Human and viral whole genome sequencing identify HPV and APOBEC as oncogenic drivers in sinonasal squamous cell carcinoma

Background: Sinonasal squamous cell carcinoma (SNSCC) is a rare, aggressive malignancy with limited molecular characterization. Emerging evidence implicates human papillomavirus (HPV) in a subset of cases, but the genomic interplay between viral and host factors remains poorly defined. Methods: We performed paired host and viral whole-genome sequencing (WGS) on 21 SNSCC tumors with matched normal samples, including ultra-deep viral WGS (10,000×) and comprehensive HPV PCR genotyping. Somatic mutations, viral integration, structural variants, and mutational signatures were analyzed using established computational pipelines. Results: Eighteen of 21 (86%) tumors were HPV-positive by WGS or PCR, with 94% concordance across assays. Unlike oropharyngeal squamous cell carcinoma (OPSCC), where HPV16 predominates, SNSCC exhibited nine HPV genotypes, including HPV11, 18, 35, 39, 45, 51, 56, and 59. Viral integration events were detected in most HPV-positive tumors, including an HPV45-TP63 fusion amplified as extrachromosomal DNA (ecDNA), representing, to our knowledge, the first HPV-associated ecDNA-like amplicon in SNSCC. Multi-genotype infections showed a single dominant integrating type, indicating that one “driver” genotype typically initiates tumorigenesis. Host mutational analysis revealed recurrent clonal mutations in PIK3CA, CHEK2, and KDM6A, with depletion of TP53 and CDKN2A alterations in high-risk HPV+ cases. Mutational signature analysis identified predominant APOBEC3 activity, independent of smoking, which extended to viral genomes, providing direct evidence of concurrent host-virus APOBEC mutagenesis. Structural variants were common, including focal PTEN loss and complex rearrangements such as chromothripsis and chromoplexy, underscoring pervasive genomic instability. Conclusions: Paired human and viral WGS reveals that HPV drives tumorigenesis in SNSCC through diverse genotypes, APOBEC-mediated mutagenesis, and integration-linked ecDNA formation. These mechanisms expand the known spectrum of viral oncogenesis beyond the oropharynx, highlighting novel routes of genomic instability and supporting the inclusion of broad HPV genotyping and viral-genomic assays in diagnostic and translational frameworks for SNSCC.