Fig 2: Differential effects of SMARCA4 mutants to rescue cell growth and chromatin accessibility loss after SMARCA2 knockdown.a Long term clonogenic growth of NCI-H1944 cells transduced with SMARCA4 WT or mutants after SMARCA2 knockdown. Representative of at least 3 replicates. b Immunoblot of cells from a (representative of at least 3 replicates). c Heatmap of ATAC-seq changes at sites after SMARCA2 knockdown in cells from a (n = 2 per construct). Values represent log2 fold-change relative to LACZ control after SMARCA2 knockdown. d Heatmap of SMARCA2 and SMARCA4 occupancy at regions with lower accessibility after SMARCA2 knockdown (sites from c) (n = 2 per construct). SMARCA2 ChIP-seq was performed in NCI-H1944 cells expressing LACZ. SMARCA4 ChIP-seq was performed in NCI-H1944 cells expressing SMARCA4 WT and doxycycline (DOX)-inducible expression of SMARCA2-targeting shRNA. Data are shown as normalized peak counts per million genomic DNA fragments in a 2 kb window around the peak center. Rows are rank ordered by SMARCA2 enrichment. R, replicate; INP, input. e Number of sites closed (left axis, blue bar, n = 2 per construct) and mean percent cell death (right axis, red dot, mean of 3 replicates) after SMARCA2 knockdown in cells from a. f Heatmap of genes downregulated after SMARCA2 knockdown in NCI-H1944 cells transduced with LACZ, WT or K785R mutant (n = 3 per construct). Data are shown as mean-centered normalized reads per kb of transcript per million mapped reads (nRPKM). g Long term clonogenic growth of CAL-12T, NCI-H1435 and HCC1897, which all harbor homozygous SMARCA4 missense mutations, after knockdown of SMARCA2 or SMARCA4 (left). Immunoblot confirming SMARCA2/SMARCA4 protein depletion (right). Data are representative of at least 2 replicates. Source data are provided as a Source Data file.

Fig 3: A947-mediated SMARCA2 degradation synergizes with MCL1 inhibition.a Cell viability in 4 SMARCA4 mutant NSCLC cell lines measured across a small-molecule library of 723 compounds screened as a dose-response in the presence or absence of 100 nM A947 for 5 days. Data are plotted as the difference in the concentration required to inhibit growth by 50% (?IC50) upon -/+ A947 treatment. Two separate MCL1 inhibitors are annotated in red. b Treatment of a representative SMARCA4-mutant cell line (NCI-H1793) with a 9 × 9 matrix titration of A947 with the MCL1 inhibitors, AMG-176 (upper plot) and S63845 (lower plot). Heatmaps depict activity in excess of the Bliss independence model to describe synergistic drug interactions (excess volume). c Live cell monitoring of apoptosis in SMARCA4-mutant NCI-H1944 (left graph) and NCI-H838 (right graph) cells grown in the presence of Caspase-3/7 Green Dye upon treatment with 100 nM A947 and/or 1 µM AMG-176. Data are presented apoptotic object count (mean ± s.d) in triplicate cultures. Significance was calculated by a two-, unpaired t-test; p = 0.0078 (NCI-H1944), p = 0.0002 (NCI-H838). Source data are provided as a Source Data file.

Fig 4: (a) Concomitant loss of SMARCA2 and SMARCA4 expression in small cell carcinoma of the ovary, hypercalcemic type measured by immunoblotting. Two high-grade serous ovarian carcinoma (HGSOC#1 and #2) cases were used as a positive control. (b) SMARCA4 overexpression in H1299 non-small cell lung carcinoma and BIN67 small cell carcinoma of the ovary, hypercalcemic type cell lines. Note the upper band in BIN67 cells blotted for SMARCA4 is non-specific. β-Actin is the loading control.

Fig 5: RNA-seq in BRG1, BRM and combined knockdown. a Western blot of HepG2 cells treated with shRNA targeting BRG1, BRM or both combined. b Log2 normalized read counts of RNA-seq data HepG2 treated with BRG1, BRM or both combined shRNA. c Morphology changes of shRNA conditions. d GSEA analysis of expression changes following shRNA targeting BRG1 and BRM. f Fold changes of genes significantly differentially expressed and bound by BRG1 and BRM. g Effect on genes in f following treatment with the individual and double knockdown shRNA