Protein primary structure correlates with calcium oxalate stone matrix preference

Yu Tian; Matthew Tirrell; Carley Davis; Jeffrey A. Wesson

doi:10.1371/journal.pone.0257515

Peer Review History

Original SubmissionMay 24, 2021
18 Jun 2021 Decision Letter - Sanjay Kumar Singh Patel, Editor PONE-D-21-15604 Protein primary structure correlates with calcium oxalate stone matrix preference PLOS ONE Dear Dr. Wesson, 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. Please submit your revised manuscript by Aug 02 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. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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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: I Don't Know 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: 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: Authors are proposing an interesting hypothesis about the initial steps of the stone formation. They are suggesting that protein-protein interaction precedes protein ions/crystal interaction. Th question is why protein protein interaction is favored over an interaction between say calcium and various calcium binding proteins/lipids. Lipids are considered to play a role in crystal nucleation and may also be in aggregation. Is there a change in urinary profile of stone formers that supports this phenomenon or is it a common occurrence in the urine. If protein contents of the stone formers urine is different from those of normal individuals, what is the source behind such a change. May I suggest that you provide the full names of the proteins, when first used in the text. Reviewer #2: The manuscript entitled “Protein primary structure correlates with calcium oxalate stone matrix preference” by Tian et al tried to examined and compared the amino acid composition in both the most abundant proteins exhibiting preference for stone matrix and the most abundant proteins exhibiting preference for the urine phase. They concluded that protein preference for stone matrix appears to correlate with high total charge content However, this reviewer feels that the manuscript needs some changes. Comments: 1. Did authors find these proteins in non-stone former urine samples? 2. Are these proteins specific to CaOx crystal stones only or they may be included in other stones matrix such as uric acid stones/ cystine stones? 3. What is the origin of these proteins, means diet origin/human origin? 4. What will be the proposed mechanism to control the stone formation and clinical relevance of this study? 5. What is the sequence of stone formation? Do proteins aggregate first followed by disposition of CaOx or vice versa? 6. Is stone formation at other organs also linked with this proposed mechanism? If yes, then include that data too. ****** 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: Yes:** Vinay Kumar [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.0257515.r001
Revision 1
1 Sep 2021 Author Response Specific comments to reviewer’s questions: Reviewer 1: “The question is why protein protein interaction is favored….” I have published several studies over many years focused specifically on characterizing the influence of proteins on calcium oxalate stone formation, and these experiments have supported the hypothesis that proteins likely assert primary influence over aggregation and growth of crystals (summarized in a review article, reference 14, in this manuscript). These studies have shown a 10,000 fold enhancement of inhibitory activities against nucleation, growth and aggregation of calcium oxalate crystal for selected relevant chemicals when comparing polymeric (30 or more residues bound in a chain structure) to monomeric forms of the same chemical, which is a direct justification for focus on the protein components. Proteins are also known to provide the dominant mass fraction to stone matrix, implying greater significance to their role in stone formation. This particular study was focused on identifying the underlying molecular interactions that likely lead to the collection of such a complex mixture of proteins in stone matrix; a mixture that is roughly duplicated by simply adding a strong polycation (polyarginine) to a solution of normal urinary proteins and studying the aggregates formed (reference 16 in this manuscript). “Is there a change in urinary profile of stone formers…?” We have published a comparison the proteomic profiles in urine samples from healthy adults and stone formers (reference 21) finding relatively trivial differences between them, and certainly no evidence for the enrichment in stone former’s urine of either highly charged polyanions or highly charged polycations that we observed at increased abundance in stone matrix (reference 8). No studies have been published to date describing changes in the proteomic profile of urine proteins with time or environmental exposure that might help explain the stone matrix proteomic profile, though my current VA grant is funding research to look at urine proteomic profiles over time in both stone forming and healthy adults. Without an observed difference, we can only speculate on sources for a change in the urine proteome distribution. We have provided the full names of proteins when they are first used in the text. Reviewer 2: 1. The urine proteomic profiles of healthy adults and stone formers are almost completely overlapping/identical, but both urine profiles are different than what we observed in stone matrix (see references 8 and 21). 2. The majority of proteins observed in stone matrix in stones of all types are found in urine, but the relative amounts of individual proteins differ greatly between urine and matrix for calcium oxalate stones, as well as other stone types. Comparable data regarding the relative abundances of individual matrix proteins in other stone types have not been published yet. We do possess such data, and substantial differences can be seen between the stone matrix proteomic profiles observed in other stone types. At present, we cannot explain such differences, though we feel that they are important. We are still preparing this manuscript for publication. 3. Certainly, the proteins in human stones are of human origin, and cat stones contain cat proteins. Many urine proteins are secreted in the tubules, while others are filtered from the blood. Whether any of these proteins are derived from diet sources vs originating from normal physiologic processes within the body is currently unknown (unreported), and there are too many proteins involved in either urine or matrix to reasonably answer this question. 4. It is difficult to define a treatment before the mechanism is understood. Certainly, the presence of a large number of proteins in stone matrix that are normally found in intracellular or nuclear compartments argues for a cell injury process (likely tubular cells) as an originating event. We introduced this speculation in reference 8, but no further studies have been reported by us or others to address this possible mechanism, though hopefully my current VA funded investigation will provide some insight upon completion. 5. This question was addressed in the Discussion in reference 8. Current data cannot distinguish between a surge of highly charged polyanions and highly charged polycations creating protein aggregates which collect crystals vs a slow accumulation of these proteins from urine on existing crystals. The conversion of the very low abundance of the highly charged polyanions and polycations in urine to the observed distribution in stone matrix could be generated by the prolonged growth times of stones (months to years) through selective adsorption to crystal surfaces. A new experiment must be designed to test this question. 6. While I suspect that it is possible that pathological crystallization processes in other parts of the body may share protein characteristics with kidney stones, I am not aware of the appropriate protein data being available for crystal deposits in other organs to facilitate such a comparison. I would like to publish the peer review process, since many questions have been posed and answered in the response to reviewers that may not fit in this manuscript specifically, but readers may find the discussions illuminating. Attachments Attachment Submitted filename: Rebuttal letter July 2021.docx https://doi.org/10.1371/journal.pone.0257515.r002
3 Sep 2021 Decision Letter - Sanjay Kumar Singh Patel, Editor Protein primary structure correlates with calcium oxalate stone matrix preference PONE-D-21-15604R1 Dear Dr. Wesson, 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, Sanjay Kumar Singh Patel, Ph.D. Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0257515.r003
Formally Accepted
15 Sep 2021 Acceptance Letter - Sanjay Kumar Singh Patel, Editor PONE-D-21-15604R1 Protein primary structure correlates with calcium oxalate stone matrix preference Dear Dr. Wesson: 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. Sanjay Kumar Singh Patel Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0257515.r004

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