Microbiome-host interactions in oral squamous cell carcinoma: a meta-transcriptomic exploratory study

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Project summary Oral cancer (predominantly squamous cell carcinoma; OSCC) is the 14th most prevalent malignancy worldwide accounting for more than 300,000 new cases and 145,000 deaths annually. Despite advances in cancer treatment modalities, OSCC continues to have poor prognosis with 5-year survival rates less than 50%. Although use of tobacco and alcohol consumption constitute the major risk factors, there is emerging evidence for the role of microbiome in OSCC. Exploration of such a role has been facilitated by the advent of next generation sequencing and availability of big data analysis tools. However, studies on the association between the microbiome and OSCC has so far focused on compositional analysis, and has been largely limited to the bacterial component of the microbiome. Furthermore, the results from these studies have not been consistent. Our preliminary work demonstrates presence of complex community of microbes other than bacteria including fungi, archaea, viruses and even protists. In addition, it shows that functional analysis generates results that are more consistent, and more importantly, that are directly relevant to the carcinogenic process. In this study, we propose to use RNA sequencing coupled with comprehensive bioinformatic analysis to study the metatranscriptome of OSCC tissues. Specifically, the study will characterize the transcriptional activity (function) as well as composition of the multi-kingdom microbiome associated with OSCC (aim 1), and correlate it with the gene expression of the host (aim 2). The study will provide a new insight into the role microbiome in OSCC by providing preliminary data on the possible mechanisms by which the tumor's microbial community may influence on its behavior.