Identification of core differentially methylated genes in glioma

Abstract

Differentially methylated genes (DMGs) serve a crucial role in the pathogenesis of glioma via the regulation of the cell cycle, proliferation, apoptosis, migration, infiltration, DNA repair and signaling pathways. This study aimed to identify aberrant DMGs and pathways by comprehensive bioinformatics analysis. The gene expression profile of GSE28094 was downloaded from the Gene Expression Omnibus (GEO) database, and the GEO2R online tool was used to find DMGs. Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DMGs were performed by using the Database for Annotation Visualization and Integrated Discovery. A protein-protein interaction (PPI) network was constructed with Search Tool for the Retrieval of Interacting Genes. Analysis of modules in the PPI networks was performed by Molecular Complex Detection in Cytoscape software, and four modules were performed. The hub genes with a high degree of connectivity were verified by The Cancer Genome Atlas database. A total of 349 DMGs, including 167 hypermethylation genes, were enriched in biological processes of negative and positive regulation of cell proliferation and positive regulation of transcription from RNA polymerase II promoter. Pathway analysis enrichment revealed that cancer regulated the pluripotency of stem cells and the PI3K-AKT signaling pathway, whereas 182 hypomethylated genes were enriched in biological processes of immune response, cellular response to lipopolysaccharide and peptidyl-tyrosine phosphorylation. Pathway enrichment analysis revealed cytokine-cytokine receptor interaction, type I diabetes mellitus and TNF signaling pathway. A total of 20 hub genes were identified, of which eight genes were associated with survival, including notch receptor 1 (NOTCH1), SRC proto-oncogene (also known as non-receptor tyrosine kinase, SRC), interleukin 6 (IL6), matrix metallopeptidase 9 (MMP9), interleukin 10 (IL10), caspase 3 (CASP3), erb-b2 receptor tyrosine kinase 2 (ERBB2) and epidermal growth factor (EGF). Therefore, bioinformatics analysis identified a series of core DMGs and pathways in glioma. The results of the present study may facilitate the assessment of the tumorigenicity and progression of glioma. Furthermore, the significant DMGs may provide potential methylation-based biomarkers for the precise diagnosis and targeted treatment of glioma.

Keywords: bioinformatics; biomarker; glioma; methylation.

Figure 1.

The PPI network of differentially methylated genes.

Figure 2.

Top four modules for differentially methylated genes were selected. (A) Module 1. (B) Module 2. (C) Module 3. (D) Module 4.

Figure 3.

Expression level of the hub genes in glioma and normal brain tissues. (A-D) Expression level of (A) NOTCH1, (B) CASP3, (C) IL1B and (D) CREB1 in glioma and normal brain tissues. Red indicates glioma, gray indicates normal brain tissue. (E) CASP3 protein was strongly upregulated in glioma tissues compared with normal brain tissues based on the Human Protein Atlas database. (F) ERBB2 protein was strongly upregulated in glioma tissues compared with normal brain tissues based on the Human Protein Atlas database. *P<0.05. GBM, glioblastoma multiforme; LGG, brain lower grade glioma; TPM, transcripts per million. NOTCH1, notch receptor 1; CASP3, caspase 3; IL1B, interleukin 1 β; CREB1, cAMP responsive element binding protein 1; ERBB2, erb-b2 receptor tyrosine kinase 2.

Figure 4.

Prognostic value of eight differentially methylated genes in patients with glioma. (A-F) High expression of (A) MMP9, (B) EGF, (C) CASP3, (D) IL6, (E) IL10 and (F) ERBB2 was significantly associated with poor prognosis in glioma patients. (G and H) High expression of (G) NOTCH1 and (H) SRC was associated with improved prognosis in glioma patients. HR, hazard ratio; TPM, Transcripts per million; MMP9, matrix metallopeptidase 9; EGF, epidermal growth factor; CASP3, caspase 3; IL6, interleukin 6; IL10, interleukin 10; ERBB2, erb-b2 receptor tyrosine kinase 2; NOTCH1, notch receptor 1; SRC, SRC proto-oncogene.

Figure 4.

Prognostic value of eight differentially methylated genes in patients with glioma. (A-F) High expression of (A) MMP9, (B) EGF, (C) CASP3, (D) IL6, (E) IL10 and (F) ERBB2 was significantly associated with poor prognosis in glioma patients. (G and H) High expression of (G) NOTCH1 and (H) SRC was associated with improved prognosis in glioma patients. HR, hazard ratio; TPM, Transcripts per million; MMP9, matrix metallopeptidase 9; EGF, epidermal growth factor; CASP3, caspase 3; IL6, interleukin 6; IL10, interleukin 10; ERBB2, erb-b2 receptor tyrosine kinase 2; NOTCH1, notch receptor 1; SRC, SRC proto-oncogene.