Peer Review History

Original SubmissionApril 19, 2024
Decision Letter - Atsushi Asakura, Editor

PONE-D-24-15862Muscleblind-like proteins are novel modulators of the tumor-immune microenvironmentPLOS ONE

Dear Dr. Bradley,

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 submit your revised manuscript by Feb 20 2025 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.

Kind regards,

Atsushi Asakura, 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. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (1) methods of sacrifice, (2) methods of anesthesia and/or analgesia, and (3) efforts to alleviate suffering.

3. Thank you for stating the following financial disclosure:

 “A.M.G and S.A.M are ARCS Foundation scholars. E.I.C is a Damon Runyon fellow. J.D.T. was supported by the NIH/NCI (K99 CA263168). R.K.B. was supported in part by the NIH/NCI (R01 CA251138), NIH/NHLBI (R01 HL128239, R01 HL151651) and the Blood Cancer Discoveries Grant program through the Leukemia & Lymphoma Society, Mark Foundation for Cancer Research, and Paul G. Allen Frontiers Group (8023-20). R.K.B is a Scholar of The Leukemia & Lymphoma Society (1344-18) and holds the McIlwain Family Endowed Chair in Data Science. Computational studies were supported in part by FHCC’s Scientific Computing Infrastructure (ORIP S10 OD028685). Experimental studies were supported in part by the Experimental Histopathology, Flow Cytometry, and Genomics Shared Resources of the Fred Hutch/University of Washington Cancer Consortium (NIH/NCI P30 CA015704). The results in this publication are based in part on data from The Cancer Genome Atlas Research Network (http://cancergenome.nih.gov).”

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

If this statement is not correct you must amend it as needed.

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

4. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“A.M.G and S.A.M are ARCS Foundation scholars. E.I.C is a Damon Runyon fellow. J.D.T. was supported by the NIH/NCI (K99 CA263168). R.K.B. was supported in part by the NIH/NCI (R01 CA251138), NIH/NHLBI (R01 HL128239, R01 HL151651) and the Blood Cancer Discoveries Grant program through the Leukemia & Lymphoma Society, Mark Foundation for Cancer Research, and Paul G. Allen Frontiers Group (8023-20). R.K.B is a Scholar of The Leukemia & Lymphoma Society (1344-18) and holds the McIlwain Family Endowed Chair in Data Science. Computational studies were supported in part by FHCC’s Scientific Computing Infrastructure (ORIP S10 OD028685). Experimental studies were supported in part by the Experimental Histopathology, Flow Cytometry, and Genomics Shared Resources of the Fred Hutch/University of Washington Cancer Consortium (NIH/NCI P30 CA015704). The results in this publication are based in part on data from The Cancer Genome Atlas Research Network (http://cancergenome.nih.gov).”

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“A.M.G and S.A.M are ARCS Foundation scholars. E.I.C is a Damon Runyon fellow. J.D.T. was supported by the NIH/NCI (K99 CA263168). R.K.B. was supported in part by the NIH/NCI (R01 CA251138), NIH/NHLBI (R01 HL128239, R01 HL151651) and the Blood Cancer Discoveries Grant program through the Leukemia & Lymphoma Society, Mark Foundation for Cancer Research, and Paul G. Allen Frontiers Group (8023-20). R.K.B is a Scholar of The Leukemia & Lymphoma Society (1344-18) and holds the McIlwain Family Endowed Chair in Data Science. Computational studies were supported in part by FHCC’s Scientific Computing Infrastructure (ORIP S10 OD028685). Experimental studies were supported in part by the Experimental Histopathology, Flow Cytometry, and Genomics Shared Resources of the Fred Hutch/University of Washington Cancer Consortium (NIH/NCI P30 CA015704). The results in this publication are based in part on data from The Cancer Genome Atlas Research Network (http://cancergenome.nih.gov).”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

5. Thank you for stating the following in the Competing Interests section:

“RKB is a founder and scientific advisor of Codify Therapeutics and Synthesize Bio and holds equity in both companies. OA-W is a founder and scientific advisor of Codify Therapeutics and holds equity in this company. RKB and OA-W have received research funding from Codify Therapeutics unrelated to the current work. OA-W has served as a consultant for Foundation Medicine Inc., Merck, Prelude Therapeutics, Amphista Therapeutics, MagnetBio, and Janssen, and is on the Scientific Advisory Board of Envisagenics Inc., Harmonic Discovery Inc., and Pfizer Boulder; OA-W has received prior research funding from H3B Biomedicine, Nurix Therapeutics, Minovia Therapeutics, and LOXO Oncology unrelated to the current manuscript. The remaining authors declare no competing interests.”

Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to  PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests).  If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared.

Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf.

6. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels.  

In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions.

7. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

8. 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.

[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

**********

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

Reviewer #1: 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: Yes

**********

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

**********

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: I have carefully reviewed the manuscript submited to Plos One by Gabel AM and his colleagues. Their study entitled ‘Muscleblind-like proteins are novel modulators of the tumor- immune microenvironment’’ is that the effect of expression changes of a novel modulator, Muscleblind-like (MBNL) proteins, on the effect of CD8 T-cells on tumor cells and tumor- immune microenvironment was investigated.

The study is well designed, many experiments have been carried out within the framework of the hypothesis and very valuable data have been obtained from the experiments. These have been systematically given in the results section of the article, but it is seen that the presented data have not been discussed in detail in the discussion part of the article in the light of the literature. Therefore, the valuable data obtained from the study should be detailly discussed in the section of the article. Also, there are a few minor grammatical errors.

**********

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

**********

[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: Review- PONE-D-24-15862.pdf
Revision 1

Please see the response to reviewer and cover letter documents for point-by-point responses to reviewer and editorial requests.

Attachments
Attachment
Submitted filename: response_to_reviewers.pdf
Decision Letter - Atsushi Asakura, Editor

Muscleblind-like proteins are novel modulators of the tumor-immune microenvironment

PONE-D-24-15862R1

Dear Dr. Bradley,

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.

Kind regards,

Atsushi Asakura, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Atsushi Asakura, Editor

PONE-D-24-15862R1

PLOS ONE

Dear Dr. Bradley,

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team.

At this stage, our production department will prepare your paper for publication. This includes ensuring the following:

* All references, tables, and figures are properly cited

* All relevant supporting information is included in the manuscript submission,

* There are no issues that prevent the paper from being properly typeset

If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps.

Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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.

If we can help with anything else, please email us at customercare@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Atsushi Asakura

Academic Editor

PLOS ONE

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .