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Article Open Access

DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme

  • Authors:
    • Shifeng Kan
    • Song Chai
    • Wenhua Chen
    • Bo Yu
  • View Affiliations / Copyright

    Affiliations: Department of Rehabilitation, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 200080, P.R. China
    Copyright: © Kan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1679-1688
    |
    Published online on: June 21, 2019
       https://doi.org/10.3892/ol.2019.10512
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Abstract

Glioblastoma multiforme (GBM) is one of the most lethal and damaging types of human cancer. The current study was conducted to identify differentially methylated genes (DMGs) between GBM and normal controls, and to improve our understanding of GBM at the epigenetic level. The DNA methylation profile of GBM was downloaded from the Gene Expression Omnibus (GEO) database using the accession number GSE50923. The MethyAnalysis package was applied to identify DMGs between GBM and controls, which were then analyzed by functional enrichment analysis. Protein‑protein interaction (PPI) networks were constructed using the hypermethylated and hypomethylated genes. Finally, transcription factors (TFs) that can regulate the hypermethylated and hypomethylated genes were predicted, followed by construction of transcriptional regulatory networks. Furthermore, another relevant dataset, GSE22867, was downloaded from the GEO database for data validation. A total of 476 hypermethylated and 850 hypomethylated genes were identified, which were mainly associated with the functions of ‘G‑protein‑coupled receptors ligand binding’, ‘cytokine activity’, ‘cytokine‑cytokine receptor interaction’, and ‘D‑glutamine and D‑glutamate metabolism’. The hypermethylated gene neuropeptide Y (NPY) and the hypomethylated gene tumor necrosis factor (TNF) demonstrated high degrees in the PPI network. Forkhead box protein A1 (FOXA1), potassium voltage‑gated channel subfamily C member 3 (KCNC3) and caspase‑8 (CASP8) exhibited high degrees in the transcriptional regulatory networks. In addition, the methylation profiles of NPY, TNF, FOXA1, KCNC3 and CASP8 were confirmed by another dataset. In summary, the present study systematically analyzed the DNA methylation profile of GBM using bioinformatics approaches and identified several abnormally methylated genes, providing insight into the molecular mechanism underlying GBM.
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Copy and paste a formatted citation
Spandidos Publications style
Kan S, Chai S, Chen W and Yu B: DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme. Oncol Lett 18: 1679-1688, 2019.
APA
Kan, S., Chai, S., Chen, W., & Yu, B. (2019). DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme. Oncology Letters, 18, 1679-1688. https://doi.org/10.3892/ol.2019.10512
MLA
Kan, S., Chai, S., Chen, W., Yu, B."DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme". Oncology Letters 18.2 (2019): 1679-1688.
Chicago
Kan, S., Chai, S., Chen, W., Yu, B."DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme". Oncology Letters 18, no. 2 (2019): 1679-1688. https://doi.org/10.3892/ol.2019.10512
Copy and paste a formatted citation
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Spandidos Publications style
Kan S, Chai S, Chen W and Yu B: DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme. Oncol Lett 18: 1679-1688, 2019.
APA
Kan, S., Chai, S., Chen, W., & Yu, B. (2019). DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme. Oncology Letters, 18, 1679-1688. https://doi.org/10.3892/ol.2019.10512
MLA
Kan, S., Chai, S., Chen, W., Yu, B."DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme". Oncology Letters 18.2 (2019): 1679-1688.
Chicago
Kan, S., Chai, S., Chen, W., Yu, B."DNA methylation profiling identifies potentially significant epigenetically‑regulated genes in glioblastoma multiforme". Oncology Letters 18, no. 2 (2019): 1679-1688. https://doi.org/10.3892/ol.2019.10512
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