Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivo

Marcos I. Petersen; Hugo A. Carignano; Claudia Mongini; Diego D. Gonzalez; Juan P. Jaworski

doi:10.1371/journal.pone.0281317

Peer Review History

Original SubmissionNovember 24, 2022
27 Dec 2022 Decision Letter - Elisabetta Pilotti, Editor PONE-D-22-32408Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivoPLOS ONE Dear Dr. Jaworski, 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. ________________________________________<ul> The authors provided novel and intriguing results by investigating the role of a potential oncogenic mechanism driven by Bovine leukemia virus infection. However, I would suggest a more in-depth discussion of the data. As known, miRNAs work in concert with each other to lead the pathological processes and their multiple targeted-mRNAs either. Since the authors pointed to the relevance of a unique genetic biomarker, I would encourage them to add some statements to highlight the importance of their work. Furthermore, I recommend citing more literature in the introduction. <li> A thorough proofreading of the English language is needed. ________________________________________ Please submit your revised manuscript by Feb 10 2023 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'. 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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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: 1. You must write P values for all figures (Figure 1, A (BLV-pol), B (viral blv-miR-b4-3p), C (host miR-29a), and E (HBP-1 mRNA)), since the graphical difference is not always so obvious, not only for Figure 1, D (PXDN mRNA). 2. Why didn't you measure DNA purity by the ratio of absorbance at 260/280 nm? This is one of the important indicators of DNA purity. 3. In the fourth sentence of the abstract: “… host ́s …” ─ should be “… host …”. 4. In the last sentence of the abstract: “… BLV-encoding miRNAs…” ─ don't generalize to everything BLV-encoding miRNAs, but only blv-miR-b4-3p: It will be more correct. Line 41: “… RNA virus” ─ does not correspond to the adhered classification, instead you should write “Deltaretrovirus genus”. If you want to emphasize that this is the RNA virus, then it is better to write additionally: “According to the Baltimore classification system, BLV is the +ssRNA virus belonging to Group IV” [Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971;35(3):235–41] Lines 45: “… novo …” ─ should be “… de novo …” Lines 45-46: Redundant information: “The novo synthesis of genomic viral RNA” and “viral transcripts” ─ rephrase this sentence. Lines 48: “… persist …” ─ should be “… persists …”. Lines 57: “... host ́s …” ─ should be “… host …”. Lines 57-61: Where is the reference to these two sentences? Lines 64: “… mRNA …” ─ should be “… mRNAs, …”. Line 248: “… that BLV-encoding miRNAs might be involved in BLV tumorigenesis during natural infection” ─ I think that herein it is more correct not to focus on all BLV-encoding miRNAs, but only on blv-miR-b4-3p. Reviewer #2: Dear Juan Pablo Jaworski, The research paper entitled "Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivo" provides a clue about the role of BLV miRNA in the development of cancer in infected animals. It is an important study and definitely adds up in the existing scientific knowledge about BLV. You are requested to improve the picture quality to 600dpi as the figures are blur and are not of good quality. Secondly discussion is week and requires further strengthening moreover the conclusion is lacking. very clear conclusion supporting your research work would be more impactful for the readers. Regards ****** 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: Yes: Nazish Bostan ******** [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: rev. res. for PONE-D-22-32408_ PlosOne Dec 2022.docx https://doi.org/10.1371/journal.pone.0281317.r001
Revision 1
4 Jan 2023 Author Response Castelar, January 2nd 2023 PLOS ONE – Editorial Office Academic Editor Dear Elisabetta Pilotti Thank you for the reviews and the opportunity to re-submit this manuscript entitled “Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivo” (PONE-D-22-32408). The manuscript has been modified in response to the Editor´s request and Reviewers´ helpful comments. On the following pages, we have addressed all of the comments from the reviewers. Reviewers´ comments are in bold and authors´ answers are in plain text below, prefaced by “AU” With these changes, my co-authors and I hope that you will find that the revised manuscript is now acceptable for publication in PLOS ONE. Thank you for considering our manuscript for review. Sincerely, Juan Pablo Jaworski, DVM MSc PhD Staff Scientist, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Instituto de Virología, C.I.C.V. y A., Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y De los Reseros s/n, Hurlingham (CP1686), Buenos Aires, Argentina. Tel. /Fax: 54 11 4621 1447 (3400) E-mail address: jaworski.juan@inta.gob.ar Editorial Comments The authors provided novel and intriguing results by investigating the role of a potential oncogenic mechanism driven by Bovine leukemia virus infection. However, I would suggest a more in-depth discussion of the data. As known, miRNAs work in concert with each other to lead the pathological processes and their multiple targeted-mRNAs either. Since the authors pointed to the relevance of a unique genetic biomarker, I would encourage them to add some statements to highlight the importance of their work. Furthermore, I recommend citing more literature in the introduction. AU: The discussion has been strengthened highlighting the importance of HBP-1 and PXDN in cancer pathways. Additionally, as suggested by Reviewer 2 a conclusion was added at the end of the discussion highlighting the main findings of current work. A thorough proofreading of the English language is needed. AU: The text has been revised accordingly 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 AU: Checked 2. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. AU: Modification of Data Availability Statement: In compliance with PLOS' data policy, all data required to replicate all study findings reported in this article (i.e., values behind the means, standard deviations, values used to build graphs, etc.) has been shared in Supporting Information files. This file (RAW data.PDF) is accessible by general software and has been included in the revised version of the manuscript. 3. 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. AU: reference list has been revised and new references have been included as requested by Editor and Reviewer 2 in order to expand the introduction and discussion of the revised manuscript 1. Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971 Sep;35(3):235–41. Available from: https://journals.asm.org/doi/10.1128/br.35.3.235-241.1971 10. Kincaid RP, Sullivan CS. Virus-Encoded microRNAs: An Overview and a Look to the Future. PLOS Pathog. 2012 Dec;8(12):e1003018. Available from: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003018 Reviewers' comments: Reviewer #1: 1. You must write P values for all figures (Figure 1, A (BLV-pol), B (viral blv-miR-b4-3p), C (host miR-29a), and E (HBP-1 mRNA)), since the graphical difference is not always so obvious, not only for Figure 1, D (PXDN mRNA). AU: P values were added for figure 1.C; 1.D and 1.E (miR-29a, PXDN and HBP-1, respectively). No P values were calculated for blv-miR-b4-3p and BLV-pol since none of these targets were detected in BLV-negative animals (BLV-). 2. Why didn't you measure DNA purity by the ratio of absorbance at 260/280 nm? This is one of the important indicators of DNA purity. AU: Thank you for pointing out this mistake/omission. As now stated in line 110 “DNA purity was assessed by the ratio of absorbance at 260/230 nm and 260/280 nm” for the detection of salt and protein contaminants, respectively. 3. In the fourth sentence of the abstract: “… host ́s …” ─ should be “… host …”. AU: corrected 4. In the last sentence of the abstract: “… BLV-encoding miRNAs…” ─ don't generalize to everything BLV-encoding miRNAs, but only blv-miR-b4-3p: It will be more correct. AU: we agree with this observation and it is now corrected as suggested Line 41: “… RNA virus” ─ does not correspond to the adhered classification, instead you should write “Deltaretrovirus genus”. If you want to emphasize that this is the RNA virus, then it is better to write additionally: “According to the Baltimore classification system, BLV is the +ssRNA virus belonging to Group IV” [Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971;35(3):235–41] AU: Now corrected as follows “Bovine leukaemia virus (BLV) belongs to the Deltaretrovirus genus, Orthoretrovirinae subfamily and Retroviridae family. BLV is related to the human T-cell lymphotropic virus (HTLV-1 and -2). According to the Baltimore classification system BLV is a +ssRNA virus (Group IV [Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971;35(3):235–41])”. New citation added to reference list. Lines 45: “… novo …” ─ should be “… de novo …” Lines 45-46: Redundant information: “The novo synthesis of genomic viral RNA” and “viral transcripts” ─ rephrase this sentence. AU: the sentence has been rephrased as follows: “The synthesis of viral transcripts and proteins is a hallmark of this stage.” Lines 48: “… persist …” ─ should be “… persists …”. AU: fixed Lines 57: “... host ́s …” ─ should be “… host …”. AU: corrected Lines 57-61: Where is the reference to these two sentences? AU: A reference was added to support both statements “Virus-Encoded microRNAs: An Overview and a Look to the Future” Kincaid and Sullivan, Plos Pathogens (REVIEW) Dec 2012; Vol: 8, Issue: 12. Lines 64: “… mRNA …” ─ should be “… mRNAs, …”. AU: fixed Line 248: “… that BLV-encoding miRNAs might be involved in BLV tumorigenesis during natural infection” ─ I think that herein it is more correct not to focus on all BLV-encoding miRNAs, but only on blv-miR-b4-3p. AU: The statement has been modified as follows: “Moreover, since PXDN has been linked to anti-tumoral pathways in B-cells, the downregulation of PXDN expression by blv-miR-b4-3p might be involved in BLV tumorigenesis in cattle during natural infection with this virus.” Reviewer #2: Dear Juan Pablo Jaworski, The research paper entitled "Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivo" provides a clue about the role of BLV miRNA in the development of cancer in infected animals. It is an important study and definitely adds up in the existing scientific knowledge about BLV. You are requested to improve the picture quality to 600dpi as the figures are blur and are not of good quality. AU: FIGURE 1 quality has been improved as requested Secondly discussion is week and requires further strengthening moreover the conclusion is lacking. very clear conclusion supporting your research work would be more impactful for the readers. Regards AU: The discussion has been strengthened highlighting the importance of HBP-1 and PXDN in cancer pathways. Additionally, as suggested by this Reviewer a conclusion was added at the end of the discussion highlighting the main findings of the current work https://doi.org/10.1371/journal.pone.0281317.r002
20 Jan 2023 Decision Letter - Elisabetta Pilotti, Editor Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivo PONE-D-22-32408R1 Dear Dr. Jaworski, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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 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, Elisabetta Pilotti Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0281317.r003
Formally Accepted
24 Jan 2023 Acceptance Letter - Elisabetta Pilotti, Editor PONE-D-22-32408R1 Bovine leukemia virus encoded blv-miR-b4-3p microRNA is associated with reduced expression of anti-oncogenic gene in vivo Dear Dr. Jaworski: I'm 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 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 plosone@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. Elisabetta Pilotti Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0281317.r004

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