Genotype and methylation interact to reconfigure transcriptional regulation in colorectal cancer

Abstract

BackgroundTranscriptional regulation is shaped by both genomic variants and the environment. Yet, how the regulatory effects of genomic variants are reconfigured by dynamic epigenomic changes during tumorigenesis remains incompletely understood. MethodsWe investigated methylation context-dependent links between genotype and gene expression in colorectal cancer (CRC) using paired tumor and normal-adjacent tissue (NAT) from 80 patients, thereby controlling for germline genomic background. By integrating promoter-targeted bisulfite sequencing with RNA-seq, we systematically compared expression quantitative trait loci (eQTLs) and methylation quantitative trait loci (mQTLs). To capture regulatory complexity beyond simple mediation, we implemented a memo-eQTL framework that explicitly models genotype x DNA methylation (GxM) interactions. ResultsWe observed extensive tissue specificity in both eQTL and mQTL landscapes; tumor-specific eGenes were significantly enriched for hallmark oncogenic pathways, including WNT and MAPK signaling. Standard mediation models explained only a minority of genotype-expression relationships, whereas our explicit interaction framework revealed widespread reconfiguration of methylation-dependent genetic effects in tumors. Memo-eQTL mapping (FDR < 0.05) identified 18 NAT and 73 tumor eGenes with significant GxM interactions, and results were consistent at a more permissive threshold (FDR < 0.2). We further developed a patient-level memo-eQTL score and found that interaction-based regulatory disruption in NAT, but not in tumor, significantly correlated with clinical stage (P = 0.035). ConclusionsGenetic regulation in cancer is reorganized through context-dependent GxM interactions. Importantly, GxM signatures in NAT are specifically linked to disease progression, offering new insights into field cancerization and the clinical consequences of regulatory reprogramming in CRC.