Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma

Abstract

Human papillomavirus (HPV) DNA is detected in up to 80% of oropharyngeal carcinomas (OPC) and this HPV positive disease has reached epidemic proportions. To increase our understanding of the disease, we investigated the status of the HPV16 genome in HPV-positive head and neck cancers (HNC). Raw RNA-Seq and Whole Genome Sequence data from The Cancer Genome Atlas HNC samples were analyzed to gain a full understanding of the HPV genome status for these tumors. Several remarkable and novel observations were made following this analysis. Firstly, there are three main HPV genome states in these tumors that are split relatively evenly: An episomal only state, an integrated state, and a state in which the viral genome exists as a hybrid episome with human DNA. Secondly, none of the tumors expressed high levels of E6; E6*I is the dominant variant expressed in all tumors. The most striking conclusion from this study is that around three quarters of HPV16 positive HNC contain episomal versions of the viral genome that are likely replicating in an E1-E2 dependent manner. The clinical and therapeutic implications of these observations are discussed.

Human Papillomavirus-Related Head and Neck Cancer

“…Also, viral oncogene expression has been shown to be independent of viral copy number and DNA integration [29]. This was confirmed by RNA-Seq and whole genome sequencing data showing that 3 possible states of the HPV genome (episomal, integrated, and a hybrid of both forms) were evenly split in HPV16-positive HNSCC [30], indicating overlapping mechanisms in HPV oncoprotein regulation (e.g., by methylation of E2 binding sites (E2BS)).…”

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

“…If this hypothesis is true, the human-viral fusion sites, that we called integration sites in this study, could instead represent chimeric human-viral episomes described in other studies (32, 47). The fact that the episomal and integrated HPV can co-exist in the same tissue or even the same cell (30, 32, 47, 48), and both can be transcribed, adds another twist to the complex picture of HPV infection in human cancers. Southern blots or FISH-based technologies followed by high-resolution microscopy might help to resolve this scientific dispute (32, 49), and should be evaluated in conjunction with H3K27ac binding sites in future studies.…”

“…A recent study supported the hypothesis that HPV is only transiently integrated into the host genome and then subsequently excised out of the human genome together with human sequences to form human-viral chimeric episomes with multiple copies of HPV (32, 47). If this hypothesis is true, the human-viral fusion sites, that we called integration sites in this study, could instead represent chimeric human-viral episomes described in other studies (32, 47).…”

“…A recent study supported the hypothesis that HPV is only transiently integrated into the host genome and then subsequently excised out of the human genome together with human sequences to form human-viral chimeric episomes with multiple copies of HPV (32, 47). If this hypothesis is true, the human-viral fusion sites, that we called integration sites in this study, could instead represent chimeric human-viral episomes described in other studies (32, 47). The fact that the episomal and integrated HPV can co-exist in the same tissue or even the same cell (30, 32, 47, 48), and both can be transcribed, adds another twist to the complex picture of HPV infection in human cancers.…”

“…Although the role of HPV-integration is controversial, recent studies have demonstrated that HPV+ HNSCC samples with episomal and integrated HPV have unique signatures of gene expression, and can be separated based on them (22, 30, 32, 47–49). Clustering of gene expression data described two HPV+ HNSCC subtypes: mesenchymal and classical (29).…”