Co-Mutation of CREBBP/EP300 and POLE/POLD1 Identifies a TMB-High Subset of MSS CRC

Identifying immunotherapy biomarkers for colorectal cancer (CRC) beyond MSI-high status is challenging. We evaluated CREBBP/EP300 and POLE/POLD1 mutations as candidate markers using public cohorts (MSK-CHORD, n = 5493; TCGA, n = 528; MetTropism, n = 24,496; ICI-treated, n = 1610). Regression with SHAP attribution, survival analyses, and pan-cancer transcriptomic profiling (n = 7628) were performed. CREBBP/EP300 mutations were independently associated with TMB-high MSS tumors (p < 0.00001). The co-mutation group (CREBBP/EP300 + POLE/POLD1; CoMut) was the strongest predictor of elevated TMB level (β = 3.63; p < 10−16; exp(β) = 37.7) with a median TMB of 155.9 vs. 7.4 and 5.4 Mut/Mb in single-mutation groups. CoMut also associated with improved survival (HR = 0.57, p = 0.035). In the ICI-treated cohort, both single-mutation groups (CREBBP/EP300-MUT-only; POLE/POLD1-MUT-only) and showed longer overall survival than wild type (34 and 28 vs. 17 months; p < 0.05), but only CREBBP/EP300 mutations independently reduced mortality risk (HR = 0.71, p = 0.0025). All groups shared immune-inflammatory transcriptomic enrichment. These findings support CREBBP/EP300 mutations as candidate immunotherapy biomarkers, and co-mutations with POLE/POLD1 define a TMB-high MSS subgroup that could refine TMB testing, pending prospective validation.