Mutated WT1, FLT3-ITD, and NUP98-NSD1 Fusion in Various Combinations Define a Poor Prognostic Group in Pediatric Acute Myeloid Leukemia

Abstract

Acute myeloid leukemia is a life-threatening malignancy in children and adolescents treated predominantly by risk-adapted intensive chemotherapy that is partly supported by allogeneic stem cell transplantation. Mutations in the WT1 gene and NUP98-NSD1 fusion are predictors of poor survival outcome/prognosis that frequently occur in combination with internal tandem duplications of the juxta-membrane domain of FLT3 (FLT3-ITD). To re-evaluate the effect of these factors in contemporary protocols, 353 patients (<18 years) treated in Germany with AML-BFM treatment protocols between 2004 and 2017 were included. Presence of mutated WT1 and FLT3-ITD in blasts (n=19) resulted in low 3-year event-free survival of 29% and overall survival of 33% compared to rates of 45-63% and 67-87% in patients with only one (only FLT3-ITD; n=33, only WT1 mutation; n=29) or none of these mutations (n=272). Including NUP98-NSD1 and high allelic ratio (AR) of FLT3-ITD (AR ≥0.4) in the analysis revealed very poor outcomes for patients with co-occurrence of all three factors or any of double combinations. All these patients (n=15) experienced events and the probability of overall survival was low (27%). We conclude that co-occurrence of WT1 mutation, NUP98-NSD1, and FLT3-ITD with an AR ≥0.4 as triple or double mutations still predicts dismal response to contemporary first- and second-line treatment for pediatric acute myeloid leukemia.

Figure 1

Study flowchart and patient characteristics. (a) Study flowchart outlining the process of patient recruitment in the data analysis. (b) WT1 mutations often co-occurred with FLT3-ITD and other genetic aberrations. AML-BFM, acute myeloid leukemia-Berlin-Frankfurt-Muenster; n, number; WT1, Wilms Tumor 1; FLT3-ITD, fms-related tyrosine kinase 3-internal tandem duplication; NPM1, nucleophosmin 1; NRAS, neuroblastoma RAS viral oncogene homolog; c-KIT, KIT proto-oncogene; CBF, core binding factor; MLL, rearrangements of MLL gene; NUP98-NSD1, Nucleoporin-Nuclear Receptor Binding SET Domain Protein 1 fusion gene; CN, cytogenetic-normal AML; AR, allelic ratio; CCR, continued complete remission; LFU, lost to followup; NR, non-response; PR, partial remission. ^aCBF aberrations include translocation of chromosomes 8 and 21 and inversion or translocation of chromosome 16. ^bOther cytogenetic aberrations such as trisomy 8, various chromosomal translocations, and complex karyotype alterations.

Figure 2

Co-occurrence of WT1 and FLT3-ITD mutations at initial diagnosis of pediatric AML predicts poor survival outcomes. (a) WT1 mutation as single factor increased the incidence of relapse, reducing the probability of survival. (b) The presence of FLT3-ITD, individually, leads to an increased chance of relapse and decreased patient survival. (c) Clinical consequences of WT1 mutations and FLT3-ITD were dependent on each other. WT1, Wilms Tumor 1; FLT3-ITD, fms related tyrosine kinase 3-internal tandem duplication; pEFS, probability of event-free survival; pOS, probability of overall survival; CIR, cumulative incidence of relapse; SE, standard error; n, number. ^aNo response to treatment was considered as the occurrence of an event at time zero.

Figure 3

Mutations in NPM1, NRAS, and c-KIT had no impact on survival. (a) Prognostic impact of mutated NPM1 on EFS, OS, and CIR. (b) Prognostic impact of mutated NRAS on EFS, OS, and CIR. (c) Prognostic impact of c-KIT mutation on EFS, OS, and CIR. NPM1, nucleophosmin 1; NRAS, neuroblastoma RAS viral oncogene homolog; c-KIT, KIT protooncogene; pEFS, probability of event-free survival; pOS, probability of overall survival; CIR, cumulative incidence of relapse; SE, standard error; n, number. ^aNo response to treatment was considered as the occurrence of an event at time zero.

Figure 4

Prognostic significance of NUP98-NSD1 fusion. (a) NUP98-NSD1 as single factor predicted poor outcomes. (b) Inclusion of NUP98-NSD1 as poor prognostic factor with WT1 mutation and FLT3-ITD, predicted poor outcomes for patients harboring all three factors in addition to patients with NUP98-NSD1 and WT1 mutation or FLT3-ITD. Patients with unknown status of NUP98-NSD1 fusion were excluded from this analysis. WT1, Wilms Tumor 1; FLT3-ITD, fms related tyrosine kinase 3-internal tandem duplication; NUP98-NSD1, Nucleoporin-Nuclear Receptor Binding SET Domain Protein 1 fusion gene; pEFS, probability of event-free survival; pOS, probability of overall survival; CIR, cumulative incidence of relapse; SE, standard error; mut, mutated; pos, positive; neg, negative. ^aNo response to treatment was considered as the occurrence of an event at time zero. ^bThree patients with NUP98-NSD1 are included in this group.

Figure 5

Prognostic significance of mutational burden of FLT3-ITD. (a) FLT3-ITD with an allelic ratio ≥0.4 as a single factor predicted poor outcomes. (b) High mutational burden of FLT3-ITD was another predictor of poor prognosis when it occurred with WT1 and/or NUP98-NSD1. Patients with an unknown FLT3-ITD AR were excluded from this analysis. NUP98-NSD1, Nucleoporin-Nuclear Receptor Binding SET Domain Protein 1 fusion gene; FLT3-ITD, fms related tyrosine kinase 3-internal tandem duplication; pEFS, probability of event-free survival; pOS, probability of overall survival; CIR, cumulative incidence of relapse; AR, allelic ratio; SE, standard error; n, number. ^aNo response to treatment was considered as the occurrence of an event at time zero. ^bThree patients with NUP98-NSD1 are included in this group.