Identification of prognostic biomarkers for nasopharyngeal carcinoma through microRNA‑mRNA network analysis combined with screening of immune‑related genes
Lihe He, Xuan Huang, Ping HuangBackground
Nasopharyngeal carcinoma (NPC) is a common head and neck cancer, and radiotherapy is its main treatment. Recurrence and metastasis are the main causes of treatment failure. Although immunotherapy can prolong patient survival, the molecular mechanisms underlying NPC development and progression remain unclear. MicroRNAs (miRNAs) and their target genes are abnormally expressed in many tumors and are closely involved in tumor development. Therefore, this study aimed to identify key miRNAs and immune-related target genes in NPC, construct miRNA–mRNA regulatory networks, and screen for and validate core immune genes to identify prognostic molecular biomarkers for NPC.
Methods
We downloaded NPC-related miRNA (GSE32960) and mRNA (GSE12452, GSE13597, GSE64634) microarray datasets from the Gene Expression Omnibus (GEO) and identified differentially expressed miRNAs (DEMs) and mRNAs (DEGs) using R. Target genes of DEMs were predicted with TargetScan, miRDB, and miRWalk, and then intersected with DEGs to identify core genes. A miRNA–mRNA regulatory network was constructed in Cytoscape. The core genes were further overlapped with immune-related gene sets, followed by functional enrichment analysis. A prognostic risk model was established using LASSO–Cox regression, and immune cell infiltration was evaluated with CIBERSORT. Model validation, immunohistochemical analysis, and drug–gene interaction analysis were also performed. In vitro, RT–qPCR was conducted in C666-1 and NP69 cell lines to verify the expression of key genes.
Results
We identified 213 potential target genes of key miRNAs. Three miRNAs (hsa-miR-30e-5p, hsa-miR-30a-5p, and hsa-miR-20a-5p) were associated with NPC prognosis, and 17 core immune-related genes were enriched in cytokine-mediated signaling, chemokine response, and JAK-STAT pathways. Five genes (CXCL11, SOCS1, ROBO1, LGR5, and RORB) showed promising diagnostic value for NPC; their expression was positively correlated (P < 0.05) with CD8 ⁺ T-cell, macrophage, and neutrophil infiltration. Drug-gene analysis predicted that 5-fluorouracil targeted LGR5 and aldesleukin targeted SOCS1. RT-qPCR demonstrated that SOCS1 was upregulated approximately 3.7-fold in NPC cells (P < 0.01).
Conclusion
This study identified potential novel key genes in nasopharyngeal carcinoma, providing new therapeutic targets for the treatment of this disease.