ART is key to clearing oncogenic HPV genotypes (HR-HPV) in anal mucosa of HIV-positive MSM

Carmen Hidalgo-Tenorio; Concepción Gil-Anguita; Miguel Angel López Ruz; Mohamed Omar; Javier López-Hidalgo; Juan Pasquau

doi:10.1371/journal.pone.0224183

Peer Review History

Original SubmissionJune 27, 2019
16 Sep 2019 Decision Letter - Jean-Luc EPH Darlix, Editor PONE-D-19-18194 ART is key to clearing oncogenic HPV genotypes (HR-HPV) in anal mucosa of HIV-positive MSM PLOS ONE Dear Dr Tenorio, 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 agreement with the reviewer, it appears that your manuscript is of interest regarding the impact of HPV anal infection in MSM . However it is clearly in need of clarifications with respect to the HPV genotypes, and the histological analyses (figures 1 & 2). The section on anal cytology and HPV genotyping by PCR (comment 6) is very hard to follow, and hence conclusions could be mistaken. This important section really needs clarification. See other comments by the reviewer. 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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: General This is a very important study exploring the natural history of anal HPV infection and anal dysplasia among HIV+ positive MSM. The study was well executed and has robust analysis. It also explored treatment of HSILs with a variety of methods including impact of giving the quadrivalent vaccine. I recommend the manuscript for publication after the comments highlighted below are addressed. Methods: Comment 1: Design: 5 paragraph last sentence: “At the same visit, biopsies were taken using an endoscopic retrograde cholangiopancreatography catheter.” What biopsies were these? Anal or liver? Comment 2: Definition of variables “Histology with anal HSIL+: from HSIL to ASCC.” “Histology with LSIL+: from LSIL to ASCC.” These are not clear and need to be updated. Results Comment 3: 5. HPV genotype distribution by histology Text in this section and reference to the tables needs to be clarified. For example the second paragraph “As depicted in Figure 1, none of the 36 HPV genotypes isolated in normal mucosa were significantly associated with this histological finding (normal mucosa), and the most frequently isolated genotypes were 6 (15.4%), 16 (21.6%), 42 (18.5%), 45 (23.2%), and 62 (31.9%).” Comment 4: The information on the most common genotypes in actually in Figure 2 not figure 1 which shows the stabilisation of the HSIL+ rates Comment 5: Again the third paragraph, “In LSIL+ mucosa samples, the most frequently isolated genotypes were 6 (19.1%), 11 (19.8%), 16 (32.3%), 31 (16.7%), 42 (19.1%), and 55 (17.3%), as shown in Figure 2. Genotype 66 was significantly associated with LSIL (12.9% vs. 5.6% p=0.001) (Figure 1).” It is not immediately clear from Figure 1 that type 66 is associated with LSIL Comment 6: 6. Correlation of anal cytology and HPV PCR with histological findings “The cytology study showed that 165 samples were normal and 232 had some degree of dysplasia. Among the patients with dysplastic samples, 36.6 % had normal anoscopy (p=0.0001), 50% LSIL (p=0.0001), and 17.2% HSIL (p=0.001).” This section is difficult to follow for the readers. For example you would need to calculate that (85/232)=36.6 had normal. There is another % i.e..43.4% which is next to 85 and can be confusing to the reader. Comment 7: Table 1: As with other abbreviations, can the authors put the full name for the SDU in table footer Comment 8: Table 5: Needs a bit of formatting so that all the text and number are of the same font. Discussion Comment 9: Second paragraph. This sentence is missing the 95% CI “The duration of ART was the sole factor favoring oncogenic virus clearance (OR 1.016; 95% CI),” Comment 10: Third paragraph. It is this sentence which explains what Figure 1 showed “However, we have observed a significant reduction in the HSIL+ rate among HIV+ MSM since the start of the program in 2010, with a stabilization since 2016” However, this is never mentioned in the results section. It then ties with observation and comments in the results section that the part 5 and 6 of the results needs to be revised as they are rather confusing to the reader. Comment 11: Fourth paragraph. The finding on nadir CD4+ is important “Factors related to infection with HPV oncogenic virus were a history of CD4 nadir < 200 cells/uL (OR: 2.363, 95% CI: 1.062-5.256), and simultaneous infection by low- and high risk HPV genotypes (OR: 1.842; 95% CI: 1.015-3.344).” Can the authors mention that this confirms previous findings and cite some few references Comment 12: Limitations paragraph: The spelling for HIV needs to be updated “A major study strength is that it reports on the first prospective cohort of VIH+ MSM, demonstrating the value of implementing a program to screen for, diagnose, treat, and follow up HSIL+ lesions.” ****** 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: Yes: Dr Admire Chikandiwa [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. Attachments Attachment Submitted filename: PONE-D-19-18194.docx https://doi.org/10.1371/journal.pone.0224183.r001
Revision 1
2 Oct 2019 Author Response We are grateful to the reviewers for their valuable comments, which have all been taken into account in our revision, as explained in our point-by-point responses.: Reviewer #1: General This is a very important study exploring the natural history of anal HPV infection and anal dysplasia among HIV+ positive MSM. The study was well executed and has robust analysis. It also explored treatment of HSILs with a variety of methods including impact of giving the quadrivalent vaccine. I recommend the manuscript for publication after the comments highlighted below are addressed. Methods: 1- Comment 1: Design: 5 paragraph last sentence: “At the same visit, biopsies were taken using an endoscopic retrograde cholangiopancreatography catheter.” What biopsies were these? Anal or liver? We have now specified in the revised text that we took biopsies of the anal mucosa, as follows: “At the same visit, biopsies of the anal mucosa were taken using an endoscopic retrograde cholangiopancreatography catheter”. 2- Comment 2: Definition of variables “Histology with anal HSIL+: from HSIL to ASCC.” “Histology with LSIL+: from LSIL to ASCC.” These are not clear and need to be updated. We have clarified these definitions. Results 3- Comment 3: 5. HPV genotype distribution by histology Text in this section and reference to the tables needs to be clarified. For example the second paragraph “As depicted in Figure 1, none of the 36 HPV genotypes isolated in normal mucosa were significantly associated with this histological finding (normal mucosa), and the most frequently isolated genotypes were 6 (15.4%), 16 (21.6%), 42 (18.5%), 45 (23.2%), and 62 (31.9%).” We have clarified the text and reference accordingly in the revised Results section. 4-Comment 4: The information on the most common genotypes is actually in Figure 2 not figure 1 which shows the stabilisation of the HSIL+ rates. We apologize for this typographic error, which has been amended. 5- Comment 5: Again the third paragraph, “In LSIL+ mucosa samples, the most frequently isolated genotypes were 6 (19.1%), 11 (19.8%), 16 (32.3%), 31 (16.7%), 42 (19.1%), and 55 (17.3%), as shown in Figure 2. Genotype 66 was significantly associated with LSIL (12.9% vs. 5.6% p=0.001) (Figure 1).” It is not immediately clear from Figure 1 that type 66 is associated with LSIL We are again grateful to the reviewer for detecting these errors. These sentences now read as follows: In LSIL+ mucosa samples, the most frequently isolated genotypes were 6 (19.1%), 11 (19.8%), 16 (32.3%), 31 (16.7%), 42 (19.1%), and 55 (17.3%), as shown in Figure 2B. Genotype 66 was significantly associated with LSIL (12.9% vs. 5.6% p=0.001). 6- Comment 6: 6. Correlation of anal cytology and HPV PCR with histological findings “The cytology study showed that 165 samples were normal and 232 had some degree of dysplasia. Among the patients with dysplastic samples, 36.6% had normal anoscopy (p=0.0001), 50% LSIL (p=0.0001), and 17.2% HSIL (p=0.001).” This section is difficult to follow for the readers. For example you would need to calculate that (85/232)=36.6 had normal. There is another % i.e..43.4% which is next to 85 and can be confusing to the reader. We have clarified the text accordingly, making these results easier to follow. 7- Comment 7: Table 1: As with other abbreviations, can the authors put the full name for the SDU in table footer. This has been done. 8- Comment 8: Table 5: Needs a bit of formatting so that all the text and number are of the same font. This has been done. Discussion 9- Comment 9: Second paragraph. This sentence is missing the 95% CI “The duration of ART was the sole factor favoring oncogenic virus clearance (OR 1.016; 95% CI),” This typographic error has now been amended. 10- Comment 10: Third paragraph. It is this sentence which explains what Figure 1 showed “However, we have observed a significant reduction in the HSIL+ rate among HIV+ MSM since the start of the program in 2010, with a stabilization since 2016” However, this is never mentioned in the results section. It then ties with observation and comments in the results section that the part 5 and 6 of the results needs to be revised as they are rather confusing to the reader. - This information is given in the Part 2 of Results under the heading “Clearance and acquisition of HR-HPV infection and prevalence of HSIL+ in anal mucosa….”: However, as depicted in Figure 1, we found significant reductions in HSIL+ cases between 2010 and 2018 (42.9% vs. 4.1%, p=0.034), between 2010 and 2013 (42.9% vs. 13.8%, p=0.003), and between 2013 and 2016 (13.8% vs. 4.8%, p=0.0001), followed by a stabilization between 2016 and 2018 (4.8% vs. 4.1%, p=0.617) (Figure 1). … We have clarified parts 5 and 6 of Results, as requested. 11- Comment 11: Fourth paragraph. The finding on nadir CD4+ is important “Factors related to infection with HPV oncogenic virus were a history of CD4 nadir < 200 cells/uL (OR: 2.363, 95% CI: 1.062-5.256), and simultaneous infection by low- and high risk HPV genotypes (OR: 1.842; 95% CI: 1.015-3.344).” Can the authors mention that this confirms previous findings and cite some few references This is done in the following paragraph: “These data confirm recent observations of the protective effects ofART and CD4 levels>500 cells/uL against infection by oncogenic HPV genotypes (26). Other studies have described the presence of genital warts (27) and a deficient immune system (28) as risk factors for developing neoplasias associated with HR-HPV infection”. 12- Comment 12: Limitations paragraph: The spelling for HIV needs to be updated “A major study strength is that it reports on the first prospective cohort of VIH+ MSM, demonstrating the value of implementing a program to screen for, diagnose, treat, and follow up HSIL+ lesions.” This has been changed to “HIV+ MSM” With Best regards Carmen Hidalgo Tenorio Attachments Attachment Submitted filename: Responses revised1019.docx https://doi.org/10.1371/journal.pone.0224183.r002
8 Oct 2019 Decision Letter - Jean-Luc EPH Darlix, Editor ART is key to clearing oncogenic HPV genotypes (HR-HPV) in anal mucosa of HIV-positive MSM PONE-D-19-18194R1 Dear Dr. Tenorio, 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. Nonetheless your manuscript requires a careful editing at this stage. 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, Jean-Luc EPH Darlix, MG, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0224183.r003
Formally Accepted
14 Oct 2019 Acceptance Letter - Jean-Luc EPH Darlix, Editor PONE-D-19-18194R1 ART is key to clearing oncogenic HPV genotypes (HR-HPV) in anal mucosa of HIV-positive MSM Dear Dr. Hidalgo-Tenorio: 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 Professor Jean-Luc EPH Darlix Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0224183.r004

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