A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes

Exitron splicing (EIS) creates a cryptic intron (called an exitron) within a protein-coding exon to increase proteome diversity. EIS is poorly characterized, but emerging evidence suggests a role for EIS in cancer. Through a systematic investigation of EIS across 33 cancers from 9,599 tumor transcriptomes, we discovered that EIS affected 63% of human coding genes and that 95% of those events were tumor specific. Notably, we observed a mutually exclusive pattern between EIS and somatic mutations in their affected genes. Functionally, we discovered that EIS altered known and novel cancer driver genes for causing gain- or loss-of-function, which promotes tumor progression. Importantly, we identified EIS-derived neoepitopes that bind to major histocompatibility complex (MHC) class I or II. Analysis of clinical data from a clear cell renal cell carcinoma cohort revealed an association between EIS-derived neoantigen load and checkpoint inhibitor response. Our findings establish the importance of considering EIS alterations when nominating cancer driver events and neoantigens. [Display omitted] •Large-scale transcriptome analysis compiles a cancer exitron-splicing landscape•Exitron splicing disrupts functional protein domains to cause cancer driver effects•Immunopeptidome analysis identifies exitron splicing-derived neoantigens•Exitron-splicing neoantigen load predicts response to checkpoint inhibitor therapy The comprehensive analysis of exitron-splicing events in cancer provides a reference of candidate cancer driver events, potential immunogenic neoantigens, and predictive signatures for immunotherapy response that are missed by genetic alteration analysis alone.