Fig. 3

HDAC1/3/7 inhibition by MS-275 represses SE-associated genes in stem-like BrCa cells. a Real-time quantitative RT-PCR analysis of MS-275 activated DHRS2, CLU, and CDKN1A genes [34], at 24 h (HMLER2 and BPLER2) and 48 h (MCF7 and SUM159) of treatment with 1 μM MS-275 in BrCa cell lines. All genes demonstrated >2.0-fold increase in transcript levels in all cell lines. b SCTF genes demonstrated 1.8- to 6.2-fold decrease in transcript levels after MS-275 treatment in CSC-like BPLER2 cells. There was no change in nsTC-like HMLER2 cells except for a 2.0-fold decrease in HOXA mRNA levels. c Real-time quantitative RT-PCR analysis of 21 BrCa/SE-associated genes, 20 of which revealed significantly reduced H3K27ac in BPLER2 cells in response to MS-275 treatment (see Supplementary Table 2), demonstrated 1.6- to 15.0-fold decrease in mRNA levels in most of the genes (15/21) and 1.6- to 2.1-fold increase in transcript levels in only ZFP36, c-JUN, and ID1. In contrast, only 4 of 21 genes demonstrated a 1.6- to 4.5-fold decrease in mRNA in HMLER2 cells. d Nine out of 18 BrCa/SE-associated genes demonstrated 1.7- to 14.3-fold decrease in transcript levels, whereas c-JUN, ZFP36, and ID1 confirmed a >2.0-fold activation in MS-275 treated, CSC-enriched SUM159 cells (black bars). Only 2 out of 18 were decreased in ERα⁺ MCF7 cells (gray bars). Transcript levels were normalized to ACTB and B2M and expressed relative to values in vehicle control (DMSO). Real-time quantitative RT-PCR with each specific set of primers were obtained from 2–5 independent biological at three technical repeats each and plotted in bar chart using logarithmic scale, error bars represent standard deviation