RNASeq as a tool to understand dysregulation of potential biomarkers in HNSC

Abstract

With its rising fatality rates, oral cancer is one of the most concerning public health issues. To reduce disease-related mortality and morbidity, advancements in screening and detection are critical. Finding specific biomarkers is one of the most successful approaches for screening, diagnosing, and staging this dreadful disease. In this study differentially expressed genes associated with oral cancer were analyzed using RNASeq to find the potential biomarkers. Functional enrichment of upregulated genes found that 253 genes were present in the plasma membrane. Three clusters were formed using KMean Clustering from the PPI networks, and highly connected hub genes were identified from each cluster. Eventually, expression and survival analyses of hub genes were performed using The Cancer Genome Atlas (TCGA) database targeting Head and Neck Squamous Cell Carcinoma. Among those genes, expression levels of eight genes SLC2A1, ITGA6, LAMC2, COL1A2, COL1A1, TNC, THY1, and CD276 have significantly changed in Head and Neck Squamous cell carcinoma. There are reports that suggest these genes were significantly dysregulated in Oral Squamous cell carcinoma and can be explored further as potential biomarkers for margin clearance.