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Our previous study revealed that CRB3 protein expression was reduced in clear cell renal cell carcinoma (ccRCC) and was associated with TNM stage, pathological grade, and poor prognosis of ccRCC. This study aimed to investigate if DNA methylation of CRB3 decreases its expression, subsequently leading to the progression and poor prognosis of ccRCC. Data for DNA methylation of CRB3, CRB3 mRNA expression, and ccRCC clinicopathological parameters were extracted from the cancer genome atlas (TCGA) database. The relationships among DNA methylation of CRB3, CRB3 mRNA expression, and ccRCC clinicopathological parameters were analyzed using UALCAN, MethHC, LinkedOmics, and Wanderer. We found that CRB3 mRNA levels were lower in ccRCC compared to normal tissues. Methylation of CRB3 increased in ccRCC, with all probes showing differences between ccRCC and normal tissues. Furthermore, CRB3 DNA methylation negatively correlated with CRB3 mRNA expression. CRB3 DNA methylation was also related to pathologic stage, T stage, N stage, and M stage of ccRCC. Overall survival was shorter in ccRCC patients with high CRB3 DNA methylation compared to ccRCC patients with low CRB3 DNA methylation. Methylation of cg24798010, a CRB3 probe, was related to laterality, pathologic stage, T stage, M stage, neoplasm-histologic-grade without N stage, and race. Furthermore, treatment with the DNA methylation inhibitor Decitabine resulted in the upregulation of CRB3 mRNA in ccRCC cell lines. These results indicate that DNA methylation of CRB3 may be both a prognostic marker and therapeutic target for ccRCC.

DNA methylation of CRB3 is a prognostic biomarker in clear cell renal cell carcinoma