B5
High throughput analysis of breast cancer epigenome
Victoria Hill1, Luke Hesson1, Ashraf Dallol1, Ivan Bieche2, Stella Tommasi3, Eamonn Maher1, John Minna4, Gerd Pfeifer3, Farida Latif1
1Institute of Biomedical Research, University of Birmingham, UK, 2Oncogenetic Laboratory, INSERM, Saint Cloud, France, 3Beckman Research Institute, City of Hope, Duarte, USA, 4Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, USA
We used a high throughput genome-wide approach (methylated-CpG island recovery assay MIRA combined with CpG island arrays) to identify epigenetically inactivated genes in sporadic breast cancer. Using this approach we identified a large number of CpG islands that demonstrated aberrant DNA methylation in breast cancer cell lines. Using a combination of COBRA and sequencing of bisulphite modified DNA, we confirmed 5 novel genes frequently methylated in breast tumours; EMILIN2, CIDE-A, SALL1, DBC1 and FBLN2. Methylation frequencies ranged from between 28% and 64% in primary breast tumours, whilst benign breast tissue DNA was either unmethylated or demonstrated a much lower frequency of methylation compared to malignant breast tissue DNA. Furthermore expression of the above 5 genes was shown to be restored following treatment with a demethylating agent in methylated breast cancer cell lines. We have expanded this analysis across a range of other epithelial cancers (lung, colorectal, kidney, brain) and demonstrate that the above genes show varying levels of methylation in these cancers.
Hence the combination of MIRA assay with CpG island arrays is a very useful technique for identifying epigenetically inactivated genes in cancer genomes and can provide molecular markers for early cancer diagnosis, prognosis and epigenetic therapy.
