“Novel structures & regulation patterns at HPV integration events in cervical cancer” was the title of Vanessa Porter’s session at London Calling 2022. Porter is a Ph.D. candidate at the University of British Columbia, Canada. They explained that HPV is “a necessary driver of cervical cancer,” and the integration of the HPV genome into the host genome is a critical event. Porter explained that in 70% of cervical cancers, HPV is found integrated. Integration requires double-stranded breaks and rearrangement. Duplications and deletions may occur. In cancer, HPV is “recurrently found near cancer genes in tumours and often corresponds with gene dysregulation.” In this study, Porter had the objective of investigating how the integration of HPV affects the structure and regulation of cervical cancer genomes using Oxford Nanopore Technology (ONT) long-read sequencing. The study explored samples from two cohorts: one with 118 cervical cancer samples collected in Uganda, and one with 192 cervical cancer samples collected in the USA. As parter of the study, Porter has sequenced 44 and 22 samples from each of the Uganda and USA cohorts, respectively. They used a pipeline with a custom modification for HPV samples. In most of their samples, HPV integrated, anad the collection of breakpoints was called integration events. The team identified six patterns in the breakpoints. The three common resolutions of two-breakpoint integrations events were a deletion, a duplication, or eccDNA (extrachromosomal circular DNA). Interestingly, eccDNA appear to have to be of a certain size to be stable within the cell. The contents of the inserted HPV sequence can be variable. Porter explained that they also identified multi-breakpoint integration events. Both the centromere and telomere have HPV integration detected by Nanopore sequencing. Some integration events are much more common than others. Also, HPV16 and HPV18 varied in their integration events, for example. Methylation is more common in genetic regions of integration HPV and in episomal HPV. Porter concluded that HPV integration events often involve structural variants that can be identified and delineated with ONT. DNA methylation across HPV integration events can help identify how HPV is affecting the epigenome. In addition, Porter concluded that “the genetic region of integrated HPV is hypermethylated when compared to episomal HPV and has some variability between HPV types.” I had not considered the power of methylation analyses of integration sites that can be used with long-read sequencing.
