Identification of biomarkers associated with inflammatory response in Parkinson’s disease by bioinformatics and machine learning

Yatan Li; Wei Jia; Chen Chen; Cheng Chen; Jinchao Chen; Xinling Yang; Pei Liu

doi:10.1371/journal.pone.0320257

Peer Review History

Original SubmissionJune 5, 2024
5 Jun 2024 Author Response https://doi.org/10.1371/journal.pone.0320257.r001
8 Dec 2024 Decision Letter - Naseem Ahamad, Editor PONE-D-24-22439Identification of biomarkers associated with inflammatory response in Parkinson's disease by bioinformatics and machine learningPLOS ONE Dear Dr. Liu, 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 Jan 22 2025 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. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Naseem Ahamad Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. 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. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 3. Thank you for stating the following financial disclosure: [Project about Parkinson's disease peripheral neuropathy drug intervention fusion research innovation team (Item Number: 2023D14006).]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in 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: [Project about Parkinson's disease peripheral neuropathy drug intervention fusion research innovation team (Item Number: 2023D14006).] We note that you have provided funding information that is not currently declared in your Funding Statement. However, 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: [Project about Parkinson's disease peripheral neuropathy drug intervention fusion research innovation team (Item Number: 2023D14006).] Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. We note that your Data Availability Statement is currently as follows: [All relevant data are within the manuscript and its Supporting Information files.] Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition). For example, authors should submit the following data: - The values behind the means, standard deviations and other measures reported; - The values used to build graphs; - The points extracted from images for analysis. Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories. If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access. 6. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. 7. 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. [Note: HTML markup is below. Please do not edit.] 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: 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: The manuscript presents a promising approach to identifying biomarkers for Parkinson's Disease (PD) using bioinformatics and machine learning. The authors leverage gene expression data from the GEO database to find differentially expressed genes (DEGs) associated with the inflammatory response in PD. They then employ machine learning to identify candidate biomarker genes for further validation. Additionally, the use of single-cell transcriptomic analysis to explore candidate gene expression in different cell types strengthens the rationale. However, a few key areas require further clarification and improvement. Specific Comments: 1. Figure Quality: The quality of the figures needs significant improvement. The current resolution makes it difficult to evaluate the data and its relationship to the presented results. Ensure figures are clear, well-labeled, and have sufficient resolution for publication. 2. Validation Analysis: The evaluation using the mRNA-miRNA network and drug sensitivity analysis requires a more elaborate discussion of the results. This includes: A detailed explanation of the findings related to observed negative correlation with drugs. How negative correlation can help in finding the drug to putative drug targets. Clarification on the rationale for considering weak correlations (Cor < 0.5) as validating evidence for drug sensitivity. Discuss about relationship between the mRNA-miRNA network and putative pathways, whether the 17 miRNAs link to the discussed pathways. 3. Single-Cell Transcriptomic Analysis: The discussion of the single-cell transcriptomic data needs further elaboration on the following aspects: � Specificity of expression of the candidate biomarker genes across different cell types. � Differential expression patterns observed in specific cell populations like neurons or glial cells. � Potential drug targets identified through drug sensitivity analysis that could be effective for these cell types. By addressing these concerns, the authors can strengthen the manuscript and enhance its clarity and impact. Reviewer #2: Reviewer Comments No. Author submission Changes needed 1 Introduction: PD has a set of well-defined features, such as bradykinesia with resting tremor, as well as nonmotor symptoms including autonomic dysfunction, incontinence, and cognitive impairme[4]. Changes need in Impairment 2 Fig 1. is not clear Image need in Higher definition 3 Provided all images in low definition, looks blurred Change into High definition with resolution more than 300dpi, follow the author instruction for preparing the Figures 4 All images provided without figure legends Provide legends on the top or bottom of the Figures 5 The author not followed the author instructions No line numbers mentioned. Use continuous line numbers 6 The author not followed reference style of the journal Follow the author instructions and reformat the references 7 Finally, the three biomarkers were found to be closely associated with excitatory neurons and microglia in single-cell transcriptomic analysis. In conclusion, IL18R1, NMUR1 and RELA could be potential therapeutic targets for PD in inflammatory response and new biomarkers for PD diagnosis. if possible show the drug target or biomarker interactions. Also show how the new biomarkers reacts with genes and show the response on inflammation. ******* 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: PK Reviewer #2: Yes: Kannan Kanthaiah ******** [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: PlosOne_PD biomarker.docx Attachment Submitted filename: Reviewer Comments.docx https://doi.org/10.1371/journal.pone.0320257.r002
Revision 1
20 Dec 2024 Author Response Reviewer #1: 1.Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1:yes Response-1:Thank you very much for recognizing our research. 2.Has the statistical analysis been performed appropriately and rigorously? Reviewer #1:yes Response-2:Thank you very much for recognizing our research. 3.Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #1:yes Response-3:Thank you very much for recognizing our research. 4.Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #1:yes Response-4:Thank you very much for recognizing our research. 5.The quality of the figures needs significant improvement. The current resolution makes it difficult to evaluate the data and its relationship to the presented results. Ensure figures are clear, well-labeled, and have sufficient resolution for publication. Response-5:Thank you for your valuable comments. We attach great importance to the quality of the graphs and have re-exported the images in tif format at dpi=300 resolution as per the requirements of the journal. 6.Validation Analysis: The evaluation using the mRNA-miRNA network and drug sensitivity analysis requires a more elaborate discussion of the results. This includes: (1)A detailed explanation of the findings related to observed negative correlation with drugs. How negative correlation can help in finding the drug to putative drug targets. (2)Clarification on the rationale for considering weak correlations (Cor < 0.5) as validating evidence for drug sensitivity. (3)Discuss about relationship between the mRNA-miRNA network and putative pathways, whether the 17 miRNAs link to the discussed pathways. Response-6: Thank you for your valuable comments. Below is a detailed response to the above questions. In addition, we have added detailed descriptions to the manuscript in the appropriate places. (1) Negative correlation helps to find potential drug targets of the drugs. The results showed that IL18R1 was negatively correlated with the drug BP-1-102 (Cor = -0.36, P = 0.004).RELA was negatively correlated with the drugs ARRY-162 (Cor = -0.37, P = 0.004) and Tamoxifen (Cor = -0.3, P = 0.018). A negative correlation means that when the expression level of the gene increases, the effect of the drug tends to diminish. Xu, F., et al. [1] found a negative correlation between camptothecin drugs and SLC1A5 expression in a drug sensitivity analysis of SLC1A5 expression with classical chemotherapeutic drugs. (2) As this study is in the pre-exploratory stage, these weak correlations are still informative and may reveal potentially complex biological mechanisms. In addition, the relationship between genes and drug responses is usually nonlinear, so a single weak correlation does not imply a lack of biological significance. For example, Song, D., et al [2], in exploring the sensitivity of small molecule drugs associated with NRAV expression, found that the drug Sapitinib, which is weakly associated with NRAV expression, induced apoptosis and inhibited phosphorylated epidermal growth factor receptor and its downstream pathway. (3) miRNAs are associated with the pathways discussed. In our study, we mainly focused on mRNA biomarkers, so the pathway analysis was performed based on mRNAs. Based on this, we mainly explored the relationship between mRNAs and their associated pathways and mined potential miRNA associations through mRNAs. However, based on your suggestion, we further explored the role of miRNA target genes in the relevant pathways (S1 Fig.tif). Through KEGG and GO analysis of miRNA target genes, we found that the pathways of miRNA target genes overlapped with the pathways we identified at the mRNA level, specifically the virus process and ECM-receptor interaction pathways. These pathways, although significant (P<0.05), were ranked low and therefore did not appear in the pathway heatmap for mRNAs. This result further supports the possible interaction of mRNA-miRNA networks in relevant biological processes. S1 Fig KEGG and GO analysis of miRNA target genes 7. Single-Cell Transcriptomic Analysis: The discussion of the single-cell transcriptomic data needs further elaboration on the following aspects: (1)Specificity of expression of the candidate biomarker genes across different cell types. (2)Differential expression patterns observed in specific cell populations like neurons or glial cells. (3)Potential drug targets identified through drug sensitivity analysis that could be effective for these cell types. By addressing these concerns, the authors can strengthen the manuscript and enhance its clarity and impact. Response-7: Thank you for your valuable comments. Below is a detailed description for the specific expression of IL18R1, NMUR1 and RELA in different cell types. In addition, we have also added a detailed description in the discussion section of Chapter 4 of the manuscript. (1) IL18R1 is specifically expressed in T cells and Endothelial cells. It suggests that IL18R1 may play an important role in the immune response, especially in T cells. T cells are key cells of the immune system and are involved in recognizing and attacking infected or tumor cells[3]. Whereas IL18R1 is a subunit of the IL-18 receptor, IL-18 is a pro-inflammatory cytokine that is commonly associated with immune response and inflammation[4]. The specific expression of IL18R1 in T cells may be related to its role in the immune response[5]. RELA is expressed in almost all cell populations.RELA is part of the NF-κB family, and NF-κB plays an important role in many biological processes, including immune response, inflammatory response, cell survival and proliferation[6]. The expression of RELA in virtually all cell populations suggests that it is a fundamental and broadly regulated factor that may maintain essential functions and responsiveness in the physiological state of the cell, especially in response to inflammation, infection, or cellular damage[7]. NMUR1 is specifically expressed in T cells.NMUR1 is usually associated with neuropeptide signaling, which may influence the immune response by regulating T cell activation, proliferation, or function[8]. (2) In single-cell transcriptome analysis, IL18R1 and NMUR1 were found to have a small amount of expression in excitatory neurons (ExN), inhibitory neurons (InN) cells, but more often found to have a high specific expression in T cells and Endothelial cells. While RELA has high expression in excitatory neurons (ExN), inhibitory neurons (InN) cells. (3) Thank you very much for your valuable questions. Our study focuses on screening biomarker genes by transcriptomics and verifying the specific expression of these markers in different cell types using single-cell transcriptomics, aiming to reveal their distribution and expression characteristics at the cellular level. Regarding drug sensitivity analysis, we have indeed performed preliminary correlation analysis at the level of transcriptomics data to identify potential drug targets. However, drug sensitivity analysis was not carried out on single-cell transcriptomics data as the main goal of this study was to validate the specific expression of the marker genes in different cell types rather than to explore the direct effects of the drugs on these cell types. However, in the future we will focus on drug sensitivity analysis on single-cell transcriptomics data. Reviewer #2: 1.Is the manuscript technically sound, and do the data support the conclusions? Reviewer #2:yes Response-1: Thank you very much for recognizing our research. 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2:yes Response-2: Thank you very much for recognizing our research. 3.Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #2:yes Response-3: Thank you very much for recognizing our research. 4.Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #2:yes Response-4: Thank you very much for recognizing our research. 5.Introduction: PD has a set of well-defined features, such as bradykinesia with resting tremor, as well as nonmotor symptoms including autonomic dysfunction, incontinence, and cognitive impairme Changes need in Impairment Response-5: Thank you for your valuable comments. We have amended the paragraph. 6.Fig 1. is not clear Image need in Higher definition Response-6: Thank you for your valuable comments. We attach great importance to the quality of the graphs and have re-exported the images in tif format at dpi=300 resolution as per the requirements of the journal. And uploaded separately in the system. 7.Provided all images in low definition, looks blurred Change into High definition with resolution more than 300dpi, follow the author instruction for preparing the Figures Response-7: Thank you for your valuable comments. We have re-exported the image to a resolution of 300 dpi as required by the journal and set the image format to tif and uploaded it separately in the system. 8.All images provided without figure legends Provide legends on the top or bottom of the Figures Response-8: Thank you for your valuable comments. We have provided legends to the right or left of the images, for example, in Figure 2A, Parkinson's patients are abbreviated as PD and the corresponding legend is in blue. Except for that, images were uploaded individually as required by the journal. Figure captions for each figure are placed in the body of the manuscript. 9.The author not followed the author instructions No line numbers mentioned. Use continuous line numbers Response-9: Thank you for your valuable comments. We have added line numbers and page numbers to the manuscript as required by the journal manuscript format. 10.The author not followed reference style of the journal Follow the author instructions and reformat the references Response-10: Thank you for your comments. We have updated the reference format and changed it to the “Vancouver” style required by the journal. 11.Finally, the three biomarkers were found to be closely associated with excitatory neurons and microglia in single-cell transcriptomic analysis. In conclusion, IL18R1, NMUR1 and RELA could be potential therapeutic targets for PD in inflammatory response and new biomarkers for PD diagnosis. if possible show the drug target or biomarker interactions. Also show how the new biomarkers reacts with genes and show the response on inflammation. Response-11: Thank you for your valuable comments. Below is a detailed response to your questions. (1) Biomarker interactions: we have mapped the correlation heatmap of differentially expressed genes for inflammatory response in Section 3.1 of the article, which includes the correlation of the biomarkers screened, IL18R1, NMUR1 and RELA. (2) Since our focus is on exploring the interactions between biomarkers and drugs, the analysis of drug-drug interactions is not addressed. In Section 3.7, the interpretation of interactions between drug targets and biomarkers is carried out. The sensitivities of three biomarkers, IL18R1, NMUR1 and RELA, corresponding to different drugs were detailed, where IL18R1 was positively associated with the Alisertib (Cor = 0.31, P = 0.016), Azacitidine (Cor = 0.33, P = 0.01) and Motesanib (Cor = 0.35, P = 0.007) drugs, IL18R1 was positively correlated with BP-1-102 (Cor = -0.36, P = 0.004) drug, NMUR1 was positively correlated with Lexibulin (Cor = 0.31, P = 0.017) and norvir (Cor = 0.48, P < 0.001) drugs, and RELA was positively correlated with CAMPTOTHECIN (Cor = 0.32, P = 0.012) and Clofarbine (Cor = 0.3, P = 0.019) drugs, and RELA was positively correlated with ARRY-162 (Cor = -0.37, P = 0.004) and Tamoxifen (Cor = -0.3, P = 0.018) and 7 other drugs were negatively correlated. (3) Biomarkers associated with inflammatory response Explanation: a. The experiments were first performed by searching for candidate genes that might serve as biomarkers among the genes associated with the inflammatory response. b. These biomarkers were found to be associated with the differential expression of Mast cells and Neutrophils cells by immune cell infiltration analysis. c. The biomarkers were found to be associated with the differential expression of Mast cells and Neutrophils cells by the immune cell infiltration analysis. Mast cells and Neutrophils cells are key cells involved in immune responses and inflammatory processes[9, 10]. Therefore, the differential expression of markers with them may imply that these markers play a role in regulating the inflammatory response. References 1. Xu, F., H. Wang, H. Pei, Z. Zhang, L. Liu, L. Tang, S. Wang, and B.-C. Ren, SLC1A5 prefers to play as an accomplice rather than an opponent in pancreatic adenocarcinoma. Frontiers in Cell and Developmental Biology, 2022. 10: p. 800925. 2. Song, D., X. Wang, Y. Wang, W. Liang, J. Luo, J. Zheng, and K. Zhu, Integrated analysis of N1-methyladenosine methylation regulators-related lncRNAs in hepatocellular carcinoma. Cancers, 2023. 15(6): p. 1800. 3. Ruf, B., T.F. Greten, and F. Korangy, Innate lymphoid cells and innate-like T cells in cancer—at the crossroads of innate and adaptive immunity. Nature Reviews Cancer, 2023. 23(6): p. 351-371. 4. Di, Y., Z. Wang, J. Xiao, X. Zhang, L. Ye, X. Wen, J. Qin, L. Lu, X. Wang, and W. He, ACSL6-activated IL-18R1–NF-κB promotes IL-18–mediated tumor immune evasion and tumor progression. Science Advances, 2024. 10(38): p. eadp0719. 5. Lutz, V., V.M. Hellmund, F.S. Picard, H. Raifer, T. Ruckenbrod, M. Klein, T. Bopp, R. Savai, P. Duewell, and C.U. Keber, IL18 receptor signaling regulates tumor-reactive CD8+ T-cell exhaustion via activation of the IL2/STAT5/mTOR pathway in a pancreatic cancer model. Cancer immunology research, 2023. 11(4): p. 421-434. 6. Guo, Q., Y. Jin, X. Chen, X. Ye, X. Shen, M. Lin, C. Zeng, T. Zhou, and J. Zhang, NF-κB in biology and targeted therapy: new insights and translational implications. Signal Transduction and Targeted Therapy, 2024. 9(1): p. 53. 7. Khan, A., Y. Zhang, N. Ma, J. Shi, and Y. Hou, NF-κB role on tumor proliferation, migration, invasion and immune escape. Cancer Gene Therapy, 2024: p. 1-12. 8. Ye, Y., Z. Liang, and L. Xue, Neuromedin U: potential roles in immunity and inflammation. Immunology, 2021. 162(1): p. 17-29. 9. Mencarelli, A., P. Bist, H.W. Choi, H.J. Khameneh, A. Mortellaro, and S.N. Abraham, Anaphylactic degranulation by mast cells requires the mobilization of inflammasome components. Nature Immunology, 2024. 25(4): p. 693-702. 10. Mihlan, M., S. Wissmann, A. Gavrilov, L. Kaltenbach, M. Britz, K. Franke, B. Hummel, A. Imle, R. Suzuki, and M. Stecher, Neutrophil trapping and nexocytosis, mast cell-mediated processes for inflammatory signal relay. Cell, 2024. 187(19): p. 5316-5335. e28. Attachments Attachment Submitted filename: Response to Reviewers.docx* https://doi.org/10.1371/journal.pone.0320257.r003
28 Jan 2025 Decision Letter - Naseem Ahamad, Editor <div>PONE-D-24-22439R1Identification of biomarkers associated with inflammatory response in Parkinson's disease by bioinformatics and machine learningPLOS ONE Dear Dr. Liu, 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 Mar 14 2025 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. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Naseem Ahamad Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. 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 ****** 5. 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 ****** 6. 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 am pleased with the justifications and improvements made to the manuscript. However, I have noticed that some of the provided justifications have not been incorporated into the manuscript text. I recommend updating the discussion section to reflect these justifications for greater clarity and alignment with the revisions. Reviewer #2: Even though the author answered all the questions raised by the reviewer, still the paper is at its best. Again, the author given All the images in lo w resolution. Kindly provide with high definition as mentioned in Author instruction. ****** 7. 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: Prince Kumar Reviewer #2: Yes: Kannan ******** [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: Untitled 1.docx https://doi.org/10.1371/journal.pone.0320257.r004
Revision 2
31 Jan 2025 Author Response Reviewer #1: 1. I am pleased with the justifications and improvements made to the manuscript. However, I have noticed that some of the provided justifications have not been incorporated into the manuscript text. I recommend updating the discussion section to reflect these justifications for greater clarity and alignment with the revisions. Response-1: Thank you so much for your positive feedback and valuable suggestions on our manuscript. We have updated Chapter 4 (Discussion) and Chapter 5 (Conclusion) of the manuscript to ensure that all the explanations we provided in our responses are fully integrated into the main text. Additionally, in response to your question, "Discuss the relationship between the mRNA-miRNA network and the putative pathways, and whether the 17 miRNAs are related to the discussed pathways," we have provided a detailed description in Section 3.8. Reviewer #2: 1.Again, the author given All the images in lo w resolution. Kindly provide with high definition as mentioned in Author instruction. Response-1: Thank you for your attention to the issue of image resolution. We have uploaded the images in TIF format with a resolution of 300 dpi, as required by the journal. However, we have noticed that the submission system compresses the images when generating the PDF, which results in a reduction of image clarity. This compression is an automatic process that we cannot control. We assure you that the original images we uploaded meet the journal’s high-resolution requirements. You can download the original images separately through the submission system, or you can click on the links to the original images within the PDF to view them in high resolution. Attachments Attachment Submitted filename: Response_to_Reviewers_auresp_2.docx https://doi.org/10.1371/journal.pone.0320257.r005
16 Feb 2025 Decision Letter - Naseem Ahamad, Editor Identification of biomarkers associated with inflammatory response in Parkinson's disease by bioinformatics and machine learning PONE-D-24-22439R2 Dear Dr. Liu, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Naseem Ahamad Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. 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 ****** 5. 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 ****** 6. 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: (No Response) Reviewer #2: The author address all the required comment given by me hence I recommend the article to accept. Kindly go with the decision of other reviewer also. ****** 7. 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: Prince Kumar Reviewer #2: Yes: Kannan Kanthaiah ******** Attachments Attachment Submitted filename: CommentsR2.docx https://doi.org/10.1371/journal.pone.0320257.r006
Formally Accepted
Acceptance Letter - Naseem Ahamad, Editor PONE-D-24-22439R2 PLOS ONE Dear Dr. Liu, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Naseem Ahamad Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0320257.r007

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .