PONE-D-24-48206In Silico Drug Repositioning-based Identification of Potentially Effective Drugs for Metabolic Dysfunction-Associated Steatotic Liver Disease against Liver CirrhosisPLOS ONE

Dear Dr. Han,

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Samuel O. Antwi, Ph.D.

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

Reviewer #2: Yes

Reviewer #3: Partly

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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: No

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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: Title & Abstract:

The abstract should explicitly state study limitations (e.g., observational design constraints) and provide more details on the in silico methodology.

Methods:

While the methods are rigorous, the manuscript should provide more details on handling multicollinearity and proportional hazard assumptions in the statistical models.

The description of the Korean NHIS database should include specifics about missing data handling and validation.

Results:

The results are clearly presented, but the clinical significance of SHR values should be discussed further.

Include subgroup-specific results in tables or figures to improve transparency.

Discussion:

The discussion highlights the significance of the findings but should expand on the biological mechanisms linking the identified drugs to reduced cirrhosis risk.

Limitations such as residual confounding and generalizability should be explicitly acknowledged.

Data Availability:

Provide clearer guidance on how external researchers can access the data through the NHIS committee.

Reviewer #2: The manuscript addresses a question of significant clinical and epidemiological relevance in a robust and methodological manner, focusing on the association of certain potential medications for the treatment of metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), and its progression to liver cirrhosis.

However, some improvements could be incorporated into the manuscript to enhance its solidity, as outlined below:

The manuscript employs an innovative and robust methodological approach. The adjustment for confounding factors and the application of advanced statistical techniques (IPTW, Fine and Gray models) strengthen the validity of the results. Nevertheless, certain aspects could be improved, such as:

-The choice of a logFC >1 and p<0.05 as criteria for gene selection could be better justified. For instance, why was a score of 0.1448 deemed sufficient to prioritize digoxin?

-Although the article mentions the identification of differentially expressed genes (DEGs) from GEO datasets, I believe some details are lacking regarding how these genes were prioritized.

-It should be explicitly stated why the cutoff point was chosen based solely on prescriptions exceeding 30 days.

-The discussion on the mechanisms by which the identified drugs (atenolol, isosorbide dinitrate) may protect against liver cirrhosis is somewhat limited. A more in-depth review of the literature on the metabolic and hepatic effects of these drugs would enrich the discussion.

The article presents a solid methodology and clinically relevant results but could benefit from a more thorough discussion of the limitations and underlying mechanisms of the findings. By implementing these improvements, the article will have a high impact on the global scientific and academic community.

Reviewer #3: Based on review of clinical health screening data, Authors propose a signature-based in silico approach to identify specific drugs that could be used to mitigate a risk of liver cirrhosis in MASLD patients. To the best of my knowledge, the study presents original research that have not been published elsewhere. Despite the evidence provided, the manuscript has several areas that require addressing.

It is unclear how the identified 415 differentially expressed genes impacted the identification of digoxin – can the authors please provide more specific information and some additional clarity on that finding? No information is provided on the DEGs that were up/down-regulated, the pathways they impact, or any commonality/relatedness between them.

The initial identification of digoxin appears somewhat random and fortuitous, as it was the only drug with a matching Korean ATC code. The basis of additional related-drug selections followed on from that initial ‘identification’. Can the authors please provide some clarity on whether any hypotheses were generated before assessing these databases on the potential drugs and/or their related mechanism of action that they expected may be implicated?

Please provide specifics on how “a meticulous validation study to assess the prospective efficacy of Digoxin using extensive patient data from the NHIS” will be performed? Also, the data provided herein indicated that use of Digoxin is associated with a higher risk of liver cirrhosis, not lower, therefore the suggestion to evaluate its ‘prospective efficacy’ seems unwarranted.

In essence, this paper is hypothesis generating, based on currently available database information, without any formal validation performed, which the authors contend that this will be provided in a follow up study. While the association data provided on the potential impact of atenolol, isosorbide dinitrate and valsartan on lowered risk of liver cirrhosis are of interest, it is unclear based on the information provided in the manuscript how the signature-based methodology played any part in supporting these findings. Additional clarity on the exact methods used to support this are crucial to supporting the overall potential of such in silico methodologies in identifying potentially effective drugs to MASLD.

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Reviewer #1: Yes:  Silvia Sovaila

Reviewer #2: No

Reviewer #3: No

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Attachments

Attachment

Submitted filename: PONE-D-24-48206 - Reviewer comments.pdf

Identification of potentially effective drugs for metabolic dysfunction-associated steatotic liver disease against liver cirrhosis: In-silico drug repositioning-based retrospective cohort study

PONE-D-24-48206R1

Dear Dr. Han,

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,

Samuel O. Antwi, Ph.D.

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 #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 #3: Yes

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

Reviewer #1: Yes

Reviewer #3: N/A

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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 #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 #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 manuscript is suitable for acceptance after the revisions, effectively addressing the previously raised concerns and significantly strengthening the overall robustness of the findings.

Reviewer #3: I acknowledge that the authors have addressed my comments and provided additional language, references and clarity on the methods used to support the manuscripts conclusions, while also acknowledging some of the limitations in the updated manuscript. I thank the authors for their responses.

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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: Yes:  Silvia Sovaila

Reviewer #3: No

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