Key Prediction Genes of Nasopharyngeal Carcinoma:Screening Based on Systematic Bioinformatics and Validation by Cell Experiments.
10.3881/j.issn.1000-503X.15503
- Author:
Zi-Kui HUANG
1
;
Fei LI
1
;
Yue-Zhou CHEN
2
;
Jia-Ming LIU
3
;
Jia-Jun LIU
4
;
Su-Zhen LAN
5
Author Information
1. Department of Traditional Chinese Medicine,Ganzhou People's Hospital,Ganzhou,Jiangxi 341000,China.
2. Shenzhen Clinical School of Medicine,Guangzhou University of Chinese Medicine,Shenzhen,Guangdong 518116,China.
3. The Second Clinical Medical College,Guangzhou University of Chinese Medicine,Guangzhou 510405,China.
4. Clinical Medical College of Acupuncture Moxibustion and Rehabilitation,Guangzhou University of Chinese Medicine,Guangzhou 510405,China.
5. Department of Oncology,Ganzhou People's Hospital,Ganzhou,Jiangxi 341000,China.
- Publication Type:Journal Article
- Keywords:
Gene Expression Omnibus;
bioinformatics analysis;
biomarkers;
differentially expressed gene;
key gene;
nasopharyngeal carcinoma;
weighted gene co-expression network analysis
- MeSH:
Humans;
Nasopharyngeal Carcinoma/genetics*;
Interleukin-15;
Dual Oxidases;
Computational Biology;
Nasopharyngeal Neoplasms/genetics*
- From:
Acta Academiae Medicinae Sinicae
2023;45(4):597-607
- CountryChina
- Language:Chinese
-
Abstract:
Objective To screen out the potential prediction genes for nasopharyngeal carcinoma(NPC)from the gene microarray data of NPC samples and then verify the genes by cell experiments.Methods The NPC dataset was downloaded from Gene Expression Omnibus,and limma package was employed to screen out the differentially expressed genes.Weighted correlation network analysis package was used for weighted gene co-expression network analysis,and Venn diagram was drawn to find the common genes.The gene ontology annotation and Kyoto encyclopedia of genes and genomes pathway enrichment were then performed for the common genes.The biomarkers for NPC were further explored by protein-protein interaction network,LASSO regression,and non-parametric tests.Real-time quantitative PCR and Western blotting were employed to determine the mRNA and protein levels of key predictors of NPC,so as to verify the screening results.Results There were 622 up-regulated genes and 351 down-regulated genes in the GSE12452 dataset.A total of 116 common genes were obtained by limma analysis and weighted gene co-expression network analysis.The common genes were mainly involved in the biological processes of cell proliferation and regulation and regulation of intercellular adhesion.They were mainly enriched in Rap1,Ras,and tumor necrosis factor signaling pathways.Six key genes were screened out,encoding angiopoietin-2(ANGPT2),dual oxidase 2(DUOX2),coagulation factor Ⅲ(F3),interleukin-15(IL-15),lipocalin-2,and retinoic acid receptor-related orphan receptor B(RORB).Real-time quantitative PCR and Western blotting showed that the NPC cells had up-regulated mRNA and protein levels of ANGPT2 and IL-15 and down-regulated mRNA and protein levels of DUOX2,F3,and RORB,which was consistent with the results predicted by bioinformatics.Conclusion ANGPT2,DUOX2,F3,IL-15 and RORB are potential predictive molecular markers and therapeutic targets for NPC,which may be involved in Rap1,Ras,tumor necrosis factor and other signaling pathways.
