PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability

Cancer Discov. 2017 Aug;7(8):884-899. doi: 10.1158/2159-8290.CD-16-1297. Epub 2017 Apr 26.


Alveolar rhabdomyosarcoma is a life-threatening myogenic cancer of children and adolescent young adults, driven primarily by the chimeric transcription factor PAX3-FOXO1. The mechanisms by which PAX3-FOXO1 dysregulates chromatin are unknown. We find PAX3-FOXO1 reprograms the cis-regulatory landscape by inducing de novo super enhancers. PAX3-FOXO1 uses super enhancers to set up autoregulatory loops in collaboration with the master transcription factors MYOG, MYOD, and MYCN. This myogenic super enhancer 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 super enhancers. Furthermore, PAX3-FOXO1 recruits and requires the BET bromodomain protein BRD4 to function at super enhancers, resulting in a complete dependence on BRD4 and a significant susceptibility to BRD inhibition. These results yield insights into the epigenetic functions of PAX3-FOXO1 and reveal a specific vulnerability that can be exploited for precision therapy.Significance: PAX3-FOXO1 drives pediatric fusion-positive rhabdomyosarcoma, and its chromatin-level functions are critical to understanding its oncogenic activity. We find that PAX3-FOXO1 establishes a myoblastic super enhancer landscape and creates a profound subtype-unique dependence on BET bromodomains, the inhibition of which ablates PAX3-FOXO1 function, providing a mechanistic rationale for exploring BET inhibitors for patients bearing PAX-fusion rhabdomyosarcoma. Cancer Discov; 7(8); 884-99. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 783.

MeSH terms

  • Animals
  • Cell Cycle Proteins
  • Cell Line, Tumor
  • Chromatin / genetics
  • Enhancer Elements, Genetic / drug effects
  • Enhancer Elements, Genetic / genetics*
  • Epigenesis, Genetic / drug effects
  • Epigenesis, Genetic / genetics
  • Female
  • Humans
  • Male
  • Mice
  • MyoD Protein / genetics
  • Myogenin / genetics
  • N-Myc Proto-Oncogene Protein / genetics
  • Nuclear Proteins / genetics*
  • Oncogene Proteins, Fusion / genetics*
  • Paired Box Transcription Factors / genetics*
  • Protein Binding / genetics
  • Protein Domains / genetics
  • Rhabdomyosarcoma, Alveolar / drug therapy*
  • Rhabdomyosarcoma, Alveolar / genetics
  • Rhabdomyosarcoma, Alveolar / pathology
  • Small Molecule Libraries / administration & dosage
  • Transcription Factors / genetics*
  • Xenograft Model Antitumor Assays


  • BRD4 protein, human
  • Cell Cycle Proteins
  • Chromatin
  • MYCN protein, human
  • MYOG protein, human
  • MyoD Protein
  • MyoD1 myogenic differentiation protein
  • Myogenin
  • N-Myc Proto-Oncogene Protein
  • Nuclear Proteins
  • Oncogene Proteins, Fusion
  • PAX3-FOXO1A fusion protein, human
  • Paired Box Transcription Factors
  • Small Molecule Libraries
  • Transcription Factors