Oligonucleotide DNA chips are useful adjuncts in epigenetic studies of glioblastomas

• Published in: Neuropathology 2006-10, Vol.26 (5), p.409-416
• Main Authors: Kim, Bomi, Kim, Hanseoung, Song, Byung Joo, Cha, Sun Ho, Lee, Mi Ok, Park, Sung-Hye
• Format: Article
• Language: English
• Subjects: Base Sequence; Brain Neoplasms - genetics; CpG Islands - genetics; DNA Methylation; DNA Primers; DNA, Neoplasm - genetics; DNA, Neoplasm - isolation & purification; Epigenesis, Genetic; epigenetic study; Gene Expression Profiling - methods; Genes, APC; Genes, p16; glioblastoma; Glioblastoma - genetics; Humans; Image Processing, Computer-Assisted; In Situ Hybridization; methylation; Molecular Sequence Data; O-Methylguanine-DNA Methyltransferase - genetics; oligoDNA chip; Oligonucleotide Array Sequence Analysis - methods; Polymerase Chain Reaction; Promoter Regions, Genetic - genetics; Tumor Suppressor Proteins - genetics
• ISSN: 0919-6544; 1440-1789
• DOI: 10.1111/j.1440-1789.2006.00707.x

Several studies have suggested that hypermethylation and hypomethylation of CpG islands within the promoters and 5′ exons of tumor‐related genes are closely associated with carcinogenesis. However, large‐scale analysis of candidate genes has been hampered by the lack of a high throughput approach for analyzing methylation patterns. Using methylation‐specific oligonucleotide (MSO) chips, we evaluated the methylation patterns of eight samples of fresh frozen glioblastoma tissue. The MSO chip used contained DNA probes with the CpG sites of p16 (p16INK4A, CDKN2A), MGMT (O6‐Methylguanine‐DNA‐methyltransferase), APC (adenomatous polyposis coil), RASSF1A (human RAS effect homolog), which are usually hypermethylated in cancer cells and MAGE (melanoma antigen), which is usually hypomethylated in cancer cells. We selected CpG sites for analysis; 28 CpG sites (263 bp) for p16, 26 CpG sites (249 bp) for MGMT, 16 CpG sites (195 bp) for APC, 22 CpG sites (262 bp) for RASSF1A and 18 CpG sites (235 bp) for MAGE. We then constructed primer sets not including CpG sites. Bisulfite modification of genomic DNA, methylation specific PCR, hybridization and image scan with data analysis and sequencing of the bisulfite modified DNA were carried out. Of the eight glioblastomas, hypermethylation of the 5′‐CpG sites of the MGMT were found in two, RASSF1A were found in five, and p16 and APC genes were not found in any cases and hypomethylation of that of the MAGE was found in eight cases. These results obtained from the oligo DNA chip study were correlated well with the sequencing data of bisulfite modified genomic DNA except in regard to the RASSF1A and MAGE genes. The devised MSO DNA chip is a useful tool for studies on methylation.