Convergent antibody evolution and clonotype expansion following influenza virus vaccination

David Forgacs; Rodrigo B. Abreu; Giuseppe A. Sautto; Greg A. Kirchenbaum; Elliott Drabek; Kevin S. Williamson; Dongkyoon Kim; Daniel E. Emerling; Ted M. Ross

doi:10.1371/journal.pone.0247253

Peer Review History

Original SubmissionOctober 16, 2020
23 Dec 2020 Decision Letter - Victor C Huber, Editor PONE-D-20-32620 Convergent antibody evolution and clonotype expansion following influenza virus vaccination PLOS ONE Dear Dr. Ross, 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. During the revision process, please address the concerns related to the analysis of public clonotype data and the availability of all underlying data related to the study. s Please submit your revised manuscript by Feb 06 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. 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Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests 3. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [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: No 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: This study by Forgacs et al. sequenced the B cell receptor repertoire of 17 participants after seasonal influenza virus vaccination. While largely descriptive, the study comprises an interesting data set that could be of interest to the field of influenza research. To allow other researchers to further study this data set, the authors should make the underlying raw data available and accessible. Minor: - Please show error bars for the HAI data in Figure 1B - Please provide specific percentages for IgG2 and IgG3. Reviewer #2: The authors present an analysis of BCR sequences following influenza vaccination, determined by B cell cloning of approximately 7,800 B cells from PBMCs. The main finding here is evidence of convergent responses, deduced from public VH genes in 10/17 donors analyzed. Overall there is a wealth of data here of interest to the field. A number of issues need to be addressed however, before the manuscript is accepted. Major: 1) Public clonotypes were defined as ...."PBs whose heavy chain variable region nucleotide pairwise identity was over 80%, and HCDR3 peptide sequence pairwise identity was over 75% compared to at least one other PB from a different participant in the same group". This is very permissive. What is the justification for such a low threshold for HCDR3 aa identity? Did the clonotypes considered as "public" share the same VJ genes. Analysis of public clonotypes with more stringent criteria, ie same V same J and >85% aa identity needs to be performed and reported. 2) Given that public VH were paired with different VL was there any analysis of Mabs to show that the binding specificity was primarily VH driven? Not an essential point, but at least should be discussed? 2) The text is excessively long, especially the Discussion. The text should be reduced by at least 30%. ****** 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.0247253.r001
Revision 1
30 Jan 2021 Author Response Athens, GA - January 29, 2021 Dear Editor: We are resubmitting a revised version of our manuscript ID PONE-D-20-32620 entitled “Convergent antibody evolution and clonotype expansion following influenza virus vaccination” to PLoS ONE after having addressed the revisions that were suggested by you and the reviewers. Below, please find a point-by-point reply to the referee comments. Editor comments: 1. We would like to update the Financial Disclosure section to state the following: This study was supported by the NIH contract HHSN272201400004C (NIAID Centers of Excellence for Influenza Research and Surveillance, CEIRS). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. The funder provided support in the form of salaries for authors [DF, RBA, GAS, GAK], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘Author contributions’ section. Some of the authors are affiliated with Atreca, Inc., however, they provided no funding for the study, only assisted with the data collection and the preparation of the manuscript. (Please note also that in the previous submission, GACRC was erroneously included in the Financial Disclosure section. While they provided assistance, it was all technical and not financial, so the statement belongs in the Acknowledgements but not in this section.) 2. In accordance to your request, we would also like to update the Competing Interests Statements to report the following: Some of the authors are affiliated with Atreca, Inc., but the company provided no funding for the study and no competing interests exist. The commercial affiliation of those authors does not alter our adherence to PLoS ONE policies on sharing data and materials. 3. The statements including the phrase “data not shown” have been replaced by the appropriate references including the data or relating to the statement (lines 534 and 631). Reviewer comments: Reviewer #1 (Response to Questions): To the question “Have the authors made all data underlying the findings in their manuscript fully available?”, Reviewer #1 answered no. This was correct at the time of the review as only placeholders were left in the manuscript while NCBI authenticated and released the 15,554 novel nucleotide sequences provided by our study. They are now all publicly available in GenBank as a Target Locus Study under accession numbers KEOV00000000 and KEOU00000000. References to those accession numbers have been included in the manuscript (line 190). Reviewer #1 (Comments to the Author): 1. Please show error bars for the HAI data in Figure 1B We thank the reviewer for having noticed that and we apologize for our oversight. Error bars have now been added to the HAI panel in Figure 1B, along with the legend now stating that all samples were run in triplicate (line 265). 2. Please provide specific percentages for IgG2 and IgG3. Specific percentages have been provided for IgG2 and IgG3 in lines 271-272. Reviewer #2 (Comments to the Author): 1. Public clonotypes were defined as ...."PBs whose heavy chain variable region nucleotide pairwise identity was over 80%, and HCDR3 peptide sequence pairwise identity was over 75% compared to at least one other PB from a different participant in the same group". This is very permissive. What is the justification for such a low threshold for HCDR3 aa identity? Did the clonotypes considered as "public" share the same VJ genes. Analysis of public clonotypes with more stringent criteria, ie same V same J and >85% aa identity needs to be performed and reported. Public convergent clonotypes are defined by three criteria, all of which had to be true in order to be considered part of the same public clonotype: 1. As Reviewer #2 stated, all B cell belonging to the same clonotype must have had identical heavy chain V and J genes. The text has been appended to include that distinction. 2. The minimum heavy chain nucleotide percent identities between two B cell had to be a minimum of 80%. 3. And in addition to strengthen our criteria, the HCDR3 amino acid identity between donors was set at a minimum of 75%. These criteria are consistent with what is recently published in the literature (e.g. Galson et al., 2020. Front. Imm.; Setliff et al., 2018. Cell Host Microbe). Increasing this cutoff to the recommended 85% would only exclude two of the 98 B cells that we found to be convergent: one from pubCDR3-1 that otherwise has an 83% heavy chain nucleotide identity, the other from pubCDR3-4 which has a staggering 93% heavy chain nucleotide identity. As both of these B cells have the same V and J genes as other members of their convergent clonotypes, as well as heavy chain nucleotide identities exceeding the published norm, we still feel strongly about including them in the analysis. However, we have included a clear description and rationale in the appropriate section (lines 230-234). 2. Given that public VH were paired with different VL was there any analysis of Mabs to show that the binding specificity was primarily VH driven? Not an essential point, but at least should be discussed? We agree that this point should be touched on, and though we have not analyzed VH/VL specificity for the purposes of this manuscript, we included a paragraph to address this point (lines 578-587). 3. The text is excessively long, especially the Discussion. The text should be reduced by at least 30%. We have done our best to shorten the Introduction, Materials and methods, as well as the Discussion sections. Though we understand that the manuscript is long, we do believe it to be free of superfluous details. We truly appreciate the lack of strict word limits for PLoS ONE publications. Sincerely, Ted M. Ross, PhD GRA Eminent Scholar in Infectious Diseases Director - Center for Vaccines and Immunology Professor - Department of Infectious Diseases University of Georgia Attachments Attachment Submitted filename: Forgacs.PLoS One Response to reviewers.docx https://doi.org/10.1371/journal.pone.0247253.r002
4 Feb 2021 Decision Letter - Victor C Huber, Editor Convergent antibody evolution and clonotype expansion following influenza virus vaccination PONE-D-20-32620R1 Dear Dr. Ross, 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, Victor C Huber Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0247253.r003
Formally Accepted
11 Feb 2021 Acceptance Letter - Victor C Huber, Editor PONE-D-20-32620R1 Convergent antibody evolution and clonotype expansion following influenza virus vaccination Dear Dr. Ross: 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. Victor C Huber Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0247253.r004

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