Abstract B018: Studying the role of FLI portion of EWS FLI in transcription regulation via modulation of chromatin 3D landscape in Ewing sarcoma

Abstract Ewing sarcoma is an aggressive bone-associated tumor currently treated with dose-intense chemotherapy, radiation, and surgery. Ewing sarcoma affects adolescents and young adults with incidence rate of 3 per million. The hallmark of Ewing sarcoma is a translocated fusion transcription factor named EWS FLI that drives the oncogenic process. The lack of efficient and targeted treatment in Ewing sarcoma directly arises from the poor understanding of how EWS/FLI regulates expression of thousands of genes as well as the current lack of effective targeting of transcription factors. We hypothesize that FLI portion of EWS::FLI containing a crucial alpha-helix plays a novel role in transcription regulation of thousands of genes by modulating chromatin looping. We postulated this hypothesis based on recent evidence from our lab that established an alpha-helix immediately downstream of DNA binding domain as an important player in regulating transcriptional activity in A673 cell line. Structure-function mapping revealed that ETS domain alone was insufficient for full transcriptional regulation. The purpose of this study is to elucidate the mechanism underlying transcriptional regulation by FLI and it is likely to guide future studies on novel therapeutics for Ewing sarcoma patients as transcriptional factors remain elusive targets of therapy. We utilized knockdown/rescue experiments in which EWS FLI was depleted with shRNA and replaced with constructs containing the ETS DNA Binding Domain (DBD) alone or DBD+ (ETS DNA Binding Domain and 4th alpha-helix). The knockdown/rescue experiments were confirmed at mRNA level using qPCR, and at protein level using immunoblots. The binding pattern and transcriptional regulation of DBD and DBD+ were assessed with RNA-Seq respectively. The extent of roles each of these construct play in organization, structure, and function of chromatin are being assessed using Micro-C technique, a variation of Hi-C with improved resolution, higher signal-to-noise ratio and more information on chromatin domain boundaries and chromatin looping. The DNA binding and genomic localization of EWS FLI was unaltered by the deletion surrounding the DNA binding domain (which contains a 4th alpha-helix) in A673 cells. Despite this similarity in genomic localization and binding, the transcriptional output driven by EWS FLI was significantly diminished by the deletion. In addition, we observed this differential transcriptional output by the EWS FLI DBD and DBD+ in another Ewing sarcoma cell line called TTC466. Current work in our lab shows that EWS FLI has a substantial role in shaping the chromatin landscape of Ewing sarcoma cells. We observed this result with Hi-C technique upon the depleting EWS FLI from A673 cells. With this current study, we hope to understand if the flanking region neighboring the DNA binding domain contributes to the chromatin architecture remodeling function of EWS FLI and whether this function could be attributed to the transcriptional output differences in the DBD and DBD+ conditions. Citation Format: Ariunaa Bayanjargal. Studying the role of FLI portion of EWS FLI in transcription regulation via modulation of chromatin 3D landscape in Ewing sarcoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B018.