Exploring the molecular subclasses and stage-specific genes of oral cancer: A bioinformatics analysis

Abstract

The rate of people getting affected by Oral cancer in Sri Lanka is growing rapidly since the root cause of such cancer, betel quid chewing is tightly coupled with the tradition of the country. The five-year survival rate of the disease is also pretty low as it is typically detected at advanced stages. This urges a comprehensive study on the marker genes of oral cancer for the successful therapeutic revisions that would potentially identify cancer in its early stages. Further, the identification of molecular subclasses can assist in individualizing the treatment for this type of fatal disease. This study uses the bioinformatics analysis on the gene expression dataset of 56 oral cancer patients from Sri Lanka and the United Kingdom to identify the differentially expressed genes where these genes are later clustered and classified into molecular subclasses. Molecular subclasses are found by clustering the genes that stratify together and the stages were identified with the use of gene co-expression networks. Five molecular subclasses of oral cancer were identified and the genes associated with each tumour stage. Out of the genes that are clustered and classified, TAGLN2, CCND2 and CCL8 were well-known tumour suppressor genes and GPX3, GRN and ITGB4 genes are involved in several carcinomas. Putative marker genes of Oral Squamous Cell Carcinoma were identified which could facilitate the medical practitioner in the early detection of oral cancer and also in the improvement of treatment methods.

Keywords

• Oral Squamous Cell Carcinoma
• Microarray
• Gene co-expression network
• Betel quid chewing
• molecular subclasses