U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations

The mechanisms by which somatic mutations of splicing factors, such as U2AF1^S34Fin lung adenocarcinoma, contribute to cancer pathogenesis are not well understood. Here, we used prime editing to modify the endogenousU2AF1gene in lung adenocarcinoma cells and assessed the resulting impact on alternative splicing. These analyses identifiedKRASas a key target modulated by U2AF1^S34F. One specificKRASmutation, G12S, generates a cryptic U2AF1 binding site that leads to skipping ofKRASexon 2 and generation of a non-functionalKRAStranscript. Expression of the U2AF1^S34Fmutant reverts this exon skipping and restores KRAS function. Analysis of cancer genomes reveals that U2AF1^S34Fmutations are enriched in KRAS^G12S-mutant lung adenocarcinomas. A comprehensive analysis of splicing factor/oncogene mutation co-occurrence in cancer genomes also revealed significant co-enrichment of KRAS^Q61Rand U2AF1^I24Tmutations. Experimentally, KRAS^Q61Rmutation leads toKRASexon 3 skipping, which in turn can be rescued by the expression of U2AF1^I24T. Analysis of genomic and clinical patient data suggests that bothU2AF1mutations occur secondary toKRASmutation and are associated with decreased overall patient survival. Our findings provide evidence that splicing factor mutations can rescue splicing defects caused by oncogenic mutations. More broadly, they demonstrate a dynamic process of cascading selection where mutational events are positively selected in cancer genomes as a consequence of earlier mutations.