Epigenetic change such as DNA methylation is one important mechanism for regulating gene expression as genetic change, such as mutation or loss of heterozygosity. Methylation of cancer-related genes has been shown to play an important role in carcinogenesis and tumor progression. Prostate cancer is not as common in Japanese as in Caucasians or African-Americans, but the number of cases is increasing every year. Genetic changes, such as point mutations, loss of heterozygosity and homozygous deletions in many tumorsuppressor genes, are associated with carcinogenesis. 1 Many studies have provided evidence of such genetic alterations in prostate cancer. 2 More recently, it has also been reported that inactivation of tumor-suppressor genes by epigenetic change due to DNA methylation could play an important role in carcinogenesis and tumor progression. 3 DNA methylation, especially in CpG-rich 5Ј regions, inhibits transcription by interfering with initiation or by reducing the binding affinity of sequence-specific transcription factors. 4 In prostate cancers, inactivation by aberrant methylation has been reported for many genes, such as RAR2, GST-P, E-cadherin and RASSF1A. [5][6][7][8] Methylation profiling analysis of multiple genes has been proposed for the purpose of evaluating biologic characteristics and identifying useful diagnostic indicators of prognosis. 9 As methods for determining genes with expression regulated by DNA methylation, restriction landmark genomic scanning (RLGS), methylated CpG island amplification (MCA)/representational difference analysis (RDA) and differential methylation hybridization (DMH) have been reported. 10 -12 MCA/RDA is useful to identify CpG-rich DNA fragments, which are methylated in only the target tissue. Toyota et al. 11 identified methylated CpG islands in colon cancer, not only in genes known to be involved in neoplasia but also other examples. To identify cancer-related genes controlled by methylation in prostate cancer, we have applied MCA/RDA to a series of prostate cancers and 2 cell lines.
MATERIAL AND METHODS
Cell lines and tissue samplesProstate cancer cell lines (LNCaP and DU145) were obtained from the American Type Tissue Culture Collection (Rockville, MD). Specimens of 63 primary prostate cancer with known clinicopathologic features (age, stage and Gleason Score) and 13 specimens of benign prostates were obtained by surgery, snapfrozen and stored at Ϫ80°C. All benign samples were examined by pathologists and determined to have no precancerous lesion such as high-grade prostatic intraepithelial neoplasia (HGPIN) and no incidental cancer.
Methylated CpG island amplification/representational difference analysis (MCA/RDA)MCA/RDA was performed as described previously. 11,13 Briefly, 5 g of DNA was digested with 100 units of SmaI and 20 units of XmaI (New England Biolabs, Beverly, MA) in this order. After these treatments, methylated CpG sites have sticky ends. The restriction fragments were ligated to the RMCA adaptor using T4 DNA ligase (New England Biolabs), and 3 l ...