MYC-regulated RNA Binding Protein Networks and Spliced Isoforms Driving Cancer

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SUMMARY Alternative RNA splicing is a key step in gene expression regulation and contributes to transcriptional diversity by selecting which transcript isoforms are produced in a specific cell at a specific time point. Aberrantly spliced isoforms can impact every one of the hallmarks of cancer, including increased cell proliferation, migration, or resistance to apoptosis. Regulatory splicing factors (SFs) have recently emerged as a new class of oncoproteins and tumor suppressors. In particular, the tumorigenic capacity of the oncogenic transcription factor MYC, which is dysregulated in >50% of human tumors, has been shown to be dependent on the splicing machinery and on at least 3 SFs directly regulated by MYC. However, we currently do not have a comprehensive understanding of which component(s) of the splicing machinery are regulated by MYC, or of the functions of MYC-induced spliced isoforms. The goal of this proposal is to systematically characterize the mechanisms by which MYC-regulated SFs and spliced isoforms drive tumor growth and maintenance. To begin to address this gap in knowledge, in our preliminary studies we used a mammary cell line harboring an inducible form of MYC to greatly expand the number of known SFs regulated by MYC. We uncovered that MYC activation promotes alternative splicing of >4,000 isoforms and expression of 125 SFs. These SFs are also upregulated in MYC-active breast tumors and can be grouped, based on co-expression, into groups or modules. Six SF-modules highly correlate with MYC activity in breast tumors and cell lines, and are enriched in triple negative breast cancer (TNBC). Which of these SFs play a role in MYC-driven transformation, and whether co-expression of multiple MYC-induced SFs has a stronger tumorigenic effect than individual SFs, is not known. Further, co-expression analysis in 33 TCGA tumors of different tissue origin identified an SF-module shared across all MYC-active tumors, suggesting a pan-cancer vulnerability. We hypothesize that MYC regulates a network of SFs which cooperate in tumor pathogenesis and that disrupting this network could provide a novel strategy to slow growth of MYC-driven tumors. Here, we will leverage our expertise in RNA splicing and cancer biology and apply a functional genomics approach to gain novel insights into MYC's oncogenicity. Aim 1 will characterize the function of 6 MYC-induced SF modules and their splicing targets in TNBC tumor growth in vitro and in vivo. Since it is unknown whether MYC regulates a shared set of isoforms in distinct tissues, Aim 2 will identify pan-cancer splicing signatures predictive of MYC activity and clinical outcomes, which may serve as clinical biomarkers, and will deliver putative neo-antigens generated from MYC-induced isoforms. Finally, Aim 3 will implement genomic approaches to determine which MYC-induced isoforms are essential for the growth of MYC-driven cancer cells and patient-derived organoids. This project will reveal fundamental mechanisms by which oncogenic SFs and their target spliced isoforms drive tumorigenesis downstream of MYC. These results could help inform development of therapeutic strategies for tumors driven by MYC, which remains an undruggable target.