Clinical and Molecular Characteristics of NPM1MTDe Novo AML ( NPM1MT dnAML) Differ from NPM1MT therapy-associated AML ( NPM1MT tAML)
Authors: Dhillon Vikram , Aguilar Jeff , Nanja Reddy Sushmitha , Potluri Lakshmi Bhavani , Dyson Gregory , Maciejewski Jaroslaw P. , Balasubramanian Suresh Kumar 
Published: December 2023

Background: NPM1-mutated AML accounts for 30% of all adult AML cases and frequently carries a favorable prognostic impact when enriched by a normal karyotype and the absence of FLT3-ITD mutations. Although the clinical and molecular characteristics of NPM1-mutated de novo AML ( NPM1MT dnAML) are well known, the impact of NPM1MT within the context of therapy-associated AML ( NPM1MT tAML) remains controversial. Recent work by Othman et al. suggests NPM1MT tAML may represent a biologically de novo leukemia, displaying similar clinical, genomic, and transcriptional profile to NPM1MT dnAML and should be treated as a single disease entity. We sought to externally validate this by analyzing the clinical outcomes, mutational landscape, and molecular features of a large cohort of patients with NPM1-mutated AML.
Methods: We conducted a large retrospective analysis of adult AML patients with NPM1MT by screening public databases, cBioPortal (Cerami et al., 2012) and AACR GENIE (v 13.1), and expanded with a published metanalytic cohort of various sub-studies from Cleveland Clinic Foundation from 2012-2021 (Awada et al., Blood 2021 and Kewan et al., Nature Communications, 2023). Baseline clinical and molecular characteristics were noted. We analyzed the molecular data in the context of overall survival (OS), clinical parameters, coexisting mutations, karyotype, AML subtypes, ELN-favorability, and gene expression data.
Results: We screened a total of 15,742 adult AML patients, and 4,135 eligible patients were separated into 5 cohorts: 2,156 patients (52%) with NPM1MT dnAML, 1233 patients (30%) with NPM1WT sAML, 289 patients (7%) with NPM1MT sAML, 397 patients (10%) with NPM1WT tAML, and 60 patients (1.5%) with NPM1MT tAML. NPM1MT dnAML and NPM1MT sAML patients had a median age of 60 and 72 yrs. [18-91 vs 27-91 yrs., p =&lt;0.0001 resp.]. NPM1MT tAML also had a median age of 72 yrs. [range 24-84]. Females were more represented in NPM1MT dnAML compared to both sAML cohorts [51% vs 45% and 39%; p =&lt;0.0001, &lt;0.0001] and both tAML cohorts. Abnormal karyotype enriched NPM1WT tAML more than NPM1MT dnAML [72% vs 27%, p =&lt;0.0001], whereas normal karyotype was more prominent in NPM1MT dnAML compared to NPM1WT sAML, NPM1MT sAML, and NPM1WT tAML cohorts [72% vs 55%, 58% and 59%; p =&lt;0.001, &lt;0.001 and 0.0243 resp.]. FLT3-ITDNEG status dominated all 5 cohorts, NPM1 MT dnAML and NPM1WT t-AML had similar FLT3-ITDNEG mutants [83% vs 86%, p =0.52], and NPM1MT sAML had the highest FLT3-ITDPOS hits (32%). NPM1WT sAML cohort was profoundly hyperproliferative in bone marrow blast response (33.5%) whereas NPM1MT dnAML and NPM1MT tAML had similar responses (73% and 73%, p =0.3). All five cohorts were pancytopenic, the degree of pancytopenia was comparable in NPM1MT dnAML vs NPM1MT t-AML as shown below in Fig 1-A.
NPM1 MT dnAML (Fig.1-B) had the best survival vs NPM1MT tAML [24.74 vs15.9 mo., p =&lt;0.0016]. NPM1MT s-AML had the worst survival across all the cohorts, although comparable to NPM1WT tAML [8.73 and 9.76 mo., p =&lt;0.0001]. When we exclude FLT-ITD, NPM1MT dnAML has the highest median OS, and median OS for NPM1MT t-AML rises as well [25 vs 23mo., p =0.0196], the remaining three cohorts had comparable OS (10.97 vs 10.63 vs 11.05 mo.). Next, we narrowed down to only ELN-favorable risk groups, median OS was only numerically higher for NPM1MT dnAML vs NPM1MT tAML [25 vs 23 mo., p-value =0.1348]. In terms of co-mutational profile, NPM1MT dnAML and NPM1MT tAML share many similarities though not with associated mutations: NPM1MT tAML is enriched by TP53 (10%), and SF3B1 (5%), and NPM1MT dnAML by RAD21 (5%) and CEBPA (5%)
To understand gene-expression differences, we analyzed publicly available RNA-seq data for dn NPM1MT AML vs NPM1MT tAML and discovered that NPM1MT dnAML had higher expression of cMYC as well as FOXO1.
Conclusion: Although dn NPM1MT AML and NPM1MT tAML appear to have distinct molecular and clinical profiles, a narrow focus on ELN-favorable patients demonstrates that both entities have similar clinicogenomic outcomes. When evaluated in a large cohort of AML patientswith added granularity from sAML cohorts, we notice several differences in survival and molecular profile that converge as more unfavorable factors, such as abnormal cytogenetics and FLT3-ITDPOS status are removed. Ongoing work at Karmanos Cancer Center is focused on evaluating differences in treatment response and gene-expression analysis based on RNA-seq.