Immune–Metabolic Profiling Reveals Functional Heterogeneity Within Colorectal Cancer Consensus Molecular Subtypes

Abstract

The Consensus Molecular Subtype (CMS) classification provides a widely used transcrip- tomic framework for colorectal cancer (CRC) stratification with clear prognostic and thera- peutic relevance. However, it does not fully capture the immune–metabolic heterogeneity underlying tumor–microenvironment interactions within each subtype. Here, we integrate a validated immune–metabolic gene signature as a functional layer to refine CMS classifica- tion and systematically characterize diversity across CMS1-4 tumors. Using transcriptomic data from 2918 CRC samples across three independent cohorts (GSE1, TCGA, and GSE2), we show that CMSs display robust yet distinct immune–metabolic distributions across datasets. CMS4 tumors exhibit glycolytic, stromal-dependent, and immunosuppressive pro- files, whereas CMS2 and CMS3 are enriched in oxidative and metabolically flexible states. Importantly, CMS1 tumors segregate into two major immune–metabolic profiles, revealing marked heterogeneity within this immune-activated subtype. These patterns are preserved in metastatic samples, supporting their stability across disease stages. Overall, integrating immune–metabolic profiling into CMSs reveals previously unrecognized functional het- erogeneity and provides a refined framework to interpret tumor–microenvironment states. This approach facilitates the identification of context-specific metabolic vulnerabilities with potential clinical relevance.