Marissa Iden

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 Technologies long-read sequencing on 72 cervical cancer genomes from a Ugandan data set that was previously characterized using short-read sequencing. We find recurrent structural rearrangement patterns at HPV integration events, which we categorize as del(etion)-like, dup(lication)-like, translocation, multi-breakpoint, or repeat region integrations. Integrations involving amplified HPV–human concatemers, particularly multi-breakpoint events, frequently harbor heterogeneous forms and copy numbers of the viral genome. Transcriptionally active integrants are 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 lack consistent methylation patterns. Furthermore, whereas transcriptional dysregulation is limited to genes within 200 kb of an HPV integrant, dysregulation of the human epigenome in the form of allelic differentially methylated regions affects 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.

Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes

Integration of human papillomavirus (HPV) into the host genome is a dominant feature of invasive cervical cancer (ICC), yet the tumorigenicity of cis genomic changes at integration sites remains largely understudied. Combining multi-omics data from The Cancer Genome Atlas with patient-matched long-read sequencing of HPV integration sites, we developed a strategy for using HPV integration events to identify and prioritise novel candidate ICC target genes (integration-detected genes (IDGs)). Four IDGs were then chosen for in vitro functional studies employing small interfering RNA-mediated knockdown in cell migration, proliferation and colony formation assays. PacBio data revealed 267 unique human-HPV breakpoints comprising 87 total integration events in eight tumours. Candidate IDGs were filtered based on the following criteria: (1) proximity to integration site, (2) clonal representation of integration event, (3) tumour-specific expression (Z-score) and (4) association with ICC survival. Four candidates prioritised based on their unknown function in ICC (BNC1, RSBN1, USP36 and TAOK3) exhibited oncogenic properties in cervical cancer cell lines. Further, annotation of integration events provided clues regarding potential mechanisms underlying altered IDG expression in both integrated and non-integrated ICC tumours. HPV integration events can guide the identification of novel IDGs for further study in cervical carcinogenesis and as putative therapeutic targets.