Nominating vulnerabilities in fusion oncoprotein-driven rhabdomyosarcoma

提名融合癌蛋白驱动的横纹肌肉瘤的脆弱性

• 批准号: 10642101
• 负责人: STEPHEN X SKAPEK
• 金额: $ 23万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-16 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10642101
• 关键词: Acetylation; Auxins; Bayesian Method; Biological; Biological Assay; Biology; CRISPR/Cas technology; Cell Line; Cell model; Cells; Child; Chimeric Proteins; Clinical Research; Clinical Trials; Clustered Regularly Interspaced Short Palindromic Repeats; Communities; Computational algorithm; Cultured Cells; DNA sequencing; Data; Data Set; Disease; Engineering; Enhancers; Epigenetic Process; Experimental Models; FOXO1A gene; Foundations; Fusion Oncogene Proteins; Future; Gene Dosage; Gene Expression; Gene Expression Profiling; Genes; Genetic; Genetic Enhancer Element; Genomics; Goals; Human; Institution; International; Knowledge; Malignant Childhood Neoplasm; Malignant Neoplasms; Mediating; Methylation; Modeling; Molecular; Molecular Biology; Mutation; Neoplastic Cell Transformation; Oncogenic; Outcome; PAX3 gene; PAX7 gene; Pediatric Oncology Group; Prognostic Marker; Reagent; Recurrence; Research; Research Project Grants; Rhabdomyosarcoma; Soft tissue sarcoma; Specimen; Subgroup; Survivors; System; Talents; Therapeutic; Translating; Translational Research; Tumor Suppressor Proteins; Work; analysis pipeline; candidate identification; computational pipelines; disorder risk; epigenome; genomic tools; high risk; innovation; next generation; next generation sequencing; novel; patient derived xenograft model; promoter; small hairpin RNA; stem; success; tool; transcriptome sequencing; tumor; young adult

Project Summary This proposal focuses on the fact that 400 children and young adults develop rhabdomyosarcoma (RMS) each year, and the vast majority of those with high-risk disease will not be long term, disease-free survivors. One of the major drivers of high-risk disease is the presence of PAX3-FOXO1 fusion protein. In what is commonly referred to as fusion-positive (FP) RMS, next generation DNA and RNA sequencing tools and molecular and cell biological approaches have yet to uncover targetable cancer drivers. As such, the treatment for these children and young adults has not fundamentally changed for several decades! Major challenges to unraveling FP-RMS and the biology of PAX3-FOXO1 are at least two-fold: First, we know much about the biology of the PAX3-FOXO1 fusion protein, including the fact that cooperating genetic or epigenetic changes are needed for it to drive RMS formation and progression. But our knowledge is not sophisticated enough to focus on the subset of cooperating genetic/epigenetic changes that can be leveraged as therapeutic vulnerabilities. Second, though some elegant, experimental models exist for FP-RMS, pure isogenic systems in which PAX3-FOXO1 expression can be quickly and completely turned “on” and “off” are not available. We are convinced that solving both of these challenges will provide a foundational step toward identifying actionable targets that are driven by the oncogenic fusion protein in FP-RMS. Over the next two years, we can accomplish this by completing two complementary but independent aims. First, we apply an innovative computational pipeline to nominate oncogenic drivers and tumor suppressors based on genetic and epigenetic changes in FP-RMS, and functionally validate them in a CRISPR/Cas9-based “mini-pool” assay using both FP and fusion-negative RMS models. Second, we will develop and validate a new degron- based system in which human PAX3-FOXO1 can be controlled in a dynamic and reversible fashion in native RMS cells and PDX models. Among other things, this system created in Aim 2 will be utilized to identify how the key drivers and suppressors from Aim 1 are controlled by PAX3-FOXO1. Our success will lay the foundation for future, hypothesis-directed studies of FP-RMS, generate sharable data and tools for the scientific community, and illustrate a general approach to tackling other translocation-driven cancers that pose challenges similar to FP-RMS.

项目摘要 该提议重点是400名儿童和年轻人发展出横纹肌肉瘤（RMS） 一年，患有高风险疾病的绝大多数人不会长期无病生存。之一 高风险疾病的主要驱动因素是PAX3-FoxO1融合蛋白的存在。在通常的 被称为融合阳性（FP）RMS，下一代DNA和RNA测序工具以及分子和细胞 生物学方法尚未发现有针对性的癌症驱动因素。因此，对这些孩子的治疗 几十年来，年轻人从根本上没有改变！ 阐明FP-RM和PAX3-FOXO1的生物学的主要挑战至少是两个倍：首先，我们知道 关于Pax3-Foxo1融合蛋白的生物学的很多内容，包括合作遗传或 需要表观遗传学变化才能驱动RMS的形成和进展。但是我们的知识不是 软化的足够专注于可以利用的遗传/表观遗传变化的子集 作为治疗脆弱性。其次，虽然有一些优雅的实验模型用于FP-RMS，但纯净 pax3-foxo1表达可以迅速而完全打开“ ON”和“ OFF”的同基因系统不是 可用的。我们坚信，解决这两个挑战将为迈向 识别由FP-RMS中的致癌融合蛋白驱动的可起作用靶标。 在接下来的两年中，我们可以通过完成两个完整但独立的目标来实现这一目标。第一的， 我们应用创新的计算管道来提名基于 FP-RMS的遗传和表观遗传变化，并在基于CRISPR/CAS9的“迷你池”中验证它们 使用FP和融合阴性RMS模型的测定。其次，我们将开发并验证新的Degron- 基于人类PAX3-FOXO1可以以动态和可逆的方式控制人类PAX3-FOXO1的系统 RMS细胞和PDX模型。除其他外，AIM 2中创建的该系统将用于确定如何确定 AIM 1的关键驱动因素和补品由PAX3-FOXO1控制。我们的成功将为 未来，假设指导的FP-RMS研究为科学界生成可共享的数据和工具， 并说明了解决其他以易位驱动的癌症的一般方法 FP-RMS。