M6A-Mediated Molecular Subtypes and Immune Microenvironment Remodeling in Colorectal Pathogenesis

Abstract

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, largely attributable to limitations in early detection and patient stratification. Although N6-methyladenosine (m6A) modification has emerged as a critical epitranscriptomic regulator in cancer biology, its role in driving molecular heterogeneity and immune microenvironment remodelling during colorectal pathogenesis remains poorly characterised. This study integrated multi-transcriptomic datasets from normal colon, adenoma, and CRC tissues to identify m6A-related differentially expressed genes (m6A-RDEGs). Using systematic bioinformatics analyses and machine learning approaches, we developed a six-gene signature to distinguish CRC from precancerous stages. Furthermore, consensus clustering based on m6ARDEG expression patterns was applied to define molecular subtypes. A robust six-gene signature effectively differentiated CRC from earlier stages. Consensus clustering revealed two distinct molecular subtypes with markedly different immune microenvironment profiles. Subtype 1 exhibited an immunosuppressive phenotype, characterized by significant M2 macrophage infiltration and enrichment of TGF-β signaling pathways, while Subtype 2 displayed divergent immunological characteristics. Functional analyses linked these subtypes to key pathways, including ferroptosis and HIF-1 signaling. Our findings establish a novel link between m6A-mediated molecular subtyping and immune microenvironment remodeling in colorectal pathogenesis. The identified signature and subtypes provide not only diagnostic biomarkers but also insights for developing subtype-specific immunotherapeutic strategies. This study elucidates the role of m6A modification in CRC heterogeneity and immune microenvironment regulation, offering potential tools for improved stratification and targeted immunotherapy in colorectal cancer.