This Article Full Text Full Text (PDF) Purchase Article View Shopping Cart Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Chen, C.-M. Articles by Huang, T. H.-M. Search for Related Content PubMed PubMed Citation Articles by Chen, C.-M. Articles by Huang, T. H.-M.

(American Journal of Pathology. 2003;163:37-45.)
© 2003 American Society for Investigative Pathology

Technical Advance

Methylation Target Array for Rapid Analysis of CpG Island Hypermethylation in Multiple Tissue Genomes

Chuan-Mu Chen^*, Hsiao-Ling Chen, Timothy H.-C. Hsiau, Andrew H.-A. Hsiau, Huidong Shi, Graham J. R. Brock, Susan H. Wei, Charles W. Caldwell, Pearlly S. Yan and Tim Hui-Ming Huang

From the Department of Life Sciences and the Institute of Biomedicine,^* National Chung Hsing University, Taiwan, Republic of China; the Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, Columbia, Missouri; and the Division of Molecular Genetics, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

Hypermethylation of multiple CpG islands is a common event in cancer. To assess the prognostic values of this epigenetic alteration, we developed Methylation Target Array (MTA), derived from the concept of tissue microarray, for simultaneous analysis of DNA hypermethylation in hundreds of tissue genomes. In MTA, linker-ligated CpG island fragments were digested with methylation-sensitive endonucleases and amplified with flanking primers. A panel of 468 MTA amplicons, which represented the whole repertoire of methylated CpG islands in 93 breast tumors, 20 normal breast tissues, and 4 breast cancer cell lines, were arrayed on nylon membrane for probe hybridization. Positive hybridization signals detected in tumor amplicons, but not in normal amplicons, were indicative of aberrant hypermethylation in tumor samples. This is attributed to aberrant sites that were protected from methylation-sensitive restriction and were amplified by PCR in tumor samples, while the same sites were restricted and could not be amplified in normal samples. Hypermethylation frequencies of the 10 genes tested in breast tumors and cancer cell lines were 60% for GPC3, 58% for RASSF1A, 32% for 3OST3B, 30% for HOXA5, 28% for uPA, 25% for WT1, 23% for BRCA1, 9% for DAPK1, and 0% for KL. Furthermore, hypermethylation of 5 to 7 loci of these genes was significantly correlated with hormone receptor status, clinical stages, and ages at diagnosis of the patients analyzed. This novel approach thus provides an additional avenue for assessing clinicopathological consequences of DNA hypermethylation in breast cancer.

This article has been cited by other articles:

				P. Stenvinkel and T. J. Ekstrom Epigenetics--a helpful tool to better understand processes in clinical nephrology? Nephrol. Dial. Transplant., May 1, 2008; 23(5): 1493 - 1496. [Full Text] [PDF]

				J.M. Ordway, J.A. Bedell, R.W. Citek, A. Nunberg, A. Garrido, R. Kendall, J.R. Stevens, D. Cao, R.W. Doerge, Y. Korshunova, et al. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets Carcinogenesis, December 1, 2006; 27(12): 2409 - 2423. [Abstract] [Full Text] [PDF]

				K. Visvanathan, S. Sukumar, and N. E. Davidson Epigenetic Biomarkers and Breast Cancer: Cause for Optimism. Clin. Cancer Res., November 15, 2006; 12(22): 6591 - 6593. [Full Text] [PDF]

				B. Khulan, R. F. Thompson, K. Ye, M. J. Fazzari, M. Suzuki, E. Stasiek, M. E. Figueroa, J. L. Glass, Q. Chen, C. Montagna, et al. Comparative isoschizomer profiling of cytosine methylation: The HELP assay Genome Res., August 1, 2006; 16(8): 1046 - 1055. [Abstract] [Full Text] [PDF]

				M. Bibikova, Z. Lin, L. Zhou, E. Chudin, E. W. Garcia, B. Wu, D. Doucet, N. J. Thomas, Y. Wang, E. Vollmer, et al. High-throughput DNA methylation profiling using universal bead arrays Genome Res., March 1, 2006; 16(3): 383 - 393. [Abstract] [Full Text] [PDF]

				A. Schumacher, P. Kapranov, Z. Kaminsky, J. Flanagan, A. Assadzadeh, P. Yau, C. Virtanen, N. Winegarden, J. Cheng, T. Gingeras, et al. Microarray-based DNA methylation profiling: technology and applications Nucleic Acids Res., January 20, 2006; 34(2): 528 - 542. [Abstract] [Full Text] [PDF]

				M. Wei, T. A. Grushko, J. Dignam, F. Hagos, R. Nanda, L. Sveen, J. Xu, J. Fackenthal, M. Tretiakova, S. Das, et al. BRCA1 Promoter Methylation in Sporadic Breast Cancer Is Associated with Reduced BRCA1 Copy Number and Chromosome 17 Aneusomy Cancer Res., December 1, 2005; 65(23): 10692 - 10699. [Abstract] [Full Text] [PDF]

				A. A. Melnikov, R. B. Gartenhaus, A. S. Levenson, N. A. Motchoulskaia, and V. V. Levenson (Chernokhvostov) MSRE-PCR for analysis of gene-specific DNA methylation Nucleic Acids Res., June 8, 2005; 33(10): e93 - e93. [Abstract] [Full Text] [PDF]

				N. Kimura, T. Nagasaka, J. Murakami, H. Sasamoto, M. Murakami, N. Tanaka, and N. Matsubara Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients Nucleic Acids Res., March 10, 2005; 33(5): e46 - e46. [Abstract] [Full Text] [PDF]

				M. Alaminos, V. Davalos, N.-K. V. Cheung, W. L. Gerald, and M. Esteller Clustering of Gene Hypermethylation Associated With Clinical Risk Groups in Neuroblastoma J Natl Cancer Inst, August 18, 2004; 96(16): 1208 - 1219. [Abstract] [Full Text] [PDF]

				S. A. Ross, P. R. Srinivas, A. J. Clifford, S. C. Lee, M. A. Philbert, and R. L. Hettich New Technologies for Nutrition Research J. Nutr., March 1, 2004; 134(3): 681 - 685. [Abstract] [Full Text] [PDF]