Rewiring the fusion oncoprotein EWS/FLI1 in Ewing sarcoma with bivalent small molecules [RNA-seq]

Deregulated transcription is a defining hallmark of cancer, especially pediatric malignancies, which are frequently driven by fusion transcription factors. Targeting transcription factors directly has been challenging as they lack druggable pockets. Recently, chemically induced proximity has enabled the rewiring of transcriptional activators to drive expression of pro-apoptotic genes using bivalent small molecules. Targeting fusion transcription factors, such as EWS/FLI in Ewing sarcoma, with these compounds, may open new therapeutic venues. Here, we develop a small molecule, EB-TCIP, that recruits FKBP12F36V-tagged EWS/FLI1 to DNA sites bound by the transcriptional regulator BCL6, leading to rapid and sustained expression of BCL6 target genes. EB-TCIP activity is dependent on ternary complex formation and specific to cells that express FKBP-EWS/FLI1. This proof-of-concept study demonstrates that EWS/FLI1 can be relocalized on chromatin to induce genes that are ordinarily regulated by a transcriptional repressor. Insights herein will guide the development of bivalent molecules for fusion transcription factors. Investigate alterations in gene expression after BCL6 knock out in two cell lines at 4 and 8 hours (in two Ewing sarcoma cell lines) and EB-TCIP gene expression changes at 8 and 24 hours with three replicates