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Background  Oral squamous cell carcinoma (OSCC) is the sixth most common cancer globally. Tobacco consumption and HPV infection, both are the major risk factor for the development of oral cancer and causes mitochondrial dysfunction. Genetic polymorphisms in xenobiotic-metabolizing enzymes modify the effect of environmental exposures, thereby playing a significant role in gene–environment interactions and hence contributing to the individual susceptibility to cancer. Here, we have investigated the association of tobacco - betel quid chewing, HPV infection,  GSTM1-GSTT1  null genotypes, and tumour stages with mitochondrial DNA (mtDNA) content variation in oral cancer patients.    Methodology/Principal Findings  The study comprised of 124 cases of OSCC and 140 control subjects to PCR based detection was done for high-risk HPV using a consensus primer and multiplex PCR was done for detection of  GSTM1-GSTT1  polymorphism. A comparative ΔCt method was used for determination of mtDNA content. The risk of OSCC increased with the ceased mtDNA copy number ( P trend   = 0.003). The association between mtDNA copy number and OSCC risk was evident among tobacco – betel quid chewers rather than tobacco – betel quid non chewers; the interaction between mtDNA copy number and tobacco – betel quid was significant ( P  = 0.0005). Significant difference was observed between  GSTM1  -  GSTT1  null genotypes ( P  = 0.04,  P =  0.001 respectively) and HPV infection ( P <0.001) with mtDNA content variation in cases and controls. Positive correlation was found with decrease in mtDNA content with the increase in tumour stages ( P <0.001). We are reporting for the first time the association of HPV infection and  GSTM1-GSTT1  null genotypes with mtDNA content in OSCC.    Conclusion  Our results indicate that the mtDNA content in tumour tissues changes with tumour stage and tobacco-betel quid chewing habits while low levels of mtDNA content suggests invasive thereby serving as a biomarker in detection of OSCC.

Mitochondrial DNA Copy Number and Risk of Oral Cancer: A Report from Northeast India