Investigating DNA Methylation Changes in a Preclinical Murine Model of Cutaneous Squamous Cell Carcinoma

  • Kevin Roth

Student thesis: Doctoral ThesisDoctor of Philosophy

Abstract

Non-melanoma skin cancers (NMSC) are the most common human malignancy. They can be divided into basal cell carcinomas (BCC) and cutaneous squamous cell carcinomas (cSCC), with the latter being responsible for the majority of NMSC deaths. Incidence rates for NMSC are rising due to increased exposure to UV radiation, caused by active sun-seeking behaviour and increased cumulative sun-exposure in aging population . In addition to the general populations, there are high risk groups, such as organ transplant recipients, who are in urgent need for strategies to treat aggressive cSCC.

Most animal models only partly reflect the complex genetic landscape of cSCC or leave out important parts of the carcinogenic process. We have developed a preclinical mouse model for cSCC by irradiating SKH-1 mice with low chronic doses of solar simulated UVR. The resulting tumors are remarkably similar to human cSCC in terms of histopathology and genetics. In this study, we provide a comprehensive analysis of global DNA methylation of this murine model and compare it to the methylome of human cSCC. We found that methylation changes in the murine cSCC tumors occur predominantly at regions of potential regulatory function, such as enhancers, promoters and intergenic regions of tumor suppressor genes that may be involved in regulation of gene expression or alternative splicing. Deactivation of tumor suppressor genes is an important feature for cancer, especially cSCC and our data suggest, that silencing of tumor suppressor genes by DNA methylation could be important in cSCC. Furthermore, we discovered differential methylation in the tumor suppressor gene Filamin A interacting protein 1 like (Filip1l). Down-regulation of the FILIP1L gene has been linked to ovarian, prostate and pancreatic cancer aggressiveness and metastatic potential and is an independent prognostic marker in ovarian cancer patients. The levels of Filip1l protein were significantly down-regulated in murine cSCC as well as in 9 out of 15 tested human cSCC cell lines. Although the exact function of the FILIP1L protein is incompletely understood, the strongest evidence points to its regulation of β-catenin stability and therefore WNT signalling activity. We found evidence that FILIP1L may regulate WNT signalling in skin, although FILIP1L did not regulate proliferation of the human cSCC cell lines that we tested.

When we compared the methylome of human cSCC patients to the methylome of mouse cSCC, the general features of the DNA methylation were similar. For example, average methylation levels increased in a subset of human cSCC cases and the mouse tumors, an effect that has been previously reported for UV irradiated skin (both human and mouse). We identified 214 genes that have at least one differentially methylated CpG in our dataset. Using R and the Ensemble gene annotation, we identified 153 of these genes that had a human orthologue. Of these 153 genes, 150 (93%) were also differentially methylated in human cSCC.

The remarkable similarities in histopathology, genetics and DNA methylation between human cSCC and the solar simulated UV induced mouse cSCC model suggest that this model could be advantageous over existing models and may provide new possibilities to investigate cSCC and develop new treatment strategies, especially for high risk groups. Furthermore, extending previous observations that most mutations in this tumor type occur not within oncogenes, but within tumor suppressor genes, our findings highlight the importance of inactivation of tumor suppressors (by both genetic and epigenetic mechanisms) for the development of cSCC.
Date of Award2019
Original languageEnglish
SponsorsBritish Skin Foundation
SupervisorAlbena Dinkova-Kostova (Supervisor) & John Hayes (Supervisor)

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