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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要该提案重点关注以下事实：每人有 400 名儿童和年轻人患有横纹肌肉瘤 (RMS) 一年中，绝大多数患有高危疾病的人都不会是长期、无病的幸存者之一。高风险疾病的主要驱动因素是常见的 PAX3-FOXO1 融合蛋白的存在。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，这些儿童的治疗方法尚未找到。而年轻人几十年来也没有根本改变！阐明 FP-RMS 和 PAX3-FOXO1 生物学的主要挑战至少有两个方面：首先，我们知道关于 PAX3-FOXO1 融合蛋白的生物学的很多内容，包括协同遗传或它需要表观遗传变化来驱动 RMS 的形成和进展，但我们的知识并非如此。足够复杂，可以专注于可以利用的合作遗传/表观遗传变化的子集其次，虽然 FP-RMS 存在一些优雅的实验模型，但纯粹是这样。在同基因系统中，PAX3-FOXO1 表达可以快速且完全地“打开”和“关闭” 我们相信，解决这两个挑战将为实现这一目标迈出基础性的一步。识别由 FP-RMS 中的致癌融合蛋白驱动的可操作靶标。在接下来的两年里，我们可以通过完成两个互补但独立的目标来实现这一目标：我们应用创新的计算流程来提名致癌驱动因素和肿瘤抑制因素 FP-RMS 中的遗传和表观遗传变化，并在基于 CRISPR/Cas9 的“迷你库”中对其进行功能验证其次，我们将开发并验证一种新的降解决定子。基于系统，其中人类 PAX3-FOXO1 可以在本地以动态和可逆的方式进行控制除其他外，Aim 2 中创建的系统将用于识别如何 Aim 1 的关键驱动器和抑制器由 PAX3-FOXO1 控制，我们的成功将为我们的成功奠定基础。未来以假设为导向的 FP-RMS 研究，为科学界生成可共享的数据和工具，并说明了应对其他易位驱动的癌症的一般方法，这些癌症带来了类似于 FP-RMS。