Clinicogenomic features and prediction model of POLE proofreading-deficient colorectal cancer
Background: Proofreading-deficient (pd) mutations in DNA polymerase epsilon (POLE) cause ultramutated colorectal cancer (CRC) characterized by high tumor mutational burden (TMB) and marked sensitivity to immune checkpoint inhibitors (ICIs). As POLEpd CRC is extremely rare and most cases are microsatellite-stable (MSS), they are unlikely to receive ICI in routine care unless genomic profiling with TMB assessment is performed. We aimed to clarify the clinicogenomic features of POLEpd CRC and to develop a prediction model to minimize missed opportunities for ICI therapy.
Methods: We retrospectively analyzed clinical and genomic data from the C-CAT registry of cases sequenced with FoundationOne between June 2019 and August 2025. Pathogenicity of POLE variants was annotated with OncoKB. Exploratory analysis of single base substitution (SBS) signature contributions was performed in cases with TMB ≥10 muts/Mb, calculated from panel sequencing data using MutationalPatterns fitted to COSMIC SBS signature v3.4.
Results: Among 9,974 CRC cases, 21 (0.2%) harbored oncogenic POLE mutations (POLEmut), while 483 (4.8%) carried variants of uncertain significance (VUS). POLEmut CRC occurred in younger, predominantly male, enriched for MSS and RAS/BRAF wild-type (WT). Mean TMB was 153 mut/Mb (95%CI 110-195), significantly higher than in POLE-VUS and POLE-WT (8.8 and 3.9 muts/Mb). The mean contributi