese homeostasis.
Phosphorus, calcium, and iron appeared at the perimeter of the lysosome, whereas sulfur, chlorine, potassium, manganese, copper, and zinc appeared to be distributed throughout the lumen of the lysosome.
This is such a neat technique and the images in figures 3 and 4 are so beautiful!
does not appear to be acidic
Has this been formally tested? If so, it would be nice to have a citation here.
In excess manganese, the expansion compartment significantly increased in volume (Figure 1A,E).
The change in CDF-2::GFP intensity is also very striking. Do you think that excess manganese promotes increased transcription and/or translation of cdf-2 mRNA?
older ncORFs with positive coding potential tend to display increased tissue specificity
Is this trend pronounced in any tissues in particular, or is this random/across all tissue types?
The majority of conditions were evaluated through liquid cultures in microplate growth assays
In future work, it would be useful to collect brightfield/DIC microscopy data for these strains to examine the ratio of spherical to filamentous cells in these diverse environmental conditions.
Of the 126 Y. lipolytica strains analyzed, 67 were newly sequenced in this study.
This is an invaluable expansion of genetic information! I think it would be neat to highlight the 67 newly sequenced strains in Figure 1 to emphasize your contributions.
Eur2/Dairy strains
It's interesting to see that one of these grows relatively well in the presence of cycloheximide. It might be neat to dig into this strain more with additional phenotypic characterization and exploration of what's conferring this fitness.
These numbers are in the same range as our own
I'm curious how many of your higher confidence dynamic proteins overlap with dynamic proteins identified in previous studies, and if there's any enrichment of proteins belonging to specific clusters in Figure 8.
We anticipate this dataset will be an important resource for cell cycle research in budding yeast.
This is a very valuable study and I'm excited to explore these data when they're publicly available!
We assembled a multi-cohort benchmark spanning 12 independent Gene Expression Omnibus GEO studies
Several studies investigate the transcriptomes of patients with not only endometriosis but also adenomyosis. I think it would be helpful to mention this here and provide some background on the co-occurrence rates of endometriosis and adenomyosis. It would be interesting if large, multi-study analyses like yours could parse out transcriptomic differences between individuals with one or both conditions.
These results suggest that the core transcriptomic signature of the drug response can be recapitulated in stromal cells from the eutopic endometrium of endometriosis patients, supporting their use as a minimally invasive source for evaluating candidate therapeutics for the disease.
Thank you for doing this work! Utilizing single-cell datasets for in silico drug prediction is a pragmatic way to help us better understand and treat endometriosis.
230 showed concordant direction of change (hypergeometric test, p = 4.43 × 10⁻³³; Jaccard index = 0.252). Notably, 381 downregulated genes displayed a highly significant overlap across tissues
Would it be possible to include these gene lists in a supplemental table?
These populations displayed strong enrichment for epithelial-mesenchymal transition (EMT) and hypoxia pathways (Figure 2, Table 1), in line with the invasive and fibrotic features of endometriotic lesions previously reported
I'm curious if your analyses were able to provide any new information about specific EMT-related factors that are enriched in these cell types. What EMT genes were consistently identified? Were there enrichment signatures you found that bulk analyses may have missed?
under general apoptotic stress, Tip30 expression significantly improved yeast resistance to acetic acid–induced growth inhibition
This is very cool! Is this experiment with wild-type or fmp52∆ cells?
Endogenous GFP tagging did not yield clear results likely due to low protein expression
It looks like there's at least one putative UPRE upstream of FMP52 (425 bases upstream of the ATG, 5'-TACGTGT-3')! I'm curious if you tried looking at endogenous Fmp52-GFP with t-2-hex or other ER stress-inducing treatment, as it may get upregulated and be more visible than in unstressed conditions? This would be consistent with your pFMP52-luciferase results.
Continued efforts on engineering LNP formulations and saRNA designs will further improve transfection efficiency, cell type specific targeting, and brain specific targeting.
It will be interesting to see how organismal age and disease state impact hm5C saRNA stability/efficacy!
robust mCherry fluorescence was present in some neurons
How does the number of saRNA-positive cells compare to the time points shown in Figure 2? It would be interesting to have micrographs from earlier time points at the same magnification of those in Supp. Fig. 1. I'm also curious if there's something measurably different about the cells still expressing saRNA after three months or if it's just a random decrease in cell cout over time.
Surprisingly, mCherry expression was also evident throughout the corpus callosum, suggesting robust labeling of neuronal axons or myelin.
These expression patterns between treatments and across time are so striking! How much does this vary between individuals? For example, the patterns between mRNA and saRNA on day 14 are very distinct from one another and I'm curious if these types of differences are consistent.
Of the 39 unique key RBPs (the union of the top 20 motif-enriched RBPs from each tissue), only five (ESRP1, FUS, MBNL1, PCBP2, RBM8A) overlapped with a previously curated list of genes whose expression correlates with MLS9.
It could be useful to also assess proteomic data for these RBPs, as RNA abundance often doesn’t correlate with protein abundance, especially in the context of aging.
although alternative first exon (AF) was the second most frequent AS event, averaging 22.8% in a single species, comparable to cassette exon (Fig. 1b), none of these were conserved
Since maximum lifespan is not a conserved phenotype, it would be interesting to see if other types of splicing events (e.g. alternative first exons) are enriched for specific biological functions, irrespective of their conservation.
our data raise the possibility that TBC1D15 localized to mitochondria in neurons treated with LLOMe
Is it possible that under these conditions, neurons transfer damaged mitochondria and/or other cellular material to astrocytes? It could be interesting to do neuron-specific labeling prior to co-culturing to track mitochondria.
Thus, the lack of robust ESCRT recruitment is not simply attributed to insufficient protein expression in neurons.
I’m curious if you looked at CHMP2B levels by western blot in addition to immunofluorescence. Is it possible that neurons express alternate mRNA isoforms and/or proteoforms (e.g. truncated CHMP2B) that disrupt canonical ESCRT recruitment?