Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation

Jamie Reilly; Louise Gallagher; Geraldine Leader; Sanbing Shen

doi:10.1371/journal.pone.0242773

Peer Review History

Original SubmissionJuly 27, 2020
4 Sep 2020 Decision Letter - Nirakar Sahoo, Editor PONE-D-20-23352 Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation PLOS ONE Dear Dr. Reilly, 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. The manuscript has been assessed by two experts in the field; please find their comments appended at the end of this email. The reviewers have identified several issues, all of which needed to be addressed in a revised version of the manuscript. In particular, I would advise you to pay attention to major comments from Reviewers. 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Nirakar Sahoo, PhD Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 ****** 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 ****** 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: In this manuscript, Reilly et. al. undertake bioinformatics analysis of susceptible genes in autism spectrum disorder (ASD) and associated co-morbidities. ASD is a genetically complex neurodevelopmental syndrome, with a wide array of central nervous system (CNS) and peripheral genes being implicated. A systematic assignment of genes responsible for comorbidities is lacking. An effort toward this direction can aid in deciphering the underlying genetic determinants and mechanisms, and could be relevant clinically. To that end, the authors analyzed five publicly available ASD databases, namely, SFARI, EXAC, Krishnan, Duda and Zhang. Based on overlap of the genes in these databases and expression profile, 292 genes were finally shortlisted for further analyses. These genes could be clustered into two sets – one expressed in the CNS and the other in the CNS as well as in peripheral tissues (PT). While both genesets included genes belonging to neuronal development, ion transport and synapse, the CNS+PT set intriguingly included additional genes related to chromatin organization and gene expression. The study represents a thorough and systematic analyses of the genes implicated in ASD using available datasets. The analysis provides a platform for further experiments looking into roles of various genes especially the ones related to chromatin organization. A couple of issues that the authors need to address: 1) It would further strengthen the analysis if the authors provide a comparison of expression profile of the genes analyzed in normal vs ASD patients. The authors could provide the comparison for whole or a subset of genes based on availability of data. This would help in narrowing down the focus on genes whose expressions vary in diseased state for future experimental studies. 2) ASD is more prevalent in males compared to females and is also characterized by an early onset with respect to age of an individual. So, it would again strengthen the manuscript if the authors analyze expression pattern in males vs. females and whether there is any difference with age. In case there is a notable difference, then the data should be presented whereas if there is no skewed behavior, that need to be mentioned appropriately in the results. Reviewer #2: In the present manuscript Reilly and co-authors analyze the existing gene expression data from autism spectrum disorder (ASD) samples. The authors presumed that dysregulation of a set of genes driving ASD should be visible in different scoring systems. By combining and reanalyzing the results of several scoring systems, the authors generated. list of genes that, in their opinion, reflects a hallmark set for ASD. Several findings in this set are intriguing, esp the possible involvement of extra-CNS tissues. The paper is methodologically sound and well written. However, in this Reviewer's opinion, in the present stage, the manuscript's scope is very limited, and it is likely that its impact will not be significant. At present, there does not seem to be a lack of candidate genes for ASD. In the present form the manuscript identifies yet another candidate set, which does not illuminate what makes ASD distinct from other neurologic diseases, or whether ASD is a set of conditions. The manuscript would benefit from an informative comparison of the author's set with other diseases, identifying unique features of ASD. As the authors indicate, it is likely that the ASD-driving dysregulation(s) occur early in development and thus, the utility of the present set is unclear. ****** 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 [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. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0242773.r001
Revision 1
21 Oct 2020 Author Response Dear Editors, thank you and the reviewers for the kind remarks and constructive comments. We have addressed the points raised by the reviewers, with point-by-point response below. We have revised the manuscript with additional data which significantly strengthen the manuscript. We hope the revised manuscript can be accepted for publication on PLOS One. Kind regards Reviewer 1 questions 1) It would further strengthen the analysis if the authors provide a comparison of expression profile of the genes analyzed in normal vs ASD patients. The authors could provide the comparison for whole or a subset of genes based on availability of data. This would help in narrowing down the focus on genes whose expressions vary in diseased state for future experimental studies. Response : We thank Reviewer 1 for raising this good point. We have now added a table and data on genes that were reported to be differentially expressed in various studies that overlap with our geneset. 2) ASD is more prevalent in males compared to females and is also characterized by an early onset with respect to age of an individual. So, it would again strengthen the manuscript if the authors analyze expression pattern in males vs. females and whether there is any difference with age. In case there is a notable difference, then the data should be presented whereas if there is no skewed behavior, that need to be mentioned appropriately in the results. Response: We have used gene lists reported by Shi et al 2016 and identified some of our ASD genes present across brain regions at prenatal stages with sex-bias expression (Fig. 8A and B). We also used CSEA webtool and found our geneset is enriched across various developmental stages in the human brain (Fig 8D). We also used GeneOveralp in Bioconductor to test significance of overlap in male biased and female biased prenatal gene sets, and identified 34 genes which are differentially spliced in male and female (Fig 8C). Reviewer 2 questions 1) At present, there does not seem to be a lack of candidate genes for ASD. In the present form the manuscript identifies yet another candidate set, which does not illuminate what makes ASD distinct from other neurologic diseases, or whether ASD is a set of conditions. The manuscript would benefit from an informative comparison of the author's set with other diseases, identifying unique features of ASD. Response: We have compared ASD geneset with genes from psychiatric conditions (via Psychgenet) and 4 peripheral conditions (Inflammatory bowel disease, arrythmia, Type 1 and Type 2 diabetes) from Harmonizome database (GWAS lists are from GWASdb dataset. We have identified subsets of genes overlapping with CNS snf peripheral conditions, as well as ASD unique genes (Fig. 9) 2) As the authors indicate, it is likely that the ASD-driving dysregulation(s) occur early in development and thus, the utility of the present set is unclear. Response: We have used CSEA to test for enrichment of the ASD geneset in various brain regions across different timepoints of brain development and showed a high enrichment to specific regions, cortex in particular (Fig. 8D) Attachments Attachment Submitted filename: Reviewer questions and responses (1).docx https://doi.org/10.1371/journal.pone.0242773.r002
10 Nov 2020 Decision Letter - Nirakar Sahoo, Editor Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation PONE-D-20-23352R1 Dear Dr. Reilly, 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, Nirakar Sahoo, PhD 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 ******** 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: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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: 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: 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: (No Response) Reviewer #2: (No Response) ****** 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 https://doi.org/10.1371/journal.pone.0242773.r003
Formally Accepted
1 Dec 2020 Acceptance Letter - Nirakar Sahoo, Editor PONE-D-20-23352R1 Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation Dear Dr. Reilly: 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 Dr. Nirakar Sahoo Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0242773.r004

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