Single Nucleotide Polymorphisms in Four Genes Associated with Survival Outcome for Patients with Head and Neck Squamous Cell Carcinoma

Abstract

Background: This study aimed to use a bioinformatics pipeline to explore the underlying mechanisms and identify genetic mutations that can be utilized to prognosticate individuals with head and neck squamous cell carcinoma (HNSCC). Methods: SNP-related data was accessed using the TCGA database. Mutation and expression analyses were performed between the mutant samples and wild-type samples. Kaplan‐Meier analysis was conducted to select the candidate mutant genes that affect overall survival. Correlation analysis, GSEA analysis and drug sensitivity analysis of the candidate genes were performed. Results: Down-regulation of FAT1, KMT2B, XIRP2 and ZNF347 expression were observed in the tumors with mutations. Kaplan‐Meier analysis indicated that reduced levels of FAT1, XIRP2 was significantly associated with better overall survival, while reduced levels of KMT2B, and ZNF347 were significantly correlated to worse overall survival. Additionally, SNPs of the four genes were found to participate in several pathways associated with HNSCC development. Furthermore, FAT1 mutation was sensitive to several anti-tumor drugs, such as PI-103, Belinostat and Ruxolitinib. Conclusion: SNPs in FAT1, KMT2B, XIRP2 and ZNF347 may be used as prognostic biomarkers in the treatment of HNSCC.