Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma

Abstract

The present study aimed to elucidate key molecular mechanisms in the progression of diffuse intrinsic pontine glioma (DIPG). The gene expression profile GSE50021, which consisted of 35 pediatric DIPG samples and 10 normal brain samples, was downloaded from the Gene Expression Omnibus database. The differentially-expressed genes (DEGs) in the pediatric DIPG samples were identified. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathways of DEGs were enriched and analyzed. The protein-protein interaction (PPI) network of the DEGs was constructed and functional modules of the PPI network were disclosed using ClusterONE. A total of 679 DEGs (454 up- and 225 downregulated) were identified in the pediatric DIPG samples. DEGs were significantly enriched in various GO terms, and KEGG and Reactome pathways. The PPI network of upregulated (153 nodes and 298 connections) and downregulated (71 nodes and 124 connections) DEGs, and two crucial modules, were obtained. Downregulated genes in module 2, such as cholecystokinin (CCK), gastrin (GAST), adenylate cyclase 2 (brain) (ADCY2) and 5-hydroxytryptamine (serotonin) receptor 7 (HTR7), were significantly enriched in the calcium signaling pathway, the neuroactive ligand-receptor interaction pathway and in GO terms, such as the G-protein coupled receptor (GPCR) signaling pathway, while upregulated genes in module 1 were not enriched in any pathways or GO terms. CCK and GAST associated with the GPCR signaling pathway, HTR7 enriched in the neuroactive ligand-receptor interaction, and ADCY2 and HTR7 involved in the calcium signaling pathway may be key mechanisms playing crucial roles in the development and progression of DIPG.

Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma

“…These studies suggest that a single gene or the interaction between more genes involved in the promotion of disease occurrence and development. In recent years, the advantage of gene chip technology and bioinformatics analysis is obviously observed, which is applied to analyze the molecular mechanism of DIPG [ 10 ]. Deng et al [ 10 ] showed cholecystokinin ( CCK ) and gastrin ( GAST ) associated with the G-protein coupled receptor ( GPCR ) signaling pathway, and 5-hydroxytryptamine (serotonin) receptor 7 ( HTR7 ) involved in the neuroactive ligand–receptor interaction might play critical roles in DIPG.…”

“…In recent years, the advantage of gene chip technology and bioinformatics analysis is obviously observed, which is applied to analyze the molecular mechanism of DIPG [ 10 ]. Deng et al [ 10 ] showed cholecystokinin ( CCK ) and gastrin ( GAST ) associated with the G-protein coupled receptor ( GPCR ) signaling pathway, and 5-hydroxytryptamine (serotonin) receptor 7 ( HTR7 ) involved in the neuroactive ligand–receptor interaction might play critical roles in DIPG. Despite a number of researches have investigated the molecular basis of DIPG, the molecular mechanisms of the disease remain not fully understood.…”

“…In the study of Buczkowicz et al [ 2 ], the gene expression profile GSE50021 was utilized only for surveying what urged DIPGs by whole-genome sequencing. In the study of Deng et al [ 10 ], GSE50021 was analyzed and revealed a potential key molecular mechanisms in DIPG by microarray analysis and bioinformatics analysis. Recently, Xi et al [ 11 ] used a novel method for extracting DEGs from GSE50021 in combination with GSE50022 that included DNA methylation.…”

The molecular classification of astrocytic tumors

“…It might provide potential treatment targets and strategies for astrocytoma patients, and its prognostic value could be validated in prospective and multicenter studies. Additionally, neuroactive ligand-receptor interaction pathway has been reported differentially expressed in diffuse intrinsic pontine glioma (DIPG) [ 22 ]and Drosophila Parkinson's disease model [ 23 ], it also deserves further research.…”

A comprehensive proteomic SWATH-MS workflow for profiling blood extracellular vesicles: a new avenue for glioma tumour surveillance

“…CCT7 expression is associated with cancer cell growth and maintenance [99], down-regulated during the DNA damage response in GBM [99] and is associated with poor clinical outcome in GBM patients [100]. CCT2 also has important functional links to cancer, including survival of breast cancer cells and negative survival associations in breast cancer [101], non-small cell lung cancer [102] and diffuse intrinsic pontine glioma [103].…”