Exploration and Characterization of the Microbiome in Oral Squamous Cell Carcinoma using 16s rRNA Gene Next-generation Sequencing

Abstract

Oral squamous cell carcinoma (OSCC) is an oral cancer with high prevalence rates in many countries, especially ones with high rates of risk factors, such as tobacco use. As OSCC is typically diagnosed in later stages and is responsible for high mortality rates, identifying biomarkers associated with OSCC could be instrumental in improving OSCC diagnosis, prognosis, and treatment. A comprehensive literature review on the use of 16s rRNA gene next generation sequencing (NGS) in studying OSCC biomarkers found that few studies to date have used rigorous scientific or biostatistical approaches, and that the high-quality studies identified have inconsistent findings. This dissertation investigated the oral microbiome of OSCC patients along with patients with a condition known to be a precursor to OSCC called oral epithelial dysplasia (OED) in the United Kingdom (UK), London. First, in substudy 1, which is a cross-sectional study, the oral microbiome of OSCC lesion tissue was compared to OED lesion tissue in terms of diversity and relative differential abundance. Next, in substudy 2, which is a case series study, the same metrics were used to compare OSCC and OED lesion tissue with healthy tissue in the same patient. Finally, in substudy 3, which is also a case series study, data obtained from a Chinese study of similar design to substudy 2 was reanalysed using the same bioinformatics and statistical approaches as used in substudy 2, and the results compared. The overall results of all three studies showed evidence that OSCC lesion tissues have statistically significantly more diversity than OED or healthy tissue. However, no specific members of the oral microbiome could be identified that appeared to be responsible for OSCC in any of the substudy analyses. Future research must tackle the challenge of using rigorous scientific methods that are replicable to identify OSCC biomarkers that have clinical utility.