 | EPIGENETICS IN CANCER PREVENTION: EARLY DETECTION AND RISK ASSESSMENT
Copyright © 2003 by the New York Academy of Sciences
description
Annals of the New York Academy of Sciences 983:131-141 (2003)
© 2003 New York Academy of Sciences
Methylation-Sensitive Representational Difference Analysis and Its Application to Cancer Research
ATSUSHI KANEDAa,b,
DAIYA TAKAIa,c,
MICHIO KAMINISHIb,
ERIKO OKOCHIa AND
TOSHIKAZU USHIJIMAa
aCarcinogenesis Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
bDepartment of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
Address for correspondence: Toshikazu Ushijima, Carcinogenesis Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan. Voice: +81-3-3547-5240; fax: +81-3-5565-1753.
tushijim{at}ncc.go.jp
cPresent address: Department of Biochemistry and Molecular Biology, University of Southern California/Norris Comprehensive Cancer Center, University of Southern California, CA 90033.
Ann. N.Y. Acad. Sci. 983: 131-141 (2003).
Methylation-sensitive representational difference analysis (MS-RDA) was previously established to detect differences in the methylation status of two genomes. This method uses the digestion of genomic DNA with a methylation-sensitive restriction enzyme, HpaII, and PCR to prepare " HpaII-amplicons," followed by RDA. An HpaII-amplicon prepared using betaine and reverse electrophoresis was enriched 3.6-fold (compared with the HpaII-amplicon prepared by the original method) with DNA fragments originating from CpG islands (CGIs). As for the specificity of MS-RDA, it was shown that DNA fragments that are unmethylated in the tester and almost completely methylated in the driver are efficiently isolated. This indicated that genes that are in biallelic methylation or in monoallelic methylation with loss of the other allele are efficiently isolated. Further, by use of two additional methylation-sensitive six-base recognition restriction enzymes, SacII and NarI, more DNA fragments were isolated from CGIs in the 5' regions of genes. After analysis of human lung, gastric, and breast cancers, 12 genes were seen to be silenced and additional genes seen to show decreased expression in association with methylation of genomic regions outside CGIs in the 5' regions of genes. MS-RDA is effective in identifying silenced genes in various cancers.
Key Words: DNA methylation • CpG island • gene silencing • cancer • genome scanning
This article has been cited by other articles:
|
|
|
|
 
M. Mihara, Y. Yoshida, T. Tsukamoto, K.-i. Inada, Y. Nakanishi, Y. Yagi, K. Imai, T. Sugimura, M. Tatematsu, and T. Ushijima
Methylation of Multiple Genes in Gastric Glands with Intestinal Metaplasia: A Disorder with Polyclonal Origins
Am. J. Pathol.,
November 1, 2006;
169(5):
1643 - 1651.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Furuta, Y. Nobeyama, Y. Umebayashi, F. Otsuka, K. Kikuchi, and T. Ushijima
Silencing of peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas.
Cancer Res.,
June 15, 2006;
66(12):
6080 - 6086.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
L. F. Zerbini and T. A. Libermann
GADD45 Deregulation in Cancer: Frequently Methylated Tumor Suppressors and Potential Therapeutic Targets
Clin. Cancer Res.,
September 15, 2005;
11(18):
6409 - 6413.
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Ying, G. Srivastava, W.-S. Hsieh, Z. Gao, P. Murray, S.-K. Liao, R. Ambinder, and Q. Tao
The Stress-Responsive Gene GADD45G Is a Functional Tumor Suppressor, with Its Response to Environmental Stresses Frequently Disrupted Epigenetically in Multiple Tumors
Clin. Cancer Res.,
September 15, 2005;
11(18):
6442 - 6449.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Miyamoto and T. Ushijima
Diagnostic and Therapeutic Applications of Epigenetics
Jpn. J. Clin. Oncol.,
June 1, 2005;
35(6):
293 - 301.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Abe, M. Ohira, A. Kaneda, Y. Yagi, S. Yamamoto, Y. Kitano, T. Takato, A. Nakagawara, and T. Ushijima
CpG Island Methylator Phenotype Is a Strong Determinant of Poor Prognosis in Neuroblastomas
Cancer Res.,
February 1, 2005;
65(3):
828 - 834.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Kaneda, K. Wakazono, T. Tsukamoto, N. Watanabe, Y. Yagi, M. Tatematsu, M. Kaminishi, T. Sugimura, and T. Ushijima
Lysyl Oxidase Is a Tumor Suppressor Gene Inactivated by Methylation and Loss of Heterozygosity in Human Gastric Cancers
Cancer Res.,
September 15, 2004;
64(18):
6410 - 6415.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
