Human papillomavirus type 16 sub-lineages and integration in cancer

Abstract

21Our lab has been intrigued by the fact that viral genomes often take on the role of mobile 22 Retroviridae (e.g., human immunodeficiency virus, HIV), it can also occur during persistent 50 infections with DNA viruses and is often associated with virally induced cancers. One such family 51 of common DNA tumour viruses, Papillomaviridae, is responsible for causing ~5% of all human 52 cancers worldwide [Ghittoni et al., 2015]. There are 660 types of papillomaviruses (PVs) 53 discovered as of June 2020 based on the PaVE reference genome database [PaVE: 54 https://pave.niaid.nih.gov, Van Doorslaer et al., 2013; 2017a]. The number of PV types, including 55 the non-human PVs (currently 215) is expected to continue rising due to high-throughput 56 genomics and sampling [Van Doorslaer and Dillner, 2019]. The majority of PVs currently identified 57 are the human papillomaviruses (HPVs) [Van Doorslaer et al., 2017b] and these types (445 to 58 date) differ in their propensity for inducing cancer as well as their epithelial tropism, with "high-59 risk" types being the primary cause of malignancies: predominantly via sexually-transmitted 60 persistent HPV type 16 (HPV16) infection of anogenital and oropharyngeal mucosa [Ndiaye et 61 al., 2014]. Although this and other HPV genomes are considered "small", only ~7.9 kb containing 62 nine open reading frames (ORFs) and a variety of alternatively spliced and multi-cistronic variant 63 transcripts [Graham & Faizo, 2017], it encodes potent oncoproteins such as E6 and E7 which 64 drive host cells to acquire the hallmarks of cancer [Hanahan and Weinberg, 2000; 2011; Mesri et 65 al., 2014]. The combined E6 and E7 actions disable protective apoptotic mechanisms and 66 promote host cell proliferation as outlined by Hoppe-Seyler and colleagues [2018]-a 67 phenomenon that could potentially be exploited therapeutically at an RNA [Togtema et al., 2018] 68 or protein-level [Togtema et al., 2019]. Of particular relevance for this study, the HPV-augmented 69 environment can permit chromosomal instability (an enabling characteristic among the hallmarks 70 157proportion of integrated cases was 1.23x higher in D2/D3-containing CESC samples (9/10, 90.0% 158 vs 51/70, 72.9% for A1), the sample size was very low rendering this initial analysis underpowered 159 and the finding as not statistically significant (P = 0.242, Χ 2 test). 160