The Mouse Papillomavirus Epigenetic Signature Is Characterised by DNA Hypermethylation after Lesion Regression

Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens

Aberrant DNA methylation is a universal feature of cancer. Here, we present a protocol for generating high-quality genome-scale DNA methylation sequencing data from a variety of human cancer biospecimens including immortalized cell lines, fresh-frozen surgical resections, and formalin-fixed paraffin-embedded tissues. We describe steps for DNA extraction considerations, reduced representation bisulfite sequencing, data processing and quality control, and downstream data analysis and integration. This protocol is also applicable for other human diseases and methylome profiling in other organisms. For complete details on the use and execution of this protocol, please refer to Rodger et al. (2023).1.

Case report: An adverse response to cyclosporin A treatment in BALB/cJ mice

Cyclosporin A (CsA) is an immunosuppressive drug that has been widely used in mice at a range of doses from 10 to 200 mg/kg. Our group carried out an experiment in 2016 where we delivered 75 mg/kg CsA (NeoralTM) to BALB/cJ mice by oral gavage to enable wart formation in mice, which was moderately well-tolerated. We recently commenced another study using the same dose and route of delivery of CsA in BALB/cJ mice in order to immune suppress mice to make them susceptible for mouse papillomavirus infection. We highlight in this case report that in contrast to our earlier study, we observed almost immediate unexpected toxicity and had to terminate the recent experiment after only five days of treatment. Seven to eight-week-old female BALB/cJ mice were treated with 75 mg/kg of CsA by oral gavage daily for five days before treatment was stopped due to body weight loss and mice becoming moribund. The probability of survival of the mice following CsA treatment was 80% in this study, compared with 98% in our 2016 study. Mice showed signs of probable acute kidney injury, which was reversible following withdrawal of CsA. Although it is unclear why the clinical response to CsA in BALB/cJ mice differed markedly between the two experiments, this case report highlights the risk of CsA to mouse welfare. CD3 depletion has been used rather than CsA treatment in other studies and should be considered as an alternative to CsA treatment as it is immune-selective, and may be more effective at enabling wart formation in mice.

A Novel In Vivo Model of Laryngeal Papillomavirus-Associated Disease Using Mus musculus Papillomavirus

Recurrent respiratory papillomatosis (RRP), caused by laryngeal infection with low-risk human papillomaviruses, has devastating effects on vocal communication and quality of life. Factors in RRP onset, other than viral presence in the airway, are poorly understood. RRP research has been stalled by limited preclinical models. The only known papillomavirus able to infect laboratory mice, Mus musculus papillomavirus (MmuPV1), induces disease in a variety of tissues. We hypothesized that MmuPV1 could infect the larynx as a foundation for a preclinical model of RRP. We further hypothesized that epithelial injury would enhance the ability of MmuPV1 to cause laryngeal disease, because injury is a potential factor in RRP and promotes MmuPV1 infection in other tissues. In this report, we infected larynges of NOD scid gamma mice with MmuPV1 with and without vocal fold abrasion and measured infection and disease pathogenesis over 12 weeks. Laryngeal disease incidence and severity increased earlier in mice that underwent injury in addition to infection. However, laryngeal disease emerged in all infected mice by week 12, with or without injury. Secondary laryngeal infections and disease arose in nude mice after MmuPV1 skin infections, confirming that experimentally induced injury is dispensable for laryngeal MmuPV1 infection and disease in immunocompromised mice. Unlike RRP, lesions were relatively flat dysplasias and they could progress to cancer. Similar to RRP, MmuPV1 transcript was detected in all laryngeal disease and in clinically normal larynges. MmuPV1 capsid protein was largely absent from the larynx, but productive infection arose in a case of squamous metaplasia at the level of the cricoid cartilage. Similar to RRP, disease spread beyond the larynx to the trachea and bronchi. This first report of laryngeal MmuPV1 infection provides a foundation for a preclinical model of RRP.