Investigation of differentially expressed genes in nasopharyngeal carcinoma by integrated bioinformatics analysis

Abstract

Nasopharyngeal carcinoma (NPC) is a common malignancy of the head and neck. The aim of the present study was to conduct an integrated bioinformatics analysis of differentially expressed genes (DEGs) and to explore the molecular mechanisms of NPC. Two profiling datasets, GSE12452 and GSE34573, were downloaded from the Gene Expression Omnibus database and included 44 NPC specimens and 13 normal nasopharyngeal tissues. R software was used to identify the DEGs between NPC and normal nasopharyngeal tissues. Distributions of DEGs in chromosomes were explored based on the annotation file and the CYTOBAND database of DAVID. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied. Additionally, a protein-protein interaction (PPI) network, constructed using the STRING database and visualized by Cytoscape, was used to identify hub genes, key modules and important transcription factors (TFs). A total of 906 DEGs were identified; 434 (47.90%) DEGs were upregulated and 472 (52.10%) were downregulated. The DEGs were demonstrated to be enriched in chromosome 7p15-p14, 2q31, 1q21-q22, 1q21, 4q21 and 1p31-p22. DEGs were mainly enriched for the following GO terms: 'Cilium movement', 'microtubule bundle formation' and 'axoneme assembly'. KEGG pathway enrichment analysis revealed that pathways for 'cell cycle', 'DNA replication', 'interleukin-17 signaling', 'amoebiasis' and 'glutathione metabolism' were enriched. In addition, a PPI network comprising 867 nodes and 1,241 edges was constructed. Finally, five hub genes (aurora kinase A, cell division cycle 6, mitotic arrest deficient 2-like 1, DNA topoisomerase 2α and TPX2 microtubule nucleation factor), 8 modules, and 14 TFs were identified. Modules analysis revealed that cyclin-dependent kinase 1 and exportin 1 were involved in the pathway of Epstein-Barr virus infection. In summary, the hub genes, key modules and TFs identified in this study may promote our understanding of the pathogenesis of NPC and require further in-depth investigation.

Keywords: Epstein-Barr virus infection; bioinformatics analysis; differential expression gene; hub gene; nasopharyngeal carcinoma; transcription factor.

Figure 1.

Heatmap of differentially expressed gene expression. Top 25 upregulated (red) and top 25 downregulated (green) genes. Orange, normal nasopharyngeal tissues; light gray, NPC specimens. NPC, nasopharyngeal carcinoma.

Figure 2.

Chromosomal distribution of DEGs in nasopharyngeal carcinoma. (A) The peak count number of DEGs was the on chromosome 1, followed by chromosome 2 and chromosome 12. (B) CYTOBAND database of DAVID revealed that the DEGs were located on 7p15-p14, 2q31, 1q21-q22, 1q21, 4q21 and 1p31-p22; P<0.025. DEGs, differentially expressed genes.

Figure 3.

Top 10 enriched GO terms and top 5 KEGG pathways for differentially expressed genes. (A-C) GO term enrichment analysis for (A) biological process, (B) molecular function, (C) cellular component. (D) KEGG pathway analysis. Node size represents gene ratio; node color represents P_adj. GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; P_adj, adjusted P-value.

Figure 4.

Protein-protein interaction network of differentially expressed genes constructed using Cytoscape. Purple nodes represent upregulated genes. Green nodes represent downregulated genes.

Figure 5.

Enriched GO terms and KEGG pathways for seven modules. (A) GO term enrichment for biological processes, molecular functions and cellular components. (B) KEGG pathway analysis. The number on the × axis is the number of enriched genes. The circle size indicates the ratio of genes in each term; colors correspond to P_adj. P-values were adjusted by the Benjamini-Hochberg method. GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; M, module; P_adj, adjusted P-value.

Figure 6.

Expression levels of candidate hub genes in the GSE13597 dataset. Five candidate hub genes were upregulated in NPC (P<0.05). AURKA, aurora kinase A; CCNA2, cyclin A2; CCNB1, cyclin B1; CDC6, cell division cycle 6; CDK1, cyclin-dependent kinase 1; H2AFZ, H2A histone family member Z; MAD2L1, mitotic arrest deficient 2-like 1; NUP107, nucleoporin 107; PRKAR2B, protein kinase cAMP-dependent type II regulatory subunit β; RACGAP1, Rac GTPase-activating protein 1 (RACGAP1); RRM2, ribonucleotide reductase regulatory subunit M2; TOP2A, DNA topoisomerase 2α; TPX2, TPX2 microtubule nucleation factor.

Figure 7.

Possible regulatory relationships between the TFs and the hub genes of nasopharyngeal cancer. Green represents TFs, purple represents candidate hub genes. TF, transcription factor.