DNA methylation status predicts survival in metastasis free clear cell renal cell carcinoma

Background: Clear cell renal cell carcinomas (ccRCCs) display divergent clinical phenotypes. Up to one third of patients with local disease at diagnosis will progress. Therefore, it is a need to identify patients at risk for recurrence. In the present study, we analyzed genome-wide promoter DNA methylation at diagnosis in relation to clinicopathological parameters, in order to identify DNA methylation profiles associated with risk for progress. Method: DNA methylation status in 155,931 CpGs located in gene promoter regions was analyzed by Illumina HumanMethylation450K arrays in diagnostic tissue samples from 115 ccRCC patients. Methylation profiles were compared with genetic aberrations and clinicopathological parameters. Results: The tumors separated into two clusters based on genome-wide promoter methylation status. The tumors in these clusters differed in tumor diameter (p < 0.001), TNM stage (p < 0.001), morphological grade (p < 0.001), and patients outcome (5 year cancer specific survival (pCSS5yr) 72 % in cluster A vs 26 % in cluster B, p < 0.001). When metastasis-status (M0/M1) and cluster A/B status at diagnosis were combined, we found poor survival in M1 patients regardless of cluster A/B status (pCSS5yr 9 % vs 6 %). In M0 patients, the cluster status clearly separated in survival (pCSS5yr 81 % vs 17 %; p < 0.001). We identified a methylation profile of 398 CpGs that was associated with progress of disease, which included differently methylated CpG sites in the SMAD6, SOCS3 and MX2 genes. An integrated genomic and epigenomic analysis revealed significant correlations between the total number of genetic aberrations and hypermethylated CpGs (R = 0.435, p > 0.001), and predicted mitotic age (R = 0.407, p < 0.001). Conclusion: DNA methylation analysis at diagnosis in ccRCC has the potential to improve outcome-prediction and therapy stratification. Bisulphite converted DNA from the clear cell renal cell carcinoma tumors and tumor free tisssue samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip