Differentially Expressed Genes in Nasopharyngeal Carcinoma Tissues and Their Correlation with Recurrence and Metastasis of Nasopharyngeal Carcinoma

Abstract

In this study, bioinformatics tools were used to identify key genes to study the molecular mechanism of nasopharyngeal carcinoma (NPC) development and to explore the correlation of these key genes with the recurrence and metastasis of NPC. The GSE61218 microarray dataset obtained from the Gene Expression Omnibus Database (GEO) was used. The limma R package was used to screen differentially expressed genes (DEGs) between NPC and normal nasopharyngeal (NP) tissues. KEGG functional enrichment was performed on these selected DEGs. Protein-protein interaction (PPI) networks were constructed using Cytoscape software to identify key node proteins. The NPC-metastasis microarray dataset GSE103611 was obtained from GEO to analyze the expression of DEGs in NPC metastasis. A total of 239 DEGs were identified. DEGs were mainly enriched in oocyte maturation-related pathways, cytokine-related pathways, cell cycle-related pathways, cancer-related pathways, and homologous recombination-related pathways. In addition, the top 10 nodes with the higher degree in the DEG PPI network were as follows: CDK1, CCNB2, BUB1, CCNA2, AURKB, BUB1B, MAD2L1, NDC80, BIRC5, and CENPF. The results indicated that DEGs may be involved in the pathogenesis of NPC by regulating cell cycle and mitosis, which can be used as molecular biomarkers for the diagnosis of NPC. In addition, we identified 87 DEGs with $\text{FC}>2$ and $P<0.01$ from the metastasis spectrum of NPC. The intersection gene between DEGs of NPC and normal NP tissue samples and those of the metastatic spectrum of NPC was identified to be VRK2. The expression of VRK2 in NPC samples was significantly higher than that in normal NP tissue, and similarly, VRK2 expression was significantly upregulated in metastatic samples compared with nonmetastatic samples ( $P<0.05$ ). Therefore, VRK2 may be a biomarker for predicting the metastasis of NPC patients after treatment.