Fig. 7

HDAC7 regulates gene expression predominantly in stem-like BrCa cells. a RNA-seq analysis after 72 h of HDAC7 knockdown with siH7 revealed predominant alteration of transcriptional activity in CSC-like BPLER2 (black circles) compared with nsTC-like HMLER2 (white circles) cells (2545 vs. 763; 328 shared), with 1068 vs. 448 repressed and 1477 vs. 315 activated genes. Otherwise, short-term HDAC1 knockdown with siH1 demonstrated comparable deregulated gene numbers in BPLER vs. HMLER cells (3187 vs. 2627; 637 shared), with 1570 vs. 1307 repressed and 1617 vs. 1320 activated transcripts in the two cell lines. b Differential expression analysis after short-term HDAC7 knockdown revealed SE-associated transcriptional alteration predominantly in CSC-rich BPLER cells (391 vs. 161; 85 shared), with >1.5-fold repression of 210 vs. 84 and activation of 181 vs. 77 SE-associated genes when compared with ns-TC-like HMLER cells. HDAC1-depleted BPLER and HMLER cells showed comparable SE-associated gene deregulation (458 vs. 404; 107 shared), although with higher number of repressed (334 vs. 142) and lower number of activated (124 vs. 262) mRNA levels in CSC-like BPLER cell line. Differential expression based on DESeq2 analysis with adjusted cutoff of p < 0.05