Defining and targeting the molecular vulnerabilities of the PAX3-FOXO1 protein in rhabdomyosarcoma

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ABSTRACT – Overall (revised) Fusion-positive alveolar rhabdomyosarcoma (ARMS) remains one of the most fatal but least understood cancers of childhood. The driving oncoprotein in ARMS is the PAX3-FOXO1 fusion protein, a chimeric transcription factor that hijacks normal gene expression and chromatin state. Five-year survival for children with PAX3-FOXO1- positive ARMS is ~30% for all-comers, and <10% when metastatic. Despite the discovery of PAX3-FOXO1 in 1993, treatment strategies for affected children remain unchanged. This deficiency stems equally from a lack of understanding of the basic biology of the disease and an inability to directly target the fusion protein. No systematic or comprehensive approach has been undertaken to identify the proteins and regulatory elements required to support PAX3-FOXO1-mediated tumorigenesis. As a result, the field has been limited to a patchwork of data with no unified scientific strategy. To overcome this, this FusOnC2 Center has an innovative team and dynamic environment in which data interpretation is informed by complementary technological approaches and by biological and clinical knowledge. This comprehensive approach will transform understanding of PAX3-FOXO1-mediated oncogenesis and create opportunities for therapeutic intervention. The Center’s overarching goal is to advance the therapeutic tractability of the PAX3-FOXO1 fusion protein in ARMS by comprehensively identifying the druggable co-regulators, modulators, and intrinsic activities of PAX3-FOXO1. To accomplish this goal, the Center includes two complementary Projects, each led by expert RMS biologists paired with specialists in pioneering experimental approaches undertaking the most cutting-edge research in cancer biology, genomics, proteomics, structural biology, and medicinal chemistry. The Projects will be supported by RMS investigators within each project who will provide curated RMS cell lines, unique human primary RMS tumor cells, and murine models to enable rapid in vitro and in vivo validation and cross-prioritization of targets. An Administrative Core will integrate and coordinate the Center components, providing leadership and oversight, and promoting cross-pollination of ideas and resources. The Overall Specific Aims are to: (1) define and target the PAX3-FOXO1 interactome; and (2) perform chemical probe discovery for PAX3-FOXO1 to create additional tools for investigating the fundamental biology and tractability of PAX3-FOXO1 and fusion-positive RMS. Approaches used include proximity labeling, saturation mutagenesis, single and combinatorial CRISPR screens, high-throughput phenotypic assays, and mechanistically unbiased approaches to chemical probe discovery using novel high-throughput binding assays. We will use information gleaned to prioritize targets and agents for validation and to inform compound optimization and PROTAC preparation. This Center’s strengths and resources will synergize with the FusOnC2 Consortium, speeding development of knowledge generalizable to the biology of multiple fusion oncoproteins in childhood cancers, accelerating advances in clinical care.