Dear Dr. van der Wijst,

Thank you very much for resubmitting your manuscript "Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board.  We also managed to secure the same two independent reviewers who commented on the previous submission. As you will read, the reviewers and editors were impressed with the extensive revisions you had made to the manuscript and I am happy to say that, based on these reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

One of the reviewers is content with the manuscript as it stands.  The other has raised additional comments, including the suggestion of more experimental work.  It is our view as an editorial board that these additional experiments are not critical for the current manuscript (whilst agreeing with the reviewer that they would undoubtedly add to the story if the data are readily available).  However, we strongly recommend that you include some text modifications to a) integrate the functional assays more with the broader manuscript and b) clarify the interpretation of Figure 3, as suggested. 

We hope that you will not find these revisions too onerous and look forward to receiving 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,

Robin Charles May

Associate Editor

PLOS Pathogens

Scott Filler

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************

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: (No Response)

Reviewer #2: The authors have addressed my comments in full and their study is of general interest to the field and warrants publication in its present form without further revisions.

**********

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: In addressing my previous major concerns, the authors have softened claims about the novelty of the importance of NK cells in candidemia while also providing more evidence for this and have now included promising data validating their claims regarding LY86. In general, the additions and edits to the manuscripts have substantially improved the paper. Most importantly, they show that knockdown of LY86 in THP-1s results in decreased CCR2 expression, causing reduced chemotaxis in response to CCL2 (MCP-1). While these experiments appear carefully done and knockdown and phenotype are robust, they should be connected more to the Candida results in the rest of the paper. Ideally, this would be done by showing migration is decreased in monocytes following stimulation with Candida, and that migration is even lower in AA individuals vs. GG individuals. If such cells are not available for that, I think that at least showing that Candida inhibits migration of THP1s to CCL2 (or citing a reference that does demonstrate that) would be valuable in providing further evidence that your model is correct, possibly revealing a mechanism of Candida immune suppression, and connecting it more to the Candida work in the rest of the paper. Additionally, Tobias Hohl’s lab seems to have provided evidence that your mechanism could be very important in vivo based on Ngo et al 2014, which you cite earlier in your paper, but not for the finding that CCR2-dependent chemotaxis of monocytes is crucial in mouse candidiasis. Again, I think the new RNAi expt is a good addition to the paper. But showing the inhibition of migration by Candida and citing how crucial CCR2+ monocytes are in systemic candidiasis could elevate the importance of your work further.

One other point regarding Figure 3D: The model does not match what is described in the Results. This figure shows a competitive model between LY86 and LY96 for binding of TLR4. It would be helpful to indicate LY86 is also known as MD-1 (and LY96 (MD-2)). More importantly, based on the Results text and a quick perusal of the literature, it would seem that a more likely model involves RP105, which appears to be a divergent TLR with most sequence similarity to TLR4. A model depicting decreased RP105/MD-1 complex signaling being downregulated by Candida, and to a greater extent with the A allele, to decrease CCR2 levels and chemotaxis would seem to be what is supported by their data and the literature.

Reviewer #2: NA

**********

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: (No Response)

Reviewer #2: NA

**********

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, PLOS recommends that you deposit 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. For instructions see http://journals.plos.org/plospathogens/s/submission-guidelines#loc-materials-and-methods

Dear Dr. van der Wijst,

We are pleased to inform you that your manuscript 'Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response' 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 within two working days 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.

Congratulations and best wishes,

Robin May

Associate Editor

PLOS Pathogens

Scott Filler

Section Editor

PLOS Pathogens

Kasturi Haldar

Editor-in-Chief

PLOS Pathogens

​orcid.org/0000-0001-5065-158X

Michael Malim

Editor-in-Chief

PLOS Pathogens

orcid.org/0000-0002-7699-2064

***********************************************************