PONE-D-20-12168

Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2

PLOS ONE

Dear Dr. Nersisyan,

Thank you for submitting your manuscript for review to PLoS ONE. Your manuscript has been reviewed by one expert and I have also personally evaluated your article. I agree with the comments raised by the reviewer and we feel that your study has merit, but is not suitable for publication as it currently stands. Therefore, my decision is "Major Revision”.

You must revise accordingly and explain your revisions in a covering letter if you wish for us to consider your paper further for publication. We invite you to submit a revised version of the manuscript that addresses the concerns raised by the reviewer. Please pay attention to all the reviewer suggestions and give them due consideration.

Specifically:

While the paper is well-written and the methodology used appears to be sound, the reviewer indicates that the work is mainly based on correlative analyses and would deserve at least one experimental validation among the different hypotheses. I agree with this criticism, in particular because the correlations found are at the tissue and not at the cell level. I thus feel that this experimental validation would strongly improve the manuscript. I can eventually propose an alternative to this main criticism if the authors are able to check at the single cell level at least some of the interesting correlations and hypotheses they have highlighted in their study. Since miRNA data sets are not available at the single cell level, the authors may use either expression of host gene in scRNA-seq database and/or use of miRNA FISH data when available.

Please submit your revised manuscript by Jul 10 2020 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Bernard Mari, Ph.D

Academic Editor

PLOS ONE

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When submitting your revision, we need you to address these additional requirements:

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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 manuscript PONE-D-20-12168 entitled “Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACES2 and TMPRSS2” by Nersisyan et al. describes putative ACE2 and TMPRSS2 expression regulation networks mediated by various miRNA isoforms (isomiR). To do this, they used publicly available paired miRNA/mRNA-sequencing data from The Cancer Genome Atlas (TCGA) project across different human organs. They claim to have identified several miRNA families targeting ACE2 and TMPRSS2 genes in multiple tissues. Their salient discovery is that the lysine-specific demethylase 5B (JARID1B), encoded by the KDM5B gene, can indirectly affect ACE2 / TMPRSS2 expression by repressing transcription of hsa-let-7e / hsa-mir-125a and hsa-mir-141 /hsa-miR-200 miRNA families which are targeting these genes.

The paper is well-written. The methodology used appears to be sound and coherent. However, the paper is very limited in scope and only generates hypothesis that would require thorough experimental validations. This limitation is, in fact, acknowledged by the authors, as their title reads “potential regulatory mechanisms”.

Although some of the hypothesis are validated by some published work, the conclusions of the paper are in my view far too definitive considering the authors describes essentially correlative studies. They do not provide any validations. I feel that this experimental validation is an absolute requirement for publication as simple bibliographic argumentation can be largely biased.

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Reviewer #1: 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.

PONE-D-20-12168R1

Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2

PLOS ONE

Dear Dr. Nersisyan,

Thank you for resubmitting your manuscript to PLOS ONE. While you have adequately addressed most of the queries in the review and that the revised manuscript is significantly improved from its original submission, some minor issues still needs to be addressed before full acceptance of the paper.

Specifically:

The authors now provide interesting data at the single cell regarding the cell types with high level of KDM5B, ACE2 and TMPRSS2 expression. They should specify in the new Table 2 the significance and the mode of calculation of these values. We also strongly encourage the authors to provide the code used in their IsomiR / miRNA analysis as a supplemental material.

Please submit your revised manuscript by Aug 02 2020 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Bernard Mari, Ph.D

Academic Editor

PLOS ONE

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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.

Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2

PONE-D-20-12168R2

Dear Dr. Nersisyan,

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,

Bernard Mari, Ph.D

Academic Editor

PLOS ONE

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