Abstract 778: Dysregulation of alternative mRNA splicing by oncogenic KRAS in lung adenocarcinoma

Abstract

Abstract Alternative mRNA splicing is dysregulated in many cancers including lung adenocarcinoma. These aberrant splicing events can sometimes be explained by mutations in splice sites or splicing factors. However, the majority of mis-splicing in cancers remains unexplained. We hypothesize that oncogenic signaling pathways play a role in regulating alternative splicing. In this study, we focus on mRNA splicing activity regulated by the Ras signaling cascade, which is frequently mutated in cancers. These pathways offer avenues for therapeutic modulation through small molecule inhibitors.We took a global proteomic and transcriptomic approach to study the effects of oncogenic Ras signaling on RNA splicing in vitro. Specifically, we performed LC-MS/MS and RNA-seq profiling on normal human lung airway epithelial (AALE) cells overexpressing wild-type or mutant KRAS or RIT1 (N = 3 replicates per allele). Phosphorylation of splicing factors was preferentially downregulated in KRASmut cells compared to KRASWT cells, suggesting that oncogenic KRAS signaling regulates splicing factor activity. Additionally, of the 2227 and 2452 skipped exon (SE) events in KRASG12V and KRASQ61H cells, respectively, compared to KRASWT overexpressing cells, 1013 events were shared between the two mutants. This statistically significant overlap (p < 0.001, hypergeometric test) indicates that KRAS has a role in splicing regulation that is disrupted when the protein is mutated. To determine how KRAS-regulated splicing activity compared to other signaling proteins and oncogenes, we also profiled the whole transcriptomes of isogenic A549 lung adenocarcinoma cell lines overexpressing 86 wild-type or variant alleles across 27 genes implicated in lung cancers (N = 4 to 8 replicates per allele). Of all pairs of mutant and wild-type alleles tested, KRASmut cells compared to KRASWT overexpressing cells exhibited the second highest levels of alternative splicing, behind only RNA binding protein RBM45 and its mutant allele RBM45M126I. In particular, ten SE events were observed to be differentially regulated in a KRAS dependent manner in both AALE and A549 cells. One of these 10 events is the differential splicing of the Myc Associated Zinc Finger (MAZ) protein to increase the expression of its splice variant that acts as a negative regulator of transcription. As MAZ regulates expression of KRAS, this splice variant may be a mechanism for the cell to modulate wild-type KRAS levels in the presence of KRAS mutants. Our proteomic and transcriptomic profiling in lung epithelial and lung adenocarcinoma cells uncovers splicing factor activity and mRNA splicing events regulated by oncogenic KRAS. With further studies of the alternative splicing events described, it will be possible to design or repurpose therapies in order to target aberrant splicing caused by disrupted Ras signaling and its downstream effectors. Citation Format: April Lo, Maria McSharry, Alice H. Berger. Dysregulation of alternative mRNA splicing by oncogenic KRAS in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 778.