PONE-D-24-15689Association of IL13 polymorphisms with susceptibility to myocardial infarction: a case-control study in Chinese population.PLOS ONE

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Additional Editor Comments:

Dear Authors,

Your manuscript has been reviewed by experts in the field and we request that you make major revisions before it is processed further. Please address all the reviewers comment that you find below.

Please revise the manuscript according to the reviewers' comments and upload the revised file within 7 days.

Reviewers comments

Reviewer One

Revision Comments for the Authors

Dear Authors,

Thank you for submitting your manuscript titled "Association of IL13 Polymorphisms with Susceptibility to Myocardial Infarction: A Case-Control Study in Chinese Population" to PLOS ONE. Your study presents important findings regarding the genetic factors contributing to myocardial infarction (MI) susceptibility. After careful review, I have some comments and suggestions that could improve the clarity and rigor of your manuscript.

Clarity and Ambiguity

1. Introduction:

- The introduction provides a good overview but could benefit from more concise language and clearer transitions between topics. For instance, the shift from discussing MI prevalence to genetic factors could be smoother.

- Clearly state the hypothesis early in the introduction to guide the reader through the rationale of the study.

2. Materials and Methods:

- Some details are missing or could be expanded for better clarity. For example, the criteria for selecting controls need to be more detailed. Explicitly mention the criteria for excluding subjects (e.g., based on BP, cholesterol, and sugar levels). - Describe the process of informed consent in more detail. This helps in understanding how ethical guidelines were followed.

3. Genotyping and ELISA Methods:

- The description of the genotyping and ELISA methods could be more detailed to ensure reproducibility. Include information about the conditions used in the TaqMan Genotyping assays and ELISA procedures.

- Clearly mention the sources and catalog numbers of the kits used for genotyping and ELISA.

4. Statistical Analysis:

- The statistical methods section should be more detailed. Explain the choice of tests (e.g., why Fisher's exact test was used) and how the Bonferroni correction was applied.

- Clarify the use of software tools, including versions and any specific settings or parameters used in the analyses.

5. Results:

- Results are presented clearly, but some sections could benefit from additional context or explanation. For example, explain the implications of the Hardy-Weinberg equilibrium results in lay terms.

- Ensure that all tables and figures are referenced in the text and include legends that are descriptive enough to be understood independently of the main text.

6. Discussion:

- The discussion is comprehensive but can be more concise. Some points are repeated or could be merged for better flow. - Discuss the limitations more explicitly and suggest future research directions based on your findings.

7. Conclusion:

- The conclusion is clear but could briefly restate the significance of the findings in the broader context of MI research.

Specific Areas of Ambiguity

1. HWE Deviation:

- The deviation from HWE for rs20541 is mentioned, but the reasons and implications are not fully explained. This could be confusing for readers not familiar with genetic studies.

2. IL-13 Levels Timing:

- It is mentioned that most patients were enrolled soon after MI, but the timing of IL-13 level measurements relative to MI onset should be more precisely described.

3. Terminology:

- Ensure that all technical terms are defined when first used. For example, "Th2 immune response" and "pleiotropic effect" might need brief explanations.

Additional Comments:

1. Sample Size Calculation and Statistical Power:

- Please include a detailed explanation of how the sample size was determined. Indicate whether a priori power analysis was conducted to ensure that the study is adequately powered to detect significant associations.

- Specify the effect size, significance level, and power used in the sample size calculation.

2. Abbreviations:

- Ensure that all abbreviations are defined at their first mention in the text. For example, abbreviations such as MI (myocardial infarction), SNP (single nucleotide polymorphism), and HWE (Hardy-Weinberg equilibrium) should be defined upon first use.

- Provide a list of abbreviations either at the beginning or end of the manuscript for reference.

3. Demographic and Clinical Characteristics:

- Provide more detailed demographic and clinical characteristics of the study participants, including information on smoking status, family history of cardiovascular diseases, and other relevant factors.

4. Genotyping Quality Control:

- Describe the quality control measures taken during genotyping to ensure accuracy and reliability of the data. This includes the handling of potential genotyping errors and missing data.

- Mention if any duplicate samples or independent replication was performed to validate the genotyping results.

5. Hardy-Weinberg Equilibrium (HWE):

- Discuss the deviation from HWE observed for the rs20541 polymorphism in more detail. Explain potential reasons for this deviation and how it might affect the study's conclusions.

- Consider conducting sensitivity analyses to determine if the HWE deviation impacts the association results.

6. Statistical Analysis:

- Provide more details on the statistical methods used for haplotype analysis and how the haplotype frequencies were compared between cases and controls.

- Clarify how the Bonferroni correction was applied and ensure that all reported p-values reflect this correction where multiple comparisons are made.

7. Plasma IL13 Quantification:

- Discuss whether IL13 levels were measured at a consistent time point post-MI for all patients to account for the dynamic changes in IL13 levels after MI.

8. Discussion and Interpretation:

- Expand on the biological plausibility of the associations found, particularly how the identified polymorphisms might influence IL13 expression and MI risk.

- Discuss the potential clinical implications of your findings and any limitations that should be considered when interpreting the results.

9. Ethical Approval:

- Include the specific ethical committee approval code for the study. This is crucial for ensuring transparency and adherence to ethical standards in research.

10. Supplementary Information:

- Provide any supplementary information or detailed protocols as supporting documents to allow for replication of your study by other researchers.

By addressing these points, you will enhance the robustness and transparency of your study. I look forward to seeing the revised version of your manuscript.

Best regards,

REVIEWER 2

The present study was a candidate gene association study for the association of IL-13 polymorphism with susceptibility to myocardial infarction (MI) in a Chinese population. Although the topic was good, there were some concerns and errors that should be addressed and revised by the authors.

Major:

1- Chinese population consists of many ethnicities and sub-populations. The sample size is not large enough for such a mixed population.

2- The effect of the studied polymorphism in genome-wide association studies (GWAS) should be mentioned in the state of the problem. Then it should be clarified whether this candidate gene association study is for confirmation of a GWAS result or is logic based unrelated to GWAS.

3- Material and methods should be started with a subsection entitled "study design". In this subsection, STREGA guideline should be mentioned.

4- The manuscript should be updated based on STREGA guideline.

5- Although TaqMan genotyping is an advanced method, I could not find any information regarding its related PCR.

6- The outcome and its measurement should be defined in material and methods.

7- I could not find study limitations in the discussion.

Minor:

1- All manufacturers and software packages should be addressed as (Company, State, Country).

2- "A P value less than 0.05 was considered statistically significant", it should be clarified that this sentence is for which test as you used Bonferroni correction for testing genotypes.

3- Table 2, why VDR?

[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: Yes

Reviewer #3: Yes

Reviewer #4: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: No

**********

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

Reviewer #4: No

**********

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

Reviewer #4: No

**********

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: Revision Comments for the Authors

Dear Authors,

Thank you for submitting your manuscript titled "Association of IL13 Polymorphisms with Susceptibility to Myocardial Infarction: A Case-Control Study in Chinese Population" to PLOS ONE. Your study presents important findings regarding the genetic factors contributing to myocardial infarction (MI) susceptibility. After careful review, I have some comments and suggestions that could improve the clarity and rigor of your manuscript.

Clarity and Ambiguity

1. Introduction:

- The introduction provides a good overview but could benefit from more concise language and clearer transitions between topics. For instance, the shift from discussing MI prevalence to genetic factors could be smoother.

- Clearly state the hypothesis early in the introduction to guide the reader through the rationale of the study.

2. Materials and Methods:

- Some details are missing or could be expanded for better clarity. For example, the criteria for selecting controls need to be more detailed. Explicitly mention the criteria for excluding subjects (e.g., based on BP, cholesterol, and sugar levels). - Describe the process of informed consent in more detail. This helps in understanding how ethical guidelines were followed.

3. Genotyping and ELISA Methods:

- The description of the genotyping and ELISA methods could be more detailed to ensure reproducibility. Include information about the conditions used in the TaqMan Genotyping assays and ELISA procedures.

- Clearly mention the sources and catalog numbers of the kits used for genotyping and ELISA.

4. Statistical Analysis:

- The statistical methods section should be more detailed. Explain the choice of tests (e.g., why Fisher's exact test was used) and how the Bonferroni correction was applied.

- Clarify the use of software tools, including versions and any specific settings or parameters used in the analyses.

5. Results:

- Results are presented clearly, but some sections could benefit from additional context or explanation. For example, explain the implications of the Hardy-Weinberg equilibrium results in lay terms.

- Ensure that all tables and figures are referenced in the text and include legends that are descriptive enough to be understood independently of the main text.

6. Discussion:

- The discussion is comprehensive but can be more concise. Some points are repeated or could be merged for better flow. - Discuss the limitations more explicitly and suggest future research directions based on your findings.

7. Conclusion:

- The conclusion is clear but could briefly restate the significance of the findings in the broader context of MI research.

Specific Areas of Ambiguity

1. HWE Deviation:

- The deviation from HWE for rs20541 is mentioned, but the reasons and implications are not fully explained. This could be confusing for readers not familiar with genetic studies.

2. IL-13 Levels Timing:

- It is mentioned that most patients were enrolled soon after MI, but the timing of IL-13 level measurements relative to MI onset should be more precisely described.

3. Terminology:

- Ensure that all technical terms are defined when first used. For example, "Th2 immune response" and "pleiotropic effect" might need brief explanations.

Additional Comments:

1. Sample Size Calculation and Statistical Power:

- Please include a detailed explanation of how the sample size was determined. Indicate whether a priori power analysis was conducted to ensure that the study is adequately powered to detect significant associations.

- Specify the effect size, significance level, and power used in the sample size calculation.

2. Abbreviations:

- Ensure that all abbreviations are defined at their first mention in the text. For example, abbreviations such as MI (myocardial infarction), SNP (single nucleotide polymorphism), and HWE (Hardy-Weinberg equilibrium) should be defined upon first use.

- Provide a list of abbreviations either at the beginning or end of the manuscript for reference.

3. Demographic and Clinical Characteristics:

- Provide more detailed demographic and clinical characteristics of the study participants, including information on smoking status, family history of cardiovascular diseases, and other relevant factors.

4. Genotyping Quality Control:

- Describe the quality control measures taken during genotyping to ensure accuracy and reliability of the data. This includes the handling of potential genotyping errors and missing data.

- Mention if any duplicate samples or independent replication was performed to validate the genotyping results.

5. Hardy-Weinberg Equilibrium (HWE):

- Discuss the deviation from HWE observed for the rs20541 polymorphism in more detail. Explain potential reasons for this deviation and how it might affect the study's conclusions.

- Consider conducting sensitivity analyses to determine if the HWE deviation impacts the association results.

6. Statistical Analysis:

- Provide more details on the statistical methods used for haplotype analysis and how the haplotype frequencies were compared between cases and controls.

- Clarify how the Bonferroni correction was applied and ensure that all reported p-values reflect this correction where multiple comparisons are made.

7. Plasma IL13 Quantification:

- Discuss whether IL13 levels were measured at a consistent time point post-MI for all patients to account for the dynamic changes in IL13 levels after MI.

8. Discussion and Interpretation:

- Expand on the biological plausibility of the associations found, particularly how the identified polymorphisms might influence IL13 expression and MI risk.

- Discuss the potential clinical implications of your findings and any limitations that should be considered when interpreting the results.

9. Ethical Approval:

- Include the specific ethical committee approval code for the study. This is crucial for ensuring transparency and adherence to ethical standards in research.

10. Supplementary Information:

- Provide any supplementary information or detailed protocols as supporting documents to allow for replication of your study by other researchers.

By addressing these points, you will enhance the robustness and transparency of your study. I look forward to seeing the revised version of your manuscript.

Best regards,

Reviewer #2: The present study was a candidate gene association study for the association of IL-13 polymorphism with susceptibility to myocardial infarction (MI) in a Chinese population. Although the topic was good, there were some concerns and errors that should be addressed and revised by the authors.

Major:

1- Chinese population consists of many ethnicities and sub-populations. The sample size is not large enough for such a mixed population.

2- The effect of the studied polymorphism in genome-wide association studies (GWAS) should be mentioned in the state of the problem. Then it should be clarified whether this candidate gene association study is for confirmation of a GWAS result or is logic based unrelated to GWAS.

3- Material and methods should be started with a subsection entitled "study design". In this subsection, STREGA guideline should be mentioned.

4- The manuscript should be updated based on STREGA guideline.

5- Although TaqMan genotyping is an advanced method, I could not find any information regarding its related PCR.

6- The outcome and its measurement should be defined in material and methods.

7- I could not find study limitations in the discussion.

Minor:

1- All manufacturers and software packages should be addressed as (Company, State, Country).

2- "A P value less than 0.05 was considered statistically significant", it should be clarified that this sentence is for which test as you used Bonferroni correction for testing genotypes.

3- Table 2, why VDR?!

Reviewer #3: After reading the paper i have come to the following conclusions:

1-This paper is Technically sound, all the steps were explained clearly and concisely in a manner that allows replication by future researchers. The limitations of the paper were also addressed as well as all supporting data in clear and chronological order.

2-Statistical analysis supported findings, with mention of methods, software and results. All results were easy to understand and thoroughly explained.

3-It was easy to read through this paper, it was well written, easy to comprehend, andI am confident that those seeking knowledge from different backgrounds will be able to reach similar conclusions to the authors with ease.

This s a job well done!

Reviewer #4: -Correlation between risk factors and IL 13 polymorphism as DM , Dyslipidemia and hypertension are not mentioned.

-Type of myocardial infarction NSTEMI, STEMI is not clear.

-Detailed data about the lipid profile (HDL,LDL TG and total cholesterol level are beneficial.

-Many studies are previously published with the same ideas and population thus this study add no much benefits .

**********

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: Yes: Seyyed Amir Yasin Ahmadi

Reviewer #3: Yes: Maha Ahmed

Reviewer #4: No

**********

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Association of IL13 polymorphisms with susceptibility to myocardial infarction: a case-control study in Chinese population.

PONE-D-24-15689R1

Dear Dr. Xiaofeng Ma,

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,

Andrea Da Porto

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

Reviewer #3: 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

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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: (No Response)

Reviewer #3: 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

Reviewer #3: 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: Dear Authors, Thank you for submitting your manuscript. Your work presents a thorough analysis and provides significant insights into the subject matter.

Best regards

Reviewer #2: My comments except Major 1 were fully resolved by the author. Acceptance of this manuscript depends on editorial decision about my comment Major 1.

Reviewer #3: The previous draft was satisfactory, but after answering all the reviewers comments ,this paper

transcended to even better levels.

I'm exited to see it replicated in other ethnic groups and maybe one day in a meta analysis.

**********

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: Seyyed Amir Yasin Ahmadi

Reviewer #3: Yes: Maha Ahmed

**********