Genomic Fabrics of the Excretory System’s Functional Pathways Remodeled in Clear Cell Renal Cell Carcinoma
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsIn this manuscript entitled “The genomic fabrics of the excretory system’s functional pathway are remodeled in clear cell renal cell carcinoma”, Dumitru et al. analyzed several samples induced by ccRCC from the perspective of the Genomic Fabric Paradigm (GFP). Compared to the traditional gene biomarker approach, GFP would offer the most theoretically possible comprehensive characterization of the transcriptome and personalized solutions for cancer gene therapy. In this study, the analyses covered five functional pathways and confirmed that even equally graded cancer nodules from the same tumor have different transcriptomic topologies.
This study is well-designed and presented. Please include the following points in the discussion section:
GFP has several advantages compared to the gene biomarker paradigm. However, the applications and publications involved in GFP are still limited. What is the reason? What are the disadvantages of GFP?
Author Response
Please see attachment
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe article explores the limitations of the gene biomarker paradigm in cancer diagnostics and therapy, specifically focusing on clear cell Renal Cell Carcinoma (ccRCC). While discussing the potential of gene therapy as an alternative, the authors criticize the reliance on gene biomarkers and propose the Genomic Fabric Paradigm (GFP) as a more comprehensive approach. The study analyzes transcriptomic data from ccRCC samples, aiming to determine the transcriptome's alteration in cancer and its impact on functional pathways.
Strengths:
- Relevance and Importance: The article addresses a crucial issue in cancer research, emphasizing the need for innovative approaches beyond traditional gene biomarkers.
- Detailed Background: The introduction provides a comprehensive overview of current cancer treatment options and highlights the challenges in addressing the disease.
- Data Utilization: The study incorporates a significant amount of transcriptomic data, offering a basis for robust analysis and conclusions.
- Novel Approach: The introduction of the Genomic Fabric Paradigm (GFP) as an alternative to gene biomarkers presents a novel perspective.
Areas for Improvement:
- Clarity in Argumentation: The article lacks a clear flow in presenting arguments. Some statements and conclusions are scattered throughout the text, making it challenging to follow the logical progression of ideas.
- Repetitive Information: Certain points, particularly regarding the limitations of gene biomarkers, are repeated, leading to redundancy. Streamlining the content would enhance the article's coherence.
- Overemphasis on Technical Details: The article delves into technical details and methodologies without sufficient explanation, making it less accessible to a broader audience. Clarifying complex terms and concepts would improve readability.
- Insufficient Explanation of GFP: While GFP is introduced as an alternative paradigm, its principles and advantages are not thoroughly explained. Providing a clearer understanding of GFP and its application would strengthen the article's core argument.
- Limited Comparison with Existing Literature: The article could benefit from a more extensive discussion of how GFP compares to other existing approaches in cancer research. This would emphasize the novelty and significance of the proposed paradigm. Please include and discuss in the section the following manuscripts: PMID: 37373581; PMID: 37685983; PMID: 37446024.
- Conclusion: The article lacks a concise conclusion that summarizes key findings and suggests future research directions. A well-structured conclusion would enhance the overall impact of the study. Please no citations in this section.
- Visualization of Data: The article contains numerous technical details and data, but visual aids, such as tables or figures, would improve the presentation of results and make the information more accessible.
Overall Assessment:
The article addresses an important topic in cancer research and proposes an intriguing alternative to conventional gene biomarkers. However, improvements in clarity, coherence, and the thorough explanation of the proposed paradigm are necessary for the article to meet the standards of a scientific publication. Additionally, a more extensive comparison with existing literature and a concise conclusion would enhance the overall impact of the study.
Author Response
Please see attachment
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript has been significantly improved compared to previous versions and is now an engaging and informative read. The topics discussed are extremely interesting, and the author has presented a unique and well-documented perspective.
