Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling

Drug resistance represents a major challenge to achieving durable responses to cancer therapeutics. Resistance mechanisms to epigenetically targeted drugs remain largely unexplored. We used bromodomain and extra-terminal domain (BET) inhibition in neuroblastoma as a prototype to model resistance to chromatin modulatory therapeutics. Genome-scale, pooled lentiviral open reading frame (ORF) and CRISPR knockout rescue screens nominated the phosphatidylinositol 3-kinase (PI3K) pathway as promoting resistance to BET inhibition. Transcriptomic and chromatin profiling of resistant cells revealed that global enhancer remodeling is associated with upregulation of receptor tyrosine kinases (RTKs), activation of PI3K signaling, and vulnerability to RTK/PI3K inhibition. Large-scale combinatorial screening with BET inhibitors identified PI3K inhibitors among the most synergistic upfront combinations. These studies provide a roadmap to elucidate resistance to epigenetic-targeted therapeutics and inform efficacious combination therapies. [Display omitted] •PI3K overexpression promotes resistance to BET inhibitors in neuroblastoma•BET inhibitor resistance engenders dependency on PI3K signaling•Enhancer remodeling is associated with transcriptional changes in BETi resistance•PI3K and BET inhibitors are synergistic in vitro and in vivo in neuroblastoma Using functional screens, profiling of drug-resistant cells, and drug combination screens in neuroblastoma, Iniguez et al. show that PI3K pathway activation via enhancer remodeling and transcriptional reprogramming confers resistance to BET inhibitors (BETi) and that PI3K inhibitors synergize with BETi.