Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [ChIP-seq]

Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth. ChIP-seq binding data to evaluate the effect of ETV6 loss in Ewing sarcoma were determined from paired-end sequencting of ChIP-seq samples in A673 and EW8 cell lines. A673 and EW8 Ewing sarcoma cells engineered to express FKBP12F36V-HA-ETV6 were treated with either DMSO control or dTAGV-1 for 6 or 72 hours to induce ETV6 degradation. Duplicates were used for paired-end ChIP-seq experiments used to evaluate differental binding with ETV6 loss. Base line ChIP-seq binding was also evaluated in parental Ewing sarcoma cell lines with single replicates. All ChIP-seq samples have matching input DNA reference sample from the same batch and treatment condition.