DNA hypermethylation is frequently observed in clear cell renal cell carcinoma (ccRCC) and correlates with poor clinical outcomes. However, the detailed function is not fully uncovered. Here, we show that the role of DNA methylation in ccRCC progression through the identification of a target(s) for DNA methyltransferases (DNMTs). Our preclinical model of ccRCC using the serial orthotopic inoculation model exhibited the up-regulation of DNMT3B in advanced ccRCC. Pre-treatment of advanced ccRCC with 5-aza-deoxycytidine attenuated a formation of a primary tumor through the induction apoptosis. DNA methylated sites were genome-widely analyzed using methylation array in reference to RNA-sequencing data. Ubiquinol cytochrome c reductase hinge protein (UQCRH), one of the components of mitochondrial complex III, was extracted as a methylation target in advanced ccRCC. Immunohistochemical analysis revealed that the expression of UQCRH in human ccRCC tissue was lower than normal adjacent tissue. Silencing of UQCRH attenuated the cytochrome c release in response to apoptotic stimuli and resulted in enhancement of primary tumor formation in vivo, implying the tumor-suppressive role of UQCRH. Moreover, DNA demethylation using 5-aza-deoxycytidine enhanced the therapeutic efficiency of mTOR inhibitor everolimus in vivo. These findings suggested that the DNMT3B-induced methylation of UQCRH may contribute to renal cancer progression and that the clinical significance of DNMT inhibitor as a therapeutic option for ccRCC.
