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.

项目总结