DNMT3A in haematological malignancies

Abstract

DNA methylation patterns are disrupted in various malignancies, suggesting a role in the development of cancer, but genetic aberrations directly linking the DNA methylation machinery to malignancies were rarely observed, so this association remained largely correlative. Recently, however, mutations in the gene encoding DNA methyltransferase 3A (DNMT3A) were reported in patients with acute myeloid leukaemia (AML), and subsequently in patients with various other haematological malignancies, pointing to DNMT3A as a critically important new tumour suppressor. Here, we review the clinical findings related to DNMT3A, tie these data to insights from basic science studies conducted over the past 20 years and present a roadmap for future research that should advance the agenda for new therapeutic strategies.

Figure 1. The structure of DNA methyltransferase proteins and their binding partners

a | Domain architecture of DNA methyltransferase 1 (DNMT1), DNMT3A1, DNMT3A2, DNMT3B and DNMT3-like (DNMT3L) and major DNMT3A splice isoforms. Note that DNMT3B has a number of additional isoforms that are not depicted here^,. Protein length is indicated (length given as number of amino acids). Domain abbreviations: ADD, ATRX-DNMT3-DNMT3L (related to the plant homology (PHD)-like domain of regulator ATRX); BAH, Bromo adjacent homology domain; DMAP, DNMT1-associated protein; PWWP, Pro-Trp-Trp-Pro. MT is the catalytic methyltransferase domain, and I, IV, VI, IX and X are motifs in the catalytic domain: motif I allows the binding of the methyl group donor AdoMet (S-adenosyl methionine). Motifs I and X are for cofactor binding, and motifs VIII and IX are for DNA binding. The catalysis of DNA methylation occurs at the IV, VI and VIII motifs. b | DNMT3A contains an amino-terminal domain that is unique to the long isoform and exhibits DNA-binding capability^,. It may also interact with transcription factors such as OCT3 (also known as OCT4 and POU5F1) in embryonic stem cells. Lysine 44 (K44) of the N-terminal domain is dimethylated by G9A and is important for interactions with G9A and/or EHMT1 (also know as GLP)^,; this interaction is necessary for the DNA methylation of some loci, such as the OCT3 promoter, which is involved in embryonic stem cell pluripotency. PWWP has diverse capabilities, including DNA and heterochromatin binding^,, as well as interactions with the histone H3 lysine 36 trimethylation (H3K36me3) and H3K9me3 marks. The ADD domain has strong affinity for histone deacetylase 1 (HDAC1) and for unmodified H3K4 (REFS –32), and is thought to positively affect DNA methyltransferase activity.This domain binds to the methyltransferase domain to act as an auto-inhibition loop in the presence of unmodified histone H3 binding; it also interacts with histone modifiers involved in gene repression, such as the histone-lysine N-methyltransferase SUV39H1 (REF. 53). Furthermore, the ADD domain binds to the histone-lysine N-methyltransferase enhancer of zeste homologue 2 (EZH2); EZH2 is part of Polycomb repressive complex 2 (PRC), which is responsible for H3K27 methylation^,.

Figure 2. Distribution of DNMT3A mutation frequency in myeloid and lymphoid leukaemia

a | Structural diagram of the location of mutations in DNA methyltransferase 3A (DNMT3A). The top band indicates amino acid position and scale. The vertical lines show the mutations mapped to DNMT3A in acute myeloid leukaemia (AML) and T cell acute lymphoblastic leukaemia (T-ALL) in the subset of patients in which the entire gene has been sequenced, as curated from the published literature. Long lines represent >0.03% frequency of mutation. Also shown is the distinct frequency of mutation at arginine 882 (R882) in AML versus T-ALL, and the minor hotspot in AML G543 (1.4%) and R736 (2.1%) residues. b | Frequency of mutations in AML, myelodysplastic syndrome (MDS) and T-ALL/lymphoma, as curated from the Catalogue of Somatic Mutations in Cancer (COSMIC) database (see Further information). ADD, ATRX-DNMT3-DNMT3L; IndelFs, insertion–deletion frameshift mutations; MT, methyltransferase; PWWP, Pro-Trp-Trp-Pro.

Figure 3. DNMT3A mutation allele and gene dosage, combined with secondary mutations, are likely to dictate the type of haematological disease

DNA methyltransferase 3A (DNMT3A) mutations (indicated by stars) are likely to arise in the pre-leukaemic haematopoietic stem cell (HSC) compartment, in which heterozygous mutations predispose the occurrence of myeloid disease and peripheral T cell lymphoma (PTCL), whereas homozygous mutations are likely to occur in T cell disease. Certain mutations in R882X, where X is an amino acid other than R, lead to the acquisition of co-mutations; that is, internal tandem duplication in the gene encoding the receptor tyrosine kinase FLT3 (FLT3^ITD) and mutations in the gene encoding nucleophosmin (NPM1). Acquisition of a secondary mutation in myeloid disease is associated with distinct myeloid neoplasms, including acute myeloid leukaemia (AML), myelodysplastic syndrome (MDS) and myeloproliferative neoplasms (MPNs). HSPC, haematopoietic stem and progenitor cell; IDH, isocitrate dehydrogenase; mut, mutant; RHOA, RAS homologue family member A; SF3B1, splicing factor 3b, subunit 1; T-ALL, T cell acute lymphoblastic leukaemia; U2AF1, U2 small nuclear RNA auxiliary factor 1.

Figure 4. Co-mutations with DNMT3A in acute myeloid leukaemia and other diseases

a | Mutations in nucleophosmin (NPM1) and internal tandem duplication in the gene encoding the receptor tyrosine kinase FLT3 (FLT3^ITD) occur more frequently in DNA methyltransferase 3A (DNMT3A)-mutant acute myeloid leukaemia (AML) than in non-DNMT3A-mutant AML. Each column represents a patient from The Cancer Genome Atlas (TCGA) database. Each coloured mark represents a mutation (light blue) or deletion (dark blue). The frequency of patients with each mutation is indicated on the left-hand side. The figure was made using cBioPortal^,. b | Frequent co-mutations with DNMT3A. AITL, angioimmunoblastic T cell lymphoma; ASXL1, additional sex combs-like transcriptional regulator 1; CDKN, cyclin-dependent kinase inhibitor; IDH, isocitratedehydrogenase; JAK2, Janus kinase 2; KMT2A, histone-lysine N-methyltransferase KMT2A (also known as MLL); MDS, myelodysplastic syndrome; MPN, myeloproliferative neoplasm; PHF6, PHD finger protein 6; PTCL, peripheral T cell lymphoma; RHOA, RAS homologue family member A; SF3B1, splicing factor 3b, subunit 1; SRSF2, serine/arginine-rich splicing factor 2; T-ALL, T cell acute lymphoblastic leukaemia; U2AF1, U2 small nuclear RNA auxiliary factor 1.*One large study showed significant association, but another study found no association. ^‡One study found a significant association with IDH2 mutations that was not confirmed in two additional large studies.