title: Quantitative assessment of RUNX3 methylation in neoplastic and non-neoplastic gastric epithelia using a DNA microarray.
abstract: Silencing of the RUNX3 gene by hypermethylation of its promoter CpG island plays a major role in gastric carcinogenesis. To quantitatively evaluate RUNX3 methylation, a fiber-type DNA microarray was used on which methylated and unmethylated sequence probes were mounted. After bisulfite modification, a part of the RUNX3 promoter CpG island, at which methylation is critical for gene silencing, was amplified by polymerase chain reaction using a Cy5 end-labeled primer. Methylation rates (MR) were calculated as the ratio of the fluorescence intensity of a methylated sequence probe to the total fluorescence intensity of methylated and unmethylated probes. Five gastric cancer cell lines were analyzed, as well as 26 primary gastric cancers and their corresponding non-neoplastic gastric epithelia. MR in four of the cancer cell lines that lost RUNX3 mRNA ranged from 99.0% to 99.7% (mean, 99.4%), whereas MR in the remaining cell line that expressed RUNX3 mRNA was 0.6%. In primary gastric cancers and their corresponding non-neoplastic gastric epithelia, MR ranged from 0.2% to 76.5% (mean, 22.7%) and from 0.7% to 25.1% (mean, 5.5%). Ten (38.5%) of the 26 gastric cancers and none of their corresponding non-neoplastic gastric epithelia had MR >30%. Most of the samples with MR >10% tested methylation-positive by conventional methylation-specific polymerase chain reaction (MSP). This microarray-based methylation assay is a promising method for the quantitative assessment of gene methylation.
authors.affiliation: Department of Pathology, Yamagata University School of Medicine, Yamagata, Japan.
authors.forename: Kanji
authors.initials: K
authors.lastname: So
authors.forename: Gen
authors.initials: G
authors.lastname: Tamura
authors.forename: Teiichiro
authors.initials: T
authors.lastname: Honda
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Homma
authors.forename: Makoto
authors.initials: M
authors.lastname: Endoh
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Togawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nishizuka
authors.forename: Teiichi
authors.initials: T
authors.lastname: Motoyama
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D045744:Cell Line, Tumor; D050677:Core Binding Factor Alpha 3 Subunit / Q000235:genetics* / Q000378:metabolism*; D004247:DNA / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000235:genetics / Q000378:metabolism; D005260:Female; D005753:Gastric Mucosa / Q000166:cytology / Q000378:metabolism* / Q000473:pathology; D020868:Gene Silencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013270:Stomach / Q000166:cytology; D013274:Stomach Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology
chemical_list: D050677:Core Binding Factor Alpha 3 Subunit; D004273:DNA, Neoplasm; D012333:RNA, Messenger; C493729:Runx3 protein, human; D004247:DNA