Journal: Cancers
Article Title: Enhancer Clusters Drive Type I Interferon-Induced TRAIL Overexpression in Cancer, and Its Intracellular Protein Accumulation Fails to Induce Apoptosis
doi: 10.3390/cancers15030967
Figure Lengend Snippet: Enhancer clusters mediate TRAIL upregulation by IFNα. ( A ) TRAIL is associated with enhancer clusters in specific cancer cell lines. Publicly available H3K27ac ChIP-seq data for several cell lines from breast cancer (MCF7, MDAMB468, T47D, ZR-75-1 and BT549) and other solid cancers (A549, HCT116, HepG2, PC-9 and SK-N-SH) were analyzed. Peaks of H3K27ac signal represent accessible chromatin and were found upstream and downstream of TRAIL (TNFSF10), which is transcribed from the opposite strand (right to left). Distal H3K27ac peaks overlapping with DNase I hypersensitive sites (a mark of open regulatory DNA) indicate accessible open DNA regions carrying putative regulatory elements. Distal DNase I hypersensitive sites, called regulatory elements 1 to 8 and shown in red in the diagram, were identified through DNase I hypersensitivity assays in 95 cell lines from ENCODE. Only distal DNase I hypersensitive regions that were found in more than 20 out of the 95 cell lines were considered as putative regulatory elements in this analysis. Regulatory elements 1 to 5 cluster together upstream of TRAIL (to the right in the figure), whereas regulatory elements 6 to 8 cluster together downstream of TRAIL (to the left in the figure). Upstream and downstream enhancer clusters are represented as pink and green lines, respectively. As observed in the H3K27ac data, MCF7, MDAMB468 and A549 cell lines show an upstream enhancer cluster, while only A549 shows a downstream enhancer cluster. ( B ) Chromatin accessibility at distal enhancer regions upstream and downstream of TRAIL-coding DNA correlates with TRAIL RNA levels in pan-cancer tumors. Scatter plots show correlation between TRAIL RNA-seq expression and ATAC-seq data on chromatin accessibility for 4 open DNA regions (regulatory elements 2, 4, 7 and 8) from 404 pan-cancer tumors from TCGA dataset. Pearson (r) and Spearman (ρ) correlation coefficients and p -values are shown for each plot. ( C ) Blocking BRD4 binding to highly acetylated enhancer regions with BET inhibitors reduced TRAIL RNA expression in MCF7 and A549, but not in BT549. Cells were treated with vehicle (DMSO), 1 μM JQ1 or 1 μM I-BET151 for 6 h. After treatment, changes in TRAIL RNA levels were analyzed using qPCR. ANOVA followed by Dunnett’s multiple comparison test was performed (**** p < 0.0001). ( D ) Enhancer clusters enhanced TRAIL upregulation by IFNα. Cells were pre-treated with vehicle (DMSO), 1 μM JQ1 or 1 μM I-BET151 for 3 h, followed by stimulation with 0.8 μg/mL IFNα2 for 6 h. After treatment, changes in TRAIL RNA levels were analyzed using qPCR. ANOVA followed by Dunnett’s multiple comparison test was performed (**** p < 0.0001).
Article Snippet: For cytokine treatment, Recombinant Human IFNα2 (Biolegend, San Diego, CA, USA), Recombinant Human soluble TRAIL (PeproTech, Cranbury, NJ, USA), Recombinant Human IFNγ (Gibco), Recombinant Human Tumor Necrosis Factor α (TNFα, PeproTech) or Recombinant Human Interleukin-6 (IL-6, PeproTech) dissolved in PBS was added to the cell media at the concentrations indicated in the figures.
Techniques: ChIP-sequencing, RNA Sequencing Assay, Expressing, Blocking Assay, Binding Assay, RNA Expression