Prognostic relevance of integrated genetic profiling in acute myeloid leukemia

Abstract

Background: Acute myeloid leukemia (AML) is a heterogeneous disease with respect to presentation and clinical outcome. The prognostic value of recently identified somatic mutations has not been systematically evaluated in a phase 3 trial of treatment for AML.

Methods: We performed a mutational analysis of 18 genes in 398 patients younger than 60 years of age who had AML and who were randomly assigned to receive induction therapy with high-dose or standard-dose daunorubicin. We validated our prognostic findings in an independent set of 104 patients.

Results: We identified at least one somatic alteration in 97.3% of the patients. We found that internal tandem duplication in FLT3 (FLT3-ITD), partial tandem duplication in MLL (MLL-PTD), and mutations in ASXL1 and PHF6 were associated with reduced overall survival (P=0.001 for FLT3-ITD, P=0.009 for MLL-PTD, P=0.05 for ASXL1, and P=0.006 for PHF6); CEBPA and IDH2 mutations were associated with improved overall survival (P=0.05 for CEBPA and P=0.01 for IDH2). The favorable effect of NPM1 mutations was restricted to patients with co-occurring NPM1 and IDH1 or IDH2 mutations. We identified genetic predictors of outcome that improved risk stratification among patients with AML, independently of age, white-cell count, induction dose, and post-remission therapy, and validated the significance of these predictors in an independent cohort. High-dose daunorubicin, as compared with standard-dose daunorubicin, improved the rate of survival among patients with DNMT3A or NPM1 mutations or MLL translocations (P=0.001) but not among patients with wild-type DNMT3A, NPM1, and MLL (P=0.67).

Conclusions: We found that DNMT3A and NPM1 mutations and MLL translocations predicted an improved outcome with high-dose induction chemotherapy in patients with AML. These findings suggest that mutational profiling could potentially be used for risk stratification and to inform prognostic and therapeutic decisions regarding patients with AML. (Funded by the National Cancer Institute and others.).

Figure 1. Mutational Complexity of Acute Myeloid Leukemia (AML)

A Circos diagram (Panel A) depicts the relative frequency and pairwise co-occurrence of mutations in patients with newly diagnosed AML who were enrolled in the Eastern Cooperative Oncology Group E1900 clinical trial. The length of the arc corresponds to the frequency of mutations in the first gene, and the width of the ribbon corresponds to the percentage of patients who also had a mutation in the second gene. Pairwise co-occurrence of mutations is denoted only once, beginning with the first gene in the clockwise direction. Panel A also shows the frequency of mutations in the test cohort. Panels B and C show the mutational events in patients with mutant DNMT3A and mutant FLT3, respectively. Since, for clarity, only pairwise mutations are encoded, the arc length was adjusted to maintain the relative size of the arc, and the correct proportion of patients with only a single mutant allele is represented by the not-otherwise-occupied space within each mutational subset (all panels). ITD denotes internal tandem duplication, PTD partial tandem duplication, and TKD tyrosine kinase domain.

Figure 2. Multivariate Risk Classification of Patients with Intermediate-Risk AML

Kaplan–Meier estimates of overall survival are shown for the risk stratification of patients with intermediate-risk AML (with P values for the comparison of all curves). Among patients with wild-type FLT3-ITD (Panel A), there were three categories: patients with mutant TET2, ASXL1, PHF6, or MLL-PTD, who had a poor prognosis for overall survival; those with mutant IDH1 or IDH2 and mutant NPM1, who had a good prognosis for overall survival; and those with any other genotypes, who had an intermediate prognosis for survival. Among patients who were positive for FLT3-ITD mutations (Panel B), there were also three categories of patients: those with mutant TET2, DNMT3A, or MLL-PTD or trisomy 8 without mutant CEBPA, who had a poor prognosis for overall survival; those with mutant CEBPA, who had an intermediate prognosis for survival; and those with any other genotypes, who also had an intermediate prognosis for survival.

Figure 3. Revised Risk Stratification of Patients with AML on the Basis of Integrated Genetic Analysis

Panel A shows a revised risk stratification on the basis of integrated cytogenetic and mutational analysis. The final overall risk groups are shown on the right. Panel B shows the effect of integrated mutational analysis on risk stratification in the test cohort of patients with AML (with P values for the comparison of all curves), and Panel C shows the reproducibility of the genetic prognostic schema in an independent cohort of 104 patients from the E1900 trial (with P values for the comparison of all curves). In Panels B and C, the black curves show the patients whose risk classification remained unchanged, the blue curve shows patients who were reclassified from intermediate risk to favorable risk, and the red curve shows patients who were reclassified from intermediate risk to unfavorable risk.

Figure 4. Molecular Determinants of Response to High-Dose Daunorubicin Induction Chemotherapy

Kaplan–Meier estimates of the probability of overall survival are shown in the entire cohort according to DNMT3A mutational status (Panel A) and according to DNMT3A status and receipt of high-dose or standard-dose daunorubicin (Panel B). The P value in Panel B is for the comparison across all groups. The rates of overall survival according to receipt of high-dose or standard-dose daunorubicin are shown among patients with DNMT3A or NPM1 mutations or MLL translocations (Panel C) and among patients without DNMT3A and NPM1 mutations and with no MLL translocations (Panel D).

Figure 5. Comprehensive Mutational Profiling for Risk Stratification and Clinical Management of AML

The use of mutational profiling delineates subgroups of patients with intermediate-risk AML, as defined according to cytogenetic analysis, who have markedly divergent prognoses and reassigns a substantial proportion of them to favorable-risk or unfavorable-risk categories (Panel A). In addition, mutational profiling identifies genetically defined subgroups of patients with AML who have improved outcomes with high-dose anthracycline induction chemotherapy (Panel B). OS denotes overall survival.