Author Response

The following is the authors’ response to the previous reviews

Reviewer #1 (Public Review):

Comments on the original submission:

Trypanosoma brucei undergoes antigenic variation to evade the mammalian host's immune response. To achieve this, T. brucei regularly expresses different VSGs as its major surface antigen. VSG expression sites are exclusively subtelomeric, and VSG transcription by RNA polymerase I is strictly monoallelic. It has been shown that T. brucei RAP1, a telomeric protein, and the phosphoinositol pathway are essential for VSG monoallelic expression. In previous studies, Cestari et al. (ref. 24) has shown that PIP5pase interacts with RAP1 and that RAP1 binds PI(3,4,5)P3. RNAseq and ChIPseq analyses have been performed previously in PIP5pase conditional knockout cells, too (ref. 24). In the current study, Touray et al. did similar analyses except that catalytic dead PIP5pase mutant was used and the DNA and PI(3,4,5)P3 binding activities of RAP1 fragments were examined. Specifically, the authors examined the transcriptome profile and did RAP1 ChIPseq in PIP5pase catalytic dead mutant. The authors also expressed several C-terminal His6-tagged RAP1 recombinant proteins (full-length, aa1300, aa301-560, and aa 561-855). These fragments' DNA binding activities were examined by EMSA analysis and their phosphoinositides binding activities were examined by affinity pulldown of biotin-conjugated phosphoinositides. As a result, the authors confirmed that VSG silencing (both BES-linked and MES-linked VSGs) depends on PIP5pase catalytic activity, but the overall knowledge improvement is incremental. The most convincing data come from the phosphoinositide binding assay as it clearly shows that N-terminus of RAP1 binds PI(3,4,5)P3 but not PI(4,5)P2, although this is only assayed in vitro, while the in vivo binding of full-length RAP1 to PI(3,4,5)P3 has been previously published by Cestari et al (ref. 24) already. Considering that many phosphoinositides exert their regulatory role by modulate the subcellular localization of their bound proteins, it is reasonable to hypothesize that binding to PI(3,4,5)P3 can remove RAP1 from the chromatin. However, no convincing data have been shown to support the author's hypothesis that this regulation is through an "allosteric switch".

Comments on revised manuscript:

In this revised manuscript, Touray et al. have responded to reviewers' comments with some revisions satisfactorily. However, the authors still haven't addressed some key scientific rigor issues, which are listed below:

1) It is critical to clearly state whether the observations are made for the endogenous WT protein or the tagged protein. It is good that the authors currently clearly indicate the results observed in vivo are for the RAP1-HA protein. However, this is not as clearly stated for in vitro EMSA analyses. In addition, in discussion, the authors simply assumed that the c-terminally tagged RAP1 behaves the same as WT RAP1 and all conclusions were made about WT RAP1.

There are two choices here. The authors can validate that RAP1-HA still retains RAP1's essential function as a sole allele in T. brucei cells (as was recommended previously). Indeed, HA-tagged RAP1 has been studied before, but it is the N-terminally HA-tagged RAP1 that has been shown to retain its essential functions. Adding the HA tag to the C-terminus of RAP1 may well cause certain defects to RAP1. For example, N-terminally HA-tagged TERT does not complement the telomere shortening phenotype in TERT null T. brucei cells, while C-terminally GFP-tagged TERT does, indicating that HA-TERT is not fully functional while TERT-GFP likely has its essential functions (Dreesen, RU thesis). Although RAP1-HA behaves similar to WT RAP1 in many ways, it is still not fully validated that this protein retains essential functions of RAP1. By the way, it has been published that cells lacking one allele of RAP1 behave as WT cells for cell growth and VSG silencing (Yang et al. 2009, Cell; Afrin et al. 2020, mSphere). In addition, although RAP1 may interact with TRF weakly, the interaction is direct, as shown in yeast 2-hybrid analysis in (Yang et al. 2009, Cell).

Alternatively, if the authors do not wish to validate the functionality of RAP1-HA, they need to add one paragraph at the beginning of the discussion to clearly state that RAP1-HA may not behave exactly as WT RAP1. This is important for readers to better interpret the results. In addition, the authors need to tune down the current conclusions dramatically, as all described observations are made on RAP1-HA but not the WT RAP1.

The results with RAP1-HA are consistent with previous knowledge of RAP1 interactions with telomeric proteins and DNA. Hence, the C-terminal HA-tagged RAP1 seems, by all measures, functional. Nevertheless, to make it clear for the reader, we added a note in the discussion, lines 244-246: “Although we showed that C-terminal HA-tagged RAP1 protein has telomeric localization (Cestari et al. 2015, PNAS) and interactions with other telomeric proteins (Cestari et al. 2019 Mol Cell Biol); we cannot rule out potential differences between HA-tagged and non tagged RAP1.”

For a similar reason, the current EMSA results truly reflect how C-terminally His6-tagged RAP1 and RAP1 fragments behave. If the authors choose not to remove the His6 tag, it is essential that they use "RAP1-His6" to refer to these recombinant proteins. It is also essential for the authors to clearly state in the discussion that the tagged RAP1 fragments bind DNA, but the current data do not reveal whether WT RAP1 binds DNA. In addition, the authors incorrectly stated that "disruption of the MybL domain sequence did not eliminate RAP1-telomere binding in vivo" (lines 165-166). In ref 29, deletion of Myb domain did not abolish RAP1-telomere association. However, point mutations in MybL domain that abolish RAP1's DNA binding activities clearly disrupted RAP1's association with the telomere chromatin. Therefore, the current observation is not completely consistent with that published in ref 29.

We stated in line 149-150 “…we expressed and purified from E. coli recombinant 6xHistagged T. brucei RAP1 (rRAP1)”. To clarify to the authors, we replaced rRAP1 with rRAP1-His throughout the manuscript and figures. As for the statement that “disruption of the MybL domain sequence did not eliminate RAP1-telomere binding in vivo" (lines 165-166).”. We removed the statement from the manuscript.

2) There is no evidence, in vitro or in vivo, that binding PI(3,4,5)P3 to RAP1 causes conformational change in RAP1. The BRCT domain of RAP1 is known for its ability to homodimerize (Afrin et al. 2020, mSphere). It is therefore possible that binding of PI(3,4,5)P3 to RAP1 simply disrupts its homodimerization function. The authors clearly have extrapolated their conclusions based on available data. It is therefore important to revise the discussion and make appropriate statements.

We did not state that PI(3,4,5)P3 causes RAP1 conformational changes. We discussed the possibility. We stated in lines 199-201: “PI(3,4,5)P3 inhibition of RAP1-DNA binding might be due to its association with RAP1 N-terminus causing conformational changes that affect Myb and MybL domains association with DNA.” This is a reasonable discussion, given the data presented in the manuscript.

Reviewer #2 (Public Review):

In this manuscript, Touray et al investigate the mechanisms by which PIP5Pase and RAP1 control VSG expression in T. brucei and demonstrate an important role for this enzyme in a signalling pathway that likely plays a role in antigenic variation in T. brucei. While these data do not definitively show a role for this pathway in antigenic variation, the data are critical for establishing this pathway as a potential way the parasite could control antigenic variation and thus represent a fundamental discovery.

The methods used in the study are generally well-controlled. The authors provide evidence that RAP1 binds to PI(3,4,5)P3 through its N-terminus and that this binding regulates RAP1 binding to VSG expression sites, which in turn regulates VSG silencing. Overall their results support the conclusions made in the manuscript. Readers should take into consideration that the epitope tags on RAP1 could alter its function, however.

There are a few small caveats that are worth noting. First, the analysis of VSG derepression and switching in Figure 1 relies on a genome which does not contain minichromosomal (MC) VSG sequences. This means that MC VSGs could theoretically be mis-assigned as coming from another genomic location in the absence of an MC reference. As the origin of the VSGs in these clones isn't a major point in the paper, I do not think this is a major concern, but I would not over-interpret the particular details of switching outcomes in these experiments.

We agree with the reviewer and thus made no speculations on minichromosomes. The data analysis must rely on the available genome, and the reference genome used is well-assembled with PacBio sequences and Hi-C data (Muller et al. 2018, Nature).

Another aspect of this work that is perhaps important, but not discussed much by the authors, is the fact that signalling is extremely poorly understood in T. brucei. In Figure 1B, the RNA-seq data show many genes upregulated after expression of the Mut PIP5Pase (not just VSGs). The authors rightly avoid claiming that this pathway is exclusive to VSGs, but I wonder if these data could provide insight into the other biological processes that might be controlled by this signaling pathway in T. brucei.

We published that the inositol phosphate pathway also plays a role in T. brucei development (Cestari et al. 2018, Mol Biol Cell; reviewed by Cestari I 2020, PLOS Pathogens)

Overall, this is an excellent study which represents an important step forward in understanding how antigenic variation is controlled in T. brucei. The possibility that this process could be controlled via a signalling pathway has been speculated for a long time, and this study provides the first mechanistic evidence for that possibility.

Reviewer #1 (Recommendations For The Authors):

Please see the public review for recommendations.1. It is critical to clearly state whether the observations are made for the endogenous WT protein or the tagged protein. It is good that the authors currently clearly indicate the results observed in vivo are for the RAP1-HA protein. However, this is not as clearly stated for in vitro EMSA analyses. In addition, in discussion, the authors simply assumed that the c-terminally tagged RAP1 behaves the same as WT RAP1 and all conclusions were made about WT RAP1.

There are two choices here. The authors can validate that RAP1-HA still retains RAP1's essential function as a sole allele in T. brucei cells (as was recommended previously). Indeed, HA-tagged RAP1 has been studied before, but it is the N-terminally HA-tagged RAP1 that has been shown to retain its essential functions. Adding the HA tag to the C-terminus of RAP1 may well cause certain defects to RAP1. For example, N-terminally HA-tagged TERT does not complement the telomere shortening phenotype in TERT null T. brucei cells, while C-terminally GFP-tagged TERT does, indicating that HA-TERT is not fully functional while TERT-GFP likely has its essential functions (Dreesen, RU thesis). Although RAP1-HA behaves similar to WT RAP1 in many ways, it is still not fully validated that this protein retains essential functions of RAP1. By the way, it has been published that cells lacking one allele of RAP1 behaves as WT cells for cell growth and VSG silencing (Yang et al. 2009, Cell; Afrin et al. 2020, mSphere). In addition, although RAP1 may interact with TRF weakly, the interaction is direct, as shown in yeast 2-hybrid analysis in (Yang et al. 2009, Cell).

Alternatively, if the authors do not wish to validate the functionality of RAP1-HA, they need to add one paragraph at the beginning of the discussion to clearly state that RAP1-HA may not behave exactly as WT RAP1. This is important for readers to better interpret the results. In addition, the authors need to tune down the current conclusions dramatically, as all described observations are made on RAP1-HA but not the WT RAP1.

The results with RAP1-HA are consistent with previous knowledge of RAP1 interactions with telomeric proteins and DNA. Hence, the C-terminal HA-tagged RAP1 seems, by all measures, functional. Nevertheless, to make it clear for the reader, we added a note in the discussion, lines 244-246: “Although we showed that C-terminal HA-tagged RAP1 protein has telomeric localization (Cestari et al. 2015, PNAS) and interactions with other telomeric proteins (Cestari et al. 2019 Mol Cell Biol); we cannot rule out potential differences between HA-tagged and non tagged RAP1.”

For a similar reason, the current EMSA results truly reflect how C-terminally His6-tagged RAP1 and RAP1 fragments behave. If the authors choose not to remove the His6 tag, it is essential that they use "RAP1-His6" to refer to these recombinant proteins. It is also essential for the authors to clearly state in the discussion that the tagged RAP1 fragments bind DNA, but the current data do not reveal whether WT RAP1 binds DNA. In addition, the authors incorrectly stated that "disruption of the MybL domain sequence did not eliminate RAP1-telomere binding in vivo" (lines 165-166). In ref 29, deletion of Myb domain did not abolish RAP1-telomere association. However, point mutations in MybL domain that abolish RAP1's DNA binding activities clearly disrupted RAP1's association with the telomere chromatin. Therefore, the current observation is not completely consistent with that published in ref 29.

We stated in lines 149-150 “…we expressed and purified from E. coli recombinant 6xHistagged T. brucei RAP1 (rRAP1)”. To clarify to the authors, we replaced rRAP1 with rRAP1-His throughout the manuscript text. As for the statement that “disruption of the MybL domain sequence did not eliminate RAP1telomere binding in vivo" (lines 165-166).”. We removed the statement from the manuscript.

2) There is no evidence, in vitro or in vivo, that binding PI(3,4,5)P3 to RAP1 causes conformational change in RAP1. The BRCT domain of RAP1 is known for its ability to homodimerize (Afrin et al. 2020, mSphere). It is therefore possible that binding of PI(3,4,5)P3 to RAP1 simply disrupts its homodimerization function. The authors clearly have extrapolated their conclusions based on available data. It is therefore important to revise the discussion and make appropriate statements.

We did not state that PI(3,4,5)P3 causes RAP1 conformational changes. We discussed the possibility. We stated in lines 199-201: “PI(3,4,5)P3 inhibition of RAP1-DNA binding might be due to its association with RAP1 N-terminus causing conformational changes that affect Myb and MybL domains association with DNA.” This is a reasonable discussion, given the data presented in the manuscript.

eLife assessment

Trypanosoma brucei evades mammalian humoral immunity through the expression of different variant surface glycoprotein genes. In this fundamental paper, the authors extend previous observations that TbRAP1 both interacts with PIP5Pase and binds PI(3,4,5)P3, indicating a role for PI(3,4,5)P3 binding. They therefore suggest that antigen switching might have a signal-dependent component. The evidence is mostly compelling, but with some caveats because tagged proteins were used.

Reviewer #1 (Public Review):

Trypanosoma brucei undergoes antigenic variation to evade the mammalian host's immune response. To achieve this, T. brucei regularly expresses different VSGs as its major surface antigen. VSG expression sites are exclusively subtelomeric, and VSG transcription by RNA polymerase I is strictly monoallelic. It has been shown that T. brucei RAP1, a telomeric protein, and the phosphoinositol pathway are essential for VSG monoallelic expression. In previous studies, Cestari et al. (ref. 24) has shown that PIP5pase interacts with RAP1 and that RAP1 binds PI(3,4,5)P3. RNAseq and ChIPseq analyses have been performed previously in PIP5pase conditional knockout cells, too (ref. 24). In the current study, Touray et al. did similar analyses except that catalytic dead PIP5pase mutant was used and the DNA and PI(3,4,5)P3 binding activities of RAP1 fragments were examined. Specifically, the authors examined the transcriptome profile and did RAP1 ChIPseq in PIP5pase catalytic dead mutant. The authors also expressed several C-terminal His6-tagged RAP1 recombinant proteins (full-length, aa1-300, aa301-560, and aa 561-855). These fragments' DNA binding activities were examined by EMSA analysis and their phosphoinositides binding activities were examined by affinity pulldown of biotin-conjugated phosphoinositides. As a result, the authors confirmed that VSG silencing (both BES-linked and MES-linked VSGs) depends on PIP5pase catalytic activity, but the overall knowledge improvement is incremental. The most convincing data come from the phosphoinositide binding assay as it clearly shows that N-terminus of RAP1 binds PI(3,4,5)P3 but not PI(4,5)P2, although this is only assayed in vitro, while the in vivo binding of full-length RAP1 to PI(3,4,5)P3 has been previously published by Cestari et al (ref. 24) already. Considering that many phosphoinositides exert their regulatory role by modulating the subcellular localization of their bound proteins, it is reasonable to hypothesize that binding to PI(3,4,5)P3 can remove RAP1 from the chromatin.

Reviewer #2 (Public Review):

In this manuscript, Touray et al investigate the mechanisms by which PIP5Pase and RAP1 control VSG expression in T. brucei and demonstrate an important role for this enzyme in a signalling pathway that likely plays a role in antigenic variation in T. brucei. While these data do not definitively show a role for this pathway in antigenic variation, the data are critical for establishing this pathway as a potential way the parasite could control antigenic variation and thus represent a fundamental discovery.

The methods used in the study are generally well-controlled. The authors provide evidence that RAP1 binds to PI(3,4,5)P3 through its N-terminus and that this binding regulates RAP1 binding to VSG expression sites, which in turn regulates VSG silencing. Overall their results support the conclusions made in the manuscript. Readers should take into consideration that the epitope tags on RAP1 could alter its function, however.

There are a few small caveats that are worth noting. First, the analysis of VSG derepression and switching in Figure 1 relies on a genome which does not contain minichromosomal (MC) VSG sequences. This means that MC VSGs could theoretically be mis-assigned as coming from another genomic location in the absence of an MC reference. As the origin of the VSGs in these clones isn't a major point in the paper, I do not think this is a major concern, but I would not over-interpret the particular details of switching outcomes in these experiments.

Another aspect of this work that is perhaps important, but not discussed much by the authors, is the fact that signalling is extremely poorly understood in T. brucei. In Figure 1B, the RNA-seq data show many genes upregulated after expression of the Mut PIP5Pase (not just VSGs). The authors rightly avoid claiming that this pathway is exclusive to VSGs, but I wonder if these data could provide insight into the other biological processes that might be controlled by this signaling pathway in T. brucei.

Overall, this is an excellent study which represents an important step forward in understanding how antigenic variation is controlled in T. brucei. The possibility that this process could be controlled via a signalling pathway has been speculated for a long time, and this study provides the first mechanistic evidence for that possibility.

Reviewer #1 (Public Review):

Summary:

The process of taste perception is significantly more intricate and complex in Lepidopteran insects. This investigation provides valuable insights into the role of Gustatory receptors and their dynamics in the sensation of sucrose, which serves as a crucial feeding cue for insects. The article highlights the differential sensitivity of Grs to sucrose and their involvement in feeding and insect behavior.

Strengths:

To support the notion of the differential specificity of Gr to sucrose, this study employed electrophysiology, ectopic expression of Grs in Xenopus, genome editing, and behavioral studies on insects. This investigation offers a fundamental understanding of the gustation process in lepidopteran insects and its regulation of feeding and other gustation-related physiological responses. This study holds significant importance in advancing our comprehension of lepidopteran insect biology, gustation, and feeding behavior.

Weaknesses:

While this manuscript demonstrates technical proficiency, there exists an opportunity for additional refinement to optimize comprehensibility for the intended audience. Several crucial sugars have been overlooked in the context of electrophysiology studies and should be incorporated. Furthermore, it is imperative to consider the potential off-target effects of Gr knock-out on other Gr expressions. This investigation focuses exclusively on Gr6 and Gr10, while neglecting a comprehensive narrative regarding other Grs involved in sucrose sensation.

eLife assessment

This important study identifies the gustatory receptors for sugar sensing in the larval and adult forms of the cotton bollworm, which is responsible for the destruction of many food crops world-wide. The authors find that the larval and adult forms utilise different receptors to sense sugars. The data are convincing and will be of interest neuroscientists working in sensory coding of sugars and to the pest management field.

Reviewer #2 (Public Review):

Summary:

To identify sugar receptors and assess the capacity of these genes the authors first set out to identify behavioral responses in larvae and adults as well as physiological response. They used phylogenetics and gene expression (RNAseq) to identify candidates for sugar reception. Using first an in vitro oocyte system they assess the responses to distinct sugars. A subsequent genetic analysis shows that the Gr10 and Gr6 genes provide stage specific functions in sugar perception.

Strengths:

A clear strength of the manuscript is the breadth of techniques employed allowing a comprehensive study in a non-canonical model species.

Weaknesses:

There are no major weaknesses in the study for the current state of knowledge in this species. Since it is much basic work to establish a broader knowledge, context with other modalities remains unknown. It might have been possible to probe certain contexts known from the fruit fly, which would have strengthened the manuscript.

Reviewer #3 (Public Review):

In this study, the authors combine electrophysiology, behavioural analyses, and genetic editing techniques on the cotton bollworm to identify the molecular basis of sugar sensing in this species.

The larval and adult forms of this species feed on different plant parts. Larvae primarily consume leaves, which have relatively lower sugar concentrations, while adults feed on nectar, rich in sugar. Through a series of experiments-spanning electrophysiological recordings from both larval and adult sensillae, qPCR expression analysis of identified GRs from these sensillae, response profiles of these GRs to various sugars via heterologous expression in Xenopus oocytes, and evaluations of CRISPR mutants based on these parameters-the authors discovered that larvae and adults employ distinct GRs for sugar sensing. While the larva uses the highly sensitive GR10a, the adult uses the less sensitive and broadly tuned GR6. This differential use of GRs are in keeping with their behavioural ecology.

The data are cohesive and consistently align across the methodologies employed. They are also well presented and the manuscript is clearly written.

Reviewer #2 (Public Review):

Summary:<br /> DAVID syndrome is a rare autosomal dominant disorder characterized by variable immune dysfunction and variable ACTH deficiency. Nine different families have been reported, and all have heterozygous mutations in NFKB2. The mechanism of NFKB2 action in the immune systems has been well-studied, but nothing is known about its role in the pituitary gland.

The DAVID mutations cluster in the C-terminus of the NFKB2 and interfere with cleavage and nuclear translocation. The mutations are likely dominant negative, by affecting dimer function. ACTH deficiency can be life-threatening in neonates and adults, thus, understanding the mechanism of NFKB2 action in pituitary development and/or function is important.

The authors use CRISPR/Cas gene editing of human iPSC-derived pituitary-hypothalamic organoids to assess the function of NFKB2 and TBX19 in pituitary development. Mutations in TBX19 are the most common, known cause of pituitary ACTH deficiency, and the mechanism of action has been studied in mice, which phenocopy the human condition. Thus, the TBX19 organoids can serve as a positive control. The Nfkb2 mouse model has a p.Y868* mutation that impairs cleavage of NFKB2 p100, and the immune phenotype mimics the patients with DAVID mutations, but no pituitary phenotype was evident. Thus, a human organoid model might be the only approach suitable to discover the etiology of the pituitary phenotype.

Overall, the authors have selected an important problem, and the results suggest that the pituitary insufficiency in DAVID syndrome is caused by a developmental defect rather than an autoimmune hypophysitis condition. The use of gene editing in human iPSC-derived hypothalamic-pituitary organoids is significant, as there is only one example of this previously, namely studies on OTX2. Only a few laboratories have demonstrated the ability to differentiate iPSC or ES cells to these organoids, and the authors have improved the efficiency of differentiation, which is also significant.

The strength of the evidence is excellent. However, the two ACTH-deficient organoid models use a single genetically engineered clone, and the potential for variability amongst clones makes the conclusions less compelling. Since the authors obtained two independent clones for NFKB2 it is not clear why only one clone was studied. Finally, the effect of TBX19 on early pituitary fate markers is somewhat surprising given the phenotype of the knockout mice and patients with mutations. Thus, the use of a single clone for that study is also worrisome.

Strengths:<br /> The authors make mutations in TBX19 and NFKB2 that exist in affected patients. The TBX19 p.K146R mutation is recessive and causes isolated ACTH deficiency. Mutations in this gene account for 2/3 of isolated ACTH deficiency cases. The NFKB2 p.D865G mutation is heterozygous in a patient with recurrent infections and isolated ACTH deficiency. NFKB2 mutations are a rare cause of ACTH deficiency, and they can be associated with the loss of other pituitary hormones in some cases. However, all reported cases are heterozygous.

The developmental studies of organoid differentiation seem rigorous in that 200 organoids were generated for each hiPSC line, and 3-10 organoids were analyzed for each time point and genotype. Differentiation analysis relied on both RNA transcript measurements and immunohistochemistry of cleared organoids using light sheet microscopy. Multiple time points were examined, including seven times for gene expression at the RNA level and two times in the later stages of differentiation for IHC.<br /> TBX19 deficient organoids exhibit reduced levels of PITX1, LHX3, and POMC (ACTH precursor) expression at the RNA and IHC level, and there are fewer corticotropes in the organoids, as ascertained by POMC IHC.

The NFKB2 deficient organoids have a normal expression of the early pituitary transcription factor HESX1, but reduced expression of PITX2, LHX3, and POMC. Because there is no immune component in the organoid, this shows that NFKB2 mutations can affect corticotrope differentiation to produce POMC. RNA sequencing analysis of the organoids reveals potential downstream targets of NFKB2 action, including a potential effect on epithelial-to-mesenchymal-like transition and selected pituitary and hypothalamic transcription factors and signaling pathways.

Weaknesses:<br /> There could be variation between individual iPSC lines that is unrelated to the genetically engineered change. While the authors check for off-target effects of the guide RNA at predicted sites using WGS, a better control would be to have independently engineered clones or to correct the engineered clone to wild type and show that the phenotypic effects are reversed.

All NFKB2 patients are heterozygous for what appear to be dominant negative mutations that affect protein cleavage and nuclear localization of processed protein as homo or heterdimers. The organoids are homozygous for this mutation. Supplemental Figure 4 indicates that one heterozygous clone and two homozygous mutant clones were obtained. Analysis of these additional clones would give more strength to the conclusions, showing reproducibility and the effect of mutant gene dosage.

Reviewer #3 (Public Review):

Summary:<br /> This manuscript by Mac et al addresses the causes of pituitary dysfunction in patients with DAVID syndrome which is caused by mutations in the NFKB2 gene and leads to ACTH deficiency. The authors seek to determine whether the mutation directly leads to altered pituitary development, as opposed to an autoimmune defect, by using mutating human iPSCs and then establishing organoids that differentiate into pituitary tissue. They first seek to validate the system using a well-characterised mutation of the transcription factor TBX19, which also results in ACTH deficiency in patients. Then they characterise altered pituitary cell differentiation in mutant NFKB2 organoids and show that these lack corticotrophs, which would lead to ACTH deficiency.

Strengths:<br /> The conclusion of the paper that ACTH deficiency in DAVID syndrome is independent of an autoimmune input is strong.

Weaknesses:<br /> 1. The authors correctly emphasise the importance of establishing the validity of an iPSC-based model in being able to recapitulate in vivo dysfunctional pituitary development through characterisation of a TBX19 knock-in mutation. Whilst this leads to the expected failure of functional corticotroph differentiation, other aspects of the normal pituitary differentiation pathway upstream of corticotroph commitment seem to have been affected in surprising ways. In particular, the loss of LHX3 and PITX1 in TBX19 mutant organoids compared with wild type requires explanation, especially as the mutant protein would only be expected to be expressed in a small proportion of anterior pituitary lineage cells. If the developmental expression profile of key transcription factors in mutant organoids does not recapitulate that which occurs in vivo, any interpretation of the relevance of expression differences in the NFKB2 organoids to the mechanism(s) leading to corticotroph function in vivo has to be questionable. It is notable that the manipulation of iPSC cells used to generate mutants through CRISPR/Cas9 editing is not applied to the control iPSC line. It is possible that these manipulations lead to changes to the iPSC cells that are independent of the mutations introduced and this may change the phenotype of the cells. A better control would have been an iPSC line with a benign knock-in (such as GFP into the ROSA26 locus).

2. In the results section of the manuscript the authors acknowledge that hypothalamic tissue in the NFKB2 mutant organoid may be having an effect on the development of pituitary tissue. However, in the discussion the emphasis is entirely on pituitary autonomous mechanisms such as pituitary HESX1 expression or POMC gene regulation; in the conclusion of the abstract, a direct role for NFKB2 in pituitary differentiation is described. Whilst the data here may suggest a non-immune mediated alteration in pituitary function in DAVID syndrome, if this is due to alteration of the developing hypothalamus then this is not direct. A fuller discussion of the potential hypothalamic contribution and/or further characterisation of this aspect is warranted.

3. qRT-PCR data presented in Figure 6A shows negligible alteration of HESX1 expression at all time points in NFKB2 mutant organoids. This is not consistent with the 2-fold increase in HESX1 expression described in day 48 organoids found by bulk RNA sequencing. How do the authors reconcile these results and why is one result focused on in the discussion where a potential mechanism for a blockade of normal pituitary cell differentiation is suggested? Further confirmation of HESX1 expression is required.

4. Throughout the authors focus on POMC gene expression and ACTH antibody immunopositive as being indicative of corticotroph cell identity. In the human fetal pituitary melanotrophs are present and most ACTH antibodies are unable to distinguish these cells from corticotrophs. Is the antibody used specifically for ACTH rather than other products of the POMC gene? It is unlikely that all the ACTH-positive cells are melanotrophs, nevertheless, it is important to know what the proportions of the 2 POMC-positive cell types are. This could be distinguished by looking for the expression of NeuroD1, which would also define whether corticotrophs are committed but not fully differentiated in the NFKB2 mutant organoids. In support of an effect on corticotrophs, it is notable that CRHR1 expression (which would be expected to be restricted to this cell type) is reduced by 84% in bulk RNAseq data (Table 1) and this may be an indicator of the loss of corticotrophs in the model.

5. Notwithstanding the caveats about whether the organoid model recapitulates in vivo pituitary differentiation (see 1 above) and whether the bulk RNAseq accurately reflects expression levels (see 3 above), there are potentially some extremely interesting changes in gene expression shown in Table 1 which warrant further discussion. For example, there is a 25-fold reduction in POU1F1 expression which may be expected to reflect a loss of somatotrophs in the organoid (and possibly lactotrophs) and highlights the importance of characterising the effect of NFKB2 on other anterior pituitary cell types within the organoid. If somatotrophs are affected, this may be relevant to the organoids as a model of DAVID syndrome as GH deficiency has been described in some individuals with NFKB2 mutations. The huge increase in CGA expression may reflect a switch in cell fate to gonadotrophs, as has been described with a loss of TPIT in the mouse. These are examples of the changes that warrant further characterisation and discussion.

6. How do the authors explain the lack of effect of NFKB2 mutation on global NFKB signalling?

eLife assessment

This valuable study examines the effects of NFKB2 mutations on pituitary gland development through hypothalamic-pituitary organoids. The evidence supporting the main conclusions is solid, although analysis of additional clones to exclude inter-clone variability would strengthen the conclusions. Insight into the mechanism of action of NFKB2 during pituitary development is incomplete. This work will be of interest to endocrinologists and biologists working on pituitary gland development and disease.

Reviewer #1 (Public Review):

Summary:<br /> NFKB mutations are thought to be one of the causes of pituitary dysfunction, but until now they could not be reproduced in mice and their pathomechanism was unknown. The authors used the differentiation of hypothalamic-pituitary organoids from human pluripotent stem cells to recapitulate the disease in human iPS cells carrying the NFKB mutation.

Strengths:<br /> The authors achieved their primary goal of recapitulating the disease in human cells. In particular, the differentiation of the pituitary gland is closely linked to the adjacent hypothalamus in embryology, and the authors have again shown that this method is useful when the hypothalamus is suspected to be involved in pituitary abnormalities caused by genetic mutations.

Weaknesses:<br /> On the other hand, the pathomechanism is still not fully understood. This study provides some clues to the pathomechanism, but further analysis of NFKB expression and experiments investigating the relevant factors in more detail may help to clarify it further.

eLife assessment

This manuscript will provide a valuable method to evaluate the safety of MR in patients with orthopaedic implants, which is required in clinics. A strength of the work is that the in-silicon testbed is solid, based on the widely available human project, and validated. In addition, the toolbox will be open for clinical practice.

Reviewer #1 (Public Review):

Summary:

In this work authors are trying to satisfy a real need in MR safety, when concerns can rise about the thermal increase due to metallic materials in patients carrying orthopedic implants. The "MR conditional" labeling of the implant obtained by ASTM in-vitro tests may help to plan the MR scan, but it is normally limited to a single specific MR sequence and a B0 value, and it is not always available. The adoption of an in-silico simulation testbed overcomes this limitation, providing a fast and reliable prediction of temperature increase from RF, in real-life scan conditions on human-like digital models. The FDA is pushing this approach.

Strengths:

The presented in-silico testbed looks valuable and validated. It is based on the widely available Visible Human Project (VHP) datasets, and the testbed is available on-line. The approval of the testbed by the FDA as a medical device development tool (MDDT) is a good premise for the large-scale adoption of this kind of solution.

Weaknesses:

A couple of limitations of the study are now clearly highlighted to the readers in this revised version of the paper. The following aspects:<br /> - the lack of the equivalent modeling for the gradients-related heating;<br /> - the way the implant is embedded in the VHP model that should take in consideration how to manage the removed and stretched tissues;<br /> are now correctly taken in consideration in the discussion, providing additional literature.

Reviewer #2 (Public Review):

Summary:

In this article, the authors provide a method of evaluating safety of orthopedic implants in relation to Radiofrequency induced heating issues. The authors provide an open source computational heterogeneous human model and explain computational techniques in a finite element method solver to predict the RF induced temperature increase due to an orthopedic implant while being exposed to MRI RF fields at 1.5 T.

Strengths:

The open access computational human model along with their semiautomatic algorithm to position the implant can help realistically model the implant RF exposure in patient avoiding over- or under-estimation of RF heating measured using rectangular box phantoms such as ASTM phantom. Additionally, using numerical simulation to predict radiofrequency induced heating will be much easier compared to the experimental measurements in MRI scanner, especially when the scanner availability is limited.

Weaknesses:

The proposed method only used radiofrequency (RF) field exposure to evaluate the heating around the implant. However, in the case of bulky implants the rapidly changing gradient field can also produce significant heating due to large eddy currents. So the gradient induced heating still remains an issue to be evaluated to decide on the safety of the patient. Moreover, the method is limited to a single human model and might not be representative of patients with different age, sex and body weights.

eLife assessment

This important work by Hann et al. advances our understanding of the role of the survival motor neuron (SMN) protein in coordinating pathogenesis of the spinal muscular atrophy (SMA). The authors provide convincing but, nevertheless, incomplete evidence in terms of skeletal analyses not being able to satisfactorily elucidate SMN regulation of bone development. The paper appears to be descriptive and will benefit from additional experiments to justify the hypothesis. With amendments, this work will be of broad interest to biologists especially those working on the SMA.

Reviewer #1 (Public Review):

Summary:<br /> The manuscript by Hann et. al examines the role of survival motor neuron protein (SMN) in lateral plate mesoderm-derived cells using the Prrx1Cre to elucidate how changing cell-specific SMN levels coordinate aspects of the spinal muscular atrophy (SMA) pathology. SMN has generally been studied in neuronal cells, and this is one of the first insights into non-neuronal cells that may contribute to SMA disease. The authors generated 3 mouse lines: a Prrx1;Smnf/f conditional null mouse, as well as, single and double copy Prrx1;Smnf/f;SMN2 mice carrying either one or two copies of a human SMN2 transgene. First, the bone development and growth of all three were assessed; the conditional null Smn mutation was lethal shortly after birth, while the SMN2 2-copy mutant did not exhibit bone growth phenotypes. Meanwhile, single-copy SMN2 mutant mice showed reduced size and shorter limbs with shorter proliferative and hypertrophic chondrocyte zones. The authors suggested that this was cell autonomous by assessing the expression of extrinsic factors known to modulate proliferation/differentiation of growth plate chondrocytes. After assessing bone phenotypes, the authors transitioned to the assessments of neuromuscular junction (NMJ) phenotypes, since there are documented neuromuscular impairments in SMA and the Prrx1Cre transgene is expressed in muscle-associated fibro-adipogenic progenitors (FAPs). Neonatal NMJ development was unchanged in mutant mice with two copies of SMN2 , but adult single-copy SMN2 mutant mice had abnormal NMJ morphology, altered presynaptic neurotransmission, and problematic nerve terminal structure. Finally, the authors sought to assess the ability to rescue NMJ phenotypes via FAP cell transplantation and showed wild-type FAPs were able to reduce pre/postsynaptic fragmentation and neurofilament varicosities.

Strengths:<br /> The conditional genetic approaches are novel and interestingly demonstrate the potential for chondrocyte and fibro-adipogenic progenitor-specific contributions to the SMA pathology.

The characterizations of the neuromuscular and NMJ phenotypes are relatively strong.

The data strongly suggest a non-neuronal contribution to SMA, which indicates a need for further mechanistic (cellular and molecular) studies to better understand SMA.

Weaknesses:<br /> The skeletal analyses are not rigorous and likely do not get to the core of how SMN regulates bone development.

The overall work is descriptive and lacks convincing mechanisms.

Additional experimentation is likely needed to fully justify the conclusions.

Reviewer #2 (Public Review):

Summary:<br /> Sang-Hyeon et al. laid out a compelling rationale to explore the role of the SMN protein in mesenchymal cells, to determine whether SMN deficiency there could be a pathologic mechanism of SMA. They crossed Smnf7/f7 mice with Prrx1Cre mice to produce SmnΔMPC mice where exon 7 was specifically deleted and thus SMN protein was eliminated in limb mesenchymal progenitor cells (MPCs). To demonstrate gene dosage-dependence of phenotypes, SmnΔMPC mice were crossed with transgenic mice expressing human SMN2 to produce SmnΔMPC mice with different copies of SMN2 (0, 1, or 2). The paper provides genetic evidence that SMN in mesenchymal cells regulates the development of bones and neuromuscular junctions. Genetic data were convincing and revealed novel functions of SMN.

Strengths:<br /> Overall, the paper provided genetic evidence that SMN deficiency in mesenchymal cells caused abnormalities in bones and NMJs, revealing novel functions of SMN and leading to future experiments. As far as genetics is concerned, the data were convincing (except for the rescue experiment, see below); the conclusions are important.

Weaknesses:<br /> The paper seemed to be descriptive in nature and could be improved with more experiments to investigate underlying mechanisms. In addition, some data appeared to be contradicting or difficult to explain. The rescue data were not convincing.

Reviewer #3 (Public Review):

Summary:<br /> SMN expression in non-neuronal cells, particularly in limb mesenchymal progenitors is essential for the proper growth of chondrocytes and the formation of adult NMJ junctions.

Strengths:<br /> The authors show copy numbers of smndelta7 in MPC influence NMJ structure.

Weaknesses:<br /> Functional recovery by FAP transplantation is not complete. Mesenchymal progenitors are heterogeneous, and how heterogeneity influences this study is not clear. Part of the main findings to show the importance of SMN expression in non-neuronal cells is partly published by the same group (Kim et al., JCI Insight 2022). In the study, the authors used Dpp4(+) cells. The difference between the current study and the previous study is not so clear.

eLife assessment

This study presents valuable data on how HSCs are expanded under PVA cultures. The functional evidence supporting the claims of the authors is solid, although an extended multi-omic data analysis could have strengthened the study. The work will be of interest to individuals within this HSC field.

Reviewer #1 (Public Review):

In 2019, Wilkinson and colleagues (PMID: 31142833) managed to break the veil in a 20-year open question on how to properly culture and expand Hematopoietic Stem Cells (HSCs). Although this study is revolutionizing the HSC biology field, several questions regarding the mechanisms of expansion remain open. Leveraging on this gap, Zhang et al.; embarked on a much-needed investigation regarding HSC self-renewal in this particular culturing setting.

The authors firstly tacked the known caveat that some HSC membrane markers are altered during in vitro cultures by functionally establishing EPCR (CD201) as a reliable and stable HSC marker (Figure 1), demonstrating that this compartment is also responsible for long-term hematopoietic reconstitution (Figure 3). Next in Figure 2, the authors performed single-cell omics to shed light on the potential mechanisms involved in HSC maintenance, and interestingly it was shown that several hematopoietic populations like monocytes and neutrophils are also present in this culture conditions, which has not been reported. The study goes on to functionally characterize these cultured HSCs (cHSC). The authors elegantly demonstrate using state-of-the-art barcoding strategies that these culturing conditions provoke heterogeneity in the expanding HSC pool (Figure 4). In the last experiment (Figure 5), it was demonstrated that cHSC not only retain their high EPCR expression levels but upon transplantation, these cells remain more quiescent than freshly-isolated controls.

Taken together, this study independently validates that the proposed culturing system works and provides new insights into the mechanisms whereby HSC expansion takes place.

Most of the conclusions of this study are well supported by the present manuscript, some aspects regarding experimental design and especially the data analysis should be clarified and possibly extended.

1. The first major point regards the single-cell (sc) omics performed on whole cultured cells (Figure 2):<br /> a. The authors claim that both RNA and ATAC were performed and indeed some ATAC-seq data is shown in Figure 2B, but this collected data seems to be highly underused.<br /> b. It's not entirely clear to this reviewer the nature of the so-called "HSC signatures"(SF2C) and why exactly these genes were selected. There are genes such as Mpl and Angpt1 which are used for Mk-biased HSCs. Maybe relying on other HSC molecular signatures (PMID: 12228721, for example) would not only bring this study more into the current field context but would also have a more favorable analysis outcome. Moreover reclustering based on a different signature can also clarify the emergence of relevant HSC clusters.<br /> c. The authors took the hard road to perform experiments with the elegant HSC-specific Fgd5-reporter, and they claim in lines 170-171 that it "failed to clearly demarcate in our single-cell multimodal data". This seems like a rather vague statement and leads to the idea that the scRNA-seq experiment is not reliable. It would be interesting to show a UMAP with this gene expression regardless and also potentially some other HSC markers.

2. During the discussion and in Figure 4, the authors ponder and demonstrate that this culturing system can provoke divert HSC close expansion, having also functional consequences. This a known caveat from the original system, but in more recent publications from the original group (PMID: 36809781 and PMID: 37385251) small alterations into the protocol seem to alleviate clone selection. It's intriguing why the authors have not included these parameters at least in some experiments to show reproducibility or why these studies are not mentioned during the discussion section.

3. In this reviewer's opinion, the finding that transplanted cHSC are more quiescent than freshly isolated controls is the most remarkable aspect of this manuscript. There is a point of concern and an intriguing thought that sprouts from this experiment. It is empirical that for this experiment the same HSC dose is transplanted between both groups. This however is technically difficult since the membrane markers from both groups are different. Although after 8 weeks chimerism levels seem to be the same (SF5D) for both groups, it would strengthen the evidence if the author could demonstrate that the same number of HSCs were transplanted in both groups, likely by limiting dose experiments. Finally, it's interesting that even though EE100 cells underwent multiple replication rounds (adding to their replicative aging), these cells remained more quiescent once they were in an in vivo setting. Since the last author of this manuscript has also expertise in HSC aging, it would be interesting to explore whether these cells have "aged" during the expansion process by assessing whether they display an aged phenotype (myeloid-skewed output in serial transplantations and/or assisting their transcriptional age).

Reviewer #2 (Public Review):

Summary:<br /> In this study, Zhang and colleagues characterise the behaviour of mouse hematopoietic stem cells when cultured in PVA conditions, a recently published method for HSC expansion (Wilkinson et al., Nature, 2019), using multiome analysis (scRNA-seq and scATACseq in the same single cell) and extensive transplantation experiments. The latter are performed in several settings including barcoding and avoiding recipient conditioning. Collectively the authors identify several interesting properties of these cultures namely: 1) only very few cells within these cultures have long-term repopulation capacity, many others, however, have progenitor properties that can rescue mice from lethal myeloablation; 2) single-cell characterisation by combined scRNAseq and scATACseq is not sufficient to identify cells with repopulation capacity; 3) expanded HSCs can be engrafted in unconditioned host and return to quiescence.<br /> The authors also confirm previous studies that EPCRhigh HSCs have better reconstitution capability than EPCRlow HSCs when transplanted.

Strengths:<br /> The major strength of this manuscript is that it describes how functional HSCs are expanded in PVA cultures to a deeper extent than what has been done in the original publication. The authors are also mindful of considering the complexities of interpreting transplantation data. As these PVA cultures become more widely used by the HSC community, this manuscript is valuable as it provides a better understanding of the model and its limitations.

Novelty aspects include:<br /> • The authors determined that small numbers of expanded HSCs enable transplantation into non-conditioned syngeneic recipients.<br /> • This is to my knowledge the first report characterising the output of PVA cultures by multiome. This could be a very useful resource for the field.<br /> • They are also the first to my knowledge to use barcoding to quantify HSC repopulation capacity at the clonal level after PVA culture.<br /> • It is also useful to report that HSCs isolated from fetal livers do expand less than their adult counterparts in these PVA cultures.

Weaknesses:<br /> • The analysis of the multiome experiment is limited. The authors do not discuss what cell types, other than functional or phenotypic HSCs are present in these cultures (are they mostly progenitors or bona fide mature cells?) and no quantifications are provided.<br /> • Barcoding experiments are technically elegant but do not bring particularly novel insights.<br /> • The number of mice analysed in certain experiments is fairly low (Figures 1 and 5).<br /> • The manuscript remains largely descriptive. While the data can be used to make useful recommendations to future users working with PVA cultures and in general with HSCs, those recommendations could be more clearly spelled out in the discussion.<br /> • The authors should also provide a discussion of the other publications that have used these methods to date.

Overall, the authors succeeded in providing a useful set of experiments to better interpret what type of HSCs are expanded in PVA cultures. More in-depth mining of their bioinformatic data (by the authors or other groups) is likely to highlight other interesting/relevant aspects of HSC biology in relation to this expansion methodology.

eLife assessment

This study presents valuable new insights into HIV-associated nephropathy (HIVAN) kidney phenotype in the Tg26 transgenic mouse model, and delineates the kidney cell types that express HIV genes and are injured in these HIV-transgenic mice. A series of compelling experiments demonstrated that PKR inhibition can ameliorate HIVAN with reversal of mitochondrial dysfunction (mainly confined to endothelial cells), a prominent feature shared in other kidney diseases. Although there are concerns regarding the specificity of C16 to PKR inhibition, as well as with the in situ hybridization studies, the data suggests that inhibition of PKR and mitochondrial dysfunction has potential clinical significance for HIVAN.

Reviewer #1 (Public Review):

Summary:

HIV-associated nephropathy (HIVAN) is a rapidly progressing form of kidney disease that manifests secondary to untreated HIV infection, and is predominantly seen in individuals of African descent. Tg26 mice carrying an HIV transgene lacking gag and pol exhibit high levels of albuminuria and rapid decline in renal function that recapitulates many features of HIVAN in humans. HIVAN is seen predominantly in individuals carrying two copies of missense variants in the APOL1 gene, and the authors have previously shown that APOL1 risk variant mRNA induces activity of the double-strand RNA sensor kinase PKR. Because of the tight association between the APOL1 risk genotype and HIVAN, the authors hypothesized that PKR activation may mediate renal injury in Tg26 mice, and tested this hypothesis by treating mice with a commonly used PKR inhibitory compound called C16. Treatment with C16 substantially attenuated renal damage in the Tg26 model as measured by urinary albumin/creatinine ratio, urinary NGAL/creatinine ratio, and improvement in histology. The authors then performed bulk and single-nucleus RNAseq on kidneys from mice from different treatment groups to identify pathways and patterns of cell injury associated with HIV transgene expression as well as to determine the mechanistic basis for the effect of C16 treatment. They show that proximal tubule nuclei from Tg26 mice appear to have more mitochondrial transcripts which was reversed by C16 treatment and suggest that this may provide evidence of mitochondrial dysfunction in this model. They explore this hypothesis by showing there is a decrease in the expression of nuclear-encoded genes and proteins involved in oxidative phosphorylation as well as a decrease in respiratory capacity via functional assessment of respiration in tubule and glomerular preparations from these mouse kidneys. All of these changes were reversed by C16 treatment. The authors propose the existence of a novel injured proximal tubule cell-type characterized by the leak of mitochondrial transcripts into the nucleus (PT-Mito). Analysis of HIV transgene expression showed high level expression in podocytes, consistent with the pronounced albuminuria that characterizes this model and HIVAN, but transcripts were also detected in tubular and endothelial cells. Because of the absence of mitochondrial transcripts in the podocytes, the authors speculate that glomerular mitochondrial dysfunction in this model is driven by damage to glomerular endothelial cells.

Strengths:

The strengths of this study include the comprehensive transcriptional analysis of the Tg26 model, including an evaluation of HIV transgene expression, which has not been previously reported. This data highlights that HIV transcripts are expressed in a subset of podocytes, consistent with the highly proteinuric disease seen in mice and humans. However, transcripts were also seen in other tubular cells, notably intercalated cells, principal cells and injured proximal tubule cells. Though the podocyte expression makes sense, the relevance of the tubular expression to human disease is still an open question.

The data in support of mitochondrial dysfunction are also robust and rely on combined evidence from downregulation of transcripts involved in oxidative phosphorylation, decreases in complex I and II as determined by immunoblot, and assessments of respiratory capacity in tubular and glomerular preparations. These data are largely consistent with other preclinical renal injury models reported in the literature as well as previous, less thorough assessments in the Tg26 model.

Weaknesses:

The key weakness of the study lies in the use of a PKR inhibitor with questionable specificity. C16 has been reported to inhibit numerous other kinases including cyclin CDKs and GSK3α and -β, and this means that the conclusions of this study with respect to the role of PKR are highly questionable. The rationale for the dose used was not provided (and is lower than used in other publications with C16), and in the absence of drug exposure data and assessment of target engagement, it is difficult to ascertain whether substantial inhibition of PKR was achieved.

A second key weakness lies in the identification of the PT-Mito cell cluster. Though the authors provide some rationale for the identification of this specific cell type, it seems equally plausible the cells merely reflect a high background capture of mitochondria in a subset of droplets. The IHC analysis that was provided is not convincing enough to support the claim and more careful high resolution imaging and in situ hybridization (with appropriate quantitation) will be needed to provide substantive support for the presence of a proximal tubule cell type with mitochondrial transcript that are trafficked to the nucleus.

Reviewer #2 (Public Review):

Summary:<br /> Numerous studies by the authors and other groups have demonstrated an important role for HIV gene expression kidney cells in promoting progressive chronic kidney disease, especially HIV-associated nephropathy. The authors had previously demonstrated a role for protein kinase R (PKR) in a non-HIV transgenic model of kidney disease (Okamoto, Commun Bio, 2021). In this study, the authors used innovative techniques including bulk and single nuclear RNAseq to demonstrate that mice expressing a replication-incompetent HIV transgene have prominent dysregulation of mitochondrial gene expression and activation of PKR and that treatment of these mice with a small molecule PKR inhibitor ameliorated the kidney disease phenotype in HIV-transgenic mice. They also identified STAT3 as a key upstream regulator of kidney injury in this model, which is consistent with previously published studies. Other important advances include identifying the kidney cell types that express the HIV transgene and have dysregulation of cellular pathways.

Strengths:<br /> Major strengths of the study include the use of a wide variety of state-of-the-art molecular techniques to generate important new data on the pathogenesis of kidney injury in this commonly used model of kidney disease and the identification of PKR as a potential druggable target for the treatment of HIV-induced kidney disease. The authors also identify a potential novel cell type within the kidney characterized by high expression of mitochondrial genes.

Weaknesses:<br /> Though the HIV-transgenic model used in these studies results in a phenotype that is very similar to HIV-associated nephropathy in humans, the model has several limitations that may prevent direct translation to human disease, including the fact that mice lack several genetic factors that are important contributors to HIV and kidney pathogenesis in humans. Additional studies are therefore needed to confirm these findings in human kidney disease.

eLife assessment

This useful article reports the possible roles of the natural product TRPV1 activator Eugenol on muscle performance and remodeling. It provides as yet incomplete evidence for eugenol, through TRPV1, but nevertheless merits future investigation.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, Huang et al have investigated the exercise mimetic role of Eugenol (a natural product) in skeletal muscle and whole-body fitness. The authors report that Eugenol facilitates skeletal muscle remodeling to a slower/oxidative phenotype typically associated with endurance. Eugenol also remodels the fat driving browning the WAT. In both skeletal muscle and fat Eugenol promotes oxidative capacity and mitochondrial biogenesis markers. Eugenol also improves exercise tolerance in a swimming test. Through a series of in vitro studies the authors demonstrate that eugenol may function through the trpv1 channel, Ca mobilization, and activation of CaN/NFAT signaling in the skeletal muscle to regulate slow-twitch phenotype. In addition, Eugenol also induces several myokines but mainly IL-15 through which it may exert its exercise mimetic effects. Overall, the manuscript is well-written, but there are several mechanistic gaps, physiological characterization is limited, and some data are mostly co-relative without vigorous testing (e.g. link between Eugenol, IL15 induction, and endurance). Specific major concerns are listed below.

Strengths:<br /> A natural product activator of the TRPV1 channel that could elicit exercise-like effects through skeletal muscle remodeling. Potential for discovering other mechanisms of action of Eugenol.

Weaknesses:<br /> (1) Figure 1: Histomorphological analysis using immunostaining for type I, IIA, IIX, and IIB should be performed and quantified across different muscle groups and also in the soleus. Fiber type switch measured based on qPCR and Westerns does not sufficiently indicate the extent of fiber type switch. Better images for Fig. 1c should be provided.

(2) Figure 2: Histomorphological analysis for SDH and NADH-TR should be performed and quantified in different muscle groups. Seahorse or oroborous respirometry experiments should be performed to determine the actually increase in mitochondrial respiratory capacity either in isolated mitochondria or single fibers from vehicle and Eugenol-treated mice. Em for mitochondrial should be added to determine the extent of mitochondrial remodeling. The current data is insufficient to indicate the extent of mitochondrial or oxidative remodeling.

(3) Figure 2: Gene expression analysis is limited to a few transcriptional factors. A thorough analysis of gene expression through RNA-seq should be performed to get an unbiased effect of Eugenol on muscle transcriptome. This is especially important because eugenol is proposed to work through CaN/NFAT signaling, major transcriptional regulators of muscle phenotype.

(4) I suggest the inclusion of additional exercise or performance testing including treadmill running, wheel running, and tensiometry. Quantification with a swimming test and measurement of the exact intensity of exercise, etc. is limited.

(5) In addition to muscle performance, whole-body metabolic/energy homeostatic effects should also be measured to determine a potential increase in aerobic metabolism over anaerobic metabolism.

(6) For the swimming test and other measurements, only 4 weeks of vehicle vs. Eugenol treatment was used. For this type of pharmacological study, a time course should be performed to determine the saturation point of the effect. Does exercise tolerance progressively increase with time?

(7) The authors should also consider measuring adaptation to exercise training with or without Eugenol.

(8) Histomorphological analysis of Wat is also lacking. EchoMRI would give a better picture of lean and fat mass.

(9) The experiments performed to demonstrate that Eugenol functions through trpv1 are mostly correlational. Some experiments are needed with trpv1 KO or KD instead of inhibitor. Similarly, KD for other trpv channels should be tested (at least 1-4 that seem to be expressed in the muscle). Triple KO or trpv null cells should be considered to demonstrate that eugenol does not have another biological target.

(10) Eugenol + trpv1 inhibition studies are performed in c2c12 cells and only looks at myofiber genes expression. This is incomplete. Some studies in mitochondrial and oxsphos genes should be done.

(11) The experiments linking Eugenol to ca handling, and calcineurin/nfat activation are all performed in c2c12 cells. There seems to be a link between Eugenol activation and CaN/NFAT activation and fiber type regulation in cells, however, this needs to be tested in mouse studies at the functional level using some of the parameters measured in aims 1 and 2.

(12) The myokine studies are incomplete. The authors show a link between Eugenol treatment and myokines/IL-15 induction. However, this is purely co-relational, without any experiments performed to show whether IL-15 mediates any of the effects of eugenol in mice.

(13) An additional major concern is that it cannot be ruled out that Engenol is uniquely mediating its effects through trpv1. Ideally, muscle-specific trpv1 mice should be used to perform some experiments with Eugenol to confirm that this ion channel is involved in the physiological effects of eugenol.

Reviewer #2 (Public Review):

Summary:<br /> The authors examined the hypothesis that eugenol enhances the metabolic profiles of skeletal muscles by activating the TRPV1-Ca2+-calcineurin-NFATc1-IL-15 signalling pathway. They first show that eugenol promotes skeletal muscle transformation and metabolic functions in mitochondria and adipose tissues by analysing changes in the expression of mRNA and proteins of relevant representative protein markers. With similar methodologies, they further found that eugenol increases the expression of mRNA and/or proteins of TRPV1, CaN, NFATC1, and IL-15. These processes were, however, prevented by inhibiting TRPV1 and CaN. Similar expression changes were also triggered by increasing intracellular Ca2+ with A23187, suggesting a Ca2+-dependent process.

Strengths:<br /> Different protein markers were used as a readout of the functions of skeletal muscles, mitochondria, and adipose tissues and analysed at both mRNA and protein levels. The results are mostly consistent though it is not always the case. Although the signaling pathway of TRPV1-Ca2+-CaN-NFAT is not new and well documented, they identified IL-15 as a new downstream target of this pathway,

Weaknesses:<br /> Apart from Fig.2A and 2B, they mostly utilised protein expression changes as an index of tissue functional changes. Most of the data supporting the conclusions are thus rather indirect. More direct functional evidence would be more compelling. For example, a lipolysis assay could be used to measure the metabolic function of adipocytes after eugenol treatment in Fig.3. Functional activation of NFAT can be demonstrated by examining the nuclear translocation of NFAT.

To further demonstrate the role of TRPV1 channels in the effects of eugenol, TRPV1-deficient mice and tissues could also be used. Will the improved swimming test in Fig. 2B and increased CaN, NFAT, and IL-15 triggered by eugenol be all prevented in TRPV1-lacking mice and tissues?

Direct evidence of eugenol activation of TRPV1 channels in skeletal muscles is also lacking. The flow cytometry assay was used to measure Ca2+ changes in the C2C12 cell line in Fig. 5A. But this assay is rather indirect. It would be more convincing to monitor real-time activation of TRPV1 channels in skeletal muscles not in cell lines using Ca2+ imaging or electrophysiology.

eLife assessment

This study presents a valuable report on the first warm autopsy case of a metastatic prostate cancer patient and the follow-up genomic and epigenomic analysis. The evidence supporting the claims of the authors is solid, although inclusion of more discussion of the study limitation and elaboration of mechanistic link for TP53, CDK12, and CDKN1B mutations would have strengthened the study. The work will be of interest to medical biologists working on prostate cancer.

Reviewer #1 (Public Review):

Summary:<br /> Zhang et al. described a warm autopsy case of a metastatic prostate cancer patient and the follow-up genomic and epigenomic analysis. The authors provided a thorough description of the warm autopsy procedure including consent process, patient evaluation, layout of operation room, specialties required to conduct a warm autopsy, and many other details. Following autopsy, they conducted a series of genomics and epigenomics experiments on selected primary tumors and metastasized tumors from different body sites. Genomic data analysis revealed several interesting results. For example, they discovered a putative metastasis driver event, CDKN1B truncation, and they provided functional relevance of this gene using cell cultures. They were able to piece together the evolutionary history and subclonal structures of the tumors in this patient, which also revealed extensive heterogeneity. They showed a strong correlation between the genetic and epigenetic distances across the tumors.

Strengths:<br /> Overall this is a very well-designed and nicely conducted study. According to the authors, warm autopsy procedures and systems are not yet well established in China. Therefore, this study represents the first warm autopsy in China, and will likely have a strong impact on similar future studies in China. The authors did a good job describing the rationale of a warm autopsy and provided a clear guideline. The genomics analyses were somewhat standard but provided interesting insights.

Weaknesses:<br /> There are several limitations that can be improved upon.

First, while this reviewer does not require the authors to increase the sample size, the authors should provide some discussion, especially on the limitation of generalizing their findings to other patients/cases/cancer types.

Second, the DNA methylation data was used to estimate clonal evolution, but the authors did not investigate whether there is any driver epigenetic events in metastasis. It seems that the authors did not generate WGBS on the primary tumors, which is another limitation.

Third, the authors generated RNA-seq data across many samples but did not provide any analysis beyond the expression level of CDKN1B. This seems to be a missed opportunity.

Fourth, the clonal relationship between the three primary tumors (PB1, PB2, and PB3) and the metastasized tumors is not very well described. Do the authors believe that the metastasis came from a subclone ancestral to the three primary tumors?

Reviewer #2 (Public Review):

Summary:<br /> The authors conducted the first warm autopsy of prostate cancer in China with clear and repeatable standard workflow, documented the transcriptional/genomic/epigenetic profiles across primary tumors and metastases, and highlighted CDKN1B mutation as a key driver mutation for prostate cancer metastases. They provided sufficient details and convincing evidence of multi-omics in their study to define a potential clonal evolution map for the metastatic progression of prostate cancer. The study will also stimulate the development of warm autopsy programs beneficial to patients in Asian populations.

Strengths:<br /> Although the overall incidence of prostate cancer is lower in Asian men compared to men in Western countries, the incidence is increasing in China recently. Therefore the autopsy program will have an important significance in boosting the understanding of molecular mechanism and drug development in prostate cancer for Asian population.<br /> 1. Clear illustration on the warm autopsy workflow and detailed documentation of patient clinical course, sample sites, and downstream analyses. This established a great standard for future expansion of similar autopsy programs and may help boost the consent of more cases.<br /> 2. Systematic and in-depth multi-omic analyses based on limited samples resulted in an impressive atlas for the intratumoral heterogeneity and clonal evolution across primary tumors and metastases. Key driver mutations were thus highlighted.

Weaknesses:<br /> 1. Although the authors highlighted TP53, CDK12, and CDKN1B mutations in the results, not much new knowledge on mechanisms is added to the field since these are already documented in previous studies. Both the unique/private and representative patterns in the single patient, compared to the publicly documented Chinese populations and other ethnical populations will add more significance to this study.

2. The authors claimed that CDKN1B mutation may be the driver event for prostate cancer metastases, but the mutation was absent in the initial bone metastases according to the evolution map created. Although the authors acknowledged this gap and mentioned an FUS mutation in the bone metastases, this compromised the strength in demonstrating the driving significance of this gene mutation. The shRNA experiments on migration<br /> and invasion were impressive but did not necessarily support the initiating potential of CDKN1B mutation in metastases to bone, which is the predominant site of metastases in prostate cancer. It might be a passenger mutation enriched in soft organ metastases or a driver mutation for the secondary metastases from bone metastases.

3. The epigenetic regulation highlighted in the study was not closely correlated to the genetic pattern highlighted (CDK12, CDKN1B, etc.).

eLife assessment

This compelling and novel mathematical method assesses drug pro-arrhythmic cardiotoxicity by examining the electrophysiology of untreated cardiac cells. It will be valuable for future drug safety design.

Reviewer #1 (Public Review):

Summary:<br /> Heitmann et al introduce a novel method for predicting the potential of drug candidates to cause Torsades de Pointes using simulations. Despite the fact that a multitude of such methods have been proposed in the past decade, this approach manages to provide novelty in a way that is potentially paradigm-shifting. The figures are beautiful and manage to convey difficult concepts intuitively.

Strengths:<br /> (1) Novel combination of detailed mechanistic simulations with rigorous statistical modeling

(2) A method for predicting drug safety that can be used during drug development

(3) A clear explication of difficult concepts.

Weaknesses:<br /> (1) In this reviewer's opinion, the most important scientific issue that can be addressed is the fact that when a drug blocks multiple channels, it is not only the IC50 but also the Hill coefficient that can differ. By the same token, two drugs that block the same channel may have identical IC50s but different Hill coefficients. This is important to consider since concentration-dependence is an important part of the results presented here. If the Hill coefficients were to be significantly different, the concentration-dependent curves shown in Figure 6 could look very different.

(2) The curved lines shown in Figure 6 can initially be difficult to comprehend, especially when all the previous presentations emphasized linearity. But a further issue is obscured in these plots, which is the fact that they show a two-dimensional projection of a 4-dimensional space. Some of the drugs might hit the channels that are not shown (INaL & IKs), whereas others will not. It is unclear, and unaddressed in the manuscript, how differences in the "hidden channels" will influence the shapes of these curves. An example, or at least some verbal description, could be very helpful.

Reviewer #2 (Public Review):

Summary:<br /> In the paper from Hartman, Vandenberg, and Hill entitled "assessing drug safety, by identifying the access of arrhythmia and cardio, myocytes, electro physiology", the authors, define a new metric, the axis of arrhythmia" that essentially describes the parameter space of ion channel conductance combinations, where early after depolarization can be observed.

Strengths:<br /> There is an elegance to the way the authors have communicated the scoring system. The method is potentially useful because of its simplicity, accessibility, and ease of use. I do think it adds to the field for this reason - a number of existing methods are overly complex and unwieldy and not necessarily better than the simple parameter regime scan presented here.

Weaknesses:<br /> The method described in the manuscript suffers from a number of weaknesses that plague current screening methods. Included in these are the data quality and selection used to inform the drug-blocking profile. It's well known that drug measurements vary widely, depending on the measurement conditions.

There doesn't seem to be any consideration of pacing frequency, which is an important consideration for arrhythmia triggers, resulting from repolarization abnormalities, but also depolarization abnormalities. Extremely high doses of drugs are used to assess the population risk. But does the method yield important information when realistic drug concentrations are used? In the discussion, the comparison to conventional approaches suggests that the presented method isn't necessarily better than conventional methods.

In conclusion, I have struggled to grasp the exceptional novelty of the new metric as presented, especially when considering that the badly needed future state must include a component of precision medicine.

eLife assessment

This study presents valuable findings on diabetogenic risk from colorectal cancer (CRC) treatment. The authors claim that postoperative screening for type 2 diabetes should be prioritized in CRC survivors with overweight/obesity, irrespective of the oncological treatment received. The evidence supporting the claims is solid but requires confirmation in different populations. These results have theoretical or practical implications and will be of interest to endocrinologists, oncologists, general practitioners, gastrointestinal surgeons, and policymakers working on CRC and diabetes.

Reviewer #1 (Public Review):

Summary:<br /> In this study, the authors set out to determine whether colorectal cancer surgery site (right, left, rectal) and chemotherapy impact the subsequent risk of developing T2DM in the Danish national health register.

Strengths:<br /> - The research question is conceptually interesting<br /> - The Danish national health register is a comprehensive health database<br /> - The data analysis was thorough and appropriate<br /> -The findings are interesting, and a little surprising that there was no impact of chemotherapy on the development of T2DM

Weaknesses:<br /> - This is not a weakness as such, but in the discussion, I would consider adding some brief comment on the international generalizability of the findings - e.g. demographic make up of the Danish population health register and background rates of DM and obesity in this population with CRC compared to countries on other continents.<br /> - A little more information would be helpful regarding how T2DM was diagnosed in the registry. If someone did develop transient hyperglycemia requiring DM medications during chemotherapy, would the investigators have been able to identify these people? Would they have been classified as T2DM based on filling a prescription for DM meds for a period of time? Also, did the authors have information regarding time to development of T2DM after surgery?<br /> - In the adjusted Models, the authors did not adjust for cancer stage, even though cancer stage appears to be very different between the chemo and no chemo groups. It would be interesting to know if it affects the results if the model adjusted for cancer stage<br /> - It would be worthwhile to report if mortality rates were different between the groups during follow up, and if the authors investigated whether perhaps differences in mortality rates led to specific groups living longer, and therefore having more time to develop DM

Overall, the authors achieved their aims, and the conclusions are supported by their results as reported.<br /> The results are unlikely to significantly change patient treatment or T2DM screening in this population. With some additional information, as described above, the results would be of interest to the community.

Reviewer #2 (Public Review):

Summary: The study showed the impact of cancer treatment on new onset of diabetes among patients with colorectal cancer using the national database. Findings reported that individuals with rectal cancer without chemotherapy were less likely to develop diabetes but among other groups, treatment didn't show any impact on the development of diabetes. BMI still played a significant role in developing diabetes regardless of treatment types.

Strengths:<br /> One of the strengths of this study is innovative findings about the prognosis of colorectal cancer treatment stratified by treatment types. Especially, as it examined the impact of treatment on the risk of new chronic disease after diagnosis, it became significant evidence that suggests practical insights in developing a proper monitoring system for patients with colorectal cancer and their outcomes after treatment and diagnosis. It is imperative for providers to guide patients and caregivers to prevent adverse outcomes like new onset of chronic disease based on BMI and types of treatment. The next strength is the national database. As the study used the national database, the generalizability is validated.

Weaknesses: Even though the study attempted to examine the impact of each treatment option, the dosage of chemotherapy and the types of chemotherapy were not able to be examined due to the data source.

eLife assessment

This important study demonstrates widespread introgression between species of cyanobacteria in hot springs in Yellowstone National Park. Using single cell sequencing of hundreds of genomes, the authors provide one of the most convincing demonstrations to date of the importance of selection and hybridization in shaping polymorphism within a natural community. The strong enthusiasm for the paper is only dampened slightly by the methods not being described in the clearest possible manner.

Reviewer #1 (Public Review):

Summary:

What are the overarching principles by which prokaryotic genomes evolve? This fundamental question motivates the investigations in this excellent piece of work. While it is still very common in this field to simply assume that prokaryotic genome evolution can be described by a standard model from mathematical population genetics, and fit the genomic data to such a model, a smaller group of researchers rightly insists that we should not have such preconceived ideas and instead try to carefully look at what the genomic data tell us about how prokaryotic genomes evolve. This is the approach taken by the authors of this work. Lacking a tight theoretical framework, the challenge of such approaches is to devise analysis methods that are robust to all our uncertainties about what the underlying evolutionary dynamics might be.

The authors here focus on a collection of ~300 single-cell genomes from a relatively well-isolated habitat with relatively simple species composition, i.e. cyanobacteria living in hotsprings in Yellowstone National Park, and convincingly demonstrate that the relative simplicity of this habitat increases our ability to interpret what the genomic data tells us about the evolutionary dynamics.

Using a very thorough and multi-faceted analysis of these data, the authors convincingly show that there are three main species of Synechococcus cyanobacteria living in this habitat, and that apart from very frequent recombination within each species (which is in line with insights from other recent studies) there is also a remarkably frequent occurrence of hybridization events between the different species, and with as of yet unidentified other genomes. Moreover, these hybridization events drive much of the diversity within each species. The authors also show convincing evidence that these hybridization events are not neutral but are driven by selected by natural selection.

Strengths:

The great strength of this paper is that, by not making any preconceived assumptions about what the evolutionary dynamics is expected to look like, but instead devising careful analysis methods to tease apart what the data tells us about what has happened in the evolution in these genomes, highly novel and unexpected results are obtained, i.e. the major role of hybridization across the 3 main species living in this habitat.

The analysis is very thorough and reading the detailed supplementary material it is clear that these authors took a lot of care in devising these methods and avoiding the pitfalls that unfortunately affect many other studies in this research area.

The picture of the evolutionary dynamics of these three Synechococcus species that emerge from this analysis is highly novel and surprising. I think this study is a major stepping stone toward the development of more realistic quantitative theories of genome evolution in prokaryotes.

The analysis methods that the authors employ are also partially novel and will no doubt be very valuable for analysis of many other datasets.

Weaknesses:

I feel the main weakness of this paper is that the presentation is structured such that it is extremely difficult to read. I feel readers have essentially no chance to understand the main text without first fully reading the 50-page supplement with methods and 31 supplementary materials. I think this will unfortunately strongly narrow the audience for this paper and below in the recommendations for the authors I make some suggestions as to how this might be improved.

A very interesting observation is that a lot of hybridization events (i.e. about half) originate from species other than the alpha, beta, and gamma Synechococcus species from which the genomes that are analyzed here derive. For this to occur, these other species must presumably also be living in the same habitat and must be relatively abundant. But if they are, why are they not being captured by the sampling? I did not see a clear explanation for this very common occurrence of hybridization events from outside of these Synechococcus species. The authors raise the possibility that these other species used to live in these hot springs but are now extinct. I'm not sure how plausible this is and wonder if there would be some way to find support for this in the data (e.g that one does not observe recent events of import from one of these unknown other species). This was one major finding that I believe went without a clear interpretation.

The core entities in the paper are groups of orthologous genes that show clear evidence of hybridization. It is thus very frustating that exactly the methods for identifying and classifying these hybridization events were really difficult to understand (sections I and V of the supplement). Even after several readings, I was unsure of exactly how orthogroups were classified, i.e. what the difference between M and X clusters is, what a `simple hybrid' corresponds to (as opposed to complex hybrids?), what precisely the definitions of singlet and non-singlet hybrids are, etcetera. It also seems that some numbers reported in the main text do not match what is shown in the supplement. For example, the main text talks about "around 80 genes with more than three clusters (SM, Sec. V; fig. S17).", but there is no group with around 80 genes shown in Fig S17! And similarly, it says "We found several dozen (100 in α and 84 in β) simple hybrid loci" and I also cannot match those numbers to what is shown in the supplement. I am convinced that what the authors did probably made sense. But as a reader, it is frustrating that when one tries to understand the results in detail, it is very difficult to understand what exactly is going on. I mention this example in detail because the hybrid classification is the core of this paper, but I had similar problems in other sections.

Although I generally was quite convinced by the methods and it was clear that the authors were doing a very thorough job, there were some instances where I did not understand the analysis. For example, the way orthogroups were built is very much along the lines used by many in the field (i.e. orthoMCL on the graph of pairwise matchings, building phylogenies of connected components of the graph, splitting the phylogenies along long branches). But then to subdivide orthogroups into clusters of different species, the authors did not use the phylogenetic tree already built but instead used an ad hoc pairwise hierarchical average linkage clustering algorithm.

Reviewer #2 (Public Review):

Summary:<br /> Birzu et al. describe two sympatric hotspring cyanobacterial species ("alpha" and "beta") and infer recombination across the genome, including inter-species recombination events (hybridization) based on single-cell genome sequencing. The evidence for hybridization is strong and the authors took care to control for artefacts such as contamination during sequencing library preparation. Despite hybridization, the species remain genetically distinct from each other. The authors also present evidence for selective sweeps of genes across both species - a phenomenon which is widely observed for antibiotic resistance genes in pathogens, but rarely documented in environmental bacteria.

Strengths:<br /> This manuscript describes some of the most thorough and convincing evidence to date of recombination happening within and between cohabitating bacteria in nature. Their single-cell sequencing approach allows them to sample the genetic diversity from two dominant species. Although single-cell genome sequences are incomplete, they contain much more information about genetic linkage than typical short-read shotgun metagenomes, enabling a reliable analysis of recombination. The authors also go to great lengths to quality-filter the single-cell sequencing data and to exclude contamination and read mismapping as major drivers of the signal of recombination.

Weaknesses:<br /> Despite the very thorough and extensive analyses, many of the methods are bespoke and rely on reasonable but often arbitrary cutoffs (e.g. for defining gene sequence clusters etc.). Much of this is warranted, given the unique challenges of working with single-cell genome sequences, which are often quite fragmented and incomplete (30-70% of the genome covered). I think the challenges of working with this single-cell data should be addressed up-front in the main text, which would help justify the choices made for the analysis. The conclusions could also be strengthened by an analysis restricted to only a subset of the highest quality (>70% complete) genomes. Even if this results in a much smaller sample size, it could enable more standard phylogenetic methods to be applied, which could give meaningful support to the conclusions even if applied to just ~10 genomes or so from each species. By building phylogenetic trees, recombination events could be supported using bootstraps, which would add confidence to the gene sequence clustering-based analyses which rely on arbitrary cutoffs without explicit measures of support.

The manuscript closes without a cartoon (Figure 4) which outlines the broad evolutionary scenario supported by the data and analysis. I agree with the overall picture, but I do think that some of the temporal ordering of events, especially the timing of recombination events could be better supported by data. In particular, is there evidence that inter-species recombination events are increasing or decreasing over time? Are they currently at steady-state? This would help clarify whether a newly arrived species into the caldera experiences an initial burst of accepting DNA from already-present species (perhaps involving locally adaptive alleles), or whether recombination events are relatively constant over time. These questions could be answered by counting recombination events that occur deeper or more recently in a phylogenetic tree. The cartoon also shows a 'purple' species that is initially present, then donates some DNA to the 'blue' species before going extinct. In this model, 'purple' DNA should also be donated to the more recently arrived 'orange' species, in proportion to its frequency in the 'blue' genome. This is a relatively subtle detail, but it could be tested in the real data, and this may actually help discern the order of the inferred recombination events.

The abstract also makes a bold claim that is not well-supported by the data: "This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species..." In fact, the two species are cohesive in the sense that they are identifiable based on clustering of genome-wide genetic diversity (as shown in Fig 1A). I agree that the mixing is 'widespread' in the sense that it occurs across the genome (as shown in Figure 2A) but it is clearly not sufficient to erode species boundaries. So I believe the data is consistent with a Biological Species Concept (sensu Bobay & Ochman, Genome Biology & Evolution 2017) that remains 'fuzzy' - such that there are still inter-species recombination events, just not sufficient to erode the cohesion of genomic clusters. Therefore, I think the data supports the emerging picture of most bacteria abiding by some version of a BSC, and is not particularly 'contrary' to the prevailing view.

The final Results paragraph begins by posing a question about epistatic interactions, but fails to provide a definitive answer to the extent of epistasis in these genomes. Quantifying epistatic effects in bacterial genomes is certainly of interest, but might be beyond the scope of this paper. This could be a Discussion point rather than an underdeveloped section of the Results.

eLife assessment

This work provides valuable insights into mucosal antibody responses against SARS-CoV-2 following intranasal immunization by characterizing a large number of monoclonal antibodies at both mucosal and non-mucosal sites. The evidence supporting the claims is overall solid, although the flow cytometric assessment of antibody-expressing cells would benefit from more rigorous controls. The demonstrated in vitro antiviral activity of antibodies characterized provides a rationale for developing mucosal vaccines, especially if confirmed in vivo and benchmarked against antibodies generated following intramuscular vaccination.

Reviewer #1 (Public Review):

Despite evidence suggesting the benefits of neutralizing mucosa-derived IgA in the upper airway in protection against the SARS-CoV-2 virus, all currently approved vaccines are administered intramuscularly, which mainly induces systemic IgG. Waki et al. aimed to characterize the benefits of intranasal vaccination at the molecular level by isolating B cell clones from nasal tissue. The authors found that Spike-specific plasma cells isolated from the spleen of vaccinated mice showed significant clonal overlap with Spike-specific plasma cells isolated from nasal tissue. Interestingly, they could not detect any spike-specific plasma cells in the bone marrow or Peyer's patches, indicating that these nose-derived cells did not necessarily home to and reside in these locations, although the Peyer's patch is not a typical plamsa cell niche - rather the lamina propria of the gut would have been a better place to look. Furthermore, they found that multimerization improves the antibody/antigen binding when the antibody is of low or intermediate affinity, but that high-affinity monomeric antibodies do not benefit from multimerization. Lastly, the authors used a competitive ELISA assay to show that multimerization could improve the neutralizing capacity of these antibodies.

The strength of this paper is the cloning of multiple IgA from the nasal mucosae (n=99) and the periphery (n=114) post-SARS-CoV-2 i.n. vaccination to examine the clonal relationship of this IgA with other sites, including the spleen. This analysis provides novel insights into the nature of the mucosal antibody response at the site where the host would encounter the virus, and whether this IgA response disseminates to other tissues.

There were also some weaknesses:

1. The finding that multimerization improves binding and neutralization is not surprising as this was observed before by Wang and Nussenzweig for anti-SARS-CoV-2 IgA (authors should cite Enhanced SARS-CoV-2 neutralization by dimeric IgA. Wang et al, Sci. Transl. Med 2021, 13:3abf1555). In addition, as far as I can tell we cannot ascertain the purity of fractions from the size exclusion chromatography thus I wasn't sure whether the input material used in Fig. 4 was a mixed population of dimer/trimer/tetramer?

2. The flow cytometric assessment of the IgA+ clones from the nasal mucosae was difficult to interpret (Fig. 1B). It was hard for me to tell what they were gating on and subsequently analysing without an IgA-negative population for reference.

3. While the i.n. study itself is large and challenging, it would have been interesting to compare an i.m. route and examine the breadth of SARS-CoV-2 variant S1 binding for IgGs as in Fig. 2A. Are the IgA responses derived from the mucosae of greater breadth than systemic IgG responses? Alternatively, and easier, authors could do some comparisons with well-characterized IgG mAb for affinity and cross-reactivity as a benchmark to compare with the IgAs they looked at.

Overall the authors did a good job of looking at a large range of systemic vs mucosal S1-specific antibodies in the context of an intra-nasal vaccination and this provides additional evidence for the utility of mucosal vaccination approaches for reducing person-to-person transmission.

Reviewer #2 (Public Review):

Summary:<br /> This research demonstrates the breadth of IgA response as determined by isolating individual antigen-specific B cells and generating mAbs in mice following intranasal immunization of mice with SARS-CoV2 Spike protein. The findings show that some IgA mAb can neutralize the virus, but many do not. Notable immunization with Wuhan S protein generates a weak response to the omicron variant.

Strengths:<br /> Detailed analysis characterizing individual B cells with the generation of mAbs demonstrates the response's breadth and diversity of IgA responses and the ability to generate systemic immune responses.

Weaknesses:<br /> The data presentation needs clarity, and results show mAb ability to inhibit SARS-CoV2 in vitro. How IgA functions in vivo is uncertain.

eLife assessment

While decades of research findings have supported the idea that action attenuates predicted touch, recent work has countered this, proposing that action actually enhances predicted touch and the previously observed attenuation is due to tactile contact. This present study resolves these contradictory claims regarding the role of prediction in perception of self-action. This important work provides compelling evidence that self-generated touch is attenuated compared to the same touch externally-generated, and a clear explanation for recent high-profile results that appeared to support the opposite view.

Reviewer #1 (Public Review):

This is a well-designed study, with clear results that is also very well-written.<br /> The authors nicely demonstrate that previous contradictory results are largely due to the lack of the proper baseline condition (Exp 1 and Exp 2). The second experiment also replicates the previous study results that had found enhancement. However, the addition of the proper baseline allows for a completely different interpretation of the same results. In the final experiment, they further probe the role of prediction in attenuation of predicted touch and demonstrate that attenuation is due to the ability to predict the consequences of active touch.

Overall, I found the paper had many strengths including the pre-registered protocols, the replication of findings both in favor of attenuation and enhancements, the inclusion of a baseline condition to compare active touch manipulations, and lastly a rigorous analysis of the data.

While in part this confirms previous results on sensory attenuation, it also helps interpret previous results that suggest the contrary. Therefore the results will be of high value to the community.

Reviewer #2 (Public Review):

Many studies have found that self-generated tactile contact is perceived as weaker than the same contact with an external source. A recent high-profile study found that a force that was predictable based on a participant's own movement but was not caused by contact was perceived as stronger than the same force in an interleaved no-go condition without movement. By combining methods from this and older studies within a single design, the present study resolves the apparent contradiction by showing that the predictable force is enhanced only relative to the no-go reference, and that forces are attenuated when self-contact occurs or is predicted.

The key strength of this work lies in the robust application of pre-registered methods to reproduce and compare findings within a single experimental setting that have been separately interpreted as enhancement or attenuation in previous work. The results are admirably clear and decisive.

I feel there is room for some conceptual clarification when it comes to the discussion of appropriate baselines. The paper tends (as does the preceding work by Thomas et al.) towards claims of the absolute kind, such as "self-generated sensation is attenuated" (or "enhanced"), that are not meaningful because the scales of sensation and stimulus are incommensurate (e.g. there is no sensation that is objectively equal to 2N of force on the finger). Rather, the only claims that can or should be made are relative ones, e.g. "self-generated sensation is attenuated *compared to* externally-generated sensation". The present results provide a strong confirmation of this existing claim while clarifying that the recent findings of Thomas et al.'s Exp 1 could be better summarized as "predictable sensations are enhanced in trials with a GO signal compared to a NOGO signal". So it is not that one study chose the "right" baseline and the other the "wrong" one, but rather that Thomas et al. extrapolated their results to comparisons other than the one they had tested.

The paper does not directly address Thomas et al.'s Exp 2, in which they observed enhanced sensation of force in an expected compared to an unexpected finger. Because there was never any (real or virtual) contact between the fingers in that experiment, the authors would probably argue that it is irrelevant to the classical "predictive attenuation" hypothesis, but the results nonetheless suggest the existence of another factor influencing force perception that is not explained by NOGO inhibition.

Reviewer #3 (Public Review):

The authors sought to directly compare the predictions of two models of somatosensory processing: The attenuation model, which states that the sensation of touch on one hand is reduced when it is the predictable result of an active movement by the other hand; and the enhancement model, which states that the sensation of touch is actually increased, as long as the active hand does not receive touch stimultaneously with the passive hand (no double stimulation). The authors achieved their aims, with results clearly demonstrating (1) attenuation in the case of self touch, (2) that previously-observed enhancement is a consequence of the comparison condition (false enhancement), and (3) that attenuation involves predictive mechanisms and does not result simply from double stimulation. These findings, and the methodology, should particularly impact future studies of perceptual attenuation, sensory prediction error, and motor control more generally. The opposite conclusions obtainable by selecting different comparison conditions is particularly striking.

Experiment 1 affirms that a touch to the passive finger caused by the active finger tapping a force sensor is perceived as weaker (attenuated) compared to a baseline not involving the active finger, but that if double stimulation is prevented (active finger moves, but no contact), neither attenuation nor enhancement occurs. Experiment 2 includes the three original conditions, plus the no-go condition used as a comparison in these earlier studies. Results suggest that the comparisons used by previous studies would result in the false appearance of enhancement. Finally, Experiment 3 tests the hypothesis that the lack of attenuation in the no-contact condition is due to the absence of double stimulation rather than predictive mechanisms. When contact and no-contact trials were mixed in an 80:20 ratio, such that participants would form predictions about the consequence of their active finger movement even if some trials lacked contact. In this case, attenuation was observed for both contact and no-contact trials, supporting the idea that attenuation is related to predictive processes linked to moving the active finger, and is not a simple consequence of double stimulation.

The methodology and analysis plans for all three experiments were pre-registered prior to data collection. We can therefore be very confident that the results were not influenced by hypotheses developed only after seeing the data. The three experiments were each performed in a new set of participants. Experiments 2 and 3 included conditions that replicated the Experiment 1 effects, allowing us to be very confident that the results are robust.

While the study has significant strengths, some aspects of the interpretation need to be clarified. In particular, the authors' interpretation depends on the idea that attenuation is absent in the no-contact condition because this action-sensory consequence relationship is an "arbitrary mapping." It is not clear what makes it arbitrary. The self-touch contact condition could also be considered somewhat arbitrary and different from real self-touch; the 2N test force was triggered by the right finger tapping a force sensor. If participants' tapping forces were recorded, it would be useful to include this information, particularly about how variable participants' taps were. In other words, unlike real self-touch, in this paradigm the force of the active finger tap did not affect the force delivered to the passive finger. One additional potential weakness is that participants' vision was occluded in Experiment 3, but not in Experiments 1 and 2. The authors do not discuss whether this difference could confound any of the analyses that compare results across experiments.

eLife assessment

This work presents useful and potentially valuable findings on how food signals may influence reproduction in the nematode C. elegans. In the current manuscript, the evidence in support of the authors' model is incomplete, and additional experimental data is needed to buttress the authors' conclusions.

Reviewer #1 (Public Review):

In this manuscript the authors perform a detailed analysis of the impact of food type on reproduction in C. elegans. They find that, in comparison with the standard OP50 strain of E. coli that is ubiquitously used to maintain C. elegans in the laboratory setting, the CS180 strain results in a reduction in the number of progeny that may be a consequence of an early transition from spermatogenesis to oogenesis that reduces total sperm number. They also find that the rate of oocyte fertilization is increased in animals fed CS180 vs. OP50. Using mutants and laser ablations, the authors show that, whereas the insulin-like peptide INS-6 acts in the ASJ sensory neurons to mediate the food type effect on total progeny and early oogenesis, the increased fertilization rate phenotype does not require ASJ or insulin-like signaling and instead requires the AWA olfactory neurons.

The major strengths of the manuscript are the establishment of INS-6 as a link between food type and reproduction and the detail and rigor with which the experiments were executed. The results presented generally support the authors' model. This role of insulin-like signaling in connecting food type and reproduction makes it a plausible target for evolutionary forces that may have shaped insulin-like signaling in invertebrates. As such, this work contributes broadly to our understanding of how insulin signaling may have evolved prior to the emergence of vertebrates.

A weakness of the work is the epistasis analysis of insulin-like pathway components, which is incomplete and at times difficult to interpret.

Reviewer #2 (Public Review):

The manuscript by Mishra et al. examines the modulation of the nervous system by different bacterial food to influence reproductive phenotypes-specifically onset of oogenesis, fertilization rate, and progeny production. Defining how animal reproduction could be modulated by bacterial food cues through neuroendocrine signaling is a fascinating subject of study for which C. elegans is well-suited. However, the overall scope of the current study is limited, and some of the central data do not provide compelling evidence for the authors' underlying hypothesis and model.

1. Two strains of E. coli are examined, the standard C. elegans bacterial food strain OP50 and an E. coli strain that Alcedo and colleagues have previously characterized to influence aging and longevity through nervous system modulation. While the authors determine that differences in LPS structure present between the strains does not account for the food-dependent effects, there is little further insight regarding the bacterial features that contribute to the observed differences in reproductive physiology. Moreover, at least two of the phenotypes examined-total progeny and fertilization rate-are known to be affected by bacterial food quality and may be affected by bacteria in many ways, so the description of these phenotypes is somewhat less compelling than the study of the onset of oogenesis.

2. The onset of oogenesis phenotype, using the lin-41::GFP reporter, seems more specific and tractable, and the authors nicely decouple this phenotype from the total progeny and fertilization rate phenotypes through experiments that shift animals to different bacterial food at specific developmental stages. However, as it stands, the data regarding the role of ins-6 and ASJ in modulating this phenotype, and the model that exposure to CS180 bacterial food causes a change in the ASJ expression of ins-6, which is sufficient to promote the earlier onset of oogenesis at the mid-L4 stage, seems somewhat incomplete and have some inconsistencies to be addressed.

a. The ins-6 mutant phenotype is rescued by genome ins-6 and partially rescued by ins-6 expressed under and ASJ-specific promoter. The lack of rescue from an ASI promoter is puzzling given the secreted nature of ins-6.

b. The ins-6 mutant phenotype with regard to delaying the early expression of lin-41::GFP on CS180 appears weaker than the daf-2 mutant phenotype. This is difficult to reconcile with what is known about the relative strength of the daf-2 mutant alleles relative to ins-6 for a wide range of phenotypes.

c. The daf-16 loss-of-function phenotype and suppression of daf-2 and ins-6 mutant phenotypes are not shown for the lin-41::GFP expression phenotype.

d. The modest difference in ins-6p::mCherry expression in the ASJ neurons (Figure 5D) make the idea that this difference causes onset of oogenesis somewhat implausible.

e. The strain carrying an genetic ablation of ASJ appears to have a markedly different baseline of kinetics of lin-41::GFP expression (even at lethargus, less than half of the animals appear to express lin-41::GFP). Given this phenotype, it seems difficult to draw conclusions about bacterial food-dependent effects on expression of lin-41::GFP. Additional characterization corroborating timing of oogenesis independent of the lin-41::GFP marker may be helpful, but something seems amiss.

Reviewer #3 (Public Review):

I very much enjoyed reading this paper by Shashwat Mishra and team from Joy Alcedo's and from Queelim Ch'ng's laboratories dissecting how sensory signals regulate reproduction in worms. The mechanisms by which sensory inputs affect the function of the germline, the balance between growth and differentiation within this tissue, are of broad interest not only to those interested in reproduction and differentiation, but also to those interested in the mechanisms of plasticity that enable organisms to adjust to changing environmental conditions. These mechanisms are only now beginning to be characterized. Here the focus is on the role of insulin signals expressed in sensory neurons. This work builds on previous findings by the Alcedo lab that sensory perception of bacterial-type dependent signals regulates C. elegans lifespan. Here their focus is on the effects on reproduction, and on the communication of that information by insulin-like signals.

Worms have a huge family of 40 insulin-like genes, which the Alcedo and Ch'ng labs have been studying for many years. The paper starts with the interesting premise that the brood size of the worms is food type dependent. The authors show that this is due to effects on the timing of the onset of oogenesis during larval development (which constrains the size of the pool of sperm available for subsequent oocyte fertilization) as well as on effects on the rate of oocyte fertilization during adulthood. Using clever timing for food switching, they show that the effects on oogenesis onset and on fertilization rate are separable. In addition, these effects did not appear to be merely the outcome of indirect effects of food ingestion, but were, instead, at least in part, due to the perception of environmental information by specific sensory neurons. Using mutants affecting transduction of sensory information in specific neurons and genetic ablation of specific neurons, the authors show that the onset of oogenesis and the rate of reproduction were controlled by different sensory neurons, ASJ and AWA, respectively. One of these neurons, ASJ, transmitted environmental information via the ins-6 neuropeptide.

Altogether, the paper advances our understanding of how environmental determinants influence reproduction.

eLife assessment

The authors studied the mechanisms by which dead cells are removed from the wounded skin in a process called efferocytosis. By analyzing different cell populations in the skin, the authors find that proteins involved in mediating the cell death and marking the cells as undergoing this process are elevated during distinct times in the wound healing program. Interestingly, these same proteins are elevated even higher in diabetic wounds. Finally the authors demonstrate that blocking the process of efferocytosis alters the wound healing program, thus illustrating its importance in effective wound repair.

Reviewer #1 (Public Review):

The manuscript by Justynski et al., addresses an important question in the field of efferocytosis, namely how does the clearance of apoptotic cells promote wound healing. A major highlight of this work is the profiling of the transcriptional heterogeneity during the inflammatory phase of the wound healing program via single cell sequencing. Many of the genes analyzed in the manuscript are well-known players in efferocytosis and wound healing so the contribution of this work is the dynamic and high resolution temporal and cell type specific responses during injury mediated inflammation.

Overall the manuscript is technically sound and the conclusions are generally supported by the data. However, the authors are cautioned to tone down some of the sentences with the human diabetic samples as they rely heavily on extrapolation rather experimental tests. Other areas of improvement include the relatively simplistic approaches and interpretation of the results. For instance, the antibody inhibition of Axl had minimal effect on the clearance of apoptotic cells in the wound and this would be expected with the redundancy endowed by other TAM receptors.

There are also some inconsistencies between the quantifications and the representative images provided. For instance, in Figure 6, the number of TUNEL+ cells seem to be higher in the IgG samples compared to the anti-Timd4 treatment, but this is not the case in the quantification.

Reviewer #2 (Public Review):

Based on their results the authors make the following statements:<br /> 1) Apoptotic pathways and efferocytosis receptors are elevated in fibroblasts and immune cells in mouse skin wounds. Based on the analysis of the scRNASeq data this is a valid conclusion.

I suggest to repeat the quantification of cells containing active caspase-3 with an anti-cleaved caspase-3 antibody. Here the authors use an antibody recognizing phospho S150 antibody, which is far from generally accepted to be a marker for active caspase-3.

It would also be good to quantify the apoptotic cells observed in the sections (Fig 1 I and J) and compare to control treatment on sections. It is not clear from the data presented whether the number of apoptotic cells increases or not in the time frame analyzed since the controls are lacking. In a FACS analysis (Fig S1 H), the authors show that there is no increase in dead cells in a time frame of 48 hrs. Could it be that the majority of the cells that may have died in vivo, were lost during the procedure of tissue digestions. Dead cells tend to aggregate.

On line 104 the authors refer to the apoptosis-inducing activity of G0s2. Please, realize that there is little or no in vivo evidence for a role of G0s2 in apoptosis.

The authors state that Axl is uniquely expressed in DC and fibroblasts (Fig 2). Are the Axl-cells positive in panel G (red, Fig 2) that do not stain for the Pdgfra marker (green) then all DCs? Please clarify or show with a triple staining that these cells are indeed DCs. In addition, it is not clear to me to what reference level exactly the expression levels are compared in Fig 2A. Is this between the 24 and 48h time points after wounding (as mentioned in the legend)? If so, the analysis may indicate up or down regulation but not necessarily expression or no expression.

2) Human diabetic wounds display increased and altered efferocytosis signaling via Axl.<br /> This conclusion is solely based on CellChat analysis and should be tuned down or validated. Tools like CellChat or NicheNet generate data that are suggestive and help scientist to build hypothesis. However, these data do not hold formal proof, but should be experimentally validated. Alternatively, the statement should be downtuned.

3) Axl expression is regulated via an TLR3-independent mechanism during wounding. This statement is supported by analysis in a genetic mouse model.

4) In mice, Axl signaling is required for wound repair but is dispensable for efferocytosis.<br /> This was concluded based on an in vivo experiment in which the authors treat the mice during wound healing with neutralizing anti-Axl antibodies that were validated in literature. The effectivity of the treatment is checked by analyzing the Axl mRNA levels since Axl activation upregulates its own mRNA expression levels. Anti-Axl therapy resulted in a downregulation of the Axl mRNA levels, while IFN-beta levels (an inducer of Axl expression) were upregulated by the treatment.<br /> The authors conclude that anti-Axl treatment leads to healing defects based on lack of granulation tissue and larger scabs, a reduction of fibroblast repopulation and revascularization. The differences in the last two parameters mentioned above are obvious, however the other parameters, as granulation tissue and scabs are less clear to me. Is this quantified in any way? In Fig S4 D there is also a large scab visible in the control treatment image. Therefore, it would be good if these parameters could be better substantiated. In view of the lack of revascularization, are there differences in the mRNA expression levels of angiogenic factors such as VEGF and others at this time point? Does revascularization occur at later stages?.<br /> Based on the FACS analysis the authors claim that there are no differences at the level of DCs. However, the plots shown in Fig 5C do not convincingly show the detection of DC (as boxed in the lower panel). Based on the density plots one would presume this is just the continuation of the CD11b+ population and not a separate CD11c+ population. To get a better view on that, it would be better to show dot plots instead of density plots.<br /> Finally, the authors state (line 265-266) that anti-Axl treatment leads to non-significantly increased expression of IL1alpha and IL6 after one day of injury (Fig S4C). If the difference between the control-treated and the anti-Axl-treated group is statistically not significant I would not conclude there is an increase. Please adapt phrasing or include more mice in the experiment (now only 4) to substantiate the observation and clarify whether it is increased or not.

5) Inhibition of the efferocytosis receptor Timd4 decreases efferocytosis and abrogates wound repair.<br /> The reason to study the effect of Timd4 was based on the fact that the authors find it upregulated on DCs during wound healing.<br /> The contribution of Timd4 in wound healing was investigated in vivo, under conditions in which the mice were treated with an anti-Timd4 antibody.<br /> The authors conclude that overall healing was not affected but that the wound beds appeared more fragile. What is meant with 'appeared more fragile' is not clear. In addition, this seems to me a quite subjective interpretation. What are the objective parameters to come this conclusion?<br /> Similar to inhibition of Axl, inhibition of Timd4 led to a defect in revascularization as witnessed by the absence of CD31 staining. Also in this experiment one can raise similar questions as in the anti-Axl experiment: 1) does revascularization occur at a later timepoint; 2) what about the expression of angiogenic factors?<br /> In the anti-Timd4 treated wounds the authors observe more TUNEL-positive cells and conclude that this is due to a defect in efferocytosis. However, the formal experimental proof for this in the current model is lacking. How do the authors exclude the possibility that anti-Timd4 treatment attracts more infiltrating cells that then undergo treatment, or that the treatment with anti-Timd4 leads to more apoptosis of certain cells in the wound bed. What is the nature of these apoptotic cells (neutrophils, T cells, others)? It has been shown that Timd4 can have stimulatory effects on other cells, such as T cells. Could deprivation of Timd4 signaling in certain conditions lead to more dying cells in this model?

Based on the comments and concerns raised above, this study appears premature at this stage.

Reviewer #3 (Public Review):

This is a clearly written report on experiments examining apoptosis and efferocytosis gene alterations in the very early stages of cutaneous wound healing. The authors have identified a number of differentially expressed genes related to apoptosis and efferocytosis in fibroblasts, neutrophils, dendritic cells and monocytes/macrophages. Additional functional experiments were carried out which show that inhibiting efferocytosis pathways can alter different aspects of wound healing, depending on the pathway that is targeted. The scRNA-seq data in mouse wounds is rigorous and follow-up functional studies in mice were done, which is an overall strength of the work. The main weaknesses were related to small sample sizes for some experiments and some conclusions that were not supported by strong data. Overall, this is interesting work that could be bolstered with additional supporting data for some key experiments.

1) The authors suggest in several places that efferocytosis must be occurring rapidly since the number of apoptotic cells are not high in their samples. There are issues with this conclusion in my opinion. They never do show that there is an increase in apoptotic cells in the wounds, which then go down (which would be a sign that the cells are being cleared via efferocytosis. In addition, they are looking for apoptotic cells at very early time points (24-48 hours), times at which large numbers of apoptotic cells would not be expected. As an example, neutrophil infiltration peaks at 24-48 hours and efferocytosis of apoptotic neutrophils would be expected after that. Other types of apoptotic cells would likely be cleared even later. Finally, several of the panels showing apoptotic cells were done with a very small number of samples (1-3 per group) in some cases so it is unclear how rigorous the data are. I would recommend that the authors at the very least soften the wording related to these conclusions and discuss the limitations of their experimental design; ideally data from more samples would be included to provide clear support those statements.

2) The human RNA-seq data is also quite limited, as non-diabetic wound tissue was all from one patient. Again, this limitation should be acknowledged. Also, there are some important published papers by Sashwati Roy's group indicating that there are defects in efferocytosis in diabetic wounds, which may go against what the authors are showing here to some degree. Discussion of the authors' work in relation to these other studies should be discussed.

3) For anti-Axl and anti-Timd4 experiments, the authors conclude that inhibition of Axl does not affect TUNEL+ cells and that Timd4 does not affect reepithelialization. However, in some cases the sample size was only 3 mice per group when measuring these parameters. That is a very small number of samples to draw conclusions about apoptotic cells or reepithelialization since these parameters are key for the overall conclusions of the experiments. Given that these are key data, it would be important to include more than n=3. Additionally, as stated above, a time point later than 24 h may be necessary to actually see changes in apoptotic cells.

4) In Fig 6, there look to be many more TUNEL+ cells in the wound bed of IgG control samples compared to anti-Timd4-treated samples, which contradicts the graph. Perhaps the authors could clarify where they were taking their measurements for panels with image analysis results. Another question related to this experiment is how it is possible that efferocytosis is so drastically different yet there are no changes in wound healing (this is one reason why a larger sample size for reepithelialization may be critical) - this would seem to suggest that efferocytosis is not important in wound healing, which is confusing. Further discussion on this might be useful.

eLife assessment

This work is fundamental in providing compelling evidence of mitochondria-encoded RNAs playing a role in controlling nuclear gene expression. How mitochondria and the nucleus communicates is an important but yet not well-appreciated area of biology. Using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by this team, the authors found that mitochondria-encoded RNAs play an unexpected role in regulating nuclear gene expressions in endothelial cells and intriguingly, depletion or overexpression of a specific mt-caRNA altered stress-induced transcription of nuclear genes encoding for innate inflammation and endothelial activation. Overall, these findings are interesting and supported by experimental confirmation, bulk-RNA-seq, and snRNA and scRNA-seq data and will be of interest to the field studying RNA regulation, gene expression and cell biology.

Reviewer #1 (Public Review):

Recently, chromatin-associated RNAs (caRNAs) were found to be involved in transcriptional regulation through multiple mechanisms, playing important roles in disease and development. Mitochondria has its own genome known as mtDNA, which codes crucial genes involved in oxidative phosphorylation. Additionally, mtDNA produces non-coding RNAs (ncRNAs), including small and long noncoding RNAs, the functions of which are still being explored. The communication between mitochondria and the nucleus is essential for coordinating gene expression and cellular function. Recent studies have identified the presence of mitochondrial RNAs (mtRNAs) in the nucleus, such as SncmtRNA, which can influence stress-induced transcription of genes related to cell adhesion.

In this manuscript, using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by the authors, they found that mitochondria-encoded lncRNA plays a role in regulating nuclear gene expressions. They then performed experimental confirmation, bulk-RNA-seq, snRNA, and scRNA-seq to demonstrate and verify the function of SncmtRNA in regulating nuclear gene expression in endothelial cells. This discovery is ground-breaking and the manuscript provides convincing evidence that mitochondrial RNAs can enter the cellular nucleus to regulate gene expression.

Reviewer #2 (Public Review):

The communication between mitochondria and the nucleus is crucial for maintaining cellular homeostasis and coordinating various cellular processes. The work by Sriram and colleagues discovers a potentially novel messenger molecule between mitochondrial-nuclear crosstalk through the widespread association of mitochondrial RNAs with nuclear chromatin. They termed this as mt-caRNAs that establishes a direct connection between mtRNA and the epigenome. These mt-caRNAs were found to preferentially attach to promoter regions, which led them to investigate how mt-caRNAs may regulate nuclear-encoded transcripts. Using an endothelial cell model, depletion/ overexpression of a specific mt-caRNA altered stress-induced transcription of nuclear genes encoding for innate inflammation and endothelial activation. Overall, these findings are interesting and warrant further investigation of the role of mt-caRNA-mediated nuclear transcription in controlling cellular processes.

eLife assessment

Brodsky and colleagues report here an unexpected cis-activation mechanism of caspase-11. The authors use cellular imaging methods and cleavage site mutants to show that the LPS-induced speck formation by caspase-11 depends on the autoprocessing between two subdomains. This new finding opens multiple doors for further investigating how this non-canonical inflammasome is regulated and activated at the molecular level.

Reviewer #1 (Public Review):

In their work, Akuma and colleagues identify the autoprocessing in cis of casp11 as a key step that allows the aggregation of casp11, and its capacity to cleave GSDMD and induce pyroptosis. The authors utilize, for the first time, a fluorescent casp11 that allowed us to visualize its aggregation (formation of specks). This is a key event that was largely overlooked for casp11. Indeed, casp11 directly binds LPS and initiates pyroptosis in the absence of other NLR members and adaptors such as ASC. While NLRs and adaptors form the structure that allows the recruitment and cleavage of casp1, how casp11 specks are formed remained unknown so far. Using casp11 mutants that lack the catalytic activity or the autoprocessing site, as well as casp11 that can be cleaved by other proteases, the authors demonstrate that self-cleavage of casp11 is a pre-requisite for aggregation and speck formation. Also, by using their mutants the authors demonstrated that casp11 acts in cis, rather than in trans, to exert this function. So far, mostly based on casp1 biology, the main view was that aggregation is a prerequisite for cleaving. Here the authors changed this view for casp11, and found that casp11 autocleavage is upstream of its aggregation induced upon LPS sensing. They found that initial dimerization and subsequent oligomerization are two distinct events and that LPS binding of casp11 is insufficient to assemble the non-canonical inflammasome.

The paper makes use of elegant mutant caspases and is based on solid bases. Some experiments lack analyses of the functional consequences of non-canonical inflammasome formation, and the paper would benefit from this type of analysis.

Another key finding is that Cys-254 plays more roles than "simply" cleaving casp11 at D285. This finding needs to be better highlighted also in the abstract because it opens more future investigations.

Also, the separation between dimerization and oligomerization may open to future studies and may be briefly mentioned also in the abstract.

Reviewer #2 (Public Review):

Casp11 is a cytosolic sensor for LPS in mice (orthologue of Casp4/5 in human). It is an important innate sensor of intracellular infection. Casp11 activity results in cleavage and activation of the pore-forming protein Gasdemin D (GSDMD) leading to lytic death (pyroptosis), of an infected cell. How exactly Casp11 signals upon LPS detection is beginning to be understood, but the picture is incomplete. Previous reports suggested that upon LPS detection, Casp11 dimerizes and undergoes auto-processing to form a pyroptosis-competent enzyme. The prediction from these studies was that the formation of a fully functional Casp11 signalling complex involves two steps: inducible dimerization and auto-processing.

In this study, authors used fluorescently tagged Casp11 reporter fusions, to report that detection of cytosolic LPS induces Casp11 assembly into a large perinuclear speck to form a signalling complex, where GSDMD can be processed. Such signalling complex resembles signalling specks formed upon the activation of other canonical inflammasomes.

Strengths:

Results are clean, experiments well controlled, and support the conclusions. Overall conclusions fit nicely in the general principle of innate signalling, whereby activation of many innate sensors results in their inducible assembly into higher-order oligomeric signalling complexes, called supra-molecular organizing centers (SMOCs).

A surprising finding from this work was that catalytically inactive Casp11 (C254A mutant) did not form signalling specks, despite being able to bind LPS and dimerise. This model is proposed where LPS binding to the CARD domain of Casp11 and Casp11 dimerization is necessary but not sufficient to mediate Casp11 speck formation within cells. The Casp11 catalytic activity is needed to facilitate the assembly of the higher-order, pyroptosis-competent Casp11 signalling platform. The model is further supported by experimental evidence that auto-processing of Casp11, by an exogenous protease TEV, (i.e. in the absence of LPS), is sufficient to mediate speck assembly in cells expressing wild type, but not catalytically inactive Casp11 mutant.

Possible technical improvements:

In general, the authors achieved their aims, and the results support the conclusions.

For technical robustness, it would be nice to consider a few controls:<br /> (a) Visualise Casp11 specks using constructs with smaller tags, and test whether tag placement on N or C terminus matters for speck formation; or<br /> (b) Biochemically crosslink and isolate endogenous, untagged Casp11 specks upon LPS transfection of primed macrophages (e.g. after priming through IFNs or TLRs). This would mimic the natural upregulation and activation of endogenous Casp11.<br /> (c) Test what happens after actual intracellular pathogen detection when the pathogen itself serves as a signalling platform? Are specks stills formed (or even needed)?

The broad impact of the work, implication, and questions for future work:

Results of this study would suggest that the enzymatic activity of Casp11 in macrophages may be highly restricted to the speck location, similar to what was described for Casp1. This may explain the very restricted substrate repertoire of Casp11 in cells, likely controlled by the substrate recruitment to the speck. This also opens avenues for follow-up work to answer several emerging questions:

1. After LPS binding and dimerization, why Casp11 must undergo intra-molecular processing to induce the formation of a pyroptosis-competent speck? Is there any substrate for LPS-bound, uncleaved Casp11 (beyond Casp11 itself), before Casp11 forms a full speck for GSDMD processing? The only currently known targets of Casp11 activity are itself, and GSDMD. Also, after intradomain linker cleavage of Casp11, what additional substrate must the cleaved Casp11 process to allow full speck formation?

2. Can activity probes be designed to detect the location of the active Casp11, and if so, would the activity of Casp11 be restricted to the speck? Is there a second cleavage event that would eventually dissociate Casp11 from the speck, to terminate its signalling? If not, how is speck activity terminated? If specks are released by lysis, are they capable of seeding new speck formation in neighbouring phagocytes, in prion-like behaviour previously described for canonical ASC speck?

3. What is the role of macrophage priming in speck formation, and what roles, if any GBPs play in speck formation?

4. Does this model apply to human orthologues, Casp4/5?

Reviewer #3 (Public Review):

Casp11 plays an important role in host defense against a wide range of pathogens; however, it also promotes autoinflammatory disorders when dysregulated. Unlike other ASC-dependent receptors, Casp11 forms a non-canonical inflammasome via LPS-indued self-assembly. Here, Brodsky and colleagues report that the catalytic activity of casp11 is required to form LPS-induced "SMOCs."

Here are my concerns/questions:

• I'm having some difficulty understanding the logic of Figure 5 in determining cis processing. It is an inverse of figure 4, and in my view, provides further evidence of trans processing. A better experiment would to be use WT-citrine tagged protein with catalytic dead mcherry and image them together. This would show WT cis processing occurs faster than trans processing as citrine specks should appear earlier than the mCherry ones. Can also do colocalization and FRET-based assays with the pair.

• Do those casp11 specks still contain CARDs?- i.e. is the second cleavage necessary for speck formation? Is CARD necessary at all? Would adding the TEV site at CDL and b/w p20 and p10 rescue? i.e. trans-activate?

• What are the equations that fit experimental data points and R2 for? E.g. Figure 1E. What are the parameters being fitted/compared and how are those interpreted? A table of fitted values and proper interpretation should be provided.

eLife assessment

This study presents a useful mathematical analysis of different signaling networks in an attempt to provide general rules that give rise to biphasic responses, a widely observed behavior in biology in which the outputs of the network depend non-monotonically on the inputs. Determining general conditions that underlie this behavior would be useful in engineering synthetic biological systems and for mechanistically understanding biphasic responses in biological systems. However, whereas the mathematical approach and methods are solid, as they stand, the analyses are inadequate to assess how these findings are applicable in nature and which are general.

Reviewer #1 (Public Review):

This paper examines different signaling networks and attempts to give general results for when the network will exhibit biphasic behavior, which is the situation when the output of the network is a non-monotonic function of its inputs. The strength of the paper is in the approach it takes. It starts with the simplest network motifs that produce biphasic behavior and then asks too what happens when these motifs are parts of larger networks. Their approach is in contrast to the usual way in which this question is tackled, which tends to be within the confines of a specific signaling network, where general results like the ones that the authors are after, might be hard to spot.

The weakness of the paper, in my opinion, is the rather formal description of the results which I am afraid will be of rather limited utility to experimental groups seeking to make use of them. The paper attempts to provide general rules for when to expect biphasic behavior and it was hard to assess to what extent such rules exist as behaviors can change depending on the context of a larger network in which the smaller biphasic one is embedded. The other thing that made assessing the generality of the results difficult is that the input-output functions shown in all the figures are computed for a specific choice of parameters and I was left wondering how different choices of parameters might change the reported behaviors. The lack of specific proposals for how their results should guide future experiments on different signaling networks is another weakness.

While I appreciate that the authors adopted a style of presenting their results such that all the mathematics is buried in the figures, I found that it made reading the paper quite difficult, and contributed to my confusion about which results are general and insensitive to parameter choices and which are not. I believe a narrative that integrated the math with some simple intuition might have been more effective. For example, when the authors say in the text that model M0 is incapable of displaying biphasic response, how general is that result? Later on, when discussing model M2, they provide a criterion for biphasic response in terms of products of rate constants satisfying an inequality, but the meaning of this condition is not described. Such things make it hard to learn from the authors' work.

The text is sprinkled with statements like "this reveals the plurality of information processing behaviors..." where the meaning is quite opaque (for this example, there is no description of "information processing" and what it might mean in this context) and therefore it makes it hard to understand what are the lessons learned from these calculations. Another example is found in the description of Erk regulation where the authors speak of "significant robustness" but what is meant by "significant" is also unclear.

Overall, I think this is an interesting attempt to provide a general mathematical framework for analyzing biphasic response of signaling networks, but the authors fall short for the reasons described above. I think a lot can be fixed by improving the way the results are presented.

Reviewer #2 (Public Review):

Biphasic responses are widely observed in biological systems and the determination of general design principles underlying biphasic responses is an important problem. The authors attempt to study this problem using a range of biochemical signaling models ranging from simple enzymatic modification and de-modification of a single substrate to systems with multiple enzymes and substrates. The authors used analytical and computational calculations to determine conditions such as network topology, range of concentrations, and rate parameters that could give rise to biphasic responses. I think the approach and the result of their investigation are interesting and can be potentially useful. However, the conditions for biphasic responses are described in terms of parameter ranges or relationships in particular biochemical models, and these parameters have not been connected to the values of concentrations or rates in real biological systems. This makes it difficult to evaluate how these findings would be applicable in nature or in experiments. It might also help if some general mechanisms in terms of competition/cooperation of time scales/processes are gleaned which potentially can be used to analyze biphasic responses in real biological systems.

eLife assessment

This paper presents valuable findings from whole-brain modeling of persistent activity states (underlying working memory) in the mouse brain. The most novel finding is that a spatial gradient of the density of inhibitory neurons supports a corresponding spatial gradient of propensity to support persistent activity. However, the evidence for this finding appears to be incomplete.

Reviewer #1 (Public Review):

This interesting manuscript sets out to develop for the mouse a series of important concepts and models that this group has previously developed for models of monkey brains, where they showed that in a large-scale model, anterior → posterior spatial gradients such as spine density (and thus inferred strength of local coupling) lead to a transition from transient stimulus responses to persistent responses, capable of supporting working memory (WM). No such spine density gradient is found in the mouse. Here, the authors propose and use modeling to explore the idea, that the corresponding gradient may be that of density of inhibitory PV cells in different regions of the brain.

The goal of the study - a large-scale, anatomically-constrained model of WM - is an extremely valuable one, and the authors' efforts in this direction should be supported. That said, some of the main claims in the manuscript were not, at least as currently written, clearly supported by the data, a number of important clarifications need to be made, and some claims of novelty are made in a way that, for a typical reader, may obscure the actual contribution being made.

The biggest issue is that one of the main claims, that together with cell-type specific long-range targeting, "density of cell classes define working memory representations" (abstract), is not terribly clear. For example, Figs. 2D and 2E show that a brain region's hierarchical location tightly predicts its persistent firing rate (2D), but that PV cell fraction has a far weaker correlation (2E). Is hierarchical location sufficient? If PV cell fraction were constant across model brain regions, would we still get persistent activity modes? It seems likely that the answer may be "yes", but the answer, easily within reach of the authors, is surprisingly not in the current version of the manuscript. Figure 3D, for the thalamocortical model, shows no significant correlation of firing rate with PV density.

Given the claim about PV density (in the abstract and the first main point of the discussion), this is a big concern. Yet it seems easily addressable: e.g. if indeed the authors found that hierarchy was sufficient and PV density immaterial, the model would be no less interesting. And if the authors demonstrated clearly that a PV density gradient is required, that would make the claim a solid one. If, within the model, such a causal demonstration is present, this reader at least missed it.

MAJOR CONCERNS:

(1) The model appears to be a model of a single side of the brain. Perhaps each brain region in the model could be considered an amalgam of that region across both sides of the brain. Yet given results like Li et al. Nature 2016, who show that persistent activity is robust to inhibition of one side, but not both sides of ALM, at the very least discussion of the issue is warranted.

(2) The authors make an interesting attempt to distinguish core WM regions from other regions such as "readout" regions, defined as showing persistent activity yet not having an effect on persistent activity elsewhere in the network.<br /> However, this definition seemed problematic: for example, consider a network that consists of 20 brain regions, all interconnected to each other, and all equivalent to each other, capable of displaying persistent activity thanks to mutual connectivity. Imagine that inhibition of any one of these regions is not sufficient to significantly perturb persistent activity in the other 19. Then they would all be labeled as "readout". Yet, by construction in this thought experiment, they are all equivalent to each other and are all core areas. Such redundancy may well be present in the brain. How would the authors address this redundancy issue?

(3) Also important to discuss would be the fact that every brain region in this model is set up as composed of two populations, and when long-range interactions are strong and the attractors strongly coupled, the entire brain is set up as a 1-bit working memory. How would results and the approach be impacted by considering WM for more flexible situations?

(4) Another concern that is important yet easily addressed is the authors' use of the term "novel cell-type specific graph theory measures". Describing in the abstract and elsewhere the fact that what they mean is to take into account the sign of connections, not just their magnitude, would transmit to readers the essence of the contribution in a manner very simple to understand. Most readers would fail to grasp the essential point of the current labeling, which sounds potentially very vague and complex.

(5) Finally, the overall significance of the study, and advances over previous work, were not entirely clear. In the discussion, the authors identify three major findings: (1) WM function is shaped by the PV cell density gradient. But as above, further work is required to make it clear that this claim is supported by the model. (2) if local recurrent excitation is insufficient to generate persistent activity, then long-range recurrent excitation is needed to generate it. I had trouble understanding why a model was needed to reach this conclusion - it seems as if it is simply a question of straightforward logic. The discussion states that in this regard, the work here "offers specific predictions to be tested experimentally", but I had trouble identifying what these specific predictions are. (3) Taking into account sign, not only magnitude, of connections, is important. This last point once again seemed a matter of straightforward logic, making its novelty difficult to assess.

Reviewer #2 (Public Review):

This paper uses the mouse mesoscale connectome, combined with data on the number and fraction of PV-type interneurons, to build a large-scale model of working memory activity in response to inputs from various sensory modalities. The key claims of the paper are two-fold. First, previous work has shown that there does not appear to be an increase in the number of excitatory inputs (spines) per pyramidal neuron along the cortical hierarchy (and this increase was previously suggested to underlie working memory activity occurring preferentially in higher areas along the cortical hierarchy). Thus, the claim is that a key alternative mechanism in the mouse is the heterogeneity in the fraction of PV interneurons. Second, the authors claim to develop novel cell type-specific graph theory.

I liked seeing the authors put all of the mouse connectomic information into a model to see how it behaved and expect that this will be useful to the community at large as a starting point for other researchers wishing to use and build upon such large-scale models. However, I have significant concerns about both primary scientific claims. With regard to the PV fraction, this does not look like a particularly robust result. First, it's a fairly weak result to start, much smaller than the simple effect of the location of an area along the cortical hierarchy (compare Figs. 2D, 2E; 3C, 3D). Second, the result seems to be heavily dependent upon having subdivided the somatosensory cortex into many separate points and focusing the main figures of the paper (and the only ones showing rates as a function of PV cell fraction) solely on simulations in which the sensory input is provided to the visual cortex. With regards to the claim of novel cell type-specific graph theory, there doesn't appear to be anything particularly novel. The authors simply make sure to assign negative rather than positive weights to inhibitory connections in their graph-theoretic analyses.

Major issues:<br /> 1) Weakness of result on effect of PV cell fraction. Comparing Figures 2D and 2E, or 3C and 3D, there is a very clear effect of cortical hierarchy on firing rate during the delay period in Figures 2D and 3C. However, in Figure 2E relating delay period firing rate to PV cell fraction, the result looks far weaker. (And similarly for Figs. 3C, 3D, with the latter result not even significant). Moreover, the PV cell fraction results are dominated by the zero firing rate brain regions (as opposed to being a nice graded set of rates, both for zeros and non-zeros, as with the cortical hierarchy results of Figures 2D), and these zeros are particularly contributed to by subdividing somatosensory (SS) into many subregions, thus contributing many points at the lower right of the graph.<br /> Further, it should be noted that Figure 2E is for visual inputs. In the supplementary Figure 2 - supplement 1, the authors do apply sensory inputs to auditory and somatosensory cortex...but then only show the result that the delay period firing rate increases along the cortical hierarchy (as in Figure 2D for the visual input), but strikingly omit the plots of firing rate versus PV cell fraction. This omission suggests that the result is even weaker for inputs to other sensory modalities, and thus difficult to justify as a defining principle.

2) Graph theoretic analyses. The main comparison made is between graph-theoretic quantities when the quantities account for or do not account for, PV cells contributing negative connection strengths. This did not seem particularly novel.

3) It was not clear to me how much the cell-type specific loop strength results were a result of having inhibitory cell types, versus were a result of the assumption ('counter-stream inhibitory bias') that there is a different ratio of excitation to inhibition in top-down versus bottom-up connections. It seems like the main results were more a function of this assumed asymmetry in top-down vs. bottom-up than it was a function of just using cell-type per se. That is, if one ignored inhibitory neurons but put in the top-down vs. bottom-up asymmetry, would one get the same basic results? And, likewise, if one didn't assume asymmetry in the excitatory vs. inhibitory connectivity in top-down versus bottom-up connections, but kept the Pyramidal and PV cell fraction data, would the basic result go away?

4) In the Discussion, there is a third 'main finding' claimed: "when local recurrent excitation is not sufficient to sustain persistent activity...distributed working memory must emerge from long-range interactions between parcellated areas". Isn't this essentially true by definition?

5) I don't know if it's even "CIB" that's important or just "any asymmetry (excitatory or inhibitory) between top-down vs. bottom-up directions along the hierarchy". This is worth clarifying and thinking more about, as assigning this to inhibition may be over-attributing a more basic need for asymmetry to a particular mechanism.

Other questions:<br /> 1) Is it really true that less than 2% of neurons are PV neurons for some areas? Are there higher fractions of other inhibitory interneuron types for these areas, and does this provide a confound for interpreting model results that don't include these other types?<br /> Maybe related to the above, the authors write in the Results that local excitation in the model is proportional to PV interneuron density. However, in the methods, it looks like there are two terms: a constant inhibition term and a term proportional to density. Maybe this former term was used to account for other cell types. Also, is local excitation in the model likewise proportional to pyramidal interneuron density (and, if not, why not?)?

2) Non-essential areas. The categorization of areas as 'non-essential' as opposed to, e.g. "inputs" is confusing. It seems like the main point is that, since the delay period activity as a whole is bistable, certain areas' contributions may be small enough that, alone, they can't flip the network between its bistable down and up states. However, this does not mean that such areas (such as the purple 'non-essential' area in Figure 5a) are 'non-essential' in the more common sense of the word. Rather, it seems that the purple area is just a 'weaker input' area, and it's confusing to thus label it as 'non-essential' (especially since I'd guess that, whether or not an area flips on/off the bistability may also depend on the assumed strength of the external input signal, i.e. if one made the labeled 'input area' a bit too weak to alone trigger the bistability, then the purple area might become 'essential' to cross the threshold for triggering a bistable-up state).

3) Relation between 'core areas' and loop strength. The measure underlying 'prediction accuracy = 0.93' in Figure 6D and the associated results seems incomplete by being unidirectional. It captures the direction: 'given high cell-type specific loop strength, then core area' but it does not capture the other direction: 'given a cell is part of a core area, is its predicted cell-type specific loop strength strong?'. It would be good to report statistics for both directions of association between loop strength and core area.

4) More justification would be useful on the assumption that the reticular nucleus provides tonic inhibition across the entire thalamus.

5) Is NMDA/AMPA ratio constant across areas and is this another difference between mice and monkeys? I am aware of early work in the mouse (Myme et al., J. Neurophys., 2003) suggesting no changes at least in comparing two brain regions' layer 2/3, but has more work been performed related to this?

6) Are bilateral connections between the left and right sides of a given area omitted and could those be important?

Reviewer #3 (Public Review):

Combining dynamical modelling and recent findings of mouse brain anatomy, Ding et al. developed a cell-type-specific connectome-based dynamical model of the mouse brain underlying working memory. The authors find that there is a gradient across the cortex in terms of whether mnemonic information can be sustained persistently or only transiently, and this gradient is negatively correlated to the local density of parvalbumin (PV) positive inhibitory cells but positively correlated with mesoscale-defined cortical hierarchy. In addition, weighing connectivity strength by PV density at target areas provides a more faithful relationship between input strength and delay firing rate. The authors also investigate a model where cortical persistent activity can only be sustained with thalamus input intact, although this result is rather separate from the rest of the study. The authors then use this model to test the causal contributions of different areas to working memory. Although some of the in silico perturbations are consistent with existing experimental data, others are rather surprising and need to be further discussed. Finally, the authors investigate patterns of attractor states as a result of different local and long-range connections and suggest that distinct attractor states could underlie different task demands.

The importance of PV density as a predictor for working memory activity patterns in the mouse brain is in contrast to recent computational findings in the primate brain where the number of spines (excitatory synapses per pyramidal cell) is the key predictor. This finding reveals important species differences and provides complementary mechanisms that can shape distributed patterns of working memory representation across cortical regions. The method of biologically-based near-whole-brain dynamical modeling of a cognitive function is compelling, and the main conclusions are mostly well supported by evidence. However, some aspects of the method, result, and discussion need to be clarified and extended.

1. Based on existing anatomical data, the authors reveal a negative correlation between cortical hierarchy (defined by mesoscale connectivity; this concept needs to be explicitly defined in the Results session, not just in the Method section) and local PV density (Fig. 1). In the dynamical model, the authors find that working memory activity is positively (and strongly) correlated with cortical hierarchy and negatively (and less strongly) correlated with PV cell density (Fig. 2), and conclude that working memory activity depends on both. But could the negative correlation between activity and PV density simply result from the inherent relationship between hierarchy and PV density across regions? To strengthen this result, the authors should quantify the predictive power of local PV density on working memory activity beyond the predictive power of cortical hierarchy.

2. In Fig. 4, the authors find that cell-type-specific graph measures more accurately predict delay-period firing rates. Specifically, the authors weigh connections with a cell-type-projection coefficient, which is smaller when the PV cell fraction is higher in the target area. Considering that local PV cell fraction is already correlated with delay activity patterns, weighing the input with the same feature will naturally result in a better input-output relationship. This result will be strengthened if there is a more independent measure of cell-type-projection coefficient, such as the spine density of PV vs excitatory cells across regions, or even the percentage of inhibitory versus excitatory cells targeted by upstream region (even just for an example set of brain regions).

3. The authors aim to identify a core subnetwork that generates persistent activity across the cortex by characterising delay activity as well as the effects of perturbations during the stimulus and delay period. Consistent with existing data, the model identifies frontal areas and medial orbital areas as core areas. Surprisingly, areas such as the gustatory area are also part of the core areas. These more nuanced predictions from the model should be further discussed. Also surprisingly, the secondary motor cortex (MOs), which has been indicated as a core area for short-term memory and motor planning by many existing studies is classified as a readout area. The authors explain this potential discrepancy as a difference in task demand. The task used in this study is a visual delayed response task, and the task(s) used to support the role of MOs in short-term memory is usually a whisker-based delayed response task or an auditory delay response task. In all these tasks, activity in the delay period is likely a mixture of sensory memory, decision, and motor preparation signals. Therefore, task demand is unlikely the reason for this discrepancy. On the other hand, motor effectors (saccade, lick, reach, orient) could be a potential reason why some areas are recruited as part of the core working-memory network in one task and not in another task. The authors should further discuss both of these points.

4. As a non-expert in the field, it is rather difficult to grasp the relationship between the results in Fig. 7 and the rest of the paper. Are all the attractor states related to working memory? If so, why are the core regions for different attractor states so different? And are the core regions identified in Fig. 5 based on arbitrary parameters that happen to identify certain areas as core (PL)? The authors should at least further clarify the method used and discuss these results in the context of previous results in this study.

eLife assessment

This important work reveals that increased flux towards one carbon metabolism improves neuronal regeneration after injury in C. elegans. The presented data are solid and provide compelling support for this conclusion. The manuscript can still be improved in order to strengthen some of the specific conclusions made and to increase the clarity of the presentation.

Reviewer #1 (Public Review):

In this manuscript, Yadav and colleagues explore the metabolic changes associated with the regeneration of mechanosensory neurons in O-GlcNAc transferase (ogt-1) mutant worms. Using in vivo laser axotomy to assess the regeneration of individual mechanosensory neurons in C elegans, the authors discovered increased regeneration in ogt-1 mutant worms diverts enhanced glycolysis towards one-carbon metabolism and the downstream transsulfuration metabolic pathway. By genetically and pharmacologically disrupting one-carbon metabolism, they were able to abrogate this phenotype. Similar results were obtained by targeting the serine synthesis pathway. Furthermore, the authors tested downstream targets of this pathway and discovered that the vitamin B12 independent shunt pathway confers regeneration competence in these neurons. They also included RNA-Seq data to support the same conclusion. Ogt-1 mutants showed profound transcriptional changes in genes related to glycolysis and one-carbon metabolism. Perhaps more excitingly, supplementation of the methioninine in wild-type worms is sufficient to recapitulate the regenerative phenotype found in ogt-1 mutants.

I found these results convincing and novel. The experimental approach is elegant and the conclusions are robust. The supplemental data support the major points of the paper. The identification of specific metabolic pathways associated with axon growth and regeneration represents a significant contribution to the Neuroscience field. Interrogation of these data sets and pathways will certainly spark new exciting research in the years to come.

Reviewer #2 (Public Review):

This is a potentially important finding regarding the roles of O-GlcNAc cycling and one-carbon metabolism in nerve regeneration. In a previous paper (Taub et al. 2018) they showed that both ogt-1 and oga-1 mutants show strong activation of a neuronal regeneration phenotype. However, the different biological processes used for the neural regeneration phenotype differed between the ogt-1 and oga-1 mutants. Several small issues emerge in the present paper which will increase the interest in the findings presented.

In summary, this paper under review is a potentially important finding which upon further documentation will be an excellent contribution.

eLife assessment

The paper introduces a new, important framework for neural modelling that promises to offer efficient simulation and analysis tools for a wide range of biologically-realistic neural networks. The paper's examples provide solid support for the ease of use and flexibility of the framework, but the comparison to existing solutions (in particular in terms of accuracy and performance) is incomplete. With a more careful evaluation of the tool's strengths and limitations, the work would be of interest to a wide range of computational neuroscientists and researchers working on biologically inspired machine learning applications.

Reviewer #1 (Public Review):

Chaoming Wang and coauthors present a new framework for modeling neurons and networks of neurons, spanning a wide range of possible models from detailed (point-neuron) models with non-linear ion channel dynamics to more abstract rate neuron models. Models are defined in an object-oriented style, familiar to users of machine-learning frameworks like PyTorch, and are efficiently executed via the just-in-time compilation framework JAX/XLA. The programming paradigm naturally supports a hierarchical style, where e.g. a network is composed of neurons that contains ion channels; each of these components can be reused in different contexts and be simulated/analyzed individually.

Strengths:<br /> Brainpy's approach is an innovative application of state-of-the-art technology widely used in the machine learning community (auto-differentation, just-in-time compilation) to modeling in computational neuroscience and could provide a useful bridge between the two domains which overlap more and more. For researchers, describing, running, and optimizing their models in Python is very convenient. The use of Numba to write efficient operators for JAX/XLA is innovative and potentially very powerful.

The modeling framework is very flexible, where most types of models commonly used in computational neuroscience can be readily expressed.

The framework supports various integration algorithms for ODEs, SDEs, and FDEs, several additional convenience tools for model training, optimization, and analysis, as well as many pre-defined ion-channel, neuron, and synapse models. The wide range of included simulation and analysis tools and pre-defined models is impressive, and exceeds those offered by most competing software. The software comes with extensive documentation, tutorials, and examples, on par with that of existing simulators that have been around for much longer.

Weaknesses:<br /> While the article clearly outlines the strengths of the chosen approach, it lacks an equally clear exposition of its limitations and a more thorough comparison to established approaches. Two examples of limitations that should be stated more clearly, in my opinion: models need to be small enough to fit on a single machine (in contrast to e.g. NEURON and NEST which support distributed computation via MPI), and only single-compartment models are supported; both limitations are mentioned in passing in the discussion, but would merit a more upfront mention. Regarding the comparison to other approaches/simulators:<br /> 1) The study does not verify the accuracy of the presented framework. While its basic approach (time-step-based simulation, standard numerical integration algorithms) is sufficiently similar to other software to not expect major discrepancies, an explicit comparison would remove any doubt. Quantitative measures of accuracies are particularly important in the context of benchmarks (see below), since simulations can be made arbitrarily fast by sacrificing performance.<br /> 2) Benchmarking against other software is obviously important, but also full of potential pitfalls. The current article does not state clearly whether the results are strictly comparable. In particular: are the benchmarks on the different simulators calculating results to the same accuracy (use of single or double precision, same integration algorithm, etc.)? Does each simulator use the fastest possible execution mode (e.g. number of threads/processes for NEST, C++ standalone mode in Brian2, etc.)? What is exactly measured (compilation time, network generation time, simulation execution time, ...) - these components will scale differently with network size and simulation duration, so summing them up makes the results difficult to interpret. Details are also missing for the comparison between the XLA operator customization in C++ vs. Python: was the C++ variant written by the authors or by someone else? Does the NUMBA→XLA mechanism also support GPUs/TPUs? This comparison also seems to be missing from the GitHub repository provided for reproducing the paper results.<br /> 3) While the authors convincingly argue for the merits of their Python-based/object-oriented approach, in my opinion, they do not fully acknowledge the advantages of domain-specific languages (NMODL, NestML, equation syntax of ANNarchy and Brian2, ...). In particular, such languages aim at a strong decoupling of the mathematical model description from its implementation and other parts of the model. In contrast, models described with BrainPy's approach often need to refer to such details, e.g. be aware of differences between dense and sparse connectivity schemes, online, or batch mode, etc. It might also be worth mentioning descriptive approaches to synaptic connectivity as supported by other simulators (connection syntax in Brian2, Connection Set Algebra for NEST).

Reviewer #2 (Public Review):

This manuscript introduces an integrative framework for modelling and analysis in neuroscience called BrainPy. It describes the many tools and utilities for building a wide range of models with an accessible and extensible unified interface written in Python. Several illustrative examples are provided for common use cases, including how to extend the existing classes to incorporate new features, demonstrating its ease of use and adherence to Python's programming conventions for integrative modelling across multiple scales and paradigms. The provided benchmarks also demonstrate that despite the convenience of presenting a high-level interpreted language to the user, it provides orders of magnitude of computational speed-up relative to three popular alternative frameworks on the chosen simulations through the extensive use of several Just In Time compilers. Computational benchmarks are also provided to illustrate the speed-up gained from running the models on massively parallel processing hardware, including GPUs, suggesting leading computational performance across a wide range of use cases.

While the results presented are impressive, publishing further details of the benchmarks in an appendix would be helpful for evaluating the claims and the overall conclusion would be more convincing if the performance benefits were demonstrated on a wider selection of test cases. Unsatisfyingly, the authors gave up on making a direct comparison to Brian running on GPUs with GeNN which would have been a fairer comparison than CPU-based simulations. The code for the chosen benchmarks is also likely to be highly optimised by the authors for running on BrainPy but less so for the other platforms - a fairer test would be to invite the authors of the other simulators to optimise the same models and re-evaluate the benchmarks. Furthermore, the manuscript reads like an advertisement for the platform with very little discussion of its limitations, weaknesses, or directions for further improvement. A more frank and balanced perspective would strengthen the manuscript and give the reader greater confidence in the platform.

Since simulators wax and wane in popularity, it would be reassuring to see a roadmap for development with a proposed release cadence and a sustainable governance policy for the project. This would serve to both clearly indicate the areas of active development where community contributions would be most valuable and also to reassure potential users that the project is unlikely to be abandoned in the near future, ensuring that their time investment in learning to use the framework will not be wasted. Similarly, a complex set of dependencies, which need to be modified for BrainPy, will likely make the project hard to maintain and so a similar plan to those given for the CI pipeline and documentation generation for automation of these modifications would be a good addition. It is also important to periodically reflect on whether it still makes sense to combine all the disparate tools into one framework as the codebase grows and starts to strain under modifications required to maintain its unification.

Finally, a live demonstration would be a very useful addition to the project. For example, a Jupyter notebook hosted on mybinder.org or similar, and a fully configured Docker image, would each enable potential users to quickly experiment with BrainPy without having to install a stack of dependencies and troubleshoot version conflicts with their pre-existing setup. This would greatly lower the barrier to adoption and help to convince a larger base of modellers of the potential merits of BrainPy, which could be major, both in terms of the computational speed-up and ease of development for a wide range of modelling paradigms.

Reviewer #3 (Public Review):

The paper presents the novel neuro-simulator BrainPy, which introduces several new concepts compared to existing simulators such as NEST, Brian, or GeNN: 1) a modular and Pythonic interface, which avoids having to use a fixed set of neural/synaptic models or using a textual equation-oriented interface; 2) a common platform for simulation, training, and analysis; 3) the use of just-in-time compilation using JAX/XLA, allowing to transparently access CPU, GPU, and TPU platforms. While none of these features is new per se (apart from TPU support, as far as I know), their combination provides an interesting new direction for the design of neuro-simulators.

Overall, BrainPy is a nice and valuable addition to the already overwhelming list of neuro-simulators, which all have their own advantages and drawbacks and are diversely maintained. The main strengths of BrainPy are 1) its multi-scale modular interface and 2) the possibility for the user to transparently use various hardware platforms for the simulation. The paper succeeds in explaining those two aspects in a convincing manner. The paper is also very didactic in explaining the different strengths and weaknesses of the current simulators, as well as the benefits of JIT compilation.

One potential issue is that the scope of the neuro-simulator is not very clearly explained and the target audience is not well defined: is BrainPy primarily intended for computational neuroscientists or for neuro-AI practitioners? The simulator offers very detailed neural models (HH, fractional order models), classical point-models (LIF, AdEx), rate-coded models (reservoirs), but also deep learning layers (Conv, MaxPool, BatchNorm, LSTM). Is there an advantage to using BrainPy rather than PyTorch for purely deep networks? Is it possible to build hybrid models combining rate-coded reservoirs or convnets with a network of HH neurons? Without such a hybrid approach, it is unclear why the deep learning layers are needed. In terms of plasticity, only external training procedures are implemented (backpropagation, FORCE, surrogate gradients). No local plasticity mechanism (Hebbian learning for rate-coded networks, STDP and its variants for spiking networks) seems to be implemented, apart from STP. Is it a planned feature? Appendix 8 refers to `bp.synplast.STDP()`, but it is not present in the current code (https://github.com/brainpy/BrainPy/tree/master/brainpy/_src/dyn/synplast). Spiking networks without STDP are not going to be very useful to computational neuroscientists, so this suggests that the simulator targets primarily neuro-AI, i.e. AI researchers interested in using spiking models in a machine learning approach. However, it is unclear why they would be interested in HH or Morris-Lecar models rather than simpler LIF neurons.

A second weakness of the paper concerns the demos and benchmarks used to demonstrate the versatility and performance of BrainPy, which are not sufficiently described. In Fig. 4, it is for example not explained how the reservoirs are trained (only the readout weights, or also the recurrent ones? Using BPTT only makes sense when the recurrent weights are also trained.), nor how many neurons they have, what the final performance is, etc. The comparison with NEURON, NEST, and Brian2 is hard to trust without detailed explanations. Why are different numbers of neurons used for COBA and COBAHH? How long is the simulation in each setting? Which time is measured: the total time including compilation and network creation, or just the simulation time? Are the same numerical methods used for all simulators? It would also be interesting to discuss why the only result involving TPUs (Fig 8c) shows that it is worse than the V100 GPU. What could be the reason? Are there biologically-realistic networks that would benefit from a TPU? As the support for TPUs is a major selling point of BrainPy, it would be important to investigate its usage further.

eLife assessment

This valuable study presents a tool for hyperaligning functional brain topography between individuals, which is based on fMRI connectivity data gathered when participants watched different movies. The tool is validated through strong correlations between functional topographic maps generated from a participant's own localizer data and those derived from other participants' data based on this hyperalignment, even when the training and target participants were drawn from different datasets. The study will potentially be of interest to researchers working with a wide range of fMRI datasets.

Reviewer #1 (Public Review):

Due complicated and often unpredictable idiosyncratic differences, comparing fMRI topography between subjects typically would require extra expensive scan time and extra laborious analyzing steps to examine with specific functional localizer scan runs that contrast fMRI responses of every subject to different stimulus categories. To overcome this challenge, hyperaligning tools have recently been developed (e.g., Guntupalli et al., 2016; Haxby et al., 2011) based on aligning in a high-dimensional space of voxels of subjects' fMRI responses to watching a given movie. In the present study, Jiahui and colleagues propose a significantly improved version of hyperaligning functional brain topography between individuals. This new version, based on fMRI connectivity, works robustly on datasets when subjects watched different movies and were scanned with different parameters/scanners at different MRI centers.

Robustness is the major strength of this study. Despite the fact that datasets from different subjects watching different movies at different MRI centers with different scan parameters were used, the results of functional brain topography from between-subject hyperalignment based on fMRI connectivity were comparable to the golden standard of within-subject functional localizations, and significantly better than regular surface anatomical alignments. These results also support the claim that the present approach is a useful improvement from previous hyperalignments based on time-locked fMRI voxel responses, which would require normative samples of subjects watching a same movie.

Given the robustness, this new version of hyperalignment would provide much stronger statistical power for group-level comparisons with less costs of time and efforts to collect and analyze data from large sample size according to the current stringent standard, likely being useful to the whole research community of functional neuroimaging. That said, more discussions of the limit of the present hyperalignment approach would be helpful to potential readers. For example, to what extend the present hyperalignment approach would be applicable to individuals with atypical functional brain topography such as brain lesion patients with e.g., acquired prosopagnosia? Even in typical populations, while bilateral fusiform face areas can be identified in the majority through functional localizer scans, the left fusiform face area sometimes cannot be found. Moreover, many top-down factors are known to modulate functional brain topography. Due to these factors, brain responses and functional connectivity may be different even when a same subject watched a same movie twice (e.g., Cui et al., 2021).

Reviewer #2 (Public Review):

Guo and her colleagues develop a new approach to map the category-selective functional topographies in individual participants based on their movie-viewing fMRI data and functional localizer data from a normative sample. The connectivity hyperalignment are used to derived the transformation matrices between the participants according to their functional connectomes during movies watching. The transformation matrices are then used to project the localizer data from the normative sample into the new participant and create the idiosyncratic cortical topography for the participant. The authors demonstrate that a target participant's individualized category-selective topography can be accurately estimated using connectivity hyperalignment, regardless of whether different movies are used to calculate the connectome and regardless of other data collection parameters. The new approach allows researchers to estimate a broad range of functional topographies based on naturalistic movies and a normative database, making it possible to integrate datasets from laboratories worldwide to map functional areas for individuals. The topic is of broad interest for neuroimaging community; the rationale of the study is straightforward and the experiments were well designed; the results are comprehensive. I have some concerns that the authors may want to address, particularly on the details of the pipeline used to map individual category-selective functional topographies.

1. How does the length of the scan-length of movie-viewing fMRI affect the accuracy in predicting the idiosyncratic cortical topography? Similarly, how does the number of participants in the normative database affect the prediction of the category-selective topography? This information is important for the researchers who are interested in using the approach in their studies.<br /> 2. The data show that category-selective topography can be accurately estimated using connectivity hyperalignment, regardless of whether different movies are used to calculate the connectome and regardless of other data collection parameters. I'm wondering whether the functional connectome from resting state fMRI can do the same job as the movie-watching fMRI. If it is yes, it will expand the approach to broader data.<br /> 3. The authors averaged the hyper-aligned functional localizer data from all of subjects to predict individual category-selective topographies. As there are large spatial variability in the functional areas across subjects, averaging the data from many subjects may blur boundaries of the functional areas. A better solution might be to average those subjects who show highly similar connectome to the target subjects.<br /> 4. It is good to see that predictions made with hyperalignment were close to and sometimes even exceeded the reliability values measured by Cronbach's alpha. But, please clarify how the Cronbach's alpha is calculated.<br /> 5. Which algorithm was used to perform surface-based anatomical alignment? Can the state-of-the-art Multimodal Surface Matching (MSM) algorithm from HCP achieve better performance?<br /> 6. Is it necessary to project to the time course of the functional localizer from the normative sample into the new participants? Does it work if we just project the contrast maps from the normative samples to the new subjects?<br /> 7. Saygin and her colleagues have demonstrated that structural connectivity fingerprints can predict cortical selectivity for multiple visual categories across cortex (Osher DE et al, 2016, Cerebral Cortex; Saygin et al, 2011, Nat. Neurosci). I think there's a connection between those studies and the current study. If the author can discuss the connection between them, it may help us understand why CHA work so well.

Reviewer #3 (Public Review):

In this paper, Jiahui and colleagues propose a new method for learning individual-specific functional resonance imaging (fMRI) patterns from naturalistic stimuli, extending existing hyperalignment methods. They evaluate this method - enhanced connectivity hyperalignment (CHA) - across four datasets, each comprising between nine (Raiders) and twenty (Budapest, Sraiders) participants.

The work promises to address a significant need in existing functional alignment methods: while hyperalignment and related methods have been increasingly used in the field to compare participants scanned with overlapping stimuli (or lack thereof, in the case of resting state data), their use remains largely tied to naturalistic stimuli. In this case, having non-overlapping stimuli is a significant constraint on application, as many researchers may have access to only partially overlapping stimuli or wish to compare stimuli acquired under different protocols and at different sites.

It is surprising, however, that the authors do not cite a paper that has already successfully demonstrated a functional alignment method that can address exactly this need: a connectivity-based Shared Response Model (cSRM; Nastase et al., 2020, NeuroImage). It would be relevant for the authors to consider the cSRM method in relation to their enhanced CHA method in detail. In particular, both the relative predictive performance as well as associated computational costs would be useful for researchers to understand in considering enhanced CHA for their applications.

With this in mind, I noted several current weaknesses in the paper:

First, while the enhanced CHA method is a promising update on existing CHA techniques, it is unclear why this particular six step, iterative approach was adopted. That is: why was six steps chosen over any other number? At present, it is not clear if there is an explicit loss function that the authors are minimizing over their iterations. The relative computational cost of six iterations is also likely significant, particularly compared to previous hyperalignment algorithms. A more detailed theoretical understanding of why six iterations are necessary-or if other researchers could adopt a variable number according to the characteristics of their data-would significantly improve the transferability of this method.

Second, the existing evaluations for enhanced CHA appear to be entirely based on image-derived correlations. That is, the authors compare the predicted image from CHA with the ground-truth image using correlation. While this provides promising initial evidence, correlation-based measures are often difficult to interpret given their sensitivity to image characteristics such as smoothness. Including Cronbach's alpha reliability as a baseline does not address this concern, as it is similarly an image-based statistic. It would be useful to see additional predictive experiments using frameworks such as time-segment classification, inter-subject decoding, or encoding models.

Addressing these concerns and considering cSRM as a comparison model would significantly strengthen the paper. There are also notable strengths that I would encourage the authors to further pursue. In particular, the authors have access to a unique dataset in which the same Raiders of the Lost Ark stimulus was scanned for participants within the Budapest (SRaiders) dataset as well as non-overlapping participants in the Raiders dataset. Exploring the relative performance for cross-movie prediction within a dataset as compared to a shared movie prediction across datasets is particularly interesting for methods development. I would encourage the authors to explicitly report results in this framework to highlight both this unique testing structure as well as the performance of their enhanced CHA method.

Overall, I share the authors' enthusiasm for the potential of cross-movie, cross-dataset prediction, and I believe that methods such as enhanced CHA are likely to significantly improve our ability to make these comparisons in the near future. At present, however, I find that the theoretical and experimental support for enhanced CHA is incomplete. It is therefore difficult to assess how enhanced CHA meets its goals or how successfully other researchers would be able to adopt this method in their own experiments.

Author Response

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

We greatly appreciate the valuable and constructive review of our manuscript. The reviewers’ comments have helped us to improve the quality of the paper. Here we provide detailed responses to the reviewers’ comments and discuss the new experiments we performed.

Reviewer #1

Summary:

In this study, the authors generate a Drosophila model to assess disease-linked allelic variants in the UBA5 gene. In humans, variants in UBA5 have been associated with DEE44, characterized by developmental delay, seizures, and encephalopathy. Here, the authors set out to characterize the relationship between 12 disease-linked variants in UBA5 using a variety of assays in their Drosophila Uba5 model. They first show that human UBA5 can substitute all essential functions of the Drosophila Uba5 ortholog, and then assess phenotypes in flies expressing the various disease variants. Using these assays, the authors classify the alleles into mild, intermediate, and severe loss-of-function alleles. Further, the authors establish several important in vitro assays to determine the impacts of the disease alleles on Uba5 stability and function. Together, they find a relatively close correlation between in vivo and in vitro relationships between Uba5 alleles and establish a new Drosophila model to probe the etiology of Uba5-related disorders.

Strengths:

Overall, this is a convincing and well-executed study. There is clearly a need to assess disease-associated allelic variants to better understand human disorders, particularly for rare diseases, and this humanized fly model of Uba5 is a powerful system to rapidly evaluate variants and relationships to various phenotypes. The manuscript is well written, and the experiments are appropriately controlled.

Recommendations For The Authors:

1) It would seem of value to determine what tissue(s) the essential function of Uba5 resides. The authors nicely detail the expression of Uba5 in a subset of neurons and glia, and indicate it is expressed in a variety of other tissues. Null mutants are embryonic lethal, suggesting an essential function. From the mouse study cited, it appears Uba5 functions early in development in the hematopoietic system. The authors can express their UAS-Uba5 rescue construct using a variety of tissue-specific Gal4 lines to determine whether the essential function of Uba5 is in the nervous system or other tissues, which would be of interest in understanding key functions of Uba5.

We thank the reviewer for the suggestion. We tried to rescue the lethality of the Uba5 mutants by expressing human UBA5 reference protein in different tissues. We found that ubiquitous expression of UBA5 (da-GAL4 or act-GAL4) successfully rescues the lethality, however, expression of UBA5 in neurons (elav-GAL4), glia (repo-GAL4), or both neurons and glia does not. In addition, expression of UBA5 in fat body (SPARC-GAL4) or muscles (Mef2-GAL4) does not rescue the lethality either. These results suggest that Uba5 is required in multiple tissues in flies. These data are included in the revised manuscript.

2). Do intermediate Uba5 alleles impact synaptic function or growth? The etiology of the disease is linked with epilepsy and neurodevelopmental disorders, and the interesting parallels the authors note between Uba5 and Para expression indicate perhaps shared roles in neurons that drive firing activity. Together, these lines of evidence may suggest the Uba5 alleles may have possible impacts on synaptic growth, morphology, and/or function. It would be of interest to examine the larval neuromuscular junction and assess NMJ growth, morphology, and perform some basic electrophysiology to determine if there are any functional defects.

Following the reviewer’s suggestion, we tested the morphology of NMJs in the humanized flies. We did not observe any obvious changes in the number or size of the synaptic boutons caused by the Group II variants. Hence, we conclude that the Uba5 variants do not cause an obvious defect in synaptic growth. The results are included in the Figure S3.

More generally, can the authors comment on the expression pattern of Uba5? One might consider something like Uba5 to be a "housekeeping" gene and expressed/required in most if not all cell types. From the data presented in Fig. 2, it appears expression is more sparse, perhaps, as the authors point out, because of roles in mature neurons that actively fire (like Para). Are neuronal targets of Uba5 known, which might suggest key pathways it modulates?

We showed that Uba5 is broadly expressed in third instar larvae. FlyAtlas2 and FlyCellAtlas datasets show that Uba5 is broadly expressed but not in all the cells. In the larval CNS and adult brain, Uba5 is not expressed in all cells either. Hence, we cannot say Uba5 is a “housekeeping” gene. Regarding the neuronal targets of Uba5, we do not know which types of neurons express Uba5 and which pathways Uba5 modulates. This could be studied in the future.

3) Does strong overexpression of the various Uba5 alleles in otherwise wild-type flies cause any phenotypes? This might support possible antimorphic/dominant negative functions of some of the variants. Is it plausible that any of the alleles could impact oligomerization of Uba5?

We have not observed compromised viability or any obvious phenotype in flies overexpressing human reference UBA5 or UBA5 variants. So, our results do not support a dominant negative effect of any of the variants.

To our knowledge, people do not have sufficient knowledge on UBA5 dimerization to speculate on whether some variants could play a dominant negative role. There is one variant, V260M, that lies at the dimer interface. We showed that the V260M variant biochemically affects ATP binding as well as UFM1 activation, but we do not have evidence to support that it causes dominant negative effects by affecting UBA5 dimerization.

Minor points:

1) Page 5 line 45: It seems a reference is missing about the temperature dependence of Gal4 activity.

We apologize for the missing reference. We have incorporated a reference to PMID 25824290.

2) It might be of interest to assay the various transgenic rescue alleles at a higher temperature (say 29C) in addition to the nice work looking at 18/25C survival. Perhaps some of the alleles display temperature sensitivity at low (18) and high (29) temperatures.

We now include the survival rate data at 29C. The enzyme dead and severe LoF variants fail to rescue the lethality at 29C, while the mild (Group IA and IB) variants fully rescue. For the three Group II variants, the survival rate at 29C is higher than that at 25C and 18C. The results support the dosage sensitive effects of UBA5 overexpression, but do not support any variant to be temperature sensitive within this range.

Reviewer #2

Relative simplicity and genetic accessibility of the fly brain make it a premier model system for studying the function of genes linked to various diseases in humans. Here, Pan et al. show that human UBA5, whose mutations cause developmental and epileptic encephalopathy, can functionally replace the fly homolog Uba5. The authors then systematically express in flies the different versions of the gene carrying clinically relevant SNPs and perform extensive phenotypic characterization such as survival rate, developmental timing, lifespan, locomotor and seizure activity, as well as in vitro biochemical characterization (stability, ATP binding, UFM-1 activation) of the corresponding recombinant proteins. The biochemical effects are well predicted by (or at least consistent with) the location of affected amino acids in the previously described Uba5 protein structure. Most strikingly, the severity of biochemical defects appears to closely track the severity of phenotypic defects observed in vivo in flies. While the paper does not provide many novel insights into the function of Uba5, it convincingly establishes the fly nervous system as a powerful model for future mechanistic studies.

One potential limitation is the design of the expression system in this work. Even though the authors state that "human cDNA is expressed under the control of the endogenous Uba5 enhancer and promoter", it is in fact the Gal4 gene that is expressed from the endogenous locus, meaning that the cDNA expression level would inevitably be amplified in comparison. The fact that different effects were observed when some experiments were performed at different temperatures (18 vs. 25) is also consistent with this. While I do not think this caveat weakens the conclusions of this paper, it may impact the interpretation of future experiments that use these tools, and thus should be clearly discussed in the paper. Especially considering the authors argue that most disease variants of UBA5 are partial loss-of-functions, the amplification effect could potentially mask the phenotypes of milder hypomorphic alleles. If the authors could also show that the T2A-Gal4 expression pattern in the brain matches well with that of endogenous RNA or protein (e.g. using HCR-FISH or antibody), it would help to alleviate this concern.

We thank the reviewer for pointing out the issue.

Regarding the humanization strategy we used in the study, we agree that this is a binary system which could induce overexpression of the target protein. However, as the reviewer also points out, this temperature sensitive system also enables us to flexibly adjust the expression level of the target protein (PMIDs 34113007, 35348658, 36206744), which is especially useful to study partial LoF variants. In our study we have successfully compared the relevant allelic strength of most of the variants.

We agree with the reviewer that a masking effect may exist in our system due to its gene overexpression nature. However, we cannot conclude that this masking effect really affects the three Group IA variants in our tests. The three variants are mild LoF, which is supported by our biochemical assays. Individuals homozygous for one of the Group IA variants, p.A371T, do not have any obvious phenotype, which is also consistent with our findings in flies.

Regarding the expression pattern of the T2A-GAL4, the Bellen lab has generated T2A-GAL4 lines for more than 3,000 genes. The expression pattern of many GAL4 lines faithfully reflect the expression pattern of the endogenous genes, which has been shown in our previous publications (PMIDs 25824290, 29565247, 31674908).

Recommendations For The Authors:

As related to the expression pattern comment in the public review, I think the authors could also take advantage of Fly Cell Atlas or other available scRNA-seq atlases of the fly brain to present a much more detailed description of the Uba5 expression profile with minimal additional effort. If the cells that express it share other features or genes (other than the para that the authors mention), this could lead to further insights about the gene's neuronal or glial functions.

In response to the reviewer, we show the expression pattern of Uba5 documented in FlyCellAtlas and another adult brain single-cell RNA seq profile (PMID 29909982) in the revised manuscript.

In addition, one of the mutants (assuming the same one) is referred to as Leu254Pro in some parts of the manuscript while in some other parts (including tables 1-2) it is Lys254Pro.

We apologize for the mistakes. The variant should be Leu254Pro and we have made these corrections in the revised manuscript.

Reviewer #3

Summary:

Variants in the UBA5 gene are associated with rare developmental and epileptic encephalopathy, DEE44. This research developed a system to assess in vivo and in vitro genotype-phenotype relationships between UBA5 allele series by humanized UBA5 fly models and biochemical activity assays. This study provides a basis for evaluating current and future individuals afflicted with this rare disease.

Strengths:

The authors developed a method to measure the enzymatic reaction activity of UBA5 mutants over time by applying the UbiReal method, which can monitor each reaction step of ubiquitination in real time using fluorescence polarization. They also classified fruit fly carrying humanized UBA5 variants into groups based on phenotype. They found a correlation between biochemical UBA5 activity and phenotype severity.

Weaknesses:

In the case of human DEE44, compound heterozygotes with both loss-of-function and hypomorphic forms (e.g., p.Ala371Thr, p.Asp389Gly, p.Asp389Tyr) may cause disease states. The presented models have failed to evaluate such cases.

We agree with the reviewer that our current system has a limitation that it evaluates one variant at a time rather than any combination of variants. However, our biochemical data do show that the three Group IA variants are mild LoF variants rather than benign variants. One of these variants, p.A371T, does not cause any obvious phenotype in homozygous individuals, which is also consistent with our findings in flies. The modeling of variant combinations, especially the Group IA/Group III combinations could be carried out in future studies.

Recommendations For The Authors:

Figure 3G. Typo. "ContonS" should be replaced by "CantonS."

We apologize for the spelling mistake. We correct the typo in the revised manuscript.

Figure 5. The labels should be in uppercase instead of lowercase.

We correct the panel labels in the revised manuscript.

Figure 6A. Is the molecular weight of UBA5~UFM1 intermediate (99 kDa) in model Figure correct? In Fig. 6B, the molecular weight of UBA5~UFM1 intermediate seems to be 70-75 kDa.

Both are correct. The molecular weight depicted in the schematic of Figure 6A is based on the UBA5 dimer, which dissociates in the SDS-PAGE gel shown in Figure 6B. We have reconfigured the schematic to make this more apparent.

Figure. 6E, F, H, and I. The time points for quantification in these figures should be specified.

We apologize for the confusion. The details on data quantification are now more thoroughly explained in the Methods.

Reviewer #3 (Public Review):

Summary:<br /> Variants in the UBA5 gene are associated with rare developmental and epileptic encephalopathy, DEE44. This research developed a system to assess in vivo and in vitro genotype-phenotype relationships between UBA5 allele series by humanized UBA5 fly models and biochemical activity assays. This study provides a basis for evaluating current and future individuals afflicted with this rare disease.

Strengths:<br /> The authors developed a method to measure the enzymatic reaction activity of UBA5 mutants over time by applying the UbiReal method, which can monitor each reaction step of ubiquitination in real time using fluorescence polarization. They also classified fruit fly carrying humanized UBA5 variants into groups based on phenotype. They found a correlation between biochemical UBA5 activity and phenotype severity.

Weaknesses:<br /> In the case of human DEE44, compound heterozygotes with both loss-of-function and hypomorphic forms (e.g., p.Ala371Thr, p.Asp389Gly, p.Asp389Tyr) may cause disease states. The presented models have failed to evaluate such cases.

eLife assessment

The authors establish a Drosophila model to assess the severity of disease-linked alleles of Uba5. Using both in vivo and in vitro experiments, this valuable study demonstrates the alleles fall into mild, intermediate, and severe classes, with convincing evidence to support their conclusion. This well-executed study establishes a model for further characterization of Uba5-related phenotypes in a powerful model system.

Reviewer #1 (Public Review):

Summary:<br /> In this study, the authors generate a Drosophila model to assess disease-linked allelic variants in the UBA5 gene. In humans, variants in UBA5 have been associated with DEE44, characterized by developmental delay, seizures, and encephalopathy. Here, the authors set out to characterize the relationship between 12 disease-linked variants in UBA5 using a variety of assays in their Drosophila Uba5 model. They first show that human UBA5 can substitute all essential functions of the Drosophila Uba5 ortholog, and then assess phenotypes in flies expressing the various disease variants. Using these assays, the authors classify the alleles into mild, intermediate, and severe loss-of-function alleles. Further, the authors establish several important in vitro assays to determine the impacts of the disease alleles on Uba5 stability and function. Together, they find a relatively close correlation between in vivo and in vitro relationships between Uba5 alleles and establish a new Drosophila model to probe the etiology of Uba5-related disorders.

Strengths:<br /> Overall, this is a convincing and well-executed study. There is clearly a need to assess disease-associated allelic variants to better understand human disorders, particularly for rare diseases, and this humanized fly model of Uba5 is a powerful system to rapidly evaluate variants and relationships to various phenotypes. The manuscript is well written, and the experiments are appropriately controlled.

Reviewer #2 (Public Review):

Relative simplicity and genetic accessibility of the fly brain makes it a premier model system for studying the function of genes linked to various diseases in humans. Here, Pan et al. show that human UBA5, whose mutations cause developmental and epileptic encephalopathy, can functionally replace the fly homolog Uba5. The authors then systematically express in flies the different versions of the gene carrying clinically relevant SNPs and perform extensive phenotypic characterization such as survival rate, developmental timing, lifespan, locomotor and seizure activity, as well as in vitro biochemical characterization (stability, ATP binding, UFM-1 activation) of the corresponding recombinant proteins. The biochemical effects are well predicted by (or at least consistent with) the location of affected amino acids in the previously described Uba5 protein structure. Most strikingly, the severity of biochemical defects appears to closely track the severity of phenotypic defects observed in vivo in flies. While the paper does not provide many novel insights into the function of Uba5, it convincingly establishes the fly nervous system as a powerful model for future mechanistic studies.

One potential limitation is the design of the expression system in this work. Even though the authors state (ln. 127-128) that "human cDNA is expressed under the control of the endogenous Uba5 enhancer and promoter", it is in fact the Gal4 gene that is expressed from the endogenous locus (which authors also note in the same paragraph 138-139), meaning that the cDNA expression level would inevitably be amplified in comparison. While I do not think this weakens the conclusions of this paper, it may impact the interpretation of future experiments that use these tools. Especially considering the authors argue that most disease variants of UBA5 are partial loss-of-functions, the amplification effect could potentially mask the phenotypes of milder hypomorphic alleles. Temperature sensitivity of Gal4 expression may allow calibrating levels to reduce the impact of this amplification, but the revised manuscript still does not openly acknowledge or discuss this potential caveat.

Author Response

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

Reviewer #1:

In this manuscript, the authors investigate differences between Tibetans and Han Chinese at altitude in terms of placental transcriptomes during full-term pregnancy. Most importantly, they found that the inter-population differentiation is mostly male-specific and the observed direction of transcriptional differentiation seems to be adaptive at high altitude. In general, it is of great importance and provides new insights into the functional basis of Tibetan high-altitude adaptations, which so far have been mostly studied via population genetic measures only. More specifically, I firmly believe that we need more phenotype data (including molecular phenotypes such as gene expression data) to fully understand Tibetan adaptations to high altitude, and this manuscript is a rare example of such a study. I have a few suggestions and/or questions with which I hope to improve the manuscript further, especially in terms of 1) testing if the observed DEG patterns are truly adaptive, and 2) how and whether the findings in this study can be linked to EPAS1 and EGLN1, the signature adaptation genes in Tibetans.

We appreciate the reviewer’s constructive comments. We have addressed these points and the details are discussed below.

Major Comments:

1) The DEG analysis is the most central result in this manuscript, but the discrepancy between sex-combined and sex-specific DEGs is quite mind-boggling. For those that were differentially expressed in the sex-specific sets but not in the sex-combined one, the authors suggest an opposite direction of DE as an explanation (page 11, Figure S5). But Figure S5A does not show such a trend, showing that down-regulated genes in males are mostly not at all differentially expressed in females. Figure S5B does show such a trend, but it doesn't seem to be a dominant explanation. I would like to recommend the authors test alternative ways of analysis to boost statistical power for DEG detection other than simply splitting data into males and females and performing analysis in each subset. For example, the authors may consider utilizing gene-by-environment interaction analysis schemes here biological sex as an environmental factor.

We agree with reviewer that the opposite direction of DEGs is likely only one of the possible explanations for the discrepancy between the sex-combined and the sex-specific DEGs. We have toned down the description of this point in the revised manuscripts.

Following the suggestion of reviewer, we performed a ANCOVA analysis to evaluate the variance explained by sex from the expression data. For each gene, univariate comparisons of the average of gene expression between Tibetans and Han Chinese were made by using the ANCOVA test in R aov function with sex as covariates: aov (Expression ~ Ethnicity + Fetal sex). We observed a significantly higher variance explained by sex than by ethnicity in six layers of the placenta (except for the CN layer) (Author response image 1). For example, in the UC layer, fetal sex can explain ~0.203 variance, while the ethnicity explains ~0.107 variance (P-value = 4.9e-4). These results suggest a significant contribution of fetal sex for the observed variance of gene expression, consist with the observed sex-biased DEG patterns.

Author response image 1.

The ANCOVA results of the seven layers of placenta. The scatter plot shows the comparison of the explained variance (y-axis) and significance (x-axis, denoted by –log10(P-value)) between ethnicity (dots in red) and fetal sex (dots in blue). Each dot represents an investigated gene, and only genes with P<0.05 in significance are shown in the plots. The table is the summary statistics of the ANCOVA analysis.

2) Please clarify how the authors handled multiple testing correction of p-values.

There were three analyses involving multiple testing in this study: 1) for the differential expression analysis, we obtained the multiple corrected p-values by Benjamini-Hochberg FDR (false discovery rate) procedure; 2) for the GO enrichment analysis, we calculated the FDR-adjusted q-values from the overall p-values to correct for multiple testing.

3) for the WGCNA analysis, considering the 12 traits were involved, including population, birth weight (BW), biparietal diameter (BPD), femur length (FL), gestation time (GT), placental weight (PW), placental volume (PLV), abdominal girth (AG), amniotic fluid maximcon depth (AFMD), amniotic fluid (AFI), fetal heart rate (FH) and fundal height (FUH). We calculated a Bonferroni threshold (p-value = 0.05/the number of independent traits) using the correlation matrix of the traits to evaluate the significant modules. We estimated the number of independent traits among the 12 investigated traits was 4 (Author response image 2). Therefore, we used a more stringent significant threshold p-value = 0.0125 (0.05/4) as the final threshold to correct the multiple testing brought by multiple traits in our WGCNA analyses. We have updated this section based on the new threshold.

Author response image 2.

The correlation matrix of 12 traits involved in the WGCNA analysis. The correlation coefficients larger than 0.2 (or smaller than -0.2) are regarded as significant correlation and marked in gradient colors.

3) The "natural selection acts on the placental DEGs ..." section is potentially misleading readers to assume that the manuscript reports evidence for positive selection on the observed DEG pattern between Tibetans and Han, which is not.

a) Currently the section simply describes an overlap between DEGs and a set of 192 genes likely under positive selection in Tibetans (TSNGs). The overlap is quite small, leading to only 13 genes in total (Figure 6). The authors are currently not providing any statistical measure of whether this overlap is significantly enriched or at the level expected for random sampling.

We understand the reviewer’s point that the observed gene counts overlapped between DEGs from the three sets (4 for female + male; 9 for male only and 0 for female only) with TSNGs should be tested using a statistical method. Therefore, we adopted permutation approach to evaluate the enrichment of the overlapped DEGs with TSNGs.

For each permutation, we randomly extracted 192 genes from the human genome, then overlapped with DEGs of the three sets (female + male; female only and male only) and counted the gene numbers. After 10,000 permutations, we constructed a null distribution for each set, and found that the overlaps between DEGs and TSNGs were significantly enriched in the “female + male” set (p-value = 0.048) and the “male only” set (p-value = 9e-4), but not in the “female only” set (p-value = 0.1158) (Author response image 3). This result suggests that the observed DEGs are significantly enriched in TSNGs when compared to random sampling, especially for the male DEGs. We added this analysis in the revised manuscript.

Author response image 3.

The distribution of 10,000 permutation tests of counts of the overlapped genes between DEGs and the 192 randomly selected genes in the genome. The red-dashed lines indicate the observed values based on the 192 TSNGs.

b) The authors are describing sets of DEGs that seem to affect important phenotypic changes in a consistent and adaptive direction. A relevant form of natural selection for this situation may be polygenic adaptation while the authors only consider strong positive selection at a single variant/gene level.

We agree with reviewer that polygenic adaptation might be a potential mechanism for DEGs to take effect on the adaptive phenotypes. Therefore, following the suggestion in the comment below, we conducted a polygenic adaptation analysis using eQTL information.

c) The manuscript is currently providing no eQTL information that can explain the differential expression of key genes. The authors can actually do this based on the genotype and expression data of the individuals in this study. Combining eQTL info, they can set up a test for polygenic adaptation (e.g., Berg and Coop; https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004412). This will provide a powerful and direct test for the adaptiveness of the observed DEG pattern.

Following the reviewer’s suggestion, we employed the PolyGraph (Racimo et al., 2018) tool to identify the signatures of polygenic selection in Tibetans using eQTL information. We conducted eQTL analysis for the seven layers, and collected a set of 5,251 eQTLs, covering the SNPs associated with gene expression with a significanct p-value < 5e-8. To obtain a list of independent eQTLs, we removed those SNPs in linkage disequilibrium (r2 > 0.2 in 1000 Genome Project). Finally, we obtained 176 independent eQTLs. At the same time, we generated a set of 1,308,436 independent SNPs of Tibetans as the control panel. The PolyGraph result showed that Tibetans have a clear signature of polygenic selection on gene expression (Bonferroni-correction p-value = 0.003) (Author response image 4).

We have added this result in the revised manuscript (Figure S4), and added a detailed description of polygenic adaption in the Methods section.

Author response image 4.

Polygraphs for the eQTLs that show evidence for polygenic adaptation in the five-leaf tree built using the allele frequency data of 1001 Tibetans (Zheng et al. 2023) and 1000 Genome Project. The colors indicate the marginal posterior mean estimate of the selection parameter for variants associated with the gene expression. r, q, s and v in the tree nodes refer to the nodes in terminal branches and internal branches. TBN, Tibetans; CHB, Han Chinese in Beijing; JPT, Japanese in Tokyo, Japan; CEU, Northern Europeans from Utah; YRI, Yoruba in Ibadan, Nigeria.

4) The manuscript is currently only minimally discussing how findings are linked to EPAS1 and EGLN1 genes, which show the hallmark signature of positive selection in Tibetans. In fact, the authors' group previously reported male-specific association between EPAS1 SNPs and blood hemoglobin level. Many readers will be intrigued to see a discussion about this point.

According to the reviewer’s suggestion, in the revised manuscript, we added a paragraph to discuss the relationship between our transcriptomic data and the two genes with strong selective signals, i.e. EPAS1 and EGLN1.

“As the gene with the strongest signal of natural selection in Tibetans, EPAS1 has been reported in numerus studies on its contribution to high altitude adaptation. In this study, we detected a significant expression reduction of EPAS1 in the Tibetan UC compared to the high-altitude Han. It was reported that the selected-for EPAS1 variants/haplotype were associated with lower hemoglobin levels in the Tibetan highlanders with a major effect (Beall et al., 2010; Peng et al., 2017), and the low hemoglobin concentration of Tibetans is causally associated with a better reproductive success (Cho et al., 2017). Therefore, we speculate that the selective pressure on EPAS1 is likely through its effect on hemoglobin, rather than directly on the reproductive traits. The down-regulation of EPAS1 in placentas likely reflects a blunted hypoxic response that may improve vasodilation of UC for better blood flow, and eventually leading to the higher BW in Tibetans (He et al., 2023). For EGLN1, another well-known gene in Tibetans, we detected between-population expression difference in the male UC layer, but not in other placental layers. Considering the known adaptation mechanism of EGLN1 is attributed to the two Tibetan-enriched missense mutations, the contribution of EGLN1 to the gene expression changes in the Tibetan UC is unexpected and worth to be explored in the future.”

Reviewer #2 (Public Review):

In this manuscript, the authors use newly-generated, large-scale transcriptomic data along with histological data to attempt to dissect the mechanisms by which individuals with Tibetan ancestry are able to mitigate the negative effects of high elevation on birth weight. They present detailed analyses of the transcriptomic data and find significant sex differences in the placenta transcriptome.

I have significant concerns about the conclusions that are presented. The analyses also lack the information necessary to evaluate their reliability.

The experimental design does not include a low elevation comparison and thus cannot be used to answer questions about how ancestry influences hypoxia responses and thus birthweight at high elevations. Importantly, because the placenta tissues (and trophoblasts specifically) are quickly evolving, there are a priori good reasons to expect to find population differences irrespective of adaptive evolution that might contribute to fetal growth protection. There are also significant details missing in the analyses that are necessary to substantiate and replicate the analyses presented.

Although the datasets are ultimately valuable as reference sets, the absence of low elevation comparisons for Tibetans and Han Chinese individuals undermines the ability of the authors to assess whether differences observed between populations are linked to hypoxia responses or variation in the outcomes of interest (i.e., hypoxia-dependent fetal growth restriction).

We understand the reviewer’s concern about the lack of low-altitude comparison. For the placenta transcriptomic data, actually, we previously studied the comparison of placenta from high-altitude Tibetans and low-altitude Han Chinese, including 63 placentas of Tibetans living at Lhasa (elevation: 3650m) and 14 placentas of Han in Kunming (elevation: 1800m) (Peng et al. 2017). The main finding was that in general, the expression profiles are similar between the high-altitude Tibetans and the low-altitude Han. In particular, most high-altitude Tibetans have a similar level of EPAS1 expression in the placenta as the lowlander Han Chinese, a reflection of Tibetans’ adaptation at altitude. In other words, (Peng et al. 2017). In this study, we observed a significant down-regulation of EPAS1 in the Tibetan UC when compared to Han Chinese living at the same high altitude. Therefore, the observed differences between Tibetans and Han Chinese placenta at high altitude are due to the adaptation of Tibetans.

For phenotypic data, we made a systematical comparison of reproductive outcomes in our previous studies (He et al., 2023; He et al., 2022). We proved that polygenic adaptation of reproduction in Tibetans tends to reduce the chance of preterm birth and eliminate the restriction on fetal development at high altitude. Compared to the high-altitude Han Chinese migrants, the high-altitude Tibetans exhibit a less birth weight reduction and infant mortality induced by hypoxia, similar with the lowland Han Chinese as reference.

In summary, although we cannot make combination analysis with our high-altitude data and the published low-altitude data because of batch effect and difference of sampling strategy, we obtained more supportive evidence for the adaptation of placenta expression regulation in Tibetans. To be objective, we have discussed the limitation of the lack of lowlander placenta data in the Discussion section.

The authors attempt to tackle this phenotypic association by looking for correlations between gene networks (WGCNA) and individual genes with birthweight and other measurements collected at birth. I have some reservations about this approach with only two groups (i.e., missing the lowland comparison), but it is further problematic that the authors do not present data demonstrating that there are differences in birthweight or any other traits between the populations in the samples they collected.

Throughout, I thus find conclusions about the adaptive value and hypoxia-responses made by the authors to be unsubstantiated and/or the data to be inadequate. There are also a gratuitous number of speculative statements about mechanisms by which differential gene expression leads to the protection of birthweight that are not evaluated and thus cannot be substantiated by the data presented.

As currently presented and discussed, these results thus can only be used to evaluate population differences and tissue-specific variation therein.

We understand the reviewer’s point that the observed differences of gene expression between Tibetan natives and Han immigrants living at high altitude might be explained by ancestral divergence, rather than hypoxia-associated response and genetic adaptation of native Tibetans.

Firstly, we conclude that Tibetans have a better reproductive outcome, not only based on the two highlander groups living at the same altitude, but also relied on the change direction compared to the lowland level. For example, we observed a significant higher BW in Tibetans than Han migrants in our dataset (35 Tibetans vs. 34 Han: p-value = 0.012) (Author response image 5), and in a larger dataset (He et al. 2023) (1,317 Tibetans vs. 87 Han: p-value = 1.1e-6), suggesting an adaptation of Tibetans because BW decreases with the increase of altitude. The logic was the same to the other traits. Following the suggestion of reviewer, we added these phenotype comparisons in the revised manuscripts. The detailed information of the investigated samples and the statistic results were also added as supplementary tables in the revised version.

For the WGCNA, we agree with the reviewer that the detected modules both showing significant correlation with population and other reproductive traits cannot be fully explained by adaptation of Tibetans. Therefore, we tuned down the description of this section and added other possible explanations, such as population differences, in the discussion.

Author response image 5.

Comparison of 11 reproductive traits between Tibetans and Han immigrants. (A) comparison based on the dataset of this study (35 Tibetans vs. 34 Han); (B) correlation between BW and altitude (left panel) and comparison analysis based on the larger sample size (the data were retrieved from (He et al., 2023)). Univariate comparisons of the average of each trait cross population were made by using the ANCOVA test in R aov function with fetal sex and maternal age as covariates.

There is also some important methodological information missing that makes it difficult or impossible to assess the quality of the underlying data and/or reproduce the analyses, further limiting the potential impact of these data:

1) Transcriptome data processing and analyses: RNA quality information is not mentioned (i.e., RIN). What # of reads are mapped to annotated regions? How many genes were expressed in each tissue (important for contextualizing the # of DE genes reported - are these a significant proportion of expressed genes or just a small subset?).

According to the reviewer’s suggestion, we added more information about transcriptome data processing and analyses in the revised Methods and Results:

“After RNA extraction, we assessed the RNA integrity and purity using 1% agarose gel electrophoresis. The RIN value of extracted RNA was 7.56 ± 0.71.”

“In total, 10.6 billion reads were mapped to the annotated regions, and 17,283 genes express in all the investigated placenta.”

“We identified 579 differentially expressed genes (DEGs) between Tibetans and Han, accounting for 3.4% of the total number of expressed genes.”

2) The methods suggest that DE analyses were run using data that were normalized prior to reading them into DESeq2. DESeq2 has an internal normalization process and should not be used on data that was already normalized. Please clarify how and when normalization was performed.

Actually, we made raw read count matrix as input file when conducting differential analysis using DESeq2, rather than using the normalized data. We have updated our description in the method section of the revised manuscript.

3) For enrichment analyses, the background gene set (all expressed genes? all genes in the genome? or only genes expressed in the tissue of interest?) has deterministic effects on the outcomes. The background sets are not specified for any analyses.

Actually, we utilized the genes expressed in placenta as the background gene set for enrichment analyses. The genes with more than two transcripts per million transcripts (TPM) were regarded as an expressed gene, which is commonly used criteria for RNA-seq data.

4) In the WGCNA analysis, P-values for correlations of modules with phenotype data (birthweight etc.) should be corrected for multiple testing (i.e., running the module correlation for each outcome variables) and p.adjust used to evaluate associations to limit false positives given the large number of correlations being run.

As we explained in response to comment#2 of Reviwer-1, we used a more stringent significant threshold of p-value = 0.0125 (0.05/4) as the final threshold to correct the multiple testing brought by multiple traits in the WGCNA analysis.

5) The plots for umbilical histological data (Fig 5 C) contain more than 5 points, but the use of replicate sections is not specified. If replicate sections were used, the authors should control for non-independence of replicate sections in their analyses (i.e., random effects model).

We did not use replicate sections. Figure 5C shows the umbilical artery intima and media. Because each human umbilical cord includes two umbilical arteries, the 5 vs. 5 individual comparison generates 10 vs. 10 umbilical artery comparison. To be clearer, we added an explanation in the revised manuscript.

On more minor notes:

There is significant and relevant published data on sex differences and hypoxia in rodents (see Cuffe et al 2014, "Mid- to late-term hypoxia in the mouse alters placental morphology, glucocorticoid regulatory pathways, and nutrient transporters in a sex-specific manner" and review by Siragher and Sferuzzi-Perro 2021, "Placental hypoxia: What have we learnt from small animal models?"), and historical work reporting sex differences in placental traits associated with high elevation adaptation in Andeans (series of publications by Moira Jackson in the late 1980s, reviewed in Wilsterman and Cheviron 2021, "Fetal growth, high altitude, and evolutionary adaptation: A new perspective").

We thank the reviewer for the constructive comments on literature review. We have cited and discussed them in the revised manuscript.

Reviewer #3 (Public Review):

More than 80 million people live at high altitude. This impacts health outcomes, including those related to pregnancy. Longer-lived populations at high altitudes, such as the Tibetan and Andean populations show partial protection against the negative health effects of high altitude. The paper by Yue sought to determine the mechanisms by which the placenta of Tibetans may have adapted to minimise the negative effect of high altitude on fetal growth outcomes. It compared placentas from pregnancies from Tibetans to those from the Han Chinese. It employed RNAseq profiling of different regions of the placenta and fetal membranes, with some follow-up of histological changes in umbilical cord structure and placental structure. The study also explored the contribution of fetal sex in these phenotypic outcomes.

A key strength of the study is the large sample sizes for the RNAseq analysis, the analysis of different parts of the placenta and fetal membranes, and the assessment of fetal sex differences.

A main weakness is that this study, and its conclusions, largely rely on transcriptomic changes informed by RNAseq. Changes in genes and pathways identified through bioinformatic analysis were not verified by alternate methods, such as by western blotting, which would add weight to the strength of the data and its interpretations. There is also a lack of description of patient characteristics, so the reader is unable to make their own judgments on how placental changes may link to pregnancy outcomes. Another weakness is that the histological analyses were performed on n=5 per group and were rudimentary in nature.

For the weakness raised by the reviewer, here are our responses:

(1) Considering that our conclusions largely rely on the transcriptomic data, we agree with reviewer that more experiments are needed to validate the results from our transcriptomic data. However, this study was mainly aimed to provide a transcriptomic landscape of high-altitude placenta, and to characterize the gene-expression difference between native Tibetans and Han migrants. The molecular mechanism exploration is not the main task of this study, and more validation experiments are warranted in the future.

(2) For the lack of description of patient characteristics, actually, we provided three level results on the placental changes of Tibetans: macroscopic phenotypes (higher placental weight and volume), histological phenotypes (larger umbilical vein walls and umbilical artery intima and media; lower syncytial knots/villi ratios) and transcriptomic phenotypes (DEG and differential modules). Combined with the previous studies, these placenta changes suggest a better reproductive outcome. For example, the placenta volume shows a significantly positive correlation with birth weight (R = 0.31, p-value = 2.5e-16), therefore, the larger placenta volume of Tibetans is beneficial to fetal development at high altitude. In addition, the larger umbilical vein wall and umbilical artery intima and media of Tibetans can explain their adaptation in preventing preeclampsia.

(3) For the sample size of histological analyses, we understand the reviewer’s concern that 5 vs. 5 samples are not large in histological analyses. This is because it was difficult to collect high-altitude Han placenta samples, and we only got 13 Han samples, from which we selected 5 infant sex matched samples.

References

Beall, C.M., Cavalleri, G.L., Deng, L.B., Elston, R.C., Gao, Y., Knight, J., Li, C.H., Li, J.C., Liang, Y., McCormack, M., et al. (2010). Natural selection on EPAS1 (HIF2 alpha) associated with low hemoglobin concentration in Tibetan highlanders. P Natl Acad Sci USA 107, 11459-11464.

Cho, J.I., Basnyat, B., Jeong, C., Di Rienzo, A., Childs, G., Craig, S.R., Sun, J., and Beall, C.M. (2017). Ethnically Tibetan women in Nepal with low hemoglobin concentration have better reproductive outcomes. Evol Med Public Health 2017, 82-96. He, Y., Guo, Y., Zheng, W., Yue, T., Zhang, H., Wang, B., Feng, Z., Ouzhuluobu, Cui, C., Liu, K., et al. (2023). Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude. Curr Biol.

He, Y., Li, J., Yue, T., Zheng, W., Guo, Y., Zhang, H., Chen, L., Li, C., Li, H., Cui, C., et al. (2022). Seasonality and Sex-Biased Fluctuation of Birth Weight in Tibetan Populations. Phenomics 2, 64-71.

Peng, Y., Cui, C., He, Y., Ouzhuluobu, Zhang, H., Yang, D., Zhang, Q., Bianbazhuoma, Yang, L., He, Y., et al. (2017). Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia. Mol Biol Evol 34, 818-830.

Racimo, F., Berg, J.J., and Pickrell, J.K. (2018). Detecting Polygenic Adaptation in Admixture Graphs. Genetics 208, 1565-1584.

eLife assessment

This fundamental study reports differential expression of key genes in full-term placenta between Tibetans and Han Chinese at high elevations, which are more pronounced in the placentae of male than in female fetuses. If validated as functionally relevant, these results will help us understand how human populations adapt to high elevation by mitigating the negative effects of low oxygen on fetal growth. At this time, while the differential gene expression analyses are solid, the downstream analyses offer incomplete support for the connection to hypoxia-specific responses and adaptive genetic variation.

Reviewer #1 (Public Review):

The revised manuscript new presented 1) a permutation-based test for the significance of the overlap between DEGs and genes with positive selection signals in Tibetans, and 2) polygenic adaptation test for the eQTLs. I make my suggestions in detail as below:

Major Comments

1. My previous concern regarding the DEG analysis remains unresolved. Although the authors agreed in their response that the difference between the male- and female-specific DEGs are insufficient to the difference between sex-combined and sex-specific DEGs (Figure S6). However, the results section still states the opposite pattern between males and females as a decisive reason for the difference (p. 9, lines 236-239). Again, I would like to recommend the authors to test alternative ways of analysis to boost statistical power for DEG detection other than simply splitting data into males and females and performing analysis in each subset. For example, the authors may consider utilizing gene by environment interaction analysis schemes here biological sex as an environmental factor.

2. Multiple testing schemes are still sub-optimal in some cases. Most of all, the p-values in the WGCNA analysis (p. 11), the authors corrected for the number of traits (n=12) after adjusting for the correlation between them. However, they did not mention whether they counted for the number of modules they tested at all (n=136 and 161 for males and females, respectively). Whether they account for the number of modules will make a substantial difference in the significance threshold, please incorporate and describe a proper multiple testing scheme for this analysis.

3. Evidence for natural selection on the observed DEG pattern is still weak and not properly described.<br /> 1) For the overlap between DEGs and TSNGs, the authors introduced a permutation-based test, but used a total set of genes in the human genome as a comparison set (p. 25, lines 699-700). I believe that the authors should sample random sets of genes from those already expressed in each tissue to make a fair comparison.<br /> 2) The entire polygraph analysis for polygenic adaptation is poorly described. The current version of the Methods does not clarify i) for which genes the eQTLs are discovered, 2) how the authors performed the eQTL analysis, iii) how the authors polarized the effect, and iv) how they set up a comparison between the eQTLs and the others.

Reviewer #2 (Public Review):

More than 80 million people live at high altitude. This impacts health outcomes, including those related to pregnancy. Longer-lived populations at high altitudes, such as the Tibetan and Andean populations show partial protection against the negative health effects of high altitude. The paper by Yue sought to determine the mechanisms by which the placenta of Tibetans may have adapted to minimise the negative effect of high altitude on fetal growth outcomes. It compared placentas from pregnancies from Tibetans to those from the Han Chinese. It employed RNAseq profiling of different regions of the placenta and fetal membranes, with some follow-up of histological changes in umbilical cord structure and placental structure. The study also explored the contribution of fetal sex in these phenotypic outcomes.

A key strength of the study is the large sample sizes for the RNAseq analysis, the analysis of different parts of the placenta and fetal membranes, and the assessment of fetal sex differences.

A main weakness is that this study, and its conclusions, largely rely on transcriptomic changes informed by RNAseq. Changes in genes and pathways identified through bioinformatic analysis were not verified by alternate methods, such as by western blotting, which would add weight to the strength of the data and its interpretations. There is also a lack of description of patient characteristics, so the reader is unable to make their own judgments on how placental changes may link to pregnancy outcomes. Another weakness is that the histological analyses were performed on n=5 per group and were rudimentary in nature.

Author Response

We thank the reviewers and editorial team for their positive and thoughtful comments and recommendations for our paper. We will provide a detailed point-to-point response accompanying a revised version of our paper to carefully incorporate all the recommendations and clarify several confusing points. Here we provide a brief provisional response to summarize the key points.

1) Are the two factors in the enslavement patterns after stroke, changes in shape (loss of complexity) and magnitude (intrusion of flexor bias), dissociable? Our results show both a loss of shape (Fig. 5) and an increase of magnitude (Fig. 7) in enslavement patterns in the paretic hand. We agree with the reviewers that the key measures for these two factors, Angular (Cosine) and Euclidean Distances, are not mathematically orthogonal because, while Angular Distance is indeed only influenced by shape, Euclidean Distance is influenced by both magnitude and shape changes of the enslavement patterns. However, our LME results show that increased flexor bias in the paretic hand strongly predicts Euclidean Distance but not Angular Distance (Fig. 9), thereby suggesting that pattern shape change cannot be fully accounted for by flexor intrusion. This analysis was also recommended by Reviewer 1. In the revised version, we will further clarify the dissociation of the two components.

2) Can biomechanical factors be ruled out from the enslavement patterns in the paretic hand? We agree with the reviewers that resting hand posture measures alone cannot fully assess biomechanical factors, given that biomechanical constraints during action and abnormal postures due to neural loss after stroke were not captured in these measures. In the paper, however, we used three analyses to justify this point. In the first analysis, we showed that resting hand posture (Mount Distance and Mount Angle) could not account for the Biases in all groups (healthy, paretic, non-paretic). In the second analysis, we showed that resting hand posture could not account for Enslavement in all groups. In the third analysis, we showed that Biases in the non-paretic hand could not predict Biases or Enslavement in the paretic hand within the same patients. The third analysis was done based on the existing literature that secondary biomechanical change after stroke was likely not the major contributor in the hand impairment, where passive muscle stimulation could successfully evoke a similar level of fingertip forces in both stroke and control hands (Hoffmann et al. 2016) and median nerve stimulation could significantly reduce intrusion of finger flexion (Kamper et al. 2003). The resting hand posture and non-paretic hand biases would include both biomechanical and neural factors, but since none of these measures could predict enslaving patterns, we maintain that biomechanical factors would not be a contribution to the enslavement in the paretic hand.

3) Neural correlates of behavioral changes were not tested, therefore claims such as "low-level," "subcortical," and "top-down cortical" contributions are not fully justified. We agree with the reviewers, and we will clear references to these neural correlates from the text of the Results section in the revised version of the paper. These neural correlates will only be discussed in the Discussion section.

4) RDM construction for "by-Target Direction" was not clearly explained. We agree with the reviewer that the diagram in Fig. 4D was a little confusing. To construct these matrices, we analyzed differences in coactivation patterns of the non-instructed fingers when two fingers move in the same target direction. A cleaner pattern comparison should exclude both the two instructed fingers to be compared from the enslavement matrices. This will be clarified in the revised version.

References

Hoffmann, Gilles, Megan O. Conrad, Dan Qiu, and Derek G. Kamper. 2016. “Contributions of Voluntary Activation Deficits to Hand Weakness after Stroke.” Topics in Stroke Rehabilitation 23 (6): 384–92. https://doi.org/10.1179/1945511915Y.0000000023.

Kamper, D G, R L Harvey, S Suresh, and W Z Rymer. 2003. “Relative Contributions of Neural Mechanisms versus Muscle Mechanics in Promoting Finger Extension Deficits Following Stroke.” Muscle & Nerve 28 (3): 309–18. https://doi.org/10.1002/mus.10443.

eLife assessment

This important study presents a new apparatus and experimental paradigm to examine deficits in finger control in stroke patients, with the goal of understanding their potential (biomechanical and neural) underpinnings. The paper presents solid experimental design and quantitative analyses to characterise these deficits and infer their origin, but a few technical aspects related to data analysis and statistics could be improved, and alternative interpretations of the results considered. In addition to the scientific results, this novel methodology can be used as a starting point for further research on hand function impairments in stroke, which is of significance for theoretical studies in neuroscience and applied research in rehabilitation.

Reviewer #1 (Public Review):

Summary:<br /> Impairment in hand function is a challenge for stroke rehabilitation, and its neural underpinnings are of paramount importance for the field of biomedical science and neuroscience. The present study uses a novel finger force measurement device to measure individual fingers' force production in three dimensions when one finger is needed to produce an independent isometric force. Enslavement, i.e., the unwanted coactivation of non-intended fingers, is exaggerated in stroke survivors. The study started out by noting that the contribution of underlying factors (the loss of corticospinal drive, intrusion of flexor synergy due to a loss of regulation on subcortical pathways, and/or biomechanical changes) is not well understood. Detailed analysis for the inter-dependence between finger forces shows that the covariation between finger forces showed stroke-specific changes in shape and magnitudes, and these changes are not caused by biomechanical constraints. The important message that the study tries to convey is that the magnitude change in finger coactivation of the paretic hand is caused by the two dissociable factors, i.e., a loss of complexity in finger control and an intrusion of flexor bias. 

Strengths:<br /> The targeted topic of individual control of fingers for stroke survivors is of both theoretical and applied importance. The methodology of using isometric finger force to fulfill simple yet relevant motor tasks for stroke patients is also novel and sound. The paper is concisely written with excellent figures.

Weaknesses:<br /> I have three major concerns about the study: 1) the link between the analysis results and two of the study's main conclusions is weak, specifically for the conclusion that a loss of complexity in finger control and the intrusion of flexor bias is dissociable. 2) using hand posture measures to quantify the influence of biomechanical factors in stroke patients is not well justified. 3) only a limited number of stroke patients were recruited (n=13). <br /> <br /> First, the conclusion that the two factors contributing to the magnitude of finger covariation pattern are dissociable is not well reasoned. For example, the reasoning is clearly stated (Line 434) as: "Given the above converging evidence that Angular Distance is a measure of complexity of the geometric shape of finger coactivation, whereas Euclidean Distance is more sensitive to the magnitude change of these patterns across task goals if the two factors are dissociable, the intrusion of flexor bias would predict the magnitude (Euclidean Distances), but not the shape (Angular Distances) of the enslavement patterns. "

The logic behind this statement is unclear. Suppose the "two factors" are the complexity loss (shown by Angular Distance) and intrusion of flexor bias (shown by Bias). In that case, we cannot just use the predictability and the lack of predictability of the measure of intrusion of flexor bias (Bias) to reach the above conclusion, i.e., the Bias (for the intrusion of flexor bias) and changes in Angular Distance (for the loss of complex loss) is dissociable. Why not just test the association between Bias and Angular Distance directly?

Another conclusion is that the changes of Euclidian Distance and Angular Distance from the pattern similarity analysis of finger coactivation patterns inform us that the coactivation shape is preserved but its magnitude is increased in the paretic hand. However, the shape measure (Angular Distance) shows a decrease in paretic hands, indicating the coactivations for different task requirements become similar in the paretic hand. It becomes similar across task conditions, but this does not mean the coactivation shape for each task requirement is preserved in patients. In fact, one possible sign of reservation might be an unchanged function of distance measure (varied by intended fingers or directions) between groups (ideally shown in the format as Figure 5B). As we can see from the figure, the shape is preserved in the mild group but not so in the severe group if we compare the data between groups. Statistically, it is better to do ANOVA and use the group*fingers and group*directions interaction to show the reservation of "shape." The same logic applies to the Euclidean Distance measure (Figure 7B and 7D). Again, the connection between data analysis results and conclusions should be clarified. <br /> <br /> Second, the use of hand posture measures to quantify biomechanical factors for hand impairments is not validated.  

Based on two hand posture measures, the study rules out the contribution of biomechanical factors for enslavement in patients entirely (Line 390). However, the alternative explanation for the negative effect of posture variables is that these two specific variables (Mount Distance and Angle) might not reflect the postural changes (and biomechanical factors in hand function) in patients. Note these two measures are not about the resting hand posture of the patient, which is often affected. It is the posture when the hand is inserted into the apparatus, and the total force readings are minimal. The force readings would be quite small if people are good at relaxing their muscles and inhibiting unwanted reflexes in a specific posture. Healthy hands can remain a small force for rather different postures. Thus, healthy hands can produce a range of possible minimum-force postures, making the reliability of these "minimum" posture measures questionable. For patients, on the other hand, since a minimum-force posture is related to the ability to relax the muscles, it probably reflects both biomechanical changes (muscles and tendons, etc.) and subcortical influence. Thus, using these two measures to rule out the possibility of biomechanical factors needs further justification. <br /> <br /> Third, the number of stroke patients is limited (n=13), especially when one important test is to compare the mild group and the moderate-severe subgroups. The group comparison thus has small statistical power with a medium split. <br /> <br /> As the study aims to tease out the contributions of biomechanical, subcortical, and cortical input to the observed impairment of enslavement, we need to be careful about whether the selected behavioral variables are justified to reflect these factors and whether the data analysis results coherently support the conclusions. As it currently stands, the paper still has room to improve to achieve its aims.

Reviewer #2 (Public Review):

Summary:<br /> This study addresses the factors affecting the loss of independent control of finger forces after stroke. As central and peripheral factors contribute to this impairment, the authors used a novel apparatus and task to rigorously quantify the specific features of loss of finger individuation across all digits. The analyses ruled out the role of biomechanical constraints and revealed that the loss of independent control of finger forces is primarily driven by the interaction of two factors: loss of complexity in finger control (shape of enslavement patterns) and involuntary coactivations of task-irrelevant fingers (flexion bias).

Strengths:<br /> 1. The device and 3D finger individuation task are major strengths of the study, setting this work apart from previous work and enabling novel insights.<br /> 2. The analyses are thorough and well-designed. Of particular value is the analysis of finger force control in 3D Cartesian space and the use of Representational Similarity Analysis of finger enslavement pattern magnitude and shape.<br /> 3. A major contribution of this work is the teasing out of the effects of top-down factors versus biomechanical constraints affecting impairment of finger force control.<br /> 4. I found the discussion about complexity of finger control (lines 541-553) very interesting. The topic of adaptability of finger coactivation patterns in the context of dexterous manipulation is a key topic in robotics and neuroscience. In robotics, finger forces are decomposed into a grasp and manipulation component. In human motor control studies, this approach has identified their temporal coordination (work by Latash and Zatsiorsky, e.g., Gao et al., 2005) and potentially distinct sensorimotor control mechanisms (Wu and Santello, 2023). The authors might wish to discuss how coactivation patterns might contribute to the coordination of grasp and manipulation forces.

Weaknesses:<br /> None (only minor clarifications, e.g., the term biomechanical constraints should be defined earlier in the paper).

Reviewer #3 (Public Review):

This paper seeks to characterize finger enslavement impairment after stroke-"the unwanted coactivation of non-intended fingers in individuated finger movements." In the past, three possible neuromuscular mechanisms contributing to finger enslavement were suggested: passive musculotendon properties, an intrusion of flexor bias, and a loss of complexity in finger control repertoire. To tease apart these factors, the authors simultaneously recorded all five fingertip forces using a sensitive isometric force measurement device, which allowed characterizing patterns of enslavement for all fingers in a variety of instructed tasks. This novel experimental design opened new opportunities to study finger enslavement in more detail. To analyze this multi-dimensional dataset, new metrics were introduced, and many detailed analyses were conducted. Here is a brief account of the important results as best as I can summarize them.

1. Gross finger individuation ability is lower in the paretic hand of stroke patients than in non-paretic or healthy hands. Enslavement worsens with the severity of overall stroke impairment.<br /> 2. The enslavement patterns - unintended finger forces as functions of an instructed force in a different finger - show smaller "complexity" in paretic than nonparetic hands. I.e., the directions of unintended finger forces in the paretic hand remain similar across various instructed tasks. This reduced complexity also correlates with the severity of stroke.<br /> 3. The enslavement patterns show larger magnitude differences in the paretic than non-paretic hands; i.e., the unintended fingers' forces show a larger shift when comparing two instructed force directions in a paretic finger.<br /> 4. Finger force biases exist in paretic and non-paretic hands and correlate with the severity of stroke. Biases are more pronounced in flexion than ab/adduction direction.<br /> 5. The resting hand posture does not correlate with finger force bias or enslavement patterns.<br /> 6. Finger force biases correlate with enslavement patterns in the paretic hand, but not in the non-paretic hand.<br /> 7. Flexor bias (force biases in flexor direction) does not correlate with gross individuation ability in the ab/adduction direction in the non-paretic hand, but it correlates with the ab/adduction individuation ability in the paretic hand.<br /> 8. Finger force biases do not correlate with directional differences in enslavement patterns on either hand. However, biases correlate with the magnitude of force shift in the enslavement pattern.<br /> 9. The intrusion of flexor bias (difference of finger force biases in paretic and non-paretic hands) does not correlate with directional differences in enslavement patterns in either hand, but it correlates with force shifts in enslavement patterns in both hands.<br /> 10. More principal components (in principal component analysis, PCA) are required to explain similar levels of variance of enslavement patterns in paretic than non-paretic hands.

Taken together, the authors use these results to claim that: 1) enslavement impairment is unrelated to passive biomechanical properties, and 2) loss of complexity and flexor bias both contribute to enslavement, but possibly via different mechanisms.

The first argument is supported by the result that resting hand posture does not explain gross individuation ability or enslavement patterns. Although these results are valid, biomechanical contributions are not ruled out altogether in my opinion. The experiment starts from the optimal posture in which minimal finger forces are recorded in a relaxed state, essentially an "equilibrium" posture where all forces from muscles, ligaments, and other soft tissues are balanced. However, this equilibrium posture alone does not represent potential asymmetry in passive biomechanical properties (e.g., at equilibrium, flexion may face less stiffness than extension), nor does it take into account complex interactions between muscles of the hand. A simple finger force requires the co-activation of several intrinsic and extrinsic hand muscles as well as those of the wrist, some of which may be weak, shortened, stiff, painful, etc. Even if neural activity is present, compensation from other muscles may be needed, which may lead to unintended forces in other fingers. Although my "hunch" agrees with the author's claim that neural contributions outweigh biomechanical factors in enslavement, I believe resting posture on its own cannot account for "all" biomechanical factors. Additionally, the results comparing biases in paretic and non-paretic hands (line 389) are unrelated to biomechanics. It is reasonable to believe that the passive biomechanical properties of the paretic hand are different from those of the non-paretic hand if long enough time has passed since the stroke. So biomechanical of one hand is not representative of the other hand. Even if biases in the non-paretic hand could explain those in the paretic hand, I find it hard to extend the conclusion that biomechanics is a factor.

The authors further presented detailed analyses to tease apart contributions of flexor bias and loss of complexity to enslavement. The flexor bias is straightforward to define, and its correlation with enslavement (or the absence of correlation in the non-paretic hand) is supported by the results. However, the arguments about complexity are less straightforward. Two separate definitions of complexity are used: one is the directional differences between enslavement patterns, and the other is based on the number of principal components. This is one source of confusion as to which definition is used when referring to "loss of complexity". Nonetheless, both complexities are shown to decrease with the severity of stroke. The first type of complexity is also shown to be uncorrelated to flexor bias. However, I did not find evidence among the results that directly linked complexity to enslavement. Could complexity, similar to biomechanical properties, be ruled out? This paper provides no evidence for or against the contribution of complexity to enslavement.

My last point is about the neural correlates of these characteristics. The authors frequently use the terms "low-level", "subcortical", "top-down cortical", etc. throughout the paper, while the results are exclusively at a behavioral level. This issue is also present in the abstract where the authors state that: "we aim to tease apart the contributions of lower biomechanical, subcortical constraints, and top-down cortical control to these patterns in both healthy and stroke hands"; however, the methods and the results are unrelated to neural aspects of control, and the authors only refer to other studied to link these behavioral effects to "potential" neural causes. Further, the intrusion of flexor bias is usually associated with "subcortical" neural pathways in Results. The authors have properly discussed these possible neural correlates in the Discussion, but mentioning these terms in the Results is unjustified and unsupported by the results or the methods. This paper does not provide any standalone evidence to directly link complexity or bias to their neural correlates.

Comments on the representational distance matrices (RDM):<br /> Two types of RDM were defined: "by-Finger" RDM (Fig 4A), and "by-Target Direction" RDM (Fig 4D). While I understand the by-Finger RDM and it physically makes sense to me, I cannot fully wrap my head around the by-Target RDM. I leave the interpretation of these results to the reader.

The distinction between the Euclidean and Angular distance is also vague to me. Angular distance is a valid similarity measure for the directions of two vectors and it is unrelated to the norms of vectors. However, Euclidean distance is not fully independent of the Angular distance as the authors claim; it changes with both the norms of the two vectors and the angle between them. If the angular distance is small, then Euclidian distance mostly represents norm differences, but the statement "Euclidean distances are sensitive to the length difference between two force vectors but insensitive to direction differences" is not generally correct. This issue is particularly important because the averaging of distances (see my next point) masks details of individual distance values, which hinders the interpretation of the results.

The enslavement patterns and RDMs are potentially valuable metrics, however, the way they are condensed in the final statistical analyses reduces their value. The way I understand it, all elements of the RDM matrix are averaged into a single value. This averaging masks the details of individual pairs of comparisons, which not only reduces the information resolution but also seriously hinders rigorous analysis and interpretation of the results.

Author Response

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

Editorial comments:

Comment 1 - Recommendations for the authors: please note that you control which revisions to undertake from the public reviews and recommendations for the authors.

We appreciate the feedback from the 3 Reviewers and Editor. We have enumerated each Reviewer comment and provide a detailed response. We endeavoured to include each suggestion into the revised manuscript. All changes in the manuscript are indicated in red font. In instances in which we respectfully disagree with the Reviewer, we have provided a fair rebuttal. We feel the comments from the Reviewers has significantly improved the clarity and quality of the manuscript.

Comment 2 - The revision process has demonstrated the value of your work, highlighting both its strengths and shortcomings. Importantly, it provides detailed and achievable suggestions for improving the current version of your contribution.

We thank the Reviewers and Editor for their time and expert input on our manuscript. We feel the suggestions from the Reviewers to address the shortcomings has resulted in a significantly improved manuscript.

Comment 3 - There is a general consensus among the reviewers on three key aspects. Firstly, the article would greatly benefit from a clearer layout of the experimental design and methodology, potentially including schematics to help readers comprehend the complexity and details of the study.

We appreciate the feedback from Reviewer 2 in particular. We have added a new schematic for Experiment 3 (see PUBLIC REVIEWS Reviewer #2 Comment 2). We have also revised the Results section by including subheadings and additional text to help explain the methods.

Comment 4 - Secondly, conducting a more comprehensive analysis of the available dataset, utilizing tools such as WGCNA to explore gene co-expression networks beyond specific genes, is recommended. Additionally, it is advised to exercise greater caution when discussing the limitations of the employed methods.

The suggestion for the WGCNA is excellent and very much appreciated. The revised manuscript includes WGCNA for both the MBH and pituitary gland. See Figures S3 & Table S6 and lines 166-182; 497-505).

Comment 5 - Thirdly, expanding the results section to create a more engaging narrative that guides readers through the numerous findings, and extending the discussion and conclusions to emphasize the ecological relevance of learning photoperiodic/seasonal responses and highlighting the presented model, would be valuable.

These were excellent suggestions that significantly improved the clarity and quality of the manuscript. The results section included several subheadings to help break up of the transitions across experiments. We have also significantly revised the introduction and discussion to include the ecological relevance and importance to consider sex as a factor in the interpretations.

Comment 6 - Finally, please pay close attention to the comment on the statistical analysis provided by Rev#2.

It is unclear why the Benjamini-Hochberg’s FDR analyses was suggested. The statistical test is a version of the Bonferroni test but is less stringent. We prefer to use conservative tests (i.e., Bonferroni correction). Moreover, the Bonferroni correction is the commonly used statistical tests in the field. To be consistent with the field and to be careful in our statistical approach, the revised manuscript did not change the post-hoc correction.

PUBLIC REVIEWS:

Reviewer #1:

Comment 1 - The authors investigated the molecular correlates in potential neural centers in the Japanese quail brain associated with photoperiod-induced life-history states. The authors simulated photoperiod to attain winter and summer-like physiology and samples of neural tissues at spring, and autumn life-history states, daily rhythms in transcripts in solstices and equinox, and lastly studies FSHb transcripts in the pituitary. The experiments are based on a series of changes in photoperiod and gave some interesting results. The experiment did not have a control for no change in photoperiod so it seems possible that endogenous rhythms could be another aspect of seasonal rhythms that lack in this study. The short-day group does not explain the endogenous seasonal response.

We thank the Reviewer for the fair assessment of the manuscript. The statement ‘the experiment did not have a control for no change in photoperiod’ is not clear to us. We think the Reviewer is arguing that prolonged constant photoperiod was not conducted to examine circannual timing in avian reproduction. The constant short photoperiod in Exp3 does provide the ability to examine the initial stages of interval timing. A different endogenous mechanism used by animals. The revised manuscript has clarified the different physiological responses.

Comment 2 - The manuscript would benefit from further clarity in synthesizing different sections. Additionally, there are some instances of unclear language and numerous typos throughout the manuscript. A thorough revision is recommended, including addressing sentence structure for improved clarity, reframing sentences where necessary, correcting typos, conducting a grammar check, and enhancing overall writing clarity.

We have incorporated the suggestions from both Reviewer 1 and Reviewer 2 that aimed to increase the clarity of the manuscript. We have provided detailed responses to each comment below and state how each comment was incorporated in the revised manuscript. We also had the manuscript reviewed by a colleague to help identify issues associated with sentence structure, grammar, and spelling.

Comment 3 - Data analysis needs more clarity particularly how transcriptome data explains different physiological measures across seasonal life-history states. It seems the discussion is built around a few genes that have been studied in other published literature on quail seasonal response. Extending results on the promotor of DEGs and building discussion is an extrapolating discussion on limited evidence and seems redundant.

A new statistical analysis (ie., WGCNA) was conducted to identify relations between photoperiod, physiology and transcripts. The focus on the few photoperiodic gene was kept in the discussion as the transcript expression is important to highlight the differences from the prevailing hypotheses and novel patterns of expression across seasonal timescales. See Figures S3 & Table S6 and lines 166-182; 497-505).

Comment 4 - Last, I wondered if it would be possible to add an ecological context for the frequent change in the photoperiod schedule and not take account of the endogenous annual response. Adding discussion on ecological relevance would make more sense.

This is an excellent suggestion. The introduction and discussion were substantially revised to include the ecological relevance.

Reviewer #2:

Comment 1 - This study is carefully designed and well executed, including a comprehensive suite of endpoint measures and large sample sizes that give confidence in the results. I have a few general comments and suggestions that the authors might find helpful.

We appreciate the Reviewers support for our manuscript. We have endeavoured to incorporate all suggestions in the revised manuscript.

Comment 2 - I found it difficult to fully grasp the experimental design, including the length of light treatment in the three different experiments (which appears to extend from 2 weeks up to 8 weeks). A graphical description of the experimental design along a timeline would be very helpful to the reader. I suggest adding the respective sample sizes to such a graphic, because this information is currently also difficult to keep track of.

We have created a new figure panel to address the Reviewer’s concern. See figure S4 panel ‘a’. The new schematic representation was designed to illustrate the similarity in experimental design used in Experiment 1 and Experiment 2. But clearly illustrates the extended short photoperiod manipulation (4 weeks and not 8 weeks). We added the sample sizes to initial drafts but felt the added text hindered the clarity of the schematic representation (particularly for Fig1a). The sample sizes for each experiment and treatment are provided in the raw data provided in the supplementary Table 1. For this reason, we have opted to not add the sample size to each diagram. We hope that the Reviewer will understand our perspective.

Comment 3 - The authors use a lot of terminology that is second nature to a chronobiologist but may be difficult for the general reader to keep track of. For example, what is the difference between "photoinducibility" and "photosensitivity"? Similarly, "vernal" and "autumnal" should be briefly explained at the outset, or maybe simply say "spring equinox" and "fall equinox."

This is a very helpful suggestion, and we thank the Reviewer. Two changes were made to the manuscript to address this comment. First, we revised the second introductory paragraph to describe the photoperiodic response and the terms used. Second, we have removed all reference to ‘vernal’ and replaced with ‘spring’. We opted to keep ‘autumn’ as the change to ‘fall’ did not provide the clarity of seasonal state in some statements (as fall is also used as a downward direction).

Comment 4 What was the rationale for using only male birds in this study? The authors may want to include a brief discussion on whether the expected results for females might be similar to or different from what they found in males, and why.

We agree with the Reviewer’s position that studies should include, or least describe, male and female biology. We have revised the text to address this comment. In the methods, we provide 2 sentences that state the photoperiodic response is the same for both male and females, and why males were selected. See lines (352-355). Then, in the discussion, we describe why females will be important to study how other supplementary environmental cues impact seasonal timing of reproduction. See lines (312-330; and 334-339).

Comment 5 - The authors used the Bonferroni correction method to account for multiple hypothesis testing of measures of testes mass, body mass, fat score, vimentin immunoreactivity and qPCR analyses in Study 1. I don't think Bonferroni is ever appropriate for biological data: these methods assume that all variables are independent of each other, an assumption that is almost never warranted in biology. In fact, the data show clear relationships between these endpoint measures. Alternatively, one might use Benjamini-Hochberg's FDR correction or various methods for calculating the corrected alpha level.

This concern is not clear to us. The Benjamini-Hochberg’s FDR is a slight modification of the Bonferroni correction. Moreover, the FDR is a less-stringent statistical test compared to the Bonferroni correction. We prefer to keep the Bonferroni approach to correct for multiple tests for two reasons. First, this test is commonly used in the field of chronobiology, and second, the Bonferroni correction is more conservative. We hope the Reviewer will appreciate our perspective to be consistent with the research field and higher stringency in our statistical approach.

Comment 6 - The graphical interpretations of the results shown in Figure 1n and Figure 3e, along with the hypothesized working model shown in Figure S5, might best be combined into a single figure that becomes part of the Discussion. As is, I do not think these interpretative graphics (which are well done and super helpful!) are appropriate for the Results section.

We appreciate the Reviewer’s suggestion. During the revision we developed a single figure to show the graphical representation for the respective experiments. Unfortunately, we found the single source to be very difficult to provide a clear description and overview of the findings. We feel that the interpretations, (admittedly unusual for Results section) are best placed in the respective figures that correspond to the different experiments.

Reviewer #3:

Comment 1a - It is well known that as seasonal day length increases, molecular cascades in the brain are triggered to ready an individual for reproduction. Some of these changes, however, can begin to occur before the day length threshold is reached, suggesting that short days similarly have the capacity to alter aspects of phenotype. This study seeks to understand the mechanisms by which short days can accomplish this task, which is an interesting and important question in the field of organismal biology and endocrinology.

We thank the Reviewer for their positive feedback.

Comment 1b - The set of studies that this manuscript presents is comprehensive and well-controlled. Many of the effects are also strong and thus offer tantalizing hints about the endo-molecular basis by which short days might stimulate major changes in body condition. Another strength is that the authors put together a compelling model for how different facets of an animal's reproductive state come "on line" as day length increases and spring approaches. In this way, I think the authors broadly fulfill their aims.

We thank the Reviewer for the positive support of our research and manuscript.

Comment 1c - I do, however, also think that there are a few weaknesses that the authors should consider, or that readers should consider when evaluating this manuscript. First, some of the molecular genetic analyses should be interpreted with greater caution. By bioinformatically showing that certain DNA motifs exist within a gene promoter (e.g., FSHbeta), one is not generating robust evidence that corresponding transcription factors actually regulate the expression of the gene in question. In fact, some may argue that this line of evidence only offers weak support for such a conclusion. I appreciate that actually running the laboratory experiments necessary to generate strong support for these types of conclusions is not trivial, and doing so may even be impossible. I would therefore suggest a clear admission of these limitations in the paper.

We agree with the Reviewer’s position. The transcription binding protein analyses was used as a means to identify potential factors involved in the regulation of transcript expression. We have written a new paragraph to address this comment. In the discussion, we that highlight the links between the well characterised circadian regulation of photoperiodic transcripts (e.g, D- & E-box elements and the photoperiodic control of TSHβ. We also indicate that our bioinformatic approach identified potentially new transcription binding motifs, and provide a clear admission and state that functional analyses are required to determine necessity of these pathways (e.g., MEF2). See lines 293-295.

Comment 2 - Second, I have another issue with the interpretation of data presented in Figure 3. The data show that FSHbeta increases in expression in the 8Lext group, suggesting that endogenous drivers likely act to increase the expression of this gene despite no change in day length. However, more robust effects are reported for FSHbeta expression in the 10v and 12v groups, even compared to the 8Lext group. Doesn't this suggest that both endogenous mechanisms and changes in day length work together to ramp up FSHbeta? The rest of the paper seemed to emphasize endogenous mechanisms and gloss over the fact that such mechanisms likely work additively with other factors. I felt like there was more nuance to these findings than the authors were getting into.

We agree with the Reviewer and a similar concern was raised by Reviewer 1. Our aim was to highlight that FSH expression increased in constant short photoperiod. We have revised the manuscript to address the concern raised by the Reviewer. We have added 2 sentences in the results to highlight the additive role of endogenous timing and photoperiodic effects on FSH expression (see lines 223-226). We have kept the text that describes endogenous increases in expression (e.g., FSH/GnRH) in response to short photoperiod in the manuscript as this observation is not influenced by long photoperiod.

Comment 3 - Third, studies 1 - 3 are well controlled; however, I'm left wondering how much of an effect the transitions in day length might have on the underlying molecular processes that mediate changes in body condition. While the changes in day length are themselves ecologically relevant, the transitions between day length states are not. How do we know, for example, that more gradual changes in day length that occur over long timespans do not produce different effects at the levels of the brain and body? This seemed especially relevant for study 3, where animals experience a rather sudden change in day length. I recognize that these experimental methods are well described in the literature, and they have been used by endocrinologists for a long time; nonetheless, I think questions remain.

There are two points raised in this comment. First, the effect of transition in day length on body condition. We are investigating the impact of photoperiodic transitions on body condition. The ongoing project has examined the changes in tissue lipid content and conducted transcriptomic analyses of multiple peripheral tissues involved in energy balance. Although we made an initial attempt to combine all the findings into a single manuscript, the large datasets resulted in an overwhelming manuscript that lacked clarity. Instead, we have opted for two manuscripts that focus on the respective physiological systems. Those data should be published shortly. We did expand the discussion by developing a single paragraph that focused on the pattern of POMC expression and changes in quail body mass and adipose tissue. See lines 300-311.

Second, the Reviewer raised the issue of more gradual changes in day length over longer timespans. The day length and duration of exposure selected was to replicate previously used photoperiod manipulations to ensure reproducibility in research programmes, and to reduce the impact of photoperiod history (see lines 367-369). The present manuscript is the first study in birds to examine multiple intervening (ie within the extreme long- and short-photoperiods) day length conditions and we feel this is a major and novel contribution to the field. We agree that other time points (e.g., 13L:11D), or quicker/longer timespans could provide additional insight into the molecular mechanisms that govern seasonal transitions in reproduction/energy balance. The question raised by the Reviewer requires the types of studies that use natural conditions from wild-caught animals (or semi-natural laboratory settings) and beyond the focus of the current manuscript.

Recommendations For The Authors:

Reviewer #1

Comment 1 - Abstract: Overall abstract needs more clarity in rationale, hypothesis, and result outcomes. How this study advances our knowledge in seasonal/ photoperiodic regulation of reproduction in birds. Particularly what knowledge gap FSHb results fill in.

We have substantially revised the abstract considering the Reviewer’s suggestions. The abstract has clarified the rationale, hypothesis and results outcomes. We have also added new introductory and concluding statements that place the work into a wider ecological context (as suggested below).

Comment 2 - In general the introduction needs more clarity and doesn't seem to cover the ecological relevance of learning photoperiodic/seasonal response.

We agree with the Reviewer the introduction could be improved. We have substantially revised the introduction with an aim to increase the clarity. This involved an addition on the ecological context, clarification of the photoperiodic states in birds, and a description of the general and specific objectives. Note we did not include an introduction to ‘learning’ of the photoperiodic response, as the term implies a cognitive component is involved which is incorrect. See lines (61-67, 71-74, 80-86, and 100-105).

Comment 3 - Line 58: What does the author mean by "future seasonal environment" Is it to introduce change in climate or future seasonal events? This sentence needs rephrasing and more clarity.

In response to Comment 2, we have revised the introductory paragraph and the sentence was removed from the text.

Comment 4 - Line 63: I would recommend the use of circannual rhythms with caution for the kind of experiments authors have proposed. The approach used here is beyond the scope of addressing circannual endogenous rhythms, which can be tested only independent of photoperiod change.

We agree with the Reviewer’s concern. The use of circannual rhythms was limited to the first paragraph (lines 56-63) only to introduce the concept of endogenous rhythmicity. We were careful to not use the term ‘circannual’ for the rest of the manuscript, as the Reviewer has indicated, would be inappropriate. We have retained the use of ‘endogenous program’ to refer to the molecular and physiological changes that can occur independent of photoperiod change (ie Experiment 3). In this case, the use of endogenous is appropriate as this form of timing adheres to an interval timer. We also provided a definition for interval timer and ecological examples to illustrate the difference between circannual rhythms and annual interval timer (see lines 71-74). We also reviewed the entire manuscript to ensure the distinction for the endogenous program was clear.

Comment 5 - Another aspect authors missed is that Quail is not an absolute photorefractory (Robinson and Follett, 1982).

We agree with the Reviewer that quail are not absolute photorefractory (but instead relative photorefractory). As our photoperiod manipulations do not address criterion 1, or criterion 2 of the avian photoperiodic response (MacDougall-Shackelton et al., 2009; see https://doi.org/10.1093/icb/icp048), we feel that adding the type of photorefractory response would be a distraction and reduce the clarity of the concepts/experimental design described in the manuscript.

Comment 6 - Line 223-234: "Chicks were raised under constant light and constant heat lamp". Constant photoperiod experienced during development raises concern on how this pretreatment would shape the adult seasonal response, which could be different in the seasonal response of birds raised in natural photoperiod. If this is correct, the results shown are not tenable for birds inhabiting the natural environment.

The light schedule used in our experiment is the most appropriate for laboratory reared chicks. The light schedule, use of an incubator and hatchery is commonly used in research laboratories. The procedure serves to increase the hatch rate and welfare of chicks. Undoubtedly there will be some early developmental programming effects on quail development. However, the gonadal response across all 3 experiments was consistent with the vast scientific literature on the avian photoperiodic response in both laboratory and wild birds. As the robust gonadal response clearly replicated previous studies, we are confident the results are tenable for birds inhabiting natural environments.

Comment 7 - Numerous studies done in mammals suggest that photoperiod experienced in the early life stage affects the circadian and seasonal response in adults (Ciarleglio et al., 2011, Perinatal photoperiod imprints the circadian clock, Nat Neurosceince; Stetson M., et al., 1986, Maternal transfer of photoperiodic information influences the photoperiodic response of prepubertal Djungarian hamsters).

We agree with the Reviewer that developmental programming in mammals is important for the photoperiodic response. However, there are vast differences between the avian and mammalian photoperiodic response. Critically, in mammals, the maternal transfer of information to the offspring is achieved via the melatonin hormone. Conversely, in birds, melatonin is not necessary, nor sufficient for photoperiodic time measurement (Juss et al., 1993; see https://doi.org/10.1098/rspb.1993.0121). It is not scientifically tenable to relate the mammalian and avian photoperiodic responses in adulthood based on early developmental programs. For this reason, we did not introduce or discuss developmental programming in our manuscript.

Comment 8 - Please give details on the month in which these birds were exposed to different short and long photoperiods. It is not clear in the method section. The birds experience long to short day transition and then back to long day in 16 weeks (~ 4 months). The annual cycle is ~12 months long in nature. Again, what is the ecological relevance of such an experimental paradigm. This could give some idea on photoperiodic response, but not on how the endogenous annual cycle would respond.

Birds were delivered in September 2019 and 2020. (We have added these details to the manuscript (see lines 351-352). We agree with the Reviewer that the ecological relevance of the experimental design is limited. Our focus was to use laboratory conditions and well characterised photoperiodic manipulations to examine the role of the environmental, initial predictive cue to time seasonal transitions in reproduction. The 2-week duration for each photoperiod state in Experiment 1 provides the ability to eliminate the impact of photoperiodic history (see lines 367-369; Stevenson et al., 2012a) and reduce the time necessary for the research project. As described above in Comment #4 – we did not examine the endogenous annual cycle – but instead focused on an endogenous interval timer. Experiment 3 was designed to best examine an endogenous interval timer.

Comment 9 - Line 251: "A jugular blood sample" Please rephrase this sentence and add 50 ul heparinized tubes

We thank the Reviewer for identifying this oversight. The text was changed accordingly.

Comment 10 - Line 259: The scale.....fat pads" - The sentence doesn't read correctly.

The sentence was revised accordingly.

Comment 11 - Line 274: Male.....six weeks. It is not clear from this sentence; what photoperiod birds were exposed to before transferring to 2 long days. Is it 16 or 14 LD.

The birds were held in 16L. The text has been revised accordingly.

Comment 12 - Line 276: It is not clear what is Home Office approved schedule 1. This may be a commonly used term for animal sacrifice protocol in UK and Europe. But it is not familiar jargon for the rest of the globe.

We apologise for the jargon. The text was revised to include the exact methods (decapitation followed by exsanguination).

Comment 13 - Line 277-284: Birds under SD for 4 weeks (8 Lext) is a bit confusing and particularly in the context of studying endogenous rhythm. Needs more clarity.

The text was revised to improve the clarity. The manuscript now states: ‘A subset of birds (n=6) was maintained in short day photoperiods for four more weeks (8Lext). This group of birds provided the ability to examine whether an endogenous increase in FSHβ expression would occur in constant short day photoperiod condition.’

Comment 14 - Line 322-323: Give RIN number (RNA integrity number) here which is a very common parameter to determine RNA degradation in RNAseq experiments. I guess, the MiniON is a portable sequencer and sequences one sample at a time. If this is true authors should consider any batch effect in sequencing and use it as a covariate in the model.

The RIN values from our extraction protocol reliably produce RIN values >9.0. The text now states: Isolated RNA reliably has RIN values >9.0 for both the mediobasal hypothalamus and pituitary gland. Our RIN values are well above the recommended 7.0 limit. The Reviewer is correct that MinION is portable, however, more than one sample can be run at a time. We stated in the text (lines 454-460) that birds were counterbalanced across Flow cells so that each sequencing run had 9 samples, one from each treatment group. Our counterbalancing approach and quality control steps prevented batch effects.

Comment 15 - Line 397-398: Adding quail or chicken-specific vimentin peptide pre-incubation with primary Ab will serve more confirming control. Omitting primary Ab doesn't address cross-reactive/ nonspecific binding issues.

We agree that a positive control (ie primary Ab) is the gold standard to support specificity of the antibody. Unfortunately, we have not found a supplier of the epitope for quail/chicken vimentin. We have conducted another in silico analysis an established that the sequences for the vimentin antibody is specific for vimentin. The next closest sequence alignment is only 68% for a protein that is not expressed in the brain. The immunoreactive pattern observed in our histology reproduces work from mammalian models in which the epitope is available. Therefore, we are confident that our immunoreactive signal for vimentin is specific. We have added the in silico analysis in the manuscript on lines 535-538.

Comment 16 - Line 430: Was the GLM model used for testing all variables? Running a statistical model to explain Differentially expressed genes, photoperiod, and physiological variables together will give a more conclusive outcome to explain the photoperiod effect and seasonal state.

A similar comment was raised by Reviewer 2. We have conducted a WGCNA analyses to examine the relationship between photoperiod, physiological variables and DEG. See Figures S3 & Table S6 and lines 166-182; 497-505).

Comment 17 - It is a bit unclear why the author used cherry-picking approach by talking about only a few genes that have been studied as key regulators of photoperiodic response in quail. What was the purpose of transcriptome? A better approach would have been to use a model to reduce the data (PCA) and explain the physiological response by regression against different PCs.

We agree with the Reviewer that other statistical approaches could be conducted, and other genes could be discussed. However, we focussed on the key regulators of the photoperiodic response in quail as these are the well characterised genes. It is important that our discussion focused on these transcripts as most do not conform to the predicted patterns of expression. We feel it is best that we keep the focus on these genes.

Comment 18 - TSHb result is inconsistent with past studies, where TSHb is the first responder gene on photoinduction. The author did not pay attention to explaining it further in the discussion.

We respectfully disagree with the Reviewer. Our results are consistent with past studies and show that TSHβ expression is a molecular marker of long day photoperiod. Our study does not examine photoinduction; which does not provide the ability to compare between our study and previous work (eg., Nakao et al., 2008; see doi: 10.1038/nature06738). We have revised the text in consideration of the concern raised by the Reviewer. The text now states ‘Previous reports established that TSHβ expression is significantly increased during the period of photoinducibility in quail (Nakao et al., 2008). Although the present study did not directly examine photoinduction, TSHβ expression was consistently elevated in long day photoperiod (i.e., 16L).’. (see lines 262-265).

Comment 19 - PRL result seems interesting and there could be more discussion in relation to the rise in PRL transcripts levels termination of breeding. Elaborating on PRL expression and breeding termination can add more information to the discussion.

This comment is not clear to us, and we would incorporate a clarified comment in a revised manuscript. The increased expression of prolactin does not occur during the termination of breeding. The increase in prolactin occurs during the vernal increase in photoperiod (ie 14L) but does not have a clear link with gonadal growth.

Comment 20 - Line 217-219: Based......respectively. Sounds like a big claim with less evidence.

We have removed the sentence from the discussion.

Comment 21 - Line 220-223: The .....Bird. The sentence is not clear about how this study would add to ecological studies. Need more clarity on the importance of such data.

The sentence was removed from the text.

Comment 22 - I think that it would be helpful to add a couple of caveats to provide more ecological context. First, the model is only based on males, and responses in females could be different.

We agree with the Reviewer there are undoubtedly sex differences in timing seasonal biology. However, the photoperiodic response (growth and regression) is similar in both males and females. Sex differences exist in response to supplementary environmental cues (e.g., temperature). Males were used in these studies as the gonadal response to changes in photoperiod manipulations are much larger compared to ovarian changes in females. The focus on males allows for fewer animals to be used in the experiments and greater statistical power. To address the Reviewers concern, we have added a paragraph in the discussion that describes the similarity in photoperiodic responses in males and females, and the importance of supplementary cues for full reproductive development in female birds. We also provide a couple sentences in the methods that describe the justification for only males in the present study. See lines (Methods 352-355; Discussion 312-330; and 334-339).

Comment 23 - Last, I wondered if it would be possible to add an ecological context for the frequent change in the photoperiod schedule and not take account of the endogenous annual response. Would the procedure simulate a similar kind of underlined molecular response for a bird under natural conditions responding to changing daylight cycles on an annual time frame?

The discussion was considerably revised to address the ecological relevance of the study, and findings. We have added a sentence at the beginning of the discussion to highlight that the laboratory-based approach and photoperiodic manipulations reliable replicate previous findings using semi-natural conditions (Robinson and Follett, 1982) (See lines 248-250). We have already reduced the focus on the endogenous annual response.

Reviewer #2:

Comment 1 - The writing is very terse and could benefit from a more narrating style, which would make it a lot easier for the reader to get through some of the very data-heavy text. Breaking up the Results with subheadings would also be helpful.

We appreciate the suggestion to add subheadings to the Results. We added 3 descriptive headings for each other studies conducted in the manuscript. We feel the added revision (e.g., ecological) has improved the narrative and made the manuscript accessible to the wider readership.

Comment 2 - The transcriptome analyses could be developed a bit more. First, using the limma package would allow the authors to apply a more complete model to the DEG analyses, which would likely be superior to EdgeR. Second, the authors may want to consider WGCNA or a similar approach to discover gene co-expression modules, and then examine whether any of the resulting module eigengenes co-vary with any morphological or physiological measures and/or vary rhythmically.

This is an excellent suggestion, and the new analyses was incorporated into the revised manuscript. Using the Langfelder and Horvath 2008 WCGNA package we conducted module-trait analyses to examine co-variation in our findings. These data are presented in Figure S# and lines 476-484. We agree that other DEG analyses would be useful; our main objectives was to use BioDare2.0 to identify rhythmic transcription in the seasonal transcriptomes. EdgR provides an excellent approach to identify transcripts and commonly used.

Comment 3 - In the Data and code availability statement (lines 226ff) the authors state that "all raw data are available in Extended data Table 1." However, they should be submitted to the GEO database or a similar public repository along with all relevant metadata. Also, and maybe I overlooked this, I did not see anywhere that the "R code used in Study 1 is freely available" (I was not sure what "the methods reference list" was supposed to refer to). Instead of stating that "the full R code used is available upon request" I suggest making all scripts available via GitHub or Dataverse, along with all non-omics data. The advantage of the latter platform is that a citable DOI is assigned to each upload.

The data are now available in the GEO database and can be accessed see GSE241775. We have added this information to the text. The R code is now provided as a Table S11 so that the reader can directly access the script.

Comment 4 - Line 191: Delete the extra "that"

We thank the Reviewer for identifying the oversight. We have revised the text accordingly.

Comment 5 - Line 24f: What does "pseudo-randomly" mean? Maybe "haphazardly" would be more appropriate here?

The term pseudo-randomly is used to describe the organized manner in which subjects are assigned to each treatment group. The aim is to ensure that a particular physiological variable, such as body mass, is evenly distributed across treatment groups. (Note although the term derived from the field of psychology). The aim is to reduce bias in the experiment due to an initial bias established when assigning treatment group. We are reluctant to replace pseudorandomly with haphazardly as the latter does not imply a logical organization. We have added text to help clarify the reason. The text now state: At the end of each photoperiodic treatment a subset of quail (n=12) body mass was used as a measure to pseudo randomly select birds for tissue collection and served to reduce the potential for unintentional bias.

Comment 6 - Figure 1e,j: The text indicates that 398 and 130 genes were "rhythmically expressed" in the MBH and pituitary, respectively, but considerably fewer genes are shown in the heatmaps in Figure 1e,j. How were these genes selected, and what was the rationale for doing so? Also, some autumnal and vernal expression patterns show some strong similarities (e.g., 16a and 16v in the MBH), which could be discussed. Consider showing the two heatmaps with the columns also hierarchically clustered in a supplementary figure.

We agree with the Reviewer that the full heatmap for the transcripts should be provided. The heat maps in Figure 1 are based on the transcripts with the most significant change; and were selected to provide a graphical representation that would be easily digested by the wide readership. We have created a new figure (ie. Fig. S1) that provides all the transcripts in heat maps for both the MBH and pituitary gland.

Reviewer #3:

Comment 1 I do not have too much to add to this section of my review. Broadly speaking, I would suggest that the authors address some of the concerns I highlight above, and integrate their thoughts into the paper more than they currently do. I think this is particularly important with respect to the limitations of many of the bioinformatic analyses.

We thank the reviewer for their input and time assessing the manuscript. We have revised the manuscript in many sections incorporating the suggestions by Reviewer 3 above, and Reviewers 1 and 2.

Comment 2 Some of the methods are also a little scant. For example, the qPCR analyses are not described in sufficient detail to replicate the study. What are the efficiencies? Were samples run in duplicate? What was the housekeeping control gene used? Was there only one, or were multiple housekeeping genes used?

We apologise for the oversight, the absence of information was a mistake that missed our previous early revisions. The revised manuscript includes all the requested information. Line 333 states that all samples were run in duplicate. The efficiency for each transcript was within the MIQE guidelines (indicated on line 342) and were within the 0.7 to 1.0 range. Actin and glyceraldehyde 3-phosphate dehydrogenase were used as the reference transcripts. The most stable reference transcript was used to calculate fold change in target gene expression (lines 343-345).

Reviewer #1 (Public Review):

This study is carefully designed and well executed, including a comprehensive suite of endpoint measures and large sample sizes that give confidence in the results. The authors have satisfactorily addressed my concerns. Specifically, the new graphical description of the experimental design along a timeline will be very helpful in guiding the reader through the paper. The narrative style is much improved and highly technical terminology is minimized. The authors now also address the question of sex differences, which will be important to study in future research. The additional analyses carried out by the authors are illuminating.

Reviewer #2 (Public Review):

It is well known that as seasonal day length increases, molecular cascades in the brain are triggered to ready an individual for reproduction. Some of these changes, however, can begin to occur before the day length threshold is reached, suggesting that short days similarly have the capacity to alter aspects of phenotype. This study seeks to understand the mechanisms by which short days can accomplish this task, which is an interesting and important question in the field of organismal biology and endocrinology.

The set of studies that this manuscript presents is comprehensive and well-controlled. Many of the effects are also strong and thus offer tantalizing hints about the endo-molecular basis by which short days might stimulate major changes in body condition. Another strength is that the authors put together a compelling model for how different facets of an animal's reproductive state come "on line" as day length increases and spring approaches. In this way, I think the authors broadly fulfill their aims.

Author Response

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

eLife assessment

In this important paper, the authors report a link between brumation and tissue size in frogs, summarizing convincing evidence that extended brumation is associated with smaller brain size and increased investment in reproduction-related tissues. The research will be of broad interest to ecologists, evolutionary biologists, and those interested in global change biology. While the dataset involves significant field work and advanced statistical analyses, the manuscript would benefit from more explanation of the models, including why frogs are a good model in which to address these questions, and from general improvement in the structure and conciseness.

We highly appreciate your positive assessment and that you considered our paper important and convincing.

Reviewer #1 (Public Review):

The authors have conducted lots of field work, lab work and statistical analysis to explore the effect of brumation on individual tissue investments, the evolutionary links between the relative costly tissue sizes, and the complex non-dependent processes of brain and reproductive evolution in anuran. The topic fits well within the scope of the journal and the manuscript is generally written well. The different parameters used in the present study will attract a board readership across ecology, zoology, evolution biology, and global change biology.

Thank you for your positive and supporting feedback.

Reviewer #2 (Public Review):

The authors set out to show how hibernation is linked to brain size in frogs. If there were broader aims it is hard to decipher them. The authors present an extremely impressive dataset and a thorough set of cutting-edge analyses. However not all details are well explained. The main result about hibernation and brain size is fairly convincing, but it is hard to think of broader implications for this study. Overall, the manuscript is very confusing and hard to follow.

Thank you for your compliments on our paper. As for your concerns, we have greatly revised our paper and, as we hope, improved its clarity. We have also added a few sentences to the conclusions to draw attention to potentially broader implications. Specifically, we describe how the focal traits of our study may all be affected by climate change. Differential constraints in necessary investments could be one of several reasons for the varying resilience to climate change between species in the same habitat.

Reviewer #1 (Recommendations For The Authors):

There are no issues on the availability of data and code.

Thank you.

Line 15: in the author contribution section, it seems that C.L.M. and J.P.Y are not in the author list.

These two authors are not part of this study. This was a mistake.

Line 24: I don't think it is vital or logical to address or compare too much on birds or mammals, which are not the focused taxa of the present study. Instead, it is better to clarify the reason why frogs and toads are ideal model taxon to this study.

The reason for comparisons with birds and mammals was that all hypotheses related to the various trade-offs tested here had been developed in these taxa. One of the points of our paper was that these needed validation beyond the two taxa, in addition to being tested against one another (each prediction had been developed in a specific group and typically in isolation of all other hypotheses).

Line 25-26: as the authors are shooting for eLife, as a general journal, it is not essential to provide the detailed methods in the abstract. But I think the authors need to strengthen the novelty of the work in the field here.

The strength of our study was that all traits were measured directly in our species, including estimates of hibernation duration. Prior studies used various proxies, categorial classification or datasets assembled from multiple sources. To us, this seemed like a sufficiently important advance in the field to mention it, but considering the reviewer’s comment, we have now removed it.

Line 28: "protracted brumation reduces brain size and instead promotes reproductive investments", as a correlative study, it is much more precise to change this sentence to a similar description as "protracted brumation is negatively correlated with brain size but is positively correlated with reproductive investments" here and related statements throughout the whole text.

We agree that, strictly speaking, a path analysis can only point toward possible causality and not provide hard evidence as experimental manipulation might. The wording may have been a bit too strong here in our attempt to minimize wordiness and because all our analyses combined very strongly pointed in this direction. However, we have now changed this as suggested even though it now reads almost as if we had done no more than conducting a simple correlation. We have further paid attention to the wording of our interpretations throughout the paper.

Line 32-33: it needs a bigger ending linking your main findings with the implication in understanding species response to the sustained environment change.

We have reworded the ending of the abstract to: “Our results provide novel insights into resource allocation strategies and possible constraints in trait diversification, which may have important implications for the adaptability of species under sustained environmental change.”

Line 63-68: this sentence is too long to understand and please simplify it.

We have split the sentence into two sentences.

Line 125-130: it is known that there are various frog reproductive modes (Crump et al. 2015) such as trade-offs between clutch size and egg size, different number of breeding during one year, etc. These different reproductive forms may also influence the brain size evolution with food availability and seasonal variations. Please clarify it.

Yes, anurans do have varying reproductive modes, but to us, there is no a priori reason to assume that such variation would have a direct effect on brain evolution. Rather, in our opinion, different reproductive modes would have indirect effects by affecting the environment in which reproduction occurs. For example, larvae developing under different environmental conditions (substrate, larval density, egg provisioning etc.) might affect developmental trajectories that could influence how resources are available and allocated to different organs, including the brain. Alternatively, reproductive modes could influence the choice of environment for reproduction, thereby possibly affecting mating strategies and ultimately trait investments associated with these strategies. Given we were asked to shorten our paper, we believe that ‘environmental effects’ remains broad enough to encompass such variation, thereby not necessitating disentangling the different, and likely primarily indirect, ways that reproductive modes could be linked to brain evolution. However, if the reviewer would find it important to go into such detail in the paper, we will be happy to do so.

Line 186-187: it is necessary to mention here that the authors also conducted sensitivity analyses to apply 2{degree sign}C or 4{degree sign}C below their experimentally derived as thresholds to test the robustness of the results to data uncertainty.

We have added “(details on methodology and various sensitivity analyses for validation in Material and Methods)” to indicate the different types of sensitivity analyses, which included more than simply 2 or 4°C difference.

Line 188: please change "In phylogenetic regressions" to "after controlling for phylogenetic autocorrelation/pseudo-replication" or similar sentence here.

Our focus here was the phylogenetically informed GLS model rather than phylogenetic control itself. In the latter case, it would still not be clear what type of model was conducted with such phylogenetic control. To avoid any shorthand, we have reworded for more precision: “We employed phylogenetic generalized least-squares (PGLS) models, …”

Line 177-287: please provide the exact variance explained by different predictor variables in brumation duration, individual tissue investments, and brain evolution. I also suggest that the authors need consider conducting multi-model inference-based model averaging analysis to test the relative importance of different variables. In addition, the present analyses did not include the interaction terms among variables, which may be more important than the effect of each individual factor.

There may be some misunderstanding as these models represent separate analyses for each predictor as indicated by the associated λ values (never more than one value per model). We conducted separate models to determine which variables might even play a role in explaining variation in the corresponding response variables. Based on relevant predictors, we then conducted path analyses rather than general multi-predictor analyses. The relative effect sizes are represented by the correlation coefficients (r values) in the tables.

Reviewer #2 (Recommendations For The Authors):

Why exactly are the pairwise comparisons positively correlated (fig. S5) and then negatively correlated (fig. 3). What is actually driving this difference? For the phylogenetic path analyses 26 candidate models are chosen without explanation. What theory or hypotheses are these based on?

We assume the reviewer is referring to the brain-body fat association. The two ‘pairwise’ analyses they mention were not the same. The correlation in Fig. S5 was a standard (albeit phylogenetically informed) partial correlation between the two focal tissues, controlling for SVL. By contrast, as described when introducing the analyses, negative associations were derived when additionally controlling for testes and hindlimb muscles, all of which deviated from isometry against body size. Here, the total mass of the four main tissues was divided by their proportional contribution to that mass in each species, then standardized for comparison across species. Since the total mass of these four tissues scaled directly with body size, larger-bodied species did not invest a proportion of their body to these tissues than smaller-bodied species, thus essentially rendering body size irrelevant for this analysis. However, the relative representation of the four traits changed between species such that more resources devoted to body fat was associated with a smaller brain, hence a negative relationship. Similarly, the multivariate analysis as well as the PCA also suggested similar trends when all four tissues were considered rather than purely pairwise comparisons.

Regarding the second comment: We indeed used 28 pre-defined predictions for our larger path analysis.

The authors haven't really provided much additional context either, and the discussion is almost entirely a rehash of the results section. I can't see the analysis code but this may be of use to people performing similar analyses.

It is true that the traits and core message of the Discussion relate directly to our results, but we believe that our Discussion provides the essential biological context to our findings and to how they are connected. We tried not to go on tangents or too much speculation as the many results provided enough material to discuss, with several different ways that we expanded the prior state-of-the-art in the field. However, we have now expanded the concluding paragraph to place our findings in the context of climate change, given that this could affect anurans and the different traits examined in many ways that are directly related to the current study. Yet, we decided to keep this short because such extrapolation of our findings

We indeed held off making the code available to the public in case dramatic changes to the paper were requested by the reviewers. However, it will be published.

Additional recommendations from the Reviewing Editor:

• One of the reviewers and I found the text a little difficult to follow. I suggest simplifying the paper by being more concise. For example, the introduction could be shortened into a 3-4 paragraphs of relevant text without overwhelming the reader. One of the reviewers wanted a better explanation of statistical models and I agree. The discussion could benefit from some structure - consider adding subheadings that would guide the reader as to the topic. Finally, the figures are difficult to see and should be made larger. For example, the graphs in Figure 1c could be on a panel below A and B so that readers can interpret the graph. In Figure 3 - the legend is far too small - please put above or below the graphs. In summary - I hope you consider a major re-write that would strengthen the accessibility of your paper to a broad audience.

We have substantially shortened the paper despite adding further details on models and a broader context to the Discussion. We also condensed the Introduction to about two thirds of the original word count. However, we did not think that shortening it even further or splitting it into 3-4 paragraphs would improve readability. We still considered it important to introduce with sufficient context all major hypotheses that were tested against one another, provide at least some information on what was or was not known about the evolution of the focal traits and their links to one another or the environmental variables. We also found it important to touch on the differences between our study organisms and those typically studied in the context of hibernation or brain evolution, as this could affect the predictions. Given the number of hypotheses and traits, cutting the number of paragraphs would have meant merging some of them into very long ones, which we did not consider helpful.

We further added short subheadings to the Discussion and adjusted the figures as requested.

eLife assessment

In this important paper, the authors report a link between brumation (or "hibernation") and tissue size in frogs, summarizing convincing evidence that extended brumation is associated with smaller brain size and increased investment in reproduction-related tissues. The research is of broad interest to ecologists, evolutionary biologists, and those interested in global change biology, as the dataset involves significant field work and advanced statistical analyses for insights into how expensive tissues in these ectothermic animals respond to environmental seasonality.

Joint Public Review:

The authors have greatly improved the manuscript after detailed revisions. I would like to discuss with the authors on how to make their findings more general across taxonomic groups. For example, whether it is possible for authors to conduct a more comprehensive analyses by including amphibians, birds, and mammals together to test the general role of the relationship between brain evolution and environmental resources, and what ecological factors determine the observed brain size variations among taxa except for their biological differences such as energetic demands. It is especially for population-level analyses when related data is available in the future, which may provide very helpful insights into the brain size biogeographic patterns and their determinants across taxa.

Author Response

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

We very much appreciate the constructive comments provided by the reviewers. We have incorporated many of their suggestions and believe the manuscript is much improved.

In brief, we updated the text as suggested and have included three additional panels in supplementary fig. S2E-G. This additional data provides further support that the ectopically persisting neuroblasts are actively dividing and that cell cycle defects alone do not account for temporal patterning phenotypes.

Reviewer #1 (Public Review):

In this manuscript, the authors are building on their previous work showing Delta-Notch regulates the entrance and exit from embryo-larval quiescence of neural stem cells of the central brain (called CB neuroblasts (NB) (PMID: 35112131)). Here they show that continuous depletion of Notch in NBs from early embryogenesis leads to cycling NBs in the adult. This - cycling NBs in the adult - is not seen in controls. The assumption here is that these Notch-RNAi NBs in adults are those that did not undergo terminal differentiation in pupal development. The authors show that Notch is activated by its ligand Delta which is expressed on the GMC daughter cell and on cortex glia. They determine that the temporal requirement for Notch activity is 0-72 hours after larval hatching (ALH) (i.e., 1st instar through mid-3rd instar at 25C). In NBs/GMCs depleted for Notch, early temporal markers were still expressed at time points when they should be off and late markers were delayed in expression. These effects were observed in ~20-40% of NBs (Figures 5 and 6). Through mining existing data sets, they found that the early temporal factor Imp - an RNA binding protein - can bind Delta mRNA. They state that Delta transcripts decrease over time (without any reference to a Figure or to published work), leading to the hypothesis that Delta mRNA is repressed by the late temporal factors. Over-expressing late factors Syp or E93 earlier in development leads to downregulation of a Delta::GFP protein trap. These results lead to a model in which Notch regulates expression of early temporal factors and early temporal factors regulate Notch activity through translation of Delta mRNA.

There are several strengths of this study. The authors report rigorous measurements and statistical analyses throughout the study. Their conclusions are appropriate for the results. Data mining revealed an important mechanism - that Imp binds Delta mRNA - supporting the model that early temporal factors promote Delta expression, which in turn promotes Notch signaling.

There are also several weaknesses:

1) The activation of Notch in NBs by Delta in GMCs was already shown by this group in their Dev 2022 paper, reducing some of the impact of this study.

In our previous work, we reported that Delta-expressing GMCs transactivate Notch in neuroblasts during the embryonic to larval transition. In the current manuscript, we show that Delta is expressed in GMCs and cortex glia and both sources transactivate Notch in neuroblasts during later developmental stages. This is in agreement with work published by others and while not novel per se, is a necessary first step for understanding which neighboring cell types control Notch pathway activity. During the embryonic to larval transition, glia do not contribute likely because they have not yet grown to ensheath CB NBs and their recently born progeny.

2) The authors do not explain their current results in context of their prior paper (2022 Dev) until the Discussion, but this would be useful to read in the Introduction. Similarly, it would be good to mention that in the 2022 paper, they find a significant number of wor>Notch RNAi NBs at 2 AHL that are cycling. Are the adult Notch RNAi in this study descended from those NBs at 2 hours ALH in the 2022 study? In other words, how does the early requirement for Notch between 0-72 hours ALH reported in the current study relate to the Notch-depleted NBs identified in the 2022 paper?

We have now included the following text in the intro: “We recently reported that Notch signaling regulates CB NB quiescence during the embryonic to larval transition (Sood et al., 2022). When Notch is knocked down, some CB NBs continue dividing during this transition. We also reported that Notch activity becomes attenuated in quiescent CB NBs because CB NBs are no longer dividing and producing Delta-expressing GMC daughters for Notch pathway transactivation. Moreover, low Notch is necessary for CB NBs to reactivate from quiescence in response to dietary nutrients (Sood et al., 2022).

Here we report that Notch signaling also regulates neurogenesis termination during pupal stages. When Notch is knocked down, CB NBs maintain early temporal factor expression longer resulting in a delay of late temporal factor expression with prolonged neurogenesis into late pupal stages and early adulthood. This defect in temporal patterning (switching from early to late) occurs after CB NB exit from quiescence suggesting that Notch is required at multiple times throughout development in controlling CB NB proliferation decisions.”

We do not know whether the neuroblasts that fail to enter quiescence are the same that fail to terminate divisions during pupal stages, however there are many more that fail to terminate divisions during pupal stages.

3) Most of the experiments rely upon continuous depletion of Notch from embryonic stage 8 until adulthood using the wor-GAL4 driver. There is no lineage tracing of this driver and there is no citation about the published expression pattern of this driver. The inclusion of these details is important for a broad audience journal.

The reference for the driver is included in supplementary data, under the heading “Experimental model:Drosophila melanogaster”. This GAL4 driver is widely used and one of the most accepted in the field.

4) Most of the experiments utilize a single RNAi transgene for Notch, Delta, Imp, Syp, E93. There are no experiments demonstrating the efficacy of the RNAi lines and no references to prior use and/or efficacy of these lines.

All RNAi lines used in these studies have been published previously, by our group as well as others and sources for the lines are listed in supplementary data, under the heading “Experimental model:Drosophila melanogaster”. Efficiency of these lines have been verified using antibody labeling (data not shown) and by assaying activity of Notch activity reporters (shown in Fig. 2).

An appraisal: The authors use temperature shifts with Gal80TS to show that Notch is required between 0-72 hours ALH. They show with the use of known markers of the temporal factors and Delta protein trap, that Imp promotes Delta protein expression and the later temporal factors reduce Delta, although the molecular mechanisms are not clearly delineated. Overall, these data support their model that the reduction of Delta expression during larval development leads to a loss of Notch activity.

As noted in the Discussion, this study raises many questions about what Notch does in larval CB NBs. For example, does it inhibit Castor or Imp? Is Notch required in certain neural lineages and not others. These studies will be of interest in the community of developmental neurobiologists.

Reviewer #2 (Public Review):

Embryonic stem cells extensively proliferate to generate the necessary number of cells that are required for organogenesis, and their proliferation must be timely terminated to allow for proper patterning. Thus, timely termination of stem cell proliferation is critical for proper development. Numerous studies have suggested that cell-extrinsic changes in the surrounding niche environment drive the termination of stem cell proliferation. By contrast, cell-intrinsic mechanisms that terminate stem cell proliferation remain poorly understood. Fruit fly larval brain neuroblasts provide an excellent model for mechanistic investigation of intrinsic control of stem cell proliferation due to the wealth of information on molecular marks, gene functions and lineage hierarchy. Sood et al. conducted a genetic screen to identify genes that are required for the termination of neuroblast proliferation in metamorphosis and found that Notch and its ligand Delta contribute to their exit from cell cycle. They showed that knocking down Notch or delta function in larval neuroblasts allows them to persist into adulthood and remain proliferative when no neuroblasts can be detected in wild-type adult brains. By carrying out a well-designed temperature-shift experiment, the authors showed that Notch is required early during larval development to promote timely exit from cell cycle in metamorphosis. The authors went on to show that attenuating Notch signaling prolongs the expression of temporal identity genes castor and seven-up perturbing the switch from Imp to Syp/E93. Finally, they showed that knocking down Imp function or overexpressing E93 can restore the elimination of neuroblasts in Notch/delta mutant brains.

Overall, the experiments are well conceived and executed, and the data are clear. However, the data reported in this study represent incremental progress in improving our mechanistic understanding of the termination of neuroblast proliferation.

We respectfully disagree with this statement. Because Notch signaling is implicated in neurogenesis termination and Notch activity is regulated by GMCs and glia, it strongly suggests that NB proliferation and timing cues are controlled in a non-autonomous manner through direct interactions with NBs and their neighbors. This is in contrast to temporal patterning during embryogenesis which is largely believed to be controlled NB-autonomously. In addition, to our knowledge, no one has yet reported that CB NBs fail to terminate cell divisions on time when Notch activity is reduced during normal development. In fact, reported NB phenotypes associated with Notch loss of function have been surprisingly subtle until now.

Some of the data seem to represent more careful analyses of previously published observations described in the Zacharioudaki et al., Development 2016 paper while others seem to contradict to the results in this study.

The Zacharioudaki et al., Development 2016 paper is terrific. One key difference between our work and theirs, is that we look at Notch pathway knockdown and loss of function phenotypes, whereas in the Zacharioudaki 2016 paper, the authors report phenotypes associated with Notch constitutive activation. It has been known for some time that constitutively active Notch leads to tumorigenic phenotypes particularly in type II lineages. Zacharioudaki and colleagues further determined that some of the classically known temporal transcription factors were ectopically expressed in these stem cell tumors.Here we show that under normal developmental conditions, Notch pathway activity controls CB NB temporal patterning.

Gaultier et al., Sci. Adv. 2022 suggested that Grainyhead is required for the termination of neuroblast proliferation in a neuroblast tumor model, and grainyhead is a direct target of Notch signaling. Thus, Grainyhead should be a key downstream effector of Notch signaling in terminating castor and seven-up expression. Identical to Notch signaling, Grainyhead is also expressed through larval development. Grainyhead can function as a classical transcription factor as well as a pioneer factor raising the possibility that temporal regulation of neurogenic enhancer accessibility might be at play in allowing Notch signaling in early larval development to set up termination of castor and seven-up expression in metamorphosis. Diving deeper into how dynamic changes in chromatin in neurogenic enhancers affect the termination of neuroblast proliferation will significantly improve our understanding of termination of stem cell proliferation in diverse developing tissue.

Reviewer #3 (Public Review):

In this study, the authors investigate the effects of Notch pathway inactivation on the termination of Drosophila neuroblasts at the end of development. They find that termination is delayed, while temporal patterning progression is slowed down. Forcing temporal patterning progression in a Notch pathway mutant restores the correct timing of neuroblast elimination. Finally, they show that Imp, an early temporal patterning factor promotes Delta expression in neuroblast lineages. This indicates that feedback loops between temporal patterning and lineage-intrinsic Notch activity fine tunes timing of early to late temporal transitions and is important to schedule NB termination at the end of development.

The study adds another layer of regulation that finetunes temporal progression in Drosophila neural stem cells. This mechanism appears to be mainly lineage intrinsic - Delta being expressed from NBs and their progeny, but also partly niche-mediated - Delta being also expressed in glia but with a minor influence. Together with a recent study (PMID: 36040415), this work suggests that Notch signaling is a key player in promoting temporal progression in various temporal patterning system. As such it is of broad interest for the neuro-developmental community.

Strengths

The data are based on genetic experiments which are clearly described and mostly convincing. The study is interesting, adding another layer of regulation that finetunes temporal progression in Drosophila neural stem cells. This mechanism appears to be mainly lineage intrinsic - Delta being expressed from NBs and their progeny, but also partly niche-mediated - Delta being also expressed in glia but with a minor influence. A similar mechanism has been recently described, although in a different temporal patterning system (medulla neuroblasts of the optic lobe - PMID: 36040415). It is overall of broad interest for the neuro-developmental community.

Weaknesses

The mechanisms by which Notch signaling regulates temporal patterning progression are not investigated in details. For example, it is not clear whether Notch signaling directly regulates temporal patterning genes, or whether the phenotypes observed are indirect (for example through the regulation of the cell-cycle speed). The authors could have investigated whether temporal patterning genes are directly regulated by the Notch pathway via ChIP-seq of Su(H) or the identification of potential binding sites for Su(H) in enhancers.

This is already known for svp and cas and we have now included this information in the discussion.Thank you.

“Whether Notch pathway activity curtails both Cas and Svp or just Cas remains an open question, however it has been reported that both cas and svp are associated with at least one enhancer that is responsive to Notch activity (Zacharioudaki et al., 2016).”

A similar approach has been recently undertaken by the lab of Dr Xin Li, to show that Notch signaling regulates sequential expression of temporal patterning factors in optic lobes neuroblasts (PMID: 36040415), which exhibit a different temporal patterning system than central brain neuroblasts in the present study. As such, the mechanistic insights of the study are limited.

Reviewer #1 (Recommendations For The Authors):

1) There are missing controls

a) Fig. 1F and Fig. 6A - The authors should generate and show images of control clones (FRT19A) stained with the same markers as Notch clones.

Fig. 1F is at 48 hours APF. In control clones, there are no Dpn positive cells present, as stated in the text and therefore no confocal images are shown. Same for Fig. 6A, there are no Dpn positive cells in control clones in the brain at this time, therefore nothing to double label.

2) This result is incorrectly described in the Results

a) P. 5 "Ectopically persisting N RNAi CB NBs expressed the NB transcription factor Deadpan (Dpn), the S-phase indicator pcnaGFP, and were small on average, similar in size to control CB NBs at earlier pupal stages (Fig. 1B,C,E)." The Notch RNAi NBs were larger (not smaller) than controls in Fig. 1E at 30, 48, 72 h APF and in adults.

Thank you for this comment. We have changed the language in the main text as follows:

“Ectopically persisting N RNAi CB NBs (CB NBs at 48 hours APF and beyond) expressed the NB transcription factor Deadpan (Dpn), the S-phase indicator pcnaGFP, and were small on average compared to control CB NBs during earlier developmental stages (L3 control, average diameter 10-15μms) (Fig. 1B,C,E). However, at 30 hours APF when control CB NBs are still present, N RNAi CB NBs were larger on average (Fig. 1B,C,E).”

3) This sentence needs clarification/editing

a) P. 4: " Independent of neurogenesis timing and the mechanism by which CB NB stop divisions, temporal patterning plays a key role". A key role in what?

Thank you again. We have changed the text to the following:

“Independent of neurogenesis timing and the mechanism by which CB NB stop divisions, temporal patterning plays a key role in controlling numbers and types of neurons made within each of the NB lineages (Maurange et al., 2008; Tsuji et al., 2008; Bahrampour et al., 2017; Yang et al., 2017; Pahl et al., 2019).”

4) Some sentences need references or data to support them.

a) P. 9 Please provide a reference to support the statement that Delta is a known Notch target

We have included a reference.

b) P. 9 - please provide a reference or data to support the statement that Delta transcripts decrease over time in larval CB NBs.

This result is shown in Fig. 7B.

5) Fig. 7A - it is difficult to appreciate the purple highlighting.

We have changed the colors as suggested.

Reviewer #2 (Recommendations For The Authors):

1) In Fig. 4C, why does late knockdown of delta lead to ectopic persistence of NBs but late knockdown of Notch has no effect?

This could be due to many things including differences in efficiency of UAS-RNAi lines. The point is that Delta/Notch is required early, but not late. Although some DeltaRNAi CB NBs are still present, the number compared to 48 hours APF is greatly reduced.

2) It is surprising that Delta expression in NBs/GMCs appears to play a more important role in activating Notch signaling in neuroblasts than Delta expression in cortex glia. Please explain how Delta can cell autonomously activate Notch signaling.

We are not proposing that Delta activates Notch cell autonomously, but are proposing that Delta in GMCs transactivates Notch in NBs. After NBs divide Delta is partitioned to GMCs. Quiescent NBs have low to no Notch pathway activity, likely because they are not producing Delta expressing GMC daughters (Sood, 2022).

Please also reconcile the difference in gene expression induced by delta[RNAi] in this study and the delta-mutant allele used in the Zacharioudaki et al study.

We are unsure what the reviewer is asking here and therefore can not reconcile any differences in gene expression between the dlRNAi line and the mutant allele. What gene expression needs to be reconciled? Zacharioudaki is listed as first author on four manuscripts. Which paper is being referred to?

3) In Fig. 2J-L, why does knocking down delta in glia lead to loss of Scrib expression in neuroblasts and their surrounding progeny?

We are not sure if it does or not. We only use Scrib as a membrane marker to identify and locate cells and neuropil regions of interest.

4) The phrase "Notch is active early" is misleading when multiple labs have shown that Notch signaling is active in neuroblasts throughout larval development.

Good point! We have rewritten the statement: “Somewhat paradoxically, we find that early Notch activity is required to terminate CB NB divisions late.”

5) Neuroblasts that persist into adulthood are "smaller and Dpn-positive/PCNA-GFP-positive". Are they really neuroblasts? Can the authors verify the identity of these "persistent neuroblasts" with other molecular markers as well as functional assessment by inducing lineage clones?

We have no doubt that these cells are NBs. Because we examine brains over time, these cells can be tracked using the markers, Scrib, Dpn, and pcna. These cells also undergo asymmetric cell division (Refer to Fig. S2F) and express other markers characteristic of CB NBs (mir and insc-not shown). We have made clones and see the same phenotype (ectopic persistence) in both MARCM clones and in “flip-out” clones.

Reviewer #3 (Recommendations For The Authors):

I have a few issues that need to be addressed to reinforce some of the conclusions:

1) It is unclear whether NBs that persist in late pupal or adult stages have just failed to differentiate or whether they continue to divide, leading to supernumerary progeny (as shown for NBs that are stalled in temporal patterning like in svp mutant NBs (Maurange et al. 2008)). EdU or PH3 staining could be done in adults to clarify this point.

In this manuscript, we make use of pcna:GFP, a reporter for E2F activity as an indicator of cell proliferation. We certainly observe Dpn positive cells that only weakly express the reporter, suggesting that these cells are not actively dividing or dividing at a reduced rate. However, by far most of the ectopically persisting CB NBs strongly express the reporter and generate pcnaGFP expressing progeny, indicating that these cells are dividing. We have also stained tissues with PH3 and have included an image of a telophase dlRNAi expressing CB NB at 48 hours APF (Fig. S2F).

2) It is unclear whether Notch signaling directly or indirectly regulates temporal transitions. One possibility is that knockdown of Notch signaling decreases cell-cycle speed leading to delayed temporal transitions. The authors should test whether Notch KD affects cell cycle speed using EdU incorporation or PH3 staining. This could be done best using Notch mutant MARCM clones as wt NBs can be used as controls.

We have quantified the number of PH3 positive CB NBs during wandering L3 stages in control and dlRNAi animals. We find that dlRNAi CB NBs are indeed proliferating at reduced rates compared to controls. To test whether reduced cell cycle times are causative for termination delay, we expressed a constitutively active form of PI3-kinase in dlRNAi animals to drive cell growth and proliferation. We found that CB NBs still ectopically persist (Fig. S2E-G).

We have included the following in the text:

“Defects in timing of temporal transitions could be due to defects in cell cycle progression, although embryonic NBs still transition independent of cell division (Grosskortenhaus et al., 2005). We used PH3 to assay CB NB mitotic activity. In Delta knock down animals, the percentage of PH3 positive CB NBs was reduced compared to control (Fig. S2E). At 48 h APF however, Delta knock down CB NBs were still dividing based on PH3 expression (Fig. S2F). To determine whether CB NBs ectopically persist due to defects in cell cycle rate, we co-expressed dp110 to constitutively activate PI3-kinase in Delta knock down animals. A significant number of pcnaGFP expressing, Dpn positive CB NBs were still observed, suggesting that defects in cell cycle timing and growth rates alone cannot account for ectopic persistence of CB NBs into later developmental stages and adulthood (Fig. S2G).”

3) Cas is expressed in NBs either during quiescence and shortly after quiescence. It is possible that the maintenance of Cas in Figure 5D, E is due to NBs that have not re-entered the cell-cycle or have exited quiescence with a strong delay.

Knockdown of Notch pathway has no effect on CB NB reactivation from developmental quiescence. In fact, low levels of Notch are required for CB NBs to reactivate in response to dietary nutrients (Sood, 2022).

Indeed, the authors have previously shown that Notch signaling is important for NB cell cycle reentry during early larval stages (PMID: 35112131). Are Cas and Svp also maintained in late larval N-/MARCM clones (MARCM clonew are made after quiescence exit)?

We have not assayed Cas or Svp expression past 48 hours ALH.

4) The authors have revisited some previously published RNA-seq data showing that Delta is temporally regulated in NB lineages. This is not clearly shown by the authors that the same is true at the protein level.

Moreover, they find that mis-expression of late temporal factors or Imp knockdown in early larval brains appear to decrease Delta expression. Such semi-quantitative analysis of gene expression by immunostainings in different conditions can be a bit complicated and not very convincing because variations on intensity levels can be due to slight variations in antibody concentration, or different parameters of image acquisition.

We totally agree, but in this case the difference compared to controls was so readily apparent, that we felt it was not necessary to carry out experiments in clones. All images were acquired with the same confocal settings, experiments were repeated, and we consistently observed the same results. The data shown in Fig. 7D-G is representative.

I suggest that the authors use clonal analysis rather than pan-neuroblast manipulation in order to have internal controls. For example, blocking temporal progression in Syp-RNAi clones (MARCM or Flp-out) and/or svp MARCM clones should lead to maintenance of Imp expression in late larval clones and maintenance of high levels of Delta, which would be easily assessed compared to surrounding NBs.

Minor points:

Fig 5: the sequential expression of Cas and Svp expression in larval NBs was first described by Maurange et al. 2008. Please cite appropriately.

We have now added the requested citation to the following:

“Over time, the percentage of Cas expressing CB NBs declined, while Svp expressing CB NBs modestly increased (Fig. 5B). Less than 1% of CB NBs co-expressed Cas and Svp at any stage and expression of both factors was absent by 48 hours ALH (Fig. 5B,C). This is consistent with work published previously (Isshiki et al., 2001; Tsuji et al., 2008; Chai et al., 2013; Maurange et al., 2008; Ren et al., 2017; Syed et al., 2017).”

Fig 6A: Please indicate which immunostainings are shown in the overlay panels.

Good catch! We have modified the figure.

P9: "Delta co-immunoprecipitated with Imp.": Add "Delta mRNA co-immunoprecipitated with Imp in RIP-seq experiments" Otherwise, it suggests that you are talking about the protein.

Done

The scheme in Figure 7H is rather complicated to understand. In my opinion, it does not clearly convey the idea that Notch signaling favors the Imp-to-Syp transition.

We have made a new model figure.

Reviewer #3 (Public Review):

In this study, the authors investigate the effects of Notch pathway inactivation on the termination of Drosophila neuroblasts at the end of development. They find that termination is delayed, while temporal patterning progression is slowed down. Forcing temporal patterning progression in a Notch pathway mutant restores correct timing of neuroblast elimination. Finally they show that Imp, an early temporal patterning factor promotes Delta expression in neuroblast lineages. This indicates that feedback loops between temporal patterning and lineage-intrinsic Notch activity fine tunes timing of early to late temporal transitions and is important to schedule NB termination at the end of development.

The study adds another layer of regulation that finetunes temporal progression in Drosophila neural stem cells. This mechanism appears to be mainly lineage intrinsic - Delta being expressed from NBs and their progeny, but also partly niche-mediated - Delta being also expressed in glia but with a minor influence. Together with a recent study (PMID: 36040415), this work suggests that Notch signaling is a key player in promoting temporal progression in various temporal patterning system. As such it is of broad interest for the neuro-developmental community.

Strengths<br /> The data are based on genetic experiments which are clearly described and mostly convincing. The study is interesting, adding another layer of regulation that finetunes temporal progression in Drosophila neural stem cells. This mechanism appears to be mainly lineage intrinsic - Delta being expressed from NBs and their progeny, but also partly niche-mediated - Delta being also expressed in glia but with a minor influence. A similar mechanism has been recently described, although in a different temporal patterning system (medulla neuroblasts of the optic lobe - PMID: 36040415). It is overall of broad interest for the neuro-developmental community.

Weaknesses<br /> The mechanisms by which Notch signaling regulates temporal patterning progression are not investigated in details. For example, it is not clear whether Notch signaling directly regulates temporal patterning genes, or whether the phenotypes observed are indirect (for example through the regulation of the cell-cycle speed). The authors could have investigated whether temporal patterning genes are directly regulated by the Notch pathway via ChIP-seq of Su(H) or the identification of potential binding sites for Su(H) in enhancers. A similar approach has been recently undertaken by the lab of Dr Xin Li, to show that Notch signaling regulates sequential expression of temporal patterning factors in optic lobes neuroblasts (PMID: 36040415), which exhibit a different temporal patterning system than central brain neuroblasts in the present study. As such, the mechanistic insights of the study are limited.

eLife assessment

This useful study reports on how Notch activity regulates the termination of neurogenesis in central brain during larval-pupal stages in Drosophila. The evidence supporting the claims is solid. The work will be of interest to developmental neurobiologists.

Reviewer #1 (Public Review):

In this manuscript, the authors are building on their previous work showing Delta-Notch regulates the entrance and exit from embryo-larval quiescence of neural stem cells of the central brain (called CB neuroblasts (NB) (PMID: 35112131)). Here they show that continuous depletion of Notch in NBs from early embryogenesis leads to cycling NBs in the adult. This - cycling NBs in the adult - is not seen in controls. The assumption here is that these Notch-RNAi NBs in adults are those that did not undergo terminal differentiation in pupal development. The authors show that Notch is activated by its ligand Delta which is expressed on the GMC daughter cell and on cortex glia. They determine that the temporal requirement for Notch activity is 0-72 hours after larval hatching (ALH) (i.e., 1st instar through mid-3rd instar at 25C). In NBs/GMCs depleted for Notch, early temporal markers were still expressed at time points when they should be off and late markers were delayed in expression. These effects were observed in ~20-40% of NBs (Figures 5 and 6). Through mining existing data sets, they found that the early temporal factor Imp - an RNA binding protein - can bind Delta mRNA. They show that Delta transcripts decrease over time, leading to the hypothesis that Delta mRNA is repressed by the late temporal factors. Over-expressing late factors Syp or E93 earlier in development leads to downregulation of a Delta::GFP protein trap. These results lead to a model in which Notch regulates expression of early temporal factors and early temporal factors regulate Notch activity through translation of Delta mRNA.

There are several strengths of this study and no major weaknesses. The authors report rigorous measurements and statistical analyses throughout the study. Their conclusions are appropriate for the results. Data mining revealed an important mechanism - that Imp binds Delta mRNA - supporting the model that that early temporal factors promote Delta expression, which in turn promotes Notch signaling.

An appraisal: The authors use temperature shifts with Gal80TS to show that Notch is required between 0-72 hours ALH. They show with the use of known markers of the temporal factors and Delta protein trap, that Imp promotes Delta protein expression and the later temporal factors reduce Delta, although the molecular mechanisms are not clearly delineated. Overall, these data support their model that the reduction of Delta expression during larval development leads to a loss of Notch activity.

As noted in the Discussion, this study raises many questions about what Notch does in larval CB NBs. For example, does it inhibit Castor or Imp? Is Notch required in certain neural lineages and not others. These studies will be of interest in the community of developmental neurobiologists.

Reviewer #2 (Public Review):

As I indicated in the initial review, the experiments are well conceived and executed, and the data are clear. I also agree with the authors that this work represents a key first step toward understanding how Notch signaling contributes to temporal control of fly neuroblasts. It is my opinion that the authors fall short of demonstrating how Notch signaling and temporal identity genes at the chromatin levels. I find this disappointing given the availability of various tools for looking at dynamic regulation of gene activity at high resolution. Given these weaknesses, my opinion is that the study is descriptive and lacks mechanistic explanation.

Author Response

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

Reviewer #1 (Public Review):

Several concerns are raised from the current study.

1) Previous studies showed that iTregs generated in vitro from culturing naïve T cells with TGF-b are intrinsically unstable and prone to losing Foxp3 expression due to lack of DNA demethylation in the enhancer region of the Foxp3 locus (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). It is known that removing TGF-b from the culture media leads to rapid loss of Foxp3 expression. In the current study, TGF-b was not added to the media during iTreg restimulation, therefore, the primary cause for iTreg instability should be the lack of the positive signal provided by TGF-b. NFAT signal is secondary at best in this culturing condition.

In restimulation, void of TGFb is necessary to cause iTreg instability. Otherwise, the setup is similar to the iTreg-inducing environment (Author response image 1). On the other hand, the ultimate goal of this study is to provide a scenario that bears some resemblance of clinical treatment, where TGFb may not be available. The reviewer is correct in stating that TGFb is essential for iTreg stability, we are studying the role played by NFAT in iTreg instability in vitro, and possibly in potential clinical use of iTreg .

Author response image 1.

Restimulation with TGFb will persist iTreg inducing environment, resulting in less pronounced instability. Sorted Foxp3-GFP+ iTregs were rested for 1d, and then rested or restimulated in the presence of TGF-β for 2 d. Percentages of Foxp3+ cells were analyzed by intracellular staining of Foxp3 after 2 d.

2) It is not clear whether the NFAT pathway is unique in accelerating the loss of Foxp3 expression upon iTreg restimulation. It is also possible that enhancing T cell activation in general could promote iTreg instability. The authors could explore blocking T cell activation by inhibiting other critical pathways, such as NF-kb and c-Jun/c-Fos, to see if a similar effect could be achieved compared to CsA treatment.

We thank the reviewer for this suggestion. We performed this experiment according to see extent of the role that NFAT plays, or whether other major pathways are involved. As Author response image 2 shows, solely inhibiting NFAT effectively rescued the instability of iTreg. The inhibition of NFkB (BAY 11-7082), c-Jun (SP600125), or a c-Jun/c-Fos complex (T5224) had no discernable effect, or in one case, possibly further reduction in stability. These results may indicate that NFAT plays a crucial and special role in TCR activation, which leads to iTreg instability. Other pathways, as far as how this experiment is designed, do not appear to be significantly involved.

Author response image 2.

Comparing effects of NFAT, NF-kB and c-Jun/c-Fos inhibitors on iTreg instability. Sorted Foxp3-GFP+ iTregs were rested for 1d, then restimulated by anti-CD3 and CD28 in the presence of listed inhibitors. Percentages of Foxp3+ cells were analyzed by intracellular staining after 2d restimulation.

3) The authors linked chromatin accessibility and increased expression of T helper cell genes to the loss of Foxp3 expression and iTreg instability. However, it is not clear how the former can lead to the latter. It is also not clear whether NFAT binds directly to the Foxp3 locus in the restimulated iTregs and inhibits Foxp3 expression.

T helper gene activation is likely to cause instability in iTregs by secreting more inflammatory cytokines, as shown in Figure Q9, for example, IL-21 secretion. Further investigation is needed to understand how these genes contribute to Foxp3 gene instability exactly. With our limited insight, there may be two possibilities. 1. IL-21 directly affects Foxp3 through its impact on certain inflammation-related transcription factors (TFs). 2. There could be an indirect relationship where NFAT has a greater tendency to bind to those inflammatory TFs when iTreg instability appears, promoting the upregulation of these Th genes like in activated T cells, while being less likely to bind to SMAD and Foxp3, representing a competitive behavior. We at the moment cannot comprehend the intricacies that lead to the differential effects on T helper genes and Treg related genes.

With that said, we have previously attempted to explore the direct effect of NFAT on Foxp3 gene locus. Foxp3 transcription in iTregs primarily relies on histone modifications such as H3K4me3 (Tone et al., 2008; Lu et al., 2011) rather than DNA demethylation (Ohkura et al., 2012; Hilbrands et al., 2016). Previous studies have reported that NFAT and SMAD3 can together promote the histone acetylation of Foxp3 genes (Tone et al., 2008). In our previous set of experiments, we simultaneously obtained information of NFAT binding sites and H3K4me3. In Foxp3 locus, we observed a decreasing trend in NFAT binding to the CNS3 region of Foxp3 in restimulated iTregs compared to resting iTregs (Author response image 3). Additionally, the H3K4me3 modification in the CNS3 region of Foxp3 decreased upon iTreg restimulation, but inhibiting NFAT nuclear translocation with CsA could maintain this modification at its original level (Author response image 3).

Author response image 3.

The NFAT binding and histone modification on Foxp3 gene locus. Genome track visualization of NFAT binding profiles and H3K4me3 profiles in Foxp3 CNS3 locus in two batches of dataset.

Based on these preliminary explorations, it is concluded that NFAT can directly bind to the Foxp3 locus, and it appears that NFAT decreases upon restimulation, resulting in a decrease in H3K4me3, ultimately leading to the close association of NFAT and Foxp3 instability. However, due to limited sample replicates, these data need to be verified for more solid conclusions. We speculate that during the induction of iTregs, NFAT may recruit histone-modifying enzymes to open the Foxp3 CNS3 region, and this effect is synergistic with SMAD. When instability occurs upon restimulation, NFAT binding to Foxp3 weakens due to the absence of SMAD's assistance, subsequently reducing the recruitment of histone modifications enzyme and ultimately inhibiting Foxp3 transcription.

Reviewer #2 (Public Review):

(1) Some concerns about data processing and statistic analysis.

The authors did not provide sufficient information on statistical data analysis; e.g. lack of detailed descriptions about

-the precise numbers of technical/biological replicates of each experiment

-the method of how the authors analyze data of multiple comparisons... Student t-test alone is generally insufficient to compare multiple groups; e.g. figure 1.

These inappropriate data handlings are ruining the evidence level of the precious findings.

We thank the reviewer for pointing out this important aspect. In the figure legend, numbers of independently-performed experiment repeats are shown as N, biological replicates of each experiment as n. Student’s t test was used for comparing statistical significance between two groups. In this manuscript, all calculations of significant differences were based on comparisons between two groups. There were no multiple conditions compared simultaneously within a single group, and thus, no other calculation methods were used.

(2) Untransparent data production; e.g. the method of Motif enrichment analysis was not provided. Thus, we should wait for the author's correction to fully evaluate the significance and reliability of the present study.

Per this reviewer’s request, we have provided detailed descriptions of the data analysis for Fig 5, including both the method section and the Figure legend, as presented below:

“The peaks annotations were performed with the “annotatePeak” function in the R package ChIPseeker (Yu et al, 2015).

The plot of Cut&Tag signals over a set of genomic regions were calculated by using “computeMatrix” function in deepTools and plotted by using “plotHeatmap” and “plotProfile” functions in deepTools. The motif enrichment analysis was performed by using the "findMotifsGenome.pl" command in HOMER with default parameters.

The motif occurrences in each peak were identified by using FIMO (MEME suite v5.0.4) with the following settings: a first-order Markov background model, a P value cutoff of 10-4, and PWMs from the mouse HOCOMOCO motif database (v11).”

Additionally, we have also supplemented the method section with further details on the analysis of RNA-seq and ATAC-seq data.

(3) Lack of evidence in human cells. I wonder whether human PBMC-derived iTreg cells are similarly regulated.

This is a rather complicated issue, human T cells express FoxP3 upon TCR stimulation (PNAS, 103(17): 6659–6664), whose function is likely to protect T cells from activation induced cell death, and does not offer Treg like properties. In contrast in mice, FoxP3 can be used as an indicator of Treg. Currently, this is not a definitive marker for Treg in human, our FoxP3 based readouts do not apply. Nevertheless, we have now investigated whether inhibiting calcium signaling or NFAT could enhance the stability of human iTreg. As shown in Author response image 4, we found that the proportion of Foxp3-expressing cells did not show significant changes across the different conditions, while the MFI analysis revealed that CsA-treated iTreg exhibited higher Foxp3 expression levels compared to both restimulated iTreg and rest iTreg. However, CM4620 had no significant effect on Foxp3 stability, consistent with the observation of its limited efficacy in suppressing human iTreg long term activation. In summary, our results suggest that inhibiting NFAT signaling through CsA treatment can help maintain higher levels of Foxp3 expression in human iTreg.

Author response image 4.

Effect of inhibiting NFAT and calcium on human iTreg stability. Human naïve CD4 cells from PBMC were subjected to a two-week induction process to generate human iTreg. Subsequently, human iTreg were restimulated for 2 days with dynabeads followed by 2 days of rest in the prescence of CsA and CM-4620. Four days later, percentages of Foxp3+ cells and Foxp3 mean fluorescence intensity (MFI) were analyzed by intracellular staining.

(4) NFAT regulation did not explain all of the differences between iTregs and nTregs, as the authors mentioned as a limitation. Also, it is still an open question whether NFAT can directly modulate the chromatin configuration on the effector-type gene loci, or whether NFAT exploits pre-existing open chromatin due to the incomplete conversion of Treg-type chromatin landscape in iTreg cells. The authors did not fully demonstrate that the distinct pattern of chromatin regional accessibility found in iTreg cells is the direct cause of an effector-type gene expression.

To our surprise, the inhibition of NFkB (BAY 11-7082), c-Jun (SP600125), and the c-Jun/c-Fos complex (T5224) resulted in minimal alterations, as shown in Fig Q1. This seems to argue that NFAT may play a more special role in events leading iTreg instability.

We hypothesize that NFAT takes advantage of pre-existing open chromatin state due to the incomplete conversion of chromatin landscape in iTreg cells. Because iTreg cells, after induction, already exhibit inherent chromatin instability, with highly-open inflammatory genes. Furthermore, when iTreg cells were restimulated, the subsequent change in chromatin accessibility was relatively limited and not rescued by NFAT inhibitor treatment (Author response image 5). Therefore, in the case of iTreg cells, we propose that NFAT exploits the easy access of those inflammatory genes, leading to rapid destabilization of iTreg cells in the short term.

In contrast, tTreg cells possess a relatively stable chromatin structure in the beginning, it would be interesting to investigate whether NFAT or calcium signaling could disrupt chromatin accessibility during the activation or expansion of tTreg cells. It is possible that NFAT might cause the loss of the originally established demethylation map and open up inflammatory loci, thereby inducing a shift in gene transcriptional profiles, equally leading to instability.

Author response image 5.

Chromatin accessibility of Rest, Retimulated, CsA/ORAIinh treated restimulated iTreg. PCA visualization of chromatin accessibility profiles of different cell types. Color indicates cell type.

To establish a direct relationship between gene locus accessibility and its overexpression, a controlled experimental approach can be employed. One such method involves precise manipulation of the accessibility of a specific genomic locus using CRISPR-mediated epigenetic modifications at targeted loci. Subsequently, the impact of this manipulation on the expression level of the target gene can be precisely examined. By conducting these experiments, it will be possible to determine whether the augmented gene accessibility directly causes the observed gene overexpression.

Reviewer #1 (Recommendations For The Authors):

1) It might be helpful to add TGF-b to the iTreg restimulation culture to remove the influence of the lack of TGF-b from the equation, and measure the influence of SOCE/NFAT on iTreg instability.

Please refer to Author response image 1.

2) Alternatively, authors can also culture iTreg cells with TGF-b for 2 weeks when they undergo epigenetic changes and become more stabilized (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). At this point, the stabilized iTregs can be used to measure the influence of SOCE/NFAT on iTreg instability.

In the study conducted by Polansky, it was observed in Figure 1 that prolonged exposure to TGF-β fails to induce stable Foxp3 expression and demethylation of the Treg-specific demethylated region (TSDR). Based on this finding, we could consider exploring alternative approaches to obtain a more stabilized iTreg population. One such approach could be isolating Foxp3+helios-Nrp1- iTreg cells directly from the peripheral in vivo, which are also known as pTregs. Generally, pTreg cells generated in vivo tend to be more stable compared to iTreg cells induced in vitro, and they already exhibit partial demethylation of the Treg signature, as shown in Fig 6C (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). Investigating the role of NFAT and calcium signaling in pTreg cells would provide further insights into the additional roles of NFAT in Treg phenotypical transitions, particularly its role in chromatin accessibility.

3) In Figure 3, NFAT binding to the inflammatory genes in iTreg cells was even stronger than in activated T conventional cells. This is possibly due to Tconv cells being stimulated only once while iTregs were restimulated. A fair comparison should be conducted with restimulated activated conventional T cells.

Figure 3 demonstrates the accessibility of inflammatory gene loci, rather than NFAT binding. Comparing restimulated Tconvs with restimulated iTreg cells is indeed a valuable suggestion, as their activation state and polarization in iTreg directions could lead to distinct chromatin accessibility. Although one is activated long term regularly and the other is activated long term under iTreg polarization, it is highly likely that the chromatin state of both activated Tconvs and iTreg cells is highly open, especially in terms of the accessibility of inflammatory genes. This may provide us with a new perspective to understand iTreg cells, but will unlikely affect our central conclusion.

4) In the in vivo experiment in Figure 6, a control condition without OVA immunization should be included as a baseline.

We have performed this experiment in the absence of OVA, as depicted in Author response image 6. In the absence of OVA immunization, both WT-ORAI and DN-ORAI iTreg exhibited substantial stability, although DN-ORAI demonstrated a slightly less stable trend. Upon activation with 40ug and 100ug of OVA, DN-ORAI iTreg demonstrated enhanced stability than WT-ORAI iTreg, maintaining a higher proportion of Foxp3 expression.

Author response image 6.

Stability of DN-ORAI iTreg in vivo with or without OVA immunization. WT-ORAI/DN-ORAI-GFP+-transfected CD45.2+ Foxp3-RFP+ OT-II iTregs were transferred i.v. into CD45.1 mice. Recipients were left or immunized with OVA323-339 in Alum adjuvant. On day 5, mLN were harvested and analyzed for Foxp3 expression by intracellular staining.

Reviewer #2 (Recommendations For The Authors):

Major

Some concerns about the data processing and statistic analysis, as mentioned in the public review. In the figure legend, what does it mean e.g. n=3, N=3? Technical triplicate experiments? Three mice? Independently-performed three experiments? The authors should define it at least in the "Statistical analysis" in the method section otherwise the readers cannot determine the reason why they mainly use SEM for the data description.

Moreover, in some cases, the number of experiments was not sure; e.g., Fig.1B, Fig. 5.

How did the authors analyze data including multiple comparisons? Student t-test alone is generally insufficient to compare multiple groups; e.g. figure 1.

We thank the reviewer for pointing out this omission. Now, in the figure legend, numbers of independently-performed experiment repeats are shown as N, biological replicates of each experiment as n. For Fig. 1B, N=2, and for Fig 5, we have acquired NFAT Cut&Tag data for 2 times, N=2. Student’s t test was used for comparing statistical significance between two groups. In this manuscript, all calculations of significant differences were based on comparisons between two groups. There were no multiple conditions compared simultaneously within a single group, and thus, no other calculation methods were involved apart from the Student's t-test.

In Figure 1A, the difference in suppressiveness seemed subtle. Data collection of multiple doses of Tconv:Treg ratio will enhance the reliability of such kind of analysis.

We have now attempted the suppression assay with varying Treg:Tconv ratios and observed that the suppressive effect of iTreg was more obvious than that of tTreg when co-cultured at a 1:1 ratio with Tconv cells. However, as the cell number of tTreg and iTreg decreased, the inhibitory effects converged.

Author response image 7.

Compare multiple dose of Tconv:Treg ratio in suppression function CFSE-labelled OT-II T cells were stimulated with OVA-pulsed DC, then different number of Foxp3-GFP+ iTregs and tTregs were added to the culture to suppress the OT-II proliferation. After 4 days, CFSE dilution were analyzed. Left, Representative histograms of CFSE in divided Tconvs. Right, graph for the percentage of divided Tconvs.

In Figure 3F, to which group did the shaded peaks belong? In this context, the authors should focus on "Activation Region" peaks (open chromatin signature in both TcAct & iTreg defined in Fig. 4D) but I did not find the peak in the focusing DNA regions in TcAct (e.g. the shaded regions in IL-4 loci). The clear attribution of the peaks to the heatmap will enhance the visibility and understanding of readers.

We have selected some typical peaks that belong to Fig 3D. These genes encompass some T-cell activation-associated transcription factors, such as Irf4, Atf3, as well as multiple members of the Tnf family including Lta, Tnfsf4, Tnfsf8, and Tnfsf14. Additionally, genes related to inflammation such as Il12rb2, Il9, and Gzmc are included. These genes show elevated accessibility upon T-cell activation, partially open in activated nTreg cells, referred to as the "Activation Region." They collectively exhibit high accessibility in iTreg cells, which may contribute to their instability.

Author response image 8.

Chromatin accessibility of some “Activation Region”. Genomic track showing chromatin accessibility of Irf4, Atf3, Lta, Tnfsf8, Tnfsf4, Tnsfsf14, Il12rb2, Il9, Gzmc in activated Tconv and iTreg.

In Figure 4A/S4A, the information on cell death will help the understanding of readers because the sustained SOCE is associated with cell survival as shown in Fig. S2. The authors can discuss the relationships between cell death and Foxp3 retention, which potentially leads to a further interesting question; e.g. the selective/resistance to activation-induced cell death as the identity of Treg cells.

As shown in Author response image 9, activated iTreg cells indeed exhibit a certain degree of cell death compared to resting iTreg cells. The inhibition of NFAT by CsA enhances the survival rate of iTreg cells, but the inhibition of ORAI by CM-4620 leads to more severe cell death. The cell death induced by CsA and CM-4620 is not consistent, indicating that there may not be a direct proportional relationship between cell death and the expression of Foxp3 and Treg identity.

Author response image 9.

Relationship of cell death and Foxp3 stability in restimulated iTregs.<br /> Sorted Foxp3-GFP+ iTregs were rested for 1d, then restimulated by anti-CD3 and CD28 in the presence of CsA or CM-4620. After 2d restimulation, live cell percentage were analyzed by staining of Live/Dead fixable Aqua, and percentages of Foxp3+ cells were analyzed by intracellular staining of Foxp3. Upper, live cell percentage of iTregs. Lower, percentages of Foxp3 in iTregs.

In Figure 5, the information for the data interpretation was insufficient.

We have provided detailed descriptions of the data analysis for Fig 5, including both the method section and the Figure legend, as presented below:

“The peaks annotations were performed with the “annotatePeak” function in the R package ChIPseeker (Yu et al, 2015). The plot of Cut&Tag signals over a set of genomic regions were calculated by using “computeMatrix” function in deepTools and plotted by using “plotHeatmap” and “plotProfile” functions in deepTools. The motif enrichment analysis was performed by using the "findMotifsGenome.pl" command in HOMER with default parameters. The motif occurrences in each peak were identified by using FIMO (MEME suite v5.0.4) with the following settings: a first-order Markov background model, a P value cutoff of 10-4, and PWMs from the mouse HOCOMOCO motif database (v11).”

Additionally, we have also supplemented the method section with further details on the analysis of RNA-seq and ATAC-seq data.

The correlation between the open chromatin status of the gene loci described in Fig.5E and the expression at mRNA level? e.g.; Do iTreg-Act cells produce a higher level of IL-21 than nTreg-act? The analysis in Fig.5F-G should be performed in parallel with nTreg cells to emphasize the distinct NFAT-chromatin regulation in iTreg cells.

We have now compared the secretion levels of IL-21 in tTreg and iTreg upon activation and treated with CsA by ELISA. As shown in Author response image 10, tTreg did not secrete IL-21 regardless of activation status (undetectable), while iTreg did not secrete IL-21 at resting state but exhibited IL-21 secretion after 48 h of activation. Moreover, the secretion of IL-21 was inhibited by CsA and CM-4620 treatment. This observation aligns with our earlier findings where we observed nuclear binding of NFAT to gene loci of these cytokines, enhancing their expression and pushing iTreg unstable under inflammatory conditions. These findings further underscore the likelihood that the inhibition of calcium and NFAT signaling might contribute to the stabilization of iTreg by suppressing the secretion of inflammatory cytokines.

Author response image 10.

IL-21 secretion in tTreg and iTreg upon activation.<br /> iTregs and tTregs were sorted and restimulated with anti-CD3 and anti-CD28 antibodies, in the presence of CsA and CM-4620. Cell culture supernatant were harvested after 2 d restimulation and IL-21 secretion was analyzed by ELISA.

Performing a parallel comparison of NFAT activity between tTreg and iTreg cells was initially part of our experimental plan. However, it proved challenging in practice, as we encountered difficulties in efficiently infecting tTreg cells with NFAT-flag. Consequently, we could not obtain a sufficient number of tTreg cells for conducting Cut&Tag experiments.

Based on our observations, we speculate that there might be substantial differences in the accessibility of genes in tTreg cells, leading to considerable variations in the repertoire of genes available for NFAT to regulate. As a result, we expect significant differences in the nuclear localization and activity of NFAT between iTreg and tTreg cells.

In Figure 6C, what does the FCM plot between Foxp3-CFSE look like?

The authors can discuss the mechanism of ORAI-DN-mediated through such analysis; e.g. the possibility that selective proliferation defect by ORAI-DN in Foxp3- cells led to an increased percentage of Foxp3, not only just unstable transcription of Foxp3.

This is an in vitro experiment to assess the suppressive effect of iTreg on Tconv proliferation. Therefore, CFSE is used to stain Tconv cells, but not iTreg cells, so we did not detect proliferation feature of iTreg.

Minor

Confusing terminology of "tTreg" at line 47, etc. "natural Treg" contains both thymic-derived Treg and periphery-derived Treg cells. (A Abbas et al. Nat Immunol. 2013)

We have now changed the designation to tTreg at line 47. tTreg refers to thymus-derived regulatory T cells, while nTreg includes both tTreg and pTreg. However, it is important to note that the Treg cells used in our study were isolated from the spleen of 2-4-month-old Foxp3-GFP or Foxp3-RFP mice. The CD4+ T cells were first enriched using the CD4 Isolation kit, and the FACSAriaII was utilized to collect CD4+ Foxp3-GFP/RFP+ Treg cells. Subsequently, Helios and Nrp-1 staining revealed that the majority of these cells were nTreg, with only approximately 6% being pTreg. Overall, we consider the cells we used as tTreg.

In all FCM analyses, the authors should clarify how to detect Foxp3 expression; Foxp3-GFP/Foxp3-RFP/Intracellular staining like Figure S5A (but not specified in the other FCM plots)

All Foxp3 expressions in the article were assessed using intracellular staining, as described in the methods section, and we have added specific descriptions to each figure legend. The reason for employing intracellular staining is that we used Foxp3-IRES-GFP mice, where GFP and Foxp3 are not fused into a single protein, existing as separate proteins after expression. Therefore, during induction, the appearance of GFP protein might potentially represent the presence of Foxp3. However, in cases of Foxp3 instability, the degradation of GFP protein may not be entirely synchronized with that of Foxp3 protein, making GFP an unreliable indicator of Foxp3 expression levels. As a result, for the purification of pure iTreg cells, we used Foxp3-GFP/RFP fluorescence, while for observing instability, we employed intranuclear staining of Foxp3.

In Figure 6B, the captions were lacking in the two graphs on the right side

The two restimulation conditions, 0.125+0.25 and 0.25+0.5, have been added into Fig 6B right side.

In Figure S2, the annotation of the x-y axis was missing.

Added.

Lack of reference at line 292.

Reference 42-46 were added.

In the method section, the authors should note the further product information of antibodies and reagents to enhance reproducibility and transparency. Making a list that clarifies the suppliers, Ab clone, product IDs, etc. is encouraged. The authors did not specify the supplier of recombinant proteins and which type of TGF-beta (TGF-beta 1, 2, or 3?).

A detailed description of the mice, antibodies, Peptide recombinant protein, commercial kit, and software has been provided and incorporated into the methods section.

In the method section, the authors should clarify which Foxp3-reporter strain. There are many strains of Foxp3-reporter mice in the world. In line 373, is the "FoxP3-IRES-GFP transgenic mice" true? Knock-in strain or BAC-transgene?

This mouse is a gift from Hai Qi Lab in Tsinghua University. They acquired this mouse strain from Jackson Laboratory, and the strain name is B6.Cg-Foxp3tm2Tch/J, Strain #:006772. An IRES-EGFP-SV40 poly A sequence was inserted immediately downstream of the endogenous Foxp3 translational stop codon, but upstream of the endogenous polyA signal, generating a bicistronic locus encoding both Foxp3 and EGFP.

The age of mice used in the experiments should be specified, and confusing words such as "young" should not be used in any method descriptions; e.g. line 405.

The detailed mouse age has been added in the methods section. “To prepare Tconv, tTreg and iTreg for experiments, spleen was isolated from 2-4-month-old Foxp3-GFP mice for Tconv and tTreg sorting, and 6-week-old mice for iTreg induction.”

The method of how the original ATAC-seq/Cut & Tag data were generated was not described in the method section.

Added in method section.

The reference section was incomplete, and the style was not unified. e.g.; ref 7, 24, 25, 26 ... I gave up checking all.

The style of ref 7, 22, 24, 26, 28, 31, 33, 35 were modified.

Changes in manuscript:

Author Name: “Huiyun Lv” to “Huiyun Lyu”.

Fig 1A was updated according to Reviwer 2’s suggestion.

Fig S3E and associated description was added according to Reviwer 2’s suggestion.

Fig S4C and associated description was added according to Reviwer 1’s suggestion.

Fig 5H and associated description was added according to Reviwer 2’s suggestion.

Fig 6D were updated according to Reviwer 1’s suggestion.

Fig 2D was corrected, the labels for gapdh and actin in the iTreg panel were inadvertently switched. The mistake has been rectified, and the original gel image will be provided.

Fig 2A and Fig 4A was updated.

The style of Fig 6B and Fig S2A was modified.

Method:

Mice: FoxP3-IRES-GFP with more description.

Flow Cytometry sorting and FACS: the detailed mouse age has been added. RNA-seq analysis, ATAC-sequencing, ATAC-seq analysis, Cut&Tag assay, Cut&Tag data analysis: more description was added.

Statistical analysis: “Numbers of independently-performed experiment repeats are shown as N, biological replicates of each experiment as n.” were added.

Reference: Ref 42-46 and 49-52 were added. The style of ref 7, 22, 24, 26, 28, 31, 33, 35 were corrected.

A detailed description of the mice, antibodies, Peptide recombinant protein, commercial kit, and software has been provided.

eLife assessment

This study presents the valuable finding that sustained calcium signaling in induced-Treg (iTreg) cells can lead to the loss of Foxp3 expression and iTreg identity by altering the chromatin landscape. The evidence supporting the claims of the authors is convincing. The work will be of interest to immunologists working on Treg cell therapy.

Reviewer #1 (Public Review):

This study revealed that one of the mechanisms for iTreg (induced-Treg) lineage instability upon restimulation is through sustained store-operated calcium entry (SOCE), which activates transcription factor NFAT and promotes changes in chromatin accessibility to activated T cell-related genes. The authors revealed that, unlike thymus-derived Tregs (tTreg) with blunted calcium signaling and NFAT activation, iTregs respond to TCR restimulation with fully activated SOCE and NFAT similar to activated conventional T cells. Activated NFAT binds to open chromatin regions in genes related to T helper cells, increases their expression, and leads to the instability of iTreg cells. On the other hand, inhibition of the SOCE/NFAT pathway by chemical inhibitors could partially rescue the loss of Foxp3 expression in iTreg upon restimulation. The conclusion of the study is unexpected since previous studies showed that NFAT is required for Foxp3 induction and iTreg differentiation (Tone Y et al, Nat Immunol. 2008, PMID: 18157133; Vaeth M et al, PNAS, 2012, PMID: 22991461). Additionally, Foxp3 interacts with NFAT to control Treg function (Wu Y et al, Cell, 2006, PMID: 16873067). The data presented in this study demonstrated the complex role NFAT plays in the generation and stability of iTreg cells.

Several concerns are raised from the current study.<br /> 1. Previous studies showed that iTregs generated in vitro from culturing naïve T cells with TGF-b are intrinsically unstable, and prone to losing Foxp3 expression due to lack of DNA demethylation in the enhancer region of the Foxp3 locus (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). It is known that removing TGF-b from the culture media leads to rapid loss of Foxp3 expression. In the current study, TGF-b was not added to the media during iTreg restimulation, therefore, the primary cause for iTreg instability should be the lack of the positive signal provided by TGF-b. NFAT signal is secondary at best in this culturing condition.

This point has been addressed in the revision. Figure Q1 could be added to the manuscript as a supplementary figure.

2. It is not clear whether the NFAT pathway is unique in accelerating the loss of Foxp3 expression upon iTreg restimulation. It is also possible that enhancing T cell activation in general could promote iTreg instability. The authors could explore blocking T cell activation by inhibiting other critical pathways, such as NF-kb and c-Jun/c-Fos, to see if a similar effect could be achieved compared to CsA treatment.

This point has been sufficiently addressed in the revision.

3. The authors linked chromatin accessibility and increased expression of T helper cell genes to the loss of Foxp3 expression and iTreg instability. However, it is not clear how the former can lead to the latter. It is also not clear whether NFAT binds directly to the Foxp3 locus in the restimulated iTregs and inhibits Foxp3 expression.

This point has been addressed in the rebuttal. Could the authors incorporate their comments in the rebuttal into the discussion section of the revised manuscript?

Reviewer #2 (Public Review):

The phenotypic instability of in vitro-induced Treg cells (iTregs) has been discussed for a long time, mainly in the context of the epigenetic landscape of Treg-signature genes; e.g. Treg-specifically CpG-hypomethylated Foxp3 CNS2 enhancer region. However, it has been insufficiently understood the upstream molecular mechanisms, the particularity of intracellular signaling of natural Treg cells, and how they connect to stable/unstable suppressive function.

Huiyun Lv et al. addressed the issue of phenotypic instability of in vitro-induced regulatory T cells (iTregs), which is a different point from the physiological natural Treg cells and an obstacle to the therapeutic use of iTreg cells. The authors focused on the difference between iTreg and nTreg cells from the perspective of their control of store-operated calcium entry (SOCE)-mediated cellular signaling, and they clearly showed that the sustained SOCE signaling in iTreg and nTreg cells led to phenotypic instability. Moreover, the authors pointed out the correlation between the incomplete conversion of chromatin configuration and the NFAT-mediated control of effector-type gene expression profile in iTreg cells. These findings potentially cultivate our understanding of the cellular identity of regulatory T cells and may shed light on the therapeutic use of Treg cells in many clinical contexts.

The authors demonstrated the biological contribution of Ca2+ signaling with the variable methods, which ensure the reliability of the results and the claims of the authors. iTreg cells sustained SOCE-signaling upon stimulation while natural Treg cells had lower strength and shorter duration of SOCE-signaling. The result was consistent with the previously proposed concept; a certain range of optimal strength and duration of TCR-signaling shape the Treg generation and maintenance, and it provides us with further in-depth mechanistic understanding.

In the later section, authors found the incomplete installment of Treg-type open chromatin landscape in some effector/helper function-related gene loci in iTreg cells. These findings propose the significance of focusing on not only the "Treg"-associated gene loci but also "Teffector-ness"-associated regions to determine the Treg conversion at the epigenetic level.

Limitations;<br /> ・NFAT regulation did not explain all of the differences between iTregs and nTregs, as the authors mentioned as a limitation.<br /> ・Also, it is still an open question whether NFAT can directly modulate the chromatin configuration on the effector-type gene loci, or whether NFAT exploits pre-existing open chromatin due to the incomplete conversion of Treg-type chromatin landscape in iTreg cells. The authors did not fully demonstrate that the distinct pattern of chromatin regional accessibility found in iTreg cells is the direct cause of an effector-type gene expression.

Author Response

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

Reviewer #1 (Public Review):

Summary:

The precise mechanism of how tetraspanin proteins engage in the generation of discs is still an open question in the field of photoreceptor biology. This question is of significance as the lack of photoreceptor discs or defects in disc morphogenesis due to mutations in tetraspanin proteins is a known cause of vision loss in humans. The authors of this study combine TEM and mouse models to tease out the role of tetraspanin proteins, peripherin, and Rom1 in the genesis of the photoreceptor discs. They show that the absence of Rom1 leads to an increase in peripherin and changes in disc morphology. Further rise in peripherin alleviates some of the defects observed in Rom1 knockout animals leading to the conclusion that peripherin can substitute for the absence of Rom1.

Strengths:

A mouse model of Rom1 generated by the McInnes group in 2000 predicted a role for Rom1 in rim closure. They also showed enlarged discs in the absence of Rom1. This study confirmed this finding and showed the compensatory changes in peripherin, maintaining the total levels of tetraspanin proteins. Lack of Rom1 leads to excessive open disks demonstrated by darkly stained tannic acid-accessible areas in TEM. Interestingly, increased peripherin expression can rescue some morphological defects, including maintaining normal disc diameters and incisures. Overall, these observations lead authors to propose a model that ROM1 can be replaced by peripherin.

Thank you for your kind summary of our work.

Weaknesses:

The compensatory increase in peripherin and morphological rescue in the absence of ROM1 is expected, given the previous work from authors showing i) absence of peripherin showing increased ROM1 and ii) "Eliminating Rom1 also increased levels of Prph2/RRCT: mean Prph2/RRCT levels in P30 Prph2+/R retinas were 34% of WT, while levels in Prph2+/R/Rom1−/− retinas were 59% of WT" from Conley, 2019. The current study provides a comprehensive quantitative analysis. However, the mechanism behind the mechanism is unclear and warrants discussion.

We referenced the result from the 2019 paper by Conley and colleagues in revision. As noted by the reviewer, new information in the current study consists of the precise quantification of the compensatory increase by a technique more accurate than semi-quantitative Western blotting. The nature of these compensatory increases is currently unknown and beyond the scope of experiments described in the current study. While this is an intriguing area for future investigation, we prefer not to speculate on the underlying mechanisms to avoid any appearance of data overinterpretation.

Photoreceptor morphology appears better when peripherin is overexpressed. Is there a rescue of rod function (assessed by ERG or equivalent measures) in peripherin OE/Rom1-/- mice? Given the extensive work in this area and the implications the authors allude to at the end, it is important to investigate this aspect.

It is indeed an interesting and potentially translationally relevant direction to address whether PRPH2 overexpression can rescue the long-term degeneration and functional defects of the loss of ROM1. Unfortunately, our work in this direction remains severely hindered by the fact that the current line of ROM1 knockout mice are notoriously poor breeders, allowing us to get only a handful of animals for each year of breeding. Therefore, we decided to limit our current study to addressing the structural roles of ROM1 and PRPH2 in supporting disc formation.

Reviewer #1 (Recommendations For The Authors):

Line 210: "ROM1 is able to form disc rims in the absence of PRPH2" is not demonstrated. The data shows that the tetraspanin domains are interchangeable similar to Conley, 2019. Similar concern for lines 225-226.

We agree with the point regarding the interchangeable tetraspanin domains and clarified it in the text by referring to the tetraspanin body of PRPH2 where applicable. However, the 2019 paper by Conley and colleagues did not show any ultrastructural images of disc rims in a mouse without at least one copy of WT PRPH2 being expressed. The presence of normally looking disc rims in the complete absence of the tetraspanin body of PRPH2 is an original observation of the present study.

Line 234: it is unclear what is meant by .."they are normally processed in the biosynthetic membranes" How does lack of ER localization lead to this conclusion?

We clarified this point by replacing “normally processed” with “not trapped”.

Lines 306-308: it is difficult to follow the rationale. How will a shift in the trafficking pathway affect disulfide bonds since these are formed in ER?

The reviewer makes a good point that at least the bulk of S-S bridge formation takes place during protein maturation in the ER and the ability of additional intramolecular S-S bond formation in the Golgi is questionable. We, therefore, removed this speculation from Discussion.

Given the poor development of OS, the authors could provide an estimate of how many OS-like structures were observed, with and without rims, in RRCT animals.

The gross development of outer segment structures in RRCT homozygous mice was part of the 2019 paper by Conley and colleagues. We prefer to limit repeating experiments from the previous study, but instead wanted to focus specifically on disc rim formation, which was not analyzed in RRCT homozygous mice in the previous study.

The term "function" is loosely defined throughout this manuscript. Specifically, the excess peripherin can resolve some of the morphological defects observed in Rom1 -/-, and these functional changes in morphology are the focus of this work.

We removed the word “function” in three occasions where there may be an ambiguity in its meaning, as noted by the reviewer.

Lines 115/116: Reference is missing for the statement that photoreceptor cell degeneration begins at P30.

These lines reference Figures 1A,B, which include quantification of the number of photoreceptor nuclei. These results show that ROM1 knockout retinas exhibit a modest but statistically significant degeneration at P30. The text is modified to eliminate any ambiguity.

Lines 143-144 are speculation and could be moved to the discussion section. "Prolonged delivery of disc membrane delivery to each disc" Any reference or experiments to support this statement?

We respectfully disagree with moving this short speculative sentence to Discussion. We believe that it helps the reader to follow the flow of the data, while being clearly presented as a potential explanation rather than a conclusion.

Line 245-246: Results explained in the following paragraph (247-254) do not answer the question "whether disc rim formation in PRPH2 2C150S/C150S knockin mice was driven by disulfide-linked ROM1 molecules", which is a valid and intriguing question. However, the results explained in 247-254 answer the question "if C150S PRPH2 can form discs in the absence of ROM1".

We changed the text to replace “To address this question” with “To explore whether disc rims can be formed in the absence of any disulfide-linked tetraspanin molecules”, which precisely reflects what was addressed.

Reviewer #2 (Public Review):

In this study, Lewis et al seek to further define the role of ROM1. ROM1 is a tetraspanin protein that oligomerizes with another tetraspanin, PRPH2, to shape the rims of the membrane discs that comprise the light-sensitive outer segment of vertebrate photoreceptors. ROM1 knockout mice and several PRPH2 mutant mice are reexamined. The conclusion reached is that ROM1 is redundant to PRPH2 in regulating the size of newly forming discs, although excess PRPH2 is required to compensate for the loss of ROM1.

This replicates earlier findings while adding rigor using a mass spectrometry-based approach to quantitate the ratio of ROM1 and PRPH2 to rhodopsin (the protein packed in the body of the disc membranes) and careful analysis of tannic acid labeled newly forming discs using transmission electron microscopy.

In ROM1 knockout mice PRPH2 expression was found to be increased so that the level of PRPH2 in those mice matches the combined amount of PRPH2 and ROM1 in wildtype mice. Despite this, there are defects in disc formation that are resolved when the ROM1 knockout is crossed to a PRPH2 overexpressing line. A weakness of the study is that the molar ratios between ROM1, PRPH2 and rhodopsin were not measured in the PRPH2 overexpressing mice. This would have allowed the authors to be more precise in their conclusion that a 'sufficient' excess of PRPH2 can compensate for defects in ROM1.

Thank you for these kind comments about our work. Regarding the stated weakness that we did not measure the molar ratios between PRPH2, ROM1 and rhodopsin in the ROM1 knockout line with PRPH2 overexpression: this is one experiment that we really hoped to do but were limited by the poor breeding of the ROM1 knockout line described above. With the current breeding rate, we estimate that we would need to wait for another year to get enough material to do this experiment, which we cannot do in the context of this manuscript revision. We hope, however, that eventually this may be a part of one of our future papers.

Reviewer #2 (Recommendations For The Authors):

The p-value for statistical significance is not listed, readers will assume the most commonly used 0.05 value was used but this should still be defined, especially since only asterisks summarizing the p-value range are provided in place of the actual p-values.

The definitions of various numbers of asterisks of significance (including p<0.05 as a minimal measure of significance) are provided in the Methods section, whereas the exact p-values are stated in figure captions.

There are 3 phrasing issues that are potentially misleading.

1) While PRHP2 and ROM1 are the most abundant tetraspanins in photoreceptors they are not the only ones. It would be more precise if for example the Table 1 title was changed to 'molar ratio of outer segment tetraspanins and rhodopsin'.

We have changed the title of Table 1 to “Quantification of molar ratios between PRPH2, ROM1 and rhodopsin in WT and Rom1-/- outer segments” to be more accurate.

2) The protein expressed in RRCT mice is described as the 'tetraspanin core' while the cartoon (and original paper) shows the protein as simply being ROM1 with a different cytoplasmic C-terminus (from PRHP2). Tetraspanin core in other places is used to mean just the transmembrane bundle or that bundle with the EC loops.

We agree that the term “tetraspanin core” may be confusing. We modified the text to not use this term and, when needed, refer to this main part of the tetraspanin molecule as a “body”.

3) Line 203-205, the 'somewhat restored' qualifier should be removed. If the authors think there is an effect that is different from chance, they should use a different alpha and justify that choice.

We removed this line, as suggested.

Reviewer #3 (Public Review):

In this manuscript, Lewis et al. investigate the role of tetraspanins in the formation of discs - the key structure of vertebrate photoreceptors essential for light reception. Two tetraspanin proteins play a role in this process: PRPH2 and ROM1. The critical contribution of PRPH2 has been well established and loss of its function is not tolerated and results in gross anatomical pathology and degeneration in both mice and humans. However, the role of ROM1 is much less understood and has been considered somewhat redundant. This paper provides a definitive answer about the long-standing uncertainty regarding the contribution of ROM1 firmly establishing its role in outer segment morphogenesis. First, using an ingenious quantitative proteomic technique the authors show PRPH2 compensatory increase in ROM1 knockout explaining the redundancy of its function. Second, they uncover that despite this compensation, ROM1 is still needed, and its loss delays disc enclosure and results in the failure to form incisures. Third, the authors used a transgenic mouse model and show that deficits seen in ROM1 KO could be completely compensated by the overexpression of PRPH2. Finally, they analyzed yet another mouse model based on double manipulation with both ROM1 loss and expression of PRPH2 mutant unable to form dimerizing disulfide bonds further arguing that PRPH2-ROM1 interactions are not required for disc enclosure. To top it off the authors complement their in vivo studies by a series of biochemical assays done upon reconstitution of tetraspanins in transfected cultured cells as well as fractionations of native retinas. This report is timely, addresses significant questions in cell biology of photoreceptors, and pushes the field forward in a classical area of photoreceptor biology and mechanics of membrane structure as well. The manuscript is executed at the top level of technical standard, exceptionally well written, and does not leave much more to desire. It also pushes standards of the field- one such domain is the quantitative approach to analysis of the EM images which is notoriously open to alternative interpretations - yet this study does an exceptional job unbiasing this approach.

According to my expertise in photoreceptor biology, there is nothing wrong with this manuscript either technically or conceptually and I have no concerns to express.

Thank you for these incredibly kind comments.

Reviewer #3 (Recommendations For The Authors):

I have no recommendations to make.

eLife assessment

This valuable study is focused on the requirement of the photoreceptor-specific tetraspanins, ROM1 and PRPH2, for the formation of light-sensitive membrane discs. The evidence supporting the claim that deficiency in one of the proteins can be compensated by the other is convincing, with both established and advanced techniques yielding results that will be of interest to those studying photoreceptor development and membrane curvature.

Reviewer #1 (Public Review):

The author studies a family of models for heritable epigenetic information, with a focus on enumerating and classifying different possible architectures. The key aspects of the paper are:

- Enumerate all 'heritable' architectures for up to 4 constituents.<br /> - A study of whether permanent ("genetic") or transient ("epigenetic") perturbations lead to heritable changes.<br /> - Enumerated the connectivity of the "sequence space" formed by these heritable architectures.<br /> - Incorporating stochasticity, the authors explore stability to noise (transient perturbations).<br /> - A connection is made with experimental results on C elegans.

The study is timely, as there has been a renewed interest in the last decade in non-genetic, heritable heterogeneity (e.g., from single-cell transcriptomics). Consequently, there is a need for a theoretical understanding of the constraints on such systems. There are some excellent aspects of this study: for instance:

- the attention paid to how one architecture "mutates" into another, establishing the analogue of a "sequence space" for network motifs (Fig 3).<br /> - the distinction is drawn between permanent ("genetic") and transient ("epigenetic") perturbations that can lead to heritable changes.<br /> - the interplay between development, generational timescales, and physiological time (as in Fig. 5).

The manuscript would be very interesting if it focused on explaining and expanding these results. Unfortunately, as a whole, it does not succeed in formalising nor addressing any particular open questions in the field. Aside from issues in presentation and modelling choices (detailed below), it would benefit greatly from a more systematic approach rather than the vignettes presented.

## Terminology<br /> The author introduces a terminology for networks of interacting species in terms of "entities" and "sensors" -- the former being nodes of a graph, and the latter being those nodes that receive inputs from other nodes. In the language of directed graphs, "entities" would seem to correspond to vertices, and "sensors" those vertices with positive indegree and outdegree. Unfortunately, the added benefit of redefining accepted terminology from the study of graphs and networks is not clear.

## Heritability<br /> The primary goal of the paper is to analyse the properties of those networks that constitute "heritable regulatory architectures". The definition of heritability is not clearly stated anywhere in the paper, but it appears to be that the steady-state of the network must have a non-zero expression of every entity. As this is the heart of the paper, it would be good to have the definition of heritable laid out clearly in either the main text or the SI.

## Model<br /> As described in the supplementary, but not in the main text, the author first chooses to endow these networks with simple linear dynamics; something like $\partial_t \vec{x} = A x - T x$, where the vector $x$ is the expression level of each entity, $A$ has the structure of the adjacency matrix of the directed graph, and $T$ is a diagonal matrix with positive entries that determines the degradation or dilution rate of each entity. From a readability standpoint, it would greatly aid the reader if the long list of equations in the SI were replaced with the simple rule that takes one from a network diagram to a set of ODEs.

The implementation of negative regulation is manifestly unphysical if the "entities" represent the expression level of, say, gene products. For instance, in regulatory network E, the value of the variable z can go negative (for instance, if the system starts with z= and y=0, and x > 0).

The model seems to suddenly change from Figure 4 onwards. While the results presented here have at least some attempt at classification or statistical rigour (i.e. Fig 4 D), there are suddenly three values associated with each entity ("property step, active fraction, and number"). Furthermore, the system suddenly appears to be stochastic. The reader is left unsure of what has happened, especially after having made the effort to deduce the model as it was in Figs 1 through 3. No respite is to be found in the SI, either, where this new stochastic model should have been described in sufficient detail to allow one to reproduce the simulation.

## Perturbations<br /> Inspired especially by experimental manipulations such as RNAi or mutagenesis, the author studies whether such perturbations can lead to a heritable change in network output. While this is naturally the case for permanent changes (such as mutagenesis), the author gives convincing examples of cases in which transient perturbations lead to heritable changes. Presumably, this is due the the underlying mutlistability of many networks, in which a perturbation can pop the system from one attractor to another.

Unfortunately, there appears to be no attempt at a systematic study of outcomes, nor a classification of when a particular behaviour is to be expected. Instead, there is a long and difficult-to-read description of numerical results that appear to have been sampled at random (in terms of both the architecture and parameter regime chosen). The main result here appears to be that "genetic" (permanent) and "epigenetic" (transient) perturbations can differ from each other -- and that architectures that share a response to genetic perturbation need not behave the same under an epigenetic one. This is neither surprising (in which case even illustrative evidence would have sufficed) nor is it explored with statistical or combinatorial rigour (e.g. how easy is it to mistake one architecture for another? What fraction share a response to a particular perturbation?)

As an additional comment, many of the results here are presented as depending on the topology of the network. However, each network is specified by many kinetic constants, and there is no attempt to consider the robustness of results to changes in parameters.

## DNA analogy<br /> At two points, the author makes a comparison between genetic information (i.e. DNA) and epigenetic information as determined by these heritable regulatory architectures. The two claims the author makes are that (i) heritable architectures are capable of transmitting "more heritable information" than genetic sequences, and (ii) that, unlike DNA, the connectivity (in the sense of mutations) between heritable architectures is sparse and uneven (i.e. some architectures are better connected than others).

In both cases, the claim is somewhat tenuous -- in essence, it seems an unfair comparison to consider the basic epigenetic unit to be an "entity" (e.g., an entire transcription factor gene product, or an organelle), while the basic genetic unit is taken to be a single base-pair. The situation is somewhat different if the relevant comparison was the typical size of a gene (e.g., 1 kb).

eLife assessment

This useful manuscript explores conditions for epigenetic inheritance by studying the stability of simple network models to permanent and transient perturbations. A novel aspect of the study is that it unifies non-genetic inheritance phenomena across cell divisions of unicellular organisms and in the germline of multicellular organisms. However, the models studied are more a collection of vignettes of numerical studies than a systematic study, therefore the evidence presented remains incomplete. This work will be of interest in the field of epigenetic inheritance as a first step towards building a more systematic theoretical framework.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript uses an interesting abstraction of epigenetic inheritance systems as partially stable states in biological networks. This follows on previous review/commentary articles by the author. Most of the molecular epigenetic inheritance literature in multicellular organisms implies some kind of templating or copying mechanisms (DNA or histone methylation, small RNA amplification) and does not focus on stability from a systems biology perspective. By contrast, theoretical and experimental work on the stability of biological networks has focused on unicellular systems (bacteria), and neglects development. The larger part of the present manuscript (Figures 1-4) deals with such networks that could exist in bacteria. The author classifies and simulates networks of interacting entities, and (unsurprisingly) concludes that positive feedback is important for stability. This part is an interesting exercise but would need to be assessed by another reviewer for comprehensiveness and for originality in the systems biology literature. There is much literature on "epigenetic" memory in networks, with several stable states and I do not see here anything strikingly new.

An interesting part is then to discuss such networks in the framework of a multicellular organism rather than dividing unicellular organisms, and Figure 5 includes development in the picture. Finally, Figure 6 makes a model of the feedback loops in small RNA inheritance in C. elegans to explain differences in the length of inheritance of silencing in different contexts and for different genes and their sensitivity to perturbations. The proposed model for the memory length is distinct from a previously published model by Karin et al. (ref 49).

Strengths:<br /> A key strength of the manuscript is to reflect on conditions for epigenetic inheritance and its variable duration from the perspective of network stability.

Weaknesses:<br /> - I found confusing the distinction between the architecture of the network and the state in which it is. Many network components (proteins and RNAs) are coded in the genome, so a node may not disappear forever.

- From the Supplementary methods, the relationship between two nodes seems to be all in the form of dx/dt = Kxy . Y, which is just one way to model biological reactions. The generality of the results on network architectures that are heritable and robust/sensitive to change is unclear. Other interactions can have sigmoidal effects, for example. Is there no systems biology study that has addressed (meta)stability of networks before in a more general manner?

- Why is auto-regulation neglected? As this is a clear cause of metastable states that can be inherited, I was surprised not to find this among the networks.

- I did not understand the point of using the term "entity-sensor-property". Are they the same networks as above, now simulated in a computer environment step by step (thus allowing delays)?

- The final part applies the network modeling framework from above to small RNA inheritance in C. elegans. Given the positive feedback, what requires explanation is how fast the system STOPs small RNA inheritance. A previous model (Karin et al., ref. 49) builds on the fact that factors involved in inheritance are in finite quantity hence the different small RNAs "compete" for amplification and those targeting a given gene may eventually become extinct.

The present model relies on a simple positive feedback that in principle can be modulated, and this modulation remains outside the model. A possibility is to add negative regulation by factors such as HERI-1, that are known to limit the duration of the silencing.

The duration of silencing differs between genes. To explain this, the author introduces again outside the model the possibility of piRNAs acting on the mRNA, which may provide a difference in the stability of the system for different transcripts.<br /> At the end, I do not understand the point of modeling the positive feedback.

- From the initial analysis of abstract networks that do not rely on templating, I expected a discussion of possible examples from non-templated systems and was a little surprised by the end of the manuscript on small RNAs.

Reviewer #2 (Public Review):

Summary:

In recent years, Auxin treatment has been frequently used for inducing targeted protein degradation in Drosophila and various other organisms. This approach provides a way to acutely alter the levels of specific proteins. In this manuscript, the authors examine the impact of Auxin treatment and provide strong evidence that Auxin treatment elicits alterations in feeding activity, survival rates, lipid metabolism, and gene expression patterns. Researchers should carefully consider these effects to design experiments and interpret their data.

Strengths:

Regarding the widespread usage of Auxin mediated gene manipulation method, it is important to address whether the application of Auxin itself causes any physiological changes. The authors provide evidence of several Auxin effects. Experiments are suitably designed with appropriate sample size and data analysis methods.

Weaknesses:

The provided information is limited and not very helpful for many applications. For example, although authors briefly mentioned aging research, feeding behavior, and lipid data, RNA seq data are provided only for short-term (48 hours) treatment. Especially, since ovary phenotype was examined with long-term treatment (15 days), authors should also show other data for long-term treatment as well.

Although the authors show that Auxin causes a change in gene expression patterns and suggests the possible alteration of Gal4 expression levels, no cell-type-specific data is provided. It would be informative if the authors could examine the expression level of major Gal4 drivers.<br /> Authors should discuss how severe these changes are by comparing them with other treatments or conditions, such as starvation or mutant data (ideally, comparing with reported data or their own data if any?).

Reviewer #4 (Public Review):

This work by Fleck et al. and colleagues documented the auxin feeding-induced effects in adult flies, since auxin could be used in temporally controlled gene expression using a modified Gal4/Gal80 system. Overall, the experiments were well-designed and carefully executed. The results were quantified with appropriate statistical analyses. The paper was also well-written and the results were presented logically. The findings demonstrate that auxin-fed flies have significantly lower triglyceride levels than the control flies using Ultra High-pressure Liquid Chromatography-Mass Spectrometry (UHPLC-MS)-based metabolomics assays. Further transcriptome analyses using the whole flies show changes in genes involved in fatty acid metabolism. However, female oogenesis and fecundity do not seem to be affected, at least using the current assays. These results indicate that auxin may not be used in experiments involving lipid-related metabolism, but could be appropriate to be applied for other biological processes.

eLife assessment

This valuable study reports that auxin exposure perturbs feeding behavior, survival rates, lipid metabolism, and gene expression patterns in adult flies. The solid results are based on proper methods and data analyses, which broadly support the conclusions with only minor weaknesses. This work should be interesting to fly geneticists who are interested in using the auxin-inducible gene expression system for inducing target protein degradation acutely.

Reviewer #1 (Public Review):

Recently the auxin-inducible gene expression system (AGES) has been frequently used for inducing target protein degradation acutely in Drosophila and other organisms. This study investigated the effects of auxin exposure on Drosophila adults, focusing on their feeding behavior, fatty acid metabolism, and oogenesis. The authors have provided strong evidence that high levels of auxin exposure perturb feeding behavior, survival rates, lipid metabolism, and gene expression patterns, providing a cautionary note for the field in using this technology.

This study documented the auxin feeding-induced effects in adult Drosophila, with a design with temporally controlled gene expression using a modified Gal4/Gal80 system. Due to the widespread usage of the auxin-mediated method, it is important to address whether the application of auxin itself causes any physiological changes.

Overall, the experiments were suitably designed with appropriate sample size and data analysis methods. The authors reported evidence of several auxin-induced effects, including strong evidence that high levels of auxin exposure perturb feeding behavior, survival rates, lipid metabolism, and gene expression patterns. For example, they found that auxin-fed flies have significantly lower triglyceride levels than the control flies using Ultra High-pressure Liquid Chromatography-Mass Spectrometry (UHPLC-MS)-based metabolomics assays. Further transcriptome analyses using the whole flies show changes in genes involved in fatty acid metabolism. However, female oogenesis and fecundity do not seem to be affected, at least using the current assays. These results indicate that auxin may not be used in experiments involving lipid-related metabolism, but could be appropriate to be applied for other biological processes.

However, this work can be improved based on the following recommendations:

1) Although authors showed that auxin causes gene expression changes including the possible alteration of Gal4 expression levels, no cell-type-specific data is provided. It would be informative to the Drosophila field if the authors could examine major Gal4 drivers in their expression levels, such as the ones used in studying metabolism and oogenesis.

2) Although the authors briefly mentioned aging research, feeding behavior, and lipid metabolism, RNA-seq data are provided only for short-term treatment (2 days). The ovary phenotype was examined with long-term treatment (15 days). It would be informative if the authors could also show other long-term treatment data.

3) The auxin used in this work is a more water-soluble version and at a high concentration (10 mM). In the C. elegans system, researchers are using a much lower concentration of auxin typically at 1 mM. Therefore, the discussion of their results in terms of potential impacts on other experimental systems should be done carefully. It would be helpful to know what impacts might be observed at a lower concentration of auxin. The recommendation would be that the authors add the 1 mM auxin data point to key elements of their analysis.

4) Another related question is whether these detected changes are reversible or not after exposure to auxin at different concentrations. This would be informative for researchers to better design their temporally controlled experiments.

5) It would also be helpful to know whether spermatogenesis is affected or not.

6) A few other points include changing the nomenclature and validating some of the key genes shown in Figure 3 using quantitative RT-PCR experiments with the tissues where the affected genes are known to be expressed and functional.

Reviewer #3 (Public Review):

In this study, Fleck and colleagues investigate the effects of auxin exposure on Drosophila melanogaster adults, focusing their analysis on feeding behavior, fatty acid metabolism, and oogenesis. The motivation for the study is that auxin-inducible transcription systems are now being used by Drosophila researchers to drive transcription using the Gal4-UAS system as a complement to Gal80ts versions of the system. I found the study to be carefully done. This study will be of interest to researchers using the Drosophila system, especially those focusing on fatty acid metabolism or physiology. The authors might address the following minor points.

1) Auxin, actually 1-naphthaleneaceid acid here, which is a more water-soluble version of auxin (indole-3-acetic acid) is used at what I consider to be a high concentration-10 mM. The problem I have is that the authors are discussing their results in terms of potential impacts on other experimental systems. At least for C. elegans, I think this is not a reasonable extension of the current dataset. In the C. elegans system, researchers are using 1 mM auxin. The authors note that their RNA-seq results suggest a xenobiotic response. Could this apparent xenobiotic response be due to a metabolic byproduct following auxin administration at high concentrations? Figure S1 A shows that there is quite a robust transcriptional response at 1 mM auxin. It would be helpful to know what impacts might be observed at this lower concentration in which the transcriptional induction could be used in the context of biologically meaningful experiments. The recommendation would be that the authors add the 1 mM auxin data point to key elements of their analysis.

2) This reviewer was confused by the genetic nomenclature the authors use. The authors have chosen to use the designation 3.1Lsp2-Gal4 (3.1Lsp2-Gal4AID). I think this is potentially confusing because a reader might think that it is the Gal4 transcription factor that is the direct target of auxin- and TIR1-mediated protein degradation, as I initially did. Rather, it is the Gal80 repressor protein that is the direct target. The authors might consider a nomenclature that is more reflective of how this system works. It would also be helpful if the full genotypes of strains were included in each figure legend.

3) The RNA-seq dataset does not appear to be validated by RT-PCR experiments. The authors should consider validating some of the key genes shown in Figure 3 using quantitative RT-PCR experiments, potentially adding a 1 mM auxin data point.

eLife assessment

This manuscript describes valuable information on how the extraocular muscles (EOM) are preserved in a mouse model of familial Amyotrophic lateral sclerosis (ALS) that carries a G93A mutation in the Sod1 gene. The authors provide convincing evidence of how the integrity of neuromuscular junction is preserved in EOM but not in limb and diaphragm muscles of G93A mice. Overall, this interesting work provides new evidence regarding the etiopathogenesis of ALS and insights for the development of therapeutic targets to slow the loss of neuromuscular function in ALS.

Reviewer #1 (Public Review):

Summary:<br /> The study explores the mechanisms that preserve satellite cell function in extraocular muscles (EOMs) in a mouse model of familial Amyotrophic lateral sclerosis (ALS) that carries the G93A mutation in the Sod1 gene. ALS is a fatal neuromuscular disorder driven by motor neuron degeneration, leading to progressive wasting of most skeletal muscles but not EOM. The study first established that integrity of neuromuscular junction (NMJ) is preserved in EOM but not in limb and diaphragm muscles of G93A mice, and sodium butyrate (NaBu) treatment partially improves NMJ integrity in limb and diaphragm muscles of G93A mice. They also found a loss of synaptic satellite cells and renewability of cultured myoblasts in hindlimb and diaphragm muscles of G93A mice, but not in EOM, and NaBu treatment restores myoblast renewability. Using RNA-seq analysis, they identify that exon guidance molecules, particularly Cxcl12, are highly expressed in EOM myoblasts, along with more sustainable renewability. Using a neuromuscular co-culture model, they convincingly show that AAV-mediated Cxcl12 expression in G93A myotubes enhances motor axon extension and innervation. Strikingly, NaBu-mediated preservation of NMJ in limb muscles of G93A mice is associated with elevated expression of Cxcl12 in satellite cells and improved renewability of myoblasts. These results together offer molecular insights into genes critical for maintaining satellite cell function and revealing a mechanism through which NaBu ameliorates ALS.

Strengths:<br /> Combination of in vivo and cell culture models.<br /> Nice imaging of NMJ and associated satellite cells.<br /> Using motoneuron-myotube coculture to establish the mechanism.<br /> Tested and illustrated a mechanism through which a clinically used drug ameliorates ALS.

Weaknesses:<br /> Data presentation could be improved (see details in the Recommendation for Authors).<br /> It would have been nice to have included G93A motoneurons in the coculture study.

Reviewer #2 (Public Review):

Summary:<br /> The work is potentially interesting as it outlines the role of satellite cells in supporting the functional decline of skeletal muscle due to the denervation process. In this context the authors analyze the functional and molecular characteristics of satellite cells in different muscle types differently affected by the degenerative process in the ALS model.

Strengths:<br /> The work illustrates a relevant aspect of the differences in stem cell potential in different skeletal muscles in a mouse model of the disease through a considerable amount of data and experimental models.

Weaknesses:<br /> However, there are some criticisms of the structuring of the results:

It is not clear how many animals were used in each experimental group (Figs 1 and 2, Fig. 2-9). In particular, it is unclear whether the dots in the histograms represent biological or technical replicates. Furthermore, the gender used in experimental groups is never specified. This last point appears to be important considering the gender differences observed in the SOD1G93A mouse model.

The first paragraph of the results lacks a functional analysis of the motor decline of the animals after the administration of sodium butyrate. The authors, in fact, administered NaBu around 90 days of age while in previous work the drug had been administered at a pre-symptomatic age. It would therefore be useful, to make the message more effective, to characterize the locomotor functions of the treated animals in parallel with the histological evidence of the integrity of the NMJ.

Figure 5 should be completed with the administration of NaBu also to the satellite cells isolated from the WT mouse, the same for figure 9 where AAV-CMV-Cxcl12 transduction of WT myotubes is missing.

In the experiment illustrated in Figure 8, treatment of cell cultures with NaBu would improve the outcome as well as the interference of Cxcl12 expression in myotubes derived from G93A EOM SC (Fig.9) would strengthen the specificity of this protein in axon guidance in this NMJ typical of a spared muscle in ALS.

In the "materials and methods" section the paragraph relating to the methods used for statistical analysis is missing.

Reviewer #3 (Public Review):

Summary:<br /> In their paper, Li et al. investigate the transcriptome of satellite cells obtained from different muscle types including hindlimb, diaphragm, and extraocular muscles (EOM) from wild-type and G93A transgenic mice (end-stage ALS) in order to identify potential factors involved in the maintenance of the neuromuscular junction. The underlying hypothesis is that since EOMs are largely spared from this debilitating disease, they may secrete NMJ-protective factors. The results of their transcriptome analysis identified several axon guidance molecules including the chemokine Cxcl12, which are particularly enriched in EOM-derived satellite cells. Transduction of hindlimb-derived satellite cells with AAV encoding Cxcl12 reverted hindlimb-derived myotubes from the G93A mice into myotubes sharing phenotypic characteristics similar to those of EOM-derived satellite cells. Additionally, the authors were able to demonstrate that EOM-derived satellite cell myotube cultures are capable of enhancing axon extensions and innervation in co-culture experiments.

Strengths:<br /> The strength of the paper is that the authors successfully isolated and purified different populations of satellite cells, compared their transcriptomes, identified specific factors released by EOM-derived satellite cells, overexpressed one of these factors (the chemokine Cxcl12) by AAV-mediated transduction of hindlimb-derived satellite cells. The transduced cells were then able to support axon guidance and NMJ integrity. They also show that administration of Na butyrate to mice decreased NMJ denervation and satellite cell depletion of hind limbs. Furthermore, the addition of Na Butyrate to hindlimb-derived satellite cell myotube cultures increased Cxcl12 expression. These are impressive results providing important insights for the development of therapeutic targets to slow the loss of neuromuscular function characterizing ALS.

Weaknesses:<br /> Several important aspects have not been addressed by the authors, these include the following points which weaken the conclusions and interpretation of the results.

a) Na Butyrate was shown to extend the survival of G93A mice by Zhang et al. Na butyrate has a variety of biological effects, for example, anti-inflammatory effects inhibit mitochondrial oxidative stress, positively influence mitochondrial function, is a class I / II HDAC inhibitor, etc. What is the mechanism underlying its beneficial effects both in the context of mouse muscle function in the ALS G93A mice and in the in vitro myotube assay? Cytokine quantification as well as histone acetylation/methylation can be assessed experimentally and this is an important point that has not been appropriately investigated.

b) In the context of satellite cell characterization, on lines 151-152 the authors state that soleus muscles were excluded from further studies since they have a higher content of slow twitch fibers and are more similar to the diaphragm. This justification is not valid in the context of ALS as well as many other muscle disorders. Indeed, soleus and diaphragm muscles contain a high proportion of slow twitch fibers (up to 80% and 50% respectively) but soleus muscles are more spared than diaphragm muscles. What makes soleus muscles (and EOMs) more resistant to ALS NMJ injury? Satellite cells from soleus muscles need to be characterized in detail as well.

Furthermore, EOMs are complex muscles, containing many types of fibers and expressing different myosin heavy chain isoforms and muscle proteins. The fact that in mice both the globular layer and orbital layers of EOMs express slow myosin heavy chain isoform as well as myosin heavy chain 2X, 2A, and 2B (Zhou et al., 2010 IOVIS 51:6355-6363) also indicates that the sparing is not directly linked to the fast or slow twitch nature of the muscle fiber. This needs to be considered.

c) In the context of myotube formation from cultured satellite cells on lines 178-179 the authors stained the myotubes for myosin heavy chain. Because of the diversity of myosin heavy chain isoforms and different muscle origins of the satellite cells investigated, the isoform of myosin heavy chain expressed by the myotubes needs to be tested and described. It is not sufficient to state anti-MYH.

d) The original RNAseq results have not been deposited and while it is true that the authors have analyzed the results and described them in Figures 6 and 7 and relative supplements, the original data needs to be shown both as an xls list as a Volcano plots (q value versus log2 fold change). This will facilitate the independent interpretation of the results by the readers as some transcripts may not be listed. As presented it is rather difficult to identify which transcripts aside from Cxcl12 are commonly upregulated. Can the data be presented in a more visual way?

e) There is no section describing the statistical analysis methods used. In many figures, more than 2 groups are compared so the authors need to use an ANOVA followed by a post hoc test.

The authors have achieved their aim in showing that satellite cells derived from EOMs have a distinct transcriptome and that this may be the basis of their sparing in ALS. Furthermore, this work may help develop future therapeutic interventions for patients with ALS.

eLife assessment

This useful study aims to advance our understanding of the structure of the native form of a viral toxin secreted from infected cells. Some of the findings confirm previous reports, but the new claims in this study are only inadequately supported by the methods and analyses used. More rigorous approaches are needed to justify the main conclusion that the structure of the viral toxin derived from infected cells in this study is distinct from previously reported structures of recombinantly expressed versions of the toxin.

Reviewer #1 (Public Review):

The authors of this study seek to visualize NS1 purified from dengue virus infected cells. They infect vero cells with DV2-WT and DV2 NS1-T164S (a mutant virus previously characterized by the authors). The authors utilize an anti-NS1 antibody to immunoprecipitate NS1 from cell supernatants and then elute the antibody/NS1 complex with acid. The authors evaluate the eluted NS1 by SDS-PAGE, Native Page, mass spec, negative-stain EM, and eventually Cryo-EM. SDS-PAGE, mas spec, and native page reveal a >250 Kd species containing both NS1 and the proteinaceous component of HDL (ApoA1). The authors produce evidence to suggest that this population is predominantly NS1 in complex with ApoA1. This contrasts with recombinantly produced NS1 (obtained from a collaborator) which did not appear to be in complex with or contain ApoA1 (Figure 1C). The authors then visualize their NS1 stock in complex with their monoclonal antibody by CryoEM. For NS1-WT, the major species visualized by the authors was a ternary complex of an HDL particle in complex with an NS1 dimer bound to their mAB. For their mutant NS1-T164S, they find similar structures, but in contrast to NS1-WT, they visualize free NS1 dimers in complex with 2 Fabs (similar to what's been reported previously) as one of the major species. This highlights that different NS1 species have markedly divergent structural dynamics. It's important to note that the electron density maps for their structures do appear to be a bit overfitted since there are many regions with electron density that do not have a predicted fit and their HDL structure does not appear to have any predicted secondary structure for ApoA1. The authors then map the interaction between NS1 and ApoA1 using cross-linking mass spectrometry revealing numerous NS1-ApoA1 contact sites in the beta-roll and wing domain. The authors find that NS1 isolated from DENV infected mice is also present as a >250 kD species containing ApoA1. They further determine that immunoprecipitation of ApoA1 out of the sera from a single dengue patient correlates with levels of NS1 (presumably COIPed by ApoA1) in a dose-dependent manner.

In the end, the authors make some useful observations for the NS1 field (mostly confirmatory) providing additional insight into the propensity of NS1 to interact with HDL and ApoA1. The study does not provide any functional assays to demonstrate activity of their proteins or conduct mutagenesis (or any other assays) to support their interaction predications. The authors assertion that higher-order NS1 exists primarily as a NS1 dimer in complex with HDL is not well supported as their purification methodology of NS1 likely introduces bias as to what NS1 complexes are isolated. While their results clearly reveal NS1 in complex with ApoA1, the lack of other NS1 homo-oligomers may be explained by how they purify NS1 from virally infected supernatant. Because NS1 produced during viral infection is not tagged, the authors use an anti-NS1 monoclonal antibody to purify NS1. This introduces a source of bias since only NS1 oligomers with their mAb epitope exposed will be purified. Further, the use of acid to elute NS1 may denature or alter NS1 structure and the authors do not include controls to test functionality of their NS1 stocks (capacity to trigger endothelial dysfunction or immune cell activation). The acid elution may force NS1 homo-oligomers into dimers which then reassociate with ApoA1 in a manner that is not reflective of native conditions. Conducting CryoEM of NS1 stocks only in the presence of full-length mAbs or Fabs also severely biases what species of NS1 is visualized since any NS1 oligomers without the B-ladder domain exposed will not be visualized. If the residues obscured by their mAb are involved in formation of higher-order oligomers then this antibody would functionally inhibit these species from forming. The absence of critical controls, use of one mAb, and acid elution for protein purification severely limits the interpretation of these data and do not paint a clear picture of if NS1 produced during infection is structurally distinct from recombinant NS1. Certainly there is novelty in purifying NS1 from virally infected cells, but without using a few different NS1 antibodies to purify NS1 stocks (or better yet a polyclonal population of antibodies) it's unclear if the results of the authors are simply a consequence of the mAb they selected.

Data produced from numerous labs studying structure and function of flavivirus NS1 proteins provide diverse lines of evidence that the oligomeric state of NS1 is dynamic and can shift depending on context and environment. This means that the methodology used for NS1 production and purification will strongly impact the results of a study. The data in this manuscript certainly capture one of these dynamic states and overall support the general model of a dynamic NS1 oligomer that can associate with both host proteins as well as itself but the assertions of this manuscript are overall too strong given their data, as there is little evidence in this manuscript, and none available in the large body of existing literature, to support that NS1 exists only as a dimer associated with ApoA1. More likely the results of this paper are a result of their NS1 purification methodology.

Suggestions for the Authors:

Major:

1. Because of the methodology used for NS1 purification, it is not clear from the data provided if NS1 from viral infection differs from recombinant NS1. Isolating NS1 from viral infection using a polyclonal antibody population would be better to answer their questions. On this point, Vero cells are also not the best candidate for their NS1 production given these cells do not come from a human. A more relevant cell line like U937-DC-SIGN would be preferable.

2. The authors need to support their interaction predictions and models via orthogonal assays like mutagenesis followed by HDL/ApoA1 complexing and even NS1 functional assays. The authors should be able to mutate NS1 at regions predicted to be critical for ApoA1/HDL interaction. This is critical to support the central conclusions of this manuscript.

3. The authors need to show that the NS1 stocks produced using acid elution are functional compared to standard recombinantly produced NS1. Do acidic conditions impact structure/function of NS1?

4. Overall, the data obtained from the mutant NS1 (contrasted to WT NS1) reveals how dynamic the oligomeric state of NS1 proteins are but the authors do not provide any insight into how/why this is, some additional lines of evidence using either structural studies or mutagenesis to compare WT and their mutant and even NS1 from a different serotype of DENV would help the field to understand the dynamic nature of NS1.

Reviewer #2 (Public Review):

Summary:

Chew et al describe interaction of the flavivirus protein NS1 with HDL using primarily cryoEM and mass spec. The NS1 was secreted from dengue virus infected Vero cells, and the HDL were derived from the 3% FBS in the culture media. NS1 is a virulence factor/toxin and is a biomarker for dengue infection in patients. The mechanisms of its various activities in the host are incompletely understood. NS1 has been seen in dimer, tetramer and hexamer forms. It is well established to interact with membrane surfaces, presumably through a hydrophobic surface of the dimer form, and the recombinant protein has been shown to bind HDL. In this study, cryoEM and crosslinking-mass spec are used to examine NS1 secreted from virus-infected cells, with the conclusion that the sNS1 is predominantly/exclusively HDL-associated through specific contacts with the ApoA1 protein.

Strengths:

The experimental results are consistent with previously published data.

Weaknesses:

CryoEM:

Some of the neg-stain 2D class averages for sNS1 in Fig S1 clearly show 1 or 2 NS1 dimers on the surface of a spherical object, presumably HDL, and indicate the possibility of high-quality cryoEM results. However, the cryoEM results are disappointing. The cryo 2D class averages and refined EM map in Fig S4 are of poor quality, indicating sub-optimal grid preparation or some other sample problem. Some of the FSC curves (2 in Fig S7 and 1 in Fig S6) have extremely peculiar shapes, suggesting something amiss in the map refinement. The sharp drop in the "corrected" FSC curves in Figs S5c and S6c (upper) indicate severe problems. The stated resolutions (3.42 & 3.82 Å) for the sNS1ts-Fab56.2 are wildly incompatible with the images of the refined maps in Figs 3 & S7. At those resolutions, clear secondary structural elements should be visible throughout the map. From the 2D averages and 3D maps shown in the figures this does not seem to be the case. Local resolution maps should be shown for each structure.

The samples were clearly challenging for cryoEM, leading to poor quality maps that were difficult to interpret. None of the figures are convincing that NS1, Ab56.2 or Fab56.2 are correctly fit into EM maps. There is no indication of ApoA1 helices. Details of the fit of models to density for key regions of the higher-resolution EM maps should be shown and the models should be deposited in the PDB. An example of modeling difficulty is clear in the sNS1ts dimer with bound Fab56.2 (figs 3c & S7e). For this complex, the orientation of the Fab56.2 relative to the sNS1ts dimer in this submission (Fig 3c) is substantially different than in the bioRxiv preprint (Fig 3c). Regions of empty density in Fig 3c also illustrate the challenge of building a model into this map.

Mass spec:

Crosslinking-mass spec was used to detect contacts between NS1 and ApoA1, providing strong validation of the sNS1-HDL association. As the crosslinks were detected in a bulk sample, they show that NS1 is near ApoA1 in many/most HDL particles, but they do not indicate a specific protein-protein complex. Thus, the data do not support the model of an NS1-ApoA1 complex in Fig 4d. Further, a specific NS1-ApoA1 interaction should have evidence in the EM maps (helical density for ApoA1), but none is shown or mentioned. If such exists, it could perhaps be visualized after focused refinement of the map for sNS1ts-HDL with Fab56.2 (Fig S7d). The finding that sNS1-ApoA1 crosslinks involved residues on the hydrophobic surface of the NS1 dimer confirms previous data that this NS1 surface engages with membranes and lipids.

Sample quality:

The paper lacks any validation that the purified sNS1 retains established functions, for example the ability to enhance virus infectivity or to promote endothelial dysfunction. Peculiarities include the gel filtration profiles (Fig 2a), which indicate identical elution volumes (apparent MWs) for sNS1wt-HDL bound to Ab562 (~150 kDa) and to the ~3X smaller Fab56.2 (~50 kDa). There should also be some indication of sNS1wt-HDL pairs crosslinked by the full-length Ab, as can be seen in the raw cryoEM micrograph (Fig S5b).

Obtaining high quality structures is often more demanding of sample integrity than are activity assays. Given the low quality of the cryoEM maps, it's possible that the acidification step in immunoaffinity purification damaged the HDL complex. No validation of HDL integrity, for example with acid-treated HDL, is reported. Acid treatment is perhaps discounted by a statement (line 464) that another group also used immunoaffinity purification in a recent study (ref 20) reporting sNS1 bound to HDL. However the statement is incorrect; the cited study used affinity purification via a strep-tag on recombinant sNS1.

Discussion:

The Discussion reflects a view that the NS1 secreted from virus-infected cells is a 1:1 sNS1dimer:HDL complex with the specific NS1-ApoA1 contacts detected by crosslinking mass spec. This is inconsistent with both the neg-stain 2D class average with 2 sNS1 dimers on an HDL (Fig S1c) and with the recent study of Flamand & co-workers showing 1-3 NS1 dimers per HDL (ref 20). It is also ignores the propensity of NS1 to associate with membranes and lipids. It is far more likely that NS1 association with HDL is driven by these hydrophobic interactions than by specific protein-protein contacts. A lengthy Discussion section (lines 461-522) includes several chemically dubious or inconsistent statements, all based on the assumption that specific ApoA1 contacts are essential to NS1 association with HDL and that sNS1 oligomers higher than the dimer necessarily involve ApoA1 interaction, conclusions that are not established by the data in this paper.

eLife assessment

This important study shows, based on analyses of single cell RNA-seq data sets of thymus cells, that transposable elements (TEs) are broadly expressed in thymic stromal cells, especially in medullary thymic epithelial cells and plasamacytoid dendritic cells. The authors also show that at least some TE-derived peptides are presented by MHC-I molecules in the thymus. The results suggest a possible role of TEs in thymic T-cell selection and immune self-tolerance, but the current analyses are incomplete and not yet fully support the claims.

Reviewer #1 (Public Review):

Summary:<br /> Transposable Elements (TEs) are exogenously acquired DNA regions that have played important roles in the evolutional acquisition of various biological functions. TEs may have been important in the evolution of the immune system, but their role in thymocytes has not been fully clarified.

Using the human thymus scRNA dataset, the authors suggest the existence of cell type-specific TE functions in the thymus. In particular, it is interesting to show that there is a unique pattern in the type and expression level of TEs in thymic antigen-presenting cells, such as mTECs and pDCs, and that they are associated with transcription factor activities. Furthermore, the authors suggested that TEs may be non-redundantly regulated in expression by Aire, Fezf2, and Chd4, and that some TE-derived products are translated and present as proteins in thymic antigen-presenting cells. These findings provide important insights into the evolution of the acquired immune system and the process by which the thymus acquires its function as a primary lymphoid tissue.

Strengths:<br /> 1. By performing single-cell level analysis using scRNA-seq datasets, the authors extracted essential information on heterogeneity within the cell population. It is noteworthy that this revealed the diversity of expression not only of known autoantigens but also of TEs in thymic antigen-presenting cells.

2. The attempt to use mass spectrometry to confirm the existence of TE-derived peptides is worthwhile, even if the authors did not obtain data on as many transcripts as expected.

3. The use of public data sets and the clearly stated methods of analysis improved the transparency of the results.

Weaknesses:<br /> 1. The authors sometimes made overstatements largely due to the lack or shortage of experimental evidence.

For example in figure 4, the authors concluded that thymic pDCs produced higher copies of TE-derived RNAs to support the constitutive expression of type-I interferons in thymic pDCs, unlike peripheral pDCs. However, the data was showing only the correlation between the distinct TE expression pattern in pDCs and the abundance of dsRNAs. We are compelled to say that the evidence is totally too weak to mention the function of TEs in the production of interferon. Even if pDCs express a distinct type and amount of TE-derived transcripts, it may be a negligible amount compared to the total cellular RNAs. How many TE-derived RNAs potentially form the dsRNAs? Are they over-expressed in pDCs?<br /> The data interpretation requires more caution to connect the distinct results of transcriptome data to the biological significance.

2. Lack of generality of specific examples. This manuscript discusses the whole genomic picture of TE expression. In addition, one good way is to focus on the specific example to clearly discuss the biological significance of the acquisition of TEs for the thymic APC functions and the thymic selection.

In figure 2, the authors focused on ETS-1 and its potential target genes ZNF26 and MTMR3, however, the significance of these genes in NK cell function or development is unclear. The authors should examine and discuss whether the distinct features of TEs can be found among the genomic loci that link to the fundamental function of the thymus, e.g., antigen processing/presentation.

3. Since the deep analysis of the dataset yielded many intriguing suggestions, why not add a discussion of the biological reasons and significance?<br /> For example, in Figure 1, why is TE expression negatively correlated with proliferation? cTEC-TE is mostly postnatal, while mTEC-TE is more embryonic. What does this mean?

4. To consolidate the experimental evidence about pDCs and TE-derived dsRNAs, one option is to show the amount of TE-derived RNA copies among total RNAs. The immunohistochemistry analysis in figure 4 requires additional data to demonstrate that overlapped staining was not caused by technical biases (e.g. uneven fixation may cause the non-specifically stained regions/cells). To show this, authors should have confirmed not only the positive stainings but also the negative staining (e.g. CD3, etc.). Another possible staining control was showing that non-pDC (CD303- cell fractions in this case) cells were less stained by the ds-RNA probe.

Reviewer #2 (Public Review):

Summary: Larouche et al show that TEs are broadly expressed in thymic cells, especially in mTECs and pDCs. Their data suggest a possible involvement of TEs in thymic gene regulation and IFN-alpha secretion. They also show that at least some TE-derived peptides are presented by MHC-I in the thymus.

Strengths: The idea of high/broad TE expression in the thymus as a mechanism for preventing TE-mediated autoimmunity is certainly an attractive one, as is their involvement in IFN-alpha secretion therein. The analyses and experiments presented here are therefore a very useful primer for more in-depth experiments, as the authors point out towards the end of the discussion.

Weaknesses: Throughout the manuscript, most conclusions are presented as proven causal relationships that the current data do not demonstrate. In the abstract, results, and discussion, the following conclusions are drawn that are not supported by the data: a) TEs interact with multiple transcription factors in thymic cells, b) TE expression leads to dsRNA formation, activation of RIG-I/MDA5 and secretion of IFN-alpha, c) TEs are regulated by cell proliferation and expression of KZFPs in the thymus. All these statements derive from correlations. Only one TF has ChIP-seq data associated with it, dsRNA formation and/or IFN-alpha secretion could be independent of TE expression, and whilst KZFPs most likely regulate TEs in the thymus, the data do not demonstrate it. The authors also seem to suggest that AIRE, FEZF2, and CHD4 regulate TEs directly, but binding is not shown. The manuscript needs a thorough revision to be absolutely clear about the correlative nature of the described associations.

On the technical side, there are many dangers about analysing RNA-seq data at the subfamily level and without stringent quality control checks. Outputs may be greatly confounded by pervasive transcription (see PMID 31425522), DNA contamination, and overlap of TEs with highly expressed genes. Whether TE transcripts are independent units or part of a gene also has important implications for the conclusions drawn. I would say that for most purposes of this work, an analysis restricted to independent TE transcripts, with appropriate controls for DNA contamination, would provide great reassurances that the results from subfamily-level analyses are sound. Showing examples from the genome browser throughout would also help.

eLife assessment

This work presents fundamental new insights into the conductivity of freshwater cable bacteria. The evidence supporting the conclusions, which was collected using appropriate techniques, is compelling. The work will be of interest to environmental microbiologists and the microbial electrochemistry community.

Reviewer #1 (Public Review):

Summary:

This work provides significant insight into freshwater cable bacteria (CB) and is an important contribution to the emerging CB literature. In this manuscript, Yang et al. describe current-voltage measurements on CB collected from two freshwater sources in Southern California. The studies use electrostatic and conductive atomic force microscopies, as well as four-probe measurements. These measurements are consistent with back-of-the-envelope calculations on conductivities needed to sustain CB function. The data shows that freshwater CB have a similar structure and function to the more studied marine cable bacteria.

Strengths:

Excellent measurements on a new class of cable bacteria.

Weaknesses:

The paper would benefit from additional analysis of the data.

Reviewer #2 (Public Review):

Summary:

In this work, Mohamed Y. El-Naggar and co-workers present a detailed electronic characterization of cable bacteria from Southern California freshwater sediments. The cable bacteria could be reliably enriched in laboratory incubations, and subsequent TEM characterization and 16S rRNA gene phylogeny demonstrated their belonging to the genus Candidatus Electronema. Atomic force microscopy and two-point probe resistance measurements were then used to map out the characteristics of the conductive nature, followed by microelectrode four-probe measurements to quantify the conductivity.

Interestingly, the authors observe that some freshwater cable bacteria filaments displayed a higher degree of robustness upon oxygen exposure than what was previously reported for marine cable bacteria. Finally, a single nanofiber conductivity on the order of 0.1 S/cm is calculated, which matches the expected electron current densities linking electrogenic sulphur oxidation to oxygen reduction in sediment. This is consistent with hopping transport.

Strengths and weaknesses:

A comprehensive study is applied to characterise the conductive properties of the sampled freshwater cable bacteria. Electrostatic force microscopy and conductive atomic force microscopy provide direct evidence of the location of conductive structures. Four-probe microelectrode devices are used to quantify the filament resistance, which presents a significant advantage over commonly used two-probe measurements that include contributions from contact resistances. While the methodology is convincing, I find that some of the conclusions seem to be drawn on very limited sample sizes, which display widely different behaviour. In particular:

The authors observe that the conductivity of freshwater filaments may be less sensitive to oxygen exposure than previously observed for marine filaments. This is indeed the case for an interdigitated array microelectrode experiment (presented in Figure 5) and for a conductive atomic force microscopy experiment (described in line 391), but the opposite is observed in another experiment (Figure S1). It is therefore difficult to assess the validity of the conclusion until sufficient experimental replications are presented.

The calculation of a single nanofiber conductivity is based on experiment and calculation with significant uncertainty. E.g. for the number of nanofibres in a single filament that varies depending on the filament size (Frontiers in microbiology, 2018, 9: 3044.), and the measured CB resistance, which does not scale well with inner probe separation (Figure 5). A more rigorous consideration of these uncertainties is required.

eLife assessment

This valuable study reports on several variants of the COVID-2 spike protein that are studied using well-established computational approaches, followed by attempts to validate the findings using experimental approaches. The evidence supporting the claims of the authors is solid, although there are known limitations of the computational approaches. The manuscript would benefit from a deeper discussion of the limitations and better contextualization of the work. The study will be of interest to biophysicists working in the general areas of allostery and protein evolution.

Reviewer #1 (Public Review):

Summary:<br /> The authors are developing differences in the dynamics and allostery of the SARS-COV-2 spike protein for several of the variants. They consider mainly the delta, omicron, and Omicron XBB, and show major differences in the dynamics of the open forms. In the most compelling step, they go further and compare against experimental values of IC50 and KD.

Overall, this is an important application of methods that were developed in the senior author's lab.

Strengths:<br /> The paper presents a strong case for the difference in the dynamical behavior of these sequence variants and relates this to available experiments.

Weaknesses:<br /> The work does not drill down to the effects of individual mutations, which might be possible and would improve our understanding of the effects of single mutations and would dissect the contributions of each single difference in sequence.

Reviewer #2 (Public Review):

The authors set out to identify CAPs (Candidate Adaptive Polymorphyisms), i.e., simply put mutations that carry a potential functional advantage, and utilize computational methods based on the perturbation of C-alpha positions with an Elastic Network Model to determine if dynamics of CAP residues are different in any way.

In my opinion this manuscript *may* suffer from fundamental flaws in the detection of CAPs, and does not provide enough analysis and discussion to determine if the methodology is applicable. A highly expanded and rewritten manuscript may help clarify the results. Lastly, the authors severely ignore the vast literature and results already in the public domain, not only with respect to the use of normal-mode analysis methods as well as the detection of functionally relevant mutations in general and to understand the evolution of the SARS-CoV-2 Spike protein in particular.

Reviewer #3 (Public Review):

Summary:<br /> The manuscript uses a combination of evolutionary approaches and structural/dynamics observations to provide mechanistic insights into the adaptation of the Spike protein during the evolution of variants.

Strengths:<br /> Very well-written text, pleasant and well-described pictures, and didactical and clear description of the methods.<br /> The citation of relevant similar results with different approaches is of note.<br /> Comparing the calculated scores with previous experimentally obtained data is one of the strongest points of the manuscript.

Weaknesses:<br /> A longer discussion of how the 19 orthologous coronavirus sequences were chosen would be helpful, as the rest of the paper hinges on this initial choice.<br /> The 'reasonable similarity' with previously published data is not well defined, nor there was any comment about some of the residues analyzed (namely 417-484).<br /> There seem to be no replicas of the MD simulations, nor a discussion of the convergence of these simulations.<br /> A more detailed description of the equilibration and production schemes used in MD would be helpful.<br /> Moreover, there is no discussion of how the equilibration procedure is evaluated, in particular for non-experts this would be helpful in judging the reliability of the procedure.

eLife assessment

This manuscript presents valuable findings that inform our understanding of the genetic underpinnings of the model plant Arabidopsis' resistance to turnip mosaic virus (TuMV). The strength of the evidence in the manuscript is convincing, with very large sample sizes, careful controls, multiple follow-up experiments, and broadening to the evolutionary context. There is very good support for each of the manuscript's conclusions and the work could pave the way for functional studies.

Reviewer #1 (Public Review):

In this manuscript, Butkovic et al. perform a genome-wide association (GWA) study on Arabidopsis thaliana inoculated with the natural pathogen turnip mosaic virus (TuMV) in laboratory conditions, with the aim to identify genetic associations with virus infection-related parameters. For this purpose, they use a large panel of A. thaliana inbred lines and two strains of TuMV, one naïve and one pre-adapted through experimental evolution. A strong association is found between a region in chromosome 2 (1.5 Mb) and the risk of systemic necrosis upon viral infection, although the causative gene remains to be pinpointed.

This project is a remarkable tour de force, but the conclusions that can be reached from the results obtained are unfortunately underwhelming. Some aspects of the work could be clarified, and presentation modified, to help the reader.

Reviewer #2 (Public Review):

The manuscript presents a valuable investigation of genetic associations related to plant resistance against the turnip mosaic virus (TuMV) using Arabidopsis thaliana as a model. The study infects over 1,000 A. thaliana inbred lines with both ancestral and evolved TuMV and assesses four disease-related traits: infectivity, disease progress, symptom severity, and necrosis. The findings reveal that plants infected with the evolved TuMV strain generally exhibited more severe disease symptoms than those infected with the ancestral strain. However, there was considerable variation among plant lines, highlighting the complexity of plant-virus interactions.

A major genetic locus on chromosome 2 was identified, strongly associated with symptom severity and necrosis. This region contained several candidate genes involved in plant defense against viruses. The study also identified additional genetic loci associated with necrosis, some common to both viral isolates and others specific to individual isolates. Structural variations, including transposable element insertions, were observed in the genomic region linked to disease traits.

Surprisingly, the minor allele associated with increased disease symptoms was geographically widespread among the studied plant lines, contrary to typical expectations of natural selection limiting the spread of deleterious alleles. Overall, this research provides valuable insights into the genetic basis of plant responses to TuMV, highlighting the complexity of these interactions and suggesting potential avenues for improving crop resilience against viral infections.

Overall, the manuscript is well-written, and the data are generally high-quality. The study is generally well-executed and contributes to our understanding of plant-virus interactions. I suggest that the authors consider the following points in future versions of this manuscript:

1. Major allele and minor allele definition: When these two concepts are mentioned in the figure, there is no clear definition of the two words in the text. Especially for major alleles, there is no clear definition in the whole text. It is recommended that the author further elaborate on these two concepts so that readers can more easily understand the text and figures.

2. Possible confusion caused by three words (Major focus / Major association and major allele): Because there is no explanation of the major allele in the text, it may cause readers to be confused with these two places in the text when trying to interpret the meaning of major allele: major locus (line 149)/ the major association with disease phenotypes (line 183).

3. Discussion: The authors could provide a more detailed discussion of how the research findings might inform crop protection strategies or breeding programs.

Reviewer #3 (Public Review):

Summary of Work<br /> This paper conducts the largest GWAS study of A. thaliana in response to a viral infection. The paper identifies a 1.5 MB region in the chromosome associated with disease, including SNPs, structural variation, and transposon insertions. Studies further validate the association experimentally with a separate experimental infection procedure with several lines and specific T-DNA mutants. Finally, the paper presents a geographic analysis of the minor disease allele and the major association. The major take-home message of the paper is that structural variants and not only SNPs are important changes associated with disease susceptibility. The manuscript also makes a strong case for negative frequency-dependent selection maintaining a disease susceptibility locus at low frequency.

Strengths and Weaknesses<br /> A major strength of this manuscript is the large sample sizes, careful experimental design, and rigor in the follow-up experiments. For instance, mentioning non-infected controls and using methods to determine if geographic locus associations were due to chance. The strong result of a GWAS-detected locus is impressive given the complex interaction between plant genotypes and strains noted in the results. In addition to the follow-up experiments, the geographic analysis added important context and broadened the scope of the study beyond typical lab-based GWAS studies. I find very few weaknesses in this manuscript.

Support of Conclusions<br /> The support for the conclusions is exceptional. This is due to the massive amount of evidence for each statement and also due to the careful consideration of alternative explanations for the data.

Significance of Work<br /> This manuscript will be of great significance in plant disease research, both for its findings and its experimental approach. The study has very important implications for genetic associations with disease beyond plants.

Author Response

We would like to thank you and the reviewers for evaluating this manuscript and providing constructive recommendations. Please see our provisional response to the major comments made by the reviewers.

Reviewer #1 (Public Review):

"…the authors never show that HFS of cortical inputs has no effect in the absence of thalamic stimulation. It appears that there is a citation showing this, but I think it would be important to show this in this study as well"

We understand that the reviewer would like us to induce an HFS protocol on cortical input and then test if there is any change in synaptic strength in thalamic input. We agree this is an important experiment which we will do.

Reviewer #2 (Public Review):

“…The experimental schemes in Figs. 1 and 3 (and Fig. 4e and extended data 4a,b) show that one group of animals was subjected to retrieval in the test context at 24 h, then received HFS, which was then followed by a second retrieval session. With this design, it remains unclear what the HFS impacts when it is delivered between these two 24 h memory retrieval sessions."

We understand that the reviewer has raised the concern that the increase in freezing we observed after the HFS protocol (ex. Fig. 1b, the bar labeled as Wth+24hHFSth) could be caused or modulated by the recall prior to the HFS (Fig. 1a, top branch).

If our interpretation of the concern is correct, we think this is unlikely to be the case. The first test, and the following HFS protocol, and the second test, (Fig. 1a, top branch) were all performed in the same chamber. For both the first and the second tests, animals received two 30-second recall trials, separated by 2 minutes (the data presented as the average of the two trials). We did not see a difference in freezing between the first and the second recall trials within each session (data not shown). It was only after the HFS protocol that we observed an increase in freezing.

This shows that in our paradigm the first recall does not impact the next recall in terms of the animals’ freezing levels. It must be noted that in cases where we did not do any testing prior to the HFS protocol, we still observed an increase in freezing after the HFS protocol (ex. Fig. 1a, middle branch and the corresponding data in Fig. 1b, the bar labeled as Wth+HFSth). Also, relevant is the data shown in Fig. 3c. Here, although animals were tested twice (Fig3. a, top branch), there was no increase in freezing in the second test (Fig. 3c, middle panel, Wth+24HFSCtx). That is, in the absence of an effective LTP, there is no significant difference between the two tests.

To further confirm this, in a new group of mice, 24 hours after weak conditioning, we will induce the HFS protocol, followed by testing (that is, no testing prior to the HFS protocol).

“The final experiment (Fig. 5a-c, extended data 5c) combines behavioral assessments with in vivo LFP recordings before and 24 h after hetero-HFS. While this experiment is demanding, it seems a bit underpowered”

We agree with the reviewer that the number of mice used in this experiment is on the lower side. However, this is not unusual for such an experimental configuration. As the reviewer mentioned, this is a demanding experiment for multiple reasons. For example, to confidently demonstrate that our HFS protocol, in addition to long-lasting behavioral changes, produces long-lasting synaptic changes, we must see a significant increase in evoked LFP after the manipulation which is predicted to last at least 24 hours. That is, the change in evoked LFP is not caused by non-related fluctuations, such as movement of the recording probe. For this reason, 3-4 days prior to conditioning, each day we measured evoked LFP. Only those mice that had a stable evoked LFP during this time were used for further conditioning. We will provide exclusion criteria for this experiment in the revised manuscript.

“ It would be critical to know if LFPs change over 24 h in animals in which memory is not altered by HFS,..”

We will perform an experiment where mice undergo a weak conditioning protocol and will record the evoked LFP 1-2 hours following the conditioning protocol, as well as the next day.

“…the slice experiments (Fig. 5d-f) are not well aligned with the in vivo experiments (juvenile animals, electrical vs. opto stimulation, different HFS protocols, timescale of hours).”

Our aim in this part was to demonstrate that the pathways we chose for our study can undergo heteroLTP. For this purpose, we used an already established protocol, which uses electrical stimulation (Fonseca, 2013). For clarification, I have tried to induce optical LTP with a high-frequency stimulation protocol in slices, but I did not succeed. I am not aware of a work that successfully induced optical LTP with a high-frequency protocol.

eLife assessment

This study presents important findings that homo- and heterosynaptic plasticity outside of the window at which a weak associative fear memory is formed can transform this memory into a stronger one, and can produce fear memory even when stimuli were not paired. This work therefore expands our views on the role of time- and input-specificity of plasticity in learning processes. The evidence, based on state-of-the-art in vivo manipulations and activity recordings in behaving mice, supporting the conclusions is solid, although further validation of the methods used is required in order to reaffirm the authors' conclusion. Once resolved, the work will be of broad interest to neuroscientists interested in activity-dependent synaptic plasticity and associative memory.

Reviewer #1 (Public Review):

Summary:

The authors' goal here was to explore how a non-hebbian form of plasticity, heterosynaptic LTP, could shape neuronal responses and learning. They used several conceptually and technically innovative approaches to answer this. First, they identified a behavioral paradigm that was a subthreshold training paradigm (stimulation of thalamic inputs with a footshock), which could be 'converted' to memory via homosynaptic LTP (HFS of thalamic inputs). They then found that stimulation of 'cortical' inputs could also convert the subthreshold stimulation to a lasting memory and that this was associated with a change in neuronal response, akin to LTP. Finally, they provided some slice work that demonstrated that stimulation of cortical inputs could stabilize LTP at thalamic inputs.

Strengths:

1) The approach was innovative and asked an important question in the field.

2) The studies are, for the most part, quite rigorous, using a novel dual opsin approach to probe multiple inputs in vivo.

3) The authors explore neural responses both in vivo and ex vivo, as well as leveraging a 'simple' behavior output of freezing.

Weaknesses:

1) There appears to be a flaw in the exploration of cortical inputs. the authors never show that HFS of cortical inputs has no effect in the absence of thalamic stimulation. It appears that there is a citation showing this, but I think it would be important to show this in this study as well.

2) It is somewhat confusing that the authors refer to the cortical input as driving heterosynaptic LTP, but this is not shown until Figure 4J, that after non-associative conditioning (unpaired shock and tone) HFS of the cortex can drive freezing and heterosynaptic LTP of thalamic inputs. Further, the authors are 'surprised' by this outcome, which appears to be what they predict.

3) 'Cortex' as a stimulation site is vague. The authors have coordinates they used, it is unclear why they are not using standard anatomical nomenclature.

4) The authors' repeated use of homoLTP and heteroLTP to define the input that is being stimulated makes it challenging to understand the experimental detail. While I appreciate this is part of the goal, more descriptive words such as 'thalamic' and 'cortical' would make this much easier to understand.

Reviewer #2 (Public Review):

Faress et al. ask the question of how synaptic plasticity (i.e. long-term potentiation, LTP) induced at different time points and different synapses in relationship to learning can transform memories supported by these circuits. The authors adopted an experimental design developed by Nabavi et al, 2014 and used male mice to optogenetically induce a weak fear memory in thalamo-LA circuits by pairing an optical conditioned stimulus (CS) at thalamo-LA synapses with a footshock unconditioned stimulus (US), or subjected the mice to an unpairing of the opto-CS and the footshock US. They then investigated how homosynaptic (thalamo-LA)- or heterosynaptic (cortico-LA) high-frequency stimulation (HFS) -that would induce LTP- delivered at different time points before and after learning can transform the opto-fear memory by using state of the art in vivo dual-wavelength optogenetics. They find that homosynaptic HFS delivered before or after learning transforms weak memories into stronger ones, whereas heterosynaptic HFS can do so when delivered immediately after learning. Both homo- and hetero-HFS delivered after unpairing produce a 24 h fear memory for the opto-CS. Lastly, they show that synaptic potentiation accompanies the strengthening of fear memory induced by hetero HFS in freely moving mice.

The significance of the study lies in showing in vivo that plasticity induced at different times or different synapses than those engaged during learning can modify memory and the synaptic strength in a synaptic pathway related to that memory. While heterosynaptic and timing-dependent effects in synaptic plasticity have been described largely ex vivo on shorter time scales, the discovery of lasting behavioral effects on memory is novel.

A strength of the study is that it uses well-defined and elegant optogenetic manipulations of distinct neural pathways in awake-behaving mice combined with in vivo recordings, which allows the authors to directly manipulate and monitor synaptic strength and memory.

The conclusions of this paper are mostly well supported by the data, but there are some aspects that should be resolved:

1. The experimental design for assessing the effects of applying HFS 24 h after conditioning should be clarified, and it should be re-evaluated which experimental groups can be compared and how. The experimental schemes in Figs. 1 and 3 (and Fig. 4e and extended data 4a,b) show that one group of animals was subjected to retrieval in the test context at 24 h, then received HFS, which was then followed by a second retrieval session. With this design, it remains unclear what the HFS impacts when it is delivered between these two 24 h memory retrieval sessions. It would be nice to see these data parsed out in a clean experimental design for all experiments (in Figs 1, 3, and 4), that means 4 groups with different treatments that are all tested only once at 24 h, and the appropriate statistical tests (ANOVA). This would also avoid repeating data in different panels for different pairwise comparisons (Fig 1, Fig 3, Fig 4, and extended Fig 4).

2. The final experiment (Fig. 5a-c, extended data 5c) combines behavioral assessments with in vivo LFP recordings before and 24 h after hetero-HFS. While this experiment is demanding, it seems a bit underpowered and not well-controlled. It would be critical to know if LFPs change over 24 h in animals in which memory is not altered by HFS, and to see correlations between memory performance and LFP changes, as two animals displayed low freezing levels. Also, the slice experiments (Fig. 5d-f) are not well aligned with the in vivo experiments (juvenile animals, electrical vs. opto stimulation, different HFS protocols, timescale of hours). They would suggest that thalamo-LA potentiation occurs directly after learning+HFS (which could be tested) and is maintained over 24 h.

3. The statistical analyses need to be clarified. All statements should be supported with statistical testing (e.g. extended data 5c, pg 7 stats are missing). The specific tests should be clearly stated throughout. For ANOVAs, the post-hoc tests and their outcomes should be stated. In some cases, 2-way ANOVAs were performed, but it seems there is only one independent variable, calling for one-way ANOVA.

4. There are a number of details in the methods and procedures that need to be elaborated on and clarified for the reader. All of them will be listed in the recommendations to the authors.

Reviewer #3 (Public Review):

Summary:

In this study, Faress and colleagues investigated the differential contributions of Hebbian and non-hebbian plasticity to long-term memory. For this, the authors relied on in vivo optogenetic manipulations of thalamic (Th) and cortical (Ctx) inputs to the lateral amygdala (LA), a circuit whose role in associative memories is well established. The authors first begin by demonstrating that following a weak association protocol (also involving opto stimulation of the Th input) high-frequency stimulation (HFS) of the Th input induces robust conditioned responses (CR) 24 hours later. The authors then use two excitatory opsins to independently manipulate Ctx and Th inputs to the LA. They show that by delivering HFS of the Ctx input, LTP can be observed at Th-LA inputs which is accompanied by long-lasting memory effects.

Strengths:

Overall, the study addresses an important scientific question and could potentially result in a very valuable contribution to the field. The combination of in vivo electrophysiology with optogenetic manipulations of individual input sources to the LA is attractive.

Weaknesses:

While the methods employed in this study are attractive, they are also associated with major weaknesses. In particular, the manuscript lacks convincing validation and sufficient controls. Specific comments are included in the "Recommendations for the authors" section.

eLife assessment

This study enhances our understanding of the relationship between cortico-hippocampal interactions and behavioral performance. Using an inter-areal coherence metric to gate trial initiation in real time, the authors provide solid evidence that links high hippocampal-prefrontal theta coherence to correct performance on spatial working memory and cue-guided decision-making tasks. Although reviewers agreed that the results do not demonstrate causality between hippocampal-prefrontal synchrony and behavioral performance, the findings are viewed as important given their potential implications for brain-machine interface applications in humans.

Reviewer #1 (Public Review):

Summary:

Information transfer between the hippocampus and prefrontal cortex is thought to be critical for spatial working memory, but most of the prior evidence for this hypothesis is correlational. This study attempts to test this causally by linking trial start times to theta-band coherence between these two structures. The authors find that trials initiated during periods of high coherence led to a dramatic improvement in performance. This applied not only to a spatial working memory task, but also to a cue-guided navigation task, suggesting that coherence in these regions may be a signature of a heightened attentional or preparatory state. The authors supplement this behavioral result with electrophysiological recordings to test whether the ventral midline thalamus is likely to mediate hippocampal-prefrontal coherence.

Strengths:

This study demonstrates a striking behavioral effect; by changing the moment at which a trial is initiated, performance on a spatial working memory task improves dramatically, from around 80% correct to over 90% correct. A smaller but nonetheless robust increase in accuracy was also seen in a texture discrimination task. Therefore, prefrontal-hippocampal synchronization in the theta band may not only be important for spatial navigation but may also be associated with improved performance in a range of tasks. If these results can be replicated using noninvasive EEG, it would open up a powerful avenue for modulating human behavior.

Weaknesses:

Ventral midline thalamic nuclei, such as reuniens, have reciprocal projections to both the prefrontal cortex and hippocampus and are therefore well-situated to mediate theta-band interactions between these structures. However, alternative mechanisms cannot be ruled out by the results of this study. For example, theta rhythms are globally coherent across the rodent hippocampus, and the ventral hippocampus projects directly to the prefrontal cortex. Theta propagation may depend on this pathway, and may only be passively inherited by VMT.

The optogenetic manipulations are intended to show that theta in VMT propagates to PFC and also affects HPC-PFC coherence. However, the "theta" induced by driving thalamic neurons at 7 Hz is extremely artificial. To demonstrate that VMT is causally involved in coordinating activity across HPC and PFC, it would have been better to optogenetically inhibit, rather than excite, these nuclei. If the authors were able to show that the natural occurrence of theta in PFC depends on activity in VMT, that would be a much more convincing test of their hypothesis.

Reviewer #2 (Public Review):

A number of previous reports have demonstrated that theta synchrony between the hippocampus (HPC) and prefrontal cortex (PFC) is associated with correct performance on spatial working memory tasks. The main goal of the current study is to examine this relationship by initiating trials either randomly (as is typically done) or during periods of high or low PFC-HPC coherence. To this end, they develop a 'brain-machine interface' (BMI) that provides real-time estimates of PFC-HPC theta coherence, which are then used to control trial onset using an automated figure-eight maze. Their main finding is that choice accuracy is significantly higher on trials initiated when theta coherence is high whereas performance on low coherence trials does not differ from randomly initiated control trials. They also observe a similar result using a non-working memory task in the same maze.

Overall the main experiments (Figures 1-4) are well designed and the BMI approach is convincingly validated. There are also appropriate controls and analyses to rule out behavioral confounds and the results clearly presented. The idea of triggering trial onset based on brain activity is an interesting idea and helps to examine how extremes in the distribution of brain states are associated with behavior, something that might be more difficult to examine if trials are initiated randomly. As such, the BMI is an interesting approach for studying the neuronal basis of behavior that could potentially be applied beyond the particular field of the study, something the authors could perhaps have elaborated on more.

That being said, although the authors have elegantly revealed an association between PFC-HPC theta synchrony and behavior using their BMI approach, it is not apparent whether these results add substantially to previous reports of similar associations, including from the author's own work. The authors sometimes seem to claim that they do; for example, in the discussion, after describing previous studies that reported an association between PFC-HPC theta synchrony and behavior, they raise the reasonable question "did mPFC-hippocampal theta coherence lead to, or coincide with, correct choice outcomes?" What they subsequently write gives the impression that their study has somehow addressed the question, whereas in fact their results still leave this question open. For example, it is entirely possible that during high-coherence trials an unobserved neural process is influencing both coherence and task performance. The authors could have made a more convincing case as to why their correlative results go beyond similar findings from previous studies, perhaps by including additional analysis to strengthen their case.

Sometimes, the authors also seem to suggest that their results establish a causal relationship between synchrony and behavior, for example when they say that they have "demonstrated for the first time that strong mPFC-hippocampal theta coherence ENHANCES memory-guided choice" (line 557, my emphasis). However, causal manipulations of PFC-HPC synchrony would be required to make such claims. I am not suggesting that the lack of such data is necessarily a weakness of the study, only that causal claims are not supported by the author's results.

In addition to the behavioral results described above, the authors also examine how HPC-PFC synchrony modulates synchrony with the ventromedial thalamus (VMT; Figure 5) and how optogenetic modulation of the VMT influences PFC-HPC synchrony (Figure 6). However, these results feel somewhat more preliminary and their relationship to the other findings in the manuscript is not always clear. For example, given that the authors demonstrate that "Prefrontal-hippocampal theta synchronization modulates prefrontal-thalamic interactions" (Figure 5) I would rather have expected the authors to manipulate HPC and/or PFC and see how this affects VMT in Figure 6. It is also difficult to draw strong conclusions about the effects of optogenetic VMT stimulation since the results presented by the authors come from only 2 rats (Figure 6D-K) and therefore feel somewhat anecdotal. I could also not find any statistical test supporting the increase in the proportion of phase-locked neurons during high theta states shown in Figure 5K.

Reviewer #3 (Public Review):

Stout et al investigate the link between prefrontal-hippocampal (PFC-HPC) theta-band coherence and accurate decision-making in spatial decision-making tasks. Previous studies show that PFC-HPC theta coherence positively correlates with learning of these tasks and correct decisions but the nature of this relation relies on correlations that cannot show whether coherence leads, coincides, or is a consequence of decision making. To investigate more precisely this link, the authors devise a novel paradigm. In this paradigm, the rat is blocked during a delay period preceding its choice and they control on a trial-by-trial basis the level of PFC-HPC theta coherence prior to the decision by allowing the rat to access the choice point only at a time when coherence reaches above or below a threshold. The design of the paradigm is very nicely controlled thanks in particular to the trial-by-trial matching of delay period durations which is crucial for the working memory task. Moreover, the behaviour of the animal is strongly similar during high and low coherence periods which bolsters the specificity of the author's interpretation. Thanks to this approach, the authors clearly demonstrate that high theta coherence prior to choice-making is strongly predictive of better decision-making both in working memory and a cue-guided version of the task.

This novel paradigm provides an improvement in the level of experimental control to analyse the coherence/choice link but the exact interpretation of the results it yields is not entirely clear in the current manuscript. Using the PFC-HPC theta coherence during the delay period to the gate when the rat accesses the choice zone clearly separates this coherence from the behavioural decision itself. This provides convincing support for the idea that PFC-HPC theta coherence prior to the behavioural decision is related to correct decision-making and is not simply temporally coincidental or a consequence of the decision output. It does not however substantially increase the weight of evidence in favour of a causal link between theta coherence and correct decisions as suggested in the abstract ("PFC-HPC theta synchronization leads to correct choices"). Indeed, the paradigm does not de-correlate PFC-HPC theta synchronization from other neurophysiological variables such as neuromodulation, arousal, synchrony with other areas, etc that could be playing the true causal role in modulating decision-making.

The question of the link between the manuscript's findings and causal involvement of PFC-HPC dialogue is interestingly highlighted by the author's unexpected result showing that their paradigm reveals a link between theta coherence even in a sensory-driven version of the task. As the authors point out, results based on muscimol inhibition have shown that neither PFC nor HPC, nor the ventral midline thalamus, that mediates communication between the two, are involved in this task. This raises the question of why coherence between two areas is predictive of choice accuracy when neither area appears to be causally involved. The manuscript does not discuss the possibility that these results could imply that theta coherence is not in fact a good causal indicator. As an illustrative example, it could be linked for example with neuromodulation (ie dopamine, see Benchenane et al, 2010) which itself causally modifies the choice process. In this case, coherence would be an excellent predictor of accuracy (as the authors show) without implying a causally important information exchange between the two regions, since inhibiting these regions is without effect.

Altogether, this novel paradigm provides finer control to analyse the role of theta coherence in behaviour. This allows pinpointing of interesting cases in which coherence increases during correct task performance although it may have at least an indirect causal role. This opens up the possibility of interrogating when inter-area synchrony is associated with information transfer and when this information is then used to drive behavioural decisions.

Author Response

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

We thank Reviewer 1 for their time reviewing our revised manuscript and appreciate their thoughtful suggestions for further clarity. In regard to the public review statement, "However, parts of the methods (e.g. assessment of blanks and data filtering) and results (e.g. visualization of plant community data) could still be polished, and the figures should be improved to increase the clarity of the manuscript", we have made small modifications in the text and figures during production of the Version of Record to address these important suggestions.

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

Reviewer #1 (Public Review):

This manuscript compiles the colonization of shrubs during the Late Pleistocene in Northern America and Europe by comparing plant sedimentary ancient DNA (sedaDNA) records from different published lake sediment cores and also adds two new datasets from Island. The major findings of this work aim to illuminate the colonization patterns of woody shrubs (Salicaceae and Betulaceae) in these sediment archives to understand this process in the past and evaluate its importance under future deglaciation and warming of the Arctic.

We greatly appreciate the time and detailed consideration of our manuscript by Reviewer 1. Our responses to individual comments are highlighted in blue, with the original comments provided by the reviewer in black.

The strength of evidence is solid as methods (sedimentary DNA) and data analyses broadly support the claims because the authors use an established metabarcoding approach with PCR replicates (supporting the replicability of PCR and thereby proving the occurrence of Salicaeae and Betulaceae in the samples) and quantitative estimation of plant DNA with qPCR (which defines the number of cycles used for each PCR amplification to prevent overamplification). However, the extraction methods need more explanation and the bioinformatic pipeline is not well-known and needs also some further description in the main text (not only referring to other publications).

Thank you for bringing this to our attention. We have now provided greater detail on our extraction methods and bioinformatic pipeline.

The authors compare their own data with previously published data to indicate the different timing of shrubification in the selected sites and show that Salicaceae occurs always like a pioneer shrub after deglaciation, followed by Betaluaceae with a various time lag. The successive colonization of Salicaceae followed by Betulaceae is explained by its differences in environmental tolerance, the time lag of colonization in the compared records is e.g. explained by varying distance to source areas.

However, there are some weaknesses in the strength of evidence because full sedaDNA plant DNA assessment, quality of the sedaDNA data (relative abundance and richness of sedaDNA plant composition) and results from Blank controls (for sedaDNA) are not fully provided. I think it is important to show how the plant metabarcoding in general worked out, because it is known that e.g. poor richness can be indicative of less preserved DNA and a full plant assessment (shown in the supplement) would be more comprehensive and would likely attract a larger readership.

Thank you for bringing these important points to our attention. The DNA dataset including the full taxa assemblage will be included with the manuscript upon publication and apologize for not including it during the review process. This dataset will also include information on positive and negative blanks used for quality control. Following suggestions from Reviewer 2, we have now also calculated some recently proposed DNA quality metrics (Rijal et al., 2021), which collectively support our earlier conclusions that our record is of sufficient quality to draw the current conclusions. We hope that the inclusion of the complete DNA dataset will indeed draw a larger readership.

Further, it would allow us to see the relative abundance in changes of plants and would make it easier to understand if the families Salicaeae and Betulaceae are a major component of the community signal. Further, the possibility to reach higher taxonomic resolution with sedaDNA compared to pollen or to facilitate a continuous record (which is different from macrofossils) is not discussed in the manuscript but should be added. Also, the taxonomic resolution within these families in the discussed datasets would be of interest, also on the sequence type level if tax. assignments are similar.

Thank you for these suggestions. We have focused on these two families as it is known from numerous pollen records and floras that they are the major component of the vascular plant communities in the regions investigated. Betula (birch) and Salix (willow) are indeed the most dominant woodland shrubs of the tundra biome, which covers expansive areas of the Arctic. For example, in Iceland natural woodlands, which cover 1.5% of the total land area, are composed of 80% birch shrubs (Snorrason et al. 2016, Náttúrufræðingurinn 86). Salix mixes in with Betula, especially around wet sites. Species from both genera are common and wide-spread throughout Iceland, but dwarf and cold tolerant species thrive best on the highland or at glacial sites, while shrub-like species are more common on the lowland, coastal area and in sheltered valleys. Flora of Iceland (http://www.floraislands.is/PDF-skjol/Checklist-vascular.pdf) lists Betula as the only genus of Betulaceae native to Iceland (page 79/80) and Salix as the major genus of Salicaceae (page 82-85), although Populus tremula (Salicaceae) exists in the wild but is rare (perhaps just a countable number of trees/shrubs in the whole country). The point is that, for Iceland, Betulaceae is Betula and Salicaceae is Salix, meaning that our sedaDNA method has the taxonomic resolution at the genus level. And with the help of pollen analysis of the site near Stóra Viðarvatn (the novel sedaDNA work of the present paper), i.e., Ytri-Áland site (Karlsdóttir et al. 2014), it is possible to interpret our results even to the species level, which we have only mention in the discussion. It has been suggested that matching sedaDNA results with botanical knowledge about the study site and the vegetation history (local reference database) is one way to increase taxonomic resolution of the sedaDNA approach (e.g. Elliott et al. 2023, Quaternary 6,7). In the same way we find our sedaDNA analysis having sufficient resolution to answer the questions asked in the present study. For the future, although we do not include it in the discussion this time, it should be possible to increase the taxonomic resolution of plant metabarcoding by priming multiple genes simultaneously like that is described as a proof of concept by Foster et al. (2021, Front Ecol Evol 9: 735744). In the revised version of the manuscript, we have now expanded on the power of sedaDNA in terms of increased taxonomic resolution and application in continuous lake sediment records in the introduction of the manuscript. Following Reviewer 2’s suggestion, we have now included the sequences used for taxonomic assignment in the supplement information.

Another important aspect is how the abundance/occurrence of Salicaceae is discussed. Many studies on sedaDNA confirm an overrepresentation of this family due to better preservation in the sediment, far-distance transport along rivers, or preferences of primers during amplification etc. As this family is the major objective of this study, such discussion should be added to the manuscript and data should be presented accordingly.

Thank you for raising this point. The reviewer is indeed correct that Salicaceae is typically overrepresented in read abundance compared to other vascular plant taxa in sedaDNA studies. However, as we mention in the Results and Interpretation section for Stóra Viðarvatn “As PCR amplification results in sequence read abundances that may not reflect original relative abundances in a sample (Nichols et al., 2018), we focus our discussion on taxa presence/absence,” we do not place weight on the indeed greater relative abundance of Salicaceae in our own dataset. As such, this different relative abundance of plant taxa reads should not influence the conclusions drawn in the manuscript.

I also miss more clarity about how the authors defined the source areas (refugia) of the shrubs. If these source areas are described in other literature I suggest to show them in a map or so. Further, it should be also discussed and explained more in detail which specific environmental preferences these families have, this is too short in the introduction and too unspecific. Also, it would be beneficial to show relative abundances rather than just highlighted areas in the Figures and it would allow us to see if Salicaeae will be replaced by Betulaceae after colonizing or if both families persist together, which might be important to understand future development of shrubs in these areas.

Thank you for allowing us to clarify. As the regions studied with the lake sediment records shown in this manuscript were all covered by extensive ice sheets during the Last Glacial Maximum (LGM, Fig. 1), plant refugia and source areas must have been located somewhere south of the ice sheet margins. Thus, we calculate our distance to source as the minimum distance from a lake site to land beyond the extent of the ice sheet during the LGM. This has now been clarified in the text and highlighted in Fig. 1. We have also added in the discussion molecular results from Thórsson et al. (2010, J Biogeogr 37) on possible source origins of Betula in Iceland. Details on taxa environmental preferences have now been expanded upon in the Discussion section where we explore the various trait-based factors that may influence the relative differences in colonization timing between Salicaceae and Betulaceae. We have now also edited Figs. 3 and 4 to include PCR replicates instead of highlighted bars to better compare the DNA and pollen datasets from Iceland.

The author started a discussion about shrubification in the future, but a more defined evaluation and discussion of how to use such paleo datasets to predict future shrubification and its consequences for the Arctic would give more significance to the work.

Thank you for this suggestion and allowing us to expand on potential future changes. We have now edited this final section of the paper to provide a little more detail on how we envision these records being used to predict future shrubification and climate change.

Reviewer #1 (Recommendations For The Authors):

I list some more specific details here.

You speak about "read counts", I guess you used relative abundance of read counts, you should state it like this.

Thank you for allowing us to clarify. The data that we refer do in terms of read counts is from the previously published studies in the circum North Atlantic. The data provided from these studies is raw read counts, and not relative abundance.

Line 100: What do you mean here: "temperature changes in prior warm periods"?

Thank you for allowing us to clarify. We have rephrased to sentence to “higher temperature in prior warm periods”, which we hope is clearer for the reader.

Line 134: How is DNA diluted by minerogenic sediment? Did the sedimentation rate increase? Typically minerogenic input should be beneficial for DNA preservation.

Thank you for allowing us to clarify. These samples were primarily comprised of tephra glass with minimal organic content. While we agree that minerogenic sediment is generally beneficial for DNA preservation, the predominance of inorganics (tephra) that fell from the sky, rather than being washed into the lake from the landscape, would not carry organic sediment with it. We have rephrased the sentence to make this clearer.

I would suggest adding more citations to the text (for example statements in lines 106, 110, 368)

Thank you for the suggestion. The manuscript has been edited accordingly.

Better divide your discussion part: discussion about dispersal mechanisms occur in both sections. Maybe you could divide it into environmental factors for colonization and traitbased factors (only an idea).

Thank you for the suggestion. We have now edited the second dispersal section to “Environmental dispersal mechanisms” to be clearer about our focus on factors such as wind, sea ice, and birds that may transport the seeds across the North Atlantic. The previous section retains the trait-based factors that may influence relative timing in colonization between Salicaceae and Betulaceae.

Which type of sequencing did you use, paired-end 76bp is unknown to me.

Methods have now been edited to clarify this, along with details related to extraction methods as requested in the Public Review.

Reviewer #2 (Public Review):

Harding et al have analysed 75 sedaDNA samples from Store Vidarvatn in Iceland. They have also revised the age-depth model of earlier pollen, macrofossil, and sedaDNA studies from Torfdalsvatn (Iceland), and they review sedaDNA studies for first detection of Betulaceae and Salicaceae in Iceland and surrounding areas. Their Store Vidarvatn data are potentially very interesting, with 53 taxa detected in 73 of the samples, but only results on two taxa are presented. Their revised age-depth model cast new light on earlier studies from Torfdalsvatn, which allows a more precise comparison to the other studies. The main result from both sedaDNA and the review is that Salicaceae arrives before Betulaceae in Iceland and the surrounding area. This is a well-known fact from pollen, macrofossil, and sedaDNA studies (Fredskild 1991 Nordic J Bot, Birks & Birks QSR 2014, Alsos et al. 2009, 2016, 2022) and as expected as the northernmost Salix reach the Polar Desert zone (zone A, 1-3oC July temperature) whereas the northernmost Betula rarely goes beyond the Southern Tundra (zone D, 8-9 oC July temperature, Walker et al. 2005 J. Veg. Sci., Elven et al. 2011 http://panarcticflora.org/ ).

We greatly appreciate the time and detailed consideration of our manuscript by Reviewer 2. Our responses to individual comments are highlighted in blue, with the original comments provided by the reviewer in black.

While we agree that previous studies have indeed indicated a relative delay in Betula colonization relative to Salix, most of these have relied on pollen and macrofossil evidence, which are complicated to use as proxies for the first appearance of a given taxa (see our Introduction in the main manuscript). A few studies have shown this also with sedaDNA (e.g., Alsos et al., 2022), which is a more robust proxy for a plant taxa’s presence, but these have been limited geographically (e.g., northern Fennoscandia). In our study, we show that this pattern is reflected in 10 different lakes across the North Atlantic, emphasizing the broad nature of Betula’s delayed colonization relative to other woody shrubs, such as Salix.

My major concern is their conclusion that lag in shrubification may be expected based on the observations that there is a time gap between deglaciation and the arrival of Salicaceae and between the arrival of Salicaceae and Betulaceae. A "lag" in biological terms is defined as the time from when a site becomes environmentally suitable for a species until the species establish at the site (Alexander et al. 2018 Glob. Change Biol.). The climate requirement for Salicaceae highly depends on species. In the three northernmost zones (A-C), it appears as a dwarf shrub, and it only appears as a shrub in the Southern Tundra (D) and Shrub Tundra (E) zone, and further south it is commonly trees. Thus, Salicaceae cannot be used to distinguish between the shrub tundra and more northern other zones, and therefore cannot be used as an indicator for arctic shrubification. Betulaceae, on the other hand, rarely reach zone C, and are common in zone D and further south. Thus, if we assume that the first Betulaceae to arrive in Iceland is Betula nana, this is a good indicator of the expansion of shrub tundra. Thus, if they could estimate when the climate became suitable for B. nana, they would have a good indicator of colonisation lags, which can provide some valuable information about time lags in shrub expansion (especially to islands). They could use either independent proxy or information from the other species recorded in sedaDNA to reconstruct minimum July temperature (see e.g. Parducci et al. 2012a+b Science, Alsos et al. 2020 QSR).

We appreciate the reviewer’s insight into the implications of our use of the word “lag”. Indeed, as we do not have site-specific climate timeseries for each lake record, we have adjusted our wording to “delay”, which we believe is more general and descriptive of our observations. We recognize the importance of independent paleotemperature records for each lake, but these are not yet available for all records, so we prefer to keep our study focused on the delay instead. In addition, we prefer not to derive temperature records from the vegetation sedaDNA records, as these are not independent and will incorporate changes driven by additional factors, such as soil and light (e.g., Alsos et al., 2022). We have added some text to the final section on Future Outlook that elaborates on the need for complimentary records of past climate to pair with paleoecological records of colonization. We hope that this motivates the community to pursue these lines of research that we agree are needed.

The study gives a nice summary of current knowledge and the new sedaDNA data generated are valuable for anyone interested in the post-glacial colonisation of Iceland. Unfortunately, neither raw nor final data are given. Providing the raw data would allow re-analysing with a more extensive reference library, and providing final data used in their publication will for sure interest many botanists and palaeoecologist, especially as 73 samples provide high time resolution compared to most other sedaDNA studies.

Finally, the raw and final data, including blank controls, used in our study for Stóra Viðarvatn will ultimately be provided with the manuscript’s publication. We apologize for not including it with the original submission.

Reviewer #2 (Recommendations For The Authors):

Line 112-113: Difference in northward expansion rate is not the same as lag. Thus, your conclusion "As a result, the biospheres role in future high latitude temperature amplification may be delayed." does not derive directly from the data you present.

Thank you for allowing us to clarify our wording. We have rephrased the sentence to align with our results more closely as stated in the Abstract of the manuscript.

.Line 133: From Figure S3, it looks like three or possibly four samples failed.

Thank you for pointing this out. First, we realized that the DNA reads originally included in Figure S3 were from after filtering. We have now updated the figure to include the total raw reads, which is a better indicator of DNA reliability (Rijal et al., 2021). Based on the total raw reads, only two samples failed with total reads of 2 and 5.

Line 141: You say you focus on presence/absence, but you do show quantitative results for Salix and Betula (0-5 PCR repeats) in Figure 2.

Thank you for allowing us to clarify. Fig 2 shows the number of replicates that meet our criteria for taxa presence, where a higher number of replicates corresponds to a higher likelihood of presence.

Line 142: Where are the other 51 taxa shown?

We are providing the full DNA record in the supplement, which will be published alongside the main manuscript. We have also now included a plot of species richness against sample depth in Fig. S2.

Line 178-179: Note that the revised date of first detection is close to what has been previously published (Salix ~10300 vs. 10227, Betula ~9500 vs 9680), so it does not make any changes to previous interpretation.

Yes, this is true. However, we still believe it is important to always consider improvements in age models to best correlate the timing of events between different paleo records.

Line 191-194 and Figure S2: I leave the evaluation of revised age-depth model to the geologist.

As this aspect was not commented on, we assume that both reviewers are satisfied.

Line 197: "Delay" is a more correct word than "lag".

Thank you, edited.

Line 210: Where do 1700 and 2500 come from? If your revised age of ice retreat is 11 800, and your revised date of Salix and Betula arrival are ~10 300 and ~9500, I make this 1500 and 2300.

Yes, this is correct. Thank you for pointing out this error.

Line 215-217: To be more certain about any bias caused by low DNA quality, I suggest you explore your data using the tools presented in Rijal et al. 2021 Science Advances. As you do not provide your data, I cannot evaluate the quality of them.

Thank you for the suggestion. We have now calculated the various DNA quality indices developed by Rijal et al. (2021). This has been added to the methods and results section for the Stóra Viðarvatn record, as well as in Fig. S3. The MTQ and MAQ scores are known to correlate with species richness when richness is low (n<30, Rijal et al., 2021), which is likely an artifact of the requirement that the 10 best represented barcode sequences are required to calculate these scores. As this correlation is observed in our dataset and given that our species richness is low (n<30, Fig. S2), the low MTQ and MAQ score are not likely indicative of low-quality DNA. We therefore judge the quality of our DNA on total raw reads and CT values, which remain relatively constant through time (Fig. S2).

Line 226: Do you mean TDV?

We intended to omit unnecessary abbreviations throughout the manuscript, such as lake names, in our original manuscript. We have now changed TORF, which we use as the lake’s abbreviation, to the full lake name, Torfdalsvatn.

Line 282-283: Given that the basal sediments of Nordivatnet are marine (Brown et al. 2022 PNAS Nexus), even a low detection may be a strong indication of local presence.

Thank you for this point. However, to standardize the records and compare across a wide range of geographical and depositional settings, we prefer to apply the same criteria for the taxa’s presence to each lake as outlined in our Methods.

Line 289: See the definition of "lag"

Changed to “delayed” per your earlier suggestion. Thank you.

Line 298-303: I agree that the late appearance of Betula at Langfjordvatnet (10 000 cal BP) is anomalously long and a bit unexpected given that it is found at five other lakes in the region 13000-10200 cal BP (Alsos et al. 2022). However, a likely explanation is the lack of area with stable soil - B. nana requires a greater degree of soil development compared to other heath shrubs (Whittaker 1993) and Langfjordvatnet is surrounded by steep scree slopes (Otterå 2012 master thesis Univ. Bergen). At Jøkelvatnet, Salix appears in the four available samples from 10453 to 9811 whereas Betula arrives 9663. Here, the arrival of Betula is just at the drop of local glacier activity and at the temperature rise, suggesting that it arrives immediately after the climate becomes suitable (Elliott et al. 2023 Quaternary). Thus, based on N Fennoscandia where we have more data available, it does not show lags and does not support delayed shrubification (which contrasts with what we have shown for many other species including common dwarf shrubs, see Alsos et al. 2022). Would be very interesting to have similar data from Iceland, which has a large dispersal barrier.

Thank you for these further considerations. We have incorporated those related to Langfjordvannet into the manuscript accordingly. We also appreciate the point regarding Jøkelvatnet. However, as stated in our Methods section for “Published sedaDNA datasets”, we do not include Jøkelvatnet in our comparison due to the impact of glacier activity as the reviewer notes: “Finally, both Jøkelvatnet and Kuutsjärvi were impacted by glacial meltwater during the Early Holocene when woody taxa are first identified (Wittmeier et al., 2015; Bogren, 2019), and thus the inferred timing of plant colonization is probably confounded in this unstable landscape by periodic pulses of terrestrial detritus.” Due to the glacier’s presence in the lake catchment, it is not possible to discern whether delay in Betulaceae would have occurred if the glacier were not present. Therefore, we prefer to keep this record excluded from our comparisons.

Line 316-319 and 344: Based on contemporary genetic patterns, Alsos et al. analyse the relative importance of adaptation to dispersal compared to other factors.

Thank for you bringing up this important point. We have now expanded our discussion to include these analyses from Alsos et al. (2022).

Line 342+350: Original publication is Alsos et al. 2007 Science

Thank you, edited.

Line 343: Alsos et al. 2009 Salix study is the wrong citation here. Eidesen et al. 2015 Mol. Ecol. shows phylogeography of Greenland population but not Baffin - I am not aware of any contemporary genetic studies of Betula from Baffin.

Thank you for pointing this out. We will also include the Eidesen et al. (2015) citation for reference to Greenland. However, there is one data point included for southern Baffin Island in Alsos et al. (2009), so we will retain this citation here as well.

Line 351-353: See comment about Betula from Baffin above. Also, I am not sure I follow here - what do you mean by "these populations" - the Svalbard ones or Iceland? Eidesen et al. 2015 is the wrong citation for Salix - use Alsos et al. 2009. Alsos et al. 2009 suggest Iceland (and E Grenland) was colonized from north Scandinavia, although this was uncertain as no data were available from Faroe/Shetland. Svalbard was colonized from N Fennoscandia (Alsos et al. 2007).

Regarding Baffin Island sources, we refer the reviewer to our response to their previous comment. We have clarified the wording of our sentence from “these populations” to “the modern populations from these locations [Baffin Island, Greenland, and Svalbard]”. We have removed reference to Eidesen et al. (2015), as this is for Betula rather than Salix. Finally, we have added a citation for Alsos et al. (2007) here for Svalbard.

Line 354-355: AFLP suggest that Baffin and W Greenland were colonised from a refugia south of the Wisconsin Ice Sheet, see Alsos et al. 2009.

Yes, we are aware, thank you. Our reference to “mid-latitude North America” in the sentence acknowledges this refugia, but we have now added “south of the Laurentide Ice Sheet” for further clarification.

Line 363-381: See comment above; your Store Vidarvatn data do currently not demonstrate a lag between environmental suitability and climate, but using the rest of the DNA record, potentially it could. Would also be good to reflect on the distance to the source area for shrubs Late Glacial/Early Holocene compared to now.

Thank you for these suggestions. We have edited this section of the manuscript to elaborate on the need for independent climate reconstructions as well as the fact that distances to plant refugia are shorter now than during the last postglacial period.

Line 396-416: I am not an expert on tephra so I will not comment on this part.

As this aspect was not commented on, we assume that both reviewers are satisfied.

Line 459-457: Please provide results of how much data is lost at each step of filtering.

We added the read loss following each filtering step as a table in the supplemental information (Table S4).

Throughout the manuscript, you go only to species level although DNA in most cases is able to distinguish to genus level within Salicaceae and Betulaceae - which sequences did you identify?

Sequences are now provided in the supplemental for Salicaceae and Betulaceae. Based on our bioinformatic pipeline, reference library and requirement for 100% match between sequence and taxonomy, we were only able to distinguish between species level.

Figure 2: The detection of Betulaceae is very sporadic in Stóra Vidarvatn with occurrence in only seven samples and hardly ever in all 5 repeats, suggesting that if you apply a statistical model to estimate first arrival (see Alsos et al. 2022), you will have a large confidence interval. Thus, these uncertainties should be considered when estimating the delayed arrival of Betula compared to Salix. The data from Torfdalsvatn (which I assume are from Alsos et al. 2021 although not specified in the figure legend), shows detection in all samples from the first appearance and mostly in 8 of 8 repeats (shown in the original publication - you could to the same here), thus providing a more accurate estimate for the time gap between arrival of Salix and Betula.

Thank you for bringing up this important point. The detection of Betulaceae is indeed sporadic, but we believe it reflects the genuine nature of its presence/absence during the Holocene in Northeast Iceland. This is supported by Betula pollen from a nearby peat record that shows a similar history (Fig. 4, Karlsdóttir et al., 2014), which we have now elaborated on in the Results and Interpretation section. As for the timing of Betulaceae colonization at this site, the first appearance in the DNA record should be a close minimum estimate as shown with modern DNA and plant survey comparisons (e.g., Sjögren et al., 2017; Alsos et al., 2018). The true first appearance could be biased by small amounts of plants being present in the early stages of colonization and not registering the sedimentary record until enough dead plant material is transported to the depocenter of the lake. However, this is likely less than age model uncertainties and therefore not likely relevant on geologic timescales as in this study. In this sense, our age models and those published for the other records indicate this is generally on the order of several hundred years. In addition, we have now added the Alsos et al. (2021) reference for Torfdalsvatn. Unfortunately, this Torfdalsvatn study does not provide number of PCR repeats so we will keep the figure as is as it best represents the available data.

Figure 5: I suggest adding lake names to the figure. Is there a dot missing for lake 5 for Salicaceae?

Thank you for the suggestion, we have added lake names to the figure. There is a dot marked for Salicaceae for lake 5, however, not for Betulaceae as this taxon was not identified. We refer the reviewer to the Discussion Section “Postglacial sedaDNA records from the circum North Atlantic” and the lake’s original publication (Volstad et al., 2020).

Figure 6: I find it more relevant to plot colonization time versus distance to LGM sheetice margin - lake number is just an arbitrary number.

We appreciate the suggestion and have modified the figure accordingly.

Author Response

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

Reviewer #1 (Public Review):

In the present manuscript, Abele et al use Salmonella strains modified to robustly induce one of two different types of regulated cell death, pyroptosis or apoptosis in all growth phases and cell types to assess the role of pyroptosis versus apoptosis in systemic versus intestinal epithelial pathogen clearance. They demonstrate that in systemic spread, which requires growth in macrophages, pyroptosis is required to eliminate Salmonella, while in intestinal epithelial cells (IEC), extrusion of the infected cell into the intestinal lumen induced by apoptosis or pyroptosis is sufficient for early pathogen restriction. The methods used in these studies are thorough and well-controlled and lead to robust results, that mostly support the conclusions. The impact on the field is considered minor as the observations are somewhat redundant with previous observations and not generalizable due to cited evidence of different outcomes in other models of infection and a relatively artificial study system that does not permit the assessment of later time points in infection due to rapid clearance. This excludes the study of later effects of differences between pyroptosis and apoptosis in IEC such as i.e. IL-18 and eicosanoid release, which are only observed in the former and can have effects later in infection.” We thank the reviewer for their time and effort in assessing our manuscript.

We agree with the reviewer’s overall assessment. One minor clarification is that the engineering used does not express the proteins in “all growth phases”, but rather only when the SPI2 T3SS is expressed; we used the sseJ promoter, which is a SPI2 effector.

Reviewer #2 (Public Review):

In this study, Abele et al. present evidence to suggest that two different forms of regulated cell death, pyroptosis and apoptosis, are not equivalent in their ability to clear infection with recombinant Salmonella strains engineered to express the pro-pyroptotic NLRC4 agonist, FliC ("FliC-ON"), or the pro-apoptotic protein, BID ("BID-ON"). In general, individual experiments are well-controlled, and most conclusions are justified. However, the cohesion between different types of experiments could be strengthened and the overall impact and significance of the study could be articulated better. ”

We thank the reviewer for their time and effort in assessing our manuscript. We agree with the reviewer’s overall assessment.

Reviewer #1 (Recommendations For The Authors):

Abstract: While new terms are sometimes useful for the visualization of concepts and I appreciate the "bucket list" analogy, it is not yet an accepted term in cell death research, and using it twice in the abstract seems out of order. ”

We opted to keep the term, but reduce its use to once in the abstract with a specific comment on the recent coining of the term: “We recently suggested that such diverse tasks can be considered as different cellular “bucket lists” to be accomplished before a cell dies.” We recently coined this term in a review in Trends in Cell Biology, where three reviewers had quite positive comments about the concept. Time will tell whether this is a useful term for the cell death field or not.

“In figure 2C-F Caspase 1 and Gsdmd deficient animals have higher levels of vector control strain than WT or Nlrc4. Could this be due to the redundancy with Nlrp3 in systemic infection described by Broz et al? Please mention in the description of the results.”

The reviewer correctly points out a trend in the data. However, our experiments are not powered to show that this difference is statistically significant. Nevertheless, we now make note of the trend, and cite prior papers that have observed NLRC4 and NLRP3 redundancy against non-engineered S. Typhimurium strains.

“The observation that apoptosis does not affect Salmonella systemically would be strengthened if the experiments using the BIDon strain could be taken out to a later time point, i.e. 72 or 96 h.”

Indeed, we wanted to extend our studies to these timepoints. However, although expression of the SspH1 translocation signal is benign for 48 h, by 72 h this causes mild attenuation (regardless of whether the BID-BH3 domain is attached as cargo). We think that the degree of difficulty for SPI2 effectors to reprogram the vacuole increases over time, and that only beyond 48 h does SPI2 need to function at peak efficiency. This observation will be reported in a second manuscript that is written and will be submitted within this month. We are happy to supply this manuscript to reviewers if they would like to see the results. We also added text to the discussion to alert the reader to the caveats of engineering S. Typhimurium at later timepoints.

“Discussion: The authors claim that pyroptotic and apoptotic signaling in IEC have the same outcome and IEC only has extrusion as a task. However, upon pyroptosis, IEC also releases IL-18 and eicosanoids, which is not the case during apoptosis. While the initial extrusion makes all the difference in early infection, Mueller et al 2016 showed that lack of IL-18 has an effect on salmonella dissemination at a 72h time point. The FlicON model can not test later time points as the bacteria will be cleared by then, but this caveat should be discussed.”

We revised the text in the discussion to make it clear that extrusion is not the only bucket list item for IECs, and that IL-18 and eicosanoids are included in the bucket list for IECs after caspase-1 activation, and add the citation to Muller et al.

Reviewer #2 (Recommendations For The Authors):

1) The manuscript is written in a rather colloquial style. Additional editing is recommended. ”

We edited the abstract to limit the use of the bucket list term and to make more clear that this is a new term that our lab has proposed in a recent review in Trends in Cell Biology. The managing editor for the current manuscript at eLife commented that the prose was lively and thoughtful. We would be happy to make edits if the reviewer has more specific suggestions.

2) It is not obvious from the Results section that all mouse infections were, in fact, mixed infections. This should be stated more clearly. Additionally, there is a minor concern regarding in vivo plasmid loss over time.

We added text to the results to make this clearer at the beginning of each in vivo figure in the paper. Our experiments are intentionally blind to any Salmonella that have lost the plasmid. These bacteria essentially convert to a wild type phenotype, and thus are no longer representative of FliCON or BIDON bacteria. We also verify the long established equal competition between pWSK29 (amp) and pWSK129 (kan) in Supplemental Figure 2A-B. Prior experiments from the laboratory of Sam Miller and others in the 1990s showed that plasmid loss occurs at a rate of less than 1%.

3) Results shown in Figure 4 are difficult to interpret. Essentially, the experiment is aimed at comparing the two engineered Salmonella strains (FliC-ON and BID-ON). However, these strains are very different from one another, which may have a confounding effect on the interpretation of the data.”

The reviewer has interpreted the experiment correctly. We wanted to make clear to the reader that the two strains induce apoptosis under different kinetics. Indeed, it would be very surprising if two different engineering methods created strains that caused apoptosis with identical kinetics. We make two text edits to the results to make this clearer, concluding with “Overall, both ways of achieving apoptosis are successful in vitro, but with slightly different kinetics.”.

4) What new insights into mechanisms of bacterial pathogenesis and host response are gained by using recombinant Salmonella (over)expressing a pro-apoptotic protein is not clearly stated.”

We modify the introduction to make this more clear, stating: “Here, we investigate whether apoptotic pathways could be useful in clearing intracellular infection. Because S. Typhimurium likely evades apoptotic pathways, we again use engineering in order to create strains that will induce apoptosis. This allows us to study apoptosis in a controlled manner in vivo.”

5) The Discussion section, while provocative, seems speculative and should be revised. Concepts of "backup apoptosis" and crosstalk between pyroptosis and apoptosis are intriguing, but it seems implausible to this reviewer that a cell might "know" that it will die, might "choose" how to die, and might aim to complete a "bucket list" before it loses all functional capacity. The usage of these types of terms does not help bolster the authors' central conclusions. ”

We agree that cells do not “choose” pathways for regulated cell death. We had over-anthropomorphized the concepts surrounding these interconnected cell death pathways that are created by evolution. We edited the introduction and discussion to remove the “choose” term. However, we kept the second phrase using “know” in the discussion with an added clarifier: “Once a cell initiates cell death signaling, it “knows” that it will die (or rather evolution has created signaling cascades that are predicated upon the initiation of RCD).”. Sometimes anthropomorphizing scientific concepts can be a useful tool to facilitate understanding of complex scientific concepts. For example, the “Red Queen hypothesis” clearly anthropomorphizes the concept of continuous evolution to maintain an evolutionary equilibrium. We have found that scientists in the cell death field often think that modes of cell death are or should be interchangeable. We hope that the idea of the “bucket list” will help to crystalize the idea that distinct processes leading up to different types of regulated cell death can have very different consequences during infection.

Additional Comments from the Reviewing Editor:

1) The authors show that FliC-ON is not cleared from the spleen of Casp1 KO or Gsdmd KO mice. The conclusion is that the backup apoptosis pathways that should be present in these mice are insufficient to clear the bacteria from the spleen. However, although it is shown that bone marrow macrophages undergo apoptosis in vitro, I believe it is not shown that the apoptotic pathways are actually activated in the spleen. This seems like an important caveat. Could it be shown (or has it previously been shown) that the cells infected in the spleens of Casp1 KO or Gsdmd KO are activating apoptosis? If not, it seems possible that the reason the bacteria are not cleared is due to a lack of apoptosis activation rather than an ineffectiveness of apoptosis, and the authors could consider explicitly acknowledging this.”

We agree, and added to the discussion “A final possibility is that our engineered strains are not successfully triggering apoptosis within splenic macrophages. This could be due to intrinsic differences between BMMs and splenic macrophages or could be due to bacterial virulence factors that fail to suppress apoptosis only in vitro. It is quite difficult to experimentally prove that apoptosis occurs in vivo due to rapid efferocytosis of the apoptotic cells.”

2) Both reviewers were somewhat unhappy about some of the new terminology/metaphors that are introduced in the manuscript. I understand the reviewers' concerns but also feel that the writing is lively and thoughtful. It is up to the authors to decide whether to retain their new terminology, but the response of two expert reviewers might give the authors some pause. At a minimum, to address the concern about an unfamiliar term being used in the abstract, perhaps explicitly state that you are introducing "bucket list" as a new concept to help explain the results. The introduction of this concept may indeed be one of the novel contributions of the manuscript.”

We opted to keep the term, but reduce its use to once in the abstract with a specific comment on the recent coining of the term: “We recently suggested that such diverse tasks can be considered as different cellular “bucket lists” to be accomplished before a cell dies.” We recently coined this term in a review in Trends in Cell Biology, where three reviewers had quite positive comments about the concept. Time will tell whether this is a useful term for the cell death field or not.

3) Perhaps this is implied in the discussion already, but it might make sense to state the obvious difference between IECs and splenic macrophages which is that the death of the former results in the removal of the cell and its contents (i.e., Salmonella) from the tissue, whereas the death of the latter does not. This seems like the simplest explanation for why apoptosis restricts bacterial replication in IECs but not macrophages, and I am not sure if introducing the concept of a "bucket list" improves the explanation or not.”

We agree that this narrative nicely distills the differences between these cell types. We edited the final paragraph of the discussion to include this narrative.

4) Lastly, some minor comments

-- p.2 "hyperactivate" instead of "hyperactive"?”

Corrected.

-- the authors may also want to mention Shigella, as it might provide another example that apoptotic C8dependent backup protects IECs”

Yes, indeed, this is a good comparison to make. We added this to the discussion.

-- p.8, in case readers are unfamiliar with the concept of a PIT, the authors should perhaps cite their own work when they first mention this concept (at the top of the page)”

Indeed, citation added.

eLife assessment

Host cell death is an effective strategy to protect against infection, and is believed to function primarily by the elimination of the intracellular niche for pathogen replication. Abele and colleagues address an important question: does the mode of cell death affect its effectiveness in pathogen clearance? Consistent with prior observations, the authors provide compelling new evidence that the answer can depend on the cell type and/or tissue involved.

Joint Public Review:

In the present manuscript, Abele et al use Salmonella strains modified to robustly induce one of two different types of regulated cell death, pyroptosis or apoptosis in all cell types to assess the role of pyroptosis versus apoptosis in systemic versus intestinal epithelial pathogen clearance. They demonstrate that in systemic spread, which requires growth in macrophages, pyroptosis is required to eliminate Salmonella, while in intestinal epithelial cells (IEC), extrusion of the infected cell into the intestinal lumen induced by apoptosis or pyroptosis is sufficient for early pathogen restriction. The methods used in these studies are thorough and well controlled and lead to robust results, that mostly support the conclusions. The impact on the field is considered minor as the observations are somewhat redundant with previous observations and and not generalizable due to cited evidence of different outcomes in other models of infection and a relatively artificial study system that does not permit the assessment of later timepoints in infection due to rapid clearance. This excludes the study of later effects of differences between pyroptosis and apoptosis in IEC such as i.e. IL-18 and eicosanoid release, which are only observed in the former and can have effects later in infection.

Author Response

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

We are very grateful to the reviewers for their thoughtful comments on the manuscript and to the editors for their assessment.

We thank the reviewers for their positive feedback and appreciate that they consider our method a valid addition to previously established systems for generating recombinant RNA viruses.

To strengthen this point, we have now included additional validation by the rescue of recombinant Chikungunya and Dengue virus from viral RNA directly, using the CLEVER protocol. This strengthens the potential of this method as a reverse genetics platform for positive-stranded viruses in general.

The supportive data has been amended in the Results section, taken into account in Materials and Methods, and the corresponding supplementary figure (Figure S4) has been added.

One key point raised by one of the reviewers, a comparison with different systems, could not be addressed in this manuscript as our lab does not at all perform BAC cloning. We currently do not have the necessary expertise to conduct an unbiased side-by-side comparison.

All other comments were addressed in detail, either by including additional data or through specific clarification in the revised text. We are grateful for the careful review and constructive criticisms raised by the reviewers and feel that the corrections and additions have significantly improved the manuscript.

We have revised the latest version posted May 30, 2023 on bioRxiv (https://doi.org/10.1101/2023.05.11.540343).

Reviewer #1:

Public Review:

In this manuscript, Kipfer et al describe a method for a fast and accurate SARS-CoV2 rescue and mutagenesis. This work is based on a published method termed ISA (infectious subgenomic amplicons), in which partially overlapping DNA fragments covering the entire viral genome and additional 5' and 3' sequences are transfected into mammalian cell lines. These DNA fragments recombine in the cells, express the full length viral genomic RNA and launch replication and rescue of infectious virus.

CLEVER, the method described here significantly improves on the ISA method to generate infectious SARS-CoV2, making it widely useful to the virology community.

Specifically, the strengths of this method are:

1) The successful use of various cell lines and transfection methods.

2) Generation of a four-fragment system, which significantly improves the method efficiency due to lower number of required recombination events.

3) Flexibility in choice of overlapping sequences, making this system more versatile.

4) The authors demonstrated how this system can be used to introduce point mutations as well as insertion of a tag and deletion of a viral gene.

5) Fast-tracking generation of infectious virus directly from RNA of clinical isolates by RT-PCR, without the need for cloning the fragments or using synthetic sequences.

One weakness of the latter point, which is also pointed out by the authors, is that the direct rescue of clinical isolates was not tested for sequence fidelity.

The manuscript clearly presents the findings, and the proof-of-concept experiments are well designed.

Overall, this is a very useful method for SARS-CoV2 research. Importantly, it can be applicable to many other viruses, speeding up the response to newly emerging viruses than threaten the public health.

We thank the reviewer for this positive feedback and the summary of the main points. Nevertheless, we would like to comment on point 5): “the direct rescue of clinical isolates was not tested for sequence fidelity”

This impression by the reviewer suggests that the data was not sufficient on this point. However, the sequence fidelity after direct rescue from RNA was indeed tested in this study, even on a clonal level (please see: Table S2, or raw NGS data SRX20303605 - SRX20303607). For higher clarity, we added the following sentence to the manuscript:<br /> “Indeed, a slight increase of unintentional mutations was observed when sequencing clonal virus populations rescued from RNA directly”.

Recommendations for the authors:

Minor Points:

1) On page 8, the authors write: "levels correlated very well with the viral phenotype". This sentence is not clear. Please clarify what you mean by "viral phenotype". Do you mean CPE on Vero cells?

We corrected the sentence to: “(…) staining intensity and patterns correlated very well with the wild-type phenotype.”

2) Page 9 "sequences were analyzed with a cut-off of 10%. Cutoff of what? please clarify.

The sentence was rephrased to: “(…)mutations with a relative abundance of >10% in the entire virus population were analyzed”

3) Page 15: The authors refer to the time required for completion of each step of the process. It would be helpful and informative for the readers to include a panel in figure 4, visualizing the timelines.

We included a timeline in Figure 4, Panel A.

4) Materials and methods, first paragraph: Please specify which human samples were collected. Do the authors refer to clinical virus isolates?

We added the following information to the Materials and Methods section:<br /> “Human serum samples for neutralization assays were collected from SARS-CoV-2 vaccinated anonymous donors (…)”

Clinical virus isolates (Material and Methods; Virus) were used for control experiments, neutralization assays, or as templates for RT-PCR.

5) Supplementary figure 4A: The color scheme makes it hard to differentiate between the BA.1 and BA.5 fragments. Please choose colors that are not as similar to each other.

Colors were adapted for better distinction.

Reviewer #2:

Public Review:

The authors of the manuscript have developed and used cloning-free method. It is not entirely novel (rather it is based on previously described ISA method) but it is clearly efficient and useful complementation to the already existing methods. One of strong points of the approach use by authors is that it is very versatile, i.e. can be used in combination with already existing methods and tools. I find it important as many laboratories have already established their favorite methods to manipulate SARS-CoV-2 genome and are probably unwilling to change their approach entirely. Though authors highlight the benefits of their method these are probably not absolute - other methods may be as efficient or as fast. Still, I find myself thinking that for certain purposes I would like to complement my current approach with elements from authors CLEVER method.

The work does not contain much novel biological data - which is expected for a paper dedicated to development of new method (or for improving the existing one). It may be kind of shortcoming as it is commonly expected that authors who have developed new methods apply it for discovery of something novel. The work stops on step of rescue the viruses and confirming their biological properties. This part is done very well and represents a strength of the study. The properties of rescued viruses were also studied using NSG methods that revealed high accuracy of the used method, which is very important as the method relies on use of PCR that is known to generate random mistakes and therefore not always method of choice.

What I found missing is a real head-to-head comparison of the developed system with an existing alternatives, preferably some PCR-free standard methods such as use of BAC clones. There are a lot of comparisons but they are not direct, just data from different studies has been compared. Authors could also be more opened to discuss limitations of the method. One of these seems to be rather low rescue efficiency - 1 rescue event per 11,000 transfected cells. This is much lower compared to infectious plasmid (about 1 event per 100 cells or so) and infectious RNAs (often 1 event per 10 cells, for smaller genomes most of transfected cells become infected). This makes the CLEVER method poorly suitable for generation of large infectious virus libraries and excludes its usage for studies of mutant viruses that harbor strongly attenuating mutations. Many of such mutations may reduce virus genome infectivity by 3-4 orders of magnitude; with current efficiencies the use of CLEVER approach may result in false conclusions (mutant viruses will be classified as non-viable while in reality they are just strongly attenuated).

We thank reviewer 2 for the careful review of our work and the valuable feedback. We agree that a direct comparison with other (PCR-free) methods such as BAC cloning, could be useful for demonstrating the unique benefits of the CLEVER method. However, as our laboratory does not use any BAC or YAC cloning methods, we could not ensure an unbiased side-byside comparison using different techniques.

We would like to highlight the avoidance of any yeast/bacterial cloning steps that render the CLEVER protocol significantly faster and easier to handle. A visualization of the key steps that could be skipped using CLEVER in comparison to common reverse genetics methods is given in Figure 6.

Further, we firmly believe that the benefits of the CLEVER method become especially apparent for large viral genomes such as the one of SARS-CoV-2, where assembly, genome amplification and sequence verification of plasmid DNA are highly inefficient and more timeconsuming than for small viruses like DENV, CHIKV or HIV.

We agree with the reviewer that the overall transfection and recombination efficiencies observed with CLEVER seemed rather low. Although data on transfection/rescue efficiency is known for many techniques and viruses, we did not find any published data on the reconstitution of SARS-CoV-2 or viruses with similar genome sizes. Therefore, a useful comparator for our observations in relation to other techniques is currently simply missing. We therefore emphasize that the efficiencies of CLEVER were achieved with one of the largest plus-stranded RNA virus genomes, and our data can’t be directly compared to transfection efficiencies of short infectious RNAs.

On the contrary, it was rather interesting to observe the very high rescue efficiency of infectious virus progeny. During the two years of establishing and validating the CLEVER protocol, we reached success rates for the genome reconstitution after transfection of >95 %. This was even obtained with highly attenuated mutants including rCoV2∆ORF3678 (joint deletion of ORF3a, ORF6, ORF7a, and ORF8) (Liu et al., 2022)(see Author response image 1). We amended this data in response to the reviewers’ comment and as an example of the successful rescue of an attenuated virus from five overlapping genome fragments (fragments A, B, C, D1, and D2∆ORF3678).

The latter data were not added to the main manuscript since in this case the deletions were introduced using a different method: from the plasmid-based DNA fragment D2∆ORF3678 and not directly from PCR-based mutagenesis.

Further, CLEVER was used for related substantial manipulations, including the complete deletion of the Envelope gene (E) which led to the creation of a single-cycle virus that may serve as a live, replication-incompetent vaccine candidate (Lett et al., 2023).

Author response image 1.

rCoV2∆ORF3678. Detection of intracellular SARS-CoV-2 nucleocapsid protein (N, green) and nuclei (Hoechst, blue) in Vero E6TMPRSS2 cells infected with rCoV2∆ORF3678 by immunocytochemistry. Scalebar is 200 µm in overview and 50 µm in ROI images.

Recommendations for the authors:

The work is nicely presented and the method authors has developed is clearly valuable. As indicated in Public review section the work would benefit from direct comparison of CLEVER with that of infectious plasmid (or RNA) based methods; direct comparison of data would be more convincing that indirect one. Authors should also discuss possible limitations of the method - this is helpful for a reader.

We were not able to perform a direct comparison of CLEVER with other methods (see our statement above).

We added the following section to the discussion: “Along with the advantages of the CLEVER protocol, limitations must be considered: Interestingly, virus was never rescued after transfecting Vero E6 cells, as has been observed previously (Mélade et al., 2022). Whether this is due to low transfection efficiency or the cell’s inability to recombine remains to be elucidated. Other cell lines not tested within this study will have to be tested for efficient recombination and virus production first. Further, the high sequence integrity of rescued virus is highly dependent on the fidelity of the DNA polymerase used for amplification. The use of other enzymes might negatively influence the sequence integrity of recombinant virus, as it has been observed for the direct rescue from viral RNA using a commercially available onestep RT-PCR kit. Another limitation when performing direct mutagenesis is the synthesis of long oligos to create an overlapping region. Repetitive sequences, for example, can impair synthesis, and self-annealing and hairpin formation increase with prolonged oligos.”

Some technical corrections of the text would be beneficial. In all past of the text the use of terms applicable only for DNA or RNA is mixed and creates some confusion. For example, authors state that "the human cytomegalovirus promoter (CMV) was cloned upstream of 5' UTR and poly(A) tail, the hepatitis delta ribozyme (HDVr) and the simian virus 40 polyadenylation signal downstream of the 3' UTR". Strictly speaking it is impossible as such a construct would contain dsDNA sequence (CMV promoter) followed by ssRNA (5'UTR, polyA tail and HDV ribozyme) and then again dsDNA (SV40 terminator). So, better to be correct and add "sequences corresponding to", "dsDNA copies of" to the description of RNA elements

We thank the reviewer for the advice but would like to state that in scientific language it is common to assume that nucleic acid cloning is based on DNA.

We have corrected the description in the Methods section: “The human cytomegalovirus promoter (CMV) was cloned upstream of the DNA sequence of the viral 5’UTR; herein, the first five nucleotides (ATATT) correspond to the 5’UTR of SARS-CoV. Sequences corresponding to the poly(A) tail (n=35), the hepatitis delta virus ribozyme (HDVr), and the simian virus 40 polyadenylation signal (SV40pA) were cloned immediately downstream of the DNA sequence of the viral 3’UTR.”

For ease of reading and for consistent terminology, we kept the original spelling in the rest of the manuscript.

In description of neutralization assay authors have used temperature 34 C for incubation of virus with antibodies as well as for subsequent incubation of infected cells. Why this temperature was used?

The following sentence was added (Materials and Methods; Cells): “A lower incubation temperature was chosen based on previous studies (V’kovski et al., 2021).”

References

Lett MJ, Otte F, Hauser D, Schön J, Kipfer ET, Hoffmann D, Halwe NJ, Ulrich L, Zhang Y, Cmiljanovic V, Wylezich C, Urda L, Lang C, Beer M, Mittelholzer C, Klimkait T. 2023. Single-cycle SARS-CoV-2 vaccine elicits high protection and sterilizing immunity in hamsters. doi:10.1101/2023.05.17.541127

Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Kurhade C, Plante JA, Bopp NE, Kalveram B, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi P-Y. 2022. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. Nat Commun 13:4337. doi:10.1038/s41467-022-31930-z

V’kovski P, Gultom M, Kelly JN, Steiner S, Russeil J, Mangeat B, Cora E, Pezoldt J, Holwerda M, Kratzel A, Laloli L, Wider M, Portmann J, Tran T, Ebert N, Stalder H, Hartmann R, Gardeux V, Alpern D, Deplancke B, Thiel V, Dijkman R. 2021. Disparate temperaturedependent virus–host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium. PLoS Biol 19:e3001158. doi:10.1371/journal.pbio.3001158

eLife assessment

This study describes CLEVER, an improved method for fast and efficient rescue and mutagenesis of SARS-CoV2. While the principle of this method is not new, this work significantly improves upon existing protocols, providing an important advancement in the field of viral infectious clones. Convincing proof-of-concept experiments were performed that demonstrate the utility and efficiency of the method.

Joint Public Review:

In this manuscript, Kipfer et al describe a method for a fast and accurate SARS-CoV2 rescue and mutagenesis. This work is based on a published method termed ISA (infectious subgenomic amplicons), in which partially overlapping DNA fragments covering the entire viral genome and additional 5' and 3' sequences are transfected into mammalian cell lines. These DNA fragments recombine in the cells, express the full length viral genomic RNA and launch replication and rescue of infectious virus.

CLEVER, the method described here significantly improves on the ISA method to generate infectious SARS-CoV2, making it widely useful to the virology community.

Specifically, the strengths of this method are:<br /> 1) The successful use of various cell lines and transfection methods.<br /> 2) Generation of a four-fragment system, which significantly improves the method efficiency due to lower number of required recombination events.<br /> 3) Flexibility in choice of overlapping sequences, making this system more versatile.<br /> 4) The authors demonstrated how this system can be used to introduce point mutations as well as insertion of a tag and deletion of a viral gene.<br /> 5) Fast-tracking generation of infectious virus directly from RNA of clinical isolates by RT-PCR, without the need for cloning the fragments or using synthetic sequences.<br /> 6) The authors further expanded this method to work on additional plus-strand RNA viruses beyond SARS-CoV-2 (CHIKV, DENV)

The manuscript clearly presents the findings, and the proof-of-concept experiments are well designed.

Overall, this is a very useful method for SARS-CoV2 research. Importantly, it can be applicable to many other viruses, speeding up the response to newly emerging viruses than threaten the public health.

Author Response

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

Note to reviewer and editor:

In the previous version of the manuscript, we referred to ‘prevalent’ disease at baseline (e.g., prevalent cardiovascular disease). We have since changed this throughout the manuscript to ‘past or prevalent’ disease. This is a more accurate description as we ascertained diseases which occurred prior to baseline but may have been resolved by the time of the accelerometry study.

Responses to reviewer 1:

• I assume that not every participant provided data on all 7 nights. Did the authors exclude those who had fewer number of nights with accelerometer data (e.g., only 2-3 days), as the SRI based on fewer nights may not reliably reflect sleep regularity compared with SRI based all 7 consecutive nights?

It is correct that not every participant provided complete accelerometry data. Most participants (88%) provided complete data. We only included participants who provided at least 2 valid measurements of the SRI (requiring valid data for at least 2 pairs of contiguous 24-hour periods). This is described in the appendix, but we have additionally now added this detail to the main text:

“Most participants (88%) provided complete accelerometry data. Participants with fewer than two valid SRI measurements (i.e., less than 2 contiguous 24-hour wear periods; <1%) were excluded.”

We would also like to note that our statistical analysis accounted, to some extent, for the lower reliability of SRI estimates in those with fewer nights of data. In those with sparse data, their estimated average SRI value would be pulled towards the overall sample average relatively more than for those with complete data. This is a consequence of the ‘partial pooling’ of the linear mixed effects model.

• The primary analysis and results were based on restricted cubic spline models that allow assessment of nonlinearity. This is different from the usual strategy that starts with the simpler linear relationship and further explores potential nonlinear relationships. Did the authors have a strong rationale for a nonlinear dose-response relationship between sleep regularity and mortality, so that the assessment of linear relationships was skipped?

We chose to model the SRI with a restricted cubic spline for two reasons. Firstly, we did expect non-linearity to be present a-priori. Partly this was because other sleep exposures (especially sleep time) have known non-linear relationships with health outcomes. We also thought that it is was plausible that a ‘plateau’ might be present, which we wanted to capture. Secondly, we decided that our primary model should be sufficiently flexible from the outset in order that we did not need to make data-driven adjustments to our model specification (e.g., adding non-linear terms depending on the results of hypothesis tests). This approach we believe to be generally safer as making data-driven changes can undermine the validity of standard errors and p-values.1

• Was the proportional hazards assumption violated in the Cox modeling? Were discrete-time hazard models used to address the violation of the modeling assumption? Please clarify.

Yes, the proportional hazards assumption was violated for all models except for the cardiovascular disease death model. This was the rationale for the use of the discrete time hazards model. They allowed for the inclusion of a flexible time by SRI interaction, allowing the hazard ratio to vary over the follow-up period. We have made this clearer in our revision. The following text has been added to the statistical methods:

“In addition to Cox models, discrete-time hazards models, including an interaction between SRI and time (aggregated into 3-month intervals and modeled with a restricted cubic spline with knots at the 5th, 35th, 65th, and 95th percentiles), were fitted to relax the assumption of proportionality and allow hazard ratios (HRs) to vary over time. The SRI by time interaction in this model provided a test of proportionality (a small p value would indicate strong evidence against the proportional hazards assumption).”

• Please provide correlations between different sleep regularity measures. Although different measures lead to the same conclusion, it is interesting that SRI appeared to provide stronger signals with mortality than the other two SD measures. In addition to what was discussed by the authors, another possibility is that SRI also captures the regularity of napping during the day which is common in older populations.

Thank you for this helpful suggestion. We have added a correlation matrix for the different sleep regularity measures (Table S1). We have additionally added the following text to the Results:

“The SRI was modestly negatively correlated with the sleep duration SD (-0.32) and sleep onset time SD ( 0.42; see correlation matrix in Table S1).”

Regarding napping during the day, the algorithm we used to make determinations of sleep and wake unfortunately is not able to identify napping. This is because, in the absence of a sleep diary, it is very difficult to distinguish napping from inactivity in accelerometry data. The algorithm that we used requires the estimation of a ‘sleep period time window’, defining the period from the beginning to the end of the main sleep bout, in which sleep can be identified. Any sleep outside of this window is treated as inactivity. While some methods have been developed to estimate napping time from accelerometry without a sleep diary, we are not aware of any that are validated for adults using wrist worn accelerometers.

This is something that was not sufficiently clear from the current manuscript. We have had added the following text to ensure this is clear in the revised version.

Methods:

“To distinguish sleep from sustained periods of inactivity without reference to a sleep diary (not available in the UKB), GGIR uses an algorithm to determine a daily ‘sleep period time window’ for each participant.11 This defines the time window between the onset and end of the main daily sleep period, during which periods of sustained inactivity are interpreted as sleep. The algorithm does not, by default, detect bouts of sleep outside of this window and hence is not able to identify naps.”

Discussion:

“In addition, sleep diaries in the UKB were not available. Consequently, the algorithm we used to determine sleep and wake relied on the identification of a main ‘sleep period time window’ and did not identify napping..”

• Table 1 - I would suggest adding additional columns showing the variable distributions across quantiles of the SRI, which can help understand the confounding structure and the covariate associations with SRI.

We agree that this is a good idea and we have adjusted Table 1 accordingly.

• Figure 1 and related supplemental Figures: it would be good to label in the figure the specific HR estimate and 95% CI mentioned in the manuscript.

Thank you for this suggestion. We agree that this would be helpful. After some consideration, we have decided to leave the figures as they are for one primary reason. This is that we want to avoid over-emphasising the 5th and 95th quantiles. As discussed above, we chose to present HRs for these quantiles as they would provide a complement to the Figures which would assist in communication (for some readers, the key results might be easier to glean from these numeric summaries than from the Figures). However, we don’t wish to overemphasise these quantiles when the full ‘dose-response’ function we believe to be of the greatest interest.

• Additional stratified analyses by main sociodemographic factors (age, sex, SES, etc) and sleep variables (sleep duration and sleep quality) would be informative to understand the population heterogeneity in the association between sleep regularity and mortality

Thank you for this suggestion. We have assessed effect modification across a range of key background variables (age, sex, household income, sleep duration, moderate to vigorous physical activity, prevalent CVD, and prevalent cancer). This has been added to the results. Where meaningful evidence of effect modification was noted, we have presented results within strata of the effect modifier.

• Some brief discussion on socioeconomic aspects of sleep is needed (the authors focused on the biological mechanisms underlying the observed association), as emerging evidence suggests that sleep health is not only a biological but also a social construct. For example, a recent study in the US found that sleep regularity is the most important contributor to racial/ethnic disparities in sleep health (see PMID: 34498675).

We agree that sleep health is both a biological and social construct. We have added the following text to the discussion to address this comment:

Discussion:

“Furthermore, identifying the determinants of poor sleep regularity may be of import, not only considering biological factors, but broader social determinants that impact circadian rhythmicity (e.g., racial/ethnic disparities32, neighbourhood factors33) and consequently overall health.”

References

1. Harrell FE. Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis. vol 608. Springer; 2001.

eLife assessment

This manuscript provides fundamental findings on the association between sleep regularity and mortality in the UK Biobank, which is a popular topic in recent sleep and circadian research in population-based studies. The study is based on a large accelerometer study with validated follow-up of incident diseases and deaths, and the data quality and large sample size are convincing and strengthen the credibility of the conclusion. This will be of wide interest to researchers in the sleep study field, epidemiologists, practicing clinicians and the general public.

Reviewer #1 (Public Review):

This manuscript provides important evidence on the association between sleep regularity and mortality in the UK Biobank, which is a popular topic in recent sleep and circadian research in population-based studies. The analysis reported robust associations between sleep irregularity and increased total, CVD and cancer mortality, and provided evidence to support the role of sleep and circadian health in disease progression and longevity in human populations. The Sleep Regularity Index (SRI) used in this study is a novel metric that quantifies the consistency in rest-activity rhythms over consecutive 24 hour periods, thus providing objective assessment of potential circadian disruption. The study is based on a large accelerometer study with validated follow-up of incident diseases and deaths. The data quality and large sample size strengthen the credibility of the conclusion. Overall, the analyses are appropriately done and the manuscript is clearly written.

Reviewer #2 (Public Review):

This interesting research commendably revealed irregular sleep-wake patterns are associated with higher mortality risk. However, as authors acknowledged, the analysis can not to accurately identify the cause and effect. In my opinion, the causality is important for this topic, cuz, sleep regularity and health (e.g. chronic disease) were long-term simultaneous status. especially given the participants are older. I suggest that the author could utilize MR analysis to find out for more evidence.

Author Response

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

Reviewer 1:

Public review:

In this study, Porter et al report on outcomes from a small, open-label, pilot randomized clinical trial comparing dornase-alfa to the best available care in patients hospitalized with COVID-19 pneumonia. As the number of randomized participants is small, investigators describe also a contemporary cohort of controls and the study concludes about a decrease of inflammation (reflected by CRP levels) aJer 7 days of treatment but no other statistically significant clinical benefit.

Suggestions to the authors:

• The RCT does not follow CONSORT statement and reporting guidelines

We thank you for this suggestion and have now amended the order and content of the manuscript to follow the CONSORT statement as closely as possible.

• The authors have chosen a primary outcome that cannot be at least considered as clinically relevant or interesting. AJer 3 years of the pandemic with so much research, why investigate if a drug reduces CRP levels as we already have marketed drugs that provide beneficial clinical outcomes such as dexamethasone, anakinra, tocilizumab and baricitinib.

We thank the reviewer for bringing up this central topic. The answer to this question has both a historical and practical component. This trial was initiated in June of 2020 and was completed in June of 2021. At that time there were no known treatments for the severe immune pathology of COVID19 pneumonia. In June 2020, dexamethasone data came out and we incorporated dexamethasone into the study design. It took much longer for all other anti-inflammatories to be tested. Hence, our decision to trial an approved endonuclease was based purely on basic science work on the pathogenic role of cell-free chromatin and NETs in murine sepsis and flu models and the ability of DNase I to clear them and reduce pathology in these animal models. In addition, evidence for the presence of cell-free chromatin components in COVID-19 patient plasma had already been communicated in a pre-print. Finally, several studies had reported the anti-inflammatory effects of dornase treatment in CF patients. Hence there was a strong case for a cheap, safe, pulmonary noninvasive treatment that could be self-administered outside the clinical se]ng.

The Identification of novel/repurposed treatments effective for COVID-19 were hampered by patient recruitment to competing studies during a pandemic. This resulted in small studies with inconclusive or contrary findings. In general, effective treatments were only picked up in very large RCTs. For example, demonstrating dexamethasone as effective in COVID-19 required recruitment of 6,425 patients into the RECOVERY study. Multiple trials with anti-IL-6 gave conflicting evidence until RECOVERY recruited 4116 adults with COVID-19 (n=2022, tocilizumab and 2094, control) similar for Baracitinib (4,148 randomised to treatment and 4,008 to standard care). Anakinra is approved for patients with elevated suPAR, based on data from one randomized clinical trial of 594 patients, of whom 405 had active treatment (PMID: 34625750). However, a systematic review analysing over 1,627 patients (anakinra 888, control 739) with COVID-19 showed no benefit (PMID: 36841793). Regarding the choice of the primary endpoint, there is a wealth of clinical evidence to support the relevance of CRP as a prognostic marker for COVID-19 pneumonia patients and it is a standard diagnostic and prognostic clinical parameter in infectious disease wards. This choice in March 2020 was supported by evidence of the prognostic value of IL-6; CRP is a surrogate of IL-6. We also provide our own data from a large study of severe COVID-19 pneumonia in figure 1, showing how well CRP correlates with survival.

In summary, our data suggest that Dornase yields an anti-inflammatory effect that is comparable or potentially superior to cytokine-blocking monotherapies at a fraction of the cost and potentially without the additional adverse effects such as the increase for co-infections.

We now provide additional justification on these points in the introduction on pg.4 as follows:

“The trial was ini.ated in June 2020 and was completed in September of 2021. At the start of the trial only dexamethasone had been proven to benefit hospitalized COVID-19 pneumonia pa.ents and was thus included in both arms of the trial. To increase the chance of reaching significance under challenging constraints in pa.ent access, we opted to increase our sample size by using a combina.on of randomized individuals and available CRP data from matched contemporary controls (CC) hospitalized at UCL but not recruited to a trial. These approaches demonstrated that when combined with dexamethasone, nebulized DNase treatment was an effec.ve an.-inflammatory treatment in randomized individuals with or without the implementa.on of CC data.”

We also added the following explanation in the discussion on pg. 16:

“Our study design offered a solution to the early screening of compounds for inclusion in larger platform trials. The study took advantage of frequent repeated measures of quantifiable CRP in each patient, to allow a smaller sample size to determine efficacy/futility than if powered on clinical outcomes. We applied a CRP-based approach that was similar to the CATALYST and ATTRACT studies. CATALYST showed in much smaller groups (usual care, 54, namilumab, 57 and infliximab, 35) that namilumab that is an antibody that blocks the cytokine GM-CSF reduced CRP even in participants treated with dexamethasone whereas infliximab that targets TNF-α had no significant effect on CRP. This led to a suggestion that namilumab should be considered as an agent to be prioritised for further investigation in the RECOVERY trial. A direct comparison of our results with CATALYST is difficult due to the different nature of the modelling employed in the two studies. However, in general Dornase alfa exhibited comparable significance in the reduction in CRP compared to standard of care as described for namilumab at a fraction of the cost. Furthermore, endonuclease therapies may prove superior to cytokine blocking monotherapies, as they are unlikely to increase the risk for microbial co-infections that have been reported for antibody therapies that neutralize cytokines that are critical for immune defence such as IL-1β, IL-6 or GM-CSF. “

• Please provide in Methods the timeframe for the investigation of the primary endpoint

This information is provided in the analysis on pg. 8:

“The primary outcome was the least square (LS) mean CRP up to 7 days or at hospital discharge whichever was sooner.”

• Why day 35 was chosen for the read-out of the endpointt?

We now state on pg. 8 that “Day 35 was chosen as being likely to include most early mortality due to COVID-19 being 4 weeks after completion of a week of treatment. ( i.e. d7 of treatment +28 (4 x 7 days))”

• The authors performed an RCT but in parallel chose to compare also controls. They should explain their rationale as this is not usual. I am not very enthusiastic to see mixed results like Figures 2c and 2d.

We initially aimed at a fully randomized trial. However, the swiJ implementation of trial prioritization strategies towards large and pre-established trial plamorms in the UK made the recruitment COVID19 patients to small studies extremely challenging. Thus, we struggled to gain access to patients. Our power calculations suggested that a mixed trial with randomized and contemporary controls was the best way forward under these restrictions in patient access that could provide sufficient power.

That being said, we also provide the primary endpoint (CRP) results in Fig. 3B as well as the results for the length of hospitalization (Fig. S3D) for the randomized subjects only.

• Analysis is performed in mITT; this is a major limitation. The authors should provide at least ITT results. And they should describe in the main manuscript why they chose mITT analysis.

We apologize if this point was confusing. We performed the analysis on the ITT as defined in our SAP: “The primary analysis population will be all evaluable patients randomised to BAC + dornase alfa or BAC only who have at least one post-baseline CRP measurement, as well as matched historical comparators.”

We understand that the reason this might be mistaken as an mITT is because the N in the ITT (39) doesn’t match the number randomised and because we had stated on pg. 8 that “ Efficacy assessments of primary and secondary outcomes in the modified inten.on-to-treat popula.on were performed.”

However, we did randomise 41 participants, but:

One participant in the DA arm never received treatment. The individual withdrew consent and was replaced. We also have no CRP data for this participant in the database, so they were unevaluable, and we couldn’t include them in the baseline table even if we wanted to. In addition, 1 participant in BAC only had a baseline CRP measurement available. Hence not evaluable as we only have a baseline CRP measurement for this participant.

We have corrected the confusing statement on pg. 8 and added an additional explanation.

“Efficacy assessments of primary and secondary outcomes in the inten.on-to-treat (ITT) popula.on were performed on all randomised par.cipants who had received at least one dose of dornase alfa if randomized to treatment. For full details see Sta.s.cal Analysis Plan. The ITT was adjusted to mi.gate the following protocol viola.ons where one par.cipant in the BAC arm and one in the DA arm withdrew before they received treatment and provided only a baseline CRP measurement available. The par.cipant in the DA arm was replaced with an addi.onal recruited pa.ent. Exploratory endpoints were only available in randomised par.cipants and not in the CC. In this case, a post hoc within group analysis was conducted to compare baseline and post-baseline measurements.”

• It is also not usual to exclude patients from analysis because investigators just do not have serial measurements. This is lost to follow up and investigators should have pre-decided what to do with lost-to-follow-up.

Our protocol pre-specified that the primary analysis population should have at least one postbaseline CRP measurement (pg. 13 of protocol). The patient that was excluded was one that initially joined the trial but withdrew consent after the first treatment but before the first post-treatment blood sample could be drawn. Hence, the pre-treatment CRP of this patient alone provided no useful information.

• In Table 1 I would like to see all randomized patients (n=39), which is missing. There are also baseline characteristics that are missing, like which other treatments as BAT received by those patients except for dexamethasone.

Table 1 includes all 39 patients plus 60 CCs.<br /> Table 2 shows additional treatments given for COVID-19 as part of BAC.

• In the first paragraph of clinical outcomes, the authors refer to a cohort that is not previously introduced in the manuscript. This is confusing. And I do not understand why this analysis is performed in the context of this RCT although I understand its pilot nature.

One of the main criticisms we have encountered in this study has been the choice of the primary endpoint. The best way respond to these questions was to provide data to support the prognostic relevance of CRP in COVID-19 pneumonia from a separate independent study where no other treatments such as dexamethasone, anakinra or anti-IL6 therapies were administered. We think this is very useful analysis and provides essential context for the trial and the choice of the primary endpoint, indicating that CRP has good enough resolution to predict clinical outcomes.

• Propensity-score selected contemporary controls may introduce bias in favor of the primary study analysis, since controls are already adjusted for age, sex and comorbidities.

The contemporary controls were selected to best match the characteristics of the randomized patients including that the first CRP measurement upon admission surpassed the trial threshold, so we do not see how this selection process introduces biases, as it was blinded with regards to the course of the CRP measurements. Given that this was a small trial, matching for baseline characteristics is necessary to minimize confounding effects.

• The authors do not clearly present numerically survivors and non-survivors at day 34, even though this is one of the main secondary outcomes.

We now provide the mortality numbers in the following paragraph on pg. 13.

“Over 35 days follow up, 1 person in the BAC + dornase-alfa group died, compared to 8 in the BAC group. The hazard ra.o observed in the Cox propor.onal hazards model (95% CI) was 0.47 (0.06, 3.86), which es.mates that throughout 35 days follow-up, there was a 53% reduced chance of death at any given .mepoint in the BAC + dornase-alfa group compared to the BAC group, though the confidence intervals are wide due to a small number of events. The p-value from a log-rank test was 0.460, which does not reach sta.s.cal significance at an alpha of 0.05.”

• It is unclear why another cohort (Berlin) was used to associate CRP with mortality. CRP association with mortality should (also) be performed within the current study.

As we explained above, the Berlin cohort CRP data serve to substantiate the relevance of CRP as a primary endpoint in a cohort that experienced sufficient mortality as this cohort did not receive any approved anti-inflammatory therapy. Mortality in our COVASE trial was minimal, since all patients were on dexamethasone and did not reach the highest severity grade, since we opted to treat patients before they deteriorated further. The overall mortality was 8% across all arms of our study, which does not provide enough events for mortality measurements. In contrast the Berlin cohort did not receive dexamethasone and all patients had reached a WHO severity grade 7 category with mortality at 30%.

My other concerns are:

• This report is about an RCT and the authors should follow the CONSORT reporting guidelines. Please amend the manuscript and Figure 1b accordingly and provide a CONSORT checklist.

We now provide a CONSORT checklist and have amended the CONSORT diagram accordingly.

• Please provide in brief the exclusion criteria in the main manuscript

We have now included the exclusion criteria in the manuscript on pg. 6.

“1.1.1 Exclusion criteria

1. Females who are pregnant, planning pregnancy or breasmeeding

2. Concurrent and/or recent involvement in other research or use of another experimental inves.ga.onal medicinal product that is likely to interfere with the study medica.on within (specify .me period e.g. last 3 months) of study enrolment 3. Serious condi.on mee.ng one of the following:

a. Respiratory distress with respiratory rate >=40 breaths/min

b. oxygen satura.on<=93% on high-flow oxygen

1. Require mechanical invasive or non-invasive ven.la.on at screening

2. Concurrent severe respiratory disease such as asthma, COPD and/or ILD

3. Any major disorder that in the opinion of the Inves.gator would interfere with the evalua.on of the results or cons.tute a health risk for the trial par.cipant

4. Terminal disease and life expectancy <12 months without COVID-19

5. Known allergies to dornase alfa and excipients

6. Par.cipants who are unable to inhale or exhale orally throughout the en.re nebulisa.on period So briefly Pa.ents were excluded if they were:

7. pregnant, planning pregnancy or breasmeeding 2. Serious condi.on mee.ng one of the following:

a. Respiratory distress with respiratory rate >=40 breaths/min

b. oxygen satura.on<=93% on high-flow oxygen

1. Require ven.la.on at screening

2. Concurrent severe respiratory disease such as asthma, COPD and/or ILD

3. Terminal disease and life expectancy <12 months without COVID-19

4. Known allergies to dornase alfa and excipients

5. Par.cipants who are unable to inhale or exhale orally throughout the en.re nebulisa.on period”

• "The final trial visit occurred at day 35." "Analysis included mortality at day 35". I am not sure I understand why. In clinicaltrials.gov all endpoints are meant to be studies at day 7 except for mortality rate day 28. Why day 35 was chosen? Please be consistent.

Thank you for identifying this inconsistency. We have amended the record on clinicaltrials.gov to read ‘’the time to event data was censored at 28 days post last dose (up to d35) for the randomised participants and at the date of the last electronic record for the CC.”

• Please provide in Methods the timeframe for the investigation of the primary endpoint

• The authors performed an RCT but in parallel chose to compare also controls. They should explain their rationale as this is not usual. I am not very enthusiastic to see mixed results like Figures 2c and 2d.

• Analysis is performed in mITT; this is a major limitation. The authors should provide at least ITT results. And they should describe in the main manuscript why they chose mITT analysis.

• It is also not usual to exclude patients from analysis because investigators just do not have serial measurements. This is lost to follow up and investigators should have pre-decided what to do with lost-to-follow-up.

• Figure 1b as in CONSORT statement, please provide reasons why screened patients were not enrolled.

• In Table 1 I would like to see all randomized patients (n=39), which is missing. There are also baseline characteristics that are missing, like which other treatment as BAT received those patients except for dexamethasone.

• In the first paragraph of clinical outcomes, the authors refer to a cohort that is not previously introduced in the manuscript. This is confusing. And I do not understand why this analysis is performed in the context of this RCT although I understand its pilot nature.

• In Figure 2 the authors draw results about ITT although in methods describe that they performed an mITT analysis. Please be consistent.

Please see answers provided to these queries above.

Reviewer #2 (Recommendations For The Authors):

1) Suppl Figure 2B would be more informative if presented as a Table with N of patients with per day sampling

We now provide the primary end point daily sampling table in Table 3.

2) The numbers at risk should figure under the KM curves

The numbers at risk for figures 1E, 2C, 2D have been added as graphs either in the main figures or in the supplement.

3) HD in Supplementary figure 3 should be explained

We apologize for this omission. We now provide a description for the healthy donor samples that we used in the cell-free DNA measurements in figure S3B on pg. 14:

“Compared to the plasma of anonymized healthy donors volunteers at the Francis Crick ins.tute (HD), plasma cf-DNA levels were elevated in both BAC and DA-treated COVASE par.cipants.

4) Presentation is inappropriate for Table S4

We thank the reviewer for pointing this issue. We have now formaxed Table S4 to be consistent with all other tables.

eLife assessment

This small-sized clinical trial comparing nebulized dornase-alfa to the best available care in patients hospitalized with COVID-19 pneumonia is valuable, but in its present form the paper is incomplete.

Joint Public Review:

In this study by Porter et al reports on outcomes from a small, open-label, pilot randomized clinical trial comparing dornase-alfa to the best available care in patients hospitalized with COVID-19 pneumonia. As the number of randomized participants is small, investigators describe also a contemporary cohort of controls and the study concludes about decrease of inflammation (reflected by CRP levels) after 7 days of treatment but no other statistically significant clinical benefit.

Suggestions to the authors:

• Please re-analyze findings by omitting from all Tables and Figures all data of comparators who were not randomized (BAC). I understand the difficulties of running this trial but the results of excess reduction of mortality do not allow the publication of a trial where comparators do not come from the randomized patient population.<br /> • The presentation remains confusing and the manuscript should be critically revised for clarity. There is a repetition of methods (e.g. lines 176-187 repeat 160-175) and redundant results (e.g. Figure S2, Table 3). At Table 4: the authors should select one method of illustration for lab results, either Table or figure, without repetitions<br /> • Regarding inclusion criteria, it is unclear whether high radiological suspicion is sufficient for inclusion or whether PCR based confirmation is required in all instances (differences in wording between lines 153 and 191), and under which oxygen requirements (lines 155 and 192)<br /> • Table 1 should be merged with Table S2 and a better description of cohort baseline severity (P/F, SOFA, APACHE, organ support, number of patients in each point of the WHO severity score) and treatments should be made available

Author Response

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

Reviewer #1 (Public Review):

The manuscript by Hage et al. presents interesting results from a foraging behavior in Marmosets that explores the interactions of saccade and lick vigor with pupil dilation and performance as well as a marginal value theory and foraging theory-inspired value-based decision-making model thereof. The results are generally robust and carefully presented and analyses, particularly of vigor, are carefully executed.

The authors constructed a model that makes two predictions: "In summary, this simple theory made two sets of predictions: in response to an increased cost of harvest, one should work longer, but move with reduced vigor. In response to an increased reward value, as in hunger, one should also work longer, but now move with increased vigor." Their behavioral data meets these predictions. It is not clear if the model was designed and tweaked in order to make those predictions and match the data, or derived from principles. Furthermore, it is not clear what other models would make similar predictions. It would help to assess what is predicted by other simple models, as well as different functional forms for the effort costs in their model.

We chose this formulation of utility (Eq. 1) because it is a normative approach that ecologists have used to understand the decisions that animals make regarding how far to travel for food, what mode of travel to use, and how long to stay before moving on to another reward opportunity (Richardson and Verbeek 1986; Stephens and Krebs 1986; Bautista et al. 2001). In a typical formulation of the theory, the numerator represents the reward gained (in units of energy), minus the effort expended (also in units of energy). The denominator represents the amount of time spent during that behavior. We represented this idea in Eq. (1) with saccades that produced reward accumulation, and licks that produced reward consumption. Thus, the utility that we are trying to maximize is the rate of energy gained.

The specific functions that we used to represent the energy acquired through reward acquisition, and the energy expended through effort expenditure, came a priori either from experiment design, or from the measurements we have made in other experiments. We modeled reward accumulation as a linear rise in energy stored because successful saccades produced a linear increase in the food cache. We modeled consumption of the food as a hyperbolic function of the number of licks to represent the fact that as the licking bout began, each successful lick depleted the food, and thus the first few licks produced a greater amount of food consumption than the last few licks. We modeled the effort cost of licking to grow linearly with the number of licks.

A critical assumption that we made is that energy spent performing the saccade trials (which grew faster than linearly as a function of the number of trials attempted), grew faster than the time spent attempting those same trials (which grew linearly with the number of trials). This assumption is based on the heuristic that the average rate of energy lost following a large number of attempted trials is greater than the average rate of energy lost following a small number of attempted trials.

Sensitivity to parameter values: The model’s simplicity provides closed-form solutions across all parameter values, allowing one to make predictions without having to fit the model to the measured data. For example, for all parameter values that produce a real solution (as opposed to imaginary), the optimal number of saccade trials increases with the square root of the cost of licking. Thus, the basic prediction of the model is that in order to maximize the capture rate, an increase in the effort that it takes to harvest the reward should produce a greater willingness to work longer, caching more food. The closed-form solutions are presented in the Mathematica supplementary document.

Other models of utility: In composing our utility (Eq. 1), we chose to combine reward and effort additively. This is in contrast to other approaches in which effort discounts reward multiplicatively (47–49). Here, let us show that multiplicative interactions may have the limitation that they are incompatible with the observation that reward invigorates movements. To compare additive and multiplicative approaches, let us consider an arbitrary function 𝑈(𝑇) that specifies how effort varies with movement duration. Typically, this is a U-shaped function that describes energy expenditure as a function of movement duration, as in Shadmehr et al. (2016). In the case of multiplicative interaction between reward and effort, we can consider the following representation of utility:

In the above formulation, reward 𝛼 is discounted hyperbolically with time, and an increase in reward increases the utility of the action. The optimum movement vigor has the duration 𝑇∗ that maximizes this utility. Notably, because increasing reward merely scales this utility, it has no effect on vigor. Thus, a utility in which reward is multiplied by a function of effort generally fails to predict dependence of movement vigor on reward.

Line 37 page 6; the link of pupil to NE/LC is tenuous. Other modulators systems and circuits may be equally important and should be mentioned (e.g. Reimer, Jacob, Matthew J. McGinley, Yang Liu, Charles Rodenkirch, Qi Wang, David A. McCormick, and Andreas S. Tolias. "Pupil fluctuations track rapid changes in adrenergic and cholinergic activity in cortex." Nature communications 7, no. 1 (2016): 13289.)

Reimer et al. (2016) used two-photon microscopy to measure activity of ACh and NE projections in layer 1 of mouse visual cortex while tracking pupil diameter fluctuations. During stillness, elevated pupil diameter was followed by cholinergic and noradrenergic axonal activity. Notably, NE activity levels were larger and with shorter latency than ACh. In primates, Joshi et al., (2016) recorded from LC during a fixation task. Using spike-triggered averaging, they found that following a spike in an LC neuron, there was pupil dilation at 200-300 ms latency. Moreover, microstimulation in LC produced pupil dilation at 500ms latency. More recently, Breton-Provencher and Sur (2019) provided causal evidence that LC activity drives pupil size. They optogenetically activated (1s) or silenced (5 sec) locus coeruleus noradrenergic neurons and found strong increase in pupil size or modest decrease: increase had a slow time scale of 1 second or more, similar slow timescale for decrease. The LC-NA neurons are surrounded by GABA-ergic neurons. Stimulation of the GABA-ergic neurons produced mild, slow constriction. They identified GABA-ergic and NA neurons by photo-tagging and then tried to identify them via spike shape and found that “spike shape of some GABA neurons were not well separated from NA neurons, demonstrating the difficulty of cell-type identification based on spike shape alone.” They noted that a subset of GABAergic neurons received coincident inputs with the NA neurons. When the GABA neurons were excited, the gain of the pupil response to an auditory tone was diminished, producing an increase as a function of tone intensity that had a lower gain. Thus, LC-NA neurons causally drive pupil size, and the GABA neurons that surround them control the gain of the response of LC-NA neurons to arousal stimuli.

Line 35 page 6-page 7 line 10 emphasizes a cognitive interpretation of the pupil dilations that is emphasized, in relation to effort costs. But there are also more concomitant vigorous movements. Could all of their pupil results be explained by motor correlates? This should be tested and ruled out before making cognitive interpretations.

Pupil dilation is a proxy for activity in the brainstem neuromodulatory system (Vazey et al., 2018) and is a measure of arousal (Mathot, 2018). Control of pupil size is dependent on spiking of norepinephrine neurons in locus coeruleus (LC-NE): an increase in the activity of these neurons produces pupil dilation (Joshi et al., 2016; Breton-Provencher and Sur, 2019). Some of these neurons show a transient change in their activity when acquisition of reward requires expenditure of physical effort (Bornert and Bouret, 2021). However, the link between effort costs and pupil size appears to go beyond motor control, as a recent paper found that pupil size increases during effortful speech perception (Contadini-Wright et al., 2023). Thus, although in our work increases in pupil size were always associated with increased movement vigor, the results from other studies suggest that economic variables such as cognitive effort in tasks in which there is no concomitant movement also drive an increase in pupil size.

Page 7, line 37-42: How would the model need to be modified in order to account for this discrepancy with the data? Ideally, this would be tested.

We comment on potential modifications that can be made to the model that may account for the discrepancy referred to by the reviewer in the discussion section: “Notably, some of the predictions of the theory did not agree with the experimental data. An increased effort cost did not accompany a reduction in the duration of harvest, and hunger did not increase saccade vigor robustly. Indeed, earlier experiments have shown that if the effort cost of harvest increases, animals who expend the effort will then linger longer to harvest more of the reward that they have earned (2). This mismatch between observed behavior and theory highlights some of the limitations of our formulation. For example, our capture rate reflected a single work-harvest period, rather than a long sequence. Moreover, the capture rate did not consider the fact that the food tube had finite capacity, beyond which the food would fall and be wasted. This constraint would discourage a policy of working more but harvesting less. Finally, if we assume that a reduced body weight is a proxy for increased subjective value of reward, it is notable that we observed a robust effect on vigor of licks, but not saccades. A more realistic capture rate formulation awaits simulations, possibly one that describes capture rate not as the ratio of two sums (sum of gains and losses with respect to sum of time), but rather the expected value of the ratio of each gain and loss with respect to time (Bateson et al., 1995 & 1996).”

Page 9, line 2-11: In this section, it would help to also consider 'baseline' pupil size (in between trials). This would give a signal that is not 'contaminated' by movements, and may reflect control state. Relatedly, changes in control state may impact and confound the movement-related dilation magnitudes due to e.g. floor and ceiling effects on pupil size, which has a strong tendency for reversion to the mean.

The experiment design included little or no between-trial periods because during the trials the subjects worked (performed saccades to accumulate reward), while after completing a few trials they stopped working and started harvesting through licking. Because primates make saccades during their entire wake state, it is probably not possible to find a significant period in which the subjects do not make any movements. We selected a window of 500 ms around each lick in the harvest period, and each saccade during the work period, and computed the average pupil size per movement, which includes data from both before and after movements. We then computed a within-session z-score by normalizing these measures by the average pupil size acquired for that day.

The hunger-related and reward-size related analyses are both heavily confounded since they were not manipulated directly and could co-vary with many latent factors. For example, why might a given Marmoset be lower weight on a given day? Could it affect sleep, stress, activity, or other factors during the preceding 24 hours? If so, could these other variables be driving the results that are interpreted as 'hunger?' Relatedly, since the reward size is determined by the animals behavior on each trial (how much they worked), factors (internal brain state, external noises, etc.) that alter how much they worked will influence the subsequent reward size. Therefore interpretations about reward expectancy are confounded. Both of these issues should be discussed and manipulations of them (different feeding schedules and reward size-work functions proposed, respectively).

Weight of the subjects was measured prior to the start of the experiment on each day. The natural fluctuations are typically the result of factors such as time of the experiment and corresponding weight measurement (AM vs PM) relative to the time of feeding on the previous day, day of the week of the experiment (following a weekend vs. during the week), and volume of food given during the previous day. Animals were maintained at 90% of their baseline weight during food restriction, and fluctuations typically occurred within that range (Sedaghat-Nejad et al., 2019). We used weight as a proxy for hunger, and thus value of reward, and the resulting analyses yielded results consistent with predictions made by our model, as seen in Fig. 5. Critically, other factors that may co-vary with lower weights, like those mentioned by the reviewer (sleep conditions, stress levels, and activity levels) often lead to very poor task performance by the subjects. In sharp contrast, the model predicted increased work period, and increased movement vigor for high reward value, both of which we observed when the subject’s weight was low. Thus, a low relative weight did not seem to impair performance, but rather act as a motivating factor. Subjects were closely monitored for well characterized stress-related behaviors and impaired attentive states by experimenters, veterinarian staff, and caretaker staff, and, in the event of abnormalities, were removed from food restriction and experimentation until behavior stabilized.

Effect of reward size: As you noted, we did not manipulate reward size directly. Rather, because our emphasis was on quantifying the effect of effort, the subjects received the same increment of reward per each completed trial, but on some sessions this reward was easy to harvest, while in other sessions the reward required greater effort to harvest. Because the reward amount accumulated during the work period, some harvests encountered a small amount of reward, while other harvests encountered a large amount of reward. Indeed, the amount of reward available for harvest depended linearly on the number of successful saccade trials completed during the work period. We found that the vigor of licks grew with the reward magnitude.

A major issue is a lack of alternative models. The authors seem to have constructed a particular model designed to capture the behavioral patterns they observed in the data. The model fails in some instances, as they point out. Even more importantly, there are no results or discussion about how other plausible models could or couldn't fit the data. The lack of model comparisons makes it difficult to interpret the conclusions or put the results in a broader context.

To model behavior, we chose a formulation of utility that represented a normative approach that ecologists have used to understand the decisions that animals make regarding how far to travel for food, what mode of travel to use, and how long to stay before moving on to another patch. In the model, the objective of decisions and actions is to maximize the sum of reward acquired, minus the efforts expended, divided by time. This is termed the capture rate. However, there are other models to consider, and thus we added a new section titled Model formulation and Other models of utility.

Reviewer #2 (Public Review):

The model proposed in the paper takes a very specific functional form that is neither motivated by the previous literature nor particularly useful for indexing the behavioral tendencies of individual monkeys (or of the same monkey in different contexts). For example, while it is clear that the saccade effort cost will need to outgrow the increase in the utility of the accumulated food for the monkey to start feeding, it is unclear why this needs to be modeled with a fixed quadratic exponent on the number of saccades? Similarly, why do licks deplete the food stash with the specific rate hard-coded in the model?

We added a section titled Model formulation and Other models of utility to better explain the rationale behind the model.

We chose this formulation of utility (Eq. 1) because it is a normative approach that ecologists have used to understand the decisions that animals make regarding how far to travel for food, what mode of travel to use, and how long to stay before moving on to another reward opportunity (Richardson and Verbeek, 1986; Stephens and Krebs, 1986; Bautista et al., 2001). In a typical formulation of the theory, the numerator represents the reward gained (in units of energy), minus the effort expended (also in units of energy), while the denominator represents the amount of time spent during that behavior. We represented this idea in Eq. (1) with saccades that produced reward accumulation, and licks that produced reward consumption. Thus, the utility that we aim to maximize is the rate of energy gained.

The specific functions that we used to represent the energy gained through reward acquisition, and the energy expended through effort expenditure, came either from experiment design, or from the measurements we have made in other experiments. We modeled reward accumulation as a linear rise in energy stored because successful saccades produced a linear increase in the food cache. We modeled consumption of the food as a hyperbolic function of the number of licks to represent the fact that as the licking bout began, each successful lick depleted the food, and thus the first few licks produced a greater amount of food consumption than the last few licks. We modeled the effort cost of licking to grow linearly with the number of licks.

A critical assumption that we made is that energy expended performing the saccade trials (which grew faster than linearly as a function of the number of trials attempted), grew faster than the time spent attempting those same trials (which grew linearly with the number of trials). This assumption is based on the heuristic that the average rate of energy lost following a large number of attempted trials is greater than the average rate of energy lost following a small number of attempted trials. A quadratic function is one example of such a function, which has the advantage of providing closed form solutions for the optimal policy.

The model’s simplicity provided closed-form solutions across all parameter values, allowing us to make predictions without having to fit the model to the measured data. Critically, for all parameter values that produce a real solution (as opposed to imaginary), the optimal number of saccade trials increases with the square root of the cost of licking. Thus, the basic prediction of the model is that to maximize the capture rate, regardless of parameter values, an increase in the effort required for harvest should be met with a greater willingness to work. The closed-form solutions are presented in the supplementary document (simulations.nb).

Finally, the proportion of successful saccades and lick events is assumed to be fixed, even though it very likely to be directly influenced by movement speed (speed- accuracy trade-off), which is also contained in the model. It would strongly increase the plausibility and potential impact of the model if the authors could clearly state where these hard-coded model terms come from. Ideally, they would formulate the model in more general terms and also consider other functional forms, as briefly suggested in the discussion. This latter point would be particularly important since not all model predictions were actually borne out in the data.

Thank you for this excellent suggestion. Regarding saccades, contrary to the speed accuracy trade-off hypothesis, we found that faster saccades were also more accurate (Fig. 3C). Thus, increased pupil size was not only associated with more vigorous saccades, but also more accurate saccades. Importantly, these vigor-related changes in accuracy were too small to affect the probability of reward: the reward area for the saccades was much larger (1.5 deg) than the endpoint accuracy changes that was produced due to changes in the food tube distance. For example, on average saccade vigor changed from 0.95 to 1.05 when the food tube distance changed from 12 mm to 8 mm. These changes in vigor would produce a fraction of degree reduction in endpoint error (Fig. 3C).

Regarding licks, we added new data to the manuscript to assess the relationship between vigor of the licks and endpoint accuracy. We saw no consistent relationship, across subjects or effort conditions, between protraction speed and the outcome of a lick, that is, if the lick was successful in making it inside the tube. On average, in subject R we observed an improvement in lick accuracy with increased vigor, and in subject M we saw no change (Fig. 4F). Thus, we used the average success rate of licks, which was roughly 30% for both subjects.

The authors derive qualitative predictions, by simulating their model with apparently arbitrary parameters. They then test these qualitative predictions with conventional statistics (e.g., t-tests of whether monkeys lick more for high vs low effort trials). The reader wonders why the authors chose this route, instead of formulating their model with flexible parameters and then fitting these to data. This would allow them (and future researchers) to test their model not just qualitatively but also quantitatively, and to compare the plausibility of different functional forms. The authors certainly have enough data and power to do this, given the vast number of sessions the monkey completed.

The model’s simplicity provides closed-form solutions across all parameter values, allowing one to make predictions without having to fit the model to the measured data. For example, for all parameter values that produce a real solution (as opposed to imaginary), the optimal number of saccade trials increases with the square root of the cost of licking. Thus, the basic prediction of the model is that to maximize the capture rate, an increase in the effort that it takes to harvest the reward should produce a greater willingness to work longer, caching more food. The closed-form solutions are presented in the Mathematica supplementary document.

The effort manipulation chosen by the authors (distance of food tube) goes hand in hand with a greater need for precision since the monkey's tongue needs to hit an opening of similar size, but now located at a greater distance. This raises the question of whether the monkeys moved slower to enhance its chance of collecting the food (in line with a speed-accuracy trade off). The manuscript would benefit from an explicit test of this possibility, for example by reporting whether for each of the two conditions, the speed of tongue movements on a trial-by-trial basis predicts the probability of food collection? At the very least, the manuscript should explicitly discuss this issue and how it affects the certainty with which effects of tube distance can be linked to anticipated effort cost alone.

Thank you for the excellent point. We looked for but found no consistent relationship, across subjects or effort conditions, between protraction speed of the tongue and the success probability of a lick (probability of insertion into the tube). Regardless, we agree with you that it is an excellent alternate hypothesis that reductions in lick vigor that accompanied increased distance of the tube may be due to a desire to maintain accuracy, and not a reflection of increased effort cost of reward. To incorporate this idea into the model, we would need a measure of speed-accuracy for the licks, something that we do not have but hope to develop in the future.

However, perhaps the most interesting aspect of our results is that when we increased tube distance, making reward more effortful, there was not only a reduction in lick vigor, but also a reduction in saccade vigor. That is, the decisions and actions during the work period responded to the increased effort cost of reward during the harvest period. These changes accompanied dilation of the pupil, both in the work period and in the harvest period. We now include a paragraph regarding this in the Discussion.

The manuscript measures pupil dilation in a time period ranging from -250ms before to 250 ms after saccade onset. However, the pupil changes strongly during saccade execution relative to the preceding baseline, leaving doubts as to whether the aggregated measure blurs several interesting and potentially different effects. It would be more conclusive if the manuscript could report the analyses of pupil size separately for a period prior to saccade onset and during/after the saccade.

Our goal was to test for general correlations between the state of the pupil and both movement vigor and decisions. We chose a window of 500 ms around saccade onset, as referred to by the reviewer, as it allowed us a large enough time window to measure pupil size outside of the movement itself (~30 ms duration), to accurately capture the state of the animal around initiation and end of a saccade. Critically, pupil tracking during a saccade itself, when using infrared eye tracking techniques, can be prone to slight measurement error in certain cases due to tracking jitter. Thus, averaging across this window, following processing of the signal, results in a more accurate measure of pupil size.

eLife assessment

This important study unravels the interaction between effort cost, pupil-indexed brain state, and movement (saccadic) vigor during foraging decisions in marmoset monkeys. Based on a normative computational model, the authors derive the prediction that anticipated effort should affect both decisions and movement vigor during foraging; and then provide solid behavioural and pupillometric evidence for this prediction in a foraging task. This paper will be of interest to decision and motor neuroscience as well as to all researchers studying animal behavior.

Reviewer #1 (Public Review):

The manuscript by Hage et al. presents interesting results from a foraging behavior in Marmosets that explores the interactions of saccade and lick vigor with pupil dilation and performance as well as a marginal value theory and foraging theory-inspired value-based decision-making model thereof. The results are generally robust and carefully presented and analyses, particularly of vigor, are carefully executed.

Reviewer #2 (Public Review):

Hage et al examine how the foraging behavior of marmoset monkeys in a laboratory setting systematically takes into account the reward value and anticipated effort cost associated with the acquisition and consumption of food. In an interesting comprehensive framework, the authors study how experimental and natural variation of these factors affect both the decisions and actions necessary to gather and accumulate food, as well as the actions necessary to consume the food.

The manuscript proposes a computational model of how the monkeys may guide all these aspects of behavior, by maximizing a food capture rate that trades off the food that can be gathered with the effort and duration of the underlying actions. They use this model to derive qualitative predictions for how monkeys should react to an increase in the effort associated with food consumption: Monkeys should work longer before deciding to consume the accumulated food, but should move more slowly. The model also predicts that monkeys should show a different reaction to an increase in reward value of the food, also working longer but moving faster. The authors test these predictions in an interesting experimental setup that requires monkeys to collect small increments of food rewards for successful eye movements to targets. The monkeys can decide freely when to interrupt work and consume the accumulated food, and the authors measure the speed of the eye movements involved in the food acquisition as well as the tongue movements involved in the food consumption.

By and large, the behavioral findings fall in line with the qualitative model predictions: When the effort involved in food consumption increases, monkeys collect more food before deciding to consume it, and they move slower both during food acquisition and food consumption. In a second test, the authors approximate the effects of reward value of the food at stake, by comparing monkey behavior during different days with natural variations in body weight. These quasi-experimental increases in the reward value of food also lead to longer work times before consumption, but to faster movements during food consumption. Finally, the authors show that these effects correlate with pupil size, with pupils dilating more for low-effort foraging actions with increased saccade speed and decreased work duration. The authors conclude that the effort associated with anticipated actions can lead to changes in global brain state that simultaneously affect decisions and action vigor.

The paper proposes an interesting model for how one unified action policy may simultaneously affect multiple types of decisions and movements involved in foraging. The methods employed to measure behavior and test these predictions are generally sound, and the paper is well written.

Reviewer #3 (Public Review):

This is a descriptive study of membrane excitability and Na+ and K+ current amplitudes of sympathetic motor neurons in culture. The main findings of the study are that neurons isolated from aged animals show increased membrane excitability manifested as increased firing rates in response to electrical stimulation and changes in related membrane properties including depolarized resting membrane potential, increased rheobase, and spontaneous firing. By contrast, neuron cultures from young mice show little to no spontaneous firing and relatively low firing rates in response to current injection. These changes in excitability correlate with significant reductions in the magnitude of KCNQ currents in aged neurons compared to young neurons. Treating cultures with the immunosuppressive drug, rapamycin, which has known antiaging effects in model animals appears to reverse the firing rates in aged neurons and enhance KCNQ current. The authors conclude that aging promotes hyperexcitability of sympathetic motor neurons.

The electrophysiological cataloging of the neuronal properties is generally well done, and the experiments are performed using perforated patch recordings which preserve the internal constituents of neurons, providing confidence that the effects seen are not due to washout of regulators from the cells. The main weakness is that this study is a descriptive tabulation of changes in the electrophysiology of neurons in culture, and the effects shown are correlative rather than establishing causality. It is difficult to know from the data presented whether the changes in KCNQ channels are in fact directly responsible for the observed changes in membrane excitability. Furthermore, a notable omission seems to be the analysis of Ca2+ currents which have been widely linked to alterations in membrane properties in aging. As well, additional experiments in slice cultures would provide greater significance on the potential relevance of the findings for intact preparations. Finally, experiments using KCNQ blockers and activators could provide greater relevance that the observed changes in KCNQ are indeed connected to changes in membrane excitability.

eLife assessment

This study presents valuable observations indicating that the electrophysiological excitability of cultured sympathetic motor neurons progressively increase during aging, and are inversely correlated with the magnitude of KCNQ currents. The alterations in membrane excitability are broadly relevant for those interested in understanding how the nervous system changes during aging. While the data as a whole are solid in showing that the excitability of sympathetic neurons increases in neurons cultured from older mice, the mechanism of the underlying changes and in vivo relevance is incomplete.

Reviewer #1 (Public Review):

Summary:<br /> The authors study age-related changes in the excitability and firing properties of sympathetic neurons, which they ascribe to age-related changes in the expression of KCNQ (Kv7, "M-type") K+ currents in rodent sympathetic neurons, whose regulation by GPCRs has been most thoroughly studied for over 40 years. The authors suggest the ingestion of rapamycin may partially reverse the age-related decrease in M-channel expression. With the rapamycin part included, it is unclear how this work will impact the field of age-related neuronal dysfunction, as the mechanistic information is not strong.

Strengths:<br /> The strengths include the rigor of the current-clamp and voltage-clamp experiments, the lovely, crisp presentation of the data, and the expert statistics. The separation of neurons into tonic, phasic, and adapting classes is also interesting, and informative. The writing is also elegant, and crisp. The above is especially true of the manuscript up until the part dealing with the effects of rapamycin, which becomes less compelling.

Weaknesses:<br /> Where the manuscript becomes less compelling is in the rapamycin section, which does not provide much in the way of mechanistic insights. As such, the effect is more of an epi-phenomenon of unclear insight, and the authors cannot ascribe a signaling mechanism to it that is supported by data. Thus, this latter part rather undermines the overall impact and central advance of the manuscript. The problem is exacerbated by the controversial and anecdotal nature of the entire mTor/aging field, some of whose findings have very unfortunately had to be recently retracted.

I would strongly recommend to the authors that they end the manuscript with their analysis of the role of M current/KCNQ channels in the numerous age-related changes in sympathetic neuron function that they elegantly report, and save the rapamycin, and possible mTor action, for a separate line of inquiry that the authors could develop in a more thorough and scholarly way.

Reviewer #2 (Public Review):

Summary:<br /> This research shows compelling and detailed evidence showing that aging influences intrinsic membrane properties of peripheral sympathetic motor neurons such that they become more excitable. Furthermore, the authors present convincing evidence that the oral administration of the anti-aging drug Rapamycin partially reversed hyperexcitability in aged neurons. This study also investigates the molecular mechanisms underlying age-associated hyperexcitability in mouse sympathetic motor neurons. In that regard, the authors found an age-associated reduction of an outward current having properties similar to KCNQ2/Q3 potassium current. They suggested a reduction of KCNQ2/Q3 current density in aged neurons as a potential mechanism behind their overactivity.

Strengths:<br /> Detailed and rigorous analysis of electrical responses of peripheral sympathetic motor neurons using electrophysiology (perforated patch and whole-cell recordings). Most of the conclusions of this paper are well supported by the data.

Weaknesses:<br /> 1) The identity of the age-associated reduced current as KCNQ2/Q3 is not corroborated by pharmacology (blocking the current with the specific blocker XE-991).<br /> 2) The manuscript does not include a direct test of the reduction of KCNQ current as the mechanism behind age-induced hyperexcitability.

eLife assessment

In Drosophila melanogaster, the Store-operated Ca2+ entry (SOCE) channel, Orai, is required for the development of flight-promoting dopaminergic neurons. Here, Mitra et al. determine that expression of a loss-of-function Orai1 mutant during the 72-96 hour window of pupal development impairs gene expression in dopaminergic flight neurons in part through the expression of Set2, a histone methyltransferase. The authors identify a large number of genes that are controlled by Set2, and show that Set2 is controlled by the Trl/GAF transcription factor. Although the findings reported here are important, the evidence supporting some of the claims is incomplete.

Author Response

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

We appreciate the critical review of our manuscript. We believe that we have addressed the questions and concerns raised by the reviewers to the best of our ability. As part of the revision, we conducted two new experiments to enhance the rigor of the conclusions and to provide more insights into the mechanism of STEAP proteins, and we reorganized the Results section, as suggested by the reviewers, following to a clearer logical thread. The new data are briefly summarized below.

1) Reduction of L230G STEAP1 by reduced FAD. We made Leu230Gly STEAP1 mutant and measured the rate of heme reduction by reduced FAD. We found that the rate of heme reduction in L230G STEAP1 is slower than that in the wild type STEAP1. Since Leu230 is solvent accessible only from the intracellular side, this result supports the conclusion that reduced FAD binds to STEAP1 on the intracellular side and reduces the heme. This result also indicates that leucine, which is found at the equivalent position in STEAP1, 2 and 3, and Phe359 in STEAP4, has a significant role in mediating electron transfer from FAD to the bound heme.

2) Reduction of STEAP2 by reduced FAD. We showed that STEAP2 can be reduced when supplied with reduced FAD, and that the rate of heme reduction is significantly slower than that of reduction of STEAP1 by reduced FAD. This result is consistent with presence of the oxidoreductase domain (OxRD)† in STEAP2, which hampers direct entrance of the isoalloxazine ring of FAD to its binding pocket in the transmembrane domain (TMD). On the other hand, the rate of heme reduction by reduced FAD is much faster than that of heme reduction in the presence of NADPH and FAD, indicating that reduction of FAD by NADPH is rate-limiting in the electron transfer chain in STEAP2.

†: To be consistent with literature, we adopted the nomenclature “oxidoreductase domain (OxRD)” for the N-terminal soluble domain in STEAP proteins. We used the term “reductase domain (RED)” in the previous version of our manuscript.

Reviewer #1 (Public Review):

This important study reveals the structure of human STEAP2 for the first time and suggests the electron transport pathway, but some questions remain regarding the interpretation of the in vitro electron transport experiments, the lack of available redox couples, and potential alternative hypotheses that would if addressed, strengthen the claims in the manuscript.

Strengths

One of the clear strengths of the manuscript that stands out is the determination of the structure of human STEAP2. The structures of some other homologs are known, but STEAP2's structure was not, and STEAP2 seems to have an unusually low activity towards certain metal chelates. The approach of producing the human STEAP2 in insect cells with the supplementation of cofactor biogenesis components nicely results in cofactor-replete protein. The structure of STEAP2 reveals a domain-swapped trimer, with the NADPH-binding domain of the neighboring protomer within electron-transport distance of the FAD-heme axis. The FAD has an interesting and somewhat unusual extended conformation and abuts a Leu residue that may regulate electron transport. Another strength of the manuscript is the demonstration that STEAP1, which does not have the internal NADPH binding domain, can interact modestly and shuttle electrons to the heme in STEAP1 through FAD. These experiments nicely expand information on the function of STEAP1 and provide a structural basis for electron transport in STEAP2.

Weaknesses

A major weakness in the manuscript lies with the kinetics data and how the data, as presented, are unclear to the reader regarding their impact and their connection to the purported electron transport scheme. While multiple sets of data are reported, the analysis in all cases is simply the reduction of a hexacoordinate heme and its related spectra and kinetic parameters. In most cases, it's unclear to the reader which part of the electron pathway is being tested in which experiment. Simple diagrams would be helpful in each case. However, it's also unclear if all of the potential order of addition experiments were actually performed; i.e., flavin but no NADPH; NADPH but no flavin; flavin before NADPH; flavin after NADPH, etc. As there are multiple permutations that should be tested to demonstrate the electron transport pathway, presenting the data in a way that makes it clear to the reader is challenging. Particularly missing are the determined redox potentials of the hemes in both STEAP1 and STEAP2. Could differences in these heme redox potentials be drivers of the difference in metal reduction rates?

We re-structured the manuscript to follow a clearer logical thread. We provided explanations for which electron transfer steps are being examined in each experiment.

We cannot reliably determine EM due to insufficient amount of purified proteins. We are inclined to think that the bound heme on STEAP1 and STEAP2 have similar EM, based on their similar coordination geometry and nearly identical UV-Vis and MCD spectra. Thus, different rates of Fe3+-NTA reduction by STEAP1 and STEAP2 are likely due to differences in substrate binding site rather than different EM.

Also, the text indicates that STEAP2 does not show a reduction rate dependence on the [Fe3+NTA], but Figure 1A shows a difference in rates dependent on [Fe3+-NTA], and the shape of the reduction curve also changes based on [Fe3+-NTA]. This discrepancy should be rectified.

We fixed this error. The reduction of Fe3+-NTA by ferrous STEAP2 shows multiple phases and the reaction rates within the initial 2 seconds are weakly dependent on [Fe3+-NTA].

A second major weakness is the lack of any verification of the relevance of the STEAP2 oligomerization to its in vivo function. Is the same domain-swapped trimer known to exist in vivo? If the protein were prepared in other detergents, is the oligomerization preserved? It is alluded to in the text that another STEAP protein is also a trimer. Was this oligomerization verified in vivo?

The domain-swapped assembly is an interesting phenomenon, and it seems to provide a solution for bringing the FAD closer to heme. The same domain swapped trimeric assembly is also observed in the structure of STEAP4, which was purified in a different detergent (Nat Commun (2018), 9, page 4337). It is likely that this feature is shared by STEAP2, 3, and 4, and preserved during the purification process.

Could this oligomerization be disrupted to impede or abrogate electron transport to underscore the oligomerization relevance? This point is germane, as it would further suggest that the domain-swapped trimer observed in the STEAP2 cryo-EM structure is physiologically relevant, especially given how far the distance between the NADPH and the FAD would otherwise be to support electron transport.

We agree with the reviewer’s reasoning that the oligomeric assembly is required for proper function of STEAPs and thus could potentially be utilized for functional regulation. However, we are not aware of any physiologically relevant stimuli or treatment that would allow regulation of STEAP functions by inducing or forming different oligomeric states. Our experience with STEAP proteins is that the trimeric assembly is stable and well-preserved during the purification process and can only be disrupted under denaturing conditions such as SDS-PAGE.

Beyond these two areas in which the manuscript could be improved there are a couple of minor considerations. First, the modest resolution of the STEAP2 structure prevents assigning the states of NADP+/NADPH and FAD/FADH2 with confidence. An orthogonal measure would be useful for modeling the accurate states in the structure.

We agree. We clarified the ambiguity and stated in the main text that the cryo-EM structure of STEAP2 was determined in the presence of NADP+ and FAD.

Finally, the BLI b5R/STEAP1 binding/unbinding fits seem somewhat poor, especially at high concentrations of b5R in the dissociation regime, which likely influences the derived value of Kd. A different fitting equilibrium might yield better agreement between the experimental and theoretical results. Moreover, whether this binding strength is influenced by the reduction state of the NADPH would be helpful in understanding and contextualizing the weak binding affinity.

We think that non-specific binding likely causes deviations from the simple binding model at higher b5R concentrations. We made a comment on this in the main text. We agree with the reviewer that the interactions between b5R and STEAP1 could be redox dependent, for example, a reduced FAD on b5R may enhance the affinity. We could implement this by performing the binding experiments in an anaerobic chamber, but this is beyond the scope of the current study.

Reviewer #2 (Public Review):

The manuscript provides new insight into a family of human enzymes. It demonstrates that STEAP2 can reduce iron and STEAP1 can be promiscuous regarding the source of electron donors that it can use. The quality of the kinetics experiment and the structural analysis is excellent. I am less enthusiastic about the interpretation of data and the take-home message that the manuscript intends to deliver. Above all, the work combines data on STEAP2 and STEAP1 and it remains unclear which questions are ultimately addressed. A second critical point is about the interpretation of the experiment demonstrating that STEAP1 can be reduced by cytochrome b5 reductase. The abstract states that "We show that STEAP1 can form an electron transfer chain with cytochrome b5 reductase" whereas the main text discusses the data by suggesting that "we speculate that FAD on b5R may partially dissociate to straddle between the two proteins". The two statements seem to be partly contradictory. Cytochrome b5 reductases do not easily release FAD but rather directly donate electrons to heme-protein acceptors (PMID: 36441026). According to the methods section, no FAD was added to the reaction mix used for the cytochrome b5 reductase experiment. Overall, the data seem to indicate that the reductase might reduce the heme of STEAP1 directly. Would it be possible to check whether FAD addition affects the kinetics of the process?

We agree with the reviewer on this point. We do not have evidence indicating that FAD fully or partially dissociates from b5R to interact with STEAP1. We removed the statement in the revision.

We have not tried to add free reduced FAD to the mixture of STEAP1/b5R/NADH, because we feel that this would increase the complexity of the system and complicate data interpretation. We are working on determining the structure of b5R in complex with STEAP1 to visualize the electron transfer pathway, and we hope that such a structure would provide a framework for understanding electron transfer between the two proteins.

And to perform a control experiment to check that NAD(P)H does not directly reduce the heme of STEAP1 (though unlikely)?

We did the control experiment and included data in Fig. S3A. No reduction of heme by NADH alone.

A final point concerns the "slow Fe3+-NTA reduction by STEAP2". The reaction is not that slow as the initial phase is 2 per second. The reaction does not show dependence on the substrate concentration suggesting "poor substrate binding". I am not convinced by this interpretation. Poor substrate binding would give rise to substrate dependency as saturation would not be achieved. A possible interpretation could be that substrate binding is instead tight and the enzyme is saturated by the substrate. Can it be that the reaction is limited by non-productive substrate-binding and/or by interconversions between active and non-active conformations? We re-analyzed the data and revised the Results and Discussion.

We agree with the reviewer on this point. We re-analyzed the data and found that the reaction rates within the first 2 seconds are weakly dependent on [Fe3+-NTA] while the rates beyond 2 seconds do not show dependence on [Fe3+-NTA]. More studies are required to unravel the mechanism that leads to the complicated kinetic data.

Reviewer #3 (Public Review):

The six-transmembrane epithelial antigen of the prostate (STEAP) family comprises four members in metazoans. STEAP1 was identified as integral membrane protein highly upregulated on the plasma membrane of prostate cancer cells (PMID: 10588738), and it later became evident that other STEAP proteins are also over expressed in cancers, making STEAPs potential therapeutic targets (PMID: 22804687). Functionally, STEAP2-4 are ferric and cupric reductases that are important for maintaining cellular metal uptake (PMIDs: 16227996, 16609065). The cellular function of STEAP1 remains unknown, as it cannot function as an independent metalloreductase. In the last years, structural and functional data have revealed that STEAPs form trimeric assemblies and that they transport electrons from intracellular NADPH, through membrane bound FAD and heme cofactors, to extracellular metal ions (PMIDs: 23733181, 26205815, 30337524). In addition, numerous studies (including a previous study from the senior authors) have provided strong implications for a potential metalloreductase function of STEAP1 (PMIDs: 27792302, 32409586).

This new study by Chen et al. aims to further characterize the previously established electron transport chain in STEAPs in high molecular detail through a variety of assays. This is a wellperformed, highly specialized study that provides some useful extra insights into the established mechanism of electron transport in STEAP proteins. The authors first perform a detailed spectroscopic analysis of Fe3+-NTA reduction by STEAP2 and STEAP1, confirming that both purified proteins are capable of reducing metal ions. A cryo-EM structure of STEAP2 is also presented. It is then established that STEAP1 can receive electrons from cytochrome b5 reductase, and the authors provide experimental evidence that the flavin in STEAP proteins becomes diffusible.

The specific aims of the study are clear, but it is not always obvious why certain experiments are performed only on STEAP2, on STEAP1, or on both isoforms. A better justification of the performed experiments through connecting paragraphs and proper referencing of the literature would improve readability of the manuscript. Experimentally, the conclusions are appropriate and mostly consistent with the experimental data, although one important finding can benefit from further clarification. Namely, the observation that STEAP1 can form an electron transfer chain with cytochrome b5 reductase in vitro is an exciting finding, but its physiological relevance remains to be validated. The metalloreductase activity of STEAP1 in vitro has been described previously by the authors and by others (PMIDs: 27792302, 32409586). However, when over expressed in HEK cells, STEAP1 by itself does not display metal ion reductase activity (PMID: 16609065), and it was also found that STEAP1 over expression does not impact iron uptake and reduction in Ewing's sarcoma (cancer) cells (PMID: 22080479). Therefore, the physiological relevance of metal ion reduction by STEAP1 remains controversial. The current work establishes an electron transfer chain between STEAP1 and cytochrome b5 reductase in vitro with purified proteins. However, the conformation of this metalloreductase activity of the STEAP1-cytochrome b5 complex will be required in a cell line to prove that the two proteins indeed form a physiological relevant complex and that the results are not just an in vitro artefact from using high concentrations of purified proteins.

The work will be interesting for scientists working within the STEAP field. However, some of the presented data are redundant with previous findings, moderating the study's impact. For instance, the new structural insights into STEAP2 are limited because the structure is virtually identical to the published structures of STEAP4 and STEAP1 (PMIDs: 30337524, 32409586), which is not surprising because of the high sequence similarity between the STEAP isoforms. Moreover, the authors provide experimental evidence to prove the previous hypothesis (PMID: 30337524) that the flavin in STEAP proteins becomes diffusible, but the molecular arrangement of a STEAP protein, in which the flavin interacts with NADPH, remains unknown. Based on the manuscript title, I would also expect the in-depth characterization of STEAP1/STEAP2 hetero trimers (first identified by the authors), but this is only briefly mentioned. When taken together, this study by Chen et al. strengthens and supports previously published biochemical and structural data on STEAP proteins, without revealing many prominent conceptual advances.

We thank the reviewer for information and the broader context. We have revised the manuscript to have a clearer logical thread.

Reviewer #1 (Recommendations For The Authors):

Please see the "Public Review" for recommendations.

Reviewer #2 (Recommendations For The Authors):

Specific suggestions

-The introduction should more clearly state which questions are being addressed and why STEAP1 and STEAP2 are investigated.

We have revised the Introduction to make that clearer.

-The manuscript should discuss more extensively and provide possible explanations for the substrate-independent kinetics of iron-reduction by STEAP2.

We re-analyzed the data and found the rate constants of the reactions before 2 s are weakly [Fe3+NTA]-dependent. We ascribe the weak [Fe3+-NTA]-dependence to the partial rate-limiting by substrate binding. However, we do not have a good interpretation for the reaction kinetics after 2 s which does not show [Fe3+-NTA]-dependence.

-"The rate of STEAP1(Fe(II)) oxidation by Fe3+-NTA is similar to those by Fe3+-EDTA or Fe3+-citrate, but the rates are significantly faster than STEAP2(Fe(II)) re-oxidation by Fe3+NTA (Fig. 1B)." The rates for STEAP1 should be given to substantiate this statement.

We added Table S1 in the supplementary materials that includes the 2nd order association (kon) and the 1st order dissociation rate constants (koff) of iron substrates in STEAP1 and STEAP2. Data on Fe3+-EDTA or Fe3+-citrate by STEAP1 are from our previous study (Biochemistry, 2016). We also calculated the KDs of different iron substrates for STEAP1 and STEAP2.

• "Our results indicate that STEAP2 can supply reduce FAD to initiate electron transfer in STEAP1." As discussed above, this statement should be discussed and analyzed

We mixed 0.9 μM STEAP1, 1.1 μM STEAP2, and 2.2 μM FAD and added 60 μM NADPH to the system and found that the heme on both STEAP1 and STEAP2 are reduced. Since adding NADPH to STEAP1 plus FAD alone does not reduce the heme (Fig. S3B), we reasoned that reduction of the heme on STEAP1 is achieved by the reduced FAD produced on STEAP2. The reduced FAD likely dissociates from STEAP2 and then bind to STEAP1.

-Experiments on "STEAP1 reduction by STEAP2" The experiments show that "STEAP2 can supply reduce FAD to initiate electron transfer in STEAP1." Could these results be explained by heterotrimer formation in agreement with the previous data published by the authors?

In our experience, STEAP1 and STEAP2 homotrimers are stable and do not form heterotrimers when mixed. STEAP1/2 heterotrimers form only when the two proteins are co-expressed in cells (Biochemistry (2016) 55, 6673-6684).

Reviewer #3 (Recommendations For The Authors):

Major points:

1) As a very general point: the order in which the results are presented could be greatly improved to increase the readability for non-experts. To elaborate: The manuscript starts with the spectroscopic characterization of STEAP2, then suddenly the reductase activities of STEAP1 and STEAP2 are compared; subsequently, experiments are described involving STEAP1 and cytochrome b5 reductase; then the cryo-EM structure of STEAP2 is presented etc. As a non-expert reader, this presentation of the results is confusing, especially because the paragraphs are not always connected well, and there is a lot of switching between STEAP1 and STEAP2 data. A more logical order would be to first present the STEAP2 spectroscopy and structural data, then write a connecting paragraph on why it is important to also study the electron transfer chain in STEAP1, followed by the comparison of the STEAP isoforms and the data on STEAP1 alone. The authors should include sentences on why they performed each experiment. For example, why did they determine the structure of STEAP2. What were they after that they could not retrieve from the homologous STEAP4 and STEAP1 structures? Justification of the performed experiments will make it easier for the reader, and will establish a better connection between the paragraphs.

We reorganized the data presentation in Results per the reviewer’s suggestions.

2) The physiological relevance of metal ion reduction by STEAP1 remains controversial. Because the current work establishes an electron transfer chain between STEAP1 and cytochrome b5 reductase, could the authors perform an easy experiment where they over express both STEAP1 and cytochrome b5 reductase in a cell line? If such an experiment would reveal STEAP1-dependent metal-ion reduction, it would greatly improve this part of the manuscript. If no activity is observed, the established electron transfer chain could just represent an in vitro artifact from using high concentrations of purified proteins.

This is an excellent point. We are not set up to perform the proposed experiment but will do so in the future.

3) The manuscript states that metal ion reduction of purified STEAP2 is slow, and the authors explain this by the absence of density for the extracellular region between helices 3 and 4 that are present in the structures of STEAP4 and STEAP1, resulting in a less-well defined substratebinding site. Can the authors exclude that the less-well defined substrate-binding site is a result of the detergent extraction of STEAP2? Would it be possible to measure the reductase activity of STEAP2 in purified membranes?

Detergent mostly interacts with the transmembrane domains and since the TMD region of STEAP2 aligns well with those of STEAP1 and STEAP4, we do not think that the disordered substrate binding region in STEAP2 is a consequence of detergent solubilization. It is difficult to conduct pre-steady state kinetic experiments using STEAP2 in membrane fractions.

4) The manuscript would greatly benefit from citing the literature more comprehensively to acknowledge insightful findings from authors in the field; for example, the important work by the Lawrence lab from 2015 (PMID: 26205815), which biochemically proved that STEAPs bind a single heme and that FAD bridges the TMD and RED, is not cited. The authors also mention that STEAP proteins belong to the same family as NOX proteins and cite some NOX structure papers. However, they fail to cite the first NOX structure paper (PMID: 28607049), as well the manuscript that structurally compares NOXs and STEAPs (PMID: 32815713). Similarly, the authors use SerialEM for their cryo-EM data collection but cite an old paper instead of the more recent (and relevant) SerialEM publication (PMID: 31086343).

We agree and added the references.

5) Generally, the data presented in the manuscript appear of good technical quality. However, a 'Table 1' with all relevant cryo-EM data collection and refinement statistics is completely missing as far as I can see. The authors should definitely add this to allow for the judgement of structural data quality. Without it, the manuscript is not suitable for publication.

We added Table S2 that includes relevant cryo-EM statistics.

Minor points:

6) The authors write in the abstract: 'STEAP2 - 4, but not STEAP1, have an intracellular domain that binds to NADPH and FAD'. This is not correct, because it has clearly been established that FAD also majorly binds to the transmembrane domain (this is even shown by the authors in the current manuscript as well).

Agree, we corrected that in the revision.

7) Sentence from the abstract and introduction state: 'It is also unclear whether STEAP1 has metal ion reductase activity' and 'it is unclear whether STEAP1 can form a competent electron transfer chain from NADPH'. The authors should definitely add "physiologically relevant" to these sentences. Namely, the senior authors themselves concluded in their 2016 Biochemistry paper (PMID: 27792302) that STEAP1 is capable of reducing metal ion complexes. Further indications that the transmembrane domain of STEAP1 displays metalloreductase activity was published by the Gros lab (PMID: 32409586), and it was also shown that fusing the RED of STEAP4 to the TMD of STEAP1 yields a functional protein in cells that reduces metal ions.

Good point and we revised the text and included the references.

8) Why is scheme 1 not just a summarizing figure?

We could change Scheme 1 to a Figure if required by the copy editor.

9) What is the purpose of Fig. 6? A larger depiction of Fig. 5e would likely be more relevant and should be considered as a replacement. Alternatively, the structure of STEAP1 (pdb 6y9b) could be shown in combination with Fig. 7, as the mutation is performed in STEAP1.

We agree and made changes to the structural figures to enhance clarity.

10) The manuscript now contains many, single panel figures. Certain main figures could easily be combined, for example, Fig. 1 and 2 and/or Fig. 3 and 4.

We agree and made changes to reduce single panel figures.

11) In Fig. 2, 3 and 4, the spectra show changes in peak heights as a result of the ferric to ferrous heme transition. However, a time component is missing in the legend. How long do these transitions take?

We added the reaction times to the figure legends.

12) The last part of the discussion states: 'The assembly of an intracellular RED with a membrane-embedded TMD observed in NOX, DUOX, and STEAPs naturally led to the notion that NADPH, FAD, and heme form an uninterrupted rigid electron-transfer chain that shuttles electron from the intracellular cellular NADPH to the extracellular substrates. While this may be true for NOX and DUOX, in which rapid supply of electrons to their extracellular substrates are essential to their biological functions, it may not apply similarly to STEAPs since it has only one heme in the TMD, and their electron transfer relies on shuttling of FAD.' The authors should mention here that the activity of NOX and DUOX is tightly regulated by accessory proteins, Ca2+ etc. Similarly, do the authors expect that the large distance between NADPH and FAD in the structures could represent a way to regulate/dampen the metal ion reduction rates of STEAPs in vivo?

We agree. We mentioned the regulation of NOX and DUOX in Discussion. We remain puzzled by the large distance between NADPH and FAD in STEAPs and are in pursuit of a structure in which the two cofactors are “in touch” for electron transfer.

eLife assessment

This study provides useful insights into the mechanisms of electron transport in STEAP proteins, consistent with current models. The work strengthens and supports previously published biochemical and structural data, and the experimental results are of solid technical quality. The manuscript will be of interest to colleagues who work on STEAP proteins and related electron transfer systems.

Reviewer #1 (Public Review):

In the revised manuscript presented by Chen, Wang, and coworkers, the authors examine two proteins, STEAP1 and STEAP2, which are transmembrane hemoproteins that are involved in Fe and Cu homeostasis and are implicated in certain cancer states. The authors produce recombinant forms of STEAP1 and STEAP2 and attempt to reconstruct the electron-transport chains of both; under certain conditions, the electron transport chain of STEAP2 consists of an internal reductase domain that binds NADPH and transfers electrons to an internal FAD molecule prior to the heme b, while STEAP1 can use an independent/external b5 reductase instead of an intrinsic reductase domain to accomplish the same electron transport pathway. A strong feature of this manuscript is the determination of the cryo-EM structure of the human STEAP2 protein resolved to 3.2 Å globally and bound to heme, FAD (in an extended conformation), and NADP+/NADPH.

This revised study aims to address the previous weaknesses that were noted, such as the unclear presentation of the kinetics data, the lack of determined redox couples, the lack of in vivo oligomerization verification, and some minor weaknesses such as the fit of the BLI data and the exact redox states of the bound coenzymes. In general, the authors have sought to rectify these weaknesses chiefly through textual edits. Through these revisions, the kinetics data are now better presented and may be more easily interpreted by the reader, how the samples for cryo-EM were prepared with the respective coenzymes is clearer, and a comparison between the oligomerization of STEAP2 and STEAP4 suggests conservation of oligomerization. The determination of the redox potentials of the hemes in both STEAP1 and STEAP2 would still be a strong addition to the data presented, but it is recognized that the limitations in the ability to prepare sufficient quantities of recombinant enzyme limits the ability to determine the measurements and may represent another publication outside of the scope of this publication.

Reviewer #2 (Public Review):

Human STEAPs form a family of transmembrane heme-bound proteins. They are implicated in cancer given their high expression levels in tumor cells. Previous work has revealed that STEAPs 1-4 are iron and copper reductases. The recent structure determination of STEAP1 and STEAP4 unveiled their trimeric arrangement. STEAP1 is an outlier because it lacks the cytosolic reductase domain present in STEAPs 2-5. The present work adds to our knowledge of the family. It reports on the cryoEM structure of STEAP2 that is similar to the known structures of STEAP4 and STEAP1. The structural analysis provides additional support to a FAD-dependent heme-reduction mechanism whereby FAD oscillates between two conformations. The excellent kinetics experiments show that STEAP1 can be promiscuous regarding the source of electron donors that it can use. Indeed, cytochrome b5 can directly reduce the heme prosthetic group of STEAP1 thereby establishing an electron transfer chain that conveys electrons from NADP(P)H to the extracellular iron. Remarkably, STEAP1 can also accept electrons from free reduced FAD. Most interestingly, the manuscript demonstrates that STEAP2 can be a source of reduced FAD so that STEAP2 can create the reducing power needed for its own activity and the activity of STEAP1. This work further convincingly shows that STEAP1 can reduce iron whereas STEAP2 is less effective in iron reduction. The manuscript indicates that STEAP2 might accept other substrates providing a hint about the distinct biochemical and physiological roles of the STEAP paralogs. The manuscript does not address this point that remains open for further investigations. Aside from this minor weakness, the manuscript will advance the fields of STEAP and iron biochemistry. It has benefited from the advice given by the Reviewers leading to a high-quality presentation and data analysis.