DNMT3A mutation is associated with increased age and adverse outcome in adult T-cell acute lymphoblastic leukemia

Abstract

The prognostic implications of DNMT3A genotype in T-cell acute lymphoblastic leukemia are incompletely understood. We performed comprehensive genetic and clinico-biological analyses of T-cell acute lymphoblastic leukemia patients with DNMT3A mutations treated during the GRAALL-2003 and -2005 studies. Eighteen of 198 cases (9.1%) had DNMT3A alterations. Two patients also had DNMT3A mutations in non-leukemic cell DNA, providing the first potential evidence of age-related clonal hematopoiesis in T-cell acute lymphoblastic leukemia. DNMT3A mutation was associated with older age (median 43.9 years vs 29.4 years, P<0.001), immature T-cell receptor genotype (53.3% vs 24.4%, P=0.016) and lower remission rates (72.2% mutated vs 94.4% non-mutated, P=0.006). DNMT3A alterations were significantly associated with worse clinical outcome, with higher cumulative incidence of relapse (HR 2.33, 95% CI: 1.05-5.16, P=0.037) and markedly poorer event-free survival (HR 3.22, 95% CI: 1.81-5.72, P<0.001) and overall survival (HR 2.91, 95% CI: 1.56-5.43, P=0.001). Adjusting for age as a covariate, or restricting the analysis to patients over 40 years, who account for almost 90% of DNMT3A-mutated cases, did not modify these observations. In multivariate analysis using the risk factors that were used to stratify treatment during the GRAALL studies, DNMT3A mutation was significantly associated with shorter event-free survival (HR 2.33, 95% CI: 1.06 - 4.04, P=0.02). Altogether, these results identify DNMT3A genotype as a predictor of aggressive T-cell acute lymphoblastic leukemia biology. The GRAALL-2003 and -2005 studies were registered at http://www.ClinicalTrials.gov as #NCT00222027 and #NCT00327678, respectively.

Figure 1.

DNMT3A mutations in T-cell acute lymphoblastic leukemia. (A) Schematic representation of the 21 mutations detected in this study. Further patient-specific details are provided in Online Supplementary Table S3. (B) Comparison of the mutational genotypes of DNMT3A altered (n=18) and DNMT3A wild-type (n=180) T-cell acute lymphoblastic leukemia. Percentage frequencies in each group are depicted. Functional categories are listed in bold.

Figure 2.

Evidence of DNMT3A mutations in non-leukemic DNA. (A) Direct sequencing of DNMT3A exons 14 and 15, NOTCH1 and NRAS in diagnostic (left panels) and remission (right panels) samples. (B) Mutational assessment of DNA extracted from leukemic and non-leukemic fractions of samples from patients with T-cell acute lymphoblastic leukemia. Sequencing results of DNMT3A and NOTCH1 in leukemic (left panels) and non-leukemic (right panels) DNA are shown. Cases are numbered according to the listing in Online Supplementary Table S3.

Figure 3.

DNMT3A mutation correlates with poor outcome in T-cell acute lymphoblastic leukemia. Comparisons of outcomes for patients with (n=18) and without (n=180) DNMT3A mutations are shown for: (A) cumulative incidence of relapse; (B) event-free survival; and (C) overall survival. The 5-year results were as follows: cumulative incidence of relapse 53.9% mutated vs. 28.7% non-mutated; event-free survival 27.8% mutated vs. 61.0% non-mutated; overall survival 38.8% mutated vs. 68.7% non-mutated. P values are indicated.

Figure 4.

DNMT3A genotype predicts outcome in the age group of patients at risk of mutation. Comparisons of outcomes for patients with (n=16) and without (n=34) mutations in patients >40 years are shown for: (A) cumulative incidence of relapse; (B) event-free survival; and (C) overall survival. The 5-year results were as follows: cumulative incidence of relapse 58.3% mutated vs. 21.7% non-mutated; event-free survival, 25.0% mutated vs. 56.7% non-mutated; overall survival 37.5% mutated vs. 62.1% non-mutated. P values are indicated.