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 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.

Clinical value and potential mechanisms of BUB1B up-regulation in nasopharyngeal carcinoma

“…Furthermore, our study shed light on the underlying upstream regulation factors of BUB1B and its potential molecular mechanisms in NPC. Before our study, only two studies focused on the role of BUB1B expression levels in NPC, both based on limited sample sizes [11,12]. The shortcomings of the previous research by Huang et al [11] and Yue et al [12] could be solved in our current study.…”

“…Before our study, only two studies focused on the role of BUB1B expression levels in NPC, both based on limited sample sizes [ 11 , 12 ]. The shortcomings of the previous research by Huang et al [ 11 ] and Yue et al [ 12 ] could be solved in our current study. Combining public high throughput data and in-house IHC, we showed the consistent up-regulation of BUB1B in NPC.…”

“…The number of cases was limited in Huang et al’s study, and the samples were recruited from a single institute, also only limited approaches were used. Yue et al confirmed that BUB1B could be a key target for promoting NPC metastasis through bioinformatics tools, but only two GEO data sets were used in the study with a small sample size [ 12 ].Further, no comprehensive analysis has been conducted to illustrate the clinical role of BUB1B expression and to explore its underlying mechanism in NPC by far.…”

Clinical value and potential mechanisms of BUB1B up-regulation in nasopharyngeal carcinoma

“…The number of cases was limited in Huang et al's study, and the samples were recruited from a single institute, also only limited approaches were used. Yue et al con rmed that BUB1B could be a key target for promoting NPC metastasis through bioinformatics tools, but only two GEO data sets were used in the study with a small sample size(Yue, Zhu, Luo et al 2022). Further, no comprehensive analysis has been conducted to illustrate the clinical role of BUB1B expression and to explore its underlying mechanism in NPC by far.…”

Screening Key Genes and Biological Pathways in Nasopharyngeal Carcinoma by Integrated Bioinformatics Analysis

“…Bioinformatics is an analytical method that uses mathematical, statistical, and computational methods to process and analyze biological data, which differs from traditional laboratory work [ 6 ]. For example, Song et al analyzed the key genes of NPC using bioinformatics [ 7 ], and Yue et al expounded on the differentially expressed genes (DEGs) in NPC tissues and their correlation with the recurrence and metastasis of NPC [ 8 ]. Although many studies have focused on identifying biomarkers related to NPC, a more comprehensive analysis is needed to explore better molecular targets to treat NPC and clarify its biological pathways.…”