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Fig. 2 | Journal of Experimental & Clinical Cancer Research

Fig. 2

From: Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis

Fig. 2

Influence of HDAC inhibitors on histone modification and expression profile. a (top) WB analysis of H3K9/14 ac, H3K27ac, H3K27me3 after HDACi treatment or solvent control (DMSO) for 17 h of three different EwS lines. β-actin served as loading control. (bottom) a table of the optical density of the individual band signals is given as the quotient of the individual value and the control (ß-actin). Values > 1.8 are shown in bold. b Volcano plots of differentially expressed genes averaged across four EwS lines (A673, CHLA-10, EW7, SK-N-MC). Each plot shows fold changes of log2 expression values (log FC) and adjusted p-values obtained from differential expression analysis comparing cell lines treated with HDACi (FK228 or MS-275, respectively) to solvent controls. Red, genes obtained adjusted p-value < 0.05 and absolute log FC > 1; blue, genes with adjusted p-value < 0.05 and absolute log FC ≤ 1; green, genes with adjusted p-value ≥0.05 and absolute log FC > 1; and in black, genes with adjusted p-value ≥0.05 and absolute log FC ≤ 1. c Heat map of 476 genes, 2-fold differentially expressed after HDACi treatment in four different EwS lines. Each column represents one individual array (robust multichip average (RMA); GSE162785). Cells were treated with DMSO or HDACi for 17-30 h. d Principal Component Analysis (PCA) plot showing the Principal Components (PC) 1 to 3. A dot represents one sample of the four different EwS lines, each treated with four HDACi, respectively (FK228, MS-275, PCI-34051, TSA). Two replicates of each cell line are shown as controls. In each cluster, a large dot in the center represents the average. Both PCA plots depict the same data from different perspectives. e Shared genes differentially expressed after individual treatment with different HDACi in four EwS lines (see [18]; GSE162785), respectively. For Venn diagram, genes ±2-fold differentially expressed were selected for analysis (http://bioinformatics.psb.ugent.be/webtools/Venn/). f GSEA enrichment plots of up- and downregulated gene sets after individual HDACi treatment. NES: normalized enrichment score. GSEA: http://www.broadinstitute.org/gsea/index.jsp

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