Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer. To resolve genome dysregulation associated with HPV integration, we performed Oxford Nanopore long-read sequencing on 72 cervical cancer genomes from an Ugandan dataset that was previously characterized using short-read sequencing. We found recurrent structural rearrangement patterns at HPV integration events, which we categorized as: del(etion)-like, dup(lication)-like, translocation, multibreakpoint, or repeat region integrations. Integrations involving amplified HPV-human concatemers, particularly multibreakpoint events, frequently harbored heterogeneous forms and copy numbers of the viral genome. Transcriptionally active integrants were characterized by unmethylated regions in both the viral and human genomes downstream from the viral transcription start site, resulting in HPV-human fusion transcripts. In contrast, integrants without evidence of expression lacked consistent methylation patterns. Furthermore, whereas transcriptional dysregulation was limited to genes within 200 kilobases of an HPV integrant, dysregulation of the human epigenome in the form of allelic differentially methylated regions affected megabase expanses of the genome, irrespective of the integrant's transcriptional status. By elucidating the structural, epigenetic, and allele-specific impacts of HPV integration, we provide insight into the role of integrated HPV in cervical cancer.