https://orcid.org/0000-0002-5863-6250
Peer Review History
| Original SubmissionFebruary 1, 2022 |
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Dear Dr. Svensson, Thank you very much for submitting your manuscript "T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations. This may include additional experiments, as suggested by the 2nd reviewer, to ensure that the PLA method is appropriately controlled. Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. When you are ready to resubmit, please upload the following: [1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out [2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file). Important additional instructions are given below your reviewer comments. Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments. Sincerely, Susan R. Ross, PhD Section Editor PLOS Pathogens Susan Ross Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************** Reviewer Comments (if any, and for reference): Reviewer's Responses to Questions Part I - Summary Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship. Reviewer #1: This study presents a new approach to understanding molecular events at the HIV LTR during reactivation of latent proviruses. The revised study addresses most of the concerns raised in the initial review. Reviewer #2: The authors have developed a J-Lat based cell system to use as a model for latency reversal. Their idea that Tat-ZFP3 PLA technique can selectively identify productive, Tat-dependent HIV-1 activation among non-physiological Tat independent activation is intriguing. However, their idea is not supported with experimental evidence – they use GFP accumulation as a control, but observe quiet significant discrepancies between Tat-ZFP3 and GFP. ********** Part II – Major Issues: Key Experiments Required for Acceptance Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions. Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject". Reviewer #1: see above Reviewer #2: The question about the specificity of the method has already been raised previously, and there (point 18 reviewer 1) the authors argued that the GFP expression occurs at different (later) time point with respect to Tat binding. This is indeed plausible, as shown also in Figure 3E, lines 257-259. However, while the levels of GFP continue to increase, Tat-ZFP3 PLA signals peak at 18hrs and then show a sharp drop. Therefore the authors opt for 16 hrs but the discrepancies remain, with their explanation being that the discrepancy between Tat-ZFP3 and GFP can be due to two mechanisms: -transient association of Tat with the TAR early in latency reversal followed by GFP accumulation -Tat-independent mechanisms leading to GFP expression This is a problem, because this leaves the authors with no appropriate controls for the PLA assay. The best way to control Tat induced transcriptional activity of the LTR promoter is to actually measure HIV-1 transcription by RT-PCR using different primers, for short (abortive) transcripts as well as long ones. The other way to control their experiments if to measure the number of viral particles, as the 1C10 cell produce and bud off non-infectious viral particles after activations (lines 266-267). Other minor points are listed bellow: • The discrepancy between the microscopy and flow cytometry data (rows 175-177 of the Msc,) could be interpreted as sensitivity of the microscope based detection, but unlikely are due to compromised cellular viability, simply because dead cells will not adhere to the slides. As these are Jurkat cells, which need to be adhered to slides, dead cells will simply not attach to slides. • It is clear already from data in Figure 1 (Figure 1E) and then later from Figure 3A and 3B that there are significant differences between Tat-ZFP3 PLA results and expression of GFP in the same cells. From the results presented in Figure 3, where different LRAs were used, it seems that GPF detection scores higher for the detection capacity of HIV-1 activation. Number of GFP + cells in PMA/i is almost 30% whereas there are less than 6% of PLATatZFP3+ cells. Also, when LRA activity was compared, it seems that the all the LRAs give some background PLA signal, while the number of real positive cells is low. Differences between LRAs are much better appreciated with GPF as a readout. How were these signals normalized? The authors need to add HIV-1 mRNA levels as a readout. They can also specifically measure the GPF signal as mRNA level • Chromatin signatures of the PLA positive cells remain very puzzling. Considering the fact that in PLA + cells GFP intensity increase upon PMAi induction concurrently with all histone marks , both activating ie K27ac and K4me3, as well as repressing, K27me3 and K9me3 is further complicating the interpretation of these data. ********** Part III – Minor Issues: Editorial and Data Presentation Modifications Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. Reviewer #1: none Reviewer #2: (No Response) ********** 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 Figure 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. 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. Data Requirements: Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5. Reproducibility: To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols References: 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. |
| Revision 1 |
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Dear Dr. Svensson, We are pleased to inform you that your manuscript 'T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin' has been provisionally accepted for publication in PLOS Pathogens. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests. Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated. IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript. Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Susan R. Ross, PhD Section Editor PLOS Pathogens Susan Ross Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************************************************** Reviewer Comments (if any, and for reference): |
| Formally Accepted |
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Dear Dr. Svensson, We are delighted to inform you that your manuscript, "T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin," has been formally accepted for publication in PLOS Pathogens. We have now passed your article onto the PLOS Production Department who will complete the rest of the pre-publication process. All authors will receive a confirmation email upon publication. The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any scientific or type-setting errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript. Note: Proofs for Front Matter articles (Pearls, Reviews, Opinions, etc...) are generated on a different schedule and may not be made available as quickly. Soon after your final files are uploaded, the early version of your manuscript, if you opted to have an early version of your article, will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers. Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens |
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