Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1

Abstract

DNA methylation patterns are frequently dysregulated in cancer, although little is known of the mechanisms through which specific gene sets become aberrantly methylated. The ecotropic viral integration site 1 (EVI1) locus encodes a DNA binding zinc-finger transcription factor that is aberrantly expressed in a subset of acute myeloid leukemia (AML) patients with poor outcome. We find that the promoter DNA methylation signature of EVI1 AML blast cells differs from those of normal CD34 ؉ bone marrow cells and other AMLs. This signature contained 294 differentially methylated genes, of which 238 (81%) were coordinately hypermethylated. An unbiased motif analysis revealed an overrepresentation of EVI1 binding sites among these aberrantly hypermethylated loci. EVI1 was capable of binding to these promoters in 2 different EVI1-expressing cell lines, whereas no binding was observed in an EVI1-negative cell line. Furthermore, EVI1 was observed to interact with DNA methyl transferases 3A and 3B. Among the EVI1 AML cases, 2 subgroups were recognized, of which 1 contained AMLs with many more methylated genes, which was associated with significantly higher levels of EVI1 than in the cases of the other subgroup. Our data point to a role for EVI1 in directing aberrant promoter DNA methylation patterning in EVI1 AMLs. (Blood. 2011;117(1):234-241) IntroductionPatterning of DNA methylation plays a critical role in epigenetic gene regulation during normal development. 1 Aberrant cytosine methylation of gene promoters occurs frequently in many forms of cancer, including acute myeloid leukemias (AMLs). 2 Several tumor suppressor genes (eg, CDKN2B and CEBPA) are found to be abnormally methylated and silenced in AML patients. 3,4 Moreover, aberrant distribution of promoter DNA methylation occurring in specific and distinct patterns has been shown to be a universal feature occurring in all AML patients. 5 However, the mechanisms that mediate these aberrant methyl cytosine patterns have not been defined.Abnormal expression of the EVI1 (ecotropic viral integration site 1) gene, as the result of inv(3)(q21q26.2)/t(3,3)(q21;q26.2) or through other unknown mechanisms, is associated with unfavorable AML outcome. 6,7 EVI1 encodes a C2H2 zinc finger transcription factor, binding DNA in a sequence-specific manner and functions as a repressor. 8-10 Retroviral insertion mutagenesis studies suggest that EVI1 deregulation plays a role in leukemogenesis. 11 The mechanism through which EVI1 mediates these effects is unknown.Given the function of EVI1 as a transcriptional repressor, we wondered whether EVI1 might be associated with aberrant epigenetic programming in AML patients. To test this hypothesis, we conducted a large-scale DNA methylation profiling study in human EVI1 AMLs. A specific promoter DNA methylation signature was uncovered in EVI1 AMLs, and evidence was provided that EVI1 contributes to aberrant promoter DNA methylation patterning in those leukemias. Methods Patient samplesDiagnostic material from 26 AML patients overexpressing EVI1 ...

Impact of MLL5 expression on decitabine efficacy and DNA methylation in acute myeloid leukemia

“…Promoter methylation was compared between patients with high or low MLL5 expression using normal CD34 + bone marrow cells (CD34 + NBM) as baseline ( Figure 5A and B). 31 In total, 341 and 71 probe sets were differentially methylated in CBF-and CN-AML patients with high MLL5 expression, respectively, with absolute difference in methylation more than 2 and adjusted P less than 0.01 ( Figure 5C). Among them, 91% (312 of 341) and 83% (59 of 71) were significantly hypermethylated in MLL5 high-expressing CBF-and CN-AML patients, respectively, whereas only 9% (29 of 341) and 17% (12 of 71) were hypomethylated.…”

Molecular Markers for Risk Stratification in Adult Acute Myeloid Leukemia with Normal Cytogenetics

“…Epigenetic modification of the CEBPA promoter regions was also described and CEBPA hypermethylation appeared to be favorable prognostic marker in addition to NPM1 mutation with lack of FLT3-ITD and CEBPA bi-allelic, double mutations (Hackanson et al, 2008;Szankasi et al, 2011). Lugthart et al (2011) found that the promoter DNA methylation signature of EVI1 AML blast cells differed from normal bone marrow cells and other AMLs and contained many hypermethylated genes. EVI1 was observed to physically interact with DNA methyltransferases 3A and 3B and colocalize with them in nuclei and complex is involved in EVI1-mediated transcriptional repression.…”

“…EVI1 was observed to physically interact with DNA methyltransferases 3A and 3B and colocalize with them in nuclei and complex is involved in EVI1-mediated transcriptional repression. Cases with the significantly higher levels of EVI1 are associated with many more methylated genes (Lugthart et al, 2011).…”

The Impact of Molecular Genetic in Acute Myeloid Leukemias

“…A recent study using DNA microarray platforms in 344 patients described 16 epigenetically distinct groups, nine of which were associated with specific molecular subgroups of AML (CEBPA, NPM1, AML-ETO1, CBFb-MYH11 and PML-RARA) [57]. A number of recent reports have also identified aberrant methylation profiling in AML associated with several molecular mutations including EVI1 [58], MLL [59] and CEBPA [60]. There are also novel approaches such as the use of deep sequencing platforms that can provide a more comprehensive coverage of methylation profiling in cancer samples.…”