Application of weighted gene co-expression network analysis to explore potential prognostic markers of head and neck squamous cell carcinoma

Currently, there are no specific head and neck squamous cell carcinoma (HNSCC) prognostic markers. We explored the potential HNSCC prognostic markers using weighted gene co-expression network analysis (WGCNA). We obtained raw datasets of HNSCC and matched normal mucosal tissues and screened out differentially expressed genes (DEGs), then analyzed DEG enrichment. DEG co-expression network modules for both tumor and normal tissues were constructed using WGCNA, then hub genes in tumor set-specific modules were selected. Key genes underwent survival analysis using the HNSCC dataset in The Cancer Genome Atlas database. The key gene expression profiles in the clinical samples were verified with RT-qPCR and western blotting. We identified 893 DEGs: 518 were upregulated (mainly distributed in the exogenous metabolic processes, epidermal development, regulation of inflammatory mediators of TRP channels, and tyrosine metabolism) and 375 were downregulated (mainly related to cell adhesion, osteoblast and adipocyte lipolysis regulation, and the RIG-I-like receptor signaling pathway). The WGCNA constructs of the HNSCC co-expression module uncovered 10 hub genes. Survival analysis determined that EOMES (eomesodermin) and SPRYD3 (SPRYD domain-containing protein 3) were closely related to HNSCC prognosis and differentially expressed in oral cancer clinical tissues. EOMES and SPRYD3 might be potential HNSCC prognostic markers and therapeutic targets.