ChIP-Sequencing of H3K27me3 and H3K9me3 repression in response to drug treatment in Ewing Sarcoma

Transcription factors are challenging drug targets in need of novel therapeutic approaches. The successful translation of transcription factor directed therapies will require an understanding of the mechanism of target suppression both to credential the therapy and to ensure sustained target suppression in vivo. We have previously shown that the small molecule trabectedin blocks the activity of the EWS-FLI1 transcription factor and reverses the expression of highly specific EWS-FLI1 target genes. In this report, we show that the drug redistributes EWS-FLI1 in the nucleus and at the same time evicts the SWI/SNF chromatin remodeling complex from chromatin to reverse the pioneer activity of this transcription factor. Importantly, these effects are concentration dependent and guide the approach to inhibit and sustain inhibition of EWS-FLI1 in vivo. Further potentiation of the effect in animal models requires the addition of a topoisomerase I inhibitor irinotecan to maintain suppression and trigger epigenetic switch leading to relatively unorganized differentiation.