To investigate the relationship between the hypoxia inducible factor-3α (HIF-3α) mRNA level and the DNA methylation level in patients with head and neck squamous cell carcinoma (HNSCC) , and to identify the potential novel prognostic biomarker for HNSCC patients.

Based on TCGA database, 530 cases of HNSCC and 50 cases of normal tissue were analyzed for the mRNA and methylation level of HIF-3α with Independent sample t-test. Pearson correlation analysis was used to explore the relationship between DNA methylation and mRNA expression of HIF-3α. Kaplan-Meier survival curves were drawn to investigate the relationship between the expression of HIF-3α, the overall and recurrence-free survival rate of patients with HNSCC by using the Log-rank test. The differentially expressed genes were detected in both the high- and low-expression groups of HIF-3α. Gene set enrichment analysis (GSEA) was performed to investigate the potential molecular function of HIF-3α in HNSCC. The online tool cBioportal was used to examine the proteins that interacted with HIF-3α.

The mRNA expression level of HIF-3α in the normal tissue (4.809 ± 0.293) was significantly higher than that of HNSCC (3.100 ± 0.092; t= 5.369, P<0.001) , whereas the DNA methylation level of HIF-3α in the normal tissue (0.158 ± 0.010) was significantly lower than the latter (0.362 ± 0.009; t= 6.806, P<0.001) . Furthermore, the expression of HIF-3α mRNA was negatively correlated to the level of DNA methylation in HNSCC tissue (r=-0.46, P<0.001) . GSEA analysis showed that the differentially expressed genes were mainly concentrated in P53 signaling pathway, apoptotic pathway and immune response pathway. Interaction protein analysis showed that HIF-3α might interact with VEGFA and CREBBP.

The decrease of HIF-3α expression was strongly related to the increase of DNA methylation in HNSCC. Patients with a low expression level of HIF-3α showed poor clinical outcomes, demonstrating that HIF-3α may be used as a prognostic indicator for HNSCC patients.