Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients

Background: Head and neck squamous cell carcinoma (HNSC) remains an important public health problem, with classic risk factors being smoking and excessive alcohol consumption and usually has a poor prognosis. Therefore, it is important to explore the underlying mechanisms of tumorigenesis and screen the genes and pathways identified from such studies and their role in pathogenesis. The purpose of this study was to identify genes or signal pathways associated with the development of HNSC. Methods: In this study, we downloaded gene expression profiles of GSE53819 from the Gene Expression Omnibus (GEO) database, including 18 HNSC tissues and 18 normal tissues. The differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Data R package. Adjusted P values <0.01 and |log2 fold change (FC)| ≥2 was regarded as the filter condition. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEGs were performed on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) online website. Protein-protein interaction (PPI) network was built to visualize the interactions between these DEGs using the STRING online website. Finally, hub genes were identified by The Cancer Genome Atlas (TCGA) database. Results: A total of 604 DEGs consisting of 159 upregulated genes and 445 downregulated genes were selected. From these DEGs, prognostic related genes could serve as potential biomarkers for the molecular diagnosis and therapeutic intervention of HNSC were identified. Including the known genes, GPR18, CNR2, RSPH4A, ULBP2, TEX101, and STC2. And the novel genes, CCR8, CCDC39, CNTN5, MSLN, and CHGB were strongly implicated in HNSC. Conclusions: In summary, we indicated genes associated with prognostic in patients, which improve our understanding of HNSC and could be used as new therapeutic targets for HNSC. Keywords: Bioinformatics analysis; biomarkers; differentially expressed genes (DEGs); head and neck squamous cell carcinoma (HNSC); microarray data.