U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations.

The mechanisms by which somatic mutations of splicing factors, such as U2AF1(S34F) in lung adenocarcinoma, contribute to cancer pathogenesis are not well understood. Here, we used prime editing to modify the endogenous U2AF1 gene in lung adenocarcinoma cells and assessed the resulting impact on alternative splicing. These analyses identified KRAS as a key target modulated by U2AF1(S34F). One specific KRAS mutation, G12S, generates a cryptic U2AF1 binding site that leads to skipping of KRAS exon 2 and generation of a non-functional KRAS transcript. Expression of the U2AF1(S34F) mutant reverts this exon skipping and restores KRAS function. Analysis of cancer genomes reveals that U2AF1(S34F) mutations 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(Q61R) and U2AF1(I24T) mutations. Experimentally, KRAS(Q61R) mutation leads to KRAS exon 3 skipping, which in turn can be rescued by the expression of U2AF1(I24T). Analysis of genomic and clinical patient data suggests that both U2AF1 mutations occur secondary to KRAS mutation 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.