Ewing’s sarcoma is an aggressive pediatric bone and soft-tissue cancer with a pathognomonic chromosomal translocation t(11;22) resulting in expression of EWS-FLI1, an “undruggable” fusion protein acting as a transcriptional modulator. Identification and ranking of repressed EWS-FLI1 target genes essential for cancer cell survival will potentially provide much-needed insights to develop novel therapeutic strategies. We performed a CRISPR activation (CRISPRa) dropout screen in Ewing cells. We generated a clonal SKNMC cell line homogenously expressing the synergistic activation mediator (SAM) CRISPRa system to functionally interrogate repressed EWS-FLI1 target genes. The systems functionality was tested using CD44, a surface marker absent on the surface of Ewing cells. We found robust and stable expression of CD44 after introduction of promoter-targeting gRNAs. The library of repressed EWS-FLI1 target genes, named LIBerty, was constructed to target 872 genes bioinformatically selected from publicly available silenced EWS-FLI1 RNA-Seq datasets as well as genes identified as repressed signature genes in Ewing’s sarcoma via meta-analysis with 3,777 unique guideRNAs. LIBerty was lentivirally delivered into SAM SKNMC cells and data from four biologic replicates were gathered at three time points: three, ten, and 21 days after infection. Cells were harvested and samples were prepared for next-generation sequencing (NGS) via PCR. The NGS data were evaluated with the analysis tool PinAPL-Py. Preliminary analysis of the screen revealed efficient selection of the positive control genes BAD and BBC3. In addition, high-ranking hits included CDKN1A and CDKN1C, both cell cycle regulators and known tumor-suppressor genes. Furthermore, we identified PCDH7 and TGFBR2, two genes already known from the literature to play a role in Ewing’s sarcoma. The presence of validated genes amid highest-ranking candidates confirms robustness of the conducted CRISPRa screen. Further analysis and validation of previously unexplored targets and pathways is currently ongoing. Our CRISPRa screen revealed both known as well as previously unknown EWS-FLI1 repressed genes whose absence of function is essential for tumor cell survival.

Citation Format: Vadim Saratov, Qui A. Ngo, Gloria Pedot, Felix K. Niggli, Beat W. Schaefer. Identification of physiologically relevant EWS-FLI1 target genes in Ewing’s sarcoma via CRISPRa screening [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B19.