Identification of key hub genes and potential therapeutic drugs for nasopharyngeal carcinoma: Insights into molecular mechanisms and treatment strategies

Abstract

Objective: Nasopharyngeal Carcinoma (NPC) is a highly malignant cancer with a high incidence in East and Southeast Asia, including southern China. Despite advances in treatment, the prognosis for advanced NPC remains poor due to high recurrence and metastasis rates. The molecular mechanisms driving NPC progression are not fully understood, and identifying key genes and potential therapeutic agents is critical. This study aims to uncover critical genes and screen therapeutic drugs, providing insights into NPC pathogenesis and novel treatment strategies.

Methods: Three GEO datasets (GSE12452, GSE53819, and GSE61218) were analyzed to identify overlapping Differentially Expressed Genes (DEGs) in NPC. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the biological roles of DEGs. Protein-Protein Interaction (PPI) and mRNA-miRNA-lncRNA interaction networks were constructed to identify key hub genes. Potential therapeutic drugs were predicted via a Drug-Gene Interaction network. The overexpression of hub genes was validated in NPC cells using CCK-8 assays, and the anti-proliferative effects of three drugs ‒ valproic acid, cyclosporine, and calcitriol ‒ were tested.

Results: Eight hub genes (ASPM, BIRC5, BUB1B, CDK1, KIF23, PBK, TOP2A, and TTK) were identified, with ASPM reported for the first time in the context of NPC. Overexpression of these genes significantly promoted NPC cell proliferation. Among the tested drugs, calcitriol exhibited the most potent anti-proliferative effect, with IC50 values of 0.90 μM, 0.47 μM, and 0.31 μM at 24-, 48-, and 72-hs, respectively.

Conclusion: This study identified eight key genes as potential biomarkers for NPC and validated calcitriol as a promising therapeutic agent, providing a foundation for further research into NPC treatment.

Level of evidence: Level 2 (Individual cross-sectional studies or systematic review of surveys that allow matching to local circumstances).

Keywords: Calcitriol; Drug screening; Key genes; Nasopharyngeal carcinoma.

Fig. 1

Identification of common DEGs in NPC from multiple datasets. (A‒C) Volcano plots showing the DEGs identified in three independent datasets (GSE12452, GSE53819, and GSE61218), comparing tumor tissues to normal tissues. (D) Venn diagram showing the overlapping high-expression DEGs across the three datasets. (E) Venn diagram showing the overlapping low-expression DEGs across the three datasets.

Fig. 2

Functional enrichment analysis of overlapping DEGs. (A) GO Biological Process (BP) enrichment analysis of overlapping DEGs. (B) GO Cellular Component (CC) enrichment analysis of overlapping DEGs. (C) GO Molecular Function (MF) enrichment analysis of overlapping DEGs. (D) KEGG pathway enrichment analysis of overlapping DEGs.

Fig. 3

Gene Set Enrichment Analysis (GSEA) of Co-expressed Genes in NPC. (A) GSEA of the PI3K-AKT signaling pathway. (B) GSEA of the p53 signaling pathway. (C) GSEA of apoptosis-related genes. (D) GSEA of cell cycle-related genes.

Fig. 4

PPI Network Construction and Hub Gene Identification. (A) Protein-Protein Interaction (PPI) network of overlapping DEGs. (B) Cluster 1 extracted from the PPI network. (C) Cluster 2 identified from the PPI network. (D) Hub genes identified from the PPI network.

Fig. 5

Construction of the ceRNA Regulatory Network. (A) Identification of miRNAs targeting hub mRNAs. (B) Selection of the top miRNAs with the highest connectivity. (C) Prediction of lncRNAs targeted by the selected miRNAs. (D) Construction of the ceRNA regulatory network encompassing mRNAs, miRNAs, and lncRNAs.

Fig. 6

Results of Drug-Gene Interaction. The network illustrates the interactions between drugs and key genes. Green lines represent drug-mediated inhibition of key genes, while red lines indicate drug-induced activation of key genes.

Fig. 7

Verification of hub genes and evaluation of potential therapeutic drug. (A) CCK-8 assay assessing the effect of overexpressing the eight hub genes on NPC cell proliferation. (B) CCK-8 assay validation of valproic acid in HK1 cells. (C) CCK-8 assay validation of cyclosporine in HK1 cells. (D) CCK-8 assay validation of calcitriol in HK1 cells.