Peer Review History

Original SubmissionJuly 26, 2019
Decision Letter - Wei Shi, Editor

PONE-D-19-21143

Airway epithelial specific deletion of Jun-N-terminal kinase 1 attenuates pulmonary fibrosis in two independent mouse models

PLOS ONE

Dear Dr. van der Velden,

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, in particular, additional information regarding materials and methods and more discussion about the potential mechanisms underlying epithelial JNK1 knockout in attenuating lung fibrosis.  

We would appreciate receiving your revised manuscript by Nov 22 2019 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Wei Shi

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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Thank you for including your ethics statement: The samples from IPF patients and non diseased controls were obtained from the National Heart Lung and Blood Institute-sponsored Lung Tissue Research Consortium (LTRC). The clinical data and specimens have been de-identified by the LTRC. LTRC protocols were approved by the institutional review boards at UVM

Please amend your current ethics statement to include the full name of the ethics committee/institutional review board(s) that approved your specific study.

Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”).

For additional information about PLOS ONE ethical requirements for human subjects research, please refer to http://journals.plos.org/plosone/s/submission-guidelines#loc-human-subjects-research.

3. 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.

4. Please include a copy of Table 1 which you refer to in your text.

5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

Additional Editor Comments (if provided):

[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

**********

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

Reviewer #1: Yes

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: Yes

Reviewer #2: 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

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: In materials and methods, chemical and antibodies, the concentration of actin antibody should be checked. 1:500 or 1:5000?

In human lung tissues, the authors should write how many patient tissues are studied.

The authors should identificate whether the patients studied are male or female.

The authors should write ethic committee approval number for clinic and all animal studies.

In phospho-JNK staining human lung tissues, the authors should write incubation time and degree of antibody. The method should write more detaily.

In animals, the authors should write male or female mice?

The start of experiment, administered substance day and end of experiment should be schematized.

In gene expression, the authors should explain to use protocol that taqman or sybr green?

In results and in figure 1, the authors Said that JNK1 (JNK1/2) and JNK2 (JNK2/1). These are not clearly. They should explain.

In figures, "the collegen content score" should be expressed instead of the score (trichrome).

"fold induction of gene expression" should be expressed instead of fold induction.

Reviewer #2: In this manuscript, the authors addressed the role of epithelial JNK1 activation in the pathogenesis of lung fibrosis using both the bleomycin and AdTGFbeta1 models. The authors demonstrated nicely that activation of JNK1 occurred in both models of lung fibrosis in mice as well as in human IPF, epithelial deletion of JNK1 protected mice from fibrosis in both models, and finally delayed epithelial deletion of JNK1 resulted in reversal of existing fibrotic response. The experiments were well-controlled, the inducible epithelial JNK1 deletion model was sufficiently described and verified, and the analyses of fibrosis were adequate and convincing. I only have one question/concern:

The fact that epithelial deletion of JNK1 offered protection against lung fibrosis induced by both bleomycin and AdTGFbeta1 suggests that JNK1 works downstream of or in concert with TGFbeta1 in the fibrotic process. The fibrotic response in the bleomycin model, however, occurs subsequent to epithelial injury and inflammation. What is the role of JNK1 activation in lung injury and inflammation induced by bleomycin? If epithelial JNK1 deletion alters the injury/inflammatory response induced by bleomycin, then its effects on fibrosis would be secondary.

**********

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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Revision 1

Editor’s comments:

Comment 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming.

Response 1: The manuscript style has been revised to the PLOS ONE requirements.

Comment 2: Thank you for including your ethics statement: The samples from IPF patients and non-diseased controls were obtained from the National Heart Lung and Blood Institute-sponsored Lung Tissue Research Consortium (LTRC). The clinical data and specimens have been de-identified by the LTRC. LTRC protocols were approved by the institutional review boards at UVM. Please amend your current ethics statement to include the full name of the ethics committee/institutional review board(s) that approved your specific study. Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”).

Response 2: The full name of the committee has been amended and the Ethics statement has been updated.

Comment 3: 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. 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.

Response 3: All the data files are uploaded in the supporting information and this is noted in the cover letter.

Comment 4: Please include a copy of Table 1 which you refer to in your text.

Response 4: Table 1 has been included in the manuscript.

Comment 5: Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

Response 5: Captions have been included for the supporting information.

Reviewer comments #1:

Comment1: In materials and methods, chemical and antibodies, the concentration of actin antibody should be checked. 1:500 or 1:5000?

Response 1: The concentration of the actin antibody is correct, 1:500.

Comment 2: In human lung tissues, the authors should write how many patient tissues are studied. The authors should identificate whether the patients studied are male or female.

Response 2: We agree with the reviewer that we should indicate the gender distribution of the analyzed samples. We included this in the methods section.

Comment 3: The authors should write ethic committee approval number for clinic and all animal studies.

Response 3: We included the Institutional Review Board Committee on Human Research in Medical Sciences approval number in the methods section.

Comment 4: In phospho-JNK staining human lung tissues, the authors should write incubation time and degree of antibody. The method should write more detaily.

Response 4: We appreciate the reviewers comment and we included a more detailed protocol with regard to incubation time and antibody specifics in the methods.

Comment 5: In animals, the authors should write male or female mice?

Response 5: we agree with the reviewer and included a statement that we use both male and female mice.

Comment 6: The start of experiment, administered substance day and end of experiment should be schematized.

Response 6: We included experimental schematics in supplemental figure 1

Comment 7: In gene expression, the authors should explain to use protocol that taqman or sybr green?

Response 7: We indicated that we used SYBR green.

Comment 8: In results and in figure 1, the authors Said that JNK1 (JNK1/2) and JNK2 (JNK2/1). These are not clearly. They should explain.

Response 8: Our apologies this is not clear, in the methods section we clearly explain why it is labeled this way together with a reference. In order to prevent confusion, we changed the labeling of figure 1A.

Comment 9: In figures, "the collegen content score" should be expressed instead of the score (trichrome). "fold induction of gene expression" should be expressed instead of fold induction.

Response 9: We appreciate the reviewer comments and corrected the figures.

Reviewer comments #2

Comment 1: The fact that epithelial deletion of JNK1 offered protection against lung fibrosis induced by both bleomycin and AdTGFbeta1 suggests that JNK1 works downstream of or in concert with TGFbeta1 in the fibrotic process. The fibrotic response in the bleomycin model, however, occurs subsequent to epithelial injury and inflammation. What is the role of JNK1 activation in lung injury and inflammation induced by bleomycin? If epithelial JNK1 deletion alters the injury/inflammatory response induced by bleomycin, then its effects on fibrosis would be secondary.

Response 1: We agree with the reviewer that this is an interesting dilemma and appreciate his comments. In previous mouse studies; both in bleomycin-induced fibrosis and house dust mite-induced allergic airway disease models we have not observed a significant impact of JNK1 on the inflammatory responses. A statement of this finding has been included in the conclusion. Further, we also have shown that JNK1 cannot only regulate the injury process via Smad and Wnt signaling pathways (reference 16 and 17) but JNK1 also plays a role in the “epithelial-ness” of cells (reference 19). In this particular study we show that JNK1 is important in the response of epithelial cells to a “diseased” extracellular matrix. These two findings combined suggest that JNK1 can act as a double edge sword. On one hand it can regulate the severity of the fibrotic injury response potentially via Smad and Wnt signaling pathways and on the other hand JNK1 can play a role in the repair process via regulating re-epithelialization. We added this to the discussion.

Attachments
Attachment
Submitted filename: Review Comments to the Author 11-01-2019.docx
Decision Letter - Wei Shi, Editor

Airway epithelial specific deletion of Jun-N-terminal kinase 1 attenuates pulmonary fibrosis in two independent mouse models

PONE-D-19-21143R1

Dear Dr. van der Velden,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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.

With kind regards,

Wei Shi

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 #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 #2: Yes

**********

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

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 #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 #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 #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 #2: No

Formally Accepted
Acceptance Letter - Wei Shi, Editor

PONE-D-19-21143R1

Airway epithelial specific deletion of Jun-N-terminal kinase 1 attenuates pulmonary fibrosis in two independent mouse models

Dear Dr. van der Velden:

I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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.

For any other questions or concerns, please email plosone@plos.org.

Thank you for submitting your work to PLOS ONE.

With kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Wei Shi

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 .