Dear Professor Weiss,

Thank you very much for submitting your manuscript "Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the 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.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. 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,

Philip K Maini

Academic Editor

PLOS Computational Biology

Jason Haugh

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: This manuscript tackles a problem of current interest in mathematical modelling of angiogenesis, namely, how the growth of the vessel sprouts couples to the mechanics of the ECM. It is well known that such feedback (i.e. how the orientation of the fibers within the ECM guides the migration of ECs and the growth of the vessels, and how the vessels deform, realign and remodel the ECM) is crucial to understand the mechanisms of angiogenesis.

The authors present a methodology that allows them to quantify the anisotropy of the orientation distribution functions of the fibrils within the ECM. To do so they introduce the so-called ellipsoid fibril distribution (EDF) and an associated Monte-Carlo sampling method. The authors claim that this methodology allows them to improve the results obtained by means of previous approaches which introduced a vector field accounting for the average local orientation, since the latter does not contain enough information about the actual distribution of orientations.

While this is an interesting approach and the results look promising, the manuscript in its current form cannot be published and major revisions regarding the presentation of their model are required.

The major concern involves the description of the model for angiogenesis. While the description of how rate the growth is influenced by both concentration of collagen and fibril orientation seems adequate, information about how the fibril orientation feeds into the model of angiogenesis is lacking. In line 477, the authors mention that "The direction a tip grows depends on a combination of persistence (prior tip direction) and fibril orientation". This needs to be further explained and substantiated, specifically regarding the EFD description and the Monte-Carlo sampling by giving the corresponding formulae (as it has been done for the rate of growth in Eq. 11). I suggest that the authors write a section on model formulation which clearly states which compartments are considered in the model, how each of this compartments is actually modelled, and, more importantly, how the different compartments are coupled and integrated within the whole model. Without the information the accuracy/validity of claims such as "These differences arose due to the dependence of the growth rate on the local anisotropy; as neovessels grew up the positive gradient, the potency of matrix growth and guidance cues increased" (lines 263 to 265) cannot be assessed.

Another issue that should be taken into account is that the concept of the "orientation distribution function" is very informally defined. While the level of information provided is probably fine for a journal with a more specialised readership, a more detailed introduction to this concept should make the paper more accessible to a more general readership

Other issues that need clarification are:

1.- The acronym "SPD" does not seem to be defined

2.- Lines 214 to 216: "As a result, these simulations were

able to accurately predict anisotropic guidance in agreement with prior experimental measures. In

contrast, simulations using the vector field approach under-predicted anisotropic guidance." What is the significance of this "under-prediction"? For example, could the simpler model reproduce some of the features in Figs. 4b and 4c?

Reviewer #2: Uploaded as an attachment

Reviewer #3: I am sorry for this very short review due to time constraints. This an elegant approach to model the effect of ECM anisotropy on angiogenesis.

I have two questions/remarks:

- I am sorry if I missed it, but it seems that in this version there is only a one-way feedback of the matrix orientations on endothelial cell migration. Then external strains can lead to ECM remodeling. However, traction on the matrix by migrating endothelial cells would also remodel the matrix. Is this part of the model already, or could the authors comment on how this can be incorporated in the model in the future?

- At present it seems there is only qualitative comparison between models and experiment. Could a more quantitative comparison be provided? Also how does matrix orientation affect cell migration velocity in vitro and in silico?

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: None

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: 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 in PLOS Biology 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

Attachments

Attachment

Submitted filename: comments.pdf

Dear Professor Weiss,

Thank you very much for submitting your manuscript "Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis" for consideration at PLOS Computational Biology. 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.

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,

Philip K Maini

Academic Editor

PLOS Computational Biology

Jason Haugh

Section Editor

PLOS Computational Biology

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

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The authors have made a thorough revision of the paper in response to the reviewers comments

Reviewer #2: The review is uploaded as an attachment.

Reviewer #3: The authors have answered comment #2 on the quantitative comparison between model and experiment satisfactorily.

Regarding my comment #1 on the feedback between vessel tip traction and ECM reorientation, we get little insight as to what extent this aspect of the model affects the results. To what extent does it matter (in the model and also in the real system) that there is a cross-talk between vessel tip traction and ECM reorientation? In its present form the study seems to focus entirely on the effect of ECM structure on cell migration/angiogenesis. This is fine, but this limitation of the study should be clarified.

I would therefore recommend that the authors either:

(a) Include a new figure comparing the behavior of the model with and without vessel tip traction to give more insight into the extent that this important feature affects the model predictions;

or (b) Clarify the limitation of the study: i.e. discuss how it currently studies the effect of ECM structure on angiogenesis, and how it could be extended to get more insights in the two-way cross-talk between endothelial cells (ECs) and ECMs, and/or discuss if and why the effect of ECM structure on EC migration (one-way) is the most important.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: None

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #3: 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 in PLOS Biology 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:

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.

Attachments

Attachment

Submitted filename: comments.pdf

Dear Professor Weiss,

We are pleased to inform you that your manuscript 'Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis' has been provisionally accepted for publication in PLOS Computational Biology.

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 Computational Biology. 

Best regards,

Philip K Maini

Academic Editor

PLOS Computational Biology

Jason Haugh

Section Editor

PLOS Computational Biology

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

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #2: The authors have responded to my comments

Reviewer #3: The authors have satisfactorily addressed all my comments. I appreciate the insightful new analysis the feedback between vessel tip traction and ECM reorientation. Thank you. Great paper!

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

Reviewer #3: None

**********

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 #2: No

Reviewer #3: Yes: Roeland Merks