Microbiome-Host Interactions in Oral Squamous Cell Carcinoma: a Metatranscriptomic Exploratory Study

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 the microbiome in OSCC. 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. The aim of this study is to characterize the transcriptional activity (function) as well as composition of the multi-kingdom microbiome associated with OSCC and correlate it with the gene expression of the host using ultra-deep metatranscriptome sequencing, which will provide new insight into the role of the microbiome in OSCC and the possible mechanisms by which the tumor’s microbial community may influence on its behavior.
This project comprises RNA-Seq data from twenty OSCC tumor/normal tissue pairs and twenty tongue scraping samples from healthy controls. However, due to consent constraints, the human sequences from the control data are filtered out.
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Inclusion Criteria:OSCC tumor/normal pair samples: Frozen tissue from 20 tumor/normal pair were received from biorepositories All the individuals were treatment naïve (no treatment received before resection), except one who received radiotherapy
Healthy control samples: Tongue scrapings were collected from 20 age, gender and ethnicity matched individuals Exclusion Criteria:Healthy control samples: SmokingHistory of previous malignancy and premalignant lesionsAny acute/chronic oral infections, including severe gingivitis/periodontitisAny history of endocarditis/valve issueHistory of antibiotic/antifungal drug intake in the last 3 months

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