Abstract 863: Neuronal splicing regulatory factors are upregulated in models of epithelial-mesenchymal transition

Abstract

Abstract Epithelial-mesenchymal transition (EMT) is an essential developmental program through which epithelial cells lose their polarity and junctions with neighboring cells and acquire migratory and invasive properties. Cancer cells hijack at least a portion of the EMT program to increase their invasive properties, acquire resistance to senescence, and metastasize. Major changes in cell signaling, transcriptional and post-transcriptional regulation occur during EMT. To study post-transcriptional changes we characterized gene expression and splicing across EMT in 3 cell culture models of EMT: the luminal epithelial MCF7ras breast cancer cell line with EMT induced by SLUG+SOX9 and in basal human mammary epithelial (HMLEras) cells, with EMT induced by either SNAIL or ZEB1. RNA-seq was performed at 2-day intervals across these transitions. We observed broad overlaps between these systems, with 821 genes that changed significantly in all three. In all three time courses, genes associated with cell cycle and growth decreased in expression, while genes associated with signaling, cell motion, adhesion, extracellular matrix organization, and differentiation increased. Intriguingly, genes associated with neurogenesis and angiogenesis were also induced in the MCF7 and HMLER-Snail time courses. Those include known axon guidance and angiogenic factors in the Robo and Slit families. We also found many alternative splicing events shared in all 3 systems, including 272 skipped exons. Sequence analysis of regions around these exons revealed binding motifs for canonical splicing regulators, including ESRP1 and ESRP2 and the RBFOX protein family, which are known to play a role in EMT. While most genes encoding RNA binding proteins decreased in expression in EMT, a small subset consistently increased in expression, including some that matched our motif analysis. Specifically, several splicing factors associated with nervous system development were upregulated, including factors of the QKI and NOVA families. We have validated the increased expression of QKI and NOVA1 proteins during EMT in vitro, and of QKI and NOVA2 in tumor sections. Further, we found that perturbation of QKI expression affects the motility of mesenchymal cancer cells in culture. Together, our results point to the existence of a program of alternative splicing shared between neuronal and mesenchymal cells. Citation Format: Yevgenia L. Khodor, Julia Froese, Frank Gertler, Robert A. Weinberg, Christopher B. Burge. Neuronal splicing regulatory factors are upregulated in models of epithelial-mesenchymal transition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 863. doi:10.1158/1538-7445.AM2017-863