NPM1 Mutated AML with Concurrent DNMT3A Mutation, and FLT3-Internal Tandem Duplication Has Outcomes Similar to European Leukemianet Adverse Risk Category
Authors: Bhanshe Prasanna , Achrekar Aarti Ramesh , Ugale Priyanka Rajesh , Kusurkar Saurabh , Joshi Swapnali , Terse Vishram , Shetty Dhanlaxmi Lalit , Jindal Nishant , Tembhare Prashant , Mirgh Sumeet , Shetty Alok , Gokarn Anant , Punatar Sachin , Nayak Lingaraj , Jain Hasmukh , Sengar Manju , Khattry Navin , Bagal Bhausaheb , Rajpal Sweta , Chatterjee Gaurav , Subramanian Papagudi Ganesan , Gujral Sumeet , Patkar Nikhil 
Published: December 2024

Introduction: Previously our group (Patkar et al, Blood Cancer Journal 2019) and others have indicated that NPM1 mutated acute myeloid leukemia (AML) with concurrent DNMT3A and FLT3-internal tandem duplication triple mutated AML (TM-AML) may have inferior outcomes. The European LeukemiaNet 2022 (ELN-22) risk stratification schema does not take DNMT3A mutations into account. Here, we demonstrate that this subset of AML has an exceedingly inferior outcome as compared to NPM1 mutated AML and should be considered as a distinct AML entity.

Methods: A total of 506 patients of adult AML (≥18 years) were accrued over 10 years (2012 - 2023). Patients were uniformly treated with “3 + 7” induction. Diagnostic samples were sequenced using a 50-gene myeloid panel (till 2020) based on single molecule molecular inversion probes and subsequently using a 135-gene hybrid capture-based panel. Based on cytogenetics and genomic information, cases were risk-stratified as per ELN-22 recommendations. MRD was evaluated at post-induction (PI) time point using 10-color or 16-color flow cytometry (PI MFC-MRD). We also compared patient characteristics (WBC counts, age) of this subset against NPM1 mutated AML using Kruskal-Wallis test for continuous variables. We also describe the genomic landscape of this subset with respect to co-occurring mutations. We compared the outcomes of TM-AML with other ELN-22 risk groups. The prognostic impact of TM-AML on overall survival (OS) and relapse-free survival (RFS) was computed using the Kaplan-Meier method and compared using log-rank test for time-to-event analyses.

Results: The median age of the overall cohort was 35.0 years (M: F, 1.6:1), with a median follow-up of 29.5 months. The median OS was 80 months (95% CI 34.8-87.3), and the median RFS was 52.3 months (95% CI 35.2-87.9). Based on ELN-22 recommendations, patients were classified as favorable (n=275), intermediate (n=157), or adverse risk (n=75). AML with NPM1 mutation was the commonest entity (n=144, 28.4%) in our cohort of which 15 cases of concurrent NPM1, FLT3-ITD, and DNMT3A triple mutated AML were detected, accounting for 10.4% of all NPM1 mutated AML. The median OS of TM-AML was 15.5 months (95% Cl; 7.1-20.5) and median RFS was 14.5 months (95% Cl; 6.2- 42.3). TM AML cases presented with a higher WBC count (p = 0.001) as compared to ELN-22 intermediate and adverse risk groups. No difference in age and bone marrow blast percentage was found compared to other ELN risk categories and NPM1 mutated AML. No additional cytogenetic abnormalities were found in TM AML cohort. In this cohort, 30% cases (n=5/15) did not achieve morphological remission. IDH1 and PTPN11 gene mutations were commonest (20%, n=3/15 each) in TM AML cases followed by TET2, WT1 and FLT3 tyrosine kinase domain (FLT3-TKD) mutations (13.3% ,n=2/15 each). In NPM1 mutated cohort, IDH2 (24.3%) was the commonest co mutation followed by mutations in TET2, (23.6%), IDH1 (19.4%) FLT3-TKD, NRAS (14.5%) and PTPN11 (13.8%) genes. PI MFC-MRD positivity (33.3%) was associated with an inferior OS (HR: 3.8 95% CI: 0.8-17.8, p = 0.02) in TM AML cohort as well as in NPM1 mutated AML (34.02%) cohort (HR: 1.9 95% CI: 1.06-3.5, p = 0.01). TM AML cases showed an inferior OS (HR: 2.9 95% CI: 0.9-8.8, p = 0.01) and RFS (HR: 4.1 95% CI: 1.09-15.8, p = 0.0001) compared to AML with NPM1 mutated cases. In comparison with ELN-22 intermediate risk AML cases, TM AML showed inferior OS (HR: 2.3 95% CI: 0.8-6.2, p = 0.01) and RFS (HR: 3.1 95% CI: 0.9-10.1, p = 0.002). No significant difference in OS (HR: 1.2,95% CI 0.5-2.6, p = 0.55) and RFS (HR:0.77; 95% CI: 0.32-1.8, p = 0.5) was found in TM AML cohort when compared with ELN-22 adverse risk category.

Conclusion: De novo AML patients with concurrent DNMT3A, FLT3 and NPM1 mutations present with higher WBC count and have outcomes comparable to ELN-22 adverse risk AML. This subtype of AML should be considered as a distinct prognostic entity for appropriate risk adapted therapy.