PPATHOGENS-D-25-02438

IL-6 is one of the Key Factors in the Formation of Gut Tissue Resident Memory T Cells from

Naïve T cells

PLOS Pathogens

Dear Dr. Cicala,

Thank you for submitting your revised manuscript to PLOS Pathogens. The manuscript was reviewed by one of the previous reviewers and I also evaluated it. After careful consideration, we feel that it has merit but does not fully meet PLOS Pathogens'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.

I had several comments that should be addressed:

1. Could you test blocking IL-6 and IFN-b together when using supernatants?

2. I would have liked the data on viability to be included in a supplementary figure or table. That way the readers can have a full appreciation of what is going on.

3. Sup. Figure 3 doesn’t discriminate between naive and memory CD4 T cells. It is unclear what is the meaning of CD4dim CD3dim since this is never discussed elsewhere in the manuscript. However, we can appreciated from the flow plot that almost all CD4 T cells seem to express IL-6R.

4. “All study participants received written informed consent.” Provided instead of received?

Please submit your revised manuscript by Mar 10 2026 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 plospathogens@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/ppathogens/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Guido Silvestri

Academic Editor

PLOS Pathogens

Susan Ross

Section Editor

PLOS Pathogens

Sumita Bhaduri-McIntosh

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0003-2946-9497

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

1) Please ensure that the CRediT author contributions listed for every co-author are completed accurately and in full.

At this stage, the following Authors/Authors require contributions: Claudia Cicala, Hans Kim, Amanda Chan, Sinmanus Vimonpatranon, Alexandre Girard, Andrew Jiang, Samuel Wertz, Il-Young Hwang, John Kehrl, Hana Schmeisser, Madelyn Seemiller, Paolo Lusso, Dawei Dawei, Danlan Wei, Livia Goes, Marcelo Soares, Elena Martinelli, and James Arthos. Please ensure that the full contributions of each author are acknowledged in the "Add/Edit/Remove Authors" section of our submission form.

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Reviewers' Comments:

Reviewer's Responses to Questions

Part I - Summary

Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship.

Reviewer #2: In this revised manuscript the authors explore the different factors that can mediate

differentiation of naive CD4T cells into GI TRM phenotype like with the ultimate goal to help

understand what intervention can help restore of increase TRM CD4 T cells in the GI which

is known to help with gut mucosa integrity and lower inflammation.

Their main findings are: In PBMCs of healthy donors, MAdCam-1 +RA prime

naïve CD4+T cells to express GI TRM cell markers and that IL-6 and TGFb promote this

differentiation. This is a well writtten paper with compelling data exposing one of potential many pathways involved in this process.

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Part II – Major Issues: Key Experiments Required for Acceptance

Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions.

Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject".

Reviewer #2: All major issues raised by reviewers were addressed by the authors.

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Part III – Minor Issues: Editorial and Data Presentation Modifications

Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity.

Reviewer #2: NA

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Reviewer #2: No

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Dear Dr. Cicala,

We are pleased to inform you that your manuscript 'IL-6 is one of the Key Factors in the Formation of Gut Tissue Resident Memory T Cells from

Naïve T cells' has been provisionally accepted for publication in PLOS Pathogens.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens.

Best regards,

Guido Silvestri

Academic Editor

PLOS Pathogens

Susan Ross

Section Editor

PLOS Pathogens

Sumita Bhaduri-McIntosh

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0003-2946-9497

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

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Reviewer Comments (if any, and for reference):