The mouse papillomavirus epigenetic signature is characterised by DNA hypermethylation after lesion regression

The {beta} genus of human papillomaviruses (HPVs) infect cutaneous epidermis. They contribute to the development of cutaneous squamous cell carcinoma (cSCC) in individuals with epidermodysplasia verruciformis, and increase susceptibility to UV-induced cSCC. This has been demonstrated in UV-exposed mice previously infected with mouse papillomavirus (MmuPV1). However, the mechanism by which {beta}-HPVs contribute to cSCC is unclear. We propose that viral infection leaves a DNA methylation signature following resolution of the active lesion that may contribute to increased susceptibility to UV-induced cSCC. To test this, we carried out Reduced Representation Bisulphite Sequencing on DNA from tail skin of mice with actively infected lesions, MmuPV1-infected then healed lesions (regressed infection), and mock-infected control mice. Genome-scale DNA methylation libraries were generated and analysed for differentially methylated regions throughout the genome, and for HPV sequences. We found that DNA of active lesions was not differentially methylated compared to matched control mice. In contrast, 834 differentially methylated fragments were identified in regressed lesions compared to mock-infected control skin. An analysis of MmuPV1 viral DNA demonstrated retention of viral DNA in some of the lesions that had regressed. Overall, the viral sequences identified showed over-representation of sequences from the E4 region. The DNA hypermethylation that we found in regressed MmuPV1 lesions may be a factor in the increased susceptibility of mice to UV-induced cSCC. AUTHOR SUMMARYPapillomavirus infections can be asymptomatic, can cause warts, and in some cases can lead to cancer. There is direct evidence for mouse papillomavirus infection resulting in increased susceptibility to UV-induced cutaneous squamous cell carcinoma in a mouse model. We propose that DNA methylation following viral infection may contribute to the increased susceptibility. We describe the DNA methylation landscape during an active infection with mouse papillomavirus and following regression of the lesion. We found that there were very few differentially methylated DNA fragments during active infection. In contrast, over 800 differentially methylated DNA fragments were identified following regression of the lesion. This is the first description of the genome-wide DNA methylation landscape for mouse papillomavirus, to our knowledge. The dramatic DNA hypermethylation that we observe following resolution of infection may contribute to a hit and run mechanism for the increased susceptibility to UV-induced cancer by papillomaviruses.