Potent Smarca2 Targeted Degraders Induce Genetic Synthetic Lethality In Smarca4 Deleted Cancer.

Abstract SWI/SNF complexes play an important role in controlling gene expression by remodeling chromatin. SMARCA2 (BRM) and SMARCA4 (BRG1) are the core subunits of the SWI/SNF complexes which contain ATPase domain and DNA binding bromodomain. SMARCA4 protein expression is lost in some cancers due to damaging mutations (e.g. nonsense, frameshift deletion, splice site mutations) and SMARCA4-deleted cancer cells are highly dependent on its paralog gene SMARCA2 for their survival. Therefore, targeting SMARCA2 in SMARCA4-deleted cancers through the use of selective SMARCA2 degraders induces synthetic lethality. We designed and synthesized a variety of novel SMARCA2 degraders and tested them for degradation potency and selectivity by high-throughput in-cell western blot and probed for both SMARCA2 and SMARCA4 proteins in SMARCA4 WT expressing non-small cell lung cancer (NSCLC) NCI-H520 cells. We identified a unique series of potent SMARCA2 degraders with 20-40 fold greater selectivity for SMARCA2 vs SMARCA4. Global proteomics analysis confirmed that these degraders are highly selective for SMARCA2, and demonstrate minimal degradation of any other protein except PBRM1, another bromodomain VIII family protein. Our data suggest that the greater degradation selectivity observed is a result of preferential SMARCA2 ternary complex formation and/or poly-ubiquitination processing. Global RNA expression analysis shows that treatment with SMARCA2 degraders downregulates gene signatures associated with the cell cycle, cell proliferation, apoptosis and cell adhesion in SMARCA4-deleted NSCLC NCI-H1693 cells. Specifically, we found a significant reduction of gene expression of AXL, SMAD3, MMP2, and KRT80, all of which are important factors for tumor cell signaling and invasion. Additionally, protein set enrichment analysis (PSEA) shows that SMARCA2 degrader-treated NCI-H1693 cells downregulate expression of cell cycle and DNA replication related protein signatures as well as upregulated antigen processing and presentation pathway. A cell line panel analysis for cell viability and clonogenicity demonstrated that our selective SMARCA2 degraders effectively inhibit proliferation of SMARCA4-deleted cancer cells with nanomolar potencies, but not SMARCA4 WT or SMARCA2/4 null cancer cells. Our SMARCA2 degraders also significantly suppressed the growth of patient derived SMARCA4-deleted NSCLC tumor cells in primary 3D culture assay. In summary, consistent with previous studies and genomic perturbation analyses, our potent and selective SMARCA2 degraders induce synthetic lethality in SMARCA4-deleted cancers in vitro. Citation Format: Koichi Ito, Anjana Agarwal, Philip Pitis, Min Wang, Jack Carter, Miles Cowart, Chaofeng Dai, William Gowen-MacDonald, Eliza Elliot, Brian Vidal, Jacob Spruance, Hsin-Yao Tang, Bruce Ruggeri, Liang Lu, Andrew Combs, Hong Lin, Peggy Scherle, Kris Vaddi. Potent SMARCA2 targeted degraders induce genetic synthetic lethality in SMARCA4 deleted cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1139.