Multi-omics analysis reveals the association between intratumoral bacteria and somatic mutational signatures in oral squamous cell carcinoma.

BACKGROUND: Oral squamous cell carcinoma (OSCC) poses significant challenges with its obscure etiology and poor prognosis. Intratumoral bacteria exert a significant influence on the progression of OSCC. Nonetheless, the precise composition and role of the intratumoral bacteria in OSCC patients remain obscure and the association between the intratumoral bacteria and somatic mutational signatures in OSCC patients has not been defined. METHODS: Paraffin-embedded tumors and adjacent normal tissues were collected retrospectively from OSCC patients. A five-region 16S rRNA gene sequencing (5R 16S rRNA-seq) approach (targeting V2, V3, V5, V6, and V8) was employed to characterize the intratumoral bacterial composition of OSCC patients, while whole-exome sequencing (WES) was utilized to identify the somatic mutational signatures of OSCC patients. Then, the multi-omics data were integrated to uncover the association between intratumoral bacterial composition and somatic mutational signatures in OSCC patients. Key findings were validated using fluorescence in situ hybridization (FISH) on tissue microarrays. RESULTS: We found significant differences in bacterial profiles between tumors and adjacent normal tissues. The diversity of the bacteria was less within tumor tissues and anaerobic bacteria and periodontopathogens (e.g., Dialister pneumosintes and Prevotella intermedia) were more prevalent in tumor tissues. And the presence of Dialister pneumosintes within tumor tissues is associated with poorer short-term disease-free survival in OSCC patients. The integrated analysis of the 5R 16S rRNA-seq and WES data revealed that tumor mutation burden was positively correlated with the α diversity of the intratumoral bacteria in OSCC patients. CONCLUSION: This study utilized a multi-omics approach to elucidate the characteristics of the intratumoral bacteria and somatic mutational signatures in OSCC patients, revealing the intricate relationships between these elements. These findings pave the way for hypothesis-driven research aiming to further elucidate the role of the intratumoral bacteria in OSCC.