Multiomics Signature Reveals Network Regulatory Mechanisms in CRC Continuum

Colorectal cancer (CRC), the third leading cause of cancer-related death globally, sporadic CRC arises through a continuum from normal tissue to adenomas, progressing from low-grade (LGD) to high-grade dysplasia (HGD), yet early epigenetic drivers of this transition remain unclear. To investigate these early events, we profiled LGD and HGD adenomas using EM-seq and identified a consensus Differential Methylation Signature (DMS) of 626 regions through two independent bioinformatics pipelines. This signature effectively distinguished LGD from HGD in both tissue and plasma-derived cell-free DNA (cfDNA), highlighting specific methylation patterns. Functional annotation indicated enrichment for regulatory elements associated with transcription factor activity and cell signaling. Applying the DMS to TCGA CRC dataset revealed three tumor subtypes with increasing hypermethylation and one normal cluster. The most hypermethylated subtype exhibited poor survival, high mutation burden, and disrupted transcriptional networks. While overlapping with classical CpG Island Methylator Phenotype (CIMP) categories, the DMS captured a broader spectrum of methylation alterations. These findings suggest that the DMS reflects early, functionally relevant epigenetic changes in CRC progression, enabling robust stratification of dysplasia severity and tumor subtypes. The DMS has the potential to improve early detection and molecular classification, warranting further validation in larger, prospective cohorts.