Decreased expression of CXCR4 by cBAF inhibition impairs leukemic cell migration toward CXCL12. (A) MA plot showing differentially expressed genes in SMARCA4/2 knockout Jurkat cells. Significantly (adjusted P < .05) upregulated and downregulated genes are highlighted in red and blue, respectively. Genes identified in the migration screen (Figure 1B) are circled in black. (B-C) CXCR4 expression levels in the indicated knockout Jurkat cells (B) and BRM014-treated T-ALL cell lines (C) by RNA-seq analysis. Data are shown as mean ± SD (n = 3). (D) Cell surface CXCR4 expression on the indicated knockout Jurkat cells. Expression was determined by flow cytometry. Data are shown as mean ± SD (n = 3). (E) Cell surface CXCR4 expression on T-ALL cell lines and T-ALL PDX cells treated with BRM014 for 2 or 4 days. Expression was determined by flow cytometry. (F) Cell surface CXCR4 expression on Jurkat cells after BRM014 withdrawal. Expression was determined by flow cytometry. (G) Cell surface CXCR4 expression on the indicated knockout Jurkat cells with exogenous CXCR4 or control cDNA expression. Data are shown as mean ± SD (n = 3). (H) Migration activity toward CXCL12 of the indicated knockout Jurkat cells with exogenous CXCR4 expression. AAVS1 knockout cells were used as a control. Data are shown as mean ± SD (n = 3). Two-tailed Student t tests were used to assess statistical significance in panels B, C, D, F, G, and H (∗∗∗P < .001; ∗∗P < .01; ∗P < .05; n.s., not significant). MA, log ratio and mean average; RNA-seq, RNA sequencing; SD, standard deviation.