Influence of Bone Marrow Blast Enumeration and Co-Occurring Myelodysplasia Related Gene Mutations in NPM1-Mutated Myeloid Malignancies

Introduction

Both World Health Organization (WHO 5th) and International Consensus Classification (ICC) guidelines recognize mutations in nucleophosmin 1 (NPM1^mut) as a class defining molecular event in acute myeloid leukemia (AML). WHO 5th omitted the blast percentage requirement and ICC lowered the blast threshold to 10%. NPM1^mut AML without FLT3 ITD or adverse risk cytogenetics is considered favorable risk in European LeukemiaNet (ELN) 2022, however co-occurring adverse-risk myelodysplasia related mutations (MR^mut) do not influence ELN 2022 risk stratification. This analysis addresses the prognostic impact of blast enumeration in NPM1^mut myeloid neoplasms (MN) with <10% blasts and influence of co-occurring mutations in NPM1^mut AML.

Methods

We interrogated publicly available data from adult (≥18 years) patients (pts) with chronic myeloid neoplasms included in the International Working Group for Prognosis in MDS (N= 3,323; Bernard et al. NEJM Evid 2022) and two independent AML cohorts (AMLSG [N=1540] Papaemmanuil et al. NEJM 2016; UKNCRI [N=2,113] Tazi et al. Nat. Commun. 2022). Between group differences were assessed using the Wilcoxon rank-sum test or Fisher’s exact test as appropriate. Time to event endpoints were analyzed using the log-rank method. Multivariate analysis (MVA) used cox proportional hazards regression.

Results

NPM1^mut was identified in 17% (N=1148) of pts (AML: 30% [1109/3653], MN with <20% blasts: 1.2% [39/3,323]). Compared to pts with NPM1^mut AML, pts with NPM1^mut MN (MDS, CMML, aCML) with blast < 20% were older (median age 65 vs. 55 years, p < 0.001), had a lower median total WBC count (5 vs. 32 x10⁹ /L, p < 0.001) and bone marrow (BM) blast percentage (8% vs. 76%, p < 0.001). No significant difference was observed between NPM1^mut AML and MN with <20% blasts in median hemoglobin (9.1 vs. 9 x10⁹, p: 0.44), platelets (62 vs. 66 x10⁹ /L, p: 0.55), or NPM1^mut variant allele frequency (VAF; 35% vs. 37%, p: 0.64).

After a median follow up of 4.7 years (range: 0-12), no difference in overall survival (OS) was observed between pts with low blast (LB; <10%) NPM1^mut MN (N=19) vs. ≥10% blasts (N=18) (median OS: 0.64 years [95% CI: 0.31-3.0] vs. 1.1 years [95% CI: 0.95-NR], p=0.32). Median leukemia free survival (LFS) was 0.81 years (95% CI: 0.67-1.5) and not significantly different between NPM1^mut MN pts with <10 vs. ≥10% blasts (median LFS: 0.55 vs. 0.91 years, p=0.27).

In pts with NPM1^mut AML (N=1109), 52% (N=581) were ELN 2022 favorable-risk; 15% (N=92) had MR^mut including SRSF2 (51%, N=47), STAG2 (21%, N=19), ASXL1 (9%, N=8), BCOR (9%, N=8), RUNX1 ( 8%, N=7), EZH2 (5%, N=5), SF3B1 (5%, N=5), U2AF1 (1%, N=1), and ZRSR2 (1%, N=1). Pts with MR^mut were older (median age 62 vs. 53 years, p < 0.001), had higher BM blasts (80% vs. 72% p=0.019), and lower platelets (45 vs. 77 x10⁹/L p < 0.001) compared to pts with NPM1^mut AML without MR^mut. No significant difference in NPM1^mut VAF was observed (34% in both groups).

After a median follow up of 3.5 years (range: 0-15), median OS was 6.2 years in pts with NPM1^mut AML (95% CI: 4.2-9.7). Inferior OS was observed in ELN favorable risk NPM1^mut pts with vs. without MR^mut, respectively (2 vs. 8.4 years, p=0.0001). When stratified by age < 60 vs. ≥ 60 years, younger pts with MR^mut had an increased risk of death (HR 1.7 95% CI: 1.1-2.8, p: 0.02). No OS difference was observed in older pts with or without MR^mut (HR: 1.2, 95% CI: 0.80-1.68, p=0.44), however OS was significantly shorter in older pts with NPM1^mut compared to younger pts (median 1.7 years vs. NR, p < 0.001). Patients with NPM1^mut /MR^mut AML had survival comparable to patients with ELN 2022 intermediate risk AML (2.0 vs. 2.1 years, p=0.35).

In MVA of NPM1^mut AML adjusted for MR^mut, BM blast percentage, age, performance status, baseline WBC, hemoglobin, platelet count, NPM1^mut VAF, and treatment setting (AMLSG or UKNCRI), the presence of an MR^mut (HR 1.39 [95% CI: 1.0-1.9], p=0.04), age < 60 (HR 0.43 [95% CI: 0.32-0.56], p < 0.001), and performance status (HR 1.35 [95% CI: 1.14-1.60], p=0.0004) retained statistical significance.

Conclusion

Pts with low blast NPM1^mut MN have outcomes similar to pts with NPM1^mut AML, supporting NPM1^mut as an AML defining event irrespective of BM blast enumeration. In patients with ELN favorable risk NPM1^mut AML, co-occurrence of MR^mut is independently associated with inferior survival, comparable to ELN intermediate risk AML. These results may inform future refinements of current consensus guidelines.