Genome-Wide Profiling of CpG Methylation Identifies Novel Targets of Aberrant Hypermethylation in Myeloid Leukemia

Abstract

The methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor suppressor genes. Because aberrant hypermethylation may be used as a marker for disease, a sensitive method for the global detection of DNA methylation events is of particular importance. We describe a novel and robust technique, called methyl-CpG immunoprecipitation, which allows the unbiased genome-wide profiling of CpG methylation in limited DNA samples. The approach is based on a recombinant, antibody-like protein that efficiently binds native CpG-methylated DNA. In combination with CpG island microarrays, the technique was used to identify >100 genes with aberrantly methylated CpG islands in three myeloid leukemia cell lines. Interestingly, within all hypermethylation targets, genes involved in transcriptional regulation were significantly overrepresented. More than half of the identified genes were absent in microarray expression studies in either leukemia or normal monocytes, indicating that hypermethylation in cancer may be largely independent of the transcriptional status of the affected gene. Most individually tested genes were also hypermethylated in primary blast cells from acute myeloid leukemia patients, suggesting that our approach can identify novel potential disease markers. The technique may prove useful for genome-wide comparative methylation analysis not only in malignancies. (Cancer Res 2006; 66(12): 6118-28)

Quantitative DNA methylation predicts survival in adult acute myeloid leukemia

“…Recent technologic advances combining acceptable spatial resolution with good quantitative accuracy such as microarray-or high-throughput sequencing-based approaches might be suitable for a refined genome-wide epigenetic marker discovery. [36][37][38] These approaches might then also be able to discriminate markers that can be used for outcome prediction within the important subgroup of CN-AML. In our model, outcome prediction was not possible within the subset of CN-AML cohort, likely because the candidate genes included in the analysis were selected based on a prognostic gene expression signature designed across all cytogenetic subgroups and not CN-AML cases only.…”

Chromatin maps, histone modifications and leukemia

“…Genome-wide DNA methylation studies have been published for solid tumors such as lung cancer, 11,12 and for leukemias. AML cell lines 13 and primary samples have been studied, and in one study relapse was associated with increased methylation of CpG islands. 14 ALL cell lines and patient samples were also evaluated.…”

Flow Cytometric and Laser Scanning Microscopic Approaches in Epigenetics Research

“…Moreover, global changes of certain epigenetic modifications may have their independent diagnostic value, especially when analyzed in correlation with other phenotypic markers, an opportunity offered by up-to-date laser scanning microscopic systems (20,21). Development of antibodies and chimeric methyl CpG-binding antibody-like proteins (24)(25)(26)(27), both recognizing CpG with high specificity, has opened novel perspectives for the diagnostic analysis of global methylation states. Anti-5mC antibodies are commercially available through various sources (e.g., Abcam and Biocarta US).…”

“…In experiments using the recombinant mCpG-binding antibody-like MBD-Fc protein (26)(27)(28), the overall level of CpG methylation has been quantified in the HCT116 cell line (Fig.7.2). As shown by confocal laser scanning microscopy …”