Identification of 5 novel genes methylated in breast and other epithelial cancers

• Published in: Molecular cancer Vol. 9; no. 1; p. 51
• Main Authors: Hill, Victoria K, Hesson, Luke B, Dansranjavin, Temuujin, Dallol, Ashraf, Bieche, Ivan, Vacher, Sophie, Tommasi, Stella, Dobbins, Timothy, Gentle, Dean, Euhus, David, Lewis, Cheryl, Dammann, Reinhard, Ward, Robyn L, Minna, John, Maher, Eammon R, Pfeifer, Gerd P, Latif, Farida
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 05-03-2010; BioMed Central; BMC
• Subjects: Biochemistry, Molecular Biology; Bioinformatics; Biomarkers; Breast cancer; Breast Neoplasms; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Cancer; Care and treatment; Cell Line, Tumor; Colorectal Neoplasms; Colorectal Neoplasms - genetics; Diagnosis; DNA Methylation; DNA Methylation - genetics; DNA microarrays; Epigenetics; Epithelial tumors; Epithelium; Epithelium - metabolism; Epithelium - pathology; Female; Gene Expression Regulation, Neoplastic; Gene loci; Genes, Neoplasm; Genes, Neoplasm - genetics; Genetic aspects; Genetic testing; Genome, Human; Genome, Human - genetics; Genomes; Genomics; Glycoproteins; Glycoproteins - genetics; Glycoproteins - metabolism; Humans; Life Sciences; Male; Mammography; Medical research; Methylation; Mortality; Physiological aspects; Primaries & caucuses; Prognosis; Risk assessment; RNA, Messenger; RNA, Messenger - genetics; RNA, Messenger - metabolism; Statistical analysis; Studies; Survival Analysis; Thermal cycling; United States; United Kingdom; Frequent Methylation; Breast Cancer Cell Line; Breast Cancer; Primary Breast Tumour; Mammary Epithelial Cell Line
• ISSN: 1476-4598; 1476-4598
• DOI: 10.1186/1476-4598-9-51

There are several high throughput approaches to identify methylated genes in cancer. We utilized one such recently developed approach, MIRA (methylated-CpG island recovery assay) combined with CpG island arrays to identify novel genes that are epigenetically inactivated in breast cancer.
Using this approach we identified numerous 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, SALL1, DBC1, FBLN2 and CIDE-A. Methylation frequencies ranged from between 25% and 63% in primary breast tumours, whilst matched normal 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 three other common epithelial cancers (lung, colorectal, prostate). We demonstrate that the above genes show varying levels of methylation in these cancers. Lastly and most importantly methylation of EMILIN2 was associated with poorer clinical outcome in breast cancer and was strongly associated with estrogen receptor as well as progesterone receptor positive breast cancers.
The combination of the 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.