Abstract 3449: Epigenomics identifies conserved DNA methylation events associated with medulloblastoma development in humans and mice
Authors: Lindsey Janet C. , Schwalbe Ed C. , Kawauchi Daisuke , Olson Jim M. , McKinnon Peter J. , Gilbertson Richard J. , Roussel Martine F. , Ellison David W. , Bailey Simon , Clifford Steven C. 
Published: June 2012

Abstract
Medulloblastoma, an invasive embryonal tumor of the cerebellum, is the most common malignant brain tumor of childhood. Genome-wide technologies have recently shown that gene-specific changes in DNA methylation status are a significant feature of medulloblastoma development. Mouse models of medulloblastoma may provide important systems in which to study the impact of these DNA methylation changes, however the epigenetic basis of these models has not been widely investigated. We therefore adopted a cross-species approach to identify epigenetic events of relevance in human and mouse tumors, and investigate their impact on medulloblastoma development.
Using Illumina Goldengate DNA methylation arrays, we first identified a series of tumor-specific DNA methylation changes (measured relative to the normal cerebellum) which are strongly associated with activation of the Sonic hedgehog (SHH) signalling pathway, which occurs in approximately 25% of human primary tumors. From these, 12 candidate CpG sites, which lay within regions orthologous to the mouse genome, were selected for further investigation, alongside RASSF1A and COL1A2 CpG sites, which show frequent methylation in human primary tumors. The methylation status of these CpG sites was confirmed to be representative of their surrounding CpG islands in human primary tumors and control cerebellar samples, using bisulfite sequencing approaches.
We next assessed whether the DNA methylation status of orthologous regions was altered in tumors from four independent mouse models driven by Shh pathway activation (Ptc1+/- Ink4c-/-; Smo/Smo; Sufu+/- p53-/-; p53-/- Ink4c-/-), compared to strain-matched control mouse cerebella. Tissue-specific methylation patterns in the normal cerebellum were conserved between mouse and human, for 10/14 of the candidate regions investigated. Three regions which showed hypermethylation in human medulloblastomas (DSC2, RASSF1A and TAL1) also showed evidence of hypermethylation in mouse tumors and five regions showed evidence of hypomethylation in both human and mouse tumors (CYP2E1, MMP9, SPDEF, TGFB1, and VAV1). CYP2E1 and VAV1 showed the most similar frequencies and patterns of methylation changes in mouse and human tumors, while other changes were either less frequent (RASSF1A), affected fewer CpG sites (TAL1, TGFB1, SPDEF) or had different tissue-specific methylation patterns (DSC2, MMP9) in mice.
Ongoing work investigates the relationship of these methylation changes to gene expression and tumorigenesis. Assessment of the conservation of epigenetic changes between human tumors and disease relevant mouse models may help highlight those alterations most important in driving tumorigenesis, and identify candidate genes to take forward for further investigation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3449. doi:10.1158/1538-7445.AM2011-3449