Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends

Colorectal cancer (CRC) is highly heterogenous with variable survival outcomes and therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus Molecular Subtypes (CMS) based on gene expression patterns. However, how these CMS categories connect to axes of phenotypic plasticity and heterogeneity remains unclear. Here, we analyze 101 bulk transcriptomic datasets, along with patient tumor samples from TCGA and single-cell RNA sequencing data, to evaluate the extent of variation among CMS subtypes across metabolic plasticity and EMT axes. Our results show that CMS2 and CMS3 samples were relatively more epithelial as compared to CMS1 and CMS4. Single-cell RNA-seq analysis of CMS1 revealed two subpopulations: one close to CMS4 (more mesenchymal) and the other closer to CMS2 or CMS3 (more epithelial), indicating a partial EMT-like behavior. Further, in our meta-analysis and in TCGA data, epithelial phenotype score was positively correlated with scores of glycolysis, OXPHOS and FAO pathways, while mesenchymal scores showed CMS subtype-specific associations with metabolic axes. PD-L1 activity scores, however, consistently correlated positively with mesenchymal signature ones and negatively with epithelial signature ones, across the four CMS categories. Together, our results quantify the patterns of two interconnected axes of phenotypic heterogeneity - EMT and metabolic reprogramming - at a CMS subtype level in CRC.