Spatiotemporal Heterogeneity of HPV Integration Architectures Drive Oncogenic Features of Oropharyngeal Cancer

The study, involving targeted capture sequencing of 197 HPV-positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC) tumors and long-read nanopore sequencing of 17 tumors and models, delved into the structural and clinical implications of viral integration within these cancer types. A novel quantitative framework was developed to classify integration structures into two types.

Type1 integration is described as simple, occurring once or in low copies, while Type2 integration involves clustered, high-copy, and rearranged patterns. FPVI integration was detected in 83% of the tumors, with recurrent hotspots including TP63, MYC, CD274, TRAF2, and KMT2C. Type2 HPV integration was notably associated with disruption of the E2 protein, focal amplifications of human genes, enhanced transcription of HPV DNA, and the emergence of noncanonical RNA fusion isoforms.

Tumors displaying Type2 integration patterns exhibited elevated expression of HPV oncogenes and activation of critical signaling pathways such as MYC, NF-{kappa}B/TNF, PI3K-AKT-mTOR, Hippo/YAP-TAZ, and those promoting epithelial stemness. Comprehensive multi-region and longitudinal analyses underscored the presence of intratumoral heterogeneity and the clonal selection of Type2 integration architectures as these cancers progressed.

This finding suggests that HPV integration structure could serve as a valuable biomarker for identifying aggressive tumor behavior and could play a role in risk stratification for patients with oropharyngeal cancer.