Mutational signature-based classification uncovers emerging oral cancer subtypes with distinct molecular patterns

Tobacco use, alcohol consumption, and infection with human papilloma virus (HPV) are well-established risk factors for head and neck squamous cell carcinomas (HNSCC). However, the incidence of oral cancer, particularly in the mobile tongue, has been rising in non-smoker/non-drinker and HPV-negative patients, suggesting the emergence of a new clinical entity. To understand in molecular terms this subtype of oral cavity squamous cell carcinomas (OCSCC) with no-identified risk factor (NIRF), we analyzed the available public head and neck cancer multi-omics data. We identified mutational signatures that stratified 253 OCSCC and 94 laryngeal cancer cases, used as tobacco-only-related controls, according to their clinico-pathological characteristics. We show that tobacco, depending on the anatomical site, triggers distinct mutational processes and further demonstrate that the single-base-substitution (SBS) signature SBS16 in OCSCC is associated with tobacco smoking, reflecting the combined effects of smoking and drinking. Importantly, we identified a tongue cancer-enriched NIRF OCSCC subgroup exhibiting significantly increased endogenous clock-like mutagenesis, while another NIRF subgroup manifested with elevated apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC)-associated mutagenesis. Both NIRF OCSCC subgroups harbored specific cancer driver mutations and distinct methylation patterns, which differed from those observed in OCSCC linked to traditional HNSCC risk factors, reflecting unique molecular programs underlying disease development. Specifically, NIRF-OSCC exhibited pronounced immune evasion strategies and antimicrobial transcriptomic responses. Our study presents the first molecular and genomic characterization of the emerging NIRF OCSCC subtype likely driven by increased endogenous mutagenesis and responses to microbial insults. These findings warrant future detailed investigations into etiology and have implications for clinical management and cancer prevention.