High-Resolution Analyses of Epigenetic Aberrations in Myelodysplastic Syndrome.

Myelodysplastic syndromes are heterogeneous groups of clonal hematopoietic disorders characterized by ineffective blood cells production and predisposition to acute myeloid leukemia, and as such, it is well established that these syndromes actually represent neoplastic processes in which a series of gene mutations accumulate in blood cell precursors, leading to neoplastic expansion of dominant clones. During the past two decades, a number of genetic abnormalities have been described in MDS cases, including copy number alterations of particular chromosomal segments, mutations of Ras, p53, runx1, and Flt3 genes, and translocation involving Evi-1 family genes, TEL, MLL and Nup98 genes. On the other hand, epigenetic abnormalities are also thought to play an important role in the pathogenesis of MDS, because demethylating agents such as 5-azacydine and decitabine are often effective for high risk MDS. Unfortunately, however, only a few genes, such as INK4B gene, have been implicated in MDS pathogenesis. Especially, no genome-wide analysis of epigenetic changes in MDS has been reported. So, in the current study, we comprehensively investigated abnormalities of DNA methylation in 30 MDS specimens, using Affymetrix tiling array combined with methylated DNA immunoprecipitation (MeDIP). In this method, genomic DNA from MDS specimens was first fragmentized with ultrasonication and immuno-precipitated with anti-methylcytosine antibody (MeDIP). The immunoprecipitated DNA was then amplified by PCR and subjected to hybridization to the promorter tiling array. In this array, regulatory regions of more than 25,000 genes are tiled by 6.5 millions of oligonucleotide probes to enable sensitive detection of target sequences and approximately 59% of CpG islands in the human genomes are covered in a single array. The extent and distribution of methylation were highly variable between specimens, although some CpG islands, such as p15INK4B and HOX gene clusters, seemed to be commonly involved in different cases (Figure). In conclusion, MeDIP on chip analysis could be a powerful method for genome-wide detection of DNA methylation and facilitate our understanding of the pathogenesis of MDS. Figure Figure