Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma

Deng, Lie; Xiong, Pengju; Luo, Yun-Hui; Bu, Xiao; Qian, Suokai; Zhong, Wuzhao

doi:10.3892/ol.2016.5024

Cited by 16 publications

(18 citation statements)

References 44 publications

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“…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.…”

Section: Introductionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Zhang

et al. 2018

Biol Res

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BackgroundDiffuse intrinsic pontine glioma (DIPG) is the main cause of pediatric brain tumor death. This study was designed to identify key genes associated with DIPG.MethodsThe gene expression profile GSE50021, which consisted of 35 pediatric DIPG samples and 10 normal brain samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified by limma package. Functional and pathway enrichment analyses were performed by the DAVID tool. Protein–protein interaction (PPI) network, and transcription factor (TF)–microRNA (miRNA)–target gene network were constructed using Cytoscape. Moreover, the expression levels of several genes were validated in human glioma cell line U251 and normal glia HEB cells through real-time polymerase chain reaction (PCR).ResultsA total of 378 DEGs were screened (74 up-regulated and 304 down-regulated genes). In the PPI network, GRM1, HTR2A, GRM7 and GRM2 had higher degrees. Besides, GRM1 and HTR2A were significantly enriched in the neuroactive ligand–receptor interaction pathway, and calcium signaling pathway. In addition, TFAP2C was a significant down-regulated functional gene and hsa-miR-26b-5p had a higher degree in the TF-miRNA-target gene network. PCR analysis revealed that GRM7 and HTR2A were significantly downregulated while TFAP2C was upregulated in U251 cells compared with that in HEB cells (p < 0.001). GRM2 was not detected in cells.ConclusionsGRM1 and HTR2A might function in DIPG through the neuroactive ligand–receptor interaction pathway and the calcium signaling pathway. Furthermore, the TFAP2C and hsa-miR-26b-5p might play important roles in the development and progression mechanisms of DIPG.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Zhang

et al. 2018

Biol Res

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“…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.…”

Section: Discussionmentioning

confidence: 99%

The molecular classification of astrocytic tumors

et al. 2017

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AimThis study will explore the genetic and epigenetic alterations in astrocytomas, and identify the critical molecular signatures and signaling pathways for prognosis assessment by multiplatform comprehensive analysis.MethodWe performed integration analyses of incorporating DNA methylation, mRNA expression, microRNA expression, and long non-coding RNA (lncRNA) expression in 33 astrocytic tumor tissues and 9 non-tumor brain tissues.ResultWe observed that 11,795 DNA methylation sites, 3,627 genes, 136 microRNAs, and 3,334 lncRNAs were significantly differential between tumors and non-tumor brain tissues, and the filtered signatures through comprehensive analysis were significantly enriched in calcium signaling pathway. Furthermore, four signatures involved in calcium signaling pathway and age could contribute to predicting the patients’ overall survival. Additionally, we identified differentially expressed signatures between IDH-mutated and IDH wild-type astrocytic tumors, and complement and coagulation cascades pathway was the most significant pathway in functional enrichment analysis using multiplatform data. The IDH wild-type astrocytomas were divided into two subtypes by Cluster of Cluster (CoC) analysis, one of which was enriched for astrocytomas overexpressed in chemokine signaling pathway.ConclusionThe calcium signaling pathway played a key role in astrocytoma tumorigenesis and prognosis. IDH mutation was a vital biomarker, and resulted in the change of expression level in complement and coagulation cascades pathway. The chemokine signaling pathway could characterize subtypes of IDH wild-type astrocytomas.

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“…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].…”

Section: T-complex Protein 1 Ring Complex (Tric) Interactome May Indimentioning

confidence: 99%

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

Hallal

Azimi

Wei

et al. 2020

Preprint

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There is a real need for biomarkers that can indicate glioma disease burden and inform clinical management, particularly in the recurrent glioblastoma (GBM; grade IV glioma) setting where treatment-associated brain changes can confound current and expensive tumour surveillance methods. In this regard, extracellular vesicles (EVs; 30-1000 nm membranous particles) hold major promise as robust tumour biomarkers. GBM-EVs encapsulate molecules that reflect the identity and molecular state of their cell-of-origin and cross the blood-brain-barrier into the periphery where they are readily accessible. Despite the suitability of circulating-EVs for GBM biomarker discovery, sample complexity has hindered comprehensive quantitative proteomic studies. Here, sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) was used in conjunction with a targeted data extraction strategy to comprehensively profile circulating-EVs isolated from plasma. Plasma-EVs sourced from pre-operative glioma II-IV patients (n=41) and controls (n=11) were sequenced by SWATH-MS, and the identities and absolute quantities of the proteins were extracted by aligning the SWATH-MS data against a custom glioma spectral library comprised of 8662 high confidence protein species. Overall, 4054 plasma-EV proteins were quantified across the cohorts, and putative circulating-EV biomarker proteins identified (adjusted p-value<0.05) included previously reported GBM-EV proteins identified in vitro and in neurosurgical aspirates. Principle component analyses showed that plasma-EV protein profiles clustered according to glioma subtype and WHO-grade, and plasma-EV proteins reflected the extent of glioma aggression. Using SWATH-MS, we describe the most comprehensive proteomic plasma-EV profiles for glioma and highlight the promise of this approach as an accurate and sensitive tumour monitoring method. Objective blood-based measurements of glioma tumour activity will support the implementation of next-generation, patient-centred therapies and are ideal surrogate endpoints for recurrent progression that would allow clinical trial protocols to be more dynamic and adapt to the individual patient and their cancer.

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Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma

Cited by 16 publications

References 44 publications

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

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

The molecular classification of astrocytic tumors

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

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