Abstract A058: Investigating the molecular role of BRD9 in synovial sarcoma

Abstract

Abstract Bromodomain-containing protein 9 (BRD9) represents a potential selective vulnerability for tumors with specific alterations in the Brahma-associated factor (BAF) chromatin remodeling complex. One example of such a modification is the incorporation of the SS18-SSX fusion into BAF complexes. This alteration is a hallmark of synovial sarcoma, and thought to drive tumorigenesis. As BRD9 is a subunit unique to ncBAF, tumors that depend on ncBAF for survival may be susceptible to BRD9 degradation. Accordingly, selective BRD9 degradation is a potential therapeutic approach to treat such diseases. Previous work has shown that loss of BRD9 causes cell and tumor proliferation defects (Brien et al. 2018, Michel et al. 2018). To explore the mechanism by which degradation of BRD9 causes cell and tumor proliferation defects in synovial sarcoma, we utilized a multi-omic approach using RNA-seq, ATAC-seq, and ChIP-seq data to understand the molecular impact of loss of BRD9 on relevant cell lines and animal model tumors. ChIP-seq revealed genome-wide colocalization of BRD9 and Myc on chromatin, and BRD9 degradation can lead to MYC loss at the majority of these co-bound regions. Genes commonly regulated in synovial cell lines treated with a BRD9 degrader in vitro and/or in vivo are enriched in MYC target genes, ribosome biogenesis genes and cell cycle genes. Furthermore, the genes commonly downregulated in synovial cell lines treated with a BRD9 degrader have notable MYC binding at their promoter regions. Therefore, we propose that these downregulated genes might be potential MYC targets, specifically in synovial sarcoma, and that downregulation leads to observed proliferation defects. Citation Format: Salih Topal, Claudia Dominici, Michael Collins, David L Lahr, Qianhe Zhou, Flore Uzan, David Mayhew, Ammar Adam, Victoria Garbitt-Amaral, Brandon Antonakos, Oliver Mikse, Hafiz Ahmad, Salonee Parikh, Mei Yun Lin, Hsin-Jung Wu, Gabriel Sandoval, Luis M. M. Soares, Jordana Muwanguzi, Huawei Chen, Zhaoxia Yang, Jason T. Lowe, Matt Netherton, Laura Zawadzke, Johannes Voigt, Liyue Huang, Sabine Ruppel, Ho Man Chan, Ryan Kruger, David S. Millan, Scott Innis, Steven F. Bellon. Investigating the molecular role of BRD9 in synovial sarcoma [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A058.