Peer Review History
| Original SubmissionMarch 26, 2024 |
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PONE-D-24-07376Beyond its preferential niche: Brucella abortus RNA down-modulates the IFN--induced expression of MHC-I in cells other than macrophages.PLOS ONE Dear Dr. Milillo, Thank you for submitting your manuscript to PLOS ONE. As you will see below, I received two very different reviews of your manuscript. After reading the reviewers' comments and reviewing the paper myself, I think that Reviewer 2's concerns can be readily addressed by revising the text and providing some important clarifications regarding the biological relevance of the experimental questions being addressed and how the results obtained are being interpreted. Doing this will help the general reader better appreciate the importance of the work. Please submit your revised manuscript by Jun 09 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:
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Sincerely, Marty Roop 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 2. Thank you for stating the following financial disclosure: "This work was financed by PB PICT-2020 SERIE A-00882 and MAM PICT-2020 SERIE A-00978 grants from the Agencia Nacional de Promoción Científica y Tecnológica (ANPCYT-Argentina)." 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. 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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. [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: No ********** 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: Brucella abortus-derived RNA (Ba RNA) is known to downregulate expression of MHCI on macrophages. Here the authors show that Ba RNA downregulates MHCI surface expression on epithelial and endothelial cells. In some cell lines, this effect was associated with retention of MHCI in the golgi. In addition, blockade of EGFR partially negated the effects of Ba RNA on MHCI surface expression. Overall, the study is generally sound and adds to the literature indicating that Ba RNA affects host responses. 1. I suggest including epithelial and endothelial cells in the title rather than “non-macrophages”. 2. Line 43-44 “… this is the first study exploring immune evasion strategies beyond monocytes….”. This statement is not entirely accurate, as Brucella is known to evade of variety of immune responses (ex. by neutrophils, dendritic cells, B cells etc). 3. Lines 145-147 “.. experiments were performed at 37C/5%CO2 and a standard medium consisting of RPMI 1640 or DMEM….”. The authors should clarify when they used media containing RPMI 1640 or DMEM”. 4. What concentration of EGFR antibody was used? 5. Why are there no error bars in Figure 2? 6. In line 269 of the Figure 3 legend the text indicates that geometric means are shown and the authors also define MFI in the legend. Is this correct or a typo resulting from carryover of text from the flow-cytometry figure legends? 7. How many cells counted were counted to generate the data in Figure 4 and Figure 5? 8. TLR8 is typically an endosomal TLR. Were the cells in Figure S2 permeabilized in order to detect TLR8 by flow cytometry? Reviewer #2: The manuscript by Serafino and colleagues describes the phenomenon of immune modulation in cells treated with RNA from the bacterial pathogen Brucella abortus. These bacteria predominantly reside in cells such as macrophages, but the authors chose to examine other cell types, including human bronchial epithelial cells (Calu-6), human alveolar epithelial cells (A-549), and endothelial cells (HMEC). RNA isolated from B. abortus was incubated with these cells, and the authors observed MHC-I was retained in the Golgi apparatus in Calu-6 and HMEC cells, but this did not occur in A-549 cells. Additionally, treatment of the cells with RNA induced the production of specific cytokines, IL-6 and IL-8. Overall, the conclusions drawn by the authors are not supported by the data, and moreover, the scientific premise for the work is not well described. The specific concerns are as follows: -The rationale for performing the study is not clear. The authors seem to argue that because there are very limited respiratory manifestations of Brucella infections, this means that the epithelial cells of the respiratory track must be infected by the bacteria. In lines 349-351, the authors state that these cells are "able to be infected with the pathogen." The data do not show this, and there are no citations to support the claim that the cell lines used support Brucella infection and/or replication. As such, it is difficult to understand why the studies were undertaken, but more importantly, it is difficult to know what the data mean in terms of Brucella biology. -The rationale for putting naked Brucella RNA onto cells and evaluating the immune response is not clear. When would cells of any type be exposed to microgram quantities of Brucella RNA? -The RNA was isolated using an organic reagent (i.e., Trizol), but there are no controls in the experiments to rule out the possibility that organic contamination or other reagent from the isolation method is what is actually stimulating the responses that were observed. An appropriate control would likely be RNA isolated using the same method from another bacterium (e.g., E. coli). This would address if this was a general RNA phenomenon or something specific to Brucella RNA isolated using that protocol. ********** 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. |
| Revision 1 |
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Beyond its preferential niche: Brucella abortus RNA down-modulates the IFN-γ-induced MHC-I expression in epithelial and endothelial cells PONE-D-24-07376R1 Dear Dr. Milillo, Thank you for your conscientious attention to the reviewers' constructive comments in preparing your revision! I'm 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, Marty Roop 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 #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: Yes 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: My concerns have been addressed, however there appears to be an errors in the Figure uploads. Figure 2 appears to have been uploaded twice. Two versions of Figure S2 are included in the manuscript, however one of these Figures appears to be Figure S3. The Figure S3 that is included appears to be a duplicate of Figure S2. Reviewer #2: The authors have addressed the concerns that were raised during the initial review of the manuscript, and there are no additional concerns. ********** 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 ********** |
| Formally Accepted |
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PONE-D-24-07376R1 PLOS ONE Dear Dr. Milillo, 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. Roy Martin Roop II Academic Editor PLOS ONE |
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