Epigenetic alterations in the methylome have been associated with tumor development and progression in renal cell carcinoma (RCC). In this study, 45 tumor samples, 12 tumor-free kidney cortex tissues, and 24 peripheral blood samples from patients with clear cell RCC (ccRCC) were analyzed by genome-wide promoter-directed methylation arrays and related to clinicopathological parameters. Unsupervised hierarchical clustering separated the tumors into two distinct methylation groups (clusters A and B), where cluster B had higher average methylation and increased number of hypermethylated CpG sites (CpGs). Furthermore, tumors in cluster B had, compared with cluster A, a larger tumor diameter (p = 0.033), a higher morphologic grade (p < 0.001), a higher tumor-node-metastasis (TNM) stage (p < 0.001), and a worse prognosis (p = 0.005). Higher TNM stage was correlated to an increase in average methylation level (p = 0.003) and number of hypermethylated CpGs (p = 0.003), whereas a number of hypomethylated CpGs were mainly unchanged. However, the predicted age of the tumors based on methylation profile did not correlate with TNM stage, morphological grade, or methylation cluster. Differently methylated (DM) genes (n = 840) in ccRCC samples compared with tumor-free kidney cortex samples were predominantly hypermethylated and a high proportion were identified as polycomb target genes. The DM genes were overrepresented by transcription factors, ligands, and receptors, indicating functional alterations of significance for ccRCC progression. To conclude, increased number of hypermethylated genes was associated with increased TNM stage of the tumors. DNA methylation classification of ccRCC tumor samples at diagnosis can serve as a clinically applicable prognostic marker in ccRCC.
Clear cell renal cell carcinoma DNA methylation Survival Predicted age Polycomb target genes
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This study was supported by grants from the Swedish Cancer Society (BL, GR), the Cancer Research Foundation in Umeå (BL, GR, SD), the Kempe Foundations (GR, SD), and the Västerbotten County Council (BL, GR).
Compliance with ethical standards
Conflicts of interest
The study was approved by the regional ethical review board in Umeå (Dnr 2011-156-31M 110523).
Informed consent was obtained from all participants included in the study.
Preprocessing of methylation data from Illumina Infinium HumanMeth27K arrays. CpG sites were excluded if ≤ 3 reported beads/array in any sample, if CpG sites had a detection p value equal to or greater than 0.05 and if CpG sites were located on sex chromosomes X and Y. (GIF 15 kb)
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