cBAF inhibition prevents RUNX1 from binding CDK6 enhancers, downregulates its expression, and affects cell-autonomous growth. (A) Venn diagram showing the overlap among Jurkat dependency genes, genes downregulated in SMARCA4/2 and ARID1A/B knockouts, genes downregulated in all 4 T-ALL cell lines treated with BRM014, and genes commonly expressed in the 4 T-ALL cell lines. The 6 genes, namely BCL11B, CCNB1IP1, CDK6, GDF11, LRP8, and SIT1, were identified. (B-C) BCL11B, CCNB1IP1, and CDK6 expression levels in BRM014-treated human T-ALL cell lines (B) and the indicated knockout Jurkat cells (C) by RNA-seq analysis. Data are shown as mean ± SD (n = 3). (D) ATAC-seq and ChIP-seq data in a 250-kb region including CDK6 enhancers. (E) CDK6 expression levels in Jurkat cells in which RUNX1 binding sites were disrupted by the CRISPR-Cas9 technology, determined by RT-qPCR. Data are shown as mean ± SD (n = 3). (F-H) ChIP-qPCR analysis of RUNX1 (F-H) and H3K27ac (G) at the CDK6 E1 and E2 in the indicated knockout Jurkat cells (F-G) and Jurkat cells treated with DMSO and BRM014 at 1 μM for 6 hours (H). Values in the control are identical with those in Figure 4F-H because the assays were performed in parallel. Data are shown as mean ± SD (n = 3-4). (I) CDK6 expression levels of DMSO- or BRM014-treated Jurkat cells with exogenous CDK6 or control cDNA expression. Data are shown as mean ± SD (n = 3). (J) Eight-day competitive coculture assay of Jurkat cells expressing exogenous CDK6 or control cDNA with control Jurkat cells under DMSO (left) or BRM014 (1μM) treatment (right). Data are shown as mean ± SD (n = 3). Two-tailed Student t test was used to assess statistical significance in panels B, C, E, F, G, H, I, and J (∗∗∗P < .001; ∗∗P < .01; ∗P < .05). cDNA, complementary DNA; DMSO, dimethyl sulfoxide; qPCR, quantitative polymerase chain reaction; RNA-seq, RNA sequencing; SD, standard deviation.