DNA methylation plays a crucial role in activating and silencing genes during normal development. Tumor virus genomes are subject to selective differential methylation with important regulatory consequences. The role of methylation in hrHPV is explored from the perspective of regulation and potential for diagnostic assays.
Review of published scientific HPV methylation papers in the context of recent research in the laboratory of the author.
HPV16 has ~113 dispersed CpG sites, many of which are differentially methylated. Increased methylation of the LI, L2 and E2 genes is consistently associated with cervical carcinogenesis. Methylation values of some CpG sites in the L1-L2 regions in normal tissues typically range from 0 to 10%, with persistent infections showing higher methylation than transient infections. Methylation values in CIN2/3 are significantly elevated compared to normal, while in cancers methylation levels often reach 50 to 100%. Methylation levels are strongly associated with HPV integration. In contrast to the L1-L2 regions the CpGs in the URR are usually unmethylated in normal and CIN specimens. However, E2 protein binding sites can show increased methylation in cancers, which facilitates continued production of HPV16 E6-E7 oncogenes. Methylation patterns in other hrHPVs resemble HPV16, being significantly higher in CIN2+ compared to <CIN2. Interestingly methylation of L1-L2 in single infections of HPV18, HPV31 or HPV45 in CIN2+ were higher than when present as combinations with HPV16, suggesting that HPV16 is usually the driver virus and is more often targeted by the cellular methylation machinery.
HPV methylation patterns are complex and strongly associated with neoplasia. Similar methylation patterns have been shown in HPV16, HPV18, HPV31, HPV33, HPV45, HPV52 and HPV58 and may be characteristic of most or all hrHPVs. There is a typical progression of methylation level with persistence and carcinogenic change. Development and validation of robust routine methylation assays may allow better disease risk profiling of hrHPV+ women.