Microarray analysis of promoter methylation in lung cancers

Masayuki Fukasawa, Mika Kimura, Sumiyo Morita, Kenichi Matsubara, Sumitaka Yamanaka, Chiaki Endo, Akira Sakurada, Masami Sato, Takashi Kondo, Akira Horii, Hiroyuki Sasaki, Izuho Hatada

Research output: Contribution to journalArticle

67 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)368-374
Number of pages7
JournalJournal of Human Genetics
Volume51
Issue number4
DOIs
Publication statusPublished - Apr 1 2006
Externally publishedYes

Fingerprint

Microarray Analysis
Methylation
Lung Neoplasms
DNA
DNA Methylation
Genes
Neoplasm Genes
Oligonucleotide Array Sequence Analysis
Genetic Promoter Regions
Epigenomics
Cell Line
Neoplasms
Small Cell Carcinoma
Gene Expression Regulation
Transcriptome
Carcinogenesis
Lung

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Fukasawa, M., Kimura, M., Morita, S., Matsubara, K., Yamanaka, S., Endo, C., ... Hatada, I. (2006). Microarray analysis of promoter methylation in lung cancers. Journal of Human Genetics, 51(4), 368-374. https://doi.org/10.1007/s10038-005-0355-4

Microarray analysis of promoter methylation in lung cancers. / Fukasawa, Masayuki; Kimura, Mika; Morita, Sumiyo; Matsubara, Kenichi; Yamanaka, Sumitaka; Endo, Chiaki; Sakurada, Akira; Sato, Masami; Kondo, Takashi; Horii, Akira; Sasaki, Hiroyuki; Hatada, Izuho.

In: Journal of Human Genetics, Vol. 51, No. 4, 01.04.2006, p. 368-374.

Research output: Contribution to journalArticle

Fukasawa, M, Kimura, M, Morita, S, Matsubara, K, Yamanaka, S, Endo, C, Sakurada, A, Sato, M, Kondo, T, Horii, A, Sasaki, H & Hatada, I 2006, 'Microarray analysis of promoter methylation in lung cancers', Journal of Human Genetics, vol. 51, no. 4, pp. 368-374. https://doi.org/10.1007/s10038-005-0355-4
Fukasawa M, Kimura M, Morita S, Matsubara K, Yamanaka S, Endo C et al. Microarray analysis of promoter methylation in lung cancers. Journal of Human Genetics. 2006 Apr 1;51(4):368-374. https://doi.org/10.1007/s10038-005-0355-4
Fukasawa, Masayuki ; Kimura, Mika ; Morita, Sumiyo ; Matsubara, Kenichi ; Yamanaka, Sumitaka ; Endo, Chiaki ; Sakurada, Akira ; Sato, Masami ; Kondo, Takashi ; Horii, Akira ; Sasaki, Hiroyuki ; Hatada, Izuho. / Microarray analysis of promoter methylation in lung cancers. In: Journal of Human Genetics. 2006 ; Vol. 51, No. 4. pp. 368-374.
@article{e37a2d59ec4a4b0aae9097ac4f822812,
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.",
author = "Masayuki Fukasawa and Mika Kimura and Sumiyo Morita and Kenichi Matsubara and Sumitaka Yamanaka and Chiaki Endo and Akira Sakurada and Masami Sato and Takashi Kondo and Akira Horii and Hiroyuki Sasaki and Izuho Hatada",
year = "2006",
month = "4",
day = "1",
doi = "10.1007/s10038-005-0355-4",
language = "English",
volume = "51",
pages = "368--374",
journal = "Journal of Human Genetics",
issn = "1434-5161",
publisher = "Nature Publishing Group",
number = "4",

}

TY - JOUR

T1 - Microarray analysis of promoter methylation in lung cancers

AU - Fukasawa, Masayuki

AU - Kimura, Mika

AU - Morita, Sumiyo

AU - Matsubara, Kenichi

AU - Yamanaka, Sumitaka

AU - Endo, Chiaki

AU - Sakurada, Akira

AU - Sato, Masami

AU - Kondo, Takashi

AU - Horii, Akira

AU - Sasaki, Hiroyuki

AU - Hatada, Izuho

PY - 2006/4/1

Y1 - 2006/4/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33646456046&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33646456046&partnerID=8YFLogxK

U2 - 10.1007/s10038-005-0355-4

DO - 10.1007/s10038-005-0355-4

M3 - Article

C2 - 16435073

AN - SCOPUS:33646456046

VL - 51

SP - 368

EP - 374

JO - Journal of Human Genetics

JF - Journal of Human Genetics

SN - 1434-5161

IS - 4

ER -