DNMT3A mutations in acute myeloid leukemia

Abstract

Background: The genetic alterations responsible for an adverse outcome in most patients with acute myeloid leukemia (AML) are unknown.

Methods: Using massively parallel DNA sequencing, we identified a somatic mutation in DNMT3A, encoding a DNA methyltransferase, in the genome of cells from a patient with AML with a normal karyotype. We sequenced the exons of DNMT3A in 280 additional patients with de novo AML to define recurring mutations.

Results: A total of 62 of 281 patients (22.1%) had mutations in DNMT3A that were predicted to affect translation. We identified 18 different missense mutations, the most common of which was predicted to affect amino acid R882 (in 37 patients). We also identified six frameshift, six nonsense, and three splice-site mutations and a 1.5-Mbp deletion encompassing DNMT3A. These mutations were highly enriched in the group of patients with an intermediate-risk cytogenetic profile (56 of 166 patients, or 33.7%) but were absent in all 79 patients with a favorable-risk cytogenetic profile (P<0.001 for both comparisons). The median overall survival among patients with DNMT3A mutations was significantly shorter than that among patients without such mutations (12.3 months vs. 41.1 months, P<0.001). DNMT3A mutations were associated with adverse outcomes among patients with an intermediate-risk cytogenetic profile or FLT3 mutations, regardless of age, and were independently associated with a poor outcome in Cox proportional-hazards analysis.

Conclusions: DNMT3A mutations are highly recurrent in patients with de novo AML with an intermediate-risk cytogenetic profile and are independently associated with a poor outcome. (Funded by the National Institutes of Health and others.).

Figure 1. DNMT3A Mutations in 188 Patients with Acute Myeloid Leukemia (AML)

Shown are data from samples banked at Washington University that were obtained from 188 patients with AML. All mutations that are shown were confirmed to be somatic. The locations of the PWWP domain (characterized by the presence of a highly conserved proline–tryptophan–tryptophan–proline motif), the ADD (ATRX, DNMT3, and DNMT3L)-type zinc finger (ZNF) domain, and the methyltransferase (MTase) domain are shown. Each patient with a DNMT3A mutation is designated with a circle. The deletion that is noted at position 1 is a 1.5-Mbp deletion that includes DNMT3A and part or all of eight other genes (for details, see Fig. 2 in the Supplementary Appendix).

Figure 2. Relationship between DNMT3A Mutations and Other Common Mutations in 188 Patients with Acute Myeloid Leukemia (AML)

Shown is the mutation status of each of 188 patients with AML on the basis of sequencing results shown in Figure 1. Red indicates the presence of the specified mutation in the designated patient, and green the absence of the mutation. For DNMT3A mutations, the presence of any R882 variant is shown in tan, and all other DNMT3A mutations are shown in blue. DNMT3A, NPM1, and IDH1/2 mutations were not detected in any sample with t(15;17), t(8;21), complex t(8;21), or inv(16). In samples with DNMT3A mutations, mutations in FLT3 (either internal tandem duplications or mutations at amino acid position D835), NPM1, and IDH1 were significantly enriched. Cytogenetic risk groups are shown at the bottom of the graph, with yellow indicating favorable risk, orange intermediate risk, and purple adverse risk. Black boxes indicate that no data were available for that sample. Mutation groups as defined by these data are designated at the top of the graph. Samples in mutation group A have cytogenetic findings associated with favorable risk and have only FLT3 mutations among the five commonly mutated AML genes. Samples in mutation group B are highly enriched for mutations in the five commonly mutated AML genes that are associated with intermediate risk. Samples in mutation group C have no mutations in any of the five common AML genes, suggesting that a different set of mutations may contribute to the pathogenesis in this group.

Figure 3. Overall Survival among Patients with Acute Myeloid Leukemia (AML) with DNMT3A Mutations

Panel A shows the overall survival among all 281 patients, including 62 with a DNMT3A mutation and 219 without a DNMT3A mutation. Panel B shows the overall survival of 120 patients with normal karyotypes, including 44 with a DNMT3A mutation and 76 without a DNMT3A mutation. Panel C shows the overall survival of 54 patients with an FLT3 internal tandem duplication mutation, including 16 with a DNMT3A mutation and 38 without a DNMT3A mutation. Panel D shows the overall survival of all 281 patients stratified according to DNMT3A mutation status and age; 72 patients were over the age of 60 years and 209 were 60 years of age or younger. All P values, which are for the comparison between any DNMT3A mutation and no mutation, were calculated by means of the log-rank test.