A16
Epigenetics in renal cell carcinoma: array-based approaches to CpG methylation profiling and candidate tumour suppressor gene identification
Mark Morris1, Fiona McRonald1, Christopher Ricketss1, Dean Gentle1, Laura Winchester2, Dilair Baban2, Jiannis Ragoussis2, Noel Clarke3, Michael Brown3, Takeshi Kishida4, Masahiro Yao4, Farida Latif1, Eamonn Maher1
1University of Birmingham, UK, 2University of Oxford, UK, 3University of Manchester, UK, 4Yokohama City University, Yokohama, Japan
Renal cell carcinoma (RCC) accounts for ~3% of all adult tumours, resulting in >4000 UK deaths per year. With the exception of VHL, mutations occur infrequently in RCC. Promoter region hypermethylation and transcriptional silencing is a frequent cause of tumour suppressor gene (TSG) inactivation in many types of human cancers. By employing microarray analysis following global de-methylation we have identified a number of putative TSGs that are silenced by promoter methylation. However, many genes whose expression is upregulated after demethylation frequently do not demonstrate promoter region methylation. Since these studies, a number of new technologies have become available which assess the methylation status of a large number of genes. We have used two such technologies to facilitate CpG profiling studies and the identification of novel candidate TSGs. We have performed high-throughput epigenetic profiling using the Illumina Goldengate Methylation Array, which provides quantitative CpG methylation data at 1505 individual CpG dinucleotides associated with 807 human genes, in 62 RCC (29 RCC from von Hippel-Lindau (VHL) disease patients, 20 sporadic clear cell RCC with wild type VHL and 13 sporadic papillary RCC). We have also performed methylated DNA Immunopercipitation (MeDIP) on 9 RCC tumours, 9 RCC-derived cell lines and 3 control kidney samples. Methylation enriched and control DNA was hybridised to a NimbleGen HG18 array. By combining these technologies with expression data from 19 RCC-derived cell lines following global de-methylation, and further analysis in a separate cohort of RCCs, we have identified a panel of genes which are specifically methylated in RCC tumours. Further characterisation of the genes identified in this, and other studies, may lead to the development of novel minimally-invasive diagnostic and prognostic tools for kidney cancer, and, in the longer term, enable more focused treatments for individual tumours.
