Purpose: Gingivo-buccal squamous cell carcinoma (GBSCC) is one of the most common oral cavity cancers in India. Even after decades of intense research, 5-year survival is less than 50%. So, it is necessary to discover therapeutic targets for better treatment of oral cancer patient. To search for therapeutic targets; expression and somatic mutations in whole transcriptomes from GBSCC of smokers and smokeless tobacco users were examined.

Methods: Whole transcriptome data from 12 pairs of GBSCC and adjacent normal tissues were generated by next generation sequencing method in Illumina platform. Data were analyzed to find out expression deregulation and somatic mutations of the transcripts.  Clustering was performed to examine whether expression of genes in different pathways could separate smokers from smokeless tobacco users.

Results: Expression of 2176 genes was significantly deregulated in cancer tissues and data analysis indicated that cell-cell adhesion and ECM-receptor processes were most aberrant pathways. Other altered pathways include AMPK, PPAR and arachidonic acid metabolism which may highlight their importance in primary GBSCC. Interestingly, smokeless tobacco users were clustered together when expression deregulation of genes involved in cell adhesion, proteoglycans, AMPK and PPAR pathways were considered for cluster analysis. We also generated cell proliferation score using expression of cell cycle progression markers and found that tumors from smokeless tobacco users tend to show higher proliferation score. Tumors from smokers and smokeless tobacco users have distinct CD47 & SIRPA and PD-1 & PDL-1 expression, respectively, and a range of variation in infiltrating immune cell signature to infer differential immune evasion strategy of the tumors. Integrative analysis of miRNA and mRNA expression helped us to identify several important miRNAs which might play important roles in shaping expression profiles of several cell adhesion, tissue architecture maintenance  and energy metabolism pathways.

Conclusion: Transcriptome analysis highlighted few potential targetable nodes and neo-antigens which could be effective precision therapeutic or immunotherapeutic targets. Further, this study also suggests that therapeutic targets might be different for oral cancer patients who used smoking or smokeless tobacco. Further, data of deleterious somatic and germline variants along with expression profile could be useful in treatment plan.