PONE-D-23-44216SOX7: Novel Autism Associated Gene Identified by Analysis of Multi-Omics DataPLOS ONE

Dear Dr. Lee,

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.

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We look forward to receiving your revised manuscript.

Kind regards,

Chunyu Liu

Academic Editor

PLOS ONE

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“This study was financially supported by the National Institutes of Health (NCATS R44TR003491 and NIDDK UH3DK119982) and the University of North Texas (Startup).”

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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: Partly

Reviewer #2: Partly

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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

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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

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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 the study of Gonzales et al., the authors analyzed the GWAS and transcriptome data and identified SOX7 as an ASD risk gene. However, the results could not robustly support SOX7 as a novel risk gene for ASD. My several comments as listed bellow:

1、It is cautious to state that SOX7 is a novel ASD risk gene. Is this study the first one to support the connection between SOX7 and ASD?

2、The authors did not perform any experiment to support their conclusion, how to support SOX7 as an ASD risk gene?

3、Correlation between SOX7 expression and ASD phenotypes may be needed to support the conclusion.

4、eQTL analysis is required for ASD-associated genetic variants and SOX7 expression.

Reviewer #2: The authors performed gene-based association test and DEG test flawlessly. However, there is one principal issue regarding to the GWAS set used and subsequent conclusions made: the PGC ASD 2017 and PGC ASD 2019 dataset are cumulative (i.e., the raw data used in ASD 2019 is a superset of ASD 2017, and I can confirm this with confidence as a PGC panel member). Therefore, the conclusion that SOX7 association has been found in both ASD 2017 and 2019 dataset is unsurprising and statistically expected. More importantly, these two dataset cannot be claimed as replicates for their inclusion (Page 14, results).

It is recommended that a "true" replicate of gene-based association test to be performed using an independent ASD dataset such as SPARK (Matoba et al. 2020 https://www.nature.com/articles/s41398-020-00953-9). I believe it should not take too much effort to repeat the analysis and the conclusions would be significantly consolidated.

Reviewer #3: In the study conducted by Samantha Gonzales and colleagues, utilizing gene-based analysis and two extensive GWAS datasets from 2019 and 2017, identifying five genes with a substantial link to autism spectrum disorder (ASD). Further, integrated two ASD and control postmortem brain gene expression data revealed that the SOX7, an (SRY-related HMG-box) family of transcription factors as a high-confidence risk gene upregulated in ASD patients. The design of this study is straightforward, but the description of the results needs to be significantly improved. For example, the scientific rationale of each section within the results needs to be more thoroughly explained. I have the following comments:

1. A major concern of this study is the reliance on two large GWAS datasets from the Psychiatric Genomics Consortium (PGC). The dataset used for discovery, dated 2019, is not independent of the dataset used for replication, dated 2017.

2. Please combine Figures 2a and 2b as one figure. Additionally, please describe the various panels within this figure, clarifying terms such as “all sample” and “white sample.”

3. Using gene expression counts in Figures 2a and 2b creates confusion, particularly as Figure 2b is presented on different scales, please address this for clarity.

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Reviewer #1: No

Reviewer #2: Yes:  Siwei Zhang

Reviewer #3: No

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PONE-D-23-44216R1SOX7: Autism Associated Gene Identified by Analysis of Multi-Omics DataPLOS ONE

Dear Dr. Lee,

Thank you for submitting your manuscript to PLOS ONE. I would recommend provisional acceptance of your paper. 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 Nov 20 2024 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:

• 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Chunyu Liu

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

I'd like to thank the authors for their efforts in addressing the reviewers' comments. While all reviewers recommended accepting the manuscript, I found that one additional concern needs to be addressed.

The MR needs to provide evaluation of instrument strength, using F-statistics. Ideally, methods like MR-Egger should be tried as well to address pleiotropy effects. The conclusion should reflect the results of these additional analyses.

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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

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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

Reviewer #3: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: (No Response)

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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: The authors have addressed my concerns. However, the abstract contains too much description about the background knowledge. Major results should be briefly summarized rather than listed all the results in the abstract.

The abstract is suggested to be revised before publication. I have no further comments.

Reviewer #2: There is one minor issue that needs to be amended before allowing publication: in Fig. 2, please plot all data points in addition to the box-whisker plot.

Reviewer #3: The authors have done an excellent job responding to my criticisms. I am happy to now recommend this manuscript for publication in Plos One.

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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: Yes:  Siwei Zhang

Reviewer #3: No

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[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.

SOX7: Autism Associated Gene Identified by Analysis of Multi-Omics Data

PONE-D-23-44216R2

Dear Dr. Lee,

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.

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Kind regards,

Chunyu Liu

Academic Editor

PLOS ONE

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