Dysregulation of viral and human genomes at HPV integration events | LC 25

Biography

Since 2022, Michelle Ng has been a postdoctoral fellow in the Marra lab at the Michael Smith Laboratories and Canada's Michael Smith Genome Sciences Centre in Vancouver, Canada. She aims to understand how HPV integration affects the 3D organization of the genome, and how this may relate to other forms of dysregulation caused by HPV. Previously, she completed her PhD at the Hannover Medical School in Germany, where she investigated the role of long non-coding RNAs in acute myeloid leukemia.

Abstract

Human papillomaviruses (HPVs) cause cervical cancer, with viral DNA integrating into the host genome in over 80% of cases. Sites of HPV integration are associated with complex genomic rearrangements, which are difficult to elucidate using short-read sequencing technologies.

To better resolve the genome dysregulation associated with HPV integration, we performed Oxford Nanopore long-read sequencing of 72 Ugandan cervical cancer genomes that were previously characterized using short-read sequencing. We identified recurrent patterns of HPV integration, which we categorized as deletion-like, duplication-like, translocation, multi-breakpoint, or repeat region events. Integrations involving amplified HPV-human concatemers, particularly multi-breakpoint events, frequently harbored heterogeneous forms and copy numbers of the viral genome.

We also observed a striking association between the methylation status and transcriptional status of integration events. Transcriptionally active integrants — determined from short-read RNA sequencing data — 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, HPV integrants without evidence of expression lacked consistent methylation patterns.

Further, whereas transcriptional dysregulation was restricted to genes within 200 kilobases of an HPV integrant, dysregulation of the human epigenome in the form of allelic differentially methylated regions spanned megabases of the genome, independent of the integrant's transcriptional status.

By elucidating the allele-specific impacts of HPV integration on the genome, epigenome, and transcriptome, we provide insight into the role of integrated HPV in cervical cancer.