Rhabdomyosarcoma (RMS) is driven by transcription factors that set up super-enhancers: large clusters of transcriptional machinery accumulated at oncogenes. Super-enhancers are also the key vulnerability of RMS, as we have revealed by CRISPR screening and chemical genomics. However, the identification of super-enhancers is inconsistent, because they are extracted from 1-dimensional ChIP-seq data, but are in fact 3D genomic objects (“super-clusters”) that form biomolecular condensates (phase-separated droplets). We have now applied new 3D genomics approaches to enable proper discovery of these epigenomic features, also yielding proper enhancer-gene connectivity maps. Furthermore, super-clusters are co-built by transcription factors recruiting p300 (acetylation writer) and BRD4 (acetylation reader). We have generated preliminary evidence that directly perturbing/degrading p300 and BRD4 are the most effective and selective means to shut down super-clusters at all oncogenes driving this childhood cancer. We applied Absolute Quantification of Architecture (AQuA) HiChIP, and were able to uncover the drug-induced 3D folding abnormalities that selectively halt RNA-Polymerase 2 at super-cluster driven oncogenes in this sarcoma.

Citation Format: Berkley E. Gryder, Issra Osman, Adam Durbin, Jun Qi. The 3D epigenome of rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR008.