All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
Congratulations on the acceptance of your manuscript.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
No comment
No comment
No comment
Article can be accepted
Dear Dr. Yue,
The study "Circular RNAs in endometriosis analyzed through RNA sequencing and bioinformatics for expression profile" by Yue et al. investigates the expression patterns and potential regulatory roles of circRNAs in endometriosis, addressing an important gap in understanding the molecular mechanisms underlying this condition. While the study is well-conceived and provides valuable insights, several aspects require further clarification, elaboration, and improvement. Please reply the concerns below as well as the two reviewers of the manuscript.,
Key Concerns and Suggestions
1. Basic Reporting
The manuscript successfully addresses the research question and employs rigorous methodologies, including RNA sequencing, qRT-PCR, and bioinformatics analyses (GO and KEGG).
However, the presentation of the results, particularly in the CircRNA-miRNA-mRNA network analysis, lacks detail on the outcomes. A more in-depth discussion is required on the biological relevance and the key signaling pathways identified. Authors should emphasize how these findings contribute to understanding the pathogenesis or offer therapeutic potential.
2. Experimental Design
Validation Criteria: Please clarify how the specific number of three upregulated and three downregulated circRNAs was chosen for qRT-PCR validation. Were additional criteria, such as biological relevance, novelty, or prior literature evidence, considered alongside fold-change and p-value?
Sample Size and Robustness: While the sequencing data and validation appear to be derived from a small cohort (3 patients), it is critical to outline plans for validation in a larger, independent cohort. Addressing this limitation will enhance the robustness and generalizability of the findings.
3. Figures and Visualizations
Although the figures are high quality, the font size in the images is too small, making some details difficult to interpret. Please increase the font size for readability.
4. Results and Discussion Section
The discussion section is insufficient in conveying the significance of the findings. For instance, in the CircRNA-miRNA-mRNA network, the outcome of the analysis and its implications are missing. Authors should elaborate on the key signaling pathways, their roles in endometriosis, and potential therapeutic targets identified in this study.
Questions for the Authors
How were the specific circRNAs chosen for validation beyond fold-change and p-value? Please elaborate.
Were the qRT-PCR validations performed on the same patient samples as those used for RNA sequencing, or on an independent cohort? This detail is crucial for understanding the validation strategy.
The study focuses on ovarian endometriosis. Are there plans to test whether the findings are applicable to other forms of endometriosis (e.g., peritoneal or rectovaginal)? If so, please discuss.
The design of this study is too simplistic. The ratio is sufficient to support the conclusion of the article.
It is suggested that the author add more other omics for other queue validation.
The experiment was too simple. More functional experiments should be added for testing. For example, selecting an important gene to knock down.
no comment.
There are too many language errors in this study, so it is recommended to ask native English speakers to polish it.
Comments
o The study provides a well-defined research question addressing the role of circular RNAs (circRNAs) in endometriosis, contributing to the understanding of its pathogenesis.
o The manuscript employs rigorous methodologies, including RNA sequencing, qRT-PCR validation, and bioinformatics analyses (GO and KEGG).
o The focus on circRNA-miRNA-mRNA networks adds depth to the analysis and introduces potential mechanistic pathways relevant to endometriosis.
o Figures and data visualizations are of high quality and effectively summarize key findings.
no comment
no comment
Questions for the Authors
1. How was the specific number of three upregulated and three downregulated circRNAs chosen for qRT-PCR validation? Were there additional criteria beyond fold-change and p-value?
2. Considering the limited sample size, are there plans to validate these findings in a larger, independent cohort to ensure robustness?
3. The study focuses on ovarian endometriosis; could the findings be extrapolated to other forms of the condition, such as peritoneal or rectovaginal endometriosis?
The research in this submission is insufficient. Authors can refer to the references below and include them in the article.
Mangeshikar A, Youssef Y, Sheth H, Mangeshikar P, Moawad G. Transvaginal Natural Orifice Specimen Extraction: A 10-step Approach for Laparoscopic Excision of Deep Endometriosis Infiltrating the Rectosigmoid. Gynecol Minim Invasive Ther. 2024 Feb 23;13(1):62-63. doi: 10.4103/gmit.gmit_52_23. PMID: 38487604; PMCID: PMC10936720.
Watanabe M. Discordance in Histopathological versus Clinical Diagnosis of a Paracolpium Endometrioma - A Diagnostic Challenge. Gynecol Minim Invasive Ther. 2024 Jan 12;13(1):64-65. doi: 10.4103/gmit.gmit_48_22. PMID: 38487603; PMCID: PMC10936722.
Abe W, Nasu K, Tsuno A, Kawano Y, Narahara H. Phosphatidylinositol-3 kinase-Akt-mammalian target of rapamycin signaling pathway mediates contractility of human endometriotic stromal cells: A promising new target for the treatment of endometriosis-associated fibrosis. Gynecol Minim Invasive Ther. 2014;3(4):115-118.
Balci BK. Is Endometriosis Telemedicine Friendly? Gynecol Minim Invasive Ther. 2022 Sep 19;11(4):224-230. doi: 10.4103/gmit.gmit_119_21. PMID: 36660334; PMCID: PMC9844039.
Singh MK, Dejenie MA, Behbehani S, Nahas S, Handler S, Stuparich MA. Treatment of Iatrogenic Pneumothorax during Resection of Diaphragmatic Endometriosis using a Laparoscopic Suction Irrigator: A Simple Approach. Gynecol Minim Invasive Ther. 2023 Jun 16;12(4):253-254. doi: 10.4103/gmit.gmit_125_22. PMID: 38034108; PMCID: PMC10683965.
[# PeerJ Staff Note: It is PeerJ policy that additional references suggested during the peer-review process should *only* be included if the authors are in agreement that they are relevant and useful #]
The manuscript “Circular RNAs in endometriosis analyzed through 1 RNA sequencing and bioinformatics for expression Profile” by Yue et al focuses on identifying potential targets for the treatment and diagnosis of endometriosis by analyzing the expression patterns of circular RNAs (circRNAs), a class of non-coding RNA with regulatory roles. Using high-throughput sequencing, the researchers compared circRNA expression in patients with endometriosis and healthy controls. They identified 371 circRNAs with increased expression and 308 with decreased expression.
The initial sequencing data was generated from 3 patients and were validate using RTqPCR, please elaborate if the validation was performed on the same samples, which is not clear in the manuscript.
Looks fine.
Regarding the Results and discussion section of the manuscript, improvement is suggested to bring the significance of the study. For example- the section “CircRNA-miRNA-mRNA network” what is the outcome of the analysis is missing. Need discussion on how this information may be useful or what are the key signaling involved. This is true for almost all the result and discussion section.
I will also suggest to make the images readable by increasing the font size.
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.