MODULATION OF CELLULAR CpG DNA METHYLATION BY KAPOSI’S SARCOMA ASSOCIATED HERPESVIRUS

Kaposi’s sarcoma associated herpesvirus (KSHV, HHV-8) is a gamma herpesvirus associated with several human malignancies. DNA methylation at CpG dinucleotides is an epigenetic mark dysregulated in many cancer types, and in KSHV infected cells. Several previous studies have analyzed in detail the CpG methylation of the KSHV episomal genome, but little is known about the impact of KSHV on the human genome. Our knowledge of cellular CpG methylation in the context of KSHV infection is currently limited to four hyper-methylated human gene promoters. Therefore, we undertook a comprehensive CpG methylation analysis of the human methylome in KSHV-infected cells and KSHV-associated primary effusion lymphoma (PEL). We performed Infinium HumanMethylation 450K and EPIC BeadChip arrays and identified panels of hyper and hypo-methylated cellular promoters in KSHV infected cells. We combined our genome wide methylation analysis with RNA-sequencing (RNA-seq) to add functional outcomes to the virally induced methylation changes. We were able to correlate many downregulated genes with promoter hyper-methylation, and upregulated genes with hypo-methylation. In addition, we show that treating the cells with a de-methylating agent leads to re-expression of these downregulated genes, indicating that indeed DNA methylation plays a role in the repression of these human genes. Comparison between de-novo infection and PEL, suggests that the virus induces initial hyper-methylation followed with a slow increase in genome wide hypo-methylation. This study extends our understanding of the relationship between epigenetic changes induced by KSHV infection and tumorigenesis.