Abstract 150: Transcriptional rewiring of BET inhibitor treated Ewing sarcoma cells augments their dependency on focal adhesion kinase
Authors: Shireen S. Ganapathi, Emma Wrenn, Nicolas Garcia, Neerja Katiyar, Aya Miyaki, Yuqi Kang, Marina Chan, Taran S. Gujral, Elizabeth R. Lawlor
Journal: Cancer Research (2024)

Abstract Outcomes for patients with recurrent and metastatic Ewing sarcoma (EwS) are dismal and novel therapies are needed. As EwS are initiated and maintained by the EWS::FLI1 transcription factor, agents that target aberrant gene transcription are of interest and bromodomain inhibitors (BETi) have shown promise in preclinical models. Nevertheless, despite initial efficacy, BETi tolerance emerges across tumor types, often via transcriptional rewiring. We reasoned that the therapeutic potential of BETi in EwS could be augmented by identifying and targeting mechanisms of drug resistance. To investigate this, we performed transcriptional and phenotypic profiling of BETi-naïve, responsive, and drug-tolerant (DT) EwS cells and used these data to nominate biologically-informed drug combinations. EwS cells (A673, CHLA10, TC32) were exposed for 72 hrs or 20 days to BMS-986158, a clinical grade BETi being tested in a phase I pediatric clinical trial (NCT0393465). A profound cytostatic effect was observed at 72 hrs but in all cell lines proliferation was restored by 20 days. RNA-seq confirmed reversion of the EWS::FLI1-dependent gene signature at 72 hrs and this was maintained at 20 days, demonstrating continued on-target effects despite restored growth of DT cells. Interrogation of differentially expressed genes between drug naïve, cytostatic, and DT cells indicated that that DT cells had been transcriptionally rewired to more mesenchymal states, with notable upregulation of genes involved in integrin signaling. In support of this, DT populations displayed more fibroblastic morphologies, increased F-actin filaments, and enhanced invasion in collagen-rich 3D culture. In parallel, an unbiased kinase inhibitor screen that exploits mathematical modeling revealed that, while BETi-treated cells were overall more resistant than parent cells to kinase inhibitors, their viability depended on focal adhesion kinase (FAK) activity. Western blot confirmed increased phospho-FAK in DT cells. We next tested BMS-986158 and the FAK-inhibitor Defactinib singly or in combination in vitro and in vivo. Defactinib induced cell death in 2D cultures and blocked invasion of 3D spheroids in collagen. Conversely, BMS-986158 enhanced invasive potential in 3D. The combination of Defactinib and BMS-986158 in naïve and DT populations was highly synergistic in 2D assays. In 3D collagen assays, viability and invasion of DT tumor spheroids were significantly reduced by the combination. Finally, ongoing studies show that the combination of FAK and BET inhibition prolongs survival of mice with EwS tumor xenografts. Thus, our studies reveal that exposure of EwS cells to BETi induces transcriptional rewiring that activates integrin and FAK signaling, restoring proliferation. This work supports further investigation of FAKi as agents that could prevent or reverse the BETi tolerant state in EwS. Citation Format: Shireen S. Ganapathi, Emma Wrenn, Nicolas Garcia, Neerja Katiyar, Aya Miyaki, Yuqi Kang, Marina Chan, Taran S. Gujral, Elizabeth R. Lawlor. Transcriptional rewiring of BET inhibitor treated Ewing sarcoma cells augments their dependency on focal adhesion kinase [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 150.