Microbiome has been shown to substantially contribute to some cancers. However, the diagnostic implications of microbiome in head and neck squamous cell carcinoma (HNSCC) remain unknown. Here, we report for the first time, the molecular difference in the microbiome of oral and non-oral HNSCC.
Primary data was downloaded from the Kraken-TCGA dataset. The molecular differences in the microbiome of oral and non-oral HNSCC were identified using the linear discriminant analysis effect size method. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUST) and ANOVA-like differential expression (ALDEx2), we predicted bacterial metabolic contributions of oral rich and non-oral rich bacteria, common rich bacteria in two groups and their pathways. A Correlation analysis was performed between RNA expression data and common bacteria data and protein-protein interaction (PPI) analysis was performed using correlated genes. Finally, to find out unique microbial signatures, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene ontology (GO) analysis using the PPI results.
The common microbiomes in oral and non-oral cancers were Fusobacterium, Treponema, and Selenomonas and Clostridium and Massilia, respectively. We found unique microbial signatures that positively and negatively correlated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in oral cancer and negatively correlated KEGG pathways in non-oral cancer. In oral cancer, positively correlated genes were mostly found in bacterial infection pathways, while negative correlated genes were involved in HTLV-I infection, signal transduction, cell adhesion, and cancer-associated pathway. In non-oral cancer, positively correlated genes did not show any significant results, and negatively correlated genes showed results from focal adhesion pathway and regulation of actin cytoskeleton pathway.
These results could help in understanding the underlying biological mechanisms of the microbiome of oral and non-oral HNSCC. Microbiome-based oncology diagnostic tool warrants further exploration.