Comprehensive identification of mRNA splicing-altering somatic intronic variants in human cancers

Abstract

A substantial fraction of somatic mutations including retrotransposition alters cancer-associated genes through abnormal splicing. Although such mutations have been characterized in human cancers, previous studies have been limited to those within splice sites and exons due to a lack of sufficient number of tumor samples profiled by whole-genome- and RNA-sequencing. To portray a landscape of splicing-altering intronic variants, we analyzed thousands of tumor samples with both the profiling data. We identified ~700 somatic intronic mutations, with 40% of them occurring in deep introns. The deep intronic mutations resulted in abnormal splicing by altering core splicing code through activating cryptic donor/acceptor splice sites and polypriminde tracts and disrupting brachpoints. Notably, deep intronic mutations were enriched toward gain of splicing enhancers and/or loss of splicing silencers. We validated pseudo exon activation by CRISPR/Cas9-mediated deletion of splicing silencer motif. These mutations account for a large fraction of tumor suppressor disruption and show signatures of both positive and purifying selection on transcripts with nonsense-mediated decay (NMD)-sensitive premature termination codon (PTC).