The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer

Abstract

The natural history of cancers associated with virus exposure is intriguing, since only a minority of human tissues infected with these viruses inevitably progress to cancer. However, the molecular reasons why the infection is controlled or instead progresses to subsequent stages of tumorigenesis are largely unknown. In this article, we provide the first complete DNA methylomes of double-stranded DNA viruses associated with human cancer that might provide important clues to help us understand the described process. Using bisulfite genomic sequencing of multiple clones, we have obtained the DNA methylation status of every CpG dinucleotide in the genome of the Human Papilloma Viruses 16 and 18 and Human Hepatitis B Virus, and in all the transcription start sites of the Epstein-Barr Virus. These viruses are associated with infectious diseases (such as hepatitis B and infectious mononucleosis) and the development of human tumors (cervical, hepatic, and nasopharyngeal cancers, and lymphoma), and are responsible for 1 million deaths worldwide every year. The DNA methylomes presented provide evidence of the dynamic nature of the epigenome in contrast to the genome. We observed that the DNA methylome of these viruses evolves from an unmethylated to a highly methylated genome in association with the progression of the disease, from asymptomatic healthy carriers, through chronically infected tissues and pre-malignant lesions, to the full-blown invasive tumor. The observed DNA methylation changes have a major functional impact on the biological behavior of the viruses.

Viral epigenomes in human tumorigenesis

“…Different viral evasion strategies have been identified, but all of them are essentially aimed at camouflaging the virus in the host cell, restricting the expression of viral genes and proteins that are indispensable for viral persistency, and avoiding the expression of genes associated with immune response. Viral DNA methylation could be the masking mechanism by which many viruses are able to achieve this (Fernandez et al, 2009).…”

“…Despite this, the virus uses DNA methylation to maximize persistence and conceal itself from immune detection, inhibiting expression of viral latency proteins that are recognized by cytotoxic T cells (Robertson and Ambinder, 1997;Paulson and Speck, 1999;Tao and Robertson, 2003;zur Hausen, 2006;Fernandez et al, 2009).…”

“…There are many studies describing the methylation profiles of specific genes, especially those associated with the type of latency state (Tao et al, 1998;Ambinder et al, 1999;Paulson and Speck, 1999;Park et al, 2007b;Fejer et al, 2008). The methylation profiles of these promoters have been analyzed by methylation-specific PCR, bisulfite sequencing and pyrosequencing (Tao et al, 1998;Ambinder et al, 1999;Paulson and Speck, 1999;Li and Minarovits, 2003;Tao and Robertson, 2003;Park et al, 2007b;Fejer et al, 2008;Niller et al, 2008;Fernandez et al, 2009).…”

“…CpG methylation switches off gene expression and induces the alternative transcription of EBNA1 from various promoters in the different latency stages that, at the same time, are associated with the pathology that the virus induces, from a simple infection to a lymphoma or carcinoma (Li and Minarovits, 2003;Yoshioka et al, 2003;Niller et al, 2008). Although Wp, Cp and Fp have been found methylated in a specific latency type, Qp remains unmethylated, irrespective of its activity, and is thought to be regulated by a putative repressor protein and specific histone modifications (Tao et al, 1998;Paulson and Speck, 1999;Salamon et al, 2001;Li and Minarovits, 2003;Tao and Robertson, 2003;Minarovits, 2006;Fejer et al, 2008;Fernandez et al, 2009). …”

“…This reactivation is initiated by the expression of the immediate-early gene BZLF1, which encodes the transcriptional activator Zta, probably by stimuli such as plasma cell differentiation, and has been found to be unmethylated (Fernandez et al, 2009). This protein, apart from affecting the expression of host genes (Chang et al, 2006), has the ability to bind to methylated sites and activate the expression of BRLF1, another of this virus's immediate-early genes, and both together then activate the expression of the remaining lytic genes, thereby inducing a lytic infection (Bhende et al, 2005;Countryman et al, 2008;Dickerson et al, 2009;Heather et al, 2009).…”