Supplementary Figure 3: Synovial sarcoma and malignant rhabdoid tumor cell lines are sensitive to ncBAF perturbation.

(a). Schematic for CRISPR-Cas9-based synthetic lethal screening. (b). CERES dependency scores for ncBAF subunits BRD9, GLTSCR1, and SMARCD1 across all soft tissue and bone cancers, ranked by BRD9 score. (c). Waterfall plots of ATARIS (Project DRIVE) scores across n = 387 cancer cell lines for indicated subunits; dashed line = −0.75 score. (d). BAF subunit perturbations in WT, SS, and MRT settings. (e). Heatmap of the z-score of CERES scores across all n = 408 cancer cell lines ranked by median z-score. (f). Immunoblot for ncBAF subunits in HEK-293T cells upon 250nM dBRD9 treatment or BRD9 KO (n = 2). See also Supplementary Figure 7m. (g). Immunoblot and proliferation on SYO-1 cells with either SS18-SSX1 (shSSX) or control (shCtrl) (n = 2 biologically independent experiments for each). Each data point represents mean ± SD from n = 3 biologically independent samples, p-value calculated by two-sided t-test on day 20. See also Supplementary Figure 7n, Supplementary Table 2. (h). Immunoblot and proliferation (n = 1 experiment) performed on SYO-1 cells treated with GLTSCR1 (shGLT1) or a non-targeting guide. Each data point is mean ± SD from n = 3 biologically independent samples, p-value calculated by two-sided t-test on day 7. See also Supplementary Table 2 (i, j). FACS-based cell cycle analysis (i) and Annexin V staining (j) for SYO-1 cells after 8 days of compound treatment (n = 1). (k). (Left) Immunoblot on G401 MRT cells treated with DMSO or dBRD9 (250 nM) (n = 2 biologically independent experiments); (Right) Proliferation experiments performed in G401, each data point represents mean ± SD from n = 3 biologically independent samples, p-value calculated by two-sided t-test on day 7. See also Supplementary Figure 7o, Supplementary Table 2. (l). Proliferation experiment in SMARCB1-intact ESX cells treated with DMSO or dBRD9 (250nM). Each data point represents mean ± SD from n = 3 biologically independent samples. (m, n). Colony formation assay (as in Fig. 3i) performed on HSSYII (m) and Aska (n) cells (n = 2 biologically independent experiments). (o, p, q). Colony formation performed on HCT-116 (n), Calu-6 (o), and RD rhabdomyosarcoma (p) cell lines (n = 2 biologically independent experiments). (r). SS18 and SMARCC1 IP/immunoblot in BRD9 KO HEK-293T cells (n = 2 biologically independent experiments). See also Supplementary Figure 7p.