Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool

Kovilen Sawmynaden; Nicholas Wong; Sarah Davies; Richard Cowan; Richard Brown; David Tang; Maud Henry; David Tickle; David Matthews; Mark Carr; Preeti Bakrania; Hong Hoi Ting; Gareth Hall

doi:10.1371/journal.pone.0288259

Peer Review History

Original SubmissionFebruary 9, 2023
28 Apr 2023 Decision Letter - Yolandy Lemmer, Editor PONE-D-23-03760Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic toolPLOS ONE Dear Dr. Hall, 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. We would like you to address the specific changes as requested by reviewer 1 with additional inputs from reviewer 2 where deemed necessary. Please submit your revised manuscript by Jun 12 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. 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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 2. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (1) methods of sacrifice, (2) efforts to alleviate suffering. 3. Thank you for stating the following financial disclosure: “I confirm that I have mentioned all organizations that funded my research in the Acknowledgements section of my submission, including grant numbers where appropriate.” At this time, please address the following queries: a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” c) If any authors received a salary from any of your funders, please state which authors and which funders. d) If you did not receive any funding for this study, please state: “The authors received no specific funding for this work.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “LifeArc provided humanisation service(s) to NanoMab under contractual arrangement. LifeArc is a self funded medical charity (registered with the Charity Commission for England and Wales no. 1015243 and a charity registered in Scotland with the Office of the Scottish Charity Regulator no. SC037861).” We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “I confirm that I have mentioned all organizations that funded my research in the Acknowledgements section of my submission, including grant numbers where appropriate.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. Thank you for stating the following in the Competing Interests section: “The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: LifeArc provided the antibody humanisation service(s) under contractual arrangement with NanoMab” Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. 6. Please amend your authorship list in your manuscript file to include author David Tickle. 7. Please include a separate caption for each figure in your manuscript. 8. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 9. 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. 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: 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: No 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: I read the article submitted by Sawmynaden et al with great interest. It describes the identification, humanisation, complex structure determination, and characterization of an anti-HER2 single-domain antibody and its target human HER2. Technically and in terms of interpretation, the article is well written and requires no further modification. My only concern is with the narrow, jargonistic linguistic style - with occasional strangely dated conjunctions. While this style may be suitable for an inner circle of aficionados, I suggest that the text could be made more accessible by replacing complex phrases with more generally comprehensible ones. Thus, "frontline treatment options" could be replaced with "current best competing antibodies," "de-risk" with "avoid immune response," "progression towards" with "proceed to" or "allow for," "chemistry, manufacturing, and control" with "pharmaceutical quality," "performed full developability profiling" with "assessed the pharmacological suitability," and "applicability" with "usefulness," among others. I also suggest removing as many brackets as possible to improve readability. For instance, instead of "show a marked increase in expression levels (2 to 20-fold)," one could say "show a two- to twenty-fold improvement in expression." On page 2, line 40, I recommend removing "As a result" or replacing it with "Correspondingly." There is no direct causal relationship between the sentences. A careful checking of the text remaining should reveal similar minor adjustments that could render the text more generally comprehensible - and hence more citable. Reviewer #2: The manuscript is well written and well presented. However, please allow me to make a few minor comments and suggestions. When reporting scientific data, it is recommended that you report in past tense and not in present tense or as absolutes; replace is with was/ were where relevant etc. Additionally, please avoid the use of pronouns e.g., we, our etc. Please see attachment for a detailed review. ****** 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: Wolf-Dieter Schubert 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. Attachments Attachment Submitted filename: Manuscript-PLOSone-Reviewer Comments-Edits.docx https://doi.org/10.1371/journal.pone.0288259.r001
Revision 1
20 Jun 2023 Author Response Dear Dr Lemmer Please find enclosed a revised version of our paper “Co-crystallisation and humanisation of an anti-HER2 single domain antibody as a theranostic tool” (Manuscript Number PONE-D-23-03760). We were pleased to read that both reviewers assessed the work with great interest and that they felt the manuscript contained important information of interest to other investigators. The reviewers had highlighted several grammatical concerns that we feel we have now addressed in a revised manuscript. We have summarised the changes made to address the reviewers’ comments below and, as requested, we have provided a copy of the original manuscript with tracked changes to facilitate the review process. In addition, we have addressed the Journal requirements below, as highlighted in your last correspondence. 1. The manuscript has been adapted to comply with PLOS ONE’s style requirements, including changing font styles, reordering sections, referencing and preparing individual .TIFF files for the figures. 2. To comply with PLOS ONE’s submission requirements, in the methods section covering animal experiments we have included further details on (1) methods of sacrifice, (2) methods of anaesthesia and/or analgesia, and (3) efforts to alleviate suffering. (1) “Mice under anaesthesia were sacrificed by cervical dislocation, after confirmation that all SPECT/CT images were technically acceptable.” (2) “Mice were subcutaneously inoculated on the right flank with BT474 cells (6 x106 cells suspended in 1:1 (v/v) matrigel:PBS) following implantation of estrogen pellets, using buprenorphine analgesic.” “Whole-body SPECT/CT images were acquired 1.5 hr post-injection in a VECTor6-CTXUHR (MILabs) preclinical imaging system under isoflurane anaesthesia.” (3) “The animals were observed daily for any abnormalities indicative of health problems, to prevent suffering. Only healthy animals were placed on the study.” 3. “I confirm that I have mentioned all organizations that funded my research in the Acknowledgements section of my submission, including grant numbers where appropriate.” a) This work was funded by the research charity LifeArc, under contractual arrangement with NanoMab. LifeArc funded the research activity carried out by the University of Leicester group. b) LifeArc and NanoMab were actively involved in the study design, data collection and analysis, as well the decision to publish and preparation of the manuscript. c) Kovilen Sawmynaden, Sarah Davies, Richard Brown, David Tang, Maud Henry, David Tickle, David Matthews and Preeti Bakrania received a salary from LifeArc. Nicholas Wong and Hong Hoi Ting received a salary from NanoMab. 4. For the Acknowledgments section: “I confirm that I have mentioned all organizations that funded my research in the Acknowledgements section of my submission, including grant numbers where appropriate.” 5. For the Competing Interests section: “The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: LifeArc provided the antibody humanisation service(s) under contractual arrangement with NanoMab. This does not alter our adherence to PLOS ONE policies on sharing data and materials.” 6. We have amended the authorship list to include David Tickle. 7. We have included a separate caption for each figure directly after the paragraph that first cites that figure, as highlighted in the style requirement. 8. We have included captions for the Supporting Information at the end of the manuscript, as highlighted in the style requirement. 9. We are happy that the reference list is complete and correct. Reviewer 1 We would like to thank the reviewer for their comments. We were pleased to read that the reviewer considered the manuscript technically well-written, although they had they felt that the linguistic style contained complex and jargonistic phrases, and that these should be replaced with more generally comprehensive ones. We agree with this comment and, as such, we have adapted the manuscript accordingly. Along with the changes suggested by the reviewer, we have also rephrased several additional sentences to improve the accessibility of the manuscript. We have also reduced the number of brackets used throughout the manuscript to improve the flow and readability. Reviewer 2 We would like to thank the reviewer for their comments. The reviewer felt that the paper was well written and well presented. We would also like to thank them for making minor suggestions regarding the use of pronouns and tenses. As a result, we have carefully ensured that the report is written in the past tense, and we have also significantly reduced the use of pronouns. In addition to changes made in response to the reviewers’ comments, we have addressed all comments made within the ‘Revised Manuscript with Tracked Changes’ document, as well as correcting additional typographical and grammatical errors identified in the original paper. We hope that the revised paper fully addresses the concerns raised by the two reviewers and is now considered acceptable for publication in PLOS ONE. Yours Sincerely, Gareth Hall Attachments Attachment Submitted filename: Response_to_Reviewers.docx https://doi.org/10.1371/journal.pone.0288259.r002
22 Jun 2023 Decision Letter - Yolandy Lemmer, Editor Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool PONE-D-23-03760R1 Dear Dr. Hall, 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, Yolandy Lemmer Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0288259.r003
Formally Accepted
7 Jul 2023 Acceptance Letter - Yolandy Lemmer, Editor PONE-D-23-03760R1 Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool Dear Dr. Hall: 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. Yolandy Lemmer Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0288259.r004

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