title: Microarray analysis of promoter methylation in lung cancers.
abstract: Aberrant DNA methylation is an important event in carcinogenesis. Of the various regions of a gene that can be methylated in cancers, the promoter is the most important for the regulation of gene expression. Here, we describe a microarray analysis of DNA methylation in the promoter regions of genes using a newly developed promoter-associated methylated DNA amplification DNA chip (PMAD). For each sample, methylated Hpa II-resistant DNA fragments and Msp I-cleaved (unmethylated+methylated) DNA fragments were amplified and labeled with Cy3 and Cy5 respectively, then hybridized to a microarray containing the promoters of 288 cancer-related genes. Signals from Hpa II-resistant (methylated) DNA (Cy3) were normalized to signals from Msp I-cleaved (unmethylated+methylated) DNA fragments (Cy5). Normalized signals from lung cancer cell lines were compared to signals from normal lung cells. About 10.9% of the cancer-related genes were hypermethylated in lung cancer cell lines. Notably, HIC1, IRF7, ASC, RIPK3, RASSF1A, FABP3, PRKCDBP, and PAX3 genes were hypermethylated in most lung cancer cell lines examined. The expression profiles of these genes correlated to the methylation profiles of the genes, indicating that the microarray analysis of DNA methylation in the promoter region of the genes is convenient for epigenetic study. Further analysis of primary tumors indicated that the frequency of hypermethylation was high for ASC (82%) and PAX3 (86%) in all tumor types, and high for RIPK3 in small cell carcinoma (57%). This demonstrates that our PMAD method is effective at finding epigenetic changes during cancer.
authors.affiliation: Laboratory of Genome Science, Biosignal Genome Resource Center, Department of Molecular and Cellular Biology, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan.|PRESTO, Japan Science and Technology Corporation (JST), Kawaguchi, Japan.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Fukasawa
authors.affiliation: Laboratory of Genome Science, Biosignal Genome Resource Center, Department of Molecular and Cellular Biology, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan.|PRESTO, Japan Science and Technology Corporation (JST), Kawaguchi, Japan.
authors.forename: Mika
authors.initials: M
authors.lastname: Kimura
authors.affiliation: Laboratory of Genome Science, Biosignal Genome Resource Center, Department of Molecular and Cellular Biology, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan.|PRESTO, Japan Science and Technology Corporation (JST), Kawaguchi, Japan.
authors.forename: Sumiyo
authors.initials: S
authors.lastname: Morita
authors.affiliation: DNA Chip Research Inc, Yokohama, Japan.
authors.forename: Kenichi
authors.initials: K
authors.lastname: Matsubara
authors.affiliation: Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.|Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan.
authors.forename: Sumitaka
authors.initials: S
authors.lastname: Yamanaka
authors.affiliation: Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
authors.forename: Chiaki
authors.initials: C
authors.lastname: Endo
authors.affiliation: Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Sakurada
authors.affiliation: Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
authors.forename: Masami
authors.initials: M
authors.lastname: Sato
authors.affiliation: Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kondo
authors.affiliation: Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Horii
authors.affiliation: Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Sasaki
authors.affiliation: Laboratory of Genome Science, Biosignal Genome Resource Center, Department of Molecular and Cellular Biology, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan. ihatada@showa.gunma-u.ac.jp.|PRESTO, Japan Science and Technology Corporation (JST), Kawaguchi, Japan. ihatada@showa.gunma-u.ac.jp.
authors.forename: Izuho
authors.initials: I
authors.lastname: Hatada
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D018288:Carcinoma, Small Cell / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D019175:DNA Methylation; D017931:DNA Primers; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004273:DNA, Neoplasm / Q000235:genetics / Q000378:metabolism; D020868:Gene Silencing; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D012985:Software Design
chemical_list: D017931:DNA Primers; D004273:DNA, Neoplasm; D004262:DNA Restriction Enzymes