Additional file 1 of Chromatin accessibility analysis identifies GSTM1 as a prognostic marker in human glioblastoma patients
Creators: name: Huang, Yin-Cheng
name: Lai, Joseph Chieh-Yu
name: Peng, Pei-Hua
name: Wei, Kuo-Chen
name: Wu, Kou-Juey
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. Analysis of RNA-seq datasets from GBM patient samples revealed the number of upregulated genes and the possibly pathways involved. a Differential gene analysis of RNA-seq datasets (tumor vs. normal and short-survival vs. long-survival tumors). The number of upregulated genes (red ink) in different gene sets were shown. b and c KEGG analysis of increased gene expression in tumor tissues (vs. normal tissues) and short-survival (vs. long-survival) tumor samples showed the possible pathways involved in GBM tumorigenesis in these two patient groups. d Ranking of genes with consistently increased chromatin accessibility on promoter through fold change of gene expression showed that more genes with consistently increased chromatin accessibility had increased gene expression through comparing different patient groups. Fig. S2. The grouping of tumor tissues (short-survival and long-survival) compared to normal tissues by PCA, the annotation of accessible regions on different genomic locations by pie plot, and the positive correlation between chromatin accessibility and gene expression by scatter plots were shown. a PCA showed the grouping of short-survival and long-survival tumor samples together, compared to the grouping of normal samples from ATAC-seq and RNA-seq datasets, respectively. Different colors represented different patient groups. The numbers representing different patients from each category were also shown in Table 1. b Pie plot showed that the accessible regions on promoters and other genomic locations from ATAC-seq analysis (see the correlation on Fig. 2b). c Scatter plots showed the positive correlation between the chromatin accessibility on promoters and gene expression from different patient groups. The numbers (in red ink) represent the number of genes with increased expression. d Positive correlations between chromatin accessibility (promoter and gene body) and gene expression were shown in the GSTM1 gene from different patient samples. Fig. S3. Representative histology of glioblastoma vs. normal brain tissue under IHC staining of GSTM1. a IHC of GSTM1 in the glioblastoma tissue: moderate to high expression (++ to +++). b IHC of GSTM1 normal brain tissue: low to negative expression (0 to +). Fig. S4. TCGA analysis showed the correlation of high GSTM1 and low ZNF727 expression with poor overall survival of GBM patients together with gene track analysis of ZNF727 locus. a TCGA analysis showed that high GSTM1 expression was correlated with poor overall survival of GBM patients. b Venn diagrams of overlapping subsets showed that 2 genes had reduced gene expression and decreased chromatin accessibility in their promoters. c Heatmap analysis showed the RNA-seq results of the two genes with reduced gene expression and decreased chromatin accessibility in their promoters (ENOSF1 and ZNF727) in different patient samples. d Comparison of representative ATAC-seq gene tracks in the ZNF727 locus from tumors (short-survival, long-survival) vs. normal samples. e TCGA analysis showed that low ZNF727 expression was correlated with poor overall survival of GBM patients. Fig. S5. Regulation of the NF-kB and STAT3 signaling pathways by GSTM1. Western blot analysis showed that knockdown of GSTM1 in U87 cells at 48 h decreased the phosphorylated NF-kB (phospho-p65) and phosphorylated STAT3 (pSer727) levels, but not the phosphorylated MAP kinase levels. These data showed the replicate and independently repeated results corresponding to Fig. 5a. Fig. S6. Original Western blotting images of Fig. 5a. Fig. S7. Original Western blotting images of Fig. S5.