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

摘要 RNA选择性剪接是基因表达调控的关键步骤，有助于转录多样性 通过选择在特定时间点在特定细胞中产生哪些转录异构体。异常拼接 异构体可以影响癌症的每个特征，包括增加细胞增殖、迁移或 对细胞凋亡的抵抗。调控剪接因子(SFS)是近年来出现的一类新的癌蛋白 和肿瘤抑制因子。特别是，致癌转录因子MYC的致瘤能力 在50%的人类肿瘤中是失调的，已被证明依赖于剪接机制和 至少3个由MYC直接监管的SFS。但我们目前对此还没有全面的认识。 剪接机械的哪个部件(S)受MYC调节，或者MYC诱导的剪接的功能 异构体。这项提案的目标是系统地描述MYC-1调节的机制。 SFS和剪接的异构体驱动肿瘤的生长和维持。为了开始解决这一知识差距，在 我们的初步研究我们使用了一种含有诱导型MYC的乳腺细胞系来极大地扩增 由MYC监管的已知SFS的数量。我们发现MYC的激活促进了选择性剪接 &gt；4,000个SFS的亚型和表达。这些SFS在MYC活动的乳腺肿瘤中也上调， 可以基于共表达将其分组为组或模块。六个SF模块与MYC高度相关 在乳腺肿瘤和细胞系中的活性，并在三阴性乳腺癌(TNBC)中丰富。这些中的哪一个 SFS在MYC驱动的转化中发挥作用，以及MYC诱导的多个SFS共表达是否具有 比单独的SFS更强的致癌作用，尚不清楚。33例TCGA肿瘤的共表达分析 不同的组织来源发现了一个在所有MYC活动肿瘤中共享的SF模块，提示是泛癌 脆弱性。我们假设MYC调节一个SFS网络，该网络在肿瘤发病机制和 破坏这一网络可以提供一种新的策略来减缓MYC驱动的肿瘤的生长。在这里，我们将 利用我们在RNA剪接和癌症生物学方面的专业知识，应用功能基因组学方法 对MYC致瘤性的新见解。目标1将描述6个MYC诱导的SF模块的功能和 它们的剪接靶点在TNBC肿瘤的体内外生长中。由于目前尚不清楚MYC是否监管 不同组织中共享的一组异构体，Aim 2将识别预测MYC的泛癌剪接特征 活动性和临床结果，可作为临床生物标记物，并将提供推定的新抗原 由MYC诱导的异构体产生。最后，目标3将实施基因组方法来确定 MYC诱导的异构体对于MYC驱动的癌细胞和患者衍生的有机化合物的生长是必不可少的。 该项目将揭示致癌SFS及其靶剪接异构体驱动的基本机制 MYC下游的肿瘤形成。这些结果可能有助于为制定治疗策略提供信息 由MYC驱动的肿瘤，它仍然是一个无法药物治疗的靶点。

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.