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

总结 选择性RNA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物同种型。异常剪接 同种型可以影响癌症的每一个特征，包括增加的细胞增殖、迁移， 抗凋亡。调节性剪接因子是近年来发现的一类新的癌蛋白 和肿瘤抑制剂。特别是，致癌转录因子MYC的致瘤能力， 在>50%的人类肿瘤中失调，已显示依赖于剪接机制和 至少3个由MYC直接调节的SF。然而，我们目前还没有全面了解， 剪接机制的哪些组分受MYC调节，或者MYC诱导的剪接机制的功能的哪些组分受MYC调节， 同种型。该提案的目标是系统地描述MYC调节的机制， SF和剪接的同种型驱动肿瘤生长和维持。为了开始填补这一知识空白， 我们的初步研究中，我们使用了一种含有可诱导MYC的乳腺细胞系， MYC调控的已知SF数量。我们发现MYC的激活促进了 > 4，000种同种型和125种SF的表达。这些SF也在MYC活性乳腺肿瘤中上调， 可以根据共表达分组为组或模块。六个SF模块与MYC高度相关 在乳腺肿瘤和细胞系中具有活性，并且在三阴性乳腺癌（TNBC）中富集。哪些 SF在MYC驱动的转化中发挥作用，并且多个MYC诱导的SF的共表达是否具有与MYC诱导的转化相关的作用。 比单个SF更强的致瘤作用尚不清楚。此外，在33个TCGA肿瘤中进行共表达分析， 不同组织来源的研究人员发现了所有MYC活性肿瘤共有的SF模块，这表明泛癌症 易损性.我们假设MYC调节SF网络，SF网络在肿瘤发病机制中起作用， 破坏这个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致癌性的新见解。目的1将描述6个MYC诱导的SF模块的功能， 它们在体外和体内TNBC肿瘤生长中的剪接靶点。由于不知道MYC是否调节 Aim 2是不同组织中的一组共享亚型，它将识别预测MYC的泛癌剪接特征 活性和临床结果，可作为临床生物标志物，并将提供推定的新抗原 由MYC诱导的同种型产生。最后，目标3将实施基因组方法，以确定 MYC诱导的亚型对于MYC驱动的癌细胞和患者来源的类器官的生长至关重要。 该项目将揭示致癌SF及其靶向剪接异构体驱动 MYC下游的肿瘤发生。这些结果可以帮助开发治疗策略， 由MYC驱动的肿瘤，这仍然是一个不可治愈的目标。

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.