Fig. 2

HDAC1/3/7 inhibition by MS-275 reduces H3K27ac on TSS, enhancers, and SEs in stem-like BrCa cells. a Heatmap of genome-wide H3K27ac ChIP-seq analysis revealed enrichment of H3K27ac around TSS (±1 kb) of 13,804 genes that was reduced following treatment with 1 μΜ MS-275 for 24 h in CSC-like BPLER cells. Coverage profiles for H3K27ac enrichment at non-TSS sites (>1 kb) also showed broad distribution of H3K27ac at 25,095 putative enhancers and SEs, which was reduced following MS-275 treatment. b ChIP-seq profiling in BPLER2 cells revealed reduction in H3K27ac peaks near TSS and to SEs of c-MYC, HDAC7, and VDR genes with MS-275 treatment. c Super-enhancers ranking plot based on H3K27ac signal using the ROSE algorithm [30, 33]. Under normal growth condition (DMSO treatment), we identified 1870 putative SE regions characterized by elevated levels of H3K27ac in CSC-like BPLER cells, which are reduced to 573 H3K27ac peak regions in cells under MS-275 treatment (see Supplementary Table 1). d Venn diagram showing the 1287 SE-associated genes (SEs) previously identified in MM, GM, and SCLC [33], among which 447 have been implicated in breast cancer (BrCa) according to the literature. Of these 447 BrCa/SE-associated genes, 361 demonstrated moderate to high H3K27ac peak levels at either proximal or overlapping SEs in BPLER2 cells (see Supplementary Table 2). With MS-275 treatment, nearly two thirds (61%) of BrCa/SE/H3K27ac associated genes (221/361) demonstrated maximum (117; ↓↓↓) to moderate (104; ↓↓) reduction in H3K27ac peaks, 136 (38%) demonstrated minimal reduction (= /↓), and four genes demonstrated an increase in H3K27ac peak levels (↑↑). The remaining 86 BrCa/SE-associated genes had no H3K27ac signal in BPLER2 cells