Peer Review History
| Original SubmissionApril 14, 2021 |
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PONE-D-21-12396 Functional predictors of causation for cis-regulatory mutations PLOS ONE Dear Dr. FitzPatrick, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jun 26 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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[Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A Reviewer #3: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This manuscript by Bengani and FitzPatrick used an updated method to determine causality of SNPs found in genomes of patients with genetically inherited intellectual disability (ID). Those are resourceful information to the other peers studying X-linked recessive forms of ID and represent diagnostic values for this particular disorder. The data in this work use a combination of zebra fish and mouse genetics models and functionally validated the clinically identified rare variants on the X chromosomes. Overall, I agree that the study is conclusive and thus recommend for acceptance. I list two minor issues and I hope the authors can address them quickly before publication. 1, An increasing body of evidences have implied brains are highly associated with somatic mutations, which often cause defects either derived from neural degeneration or development. Dr. Christopher Walsh from Harvard University is an expert in this field. The point is brain genomes are not identical to genomes of other tissue types as the method presented in this study used nonbrain tissues for sequencing. Would the authors comments on this point with respect to performance of gnomAD2.1 in the discussion section? 2, The quality/resolution of some figures are low, e.g. fig. 1, 3, 4 and 5. Is there any way to increase the readability of these figures? Reviewer #2: Bengani et al. performed a study for the identification of functional cis-regulatory mutations involved in the development of X-linked intellectual disability. The task is definitely very interesting, but also very challenging and time consuming. Indeed, it took several years and two different in vivo models to find data supporting a causative role for one out of 31 highly conserved CRE initially identified, the FMR1-CRE variant. I think that this manuscript is worth publishing because it has a quite strong rationale behind the selection of the non-coding variants to be tested and it shows that it is possible to make functional sense of mutations in regulatory elements. However, the phenotype for which the authors are trying to find a genetic evidence in CRE is very complex and very hard to dissect. Indeed, it is very difficult to find a straightforward link with a single variant in CRE. The phenotypes observed in the mouse model and the link to the human disease appears quite weak. I think this should be clearly underlined in the manuscript and better explained. Moreover, I think that the title, being very general, overstates the results of the manuscript and it should be changed to make it more related to the findings. The description of the statistical analysis applied by the authors is lacking. Moreover, I would suggest to check the statistical methods used for the analysis, in general, and, in particular, for Fmr1 transcription by qPCR (Fig. S41): some differences between wt and mutants would seem significant (i.e. in Hind brain P7), especially compared to other data reported as significant in the manuscript (i.e. Fig. 4H). Based on these reevaluations, some results and some statement in the paper might need to be revised. Reviewer #3: Manuscript Summary: Identifying causative variants in cis -regulatory elements (CREs) in neurodevelopmental disorders has proven challenging. Bengani, Grozeva, Moyon, and Bhatia et al. used a translational bridge between humans-zebrafish-mice, with the aid of model systems, and circling back to humans to identify and evaluate the pathological implications of chromosome X-resident CRE mutations that cause X-linked intellectual disability (XLID). Overall, this manuscript is perfectly suited for the scope of PLOS ONE. The translational approach that the authors have taken in this study is albeit challenging but particularly well appreciated. Studies such as these would certainly enhance the field's understanding of pathogenic variants implicated in neurodevelopmental disorders. In addition, the methodology employed in this study is thorough and the authors present the data/findings objectively. Major Comments and Questions: 1) 1a) Figures 2F and 2G: The authors use Six3-targeting morpholinos to demonstrate that six3-knockdown rescues the activity of mutant TENM1-CRE, the latter of which is quite convincing. However, there is no validation data provided to demonstrate that the concentration of the six3-morpholino used post-optimizations indeed led to a sufficient knockdown of six3. 1b) Additional note 1 (not required for the acceptance of this manuscript for publication): While I can understand the following might be outside the scope of this manuscript, an IP-seq experiment to pull down six3-bound to either TENM1-WT or TENM1-CRE would provide irrefutable evidence to substantiate the author's hypothesis that TENM1-CRE introduces a novel binding site of the repressor, six3. 1c) Additional note 2: The following could be addressed in the discussion, as per the authors' discretion. While TENM1-CRE led to a consistent loss of tenm1-expression in the mid-brain and hind-brain (table 1), it did not lead to a loss of tenm1-expression in the neural tube. Is six3 and six6 not expressed in the neural tubes and what additional six3/six6-independent mechanisms could be at play here? 2) In the figure legend for Fig. 6C: The authors state that there was "No significant difference was observed in audiogenic seizure incidence in the hemizygous mice with the variant Fmr1CRE compared to wild-type littermates (lines 447 - 449)." However, as per Fig. 6C, the Fmr1-CRE did display a statistically-significant decrease in the predisposition to audiogenic seizures (AGS), starkly contrasting the anticipated results of an increase in AGS derived from Fmr1-null mice. The data and results appears to contradict the figure legend and the authors' interpretation. 3) It is nice that the authors took a bench-to-bedside approach to re-evaluate the individuals within the FMR1-CRE-segregating family. Did these individuals not have any olfactory disorders, which may recapitulate the phenotype observed in Fig. 5A,B? And, following up from the precedence derived from Fig. 6C, did the affected individuals also display a resistance to the development of AGS? 4) The six3 piece of data from the zebrafish study was intriguing (Fig. 2). Was there no correlative evidence of a similar interplay between Six3 and Tenm1 in mice and/or humans? Could murine and human SIX3 exhibit a non-overlapping pattern of expression with TENM1, which might explain the lack of a phenotype in Tenm1-CRE mice? What are the authors thoughts on the Six3/Six6-dependent and -independent mechanisms of tenm1-CRE in zebrafish and how these mechanisms translate to mammalian species (e.g. mice and humans)? Minor Comments and Questions: 1) Formatting: It would be nice to keep the text format used in all figures, either in the main text or in the supplement, consistent in size and style. 2) It would be nice to spell out the full names of the protein abbreviations used, such as FMR1, FMRP, TENM1. All additional major and minor comments from me were either fully or partially overlapping with those raised by the reviewers during the peer-review for the PLOS Genetics submission and have been addressed by the authors. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No Reviewer #3: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. 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| Revision 1 |
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Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability PONE-D-21-12396R1 Dear Dr. FitzPatrick, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Chaeyoung Lee Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: (No Response) Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: (No Response) Reviewer #3: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: (No Response) Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: (No Response) Reviewer #3: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: All of my minor concerns have been addressed in this revisedmanuscript. I have no further question. Reviewer #2: (No Response) Reviewer #3: The authors have sufficiently and more than satisfactorily addressed all my comments and questions. Overall, this manuscript is perfectly suited for the scope of PLOS ONE. The translational approach that the authors have taken in this study is albeit challenging but particularly well appreciated. Studies such as these would certainly enhance the field's understanding of pathogenic variants implicated in neurodevelopmental disorders. In addition, the methodology employed in this study is thorough and the authors present the data/findings objectively. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No Reviewer #3: No |
| Formally Accepted |
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PONE-D-21-12396R1 Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability Dear Dr. FitzPatrick: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Prof. Chaeyoung Lee Academic Editor PLOS ONE |
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