SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily A member 2 (SMARCA2) is an ATP-dependent DNA helicase and a catalytic component of the SWI/SNF complex. SWI/SNF-mediated nucleosome remodeling is a critical regulator of chromatin accessibility resulting in transcriptional regulation of gene sets that determine and maintain cell state. SMARCA2's role as the catalytic driver of SWI/SNF activity is mutually exclusive with that of its close paralog, SMARCA4. Here, we show that the synthetic lethal relationship between SMARCA2 and SMARCA4 can be genetically engineered bi-directionally in SMARCA2/SMARCA4 wild type (WT) cell lines. While knockout (KO) of either protein individually minimally affects cell growth, a genetically engineered cell line with loss of either SMARCA2 or SMARCA4 becomes sensitive to loss of its paralog. While SMARCA2 is infrequently lost through genetic mutation, SMARCA4 mutations occur in a wide variety of cancer types. We present CRISPR-Cas9 pooled screening data showing that cell lines with SMARCA4 mutations have a selective sensitivity to loss of SMARCA2 across multiple cancer indications, including NSCLC and ovarian carcinoma. SMARCA2 and SMARCA4, though partially redundant, also play unique roles within the cell as is evidenced by the unique set of transcriptional changes that occur in the SMARCA2/4 isogeneic cell lines, including the differential modulation of genes involved in TGFB signaling, regulation of angiogenesis, and in determinants of epithelial or mesenchymal cell state. ChIP-seq studies show changes in SWI/SNF occupancy as well as in the chromatin landscape that are specific to the loss of either SMARCA2 or SMARCA4. These isogenic cell lines also respond differently to treatment with a novel SMARCA2/4 inhibitor, Compound 1, in transcriptional as well as functional effects, providing evidence that dual inhibition with a small molecule may not be equivalent to the complete genetic ablation of these two proteins The NCI-H358 NCSLC cell line expresses WT SMARCA2 and SMARCA4 and is weakly sensitive to treatment with Compound 1. CRISPR-Cas9 mediated KO of SMARCA4 confers several-fold greater sensitivity to treatment with the novel inhibitor compared to the parental cell line. Surprisingly, KO of SMARCA2 does not confer sensitivity to inhibitor treatment. This selectivity sensitivity to treatment with Compound 1 that we observe in the SMARCA4-KO cell line is also observed across a panel of SMARCA4-mutant NSCLC. The relationship between the transcriptional and phenotypic changes that occur in these isogenic knockout lines as well as in SMARCA4-mutated NSCLC cell lines in response to SMARCA2/4 inhibitor treatment have revealed novel mechanisms driven by specific SWI/SNF complexes. These data have allowed us to better understand the potential therapeutic utility of a SMARCA2/4 inhibitor in both a SMARCA4-mut and SMARCA4-wt NSCLC patient population.
Citation Format: Lindsey W. Eichinger, Chloe Pantano, Vinny Motwani, Dorothy Brach, Selene Howe, Alejandra Raimondi, Daniel T. Dransfield, Kenneth W. Duncan, Kim Stickland, Cuyue Tang, Neil A. Farrow, John Lampe, Suzanne L. Jacques, Allison E. Drew. Aberrant SWI/SNF complexes lacking SMARCA2 or SMARCA4 differentially affect cell state and response to a novel SMARCA2/4 inhibitor [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2924.