Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events

Tigran Makunts; Keith Burkhart; Ruben Abagyan; Peter Lee

doi:10.1371/journal.pone.0263402

Peer Review History

Original SubmissionAugust 16, 2021
17 Nov 2021 Decision Letter - Yoshihiko Hirohashi, Editor PONE-D-21-24932 Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events PLOS ONE Dear Dr. Tigran Makunts, 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 Dec 25 2021 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. 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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: Partly 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). 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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 this paper, the authors performed retrospective analysis of clinical trial safety data and found a significant association of co-occurring infections with immune related adverse event (irAE) in pembrolizumab treated cancer patients. Although this manuscript contains some interesting findings, the authors should consider the following point. 1. Is the association between irAEs and infections characteristic of pembrolizumab? If the authors want to prove the irAE/infection association while using immune checkpoint inhibitors, they should also analyze the clinical trial data of other immune checkpoint inhibitors including nivolumab, cemiplimab, anti-PD-L1 antibodies and anti-CTLA-4 antibodies and compare those results. It is very important to clarify the association between irAEs and infections in other immune checkpoint inhibitors in this paper. 2. Is there any difference between irAEs with infection and irAEs without infection in the type of irAEs? Reviewer #2: In this manuscript, the authors have claimed that infection may increase the risk of developing an irAE. Infection undoubtedly activate immunity. Therefore, the claim themselves would be not surprising but may confer important reference in the future studies. This reviewer has some concerns as listed below. 1. As the authors mentioned in the manuscript at around line 180 to 190, this reviewer wonders whether infection is a cause or a result of irAE. As shown in Table 5, mean days at 1st of infection delayed to that of 1st irAE. This reviewer suggests that only cases in which infection precedes irAE should be analyzed. The causal relationship between infection and irAE should be at least consistent from view of time series. If this point is not clarified, the authors' claim would be an overstatement and should not be published. 2. Is it possible that pembrolizumab exacerbate inflammatory reaction of subclinical infection? In such case, enhanced inflammation of subclinical infection by pembrolizumab is a result of irAE. 3. This reviewer is interested whether there is a difference in the clinical effect of pembrolizumab depending on the presence or absence of infection. This point would certainly improve the importance of the manuscript. ****** 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. https://doi.org/10.1371/journal.pone.0263402.r001
Revision 1
26 Dec 2021 Author Response Responses to reviewer comments Reviewer #1: In this paper, the authors performed retrospective analysis of clinical trial safety data and found a significant association of co-occurring infections with immune related adverse event (irAE) in pembrolizumab treated cancer patients. Although this manuscript contains some interesting findings, the authors should consider the following point. 1. Is the association between irAEs and infections characteristic of pembrolizumab? If the authors want to prove the irAE/infection association while using immune checkpoint inhibitors, they should also analyze the clinical trial data of other immune checkpoint inhibitors including nivolumab, cemiplimab, anti-PD-L1 antibodies and anti-CTLA-4 antibodies and compare those results. It is very important to clarify the association between irAEs and infections in other immune checkpoint inhibitors in this paper. We agree with reviewer 1 that analyzing clinical trial data for other checkpoint inhibitors would be helpful. However, the study was constrained by data availability for each treatment, and the processing effort required for clinical data. We chose the antibody with the largest number of clinical trials and safety reports to ensure statistical significance and narrow 95% confidence intervals. The current study used data from every pembrolizumab clinical trial submitted to the US FDA. It took nearly 2 years of data preparation and internal government regulatory review. We do agree that not including every other chemotherapy in the analysis is a limitation and amended the Study limitations section with the following: “The study focused on only one of the currently approved antibodies in immune oncology with the goal of quantifying and establishing a signal that can be investigated further. Future studies are needed to confirm whether the observed irAE/infection association is preserved in subjects administered other anti-PD-1, -PD-L1, and -CTLA-4 cancer immunotherapy.” 2. Is there any difference between irAEs with infection and irAEs without infection in the type of irAEs? It is definitely an interesting question. In fact, asking that question was the part of the original design of the study. Unfortunately, the paucity and ambiguity of the annotations of AE reports made it difficult to generate and any meaningful statistical analysis. The irAEs based on AEHLT designations were pooled together under the irAE umbrella term to allow for sufficient number of reports and reasonable 95% confidence intervals. For clarity, we improved the Measured outcomes section to explain the rationale of clustering irAEs together: “The irAEs based on AEHLT designations were pooled together under the irAE umbrella term to allow for sufficient number of reports and reasonable 95% confidence intervals. The limited number of reports with organ specific irAE terms prevented any higher resolution analysis.” Reviewer #2: In this manuscript, the authors have claimed that infection may increase the risk of developing an irAE. Infection undoubtedly activate immunity. Therefore, the claim themselves would be not surprising but may confer important reference in the future studies. This reviewer has some concerns as listed below. Indeed, the infection and irAE association makes sense both intuitively and etiologically. However, it has never been properly quantified using a comprehensive set of reports from over a hundred controlled clinical trials for 11 types of cancers. 1. As the authors mentioned in the manuscript at around line 180 to 190, this reviewer wonders whether infection is a cause or a result of irAE. As shown in Table 5, mean days at 1st of infection delayed to that of 1st irAE. This reviewer suggests that only cases in which infection precedes irAE should be analyzed. The causal relationship between infection and irAE should be at least consistent from view of time series. If this point is not clarified, the authors' claim would be an overstatement and should not be published. We agree that association does not necessarily indicate causation. In our study we focused on statistically significant associations that need to be further studied. Unfortunately, the paucity of sufficient longitudinal data prevented further assignment of the causality. We do mention this limitation in the results section. In the revised version we expanded the Study limitations section. See additional lines 249-251 in the Study limitations. 2. Is it possible that pembrolizumab exacerbate inflammatory reaction of subclinical infection? In such case, enhanced inflammation of subclinical infection by pembrolizumab is a result of irAE. Thank you for the great question. A possibility of immune activation worsening certain subtypes of inflammation from infection is plausible. However, the inflammation pathways related to infections may not be the same as the immune activation through PD-1 blockade. In our study we demonstrate that in most cases infections precede the irAE, however the lack of AE duration end dates made the definite quantification of this observation challenging. 3. This reviewer is interested whether there is a difference in the clinical effect of pembrolizumab depending on the presence or absence of infection. This point would certainly improve the importance of the manuscript. We agree with the reviewer that looking at efficacy as a function of existing infection would be very interesting and potentially useful. Multiple immune oncology studies have observed a positive association of severity of irAEs with efficacy. Additionally, introduction of gut microbiota concurrent with immunotherapy has shown a similar effect (see references 41 and 42). Therefore, infection may facilitate enhanced immune activation and efficacy indirectly through the above-mentioned mechanism. The study of this potential synergy was beyond the scope of our study, but definitely deserves further analysis of controlled trial data. Attachments Attachment Submitted filename: Responses to reviewer comments.docx https://doi.org/10.1371/journal.pone.0263402.r002
19 Jan 2022 Decision Letter - Yoshihiko Hirohashi, Editor Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events PONE-D-21-24932R1 Dear Dr. Makunts, 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, Yoshihiko Hirohashi, M. D., Ph. D. Academic Editor PLOS ONE Additional Editor Comments (optional): The authors addressed concerns. Reviewers' comments: https://doi.org/10.1371/journal.pone.0263402.r003
Formally Accepted
27 Jan 2022 Acceptance Letter - Yoshihiko Hirohashi, Editor PONE-D-21-24932R1 Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events Dear Dr. Makunts: 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. Yoshihiko Hirohashi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0263402.r004

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