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

MYC 调节的 RNA 结合蛋白网络和剪接亚型导致癌症

基本信息

批准号：
10348197
负责人：
OLGA ANCZUKOW-CAMARDA
金额：
$ 51.88万
依托单位：
JACKSON LABORATORY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-02-10 至 2026-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10348197
关键词：
3-Dimensional Address Alternative Splicing Apoptosis Automobile Driving Binding Binding Sites Biological Assay Breast Breast Cancer Cell Breast Cancer Model Breast Cancer cell line Breast Epithelial Cells Cancer Biology Cancer Cell Growth Cancer Patient Cell Line Cell Proliferation Cell model Cells Clinical Clustered Regularly Interspaced Short Palindromic Repeats DNA Data Data Set Development Diagnostic Neoplasm Staging Distant Metastasis Dropout Excision Exons FDA approved Failure Gene Expression Regulation Genes Genetic Transcription Genomic approach Goals Growth Human Image In Vitro Individual Knowledge MYC gene Maintenance Malignant Neoplasms Mammary Neoplasms Methods Molecular Neoplasm Metastasis Oncogenic Oncoproteins Organoids Outcome Pathogenesis Patient-Focused Outcomes Play Primary Neoplasm Process Protein Isoforms Proteins Proteomics Proto-Oncogene Proteins c-myc RAS genes RNA RNA Splicing RNA-Binding Proteins Regulation Research Resistance Role Signal Transduction Spliced Genes Testing The Cancer Genome Atlas Therapeutic Studies Time Tissues Transcript Tumor Markers Tumor Suppressor Proteins base cancer cell cell growth chemical standard clinical biomarkers clinical diagnosis clinically relevant functional genomics in vivo inhibitor insight knock-down malignant breast neoplasm mammary migration neoantigens novel novel marker novel strategies novel therapeutic intervention overexpression patient prognosis predictive signature public database targeted treatment therapeutic development therapeutic target tool transcription factor transcriptome sequencing triple-negative invasive breast carcinoma tumor tumor growth tumorigenesis tumorigenic

项目摘要

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.

概括选择性 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特定细胞中产生哪些转录亚型。异常拼接同种型可以影响癌症的每一项特征，包括细胞增殖、迁移或增加对细胞凋亡的抵抗。调节剪接因子（SF）最近作为一类新的癌蛋白出现和肿瘤抑制剂。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，已被证明依赖于剪接机制和至少 3 个由 MYC 直接监管的 SF。但目前我们还没有全面了解剪接机制的哪些组件受 MYC 调节，或 MYC 诱导剪接的功能同工型。该提案的目标是系统地描述 MYC 调节的机制 SF 和剪接异构体驱动肿瘤生长和维持。为了开始解决这一知识差距，在我们的初步研究中，我们使用了含有可诱导形式 MYC 的乳腺细胞系来极大地扩展 MYC 监管的已知 SF 数量。我们发现 MYC 激活促进选择性剪接 >4,000 种异构体和 125 种 SF 的表达。这些 SF 在 MYC 活性乳腺肿瘤中也上调可以基于共表达分为组或模块。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。其中哪一个 SF 在 MYC 驱动的转化中发挥作用，多个 MYC 诱导的 SF 的共表达是否具有是否比单个 SF 具有更强的致瘤作用尚不清楚。此外，33 个 TCGA 肿瘤中的共表达分析不同组织来源的细胞鉴定出所有 MYC 活性肿瘤共有的 SF 模块，表明存在泛癌脆弱性。我们假设 MYC 调节 SF 网络，这些 SF 协同参与肿瘤发病机制并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，并应用功能基因组学方法来获得对 MYC 致癌性的新见解。目标 1 将表征 6 个 MYC 诱导的 SF 模块的功能和它们在体外和体内 TNBC 肿瘤生长中的剪接靶标。由于尚不清楚 MYC 是否监管不同组织中共享的同种型集，目标 2 将识别预测 MYC 的泛癌剪接特征活动和临床结果，可作为临床生物标志物，并将提供假定的新抗原由 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哪些 MYC 诱导的异构体对于 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 及其目标剪接亚型驱动的基本机制 MYC 下游的肿瘤发生。这些结果可能有助于为治疗策略的制定提供信息 MYC 驱动的肿瘤仍然是一个无法成药的靶点。