Novel biomarker identification for oral squamous cell carcinoma development in nonsmoker, nondrinker, and nonchewer patients using third-generation sequencing of oral microbiome.

Abstract

Background/objective: Oral squamous cell carcinoma (OSCC) in patients without tobacco, alcohol, or betel-quid habits is poorly understood and difficult to detect early. This study aimed to identify microbial biomarkers specific to this habit-free population using third-generation sequencing (TGS).

Patients/materials and methods: Twenty-seven habit-free OSCC patients were recruited at National Taiwan University Hospital (NTUH). Paired tumor and adjacent normal tissues were collected with informed consent and NTUH Research Ethics Committee approval (IRB 201902080RINC, 201304078RIND). Full-length 16S rRNA sequencing (PacBio Sequel IIe) was processed with DADA2 and SILVA. Biomarkers were identified using sparse partial least squares discriminant analysis (sPLS-DA) and random forest with cross-validation, and validated against three public OSCC cohorts.

Results: A three-species panel-Eikenella corrodens, Slackia exigua, and Eggerthia catenaformis-discriminated tumor from normal tissues (AUC = 0.905 training; 0.733 testing). Functional and network analyses showed tumor-enriched taxa forming pro-inflammatory clusters linked to lipid and glutamine metabolism, while commensals correlated with homeostatic pathways. Cross-cohort comparison confirmed this panel's specificity to habit-free OSCC.

Conclusions: Using TGS, we revealed distinct microbial signatures in habit-free OSCC that may aid early diagnosis and underscore the role of microbiome-host interactions in carcinogenesis.