Abstract
To detect genes with CpG sites that display methylation patterns that are characteristic of acute lymphoblastic leukemia (ALL) cells, we compared the methylation patterns of cells taken at diagnosis from 20 patients with pediatric ALL to the methylation patterns in mononuclear cells from bone marrow of the same patients during remission and in non-leukemic control cells from bone marrow or blood. Using a custom-designed assay, we measured the methylation levels of 1,320 CpG sites in regulatory regions of 413 genes that were analyzed because they display allele-specific gene expression (ASE) in ALL cells. The rationale for our selection of CpG sites was that ASE could be the result of allele-specific methylation in the promoter regions of the genes. We found that the ALL cells had methylation profiles that allowed distinction between ALL cells and control cells. Using stringent criteria for calling differential methylation, we identified 28 CpG sites in 24 genes with recurrent differences in their methylation levels between ALL cells and control cells. Twenty of the differentially methylated genes were hypermethylated in the ALL cells, and as many as nine of them (AMICA1, CPNE7, CR1, DBC1, EYA4, LGALS8, RYR3, UQCRFS1, WDR35) have functions in cell signaling and/or apoptosis. The methylation levels of a subset of the genes were consistent with an inverse relationship with the mRNA expression levels in a large number of ALL cells from published data sets, supporting a potential biological effect of the methylation signatures and their application for diagnostic purposes.
Highlights
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy accounting for 25% of all childhood cancers in developed countries
We investigated how the methylation status of the 1,320 CpG sites in genes with allele-specific gene expression (ASE) differs between ALL samples taken at diagnosis and matched bone marrow samples from the same patients during and after induction therapy, when the patients were in remission, and in control cells from bone marrow or blood of non-leukemic individuals
To identify genes with differential DNA methylation, we compared the methylation levels of 1,320 CpG sites in mononuclear cells from bone marrow taken at the time of ALL diagnosis to bone marrow mononuclear cells from the same patients at day 29, 50 or 106 of therapy, when the patients were in remission, and to bone marrow and peripheral blood mononuclear cells from non-leukemic controls
Summary
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy accounting for 25% of all childhood cancers in developed countries. Most of the known large scale genetic aberrations in ALL are not alone sufficient to induce the disease [2], suggesting that there are other genetic or epigenetic alterations that act in leukemic transformation. Methylation of the C-residue in CpG dinucleotides plays an important role in regulating gene expression [3,4]. Alterations in the expression of DNMTs in blood progenitor cells results in extensive changes in methylation patterns, which may lead to leukemogenesis [5]. Treatment with inhibitors of DNA methylation, such as 59-azacytidine have therapeutic benefits in leukemia [6], indicating that the methylation changes are functionally important. Epigenetic perturbation of DNA methylation can be a valuable source of information for understanding the biology of gene regulation, phenotypic diversity, and treatment outcome in pediatric ALL
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
