Data from DNA Methylation of the <i>SLC16A3</i> Promoter Regulates Expression of the Human Lactate Transporter MCT4 in Renal Cancer with Consequences for Clinical Outcome

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<div>Abstract<p><b>Purpose:</b> The monocarboxylate transporter 4 (MCT4) is a metabolic target in tumor biology because it mediates lactate transport across membranes resulting in antiapoptotic effects. Cell experiments support the importance of MCT4 in clear cell renal cell carcinoma (ccRCC). In this study, we assessed the prognostic potential of MCT4 expression in ccRCC and its epigenetic regulation by DNA methylation as novel predictive marker for patient outcome using independent ccRCC cohorts.</p><p><b>Experimental Design:</b> MCT4 protein expression was quantified in 207 ccRCC and corresponding nontumor tissues. Data of an independent ccRCC cohort from The Cancer Genome Atlas (TCGA) were analyzed on MCT4 mRNA (<i>n</i> = 482) and DNA methylation (<i>n</i> = 283) level. The findings on MCT4 expression and DNA methylation in the <i>SLC16A3</i> promoter were validated in a third cohort (<i>n</i> = 64). Promoter activity assays were conducted in four RCC cell lines.</p><p><b>Results:</b> MCT4 protein expression was upregulated (<i>P</i> < 0.0001) in ccRCC and showed significant association with cancer-related death. Upregulation of MCT4 mRNA expression (<i>P</i> < 0.00001) was confirmed in the TCGA cohort. Single CpG sites correlated inversely with mRNA expression and were associated with overall survival in Kaplan–Meier analyses [HR = 0.39; 95% confidence interval (CI), 0.24–0.64; <i>P</i>[log-rank] = 1.23e<sup>−04</sup>]. Promoter activity studies confirmed MCT4 regulation by DNA methylation. The significant correlation between MCT4 protein and gene expression or DNA methylation at single CpG sites was validated in a third cohort. Again, higher methylation at individual CpG sites was associated with prolonged survival [HR = 0.05; 95% CI, 0.01–0.40; <i>P</i>[log-rank] = 6.91e<sup>−05</sup>].</p><p><b>Conclusion:</b> We identified <i>SLC16A3</i> promoter DNA methylation as a novel epigenetic mechanism for MCT4 regulation in ccRCC with first evidence of a biological rationale for prognosis and clinical outcome. <i>Clin Cancer Res; 19(18); 5170–81. ©2013 AACR</i>.</p></div>