Mentor Name: Jun Qi

Rhabdomyosarcoma (RMS) is a pediatric tumor reminiscent of immature skeletal muscle. The most aggressive subtype contains gene fusions between PAX3/7 and FOXO1 (termed fusion protein RMS or FP-RMS), which predict poor 5-year survival rates approximated at 20-30%. The current treatment options do not guarantee long-term disease-free survival and are often harsh, significantly hurting the quality of life for these young patients. Thus, there is a critical unmet need to understand the function of this fusion protein and develop a more targeted precision medicine approach for treating these aggressive pediatric tumors. In this study, we will mainly focus on models of FP-RMS that contain the PAX3-FOXO1 fusion. Within these cell lines, the survival of some cell lines is dependent on PAX3-FOXO1 functions, such as RH4, RH28 while others may survive even with the loss of FP function, such as RH30. Thus, the key survival and tumor maintenance function of PAX3-FOXO1 remains unclear. While FP-RMS has been reported to depend on chromatin remodeling complexes, such as SWI/SNF (also-called BAF) complex, we discovered that key functions of PAX3-FOXO1 in FP-RMS cells rely more on other chromatin remodeling complexes, such as the Nuclear Remodeling (NURF) complex, a member of Imitation SWItch (ISWI) chromatin remodeling complexes. Particularly, PAX3-FOXO1 is directly interacting with bromodomain PHD-finger transcription factor (BPTF). The loss of BPTF induced by a small molecule selective proteolysis targeting chimera (PROTAC) degrader we developed disassociates PAX3-FOXO1 from histones. This displacement of PAX3-FOXO1 induces cell death in PAX3-FOXO1-dependent cell lines, while the PAX3-FOXO1 independent FP-RMS line did not show any anti-proliferative response toward BPTF degradation. Our exciting findings lead to our key hypothesis that BPTF is a regulator of PAX3-FOXO1 in FP-dependent RMS. We predict that our novel BPTF degrader can effectively interrupt the key function of PAX3-FOXO1. We will use our chemical biology tool together with genetic methods to ask, “What is the molecular mechanism that creates the dependency of FP-RMS on BPTF?” (Aim 1). “Can we further optimize our BPTF degrader to fully assess the therapeutic potential of BPTF PROTAC in FP-RMS in vitro and in vivo?” (Aim 2). We will fully assess the therapeutic potential of BPTF PROTAC in FP-RMS xenograft model. Overall, we identified a novel target BPTF and identify a strategy to target it. Our study could lead to develop a promising precision medicine strategy that interrupts the key functions of fusion proteins and generate effective and low toxic treatment development.