Peer Review History
| Original SubmissionJuly 22, 2025 |
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Integrated Multi-omics Analysis Reveals Necroptosis-Related Biomarker BIRC3 for Early Diagnosis and Therapeutic Targeting in Preeclampsia PLOS ONE Dear Dr. Shi, 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 Nov 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:
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Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: No Reviewer #2: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ********** Reviewer #1: The authors investigate the role of necroptosis in preeclampsia (PE) by integrating bulk transcriptomics (GSE66273), necroptosis-related gene mapping, functional enrichment, immune-cell deconvolution (ssGSEA/xCell), single-cell analysis (GSE173193), PPI/network inference with machine-learning prioritization, and exploratory drug prediction with molecular docking, culminating in the nomination of BIRC3 as a putative diagnostic biomarker and mechanistic node. The topic is clinically relevant, the workflow is clearly laid out, and the figures are generally intelligible. That said, several issues limit scientific robustness and reproducibility, including the very small discovery cohort, limited statistical stringency (e.g., multiple-testing control), lack of external/orthogonal validation (at protein or functional levels), heavy reliance on database-predicted interactions, and overinterpretation of in silico docking. My detailed, section-by-section comments below focus on methodological transparency, statistical rigor, and the extent to which conclusions are supported by the presented data, in keeping with PLOS ONE’s criteria for scientific soundness. The introduction provides a clear overview of preeclampsia and appropriately emphasizes its clinical significance. The description of molecular mechanisms such as oxidative stress, apoptosis, and necroptosis is informative and leads the reader toward the study’s objectives. However, the research gap is only broadly stated (“necroptosis in PE is rarely reported”) without sufficient critical appraisal of prior work. The transition to bioinformatics is abrupt and requires stronger justification, and the final paragraph enumerates methodological steps rather than presenting a concise research question or hypothesis. In addition, the introduction does not sufficiently align with the studies later cited in the discussion, creating a citation gap. Overall, the section would benefit from a more focused articulation of the novelty, an updated review of the literature, and clearer framing of the study’s hypotheses. the criterion for defining DEGs is based solely on p<0.05 without mention of multiple testing correction, raising the risk of false positives. Details of preprocessing steps (quality control, probe annotation, and batch effect adjustment) are insufficient. The selection of necroptosis-related genes from GeneCards is not adequately defined, as this database aggregates heterogeneous evidence and requires clear filtering criteria. Finally, while the authors correctly note that public datasets do not require new ethics approval, it would be appropriate to clarify that the original dataset had obtained ethical clearance. The scRNA-seq workflow is incompletely described; critical quality control criteria (e.g., mitochondrial content, number of detected cells, and justification for principal component selection) are missing, and annotation methods lack validation. Immune infiltration analysis with xCell may be limited in accuracy for placental tissues, and no sensitivity analyses are described. For the PPI network, the confidence score threshold for STRING interactions is unspecified, and hub gene identification relies solely on network topology without independent validation. ROC curves were generated only within the discovery dataset without external validation, raising overfitting concerns and limiting clinical generalizability. The TF–mRNA, miRNA–mRNA, and RBP–mRNA networks were constructed purely from prediction databases, with no reported filtering criteria, confidence thresholds, or experimental validation, making their biological significance uncertain. Similarly, the drug prediction based on DGIdb is exploratory and lacks pharmacological plausibility or validation. The docking analysis is described superficially, with incomplete reporting of grid parameters, scoring criteria, and validation steps, and it focuses on a single target-ligand pair, which provides only preliminary and hypothetical insights. Functional enrichment based on only six genes is inherently unstable and should be interpreted cautiously. The workflow to define hub genes is complex but insufficiently detailed, raising concerns about reproducibility. Moreover, the random forest analysis on such a small dataset risks overfitting, and the ROC result (AUC = 0.933) appears overly optimistic given the lack of independent validation. The Discussion narrative around macrophage imbalance (M1/M2), Hofbauer cells, and immune microenvironment remodeling is convincing and clinically relevant. Additionally, the authors appropriately acknowledge the translational potential of natural compounds identified by docking, while also noting the need for further validation. Despite these strengths, several weaknesses remain: The claim that this is the “first comprehensive multi-omics study” linking necroptosis to PE is ambitious and should be moderated, as there are emerging studies on regulated cell death pathways in PE. A more nuanced positioning would strengthen credibility. The reported AUC of 0.933 for BIRC3 as a diagnostic marker is very high, but it derives from a small dataset without independent validation. This limitation should be emphasized more strongly to avoid overstating clinical applicability. Although limitations are briefly acknowledged at the end, they are underdeveloped. Key issues such as small sample size, lack of external datasets, absence of protein-level validation, and potential biases from database-driven predictions deserve fuller elaboration. Reviewer #2: This is an ambitious and well-written study integrating bulk transcriptomics, single-cell RNA-seq, immune infiltration analysis, and molecular docking to identify BIRC3 as a necroptosis-related biomarker and potential therapeutic target in preeclampsia. The topic is novel and relevant, as necroptosis is underexplored in PE pathogenesis. However, there are significant concerns about dataset size, methodological clarity, and overinterpretation of in silico findings without experimental validation. 1. The bulk transcriptomic dataset (GSE66273) includes only 6 PE vs. 5 controls, which substantially limits statistical robustness. This limitation should be acknowledged more explicitly in the Discussion. The generalizability of findings should be presented cautiously. Validation in larger independent cohorts (if available) is strongly recommended, or at least a justification for using this dataset should be provided. 2. Necroptosis-related genes were sourced from GeneCards, which aggregates heterogeneous evidence and may include weak associations. A curated pathway reference (e.g., KEGG Necroptosis pathway, Reactome, or literature-defined necroptosis gene lists) would provide stronger rigor. Please justify the choice of GeneCards and consider cross-validating with a curated set. 3. The reported AUC = 0.933 for BIRC3 is based on a very small cohort (n=11). Such results are prone to overfitting and may not reflect true predictive value. The claim of “exceptional diagnostic potential” should be tempered and described as preliminary until validated in independent cohorts. 4. Docking scores alone are not sufficient to infer therapeutic relevance. Binding affinity does not necessarily confirm biological activity, specificity, or safety—particularly in pregnancy. The docking results should be framed as hypothesis-generating only, without implying clinical readiness of Withanolide D, Baicalin, or Mangostin. 5. Both ssGSEA and xCell were applied, but the rationale for using two methods and how differences were reconciled is not clearly explained. Please clarify why both were used and provide a stronger justification for interpreting correlations between BIRC3 expression and immune cell scores. 6. While GSE173193 is an appropriate dataset, the scRNA-seq analysis is largely descriptive. Statistical comparisons (e.g., differential expression of BIRC3 across PE vs. controls) should be included to strengthen claims. 7. Several figures (particularly heatmaps and pathway plots) appear blurred and difficult to interpret. High-resolution versions should be provided to ensure readability and clarity. ********** 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 ********** [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. |
| Revision 1 |
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<p>Integrated multi-omics analysis reveals necroptosis-related biomarker BIRC3 for early diagnosis and therapeutic targeting in preeclampsia PONE-D-25-39907R1 Dear Dr. Shi, 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. For questions related to billing, please contact billing support . 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, Yanggang Hong Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer #1: The authors have provided satisfactory, point-by-point responses and implemented substantive revisions that address the core concerns raised in Round 1. Key improvements include: (i) a sharper Introduction with a defined hypothesis and literature alignment; (ii) clarified criteria for necroptosis gene selection and updated analyses; (iii) expanded scRNA-seq methods; (iv) triangulated immune deconvolution (adding CIBERSORTx) with appropriate caveats; (v) explicit STRING thresholds for PPI and a multi-step hub-gene workflow; (vi) independent external validation of BIRC3 in GSE44711 (AUC ≈ 0.84); (vii) reframing TF/miRNA/RBP networks and docking as hypothesis-generating; (viii) strengthened limitations and ethics statements; and (ix) upgraded figure quality and supplemental captions. Collectively, the revisions bring the manuscript in line with PLOS ONE’s standard for methodological soundness and transparency. I recommend acceptance. |
| Formally Accepted |
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PONE-D-25-39907R1 PLOS ONE Dear Dr. Shi, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Yanggang Hong Academic Editor PLOS ONE |
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