Identification and Validation of Tumor Microenvironment-Associated Signature in Clear-Cell Renal Cell Carcinoma through Integration of DNA Methylation and Gene Expression

• Published in: International journal of molecular sciences 2024-06, Vol.25 (12), p.6792
• Main Authors: Ye, Zijian, Xu, Jialiang, Zhang, Xin, Zhang, Yifan, Ivanova, Deyana, Lu, Weiyu, Zhang, Jianning, Li, Fangfang, Chen, Xuemei, Wang, Yingxiong, Wang, Meijiao, Xie, Biao
• Format: Article
• Language: English
• Subjects: Antimitotic agents; Antineoplastic agents; Biomarkers, Tumor - genetics; Cancer; Carcinoma, Renal Cell - genetics; Carcinoma, Renal Cell - metabolism; Carcinoma, Renal Cell - pathology; Chemotherapy; clear-cell renal cell carcinoma; Correlation analysis; Cytokines; Development and progression; DNA; DNA Methylation; Epigenetics; Extracellular matrix; Female; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic; Genetic aspects; Genomics; Humans; Immunotherapy; Indazoles - pharmacology; Indazoles - therapeutic use; Kidney cancer; Kidney Neoplasms - genetics; Kidney Neoplasms - pathology; Kinases; Lymphocytes; Male; Medical prognosis; Metastasis; Methylation; molecular docking; Molecular Docking Simulation; Patients; prognostic signature; Protein binding; Proteins; Pyrimidines - therapeutic use; Regression analysis; Sulfonamides - pharmacology; Sulfonamides - therapeutic use; Survival analysis; tumor microenvironment; Tumor Microenvironment - genetics; Tumors
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25126792

The tumor microenvironment (TME) is crucial in tumor development, metastasis, and response to immunotherapy. DNA methylation can regulate the TME without altering the DNA sequence. However, research on the methylation-driven TME in clear-cell renal cell carcinoma (ccRCC) is still lacking. In this study, integrated DNA methylation and RNA-seq data were used to explore methylation-driven genes (MDGs). Immune scores were calculated using the ESTIMATE, which was employed to identify TME-related genes. A new signature connected with methylation-regulated TME using univariate, multivariate Cox regression and LASSO regression analyses was developed. This signature consists of four TME-MDGs, including , , , and , which exhibit high methylation and low expression in tumors. Validation was performed using qRT-PCR which confirmed their downregulation in ccRCC clinical samples. Additionally, the signature demonstrated stable predictive performance in different subtypes of ccRCC. Risk scores are positively correlated with TMN stages, immune cell infiltration, tumor mutation burden, and adverse outcomes of immunotherapy. Interestingly, the expression of four TME-MDGs are highly correlated with the sensitivity of first-line drugs in ccRCC treatment, especially pazopanib. Molecular docking indicates a high affinity binding between the proteins and pazopanib. In summary, our study elucidates the comprehensive role of methylation-driven TME in ccRCC, aiding in identifying patients sensitive to immunotherapy and targeted therapy, and providing new therapeutic targets for ccRCC treatment.