Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis.
Oligonucleotide microarray-based hybridization is an emerging technology for genome-wide detection of DNA variations. We have extended this principle and developed a novel approach, called methylation-specific oligonucleotide (MSO) microarray, for detecting changes of DNA methylation in cancer. The method uses bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. The amplified product, therefore, may contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status. A test sample is hybridized to a set of oligonucleotide (19-23 nucleotides in length) arrays that discriminate methylated and unmethylated cytosine at specific nucleotide positions, and quantitative differences in hybridization are determined by fluorescence analysis. A unique control system is also implemented to test the accuracy and reproducibility of oligonucleotides designed for microarray hybridization. This MSO microarray was applied to map methylated CpG sites within the human estrogen receptor alpha (ERalpha) gene CpG island in breast cancer cell lines, normal fibroblasts, breast tumors, and normal controls. Methylation patterns of the breast cancer cell lines, determined by MSO microarray, were further validated by bisulfite nucleotide sequencing (P <0.001). This proof-of-principle study shows that MSO microarray is a promising technique for mapping methylation changes in multiple CpG island loci and for generating epigenetic profiles in cancer.
Gitan
Raad S
RS
Department of Pathology, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia 65203, USA.
Shi
Huidong
H
Chen
Chuan-Mu
CM
Yan
Pearlly S
PS
Huang
Tim Hui-Ming
TH
D001483:Base Sequence; D001943:Breast Neoplasms / Q000737:chemistry / Q000235:genetics; D002460:Cell Line; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000032:analysis; D047628:Estrogen Receptor alpha; D005260:Female; D005347:Fibroblasts; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011960:Receptors, Estrogen / Q000032:analysis / Q000235:genetics; D014407:Tumor Cells, Cultured
D004273:DNA, Neoplasm; D047628:Estrogen Receptor alpha; D011960:Receptors, Estrogen