Somatic alterations in TP53, PIK3CA, and CCND1 reveal exposure-driven patterns in oral and oropharyngeal tumors

: Tobacco, alcohol, and human papillomavirus (HPV) are major risk factors for oral cavity (OC) and oropharyngeal (OPC) cancers, yet their specific contributions to the tumor molecular landscape remain incompletely understood. We analyzed somatic alterations in 1,086 tumors (606 OC, 480 OPC, including 287 HPV(+)OPC) profiled with a 1,109-gene panel and evaluated their associations with exposures. PIK3CA alterations were widespread but context-specific: HPV(+)OPC featured APOBEC-driven mutations and co-occurrence of FGFR3 mutations in a subset of cases, while HPV(-)OPC and OC were marked by 3q26/28 (PIK3CA/TP63/SOX2) amplifications. TP53 was the most frequently mutated gene in HPV(-) tumors, with strong enrichment among smokers in HPV(-)OPC, whereas TP53 mutation frequencies in OC were consistently high regardless of smoking status. CCND1 amplifications were largely restricted to HPV(-) tumors and were most frequent in individuals reporting combined tobacco/alcohol use. This combined effect was replicated in the TCGA OC-OPC cohort and mirrored at the transcriptomic level, where CCND1 mRNA expression was highest in dual users. Within OC, characterization of one of the largest cohorts of tumors from never smoker-never drinkers to date (N = 100) showed they were more likely to be from female patients and to exhibit enrichment for FAT1 and CASP8 mutations compared to tumors from ever smoker-ever drinkers (N = 353). Together, these findings define distinct, exposure-driven patterns of somatic alterations by subsite and HPV status, and provide a molecular framework that may inform etiologic-based risk stratification in head and neck cancer.