Alveolar rhabdomyosarcoma is a life-threatening myogenic cancer of children and adolescent young adults, driven primarily by the chimeric transcription factor PAX3-FOXO1 (P3F). The mechanisms by which P3F dysregulates chromatin are unknown. We find P3F reprograms the cis-regulatory landscape by inducing (de novo) super enhancers (SEs). P3F uses SEs to setup auto-regulatory loops in collaboration with master transcription factors MYOG, MYOD and MYCN. This myogenic SE circuitry is consistent across cell lines and primary tumors. Cells harboring the fusion gene are selectively sensitive to small molecule inhibition of protein targets induced by, or bound to, PAX3-FOXO1 occupied SEs. Furthermore, P3F recruits and requires BET bromodomain protein BRD4 to function at SEs, resulting in a complete dependence on BRD4 and a significant susceptibility to BRD inhibition. These results yield novel insights into the epigenetic functions of P3F, and reveal a specific vulnerability that can be exploited for precision therapy.

Gryder, Berkley E; Yohe, Marielle E; Chou, Hsien-Chao; Zhang, Xiaohu; Marques, Joana; Wachtel, Marco; Schaefer, Beat; Sen, Nirmalya; Song, Young K; Gualtieri, Alberto; Pomella, Silvia; Rota, Rossella; Cleveland, Abigail; Wen, Xinyu; Sindiri, Sivasish; Wei, Jun S; Barr, Frederic G; Das, Sudipto; Andresson, Thorkell; Guha, Rajarshi; Lal, Madhu; Ferrer-Alegre, Marc; Shern, Jack F; Zhao, Keji; Thomas, Craig; Khan, Javed;