Intratumoral heterogeneity and clonal evolution induced by HPV integration

The human papillomavirus (HPV) genome is integrated into host DNA in most HPV-positive cancers, but the consequences for chromosomal integrity are unknown. Continuous long-read sequencing of oropharyngeal cancers and cancer cell lines revealed interrelated but heterogeneous genomic structures comprising repetitive patterns of concatemerized virus and host segments. Evidence of this novel form of structural variation – termed “circacatena” here -- was detected in extrachromosomal and intrachromosomal DNA and at chromosomal rearrangements. Unique breakpoint sequences shared across structurally diverse virus-host concatemers facilitated stepwise reconstruction of their evolution from common molecular ancestors. This analysis revealed that concatemerized HPV genomes are unstable and, upon insertion into and excision from chromosomes, facilitate capture, rearrangement, and rolling-circle amplification of host DNA. The data indicate that circacatena is driven by the dynamic, aberrant replication and recombination of an oncogenic DNA virus, thereby extending known consequences of HPV integration to include promotion of intratumoral heterogeneity and clonal evolution. ### Competing Interest Statement : F.S. receives research support from Illumina, PacBio and Oxford Nanopore. M.L.G. serves as consulting, advisory board roles for LLX Solutions, LLC (Pending), Sensei, Mirati Therapeutics, BioNTech AG, Shattuck Labs Inc., EMD Serono Inc., Debiopharm, Kura Oncology, Merck Co., Ipsen Biopharmaceuticals Inc., Bristol-Myers Squibb, Bicara Therapeutics, Bayer HealthCare Pharmaceuticals, Roche, Roche Diagnostics GmbH, Genocea Biosciences, Inc., NewLink Genetics Corporation, Aspyrian Therapeutics, TRM Oncology, Amgen Inc., AstraZeneca Pharmaceuticals, and Celgene Corp.; and research funding from Genocea, BMS, Kura, Cullinan, Genentech, BioNtech, and Gilead.