Title: The role of m6A regulators mRNA expression in peripheral blood mononuclear cells in
chronic hepatitis B: A novel Diagnostic and prognostic indicator
Version: 3 Date: 14 Mar 2025
Reviewer:  Shah Jahan
Reviewer's report:
The study investigates the role of m6A regulators in peripheral blood mononuclear cells
(PBMCs) of patients with chronic hepatitis B (CHB) and their potential as diagnostic and
prognostic indicators. The research question is relevant, and the methodology is generally
sound. The authors have adequately addressed many of the reviewers’ concerns, significantly
improving the manuscript. However, further refinements are necessary to strengthen the clarity,
interpretation, and reproducibility of the findings.
Major Revisions
1. Mechanistic Insight on METTL3 and Inflammatory Markers
o The expanded discussion on METTL3’s role in inflammation is commendable. However, the
proposed mechanisms remain speculative and would benefit from additional citations
o Suggested Revision: Clearly state the limitations of current knowledge regarding METTL3’s
role in inflammation and provide a roadmap for validating these mechanisms in future studies.
2. Multiple Comparison Corrections
o The authors appropriately applied the Bonferroni correction, but it would be beneficial to
discuss why this method was chosen over alternatives like FDR, which is often more suitable
for biological datasets.
o Suggested Revision: Include a brief justification for the use of Bonferroni correction and
acknowledge any trade-offs regarding statistical power.
3. Sample Size and Statistical Power
o The inclusion of a post-hoc power analysis strengthens the manuscript. However, a power
calculation before data collection would have been preferable.
o Suggested Revision: Consider adding a discussion on how future studies can be designed with
an a priori power analysis to optimize sample size and statistical validity.
4. GEO Dataset Analysis
o The newly added details on the GSE267808 dataset analysis enhance reproducibility.
However, information on quality control steps, normalization, and potential batch effects should
be elaborated.
o Suggested Revision: Provide a brief explanation of how batch effects were assessed and
corrected and whether normalization methods were compared for robustness.
Minor Revisions
1. Clarifying the Novelty of PBMC-based Analysis
o The revision emphasizing PBMCs' advantages over liver tissue is well-explained. However,
further elaboration on how PBMC-based biomarkers compare to existing serum biomarkers
would add clarity.
o Suggested Revision: Briefly compare the predictive value of PBMC m6A regulators versus
conventional serum biomarkers in CHB diagnosis and prognosis.
2. Correction of LC Group Size
o The correction from 26 to 27 patients is appropriate, but the discrepancy should be briefly
acknowledged in the manuscript.
o Suggested Revision: Add a sentence in the results section to acknowledge and clarify the error
correction.
3. Discussion on m6A-specific Assays
o The limitations regarding indirect m6A measurement are well stated. Adding references to
recent m6A-specific methods applicable to PBMCs would be beneficial.
o Suggested Revision: Cite recent advancements in MeRIP-seq or other m6A detection methods
and discuss their potential in future validation studies.
Final Recommendation
The manuscript has significantly improved, and with the suggested refinements, it will be well-
prepared for acceptance. justify statistical choices, and further enhance the reproducibility of
the analysis. Upon addressing these points, the study will make a strong contribution to the field
of CHB biomarker research.
Recommendation: Minor Revisions Required
Title: The role of m6A regulators mRNA expression in peripheral blood mononuclear cells in
chronic hepatitis B: A novel Diagnostic and prognostic indicator
Version: 3 Date: 14 Mar 2025
Reviewer:  Shah Jahan
Reviewer's report:
The study investigates the role of m6A regulators in peripheral blood mononuclear cells
(PBMCs) of patients with chronic hepatitis B (CHB) and their potential as diagnostic and
prognostic indicators. The research question is relevant, and the methodology is generally
sound. The authors have adequately addressed many of the reviewers’ concerns, significantly
improving the manuscript. However, further refinements are necessary to strengthen the clarity,
interpretation, and reproducibility of the findings.
Major Revisions
1. Mechanistic Insight on METTL3 and Inflammatory Markers
o The expanded discussion on METTL3’s role in inflammation is commendable. However, the
proposed mechanisms remain speculative and would benefit from additional citations
o Suggested Revision: Clearly state the limitations of current knowledge regarding METTL3’s
role in inflammation and provide a roadmap for validating these mechanisms in future studies.
2. Multiple Comparison Corrections
o The authors appropriately applied the Bonferroni correction, but it would be beneficial to
discuss why this method was chosen over alternatives like FDR, which is often more suitable
for biological datasets.
o Suggested Revision: Include a brief justification for the use of Bonferroni correction and
acknowledge any trade-offs regarding statistical power.
3. Sample Size and Statistical Power
o The inclusion of a post-hoc power analysis strengthens the manuscript. However, a power
calculation before data collection would have been preferable.
o Suggested Revision: Consider adding a discussion on how future studies can be designed with
an a priori power analysis to optimize sample size and statistical validity.
4. GEO Dataset Analysis
o The newly added details on the GSE267808 dataset analysis enhance reproducibility.
However, information on quality control steps, normalization, and potential batch effects should
be elaborated.
o Suggested Revision: Provide a brief explanation of how batch effects were assessed and
corrected and whether normalization methods were compared for robustness.
Minor Revisions
1. Clarifying the Novelty of PBMC-based Analysis
o The revision emphasizing PBMCs' advantages over liver tissue is well-explained. However,
further elaboration on how PBMC-based biomarkers compare to existing serum biomarkers
would add clarity.
o Suggested Revision: Briefly compare the predictive value of PBMC m6A regulators versus
conventional serum biomarkers in CHB diagnosis and prognosis.
2. Correction of LC Group Size
o The correction from 26 to 27 patients is appropriate, but the discrepancy should be briefly
acknowledged in the manuscript.
o Suggested Revision: Add a sentence in the results section to acknowledge and clarify the error
correction.
3. Discussion on m6A-specific Assays
o The limitations regarding indirect m6A measurement are well stated. Adding references to
recent m6A-specific methods applicable to PBMCs would be beneficial.
o Suggested Revision: Cite recent advancements in MeRIP-seq or other m6A detection methods
and discuss their potential in future validation studies.
Final Recommendation
The manuscript has significantly improved, and with the suggested refinements, it will be well-
prepared for acceptance. justify statistical choices, and further enhance the reproducibility of
the analysis. Upon addressing these points, the study will make a strong contribution to the field
of CHB biomarker research.
Recommendation: Minor Revisions Required
Please review this paper.
user
Title: The role of m6A regulators mRNA expression in peripheral blood mononuclear cells in
chronic hepatitis B: A novel Diagnostic and prognostic indicator
Version: 3 Date: 14 Mar 2025
Reviewer:  Shah Jahan
Reviewer's report:
The study investigates the role of m6A regulators in peripheral blood mononuclear cells
(PBMCs) of patients with chronic hepatitis B (CHB) and their potential as diagnostic and
prognostic indicators. The research question is relevant, and the methodology is generally
sound. The authors have adequately addressed many of the reviewers’ concerns, significantly
improving the manuscript. However, further refinements are necessary to strengthen the clarity,
interpretation, and reproducibility of the findings.
Major Revisions
1. Mechanistic Insight on METTL3 and Inflammatory Markers
o The expanded discussion on METTL3’s role in inflammation is commendable. However, the
proposed mechanisms remain speculative and would benefit from additional citations
o Suggested Revision: Clearly state the limitations of current knowledge regarding METTL3’s
role in inflammation and provide a roadmap for validating these mechanisms in future studies.
2. Multiple Comparison Corrections
o The authors appropriately applied the Bonferroni correction, but it would be beneficial to
discuss why this method was chosen over alternatives like FDR, which is often more suitable
for biological datasets.
o Suggested Revision: Include a brief justification for the use of Bonferroni correction and
acknowledge any trade-offs regarding statistical power.
3. Sample Size and Statistical Power
o The inclusion of a post-hoc power analysis strengthens the manuscript. However, a power
calculation before data collection would have been preferable.
o Suggested Revision: Consider adding a discussion on how future studies can be designed with
an a priori power analysis to optimize sample size and statistical validity.
4. GEO Dataset Analysis
o The newly added details on the GSE267808 dataset analysis enhance reproducibility.
However, information on quality control steps, normalization, and potential batch effects should
be elaborated.
o Suggested Revision: Provide a brief explanation of how batch effects were assessed and
corrected and whether normalization methods were compared for robustness.
Minor Revisions
1. Clarifying the Novelty of PBMC-based Analysis
o The revision emphasizing PBMCs' advantages over liver tissue is well-explained. However,
further elaboration on how PBMC-based biomarkers compare to existing serum biomarkers
would add clarity.
o Suggested Revision: Briefly compare the predictive value of PBMC m6A regulators versus
conventional serum biomarkers in CHB diagnosis and prognosis.
2. Correction of LC Group Size
o The correction from 26 to 27 patients is appropriate, but the discrepancy should be briefly
acknowledged in the manuscript.
o Suggested Revision: Add a sentence in the results section to acknowledge and clarify the error
correction.
3. Discussion on m6A-specific Assays
o The limitations regarding indirect m6A measurement are well stated. Adding references to
recent m6A-specific methods applicable to PBMCs would be beneficial.
o Suggested Revision: Cite recent advancements in MeRIP-seq or other m6A detection methods
and discuss their potential in future validation studies.
Final Recommendation
The manuscript has significantly improved, and with the suggested refinements, it will be well-
prepared for acceptance. justify statistical choices, and further enhance the reproducibility of
the analysis. Upon addressing these points, the study will make a strong contribution to the field
of CHB biomarker research.
Recommendation: Minor Revisions Required
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