Fig. 5: BRD9 binds a gene quartet on chromosome 1 and displays selective dependency in DepMap.

A Volcano plot depicting differentially expressed genes between 18 SF3B1^MUT and 17 SF3B1^WT subset #2 cases with 22 downregulated and 55 upregulated genes ( | log₂FC | ≥ 0.58 and FDR < 0.01). B Unsupervised clustermap illustrating the distinct clustering of SF3B1^MUT and SF3B1^WT subset #2 cases based on differential gene expression. The four neighboring genes, NOL9, TAS1R1, ZBTB48, and KLHL21, located on chromosome 1 are depicted in color. The Ward method and the Euclidean metric were employed. C Karyoplot of chromosome 1 displaying differentially expressed genes between SF3B1^MUT and SF3B1^WT subset #2 cases. Examination of chromosomal positions revealed four neighboring genes, NOL9, TAS1R1, ZBTB48, and KLHL21. D Venn diagram showing the overlap of genes with differential expression between SF3B1^MUT and SF3B1^WT cases in three independent datasets; subset #2 CLL, ICGC CLLE-ES [30, 31], and TCGA CLL [29, 33, 34]. For the differential gene expression analyses of the latter two datasets see Supplementary Fig. 10A–E. ZBTB48 appeared upregulated in all three datasets, while TAS1R1 in subset #2 CLL and ICGC CLLE-ES. E Venn diagram showing the overlap of genes with higher expression levels in SF3B1^MUT subset #2 cases and increased chromatin accessibility in SF3B1^MUT CLL cases from Beekman et al. [47]. The overlap comprises NOL9, TAS1R1, ZBTB48, and KLHL21. F Coverage tracks from ChIP-seq data sourced from the ENCODE database [35, 36], based on the CML cell line K562, illustrating the binding of BRD9 and the ncBAF complex subunits SMARCA4 and SMARCC2 to the gene quartet region on chromosome 1. The promoters for these genes appear active based on the signal for H3K27ac, H3K4me3, H3K9ac, and H3K79me2, and transcriptionally active based on the H3K36me3 signal, whereas transcriptional repression is low based on the low signal for H3K27me3 and H3K9me3. G Gene essentiality map showing the relationship between efficacy and selectivity of genes in shinyDepMap [37, 38]. SF3B1 appears as a non-selective dependency with high efficacy, while BRD9 as a selective dependency with high efficacy. BRD9 is in the dependency region of PIK3R1, EZH2, and FBXW7. H Functional similarity clustering showing a chromatin remodeling dependency cluster connected to the BRD9 dependency signature in shinyDepMap. BRD9 clusters with SMARCD1, a BAF complex subunit, subunits of the Mediator complex, p300/CBP subunits, and subunits of the SAGA complex. I BRD9 dependency ranking of the 1086 DepMap (22Q2) cell lines. For CLL cell lines, gene effect scores are given within the parenthesis. WT: wildtype; MUT: mutated; FDR: false discovery rate; FC: fold change.