Figure 6. Independent validation and replication of retroelement (RE) methylation subtypes in the DCC ccRCC cohort.

A NEMO-based clustering (k = 2) of REMP-predicted Alu, LINE-1 (L1), and LTR methylation in the Dartmouth Cancer Center (DCC) cohort identifies two RE-defined subtypes, Repressed and Active, with coordinated global methylation patterns across RE classes. B Kaplan, Meier overall survival analysis based on cohort-intrinsic DCC. C Kaplan, Meier overall survival analysis after restricting DCC clustering to RE-associated CpG loci shared with TCGA. D-K Violin and box plots show molecular and immune features across DCC RE subtypes, including D EPAS1 (HIF2A) mRNA expression, E PDCD1 (PD-1) mRNA expression, F Treg proportions, G CD8+ T cell proportions, H progenitor exhaustion scores, I terminal exhaustion scores.