Role of DNMT3A, TET2, and IDH1/2 mutations in pre-leukemic stem cells in acute myeloid leukemia

Abstract

Aberrant changes in the epigenome are now recognized to be important in driving the development of multiple human cancers including acute myeloid leukemia. Recent advances in sequencing technologies have led to the identification of recurrent mutations in genes that regulate DNA methylation including DNA methyltransferase 3A (DNMT3A), ten-eleven translocation 2 (TET2), and isocitrate dehydrogenase 1 (IDH1) and IDH2. These mutations have been shown to promote self-renewal and block differentiation of hematopoietic stem/progenitor cells. Acquisition of these mutations in hematopoietic stem cells can lead to their clonal expansion resulting in a pre-leukemic stem cell (pre-LSC) population. Pre-LSCs retain the ability to differentiate into the full spectrum of mature daughter cells but can become fully transformed with the acquisition of additional driver mutations. Here, we review the effects of mutations in DNMT3A, TET2, and IDH1/2 on mouse and human hematopoiesis, the current understanding of their role in pre-LSCs, and therapeutic strategies to eliminate this population which may serve as a cellular reservoir for relapse.

Figure 1. Model of step-wise acquisition of mutations in the development of pre-leukemic stem cells (pre-LSCs) and fully transformed leukemic stem cells (LSCs) from hematopoietic stem cells (HSCs)

Acquisition of mutations in genes involved in regulation of DNA methylation (TET2, DNMT3A, and IDH1/2) in HSCs leads to enhanced self-renewal and clonal expansion of a pre-LSC population. By definition, pre-LSCs do not cause overt disease and retain the ability to differentiate into lymphoid and myeloid lineages. However, they may skew towards myeloid development in some circumstances (e.g. TET2 mutations). Acquisition of additional cooperating mutations (e.g. FLT3-ITD) converts a pre-LSC into a fully transformed LSC with unlimited self-renewal potential and impaired differentiation. The eradication of both pre-LSCs and LSCs may be required to prevent disease relapse as both populations may serve as a cellular reservoir for relapse.

Figure 2. Mechanism of gene expression dysregulation by DNMT3A mutations

DNMT3A catalyzes de novo methylation of DNA at the 5-position of cytosine in the context of CpG dinucleotides. DNA methylation is generally associated with transcriptional repression and can suppress the expression of self-renewal genes or genes that negatively regulate differentiation. DNMT3A activity appears to be necessary for normal hematopoietic stem cell (HSC) differentiation. Mutations in DNMT3A that disrupt enzymatic activity may promote self-renewal and block differentiation of HSCs by modifying DNA methylation at gene regulatory regions and thereby increasing the transcription of self-renewal genes and negative regulators of differentiation.

Figure 3. Mechanism of gene expression dysregulation by TET2 and IDH1/2 mutations

(A) TET2 catalyzes the hydroxylation of 5-methylcytosine (5-mC) in DNA resulting in the formation of 5-hydroxymethylcytosine (5-hmC). α-ketoglutarate (α-KG) is an essential cofactor in this reaction. 5-hmC appears to be an intermediate product in the DNA demethylation pathway which involves enzymes in the base excision repair (BER) pathway. TET2-mediated DNA demethylation may be necessary for the expression of genes that promote differentiation and genes that suppress self-renewal in normal hematopoiesis. (B) Mutations that disrupt TET2 activity impair hydroxylation of 5-mC and consequently DNA demethylation at gene regulatory regions. This can result in transcriptional down-regulation of genes that promote differentiation and genes that negatively regulate self-renewal. Mutant IDH1 or IDH2 gain a neomorphic activity that catalyzes the conversion of α-KG to the oncometabolite, D-2-hydroxyglutarate (D-2-HG). D-2-HG inhibits the activity of α-KG dependent dioxygenases including TET2, which leads to changes in DNA methylation and gene expression similar to those seen with TET2 mutations.

Figure 3. Mechanism of gene expression dysregulation by TET2 and IDH1/2 mutations

(A) TET2 catalyzes the hydroxylation of 5-methylcytosine (5-mC) in DNA resulting in the formation of 5-hydroxymethylcytosine (5-hmC). α-ketoglutarate (α-KG) is an essential cofactor in this reaction. 5-hmC appears to be an intermediate product in the DNA demethylation pathway which involves enzymes in the base excision repair (BER) pathway. TET2-mediated DNA demethylation may be necessary for the expression of genes that promote differentiation and genes that suppress self-renewal in normal hematopoiesis. (B) Mutations that disrupt TET2 activity impair hydroxylation of 5-mC and consequently DNA demethylation at gene regulatory regions. This can result in transcriptional down-regulation of genes that promote differentiation and genes that negatively regulate self-renewal. Mutant IDH1 or IDH2 gain a neomorphic activity that catalyzes the conversion of α-KG to the oncometabolite, D-2-hydroxyglutarate (D-2-HG). D-2-HG inhibits the activity of α-KG dependent dioxygenases including TET2, which leads to changes in DNA methylation and gene expression similar to those seen with TET2 mutations.