Comprehensive characterization of posttranscriptional impairment-related 3′-UTR mutations in 2413 whole genomes of cancer patients

The 3′ untranslated region (3′-UTR) is the vital element regulating gene expression, but most studies have focused on variations in RNA-binding proteins (RBPs), miRNAs, alternative polyadenylation (APA) and RNA modifications. To explore the posttranscriptional function of 3′-UTR somatic mutations in tumorigenesis, we collected whole-genome data from 2413 patients across 18 cancer types. Our updated algorithm, PIVar, revealed 25,216 3′-UTR posttranscriptional impairment-related SNVs (3′-UTR piSNVs) spanning 2930 genes; 24 related RBPs were significantly enriched. The somatic 3′-UTR piSNV ratio was markedly increased across all 18 cancer types, which was associated with worse survival for four cancer types. Several cancer-related genes appeared to facilitate tumorigenesis at the protein and posttranscriptional regulation levels, whereas some 3′-UTR piSNV-affected genes functioned mainly via posttranscriptional mechanisms. Moreover, we assessed immune cell and checkpoint characteristics between the high/low 3′-UTR piSNV ratio groups and predicted 80 compounds associated with the 3′-UTR piSNV-affected gene expression signature. In summary, our study revealed the prevalence and clinical relevance of 3′-UTR piSNVs in cancers, and also demonstrates that in addition to affecting miRNAs, 3′-UTR piSNVs perturb RBPs binding, APA and m6A RNA modification, which emphasized the importance of considering 3′-UTR piSNVs in cancer biology.