Human papillomavirus type 16 sub-lineages and integration in cancer

ABSTRACT Our lab has been intrigued by the fact that viral genomes often take on the role of mobile elements to perpetuate their existence in a complex organism’s genome. Multiple DNA viruses such as Epstein-Barr virus, hepatitis B virus, and human papillomavirus (HPV) can invade their host genome, as “genomic parasites”. We have been investigating HPV type 16 (HPV16), which is a prominent human tumour virus. In our recent in vitro work using 3D organoids, a common variant of HPV16’s coding region elicited early integration into the host genome compared to the HPV16 prototype sequence. Next-generation sequencing (NGS) data confirmed a transcriptomic profile of increased proliferation and chromosomal instability—both hallmarks of cancer. Epidemiologically, this variant is associated with a high cervical cancer incidence. To take inquiries a step further, we investigated variant-specific integration across HPV16-related cancers using NGS data from population-derived clinical samples in The Cancer Genome Atlas (TCGA)-curated database. Data were analyzed for HPV16 positivity, sub-lineage, and viral-host integration using a bioinformatic pipeline of open-source tools, including HPVDetector. Here, we report the analysis of 120 cervical cancer cases comprising HPV16 positive and negative samples as well as their different sub-lineage and integration status. The integration signature between variant and prototype did not differ quantitatively but qualitatively: that of the variant being related to hypoxia/energetics (Warburg effect) and that of the prototype being much more varied to include host immune abrogation and cancer pathways activation. We conclude by discussing challenges and future directions for expanding these analyses.