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Thank you for your revisions. I judge that you have adequately responding to the reviewers' comments and that the manuscript is ready for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Brenda Oppert, a PeerJ Section Editor covering this Section #]
The authors have done alterations that i suggested.
The authors have done alterations that i suggested.
The authors have done alterations that i suggested.
The revised article is still not written in clear English and does not conform to professional standards. In the references, no sufficient field background is provided. There are no hypotheses related to the presented results.
Research questions are still not well defined
Impact and novelty of the revised manuscript remain unclear.
I am not convinced by the authors' response to the comments of reviewers and the revision the manuscript.
Please pay careful attention to the reviewers' comments. Note that while the first reviewer writes in an understated and more general way compared to the second reviewer, their comments should not underemphasized. Following the advice of both reviewers should will, I think, substantially improve the manuscript.
The article titled "Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses” aims to identify key autophagy-related genes (ATGs) associated with CAS using bioinformatics analyses, in vivo AS mouse models and in vitro experiments. To this end, the authors analysed datasets GSE100927 and GSE28829 from the Gene Expression Omnibus (GEO) database. An integrated bioinformatic analysis of the diûerentially expressed ATGs (DEATGs) was performed. Gene enrichment analyses were performed in Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) to identify the associated biological processes and pathways. 3 major CAS-associated ATGs were identified and validated, namely CCL2, LAMP2 and CTSB with high diagnostic value. These 3 important CAS-associated ATGs are promising diagnostic markers and therapeutic targets for patients with CAS.
It is not clear what the novelty or added value is compared to https://doi.org/10.1186/s13023-023-02660-2.
- A summary picture could be created to illustrate the data and translate it.
- How do they translate to clinical practice?
It is not clear what the novelty or added value is compared to https://doi.org/10.1186/s13023-023-02660-2.
- A summary picture could be created to illustrate the data and translate it.
- How do they translate to clinical practice?
See Additional comments
See Additional comments
See Additional comments
The manuscript ((#102081) describes a comprehensive study investigating autophagy-related genes (ATGs) associated with carotid atherosclerosis (CAS). Authors conclude that CCL2, LAMP2, and CTSB are promising diagnostic markers and therapeutic targets for CAS.
1. The manuscript describes using human data from GEO (GSE100927 and GSE28829), but there is no mention of ethical approval or patient consent for the original data collection. Even though the data are public, it's good practice to mention how the study complies with ethical standards for human data.
2. In section 2.2, the overlap between DEGs and the 222 ATGs is described. However, it might be helpful to specify whether this overlap was done using a specific statistical test or simply by comparing lists. Including more details about how significant overlaps were determined would clarify this step.
3. Section 2.6 mentions the use of CIBERSORT for immune cell infiltration analysis. While the process is briefly described, it would be beneficial to include a few more specifics, such as how you handled potential batch effects or normalized gene expression data across the two datasets
4. The choice of thresholds for DEGs should be justified or referenced. Why were these specific cutoffs chosen?
5. More details on the justification for the specific number of animals used would be helpful. For instance, was a power analysis conducted to determine sample size?
6. Regarding the results of validation by in vitro and in vivo experiments showed in Fig 8 why did CCL2 in ECs and SMCs in western blot so similar?
7. The manuscript identifies key DE-ATGs such as CTSB, CCL2, and LAMP2, but further discussion on their specific biological roles in CAS would be valuable. For example, explaining how these genes mechanistically contribute to CAS development based on previously publications (through LMP or inflammation) would provide a more comprehensive understanding of their significance.
8. While the ROC curves show good diagnostic performance, it would be helpful to discuss the clinical relevance of these findings. Is the outcome of the study binary? How could these biomarkers be applied in a clinical setting for early detection or monitoring of CAS? What are the limitations of ROC analysis in terms of clinical translation?
9. The in vitro and in vivo validations provide compelling data, but it would be helpful to mention the number of replicates and the statistical power of these experiments. Were enough biological replicates used to ensure the robustness of the findings?
10. While the authors cite some new relevant studies, some important classical references are missing which are key papers on reported findings in atherosclerosis could have been cited. If your search for “carotid atherosclerosis and lysosome”, and “carotid atherosclerosis and cathepsins”, it will help to improve the understanding of staring research process of these research areas and the interpretation of the results reported in this manuscript.
11. In the discussion, the authors focus primarily on studies that support their findings. They could strengthen the discussion by addressing conflicting studies or potential caveats regarding the role of autophagy in CAS. For instance, there is evidence that autophagy can have both protective and harmful effects depending on the stage of atherosclerosis.
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