Related Experiment Video
Updated: Sep 12, 2026
Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
A transcriptomic analysis based on aberrant methylation levels revealed potential novel therapeutic targets for
Mo Lyu1,2, Xinzhu Yi2, Zhiwei Huang1,3
1Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.
Background:
This study aimed to identify potential novel therapeutic targets for nasopharyngeal carcinoma (NPC) by identifying aberrantly methylated-differentially expressed genes (DEGs) and pathways based on a comprehensive bioinformatics analysis.
Methods:
Eight gene expression data sets and 2 methylation microarray data sets that included NPC and control groups from the Gene Expression Omnibus were identified. Meta-analyses of the DEGs were performed using the online analysis database "NetworkAnalyst". Aberrantly methylated gene loci were obtained from the GEO2R. Aberrantly methylated DEGs were obtained from Venn diagrams. The enrichment analysis was carried out on the "Metascape" website, and the protein-protein interaction (PPI) network construction, network analysis, and visualization of the analysis results were carried out on the "String" website using "Cytoscape" software.
Results:
In total, 544 hypomethylation high-expression genes and 164 hypermethylation low-expression genes were obtained. The enrichment and PPI network analyses suggested that several pathways and hub genes with abnormal gene expression accompanied by methylation change, including inositol-trisphosphate 3-kinase B (ITPKB), G protein subunit beta 5 (GNB5), FYN proto-oncogene, Src family tyrosine kinase (FYN), LCK proto-oncogene, Src family tyrosine kinase (LCK), nuclear factor of activated T cells 1 (NFATC1), GNAS complex locus (GNAS), protein kinase C beta (PRKCB), zeta chain of T cell receptor associated protein kinase 70 (ZAP70), lysophosphatidic acid receptor 1 (LPAR1), protein kinase C epsilon (PRKCE), tumor protein p53 (TP53), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fibronectin 1 (FN1), cyclin D1 (CCND1), vascular endothelial growth factor A (VEGFA), HRas proto-oncogene, GTPase (HRAS), signal transducer and activator of transcription 3 (STAT3), fibroblast growth factor 2 (FGF2), amyloid beta precursor protein (APP), and matrix metallopeptidase 2 (MMP2), may be related to the occurrence of nasopharyngeal carcinoma .
Conclusions:
The identification of novel and important pathways and hub genes and their roles in the occurrence and development of NPC will guide clinical research and the development of pharmaceutical targets.
Insights
This bioinformatics study identified key genes and pathways linked to nasopharyngeal carcinoma (NPC) development. These findings highlight potential new therapeutic targets for NPC treatment.
Area of Science:
- Oncology
- Bioinformatics
- Genomics
Background:
- Nasopharyngeal carcinoma (NPC) is a complex malignancy.
- Identifying novel therapeutic targets is crucial for improving NPC treatment outcomes.
Purpose of the Study:
- To identify potential novel therapeutic targets for NPC.
- To identify aberrantly methylated-differentially expressed genes (DEGs) and pathways in NPC through bioinformatics analysis.
Main Methods:
- Utilized eight gene expression and two methylation microarray datasets from the Gene Expression Omnibus (GEO).
- Performed meta-analyses of DEGs using NetworkAnalyst.
- Identified aberrantly methylated gene loci and DEGs using GEO2R and Venn diagrams.
- Conducted enrichment analysis via Metascape and constructed protein-protein interaction (PPI) networks using String and Cytoscape.
Main Results:
- Identified 544 hypomethylation high-expression genes and 164 hypermethylation low-expression genes.
- Enrichment and PPI analyses revealed pathways and hub genes (e.g., ITPKB, GNB5, FYN, LCK, NFATC1, GNAS, PRKCB, ZAP70, LPAR1, PRKCE, TP53, GAPDH, FN1, CCND1, VEGFA, HRAS, STAT3, FGF2, APP, MMP2) associated with NPC.
- These genes exhibit abnormal expression and methylation changes potentially driving NPC development.
Conclusions:
- The study identified novel pathways and hub genes implicated in NPC.
- These findings provide a foundation for future clinical research and the development of targeted pharmaceutical therapies for nasopharyngeal carcinoma.
More Related Videos
13:21Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
Published on: June 16, 2017
06:07Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors
Published on: August 5, 2022
