Fig. 3

BET and CDK7 inhibitors synergistically suppresses SE-driven core transcriptional regulatory network of G3-MB. a Heatmap of significantly differential genes actively expressed (mean FPKM ≥ 1, adjusted p-value ≤ 0.05) in D425 treated with DMSO, 1 μM JQ1 for 24 h or 0.1 μM THZ1 for 6 h. vSE genes are highlighted. b Groupwise GSEA analysis of SE signatures as labeled in D425 treated with either JQ1 (upper panels) or THZ1 (lower panels) versus DMSO. D425_TE signature serves as control. c Plots on expression (left Y axis, violin) and percentage of significantly downregulated genes (log2_FC < -1, FDR < 0.05) (right Y axis, dot) of different SE signatures genes from D425 treated same as in a. d RT-qPCR analysis of vSE genes in MB002 and D425 treated with 1 μM JQ1 or 0.1 μM THZ1 for 6 h. MYC and OTX2 are highlighted. e Immunoblot of MYC and OTX2 in MB002 and D425 treated with the same drugs and dosages as in (d) for the indicated time. f Cell viability and corresponding CI of MB002 and D425 cells treated with THZ1 and JQ1 at the indicated concentrations for 72 h. A CI value of less than 1 indicates synergy. g Day0-normalized cell viability of MB002 and D425 single- or combo-treated with THZ1 (12.5 or 15 nM for each cell line) and 0.5 μM JQ1. h-i FACS analyses on cell proliferation (h) and apoptosis (i) of MB002 cells with labeled treatments. j RT-qPCR analysis of vSE genes in MB002 cells single- or combo-treated with 1 μM JQ1 and 25 nM THZ1 for 6 h. k Immunoblot of MYC and OTX2 in MB002 cells treated with 0.5 μM JQ1 or 0.05 μM THZ1 for 8 h. RT-qPCR and cell viability assays were performed in triplicate and the data are presented as mean ± SD. Statistical significance is determined either by two-tailed paired t test (c) or one-way ANOVA (j)