PONE-D-24-02154Efficacy and safety of berberine for ulcerative colitis: A systematic review and meta-analysisPLOS ONE

Dear Dr. Yang,

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.

Please respond to each of the reviewer comments, including the detailed uploaded response provided by Reviewer 1. I concur that all of the criticisms provided by the reviewers are necessary and constructive. In addition to the reviewers' comments, I have the following points that should be addressed.

First, I must emphasize a couple of important issues raised in the review process noticed by multiple parties including the reviewers and myself: (1) that some of the subject studies are not in English is a barrier to many other researchers; (2) overstatement of claims about use context of berberine (BBR). The latter issue can be addressed by carefully moderating the language of the manuscript (including title) to indicate the actual use of BBR here as a complementary therapeutic. The former issue can be addressed in a variety of ways, one which will improve PRISMA reporting. You note that data, code, and other materials are not available in the PRISMA checklist, which is not best practice for PLOS or principles of open science broadly. Providing such information from all studies and translated (with publisher permission) from the non-English studies could ameliorate both the Chinese language and PRISMA issues.

Additionally, I have the following questions comments that should be addressed:

• Regarding the section on adverse events, did any of the studies report glycemic control indicators (glucose, insulin, HOMA-IR, etc.) or changes in body mass/weight?
• I think that you need to carefully re-visit the T cell section. First, the claim that BBR “augmented” CD8+ is not supported by simple visual inspection of the data; further even if some statistical test alleges significant difference here, it is not supported by the actual numbers/biology whose differences are not truly substantive.   Second, CD4+ changes could include changes in T regulatory (Treg) cell populations. Did any studies report FOXP3 and/or CD25 expression? This should be examined and discussed, even if none of the reported studies indicated such. These are important cells to consider in pathologies such as UC. Finally, what do increased CD4+ mean in the context of “favours control” as depicted in the figure? The statements and the figure do not seem to be in agreement. Without further details as to the phenotypes of CD4+ T cells, once cannot really say much about favoring one group vs. another; for example, an increase in Th17 cells could actually indicate worsening of cellular pathology, where as an increase in Treg may indicate amelioration.
• Line 120: be more detailed as to what is meant by “statistical inaccuracies”.
• Lines 148-152 need to be re-written to indicate the subject studies used these techniques. As currently written the statements could be construed that you conducted these experiments.
• Table 1 descriptors need to be re-written in English.
• I suggest combining Figures 3, 4, and 5 into a single figure.
• Lines 256-257: more should be stated about the IL-10 results, particularly discordance between control and BBR intervention.
• Delete the first sentence of line 340. It is unnecessary.
• There are currently no detailed figure legends. This should be addressed.

Please submit your revised manuscript by Apr 01 2024 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: 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.

Sincerely,

Nicholas A. Pullen, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf.

2. We note that your Data Availability Statement is currently as follows: [All relevant data are within the manuscript and its Supporting Information files.]

Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition).

For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study.

If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories.

If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

3. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files.

Additional Editor Comments (if provided):

Dear Dr. Yang,

Please respond to each of the reviewer comments, including the detailed uploaded response provided by Reviewer 1. I concur that all of the criticisms provided by the reviewers are necessary and constructive. In addition to the reviewers' comments, I have the following points that should be addressed.

First, I must emphasize a couple of important issues raised in the review process noticed by multiple parties including the reviewers and myself: (1) that some of the subject studies are not in English is a barrier to many other researchers; (2) overstatement of claims about use context of berberine (BBR). The latter issue can be addressed by carefully moderating the language of the manuscript (including title) to indicate the actual use of BBR here as a complementary therapeutic. The former issue can be addressed in a variety of ways, one which will improve PRISMA reporting. You note that data, code, and other materials are not available in the PRISMA checklist, which is not best practice for PLOS or principles of open science broadly. Providing such information from all studies and translated (with publisher permission) from the non-English studies could ameliorate both the Chinese language and PRISMA issues.

Additionally, I have the following questions comments that should be addressed:

• Regarding the section on adverse events, did any of the studies report glycemic control indicators (glucose, insulin, HOMA-IR, etc.) or changes in body mass/weight?

• I think that you need to carefully re-visit the T cell section. First, the claim that BBR “augmented” CD8+ is not supported by simple visual inspection of the data; further even if some statistical test alleges significant difference here, it is not supported by the actual numbers/biology whose differences are not truly substantive. Second, CD4+ changes could include changes in T regulatory (Treg) cell populations. Did any studies report FOXP3 and/or CD25 expression? This should be examined and discussed, even if none of the reported studies indicated such. These are important cells to consider in pathologies such as UC. Finally, what do increased CD4+ mean in the context of “favours control” as depicted in the figure? The statements and the figure do not seem to be in agreement. Without further details as to the phenotypes of CD4+ T cells, once cannot really say much about favoring one group vs. another; for example, an increase in Th17 cells could actually indicate worsening of cellular pathology, where as an increase in Treg may indicate amelioration.

• Line 120: be more detailed as to what is meant by “statistical inaccuracies”.

• Lines 148-152 need to be re-written to indicate the subject studies used these techniques. As currently written the statements could be construed that you conducted these experiments.

• Table 1 descriptors need to be re-written in English.

• I suggest combining Figures 3, 4, and 5 into a single figure.

• Lines 256-257: more should be stated about the IL-10 results, particularly discordance between control and BBR intervention.

• Delete the first sentence of line 340. It is unnecessary.

• There are currently no detailed figure legends. This should be addressed.

[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: Partly

Reviewer #2: Yes

**********

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

Reviewer #1: I Don't Know

Reviewer #2: Yes

**********

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: No

Reviewer #2: 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

**********

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: There is an attached review file with detailed comments by line/section of the article. However, below are a few general comments:

Overall, I think this analysis is of interest to the field and a good contribution to the literature. However, there are a few overarching concerns (“General Comments”) that must be addressed before I can recommend for the publication, in addition to a detailed breakdown of items associated with each section of the manuscript (“Detailed Comments”) in the attached review file.

GENERAL COMMENTS (again, PLEASE see detailed comments in the attached review file).

1. There are many locations where the authors overstate the findings/context of the study to implicate “BBR as a therapy for UC” when the study actually evaluates the efficacy of “BBR as a complementary therapy to support/enhance standard treatments.” Because BBR is being used in addition to standard treatment in all studies and is not being used alone in comparison to standard treatment, you are not evaluating BBR as an alternative therapy. So, in locations where it is implied the study is evaluating BBR in "treating disease,” it should be reworded to something like, "supporting disease management". The locations of these overstatements in the manuscript are highlighted in detail in “Detailed Comments.”

2. Many issues with citations: There is a considerable lack of citations for physiological and mechanistic statements throughout the article. These are highlighted in detail in “Detailed Comments.” Also, two of the ten articles included in the analysis are not properly cited in the References (in-text Figures include different author names for references 22 and 24)

3. Need additional details in Methods for reproducibility (These are highlighted in detail in “Detailed Comments.”), especially around data extraction and additional clarity around the inclusion criteria.

4. The lack of availability of many of these articles in the English language and/or on many databases common to Europe and the Americas presents a major barrier to researchers outside of China/Asia who may want to follow up on these articles. I unsuccessfully tried to search for many of these articles through Medline, EMBASE, PubMed, Google Scholar, and three separate university libraries for institutions that I am affiliated with (one of them being a major medical school library)—so, I was unable to confirm many methods or double-check measures. Because of this, authors must include which database they accessed each article from and any identifiable database numbers (e.g., DOI) in Table 1 to facilitate the reproducibility of the search and access to these papers.

5.In the introduction, authors must place the current review/meta-analysis in the context of any existing systematic reviews and meta-analysis on similar content (which do exist)—Describe what content those reviews/meta-analysis include, and how this current meta-analysis is different and contributes to the literature.

6. Highlight limitations in discussion or conclusion

Reviewer #2: 1. Authors should provide more detailed information on the sources of BBR in each study.

2. It is recommended to include the UC pathological staging of patients before treatment in the study.

3. Please calibrate the reference format in the manuscript to maintain consistency.

4. The title is "Efficacy and safety of berberine for ulcerative colitis: A systematic review and meta-analysis", but the majority of the data included in the meta-analysis is related to the combined treatment of BBR and 5-ASA. How to demonstrate the efficacy and safety of BBR through the use of BBR in combination with 5-ASA data? Please use concise and succinct language to describe your research findings regarding this matter.

**********

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: 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.

Attachments

Attachment

Submitted filename: PLOS One Review_ BBR and UC.docx

PONE-D-24-02154R1Efficacy and safety of berberine plus 5-ASA for ulcerative colitis : A systematic review and meta-analysisPLOS ONE

Dear Dr. Yang,

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. Thank you for your improved, revised submission. Substantial English language editing will still be required for me to endorse the paper further. Additionally, while you have figure titles, you still do not have figure legends. Please add these. I refer you to the PLOS page on this: https://journals.plos.org/plosone/s/figures. Specifically, from the page, under Figure legend tips: "Describe the key messages of a figure: provide a description of the figure that will allow readers to understand it without referring to the text."

Please submit your revised manuscript by Aug 23 2024 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: 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.

Sincerely,

Nicholas A. Pullen, Ph.D.

Academic 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.

Additional Editor Comments:

Thank you for your improved, revised submission. Substantial English language editing will still be required for me to endorse the paper further. Additionally, while you have figure titles, you still do not have figure legends. Please add these. I refer you to the PLOS page on this: https://journals.plos.org/plosone/s/figures. Specifically, from the page, under Figure legend tips: "Describe the key messages of a figure: provide a description of the figure that will allow readers to understand it without referring to the text."

[Note: HTML markup is below. Please do not edit.]

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

**********

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: Yes

Reviewer #2: 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: No

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 have made tremendous improvements to enhance the transparency and reproducibility of their methods, which now reflect the rigor required for a systematic review.

The authors have also thoroughly addressed previous reviewer comments and have improved the clarity and organization of their manuscript.

While the clarity of the manuscript is greatly improved, there are still several grammatical errors throughout. These include punctuation errors, issues with spacing (or lack thereof) between characters, missing prepositions or conjunctions, and incorrect numbering of lists (e.g., under Primary Outcome Measures there are two #1’s). Once these minor issues are fixed, I believe the article will be ready for publication.

Some examples are below, although more instances can be found in the manuscript:

-Under the Inclusion Criteria section-- No need to use colons (the “:” symbol) after symptomatic relief, serological indicators, etc., because the lists that follow are encapsulated in parentheses.

-Under the Exclusion Criteria section-- Line 117, there is a period where there should be a semi-colon.

-Under the Primary Outcome Measures section-- Check the numbering. Both “clinical efficacy rate” and “complete remission” are labeled with the number 1.

-Character spacing throughout the manuscript -- There are many locations where there is no space between characters that should have spaces (e.g., between a period and a new word, or between a colon and a new word, etc.).

-In the Discussion, line 379-- Currently “effector cells, memory cells” --> “effector cells AND/OR memory cells.”

Reviewer #2: (No Response)

**********

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.

Efficacy and safety of berberine plus 5-ASA for ulcerative colitis : A systematic review and meta-analysis

PONE-D-24-02154R2

Dear Dr. Yang,

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.

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org.

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.

Sincerely,

Nicholas A. Pullen, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you for your judicious attention to previous comments.

Reviewers' comments: