Comprehensive analysis of m6A RNA methylation regulators for prognostic risk stratification and immune microenvironment characterization in colorectal cancer

Abstract Objectives Despite mounting evidence of N6-methyladenosine (m6A) dysregulation in colorectal cancer (CRC), comprehensive prognostic association analysis remains limited. We systematically investigated m6A modification patterns and developed a robust risk stratification model. Methods We analyzed 27 m6A regulators in 488 CRC samples and 42 normal controls from TCGA, with external validation in two independent cohorts (n=762). Consensus clustering identified distinct m6A modification patterns. A prognostic risk model incorporating 268 m6A-associated genes was constructed using multivariate Cox regression. Results 24 of 27 m6A regulators exhibited significant differential expression (p<0.001). Multivariate analysis identified ZC3H13, LRPPRC, and IGFBP3 as independent prognostic factors. The risk model showed exceptional performance across all validation cohorts (HR: 8.59–14.27, p<0.0001), maintaining significance in early-stage patients. High-risk patients exhibited significantly elevated PD-L1 expression levels (p=5.7 × 10 −9 to 5 × 10 −7 ) and altered immune cell infiltration patterns. Conclusions Our findings reveal pervasive m6A dysregulation with superior predictive performance compared to conventional approaches. The links between RNA methylation and tumor immunity establish m6A signatures as actionable biomarkers for precision oncology.