Changes in DNA Methylation of Repetitive Elements during the Progression of Chronic Myelogenous Leukemia.

Epigenetic changes are a common finding in cancer, and promoter hypermethylation of tumor suppressor genes leads to aberrant gene silencing. In contrast to gene promoter hypermethylation, global hypomethylation is also a well-described phenomenon in cancer. Measurement of total 5-methylcytosine in the DNA show decreases in cancer despite increases in gene specific methylation. This discrepancy can be accounted for by the decrease of DNA methylation found in DNA repetitive elements, which make up approximately over half of the human genome. Decreases in repetitive element DNA methylation are a sensitive surrogate marker of global methylation, and have been used to measure DNA methylation changes induced by chemotherapy, dietary folate and environmental exposure. Decreases in LINE1 methylation have been described in numerous human cancers. In CML decrease in LINE1 methylation has been associated with progression to blast crisis. We investigated the DNA methylation changes of DNA repetitive elements in CML during the progression of CML from chronic phase to accelerated phase and finally blast crisis. We used a previously described assay (Yang et al. 2004) employing Bisulfite-PCR Pyrosequencing to quantitatively study the DNA methylation changes associated with the LINE1, Alu, D4Z4, and NBL-2 repetitive elements (See table).

LINE1 and Alu hypomethylation was significantly associated with the progression of CML. Surprisingly, we found that NBL-2 and D4Z4 hypermethylation significantly increased during the progression of CML. Interestingly, these two repetitive elements were found to be specifically hypomethylated in immunodeficiency, centromeric instability and facial abnormalities (ICF) syndrome which is caused by a germline mutation of DNA methyltransferase 3b (DNMT3b) (Kondo T et al, 2000). This result suggests that DNMT3b may be involved in the progression of CML.