Abstract 6227: A systems biology approach for identifying targetable vulnerabilities in Ewing sarcoma

Abstract

Abstract Background: Targeting fusion oncoproteins like the canonical EWS/ETS fusions in Ewing sarcoma remain an elusive challenge. To circumvent these challenges, we have utilized transcriptome-based systems biology approaches that identify targetable Master Regulator proteins (MRs) critical to maintaining the cancer cell state. OncoTarget analysis generates a rank order list of targetable MRs while OncoTreat analysis uses cognate cell lines matched to patient tumors to identify drugs that invert the MR signature. We used OncoTarget and OncoTreat analyses to identify existing drugs which could be repurposed to target MRs active in Ewing sarcoma. Methods: A gene regulatory interactome was developed from 122 pediatric sarcoma samples to enable identification of MR targets using OncoTarget. To enable OncoTreat analysis, 2 cognate cell lines were subjected to high-throughput drug perturbational screens. Cells were treated with sub-lethal concentrations of 335 compounds (FDA approved or investigational drugs). Ex vivo drug screens using PDX-derived cells were performed as a complementary assay to validate predictions. In vivo validation was performed in Ewing sarcoma PDXs. Results: The MR architecture of 3 Ewing sarcoma PDX models was evaluated using OncoTarget. OncoTreat analysis identified 43 drugs predicted to be active in at least 1 Ewing sarcoma PDX while OncoTarget analysis identified 20 MR targets predicted in at least 1 Ewing sarcoma PDX. DOT1L and AURKB were predicted targets across multiple Ewing sarcoma PDXs. Ex vivo screening of dissociated cells from 2 Ewing sarcoma PDXs was performed to select the most potent agents for in vivo validation. Three OncoTreat (clarithromycin, tivozanib and obataclax) and two OncoTarget (DOT1L targeted with EPZ-5676 and AURKB targeted with baracertib) predicted drugs were evaluated in a STAG2 mutant Ewing sarcoma PDX and all demonstrated significant abrogation of tumor growth including complete regression in baracertib-treated animals (p<0.01). Conclusion: These systems biology approaches can identify non-oncogene encoded vulnerabilities in Ewing sarcoma and hold the potential for expanding the number of therapeutic options for tumors driven by untargetable oncoproteins. Citation Format: Filemon S. Dela Cruz, Prabhjot S. Mundi, Armaan Siddiquee, Kristina Guillan, Daoqi You, Glorymar Ibanez Sanchez, Andoyo Ndengu, Andrea Califano, Andrew L. Kung. A systems biology approach for identifying targetable vulnerabilities in Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6227.