PONE-D-21-20087Genetically regulated gene expression and proteins revealed discordant effectsPLOS ONE

Dear Dr. Pott,

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. You may notice the reviewer raised some concerns regarding the methodology. I agree with these points, especially it would be useful to know whether the use of GTEx V8 can replicate the findings based on GTEx V7, as well as the basis of outcome selection.

Please submit your revised manuscript by 25 Dec 2021. 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.

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We look forward to receiving your revised manuscript.

Kind regards,

Jie V Zhao

Academic Editor

PLOS ONE

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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: Yes

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

Reviewer #1: 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

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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

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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: The authors did an extensive work to study the 92 proteins in the whole blood from 2014 participants in both SNP level and locus level. Of which, 63 proteins were genetically regulated, and 3 sex specific effects were identified. The authors then tested for the colocalization between pQTLs and eQTLs and found evidence of both independent and shared signals. Additionally, the authors tested for the association of genetically regulated gene expression (GE) across tissues and identified 10 proteins of negative correlations. Finally, the authors tested the causal link of genomics, transcriptome, proteome to coronary artery disease (CAD) risk and confirmed a negative causal effect of GE on protein level for 5 genes. The main finding was the gene IL6R.

Comment 1: In the statistical analysis, the population stratification (PS) is not considered. It would be great if the authors can include more details to justify why PS is not a concern in the study. Otherwise, if there exists any PS, not adjusting for it could induce significant bias.

Comment 2: GTEx v8 data has been released for quite a while. I wonder why the authors used v7 instead of v8?

Comment 3: The proteins in the study were supposed to be cardiovascular (CVD) biomarkers and the authors tried to establish the link from genomics, transcriptome, proteome to CAD risk. I wonder why the authors included CVD-unrelated tissues, especially when testing for the causal path involving CAD, how does the GE and PE in colon, lung and testis contribute to CAD outcome?

Comment 4: The authors may need to review and correct the typos and formatting issues throughout. For example, 1) in the abstract, CAD is first mentioned and needs to be defined; 2) The table 2 needs to be re-formatted and the minor allele of CCL15 does not look right. In line 238, the results show ten genes instead of eight; 3) The gene names should be in italics format throughout; 4) The figure 2-4 in the main text are mis-numbered as figure 1-3.

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Reviewer #1: No

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PONE-D-21-20087R1Genetically regulated gene expression and proteins revealed discordant effectsPLOS ONE

Dear Dr. Pott,

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. As you can see, one reviewer has pointed out some wording issues and consistency throughout the paper, please revise accordingly.

Please submit your revised manuscript by 10 May. 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,

Jie V Zhao

Section 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.

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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

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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

**********

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: No

Reviewer #2: No

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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

**********

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 did extensive work to revise the manuscript. Now the manuscript looks great. I do not have further question.

Reviewer #2: In the revised version of their manuscript the authors have addressed the comments raised by the reviewer and doing so the quality and clarity of the manuscript have improved substantially.

I have only a couple of (very) minor further comments:

1. Figure numbers in the main text are still not correct.

2. The authors may want to present numbers in a consistent way throughout the manuscript, either as e.g. "2384" or "2,384".

3. It seems at several occasions there is a typo with r22 instead of r2 (when referring to LD), and line 313 “data WERE available”.

4. The authors may want to check for consistent use of past tense in the material and methods section, e.g. line 135 and line 196 in the revised version of the manuscript.

5. Data from the 1000 Genome Project Phase 3 have been used for genotype imputation. I wonder, why this rather old dataset was used instead of a more updated sources for imputation, e.g. the Haplotype reference consortium r1.1 .

6. I find the term "best eQTL" a bit unclear and would like the authors to specify whether they refer to strongest/most significant eQTL and/or largest effect size.

7. A more cautious wording with regard to Mendelian Randomization may be more adequate, as this methods gives an estimate of causation/causality but does not prove or guarantee such relationship, e.g. line 349 "IL6R was the only protein that showed causality in all three settings".

8. In the part of the discussion section where the authors refer to TPM values of several genes in several tissues, many new results are reported (that otherwise have only appeared in supplementary material). I suggest to limit the content of new data presented here and instead report these findings in the results section.

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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: 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.

Genetically regulated gene expression and proteins revealed discordant effects

PONE-D-21-20087R2

Dear Dr. Pott,

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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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,

Jie V Zhao

Section Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: