NPM1-mutated Acute Myeloid Leukemia Research Articles

Venetoclax–based low intensity therapy in molecular failure of NPM1-mutated AML

AbstractMolecular failure in NPM1-mutated acute myeloid leukemia (AML) inevitably progresses to frank relapse if untreated. Recently published small case series show that venetoclax combined with low-dose cytarabine or azacitidine can reduce or eliminate measurable residual disease (MRD). Here, we report on an international multicenter cohort of 79 patients treated for molecular failure with venetoclax combinations and report an overall molecular response (≥1-log reduction in MRD) in 66 patients (84%) and MRD negativity in 56 (71%). Eighteen of 79 patients (23%) required hospitalization, and no deaths were reported during treatment. Forty-one patients were bridged to allogeneic transplant with no further therapy, and 25 of 41 were MRD negative assessed by reverse transcription quantitative polymerase chain reaction before transplant. Overall survival (OS) for the whole cohort at 2 years was 67%, event-free survival (EFS) was 45%, and in responding patients, there was no difference in survival in those who received a transplant using time-dependent analysis. Presence of FLT3-ITD mutation was associated with a lower response rate (64 vs 91%; P < .01), worse OS (hazard ratio [HR], 2.50; 95% confidence interval [CI], 1.06-5.86; P = .036), and EFS (HR, 1.87; 95% CI, 1.06-3.28; P = .03). Eighteen of 35 patients who did not undergo transplant became MRD negative and stopped treatment after a median of 10 months, with 2-year molecular relapse free survival of 62% from the end of treatment. Venetoclax–based low intensive chemotherapy is a potentially effective treatment for molecular relapse in NPM1-mutated AML, either as a bridge to transplant or as definitive therapy.

Intensive Induction Chemotherapy Vs Hypomethylating Agents + Venetoclax (HMA/VEN) in NPM1-Mutant Newly Diagnosed Acute Myeloid Leukemia (AML) - a Multicenter Cohort Study

Introduction: Intensive induction chemotherapy (IC) with cytarabine + anthracycline remains the standard of care for younger and fit patients (pts) with acute myeloid leukemia (AML). Post-hoc analyses from clinical trials evaluating venetoclax (VEN)-based therapies in AML have identified mutations in NPM1 as being associated with high rates of durable responses. However, these trials were conducted in pts age ≥75 years or unfit for IC. Thus, it is unknown whether IC or hypomethylating agent (HMA)+VEN is the optimal frontline treatment for pts with NPM1-mutant AML. We performed a large multicenter retrospective cohort study dedicated to pts with newly diagnosed AML with NPM1 mutations, comparing treatment modalities and assessing the impact of clinical and molecular characteristics on response and survival. Methods: We included pts with newly diagnosed, NPM1-mutant AML who were treated at 4 large academic centers with IC (either conventional 7+3 or liposomal cytarabine/daunorubicin [CPX-351]) or HMA+VEN. Detection of NPM1 mutations was performed at the participating sites either by polymerase chain reaction (PCR) or next-generation sequencing (NGS) per local standards. Composite complete response (cCR) was defined as complete response (CR) + CRi (CR with incomplete count recovery) per European LeukemiaNet 2017 criteria. Overall survival (OS) was compared between groups by log-rank test. Cox regression multivariable model for OS was fitted using a stepwise backward selection to evaluate the effect of treatment, allogeneic stem cell transplantation (allo-SCT) as a time-varying covariate and additional covariates with a p&amp;lt;0.1 in the univariate model. Results: We reviewed 1132 pts with AML and included 225 pts with NPM1-mutant AML in the final analysis ( Table 1). Among these pts, 71% (n=160) and 29% (n=65) received IC and HMA+VEN, respectively. Some pts (22%) in the IC group also received midostaurin compared to 0% in the HMA+VEN group. Pts who received IC for NPM1-mutant AML were younger (median age 61 years [Range: 22 -76] vs 74 years [33 -89]; p&amp;lt;0.001) when compared to HMA+VEN and less likely to have prior myelodysplastic syndrome (MDS) or myeloproliferative neoplasms (MPN; 10% vs 20%, p=0.042), and SF3B1 mutations (3.1% vs 15%; p=0.002). There was no difference in the rate of FLT3-ITD mutations between groups (36% vs 29%; p=0.36). Rates of cCR and CR were higher for IC than HMA+VEN-treated pts (cCR: 87% vs 74%; p=0.018; CR: 83% vs 52%; p&amp;lt;0.001), as well as rates of allo-SCT (56% vs 23%; p&amp;lt;0.001). Median OS was 31 months (95% CI: 24 months [mo] - not reached [NR]) for the total cohort of pts with NPM1-mutant AML and was better in pts treated with IC vs HMA+VEN (IC: 24 mo OS 65% [95% CI: 57 - 74%] vs HMA+VEN: 24 mo OS 38% [95% CI: 26 - 55%]; p&amp;lt;0.001). While the median OS remained favorable for IC among pts age &amp;gt; 60 years with NPM1-mutant AML (34 mo [95% CI: 24 mo - NR] vs 15 mo [13 mo - 28 mo]; p=0.015), there was no difference in OS by treatment type among the pts undergoing allo-SCT (IC: median OS not reached; 24 mo OS: 72% [95% CI: 63-83%] vs HMA+VEN: median OS 29 mo; 24 mo OS 69% [95% CI: 48-100%]; p=0.55). In the univariate analysis, treatment (HMA+VEN vs IC), age, prior chemotherapy exposure, abnormal cytogenetics, SF3B1, TET2 and RNA splicing mutations were associated with worse outcomes ( Table 2). Of note, neither the presence of concurrent FLT3 or IDH1/2 mutations nor allo-SCT as a time-varying covariate had a statistically significant impact on OS. In the multivariable analysis, treatment with HMA+VEN vs. IC retained its predictive value (hazard ratio: 2.00; 95% CI: 0.92 - 3.03; p=0.006), as well as prior chemotherapy and abnormal cytogenetics ( Table 2). Conclusion: In pts with newly diagnosed NPM1-mutant AML, treatment with IC was associated with higher cCR rates and favorable OS when compared with HMA+VEN in multivariable regression analysis. However, as residual confounding cannot be excluded given the significant differences in baseline patient and disease characteristics between the two groups, a randomized clinical trial is needed to definitively verify the potential superiority of IC vs HMA+VEN in pts with newly diagnosed NPM1-mutant AML.

Genomic Analyses Unveil the Pathogenesis and Inform on Therapeutic Targeting in KMT2A-PTD AML

A partial tandem duplication (PTD) in the KMT2A gene is detected in approximately 5-10% of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Previous studies revealed that HOX-genes are highly expressed in KMT2A-PTD AML similar to KMT2A-rearranged or NPM1-mutated AML. While the overexpression of HOX-genes is a convergent oncogenic pathway shared by these molecular subtypes of AML, the mechanism by which KMT2A-PTD induces high expression of the HOX-genes remains unclear and may be distinct from that mediated by balanced KMT2A-translocations, and NPM1 mutations. We stipulated that analysis of common molecular features of KMT2A-PTD will help identifying mechanistic intersections pointing towards possible targeted therapies. In a total of 5420 AML cases 1 including 793 cases from publicly available sources (Beat AML 2 and TCGA 3), we identified 254 cases of KMT2A-PTD. Somatic mutational screening and karyotype analysis showed co-occurrence with DNMT3A (31%), FLT3-ITD (32%), IDH1/2 (26%), RUNX1 (28%), TET2 (18%), SRSF2, STAG2, U2AF1 mutations and deletion 5q. Strong leukemic initiators such as KMT2A-rearrangement, CBFB-MYH11, PML-RARA, RUNX1-RUNX1T1, trisomy 8 and NPM1 mutations were mutually exclusive with KMT2A-PTD and did not rely on acquisition of additional mutations linked to secondary AML ontogenesis ( e.g., ASXL1, RUNX1, SRSF2, and STAG2) different from KMT2A-PTD. Next, we analyzed bulk mRNA-expression between mutually exclusive KMT2A-PTD, KMT2A-rearranged or NPM1-mutant high HOX-genes expressors. While several differentially expressed genes (DEG) between KMT2A-PTD and KMT2A-rearranged cases were detected, there were few DEG between KMT2A-PTD and NPM1-mutated cases. Compared to KMT2A-rearrenged cases, KMT2A-PTD had higher expression of CD34 and KIT in addition to some HOX-genes such as HOXB2 or NKX2-3. In contrast, expression of CD1D, CD14, and immune checkpoint genes including LILRB4, CD276, CD86, and SIGLEC7 was much higher in KMT2A-rearranged than KMT2A-PTD cases. These results prompted us to analyze the hematopoietic differentiation status. For this purpose, we defined three gene signatures along the HOX-targeted genes axis, termed as HOX-primitive, HOX-transient, and HOX-committed profiles. Differentiation analysis revealed almost all of KMT2A-PTD cases could be subclassified into HOX-transient stage while most of KMT2A-rearranged cases were HOX-committed. However, NPM1-mutated cases were interspersed in all the differentiation stages along the HOX-axis. We therefore assumed that there were a few DEG shared between KMT2A-PTD and NPM1-mutated cases as some NPM1-mutated AML clustered in the HOX-transient expression profile group. Intriguingly, DEG analysis was concordant with the hierarchical clustering based on the HOX-gens axis. Indeed, CD34 and KIT were highly expressed in the HOX-transient cases, and CD1D and CD14 in the HOX-committed cases, consistent with the enrichment of KMT2A-PTD and KMT2A-rearranged AML, respectively. We can conclude that the observed signatures were unique to the HOX-stages rather than the molecular abnormalities such as KMT2A-PTD and KMT2A-rearrangements. For example, CD34 upregulation was a feature shared transversally by all HOX-transient cases, including both KMT2A-rearranged and NPM1-mutated cases. As shown in Figure, KMT2A-rearranged, KMT2A-PTD, and NPM1-mutated cases were more clearly classified in HOX-profiles than molecular abnormalities. Additionally, among the cases which molecular subtypes were not clear, those with high HOX-genes expression revealed higher MEN1 expression. In conclusion, despite molecularly different, KMT2A-PTD, KMT2A-rearranged, and NPM1-mutated AML have similar expression patterns defined by each HOX differentiation stage. Like core binding factor AML such as RUNX1-RUNX1T1 and CBFB-MYH11, AML with higher expression of HOX-genes should be classified in the same group, HOX-AML. Given the results obtained with menin inhibitors in KMT2A-rearranged and NPM1-mutated AML, our findings open an opportunity for exploiting a therapeutic vulnerability in all HOX-AML including KMT2A-PTD AML or AML with high MEN1 expression. Since HOX-AML highly express genes according to the HOX differentiation profile, stage-specific surface proteins coded by these genes would be promising targets.

Biological and Therapeutic Implications of NPM1-Mutated AML Receiving Allogeneic Hematopoietic Cell Transplantation

Background: The nucleophosmin 1( NPM1) gene mutations are the most common gene alteration in acute myeloid leukemia (AML) patients, occurring in approximately 30%-35% of adult AML cases. However, molecular and response to therapy heterogeneity are existed in this distinct group. Response to therapy, differing patterns of co-mutation and the prognosis of NPM1-mutated AML patients receving allogeneic hematopoietic stem cell transplantation (allo-HSCT) treatment were unknown. Aims: To evaluate prognostic factors in the NPM1-mutated AML who underwent allo-HSCT treatment. Methods: A total of 115 consecutive NPM1-mutated AML patients who underwent allo-HSCT from 2016 to 2022 were enrolled in this study. The primary endpoint was the cumulative incidence of relapse (CIR). Results: The median patient age was 46 (IQR: 36-50) years. The most frequent co-mutations were FLT3-ITD(58.3%) and DNMT3A (40.0%), followed by IDH2(18.3%), NRAS (13.9%) and IDH1 (11.3%). The overall 3-year cumulative incidence of relapse (CIR) and leukemia-free survival (LFS) was 17.3% and 77.2%. The 3-year CIR of patients with FLT3-ITD was significantly higher than that without FLT3-ITD (24.3% vs. 7.0%; P=0.023). The 3-year CIR of patients with DTA mutations ( DNMT3A, TET2, and ASXL1) was significantly higher than that without DTA mutations (24.7% vs. 11.2%; P=0.030). Patients who received matched sibling donor (MSD) allo-HSCT had the highest CIR compared with unrelated donor (URD) allo-HSCT and haploidentical (HRD) allo-HSCT (46.2%, 10.0% and 11.2%, P=0.002). The 3-year CIR in patient with pre-HSCT measurable residual disease negative (MRD-), MRD+ and non-remission was 10.9%, 30.0% and 72.2%(P&amp;lt;0.001). After multivariable adjustment, DTA mutations, pre-MRD+ or non-remission, MSD allo-HSCT remained statistically significantly associated with higher CIR as well as lower LFS and OS. In univariate and multivariate analyses, the cell of origin of AML did not impact the outcomes of NPM1-mutated AML patients accept allo-HSCT treatment . Conclusion: The DTA mutations ( DNMT3A, TET2, and ASXL1) were identified a distinct group of patients with adverse prognosis in NPM1-mutated AML patients who received allo-HSCT. Our results indicate that NPM1-mutated patients accept HRD/URD donors can achieve lower CIR than MSD donors in transplantation. HRD allo-HSCT may suitable for high risk patients within this group.

Combined Single Cell Flow Cytometry and Imaging Analyses Reveal Immunomodulatory Effects Exerted By Targeted Phospho-SYK Inhibitors with Elevated Sensitivity in NPM1 Mutated AML

Acute myeloid leukemia (AML) is driven by genetic lesions that can result in addiction to signaling pathways that lead to aberrant proliferation and survival. Several new targeted drugs are being assessed for activity in AML with some recently approved for the treatment of subgroups of patients with specific genetic features, such as mutations in FLT3, IDH1 or IDH2. Entospletinib (ENTO) and lanraplenib (LANRA) are inhibitors of spleen tyrosine kinase (SYK); the latter is a next-generation SYK inhibitor and is currently being evaluated in combination with gilteritinib (GILT) in patients with relapsed or refractory FLT3-mutated AML (NCT05028751). Although SYK is rarely mutated, it has been found to cooperate with FLT3, and is highly active especially in AML patients with mutated FLT3. In addition, SYK is important for immune cell signaling through antibody constant region Fc and B cell receptors. To examine the multi-modulatory effect of pSYK inhibitors in AML, we used combined high parameter flow cytometry (HP-FC) and single cell miniaturized imaging (sc-MI) approaches to profile the immunologic, mutation, and functional protein pathway targets of ENTO and LANRA. Two different AML patient cohorts were assessed by ex vivo treatment with ENTO, LANRA and combinations of LANRA (trametinib, gilteritinib (GILT), aPD-1) over a range of time points (2h, 4h, 3d and 9d) and readouts for cellular phenotype (e.g., differentiation state, immune cell populations) and functional readouts (pSYK, viability) for each cohort were analyzed by HP-FC and sc-MI and associated with available mutation information (bulk gene and single cell RNA sequencing). Differential analyses of data from flow cytometry (AML-HP-FC Cohort) and single cell imaging (AML-sc-MI Cohort) demonstrated: 1) sensitivity to ENTO and LANRA (³ 1uM) was higher in NPM1 and FLT3 mutated AML samples, as measured via cell viability and pSYK target inhibition; sensitivity was not drastically altered in the presence of other mutations (e.g. IDH1/2, MLL); 2) lower doses of ENTO and LANRA (&amp;lt;1uM) induced proliferation in specific cell types, including progenitor myeloid cells, and T and B lymphocytes, but induced more T cell proliferation in AML samples that have low baseline proliferation; analysis with next generation bulk gene and single cell RNA sequencing suggested downregulation of STAT1expression, downregulation of MYC- and mTOR-dependent pathways, and upregulation of IL-1 pathway genes; and 3) LANRA was more broadly effective at targeting pSYK inhibition than ENTO; however, both were effective in combinations (ENTO with trametinib and GILT, and LANRA with aPD-1). In sum, analysis using collective flow and single cell imaging provides corroboratory and complementary information revealing new roles for ENTO and LANRA as immune modulating agents supporting B and T cell proliferation at lower dosages, and with demonstrated greater effect in individuals with NPM1 and FLT3 mutations. These support studies investigating the use of pSYK inhibitors in combination with other therapies to reduce tumor burden, and as an improved line of treatment for AML. Acknowledgements: We are appreciative of the patients and families for their time and participation.

Establishment of an NPM1 Mutation Copy Number Estimator for Xpert ® NPM1 Mutation Test

Objectives: The nucleophosmin ( NPM1)is the most mutated gene (~30%) in Acute Myeloid Leukemia (AML) 1. Three NPM1 mutations (type A, B, and D) represent ~84% in NPM1-mutated AML cases while other uncommon subtypes occupy ~16% 2. Xpert® NPM1 mutation, an automated cartridge-based test for measuring NPM1 mutation transcript levels (type A, B and D), is standardized to quantify the amount of mutated NPM1 relative to ABL1 control gene based on delta Ct in peripheral blood 3. Since mutated NPM1 level is crucial for risk assessment, medication selection, and ongoing therapeutic monitoring in AML 4,5, it is important to obtain the NPM1 mutation copy number (CN). The aim of this work is to develop NPM1 mutation CN estimator and to compare %NPM1 mutation/ABL1 reporting between delta Ct-based and CN-based methods. Methods: Five levels of NPM1 mutations (A, B, D) and ABL1 IVT-RNA panels as well as two lots of Xpert® NPM1 mutation tests were used to generate standard curves for CN and %CN reporting. The cell lysates from cell lines carrying either NPM1 mutation A, B, or D and AML clinical samples containing NPM1 mutations were examined to evaluate the CN and %CN between two lots of the Xpert® NPM1 mutation tests and to compare the delta Ct-based and CN-based methods for reporting %NPM1 mutation/ABL. Results: Linearity was demonstrated in Ct vs CN input for NPM1 mutation and ABL1 with R 2 above 0.96 for Lot1 and Lot2. Less than 3-fold difference was exhibited for CN and %CN across two lots of Xpert® NPM1 mutation test. Less than 3-fold difference was observed in %NPM1 mutation/ABL1 reporting between delta Ct-based and CN-based approaches. Conclusion: An NPM1 mutation copy number estimator for Xpert® NPM1 mutation test was established, which will provide diagnostic and prognostic values for NPM1-mutated AML patients.

Only FLT3-ITD Mutation Did Not Have a Deleterious Effect on Acute Myeloid Leukemia Patients with NPM1 Mutation, but Concomitant with DNMT3A Mutation or a＜3log Reduction of MRD2 Predicted Poor Survival

Background Co-occurring mutations were observed in NPM1-mutated acute myeloid leukemia (AML) frequently, and the measurable residual disease (MRD) for NPM1 is effective for the prognosis of NPM1-mutated AML. However, the combined effects of co-occurring gene mutation at the baseline and MRD on survival are unclear. We investigated the impact of gene mutation status and NPM1 MRD on predictive value of AML patients with NPM1 mutation. Methord A single-center, retrospective cohort study was carried out in patients diagnosed as AML with NPM1 mutation in Peking University Peoples'hospital. Patients were treated by an anthracycline and cytarabine-based or homoharringtonine and cytarabine-based induction chemotherapy regimen and followed by high dose cytarabine as consolidation therapy. Patients who had the indications of allogeneic hematopoietic stem cell transplantation (allo-HSCT) underwent allo-HSCT. A small part of patients with FLT3-ITD mutation received FLT3 inhibitor. Targeted next-generation sequencing (NGS) were analyzed at diagnosis, and quantitative NPM1 mutation (A, B, and D type) were detected at diagnosis and each end of chemotherapy cycle. As MRD for NPM1 rare type (NPM1 RT) was not available, MRD, relapse free survival (RFS) or overall survival (OS) analysis were conducted in patients received chemotherapy only (NGS chemo), excluding harboring NPM1 RT. Results A total of 234 patients, with NGS results, diagnosed as NPM1-mutated AML were included. 68.4% (160/234) patients including 17 patients with NPM1 RT received chemotherapy only, and NGS chemo patients were 143. After chemotherapy, 31.6% (74/234) patients underwent allo-HSCT. 1.7% (4/234) patients died of infection or hemorrhage during induction therapy. 15.8% (37/234) patients received FLT3 inhibitor，and 92.2% (212/230) patients achieved complete remission rate (CR) or incomplete hematologic recovery (CRi). During median follow-up time of 24.9 [interquartile range (IQR) 11.6-47.8] months, 40.6% (95/234) patients died. Median transcription of NPM1 at diagnosis was 31.13 (IQR 17.23-56.91)%, and would take a median time of 4.1 (IQR 2.6-5.6) months to converted to negativity.Reduction of MRD at the end of second cycle of consolidation (MRD2) ≥3log associated with higher RFS (3-year RFS rate 66.3% vs. 11.1%, p＜0.001) and OS (3-year OS rate 78.4% vs. 32.4%, p＜0.001) than reduction＜3log, and consistent negativity of MRD also predicted higher RFS (3-year RFS rate, 98.1% vs. 42.3%, p＜0.001) and OS (3-year OS rate, 100% vs. 67.7%, p＜0.001) than those whose MRD turned from negativity to positivity. 9 genes were mutated in＞10% in 234 patients, and DNMT3A and FLT3-ITD were the most prevalence (Figure 1). Univariate analysis showed FLT3-ITD, DNMT3A and reduction of MRD2＜3log were associated with poorer RFS and OS in 143 NGS chemo patients. But In multivariate analysis, only DNMT3A mutation [RFS, hazard ratio (HR)=1.9, p =0.023; OS, HR=2.1, p =0.032] and reduction of MRD2 ≥3log（RFS, HR=0.1; OS, HR =1.9, both p＜0.001）were independent prognostic factors for survival. Four subgroups were divided by different status of DNMT3A and FLT3-ITD, that were both FLT3-ITD and DNMT3A negative, FLT3-ITD positive and DNMT3A negative, FLT3-ITD negative and DNMT3A positive, and both FLT3-ITD and DNMT3A positive. The concurrence of FLT3-ITD and DNMT3A was associated with lowest RFS and OS (3-year RFS rate 29.2%, p＜0.001; 3-year OS rate 53.5%, p＜0.001). However, patients with only FLT3-ITD mutation did not contribute to poor survival compared with patients without FLT3-ITD mutation (3-year RFS rate 71.4% vs. 74.4%, p＜0.843; 3-year OS rate 74.5% vs.75.8%, p = 0.759). Three risk group were re-stratified by the gene mutation and gene reduction of MRD2 (Figure2), and the RFS and OS of the poor risk group, defined by patients with ＜3log reduction of MRD2, or with both FLT3-ITD and DNMT3A mutation, could be improved by allo-HSCT(3-year RFS rate, 56.4% vs. 29.2%, p = 0.015; 3-year OS rate, 72.0% vs. 31.6%, p = 0.001). Conclusion In AML patients with NPM1 mutation, the deleterious effect of FLT3-ITD could be pronounced in patients concomitant with DNMT3A mutation. A＜3log reduction of MRD2 was also another independent poor prognostic factor for survival, which could be improved by allo-HSCT. Meanwhile, the conversion of MRD for NPM1 from negative to positive might be a poor prognostic factor, but it requires to be validated by multivariate analysis.

Ubtf tandem Duplications Define a Novel Subtype of Acute Myeloid Leukemia Associated with Younger Age, WT1 Mutations and HOXA9 Marked Overexpression

Background Upstream Binding Transcription Factor ( UBTF) gene plays an important role in ribosomal RNA transcription. UBTF tandem duplications (TD) have been recently described as a recurrent genetic lesion in acute myeloid leukemia (AML). UBTF-TDs appear to be mutually exclusive with other class-defining lesions in AML and display a unique comutational signature. UBTF-mutated AML affects predominantly younger patients and is associated with trisomy 8, internal tandem duplication of FLT3 ( FLT3-ITD), mutations in WT1 and poor prognosis. Moreover, HOX and MEIS genes seem to be overexpressed in AML with UBTF-TD similarly to NPM1-mutated ( NPM1m) or KMT2A-rearragend ( KMT2Ar) AML, suggesting potential sensitivity to menin inhibitors. In this study we sought to characterize UBTF-TDs in our AML cohort. Methods We studied 456 adult patients (median age 54 years; range 18-70) diagnosed with de novo AML and included in AML-12 protocol from CETLAM group. All patients from the 2012-2017 period (n=403) were consecutively studied and we also selected 53 cases of WT1-mutated AML from the 2017-2020 period, given the strong association with UBTF-TD. Screening for UBTF-TD was performed on bone marrow (BM) or peripheral blood (PB) genomic DNA samples. Exon 13 of UBTF gene was amplified and analysed by Polymerase chain reaction (PCR) and subsequent fragment length analysis by capillary electrophoresis. Mutated samples were confirmed through Sanger sequencing. Further, RNA from 9 UBTF-TD cases was available and HOXA9 and MEIS1 gene expression analysis was performed by Real-Time Polymerase Chain Reaction (RT-qPCR). Clinical and biological data were obtained from CETLAM registry. Results UBTF-TD was found in 13 patients from our cohort whose characteristics are detailed in Table 1. UBTF-TDs range from 45 base pairs (bp) to 365 bp, being the 48 bp the most recurring size. As described, although small UBTF-TDs are in frame insertions, the largest ones are not multiple of 3. Notably, most UBTF-TDs presented small insertions and deletions among the duplication. Presence of UBTF-TD was associated with younger age (36 vs 55 years; p&amp;lt;0.001) and BM dysplastic changes (80% of U BTFMUT). UBTF-TD was particularly frequent (8.9% of all cases) in patients below 40 years, compared to other lesions as CEBPA mutations (1.1%). Eleven (85%) U BTFMUT patients presented intermediate cytogenetics, being trisomy 8 (5), normal karyotype (3) and 9q deletion (2) the most recurrent findings. Two cases of adverse karyotype with MECOM-rearrangements were found. As previously described, there was a strong association between UBTF-TD and of FLT3-ITD (38.5%). Other recurrent genetic lesions in AML like NPM1 and CEBPA mutations or core-binding factor (CBF) rearrangements were exclusive of UBTF wild type patients. Further, we found that UBTFMUT leukemias showed marked overexpression of HOXA9 compared with other AML subtypes (22.1-fold vs 5.0-fold; p&amp;lt;0.001; Fig. 1) and similar to NPM1m AML (22.3-fold). On the other hand, MEIS expression did not differ significantly among groups. Conclusions In our cohort of adult AML patients, UBTF-TDs are found in 1.8% of cases and are especially frequent in younger individuals in absence of other class-defining genetic lesions. The presence of UBTF-TD is strongly associated with cytomorphological dysplasia and co-occurrence of FLT3-ITD and WT1 mutations, while NPM1 and CEBPA mutations and CBF rearrangements appear to be mutually exclusive. HOXA9 upregulation could be a leukemogenic event in UBTF-TD AML, as described in NPM1-m and KMT2A-r AML, suggesting potential utility of menin inhibitors in this subset of patients. Screening for UBTF-TD is going to be incorporated in our molecular diagnostic panel for new AML cases.

Synergistic Growth Inhibition of NPM1 Mutant AML PDX By Combined Therapy with BCL-2 Inhibitor Venetoclax (ABT-199) and Menin Inhibitor DS-1594b In Vivo

Introduction: Mixed-lineage-leukemia (MLL) translocations are prevalent in hematologic malignancies, resulting in aggressive leukemias resistant to standard therapies and low 5-year survival rates. These translocations lead to the production of MLL fusion proteins that promote leukemia development by enhancing proliferation, inhibiting hematopoietic differentiation, and driving leukemogenesis. Acute myeloid leukemia (AML), an aggressive blood cancer with a grim prognosis, particularly in elderly patients, frequently involves mutations in the nucleophosmin (NPM1) gene. Importantly, the interaction between Menin, MLL, and MLL fusion proteins play a crucial role in the pathogenesis of AML, both with MLL rearrangements (MLLr) and in leukemias carrying NPM1 mutations. Inhibition of the Menin-MLL interaction using novel Menin inhibitors has demonstrated efficacy in pre-clinical and clinical studies for both AML subsets. In this study, we investigate the effectiveness of the novel Menin-MLL inhibitor DS-1594b, developed by Daiichi Sankyo Co. Ltd., in combination with the BCL-2 antagonist venetoclax (ABT-199), in a patient-derived xenograft (PDX) model of NPM1-mutated acute leukemia. We have previously reported synergistic lethality and differentiation-inducing effects of this drug combination in both AML cell lines and primary leukemia samples in vitro (Ciaurro et al., Blood 2022). Our findings shed light on the potential of this therapeutic combination for the targeted treatment of AML with NPM1 mutations. Methods: NSG mice (female, 8-10 weeks old) were purchased from Jackson Laboratory. Mice were inoculated via the tail vein with NPM1m PDX/luc/GFP (3×10 6 cells). Once leukemia engraftment was confirmed by bioluminescent imaging mice were randomized in 4 groups: vehicle, ABT199, DS-1594b alone, and combination. After 12 days drugs were administered as follows: DS1594b at a dosage of 50 mg/kg by oral gavage for 4 weeks; ABT-199 at a dosage of 50 mg/kg by oral gavage for 2 weeks and 100mg/kg for the other 2 weeks. NSG mice were euthanized by CO 2 inhalation at the endpoint of the study in accordance with IACUC protocols. BM and spleens were harvested in a sterile environment and flushed in HBSS with 1% FBS. For CyTOF data spleen cells were initially barcoded and stained with metal-conjugated antibodies according to Fluidigm's protocols and samples were analyzed by CyTOF (Helios) Mass Cytometer. Results: New in vitro data confirmed synergistic lethality on additional AML cell lines and demonstrated upregulation of PARP-C and Caspase3-C apoptosis pathways using western blot analysis. Further, additional 3 primary AML patient samples showed additive or synergistic growth inhibition when treated with combination of drugs. In the in vivo experiment with NPM1m PDX/luc/GFP AML PDX model, we found that co-treatment with DS-1594b and venetoclax for four weeks resulted in a greater reduction in AML burden compared to treatment with either agent alone or a vehicle control as shown by Bioluminescence imaging. Moreover, weight of mice in the combo group was not significantly affected, while mice lost weight in vehicle and in single agent cohort due to rapid disease progression. The survival curve clearly demonstrated the benefits of the combination treatment, with the DS-1594b group having modest anti-tumor efficacy, and the combination group showing the greatest efficacy (Fig. 1A). To study the effects on cell differentiation, we used CyTOF technique, which allowed us to analyze a complete panel of 30 markers. We found two populations of cells, which we named populations (pop) 3 and pop 4, that were enriched in the group treated with the combination of drugs compared to the control group (Fig 1B). These populations of cells had higher levels of expression of CD33 and CD38, which are well-known markers of cellular differentiation. Conclusions: In this study, we present the in vivo effectiveness of DS-1594b in combination with venetoclax in a PDX model of NPM1-mutated AML. Moreover, the combination treatment exhibits differentiation-inducing effects, which contribute to its therapeutic effectiveness, and was safe. Overall, our findings strongly indicate that the combination of DS-1594b and venetoclax exhibits promising anti-leukemic activity in vivo and holds potential as a therapeutic strategy for AML patients with mtNPM1 mutations.

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 ( NPM1mut) 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%. NPM1mut 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 NPM1mut myeloid neoplasms (MN) with &amp;lt;10% blasts and influence of co-occurring mutations in NPM1mut 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 &amp;lt;20% blasts: 1.2% [39/3,323]). Compared to pts with NPM1mut AML, pts with NPM1mut MN (MDS, CMML, aCML) with blast &amp;lt; 20% were older (median age 65 vs. 55 years, p &amp;lt; 0.001), had a lower median total WBC count (5 vs. 32 x10 9 /L, p &amp;lt; 0.001) and bone marrow (BM) blast percentage (8% vs. 76%, p &amp;lt; 0.001). No significant difference was observed between NPM1mut AML and MN with &amp;lt;20% blasts in median hemoglobin (9.1 vs. 9 x10 9, p: 0.44), platelets (62 vs. 66 x10 9 /L, p: 0.55), or NPM1mut 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; &amp;lt;10%) NPM1mut 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 NPM1mut MN pts with &amp;lt;10 vs. ≥10% blasts (median LFS: 0.55 vs. 0.91 years, p=0.27). In pts with NPM1mut 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 &amp;lt; 0.001), had higher BM blasts (80% vs. 72% p=0.019), and lower platelets (45 vs. 77 x10 9/L p &amp;lt; 0.001) compared to pts with NPM1mut AML without MR mut. No significant difference in NPM1mut 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 NPM1mut AML (95% CI: 4.2-9.7). Inferior OS was observed in ELN favorable risk NPM1mut pts with vs. without MR mut, respectively (2 vs. 8.4 years, p=0.0001). When stratified by age &amp;lt; 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 NPM1mut compared to younger pts (median 1.7 years vs. NR, p &amp;lt; 0.001). Patients with NPM1mut /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 NPM1mutAML adjusted for MR mut, BM blast percentage, age, performance status, baseline WBC, hemoglobin, platelet count, NPM1mut 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 &amp;lt; 60 (HR 0.43 [95% CI: 0.32-0.56], p &amp;lt; 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 NPM1mut MN have outcomes similar to pts with NPM1mut AML, supporting NPM1mut as an AML defining event irrespective of BM blast enumeration. In patients with ELN favorable risk NPM1mut 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.

The Genomic Landscape and Its Clinical Implication in NPM1-Mutated AML Patients: A Study within the AMLSG 09-09 Clinical Trial

Background: Mutations in the Nucleophosmin 1 gene ( NPM1 mut ) represent one of the most common genetic lesions in acute myeloid leukemia (AML).Based on its characteristic clinico-pathologic features, NPM1 mutAML has been recognized as a distinct entity among the category “AML with recurrent genetic abnormalities”. According to the ELN 2022 genetic risk-stratification, NPM1 mut AML, in the absence of FLT3-ITD mutation, is associated with a favorable prognosis. However, a significant proportion of these patients (pts) relapse after intensive therapy suggesting that other co-mutations may have an impact on outcome. Aims: To comprehensively characterize the genomic landscape and leukemogenic trajectoriesin a large cohort of NPM1 mut AML pts and to investigate its prognostic and predictive impact on outcome. Methods: Targeted DNA sequencing (mean read depth: 1817) on the entire coding region of 263 genes was performed in 568 NPM1 mut AML pts (median age: 58.7 years; 18-60 years, n=317; &amp;gt;60 years, n=251). All pts were enrolled in the randomized open-label Phase 3 AMLSG 09-09 trial [NCT00893399; Döhner H et al. Lancet Haematol 2023]. In this trial, pts were assigned to intensive chemotherapy plus all- trans retinoic acid with or without gemtuzumab ozogamicin; none of the pts received midostaurin. Results: In total n=3,058 variants (variant allele frequency of ≥1%) were identified in 195/263 genes. The median number of co-mutations was 3 (range 0-11). The most common co-mutated genes were DNMT3A (49.5%), FLT3-TKD (42.8%) PTPN11 (24.8%), NRAS (22.7%) TET2 (21.7%), IDH2 (21.3%), IDH1 (18%), and FLT3-ITD (17.3%). DNMT3AR882 hotspot mutations occurred more frequently in younger pts (36.6% vs 17.1%), while there was no difference for DNMT3AnonR882 mutations between the two age groups (21.8% and 21.9%). An age-dependent difference was also identified for mutations in myelodysplasia-related genes ( ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, and ZRSR2) as defined by the ICC, occurring with a higher incidence in older pts (30.3% vs 12.3% in younger pts). Analyzing the mutational pattern of co-mutations, we found statistically significant tertiary gene-gene interactions: e.g., NPM1- NFE2- STAG2 (p&amp;lt;.001), NPM1- IDH2- SRSF2 (p&amp;lt;.001), NPM1- CEBPA- TET2 (p&amp;lt;.001), NPM1- DNMT3AR882- NRAS (p=.002), and NPM1- ASXL1- SRSF2 (p=.004); mutual exclusivities were identified for NPM1- DNMT3AR882- DNMT3AnonR882 (p&amp;lt;.001), NPM1- IDH2- TET2 (p&amp;lt;.001), NPM1- DNMT3AR882- SRSF2 (p&amp;lt;.001), NPM1- IDH1- TET2 (p&amp;lt;.001), and NPM1- FLT3-ITD- KRAS (p&amp;lt;.002). Correlating co-mutation data with outcome, we found that DNMT3AR882 hotspot mutations confer inferior event-free (EFS) and overall survival (OS) only in younger pts (EFS, p&amp;lt;.001 vs p=.11, Figure 1a; OS, p=.003 vs p=.8), whereas DNMT3AnonR882 mutations did not impact prognosis within the two age groups. We also found a negative prognostic impact of IDH1 mutations which was restricted to younger pts (EFS, p=.05), whereas IDH2 mutations were associated with superior EFS in older pts (p=.04) and superior OS in both groups (p=.05 and p=.03). Of note, co-mutations occurring in one or more of the myelodysplasia-related genes did not impact EFS or OS (Figure 1b). In multivariable analysis (all pts) including age, WBC, LDH, allogeneic transplantation in CR1, and mutations with an incidence of at least 3% as covariables, age (HR,1.03; p&amp;lt;.001), DNMT3AR882 (HR, 1.86; p&amp;lt;.001), FLT3-ITD (HR, 1.54; p=.012), IDH1 (HR, 1.48; p=.009), MYC (HR, 1.83; p=.032), and WT1 (HR, 1.73; p=.012), were associated with an inferior EFS, while SMC3 mutation showed favorable EFS (HR, 0.44; p=.019). To further study the leukemogenic trajectories, we used an oncogenetic tree modeling algorithm, which yielded a tree with several main branches including DNMT3AR882, DNMT3AnonR882, FLT3-TKD , IDH1, IDH2, PTPN11, and TET2. These mutations might represent initiating events which predispose to additional events with further distinct branches. Conclusions: Our study provides comprehensive data on the genomic landscape and its clinical impact in pts with NPM1mut AML fit for intensive chemotherapy. The co-mutational pattern clearly differs between younger and older NPM1 mutAML pts. Using this large dataset allowed the identification of secondary and tertiary gene-gene interactions with significant impact on outcome. Further data analysis is ongoing and will be presented at the meeting.

NPM1-Mutated Myeloid Neoplasms: Updated Outcomes with High-Intensive Chemotherapy Regardless of the Blast Percentage

Background: The most recent World Health Organization (WHO) classification has stablished NPM1-mutated myeloid neoplasms (MNs) to be acute myeloid leukemia (AML) regardless of bone marrow (BM) blast percentage. In contrast, the new International Consensus Classification (ICC) considers NPM1-mutant MNs as AML only in the presence of ≥10% BM blasts. Previous studies from our group and others have reported favorable outcomes of NPM1-mutant MNs with &amp;lt;20% blasts when treated with intensive chemotherapy. Here we seek to further evaluate clinical outcomes of this group of pts. Methods: We retrospectively re-evaluated the patient's characteristics, disease features and outcomes in patients with NPM1-mutated oligoblastic AML (&amp;lt;20% blasts) (oligo-AML). In addition, we also evaluated the clinicopathological characteristics in a cohort of patients with secondary NPM1-mutated AML (sAML), the majority of which had received treatment before progressing to AML. The Kaplan-Meier method was used to estimate the overall survival (OS), event-free survival (EFS) and relapse-free survival (RFS). Results: We identified 54 patients with NPM1-mutated oligo-AML. Median age was 62 years (range, 19-87) and most of them were female (59%). Median bone marrow (BM) blasts was 10%. Most patients could have been classified as CMML-2 (7/54, 13%), MDS-EB1 (7/54, 13%) and MDS-EB2 (24/54, 44%), based on the 2016 WHO classification. Median NPM1 variant allele frequency (VAF) was 0.38 (range, 0.05-0.52) and 38 patients (70%) had normal karyotype. These patients harbored a median of 1 co-mutation (range, 0-5), predominantly DNA methylation pathway, such as DNMT3A (31%) or TET2 (23.5%), or RAS pathway, mainly NRAS (25.5%), but rarely exhibited mutations in other functional pathways (Figure 1). Twenty-three patients (43%) progressed to AML with &amp;gt;20% BM blasts within a median of 10.7 months. Of 54 patients, 46 patients (82%) received chemotherapy-based regimens [61% low-intensity chemotherapy (LI-Chemo) based on hypomethylating agents or low-dose cytarabine and 21% high-intensity chemotherapy (HI-Chemo)] and 21 patients (39%) received a stem cell transplant (SCT). With a median follow up of 67.6 months (LI-Chemo of 48.3 months; HI-Chemo of 71.4 months), the median OS, EFS and RFS was 30.4 months, 30.4 months and 14.7 months for the LI-Chemo group, respectively, but median OS, EFS and RFS were not reached (NR) for HI-Chemo group. However, when compared by age, patients with &amp;lt;60 years had trends to have better OS with LI-Chemo or HI-Chemo than patients aged ≥60 years (Figure 2). In addition, 5 patients received chemotherapy-based regimens with venetoclax, however improved OS was only seen when combined with HI-Chemo and SCT (n=2, with a median OS NR without deaths, likely related to younger people). In parallel, we identified 31 patients with NPM1-mutated sAML progressed from oligo-AML. Median age was 67 years (range, 31-83) and female were 58%. Median BM blasts was 40%. Median NPM1 VAF was 0.38 (range, 0.02-0.56). Most patients did not exhibit clonal cytogenetic evolution and remained with a diploid karyotype (65%). Seventy-four percent of patients (17 out of 23 tested) had known prior NPM1-mutated oligo-AML, and in 6 patients NPM1 mutation was acquired at progression. Median number of co-mutations were 3 (range, 0-7). DNTM3A (65%) or TET2 (33.3%) mainly co-occurred with RAS pathway mutations, and in particular FLT3-ITD (26.7%) or FLT3-TKD (13.3%) (Figure 1). Eleven of 31 patients (36%) received LI-Chemo regimens, whereas 15 of 31 patients (48%) had HI-Chemo regimens. Nine patients (29%) underwent SCT. With a median follow up of 39.6 months (LI-Chemo of 55.5 months; HI-Chemo of 39.4 months), the median OS, EFS and RFS was 11.4 months, 12.4 months and NR for LI-Chemo, respectively; and 13.2 months, 6.5 months and NR for HI-Chemo, respectively. No significant differences were seen depending on the number of therapies received for previous oligo-AML. Previously untreated patients who received a venetoclax-based regimen with SCT had prolonged survival (n=4, median OS NR, with median follow up of 41 months). Conclusions: NPM1-mutated acute myeloid leukemia can be treated as such irrespective of blasts burden. For these cases, especially young patients, should be treated with intensive chemotherapy and subsequent allogeneic stem cell transplant as a clear curative approach.

Molecular Relapse after First-Line Intensive Therapy in Patients with Core-Binding Factor and NPM1-Mutated Acute Myeloid Leukemia - a Filo Study

Background: Patients with Core-Binding Factor (CBF) and NPM1-mutated acute myeloid leukemia (AML) are considered as favorable or intermediate-risk according to the European LeukemiaNet (ELN) 2022 classification and allogeneic hematopoietic cell transplantation (HCT) is usually not considered in those achieving first complete remission (CR) with good molecular response. Close molecular monitoring by quantitative PCR has been widely implemented over time and approximately 30% of patients will experience molecular relapse. However, there is no recommendation on how to manage these patients due to the lack of data from large patient series or clinical trials. In this study, we retrospectively analyzed the outcome of CBF or NPM1-mutated AML patients who had MRD monitoring after having achieved first CR. Methods: All CBF and NPM1-mutated AML patients, aged 18-60 years, who had MRD molecular monitoring (RT-qPCR of RUNX1-RUNXT1 or CBFB-MYH1 transcripts or classical NPM1 mutations) after first-line therapy including induction therapy with daunorubicin/idarubicin and cytarabine followed by intermediate or high-dose cytarabine consolidation, without allogeneic HCT in first CR, were included. MRD measurements were generally performed every three months during follow-up for 24 months in either bone marrow (BM) or peripheral blood (PB). Molecular relapse was defined according to ELN recommendations (Heuser M, Blood 2021) as a conversion from MRD negativity to positivity or an increase in MRD copy numbers &amp;gt;1 log between two positive samples. Results: Between 2010 and 2019, 303 patients from 9 centers with newly diagnosed CBF or NPM1-mutated AML ( RUNX1-RUNX1T1, 19%; CBFB-MYH11, 27%; NPM1, 53%) and available MRD monitoring after first-line therapy were included. Among these patients, 153 (51%) never relapsed, 95 (31%) had molecular relapse, with a median of 326 days (interquartile range [IQR]: 276-438) from initial diagnosis, and 55 (18%) had upfront morphologic relapse (i.e., without prior molecular relapse detected), with a median of 388 days (IQR: 280-559). Patients with molecular and upfront morphologic relapse had higher white blood cell (WBC) count at diagnosis (12 vs. 22 vs. 30 G/l in those without relapse, molecular relapse, and morphological relapse, respectively, P=0.003) and were more likely to have a FLT3-ITD mutation (7% vs. 25% vs. 19%, respectively, P=0.001). In addition, patients with upfront morphologic relapse had a lower log-reduction of MRD during first-line treatment (4.90 vs. 4.93 vs. 3.77, respectively, P=0.009) and were more likely to have CR with positive MRD at the end of treatment in peripheral blood (2% vs. 16% vs. 32%, respectively, P&amp;lt;0.001). Overall survival (OS) was significantly different according to whether patients never relapsed, had molecular relapse, or had upfront morphological relapse (three-year OS of 100% vs. 75% vs. 60%, P&amp;lt;0.001; Figure A). Among the 95 patients with molecular relapse, 53 (56%) received preemptive therapy (median of 48 days [IQR:24-68] from molecular relapse to treatment initiation) and 42 (44%) progressed to morphologic relapse before treatment was initiated (median of 58 days [IQR:36-134] from molecular to morphologic relapse). Patients who received preemptive therapy had a better OS than those who received salvage therapy after having progressed from molecular to morphologic relapse, and those who had upfront morphologic relapse (78% vs. 51% vs. 51% at three years, respectively, P=0.01; Figure B). Preemptive therapy included upfront allogeneic HCT (n=19), intensive chemotherapy (n=21), and non-intensive therapy (n=13) with different OS rates that did not reach statistical significance (92% vs. 79% vs. 58% at three years for upfront allogeneic HCT, intensive chemotherapy, and less intensive therapy, respectively, P=0.09). Conclusion: Up to 30% of patients with CBF or NPM1-mutated AML experienced molecular relapse in our cohort and more than 50% of them received preemptive therapy. Patients treated preemptively at molecular relapse had a better OS than those treated with active disease. Although these results need to be confirmed in larger studies, it supports molecular monitoring during follow-up to start preemptive therapy before overt morphologic relapse. Other techniques for MRD monitoring are urgently needed for AML patients who cannot be monitored by qPCR.

APL-like Subset within NPM1-Mutated Acute Myeloid Leukemia: A Distinct Phenotypic Signature Correlating with Early-Onset Vascular Complications

Background: NPM1 mutations represent the most common genetic alteration in adult acute myeloid leukemia (AML), often in co-occurrence with FLT3-ITD and mutations in genes influencing DNA methylation ( DNMT3A, IDH1, IDH2 and TET2). Whether these genetic alterations correlate with distinct immunophenotypic and clinical features is still a matter of debate. There is growing evidence of distinct immunophenotypic subsets driven by co-occurring genetic mutations in NPM1-mutated AML, potentially accounting for the heterogeneity of clinical presentations and outcome. Mason et alhave described a subtype of NPM1-mutated AML, displaying an immunophenotypic profile resembling that of acute promyelocytic leukemia, specifically, the negativity for both CD34 and HLA-DR, and as such defined APL-like. Aims: We studied the characteristics of a series of patients with APL-like NPM1-mutated AML, focusing on the incidence of vascular events at disease onset, and investigated the impact of some markers (blood counts, coagulation parameters and LDH) reported to correlate with coagulopathy in APL. Methods: The study cohort included patients diagnosed with NPM1-mutated AML at our Centre according to conventional morphological, immunophenotypic, cytogenetic and molecular criteria. Vascular events were defined according to the revised World Health Organization (WHO) bleeding scale and to the CTCAE grading of thromboembolic events. Results: From April 2007 to May 2023, 139 patients with a diagnosis of NPM1-mutated AML were enrolled, of whom 31 (22.3%) featured by APL-like phenotype. Their characteristics are detailed in Table 1. APL-like patients were older (64 y) compared to non-APL-like (57 y, P=0.002) NPM1-mutated patients; no further difference emerged for baseline blood count parameters. Vascular complications (n=22 bleeding events and n=2 thrombotic events) were significantly more frequent in the APL-like (n=10, 34.5%) than non-APL-like (n=16, 13.6%, P=0.015) group. There was a trend for more severe (G3-G4) vascular events in APL-like (3/31, 9.7%) vs non-APL-like (3/108, 2.8%, P=0.12). Also, abnormal coagulopathy-related parameters, including INR ≥1.5 and/or fibrinogen below normal level) were more frequent in APL-like patients (27.6% versus 15.7%,). D-dimer levels resulted significantly higher in APL-like patients (median 5998 ng/ml versus 2287 ng/ml, P=.005). The D-dimer/fibrinogen ratio (DD/FBG) showed significantly higher level in APL-like (median 16.84) vs non-APL-like (4.4, P=.017) patients. Of note, in multivariate analysis, APL-like phenotype maintained a value (OR=2.67, P=0.007) on DD levels from WBC count (OR=2.37, P=0.017), thus suggesting an effect independent from leukocytosis. Also, APL-like subset maintained an age-independent impact (OR=2.77, P=0.041) on the rate of vascular events. Among the 85 patients with full molecular information, there was a significant enrichment IDH1 (36.8%, P=0.002) and IDH2 (47.6%, P=.001) mutations in APL-like vs non-APL-like (6.1% and 8.6%, respectively) patients. No difference in the incidence of TET2 mutations was observed (18.8% and 25% in APL-like and non-APL-like, respectively, P=0.744). As regards outcome, complete remission rate was 85.7% and 78.9% in APL- and non-APL-like (P=0.43). We did not observe any significant difference between APL- and non-APL-like patients in disease-free (13.2 vs 22.0 months; P=0.83) or overall (15.9 vs 15.1 months, respectively; P=0.38) survival. Conclusions: Our findings suggest APL-like signature to be a potential predictor of susceptibility to vascular events within NPM1-mutated AML. Our results deserve validation in a larger patient set and might indicate the utility of an intensive monitoring and supportive care to prevent early vascular, especially hemorrhagic, events in this patient category.

Chronic Mitochondrial Dysfunction Renders Acute Myeloid Leukemia Resistant to Multipronged Inhibition of Mitochondrial Metabolism

Acute Myeloid Leukemia (AML) is a genetically diverse and aggressive myeloid neoplasm that awaits novel therapeutics to improve patient survival. Targeting AML metabolic aberrations as a genotype-agnostic strategy has shown promise, evidenced by the clinical success of venetoclax and the rapid pre-clinical development of other mitochondrial (mt) metabolism targeted therapies. However, the mechanism of how AML develops resistance to drugs targeting key mt metabolic pathways is not fully understood. We previously identified sirtuin 5 (SIRT5), a deacylase that regulates several pathways of mt metabolism in AML including oxidative phosphorylation and glutamine metabolism. In AML, it functions as a master metabolic regulator that is necessary for leukemic stem cell survival. Genetic or pharmacological inhibition of SIRT5 leads to rapid AML cell apoptosis in vitro and disease regression in multiple AML mouse models. However, a subset of AML cell lines and primary samples can survive SIRT5 inhibition, indicating an unusual intrinsic resistance to mt dysfunction. To provide a mechanistic explanation, we first compared the molecular features between SIRT5-dependent and independent cases. Among the 25 primary AML samples we tested, NPM1c mutation, but not FLT3-ITD, TP53, WT1, NRAS, or IDH1 mutations, is significantly enriched in SIRT5-independent samples. Accordingly, among the panel of 22 AML cell lines we tested, the only NPM1 mutant cell line (OCI-AML3) sits at the most SIRT5-independent extreme of the spectrum. NPM1 mutant AML cells have increased cytoplasmic mitochondrial DNA (mtDNA) and fragmented mt morphology, indicating chronic mt damage (Wu H et al. Cancer Discovery. 2021). Because SIRT5 exerts its metabolic maintenance functions within the mt, we hypothesize that AML cells that can adapt to chronic, sublethal mt dysfunction will be capable of proliferation without SIRT5. To test this, we took three orthogonal approaches: (1) introducing NPM1c mutation, (2) using low concentrations of ethidium bromide (EtBr) to selectively block mtDNA replication, or (3) genetically inducing chronic mt dysfunction by silencing the essential mt transcription factor TFAM in 3 AML cell lines that are heavily dependent on SIRT5 - OCI-AML2, CMK, and SKM-1. SIRT5-dependent cells expressing ectopic NPM1c exhibit mt dysfunction as evidenced by decreased oxygen consumption rate (OCR) measured using the Seahorse metabolic flux assay. Also, the lethal effect of SIRT5 depletion is rescued in these cells. Pharmacologically blocking NPM1c nuclear export with selinexor in the typically SIRT5-independent OCI-AML3 cells sensitizes them to the lethal effect of SIRT5 depletion. After culturing in 100 ng/mL EtBr for 3, 5, or 11 days, cells had significantly decreased mt abundance as measured by mtDNA content relative to nuclear DNA and had significantly decreased OCR and extracellular acidification rate (ECAR). SIRT5-dependent cells cultured in EtBr survived shRNA-induced SIRT5 depletion, in contrast to the rapid lethality of cells not cultured in EtBr. Additionally, cells initially cultured in EtBr and allowed to recover in the absence of EtBr assume their original phenotype of SIRT5 dependence. However, inhibiting specific subunits of the mt using potent complex I and III inhibitors (rotenone and antimycin A) shows no effect on SIRT5 dependence. Together these data suggest that mt damage, rather than loss of function in one pathway, is needed to convert SIRT5-dependent cells to SIRT5 independence. TFAM, a nuclearly coded transcription factor for mtDNA, is necessary for the replication and transcription of mt genes. We used cas13d-mediated knockdown of TFAM to deplete mtDNA and induce mt dysfunction. Experiments that investigate how this method of inducing mt dysfunction affects OCR, ECAR, and SIRT5-dependent cell line proliferation are currently underway and will be presented at the ASH conference. In summary, we present a mechanism of how NPM1 mutation-associated or experimentally induced chronic sublethal mt dysfunction renders AML resistant to therapies targeting vital mt metabolic pathways, such as SIRT5 inhibitors, demonstrating AML's metabolic flexibility. Experiments are scheduled to validate these findings in primary samples and additional metabolomic and transcriptional studies will be done to deduce the mechanism for SIRT5 dependence in AML.

Secondary-Type Mutations Do Not Impact the Favorable Outcome of NPM1-Mutated Acute Myeloid Leukemia Patients - Results from a Large Cohort of Intensively Treated Patients

Introduction: In 2022, the ELN risk classification for AML was updated for the second time. One of the major novelties of the ELN2022 is that all secondary-type mutations (STMs, i.e., mutations in the genes SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, and STAG2) were now added to the adverse risk characteristics. However, a pertinent question also raised by the ELN expert panel is whether STMs abrogate the positive prognostic value of co-occurring, favorable NPM1 mutations. Aim: The aim of this study was to analyze the prognostic value of STMs in AML patients (pts) who also harbor an NPM1 mutation. Methods: We investigated a pooled cohort of 936 NPM1-mutated AML pts who were treated in previously reported multicenter trials of the Study Alliance Leukemia or the AML Cooperative Group. Eligibility was determined based on diagnosis of non-APL, age ≥ 18 years, NPM1 mutation detected in targeted sequencing, curative treatment intent, and available biomaterial at diagnosis. Standard techniques for chromosome banding and fluorescence-in-situ-hybridization (FISH) were used for karyotyping. Next-generation panel sequencing was performed to detect genetic alterations that are recurrently found in myeloid neoplasms. Results: In our multicenter cohort of 936 NPM1-mutated AML pts, median follow-up for the entire cohort was 8.0 years. We found 125 patients (13.4%) harboring at least one STM ( SRSF2 [n=48; 5.1%], STAG2 [n=32; 3.2%], EZH2 [n=22, 2.4%], BCOR [n=16; 1.7%], SF3B1 [n=13; 1.4%], ASXL1 [n=12; 1.3%], ZRSR2 [n=5; 0.5%], and U2AF1 [n=4; 0,4%]). A comparison of pretreatment clinical and genetic features revealed that pts with a STM were significantly older ( p=.003, median 59 vs. 55 years), had lower white blood cell counts ( p&amp;lt;.001, 22.2*10 9/L vs. 39.7*10 9/L,) and platelet counts ( p&amp;lt;.001, 46.5*10 9/L vs. 65.0 10 9/L). The strongest pair-wise associations between gene mutations were observed between U2AF1 and RUNX1 ( p&amp;lt;.001) as well as SRSF2 and IDH2 ( p&amp;lt;.001). With respect to outcome, complete remission (CR) rate did not differ significantly between NPM1-mutated patients with or without additional STMs ( p=.41, 74.4% vs. 77.7%, OR 0.83 [95%-CI 0.54-1.29]). Median RFS for NPM1-mutated pts with STMs was 32.9 months (95%-CI: 13.0-46.0) while patients without STMs had a median RFS of 24.3 months (95%-CI: 18.7-33.3) corresponding to a HR of 1.04 ( p=0.80, 95%-CI 0.79-1.37; Figure A). Median OS for NPM1-mutated pts with or without STMs was 27.2 months (95%-CI: 14.2-49.0) and 29.1 months (95%-CI: 23.5-41.4), respectively, corresponding to a HR of 1.11 ( p=.37, 95%-CI 0.88-1.41; Figure B). To focus solely on the impact of STMs, we subsequently excluded patients with co-occurring mutations in TP53 or myelodysplasia-related cytogenetics, which all define an ELN adverse risk. Again, we observed no differences in CR rate ( p=.54, 78% vs. 75.4%), RFS ( p=.59, median 33.2 months vs. 26.6 months), or OS ( p=.33, median 27.4 month vs. 32.6 month) between NPM1-mutated patients with or without STMs. Next, we restricted our analysis to pts who are classified favorable risk according to ELN2022. Again, we found no significant outcome differences based on the STM status (unmutated vs. mutated: CR rate, 80% vs. 70.7% [ p=.072]; RFS, median 49.7 months vs. 46.0 months [ p=.702]; OS, median 45.3 months vs. 59.8 months [ p=.092]). Conclusion: NPM1 mutations rank as the second most frequent mutations in AMLand the most common in patients with a normal karyotype and serve as an established favorable prognostic marker. Our data from a large cohort demonstrate that additional STMs have no adverse effect on the clinical outcome of NPM1-mutated patients. As a result, these patients should still be considered ELN favorable risk.

Effect of clonal hematopoiesis in remission on hematopoiesis recovery in patients with NPM1 mutated acute myeloid leukemia after chemotherapy

Objective: To investigate the effect of clonal hematopoiesis (CH) in remission on hematopoiesis recovery in patients with NPM1 mutated acute myeloid leukemia (AML) after chemotherapy. Methods: Retrospective analysis was performed on 86 patients with NPM1(mut) AML newly diagnosed and treated in the First Affiliated Hospital of Soochow University between July 2016 and June 2019. Their clinical data and NGS test results at diagnosis were analyzed. Moreover, bone marrow samples in remission were tested using Sanger sequencing. The log-rank test was used to analyze the difference in hematopoietic recovery, and Cox proportional hazard models were used to analyze the prognostic factors affecting hematopoietic recovery. Results: The median age of the 86 NPM1(mut) AML patients was 50 years (15-69 years). There were 39 males and 47 females. Forty-one patients were induced with intensity chemotherapy ("7 + 3"), whereas 45 patients were treated with low-dose cytarabine-based induction chemotherapy. At diagnosis, The most common mutations in the patients were FLT3, DNMT3A, TET2, and IDH1/IDH2 mutations. CH-associated mutations persisted in 21 patients during remission, and the mutations were DNMT3A, TET2, ASXL1, and IDH1/IDH2. The recovery time of neutrophils in patients with CH-associated mutations in remission was consistent with that in patients without CH in remission (P=0.282) but the recovery time of platelets in patients with CH in remission was significantly longer[26 (95% CI 21-32) days vs 25 (95% CI 23-26) days, P=0.032]. Furthermore, univariate analysis indicated that age, induced chemotherapy program, and CH in remission were risk factors for platelet recovery, whereas multivariate analysis indicated that induced chemotherapy program and CH in remission were independent risk factors for platelet recovery (HR=0.454, P=0.001 and HR=0.520, P=0.027, respectively) . Conclusion: CH in remission delays the hematopoietic recovery of patients with NPM1(mut) AML after chemotherapy.

The effect of small molecule inhibitor NSC348884 on nucleophosmin 1-mutated acute myeloid leukemia cells.

Nucleophosmin 1 (NPM1) is a common shuttling protein. Mutation in the NPM1 gene is the most frequent gene alteration in acute myeloid leukemia (AML). This study aims to explore the inhibitory effects of small molecule NSC348884 on wild-type and NPM1-mutated AML cells. Immunofluorescence was used to determine the intracellular localization of NPM1 protein in wild-type (OCI-AML2) and NPM1-mutated (OCI-AML3) AML cell lines. The oligomerization state of NPM1 was assessed by Western blot analysis, and the inhibitory effect of NSC348884 on the proliferation of AML cells was evaluated by Cell-counting kit-8 (CCK-8). Flow cytometry was used to detect the proapoptotic effect of NSC348884 on AML cells. Western blot results showed a significant reduction in the levels of the oligomeric NPM1 protein after the treatment with NSC348884. NSC348884 had an inhibitory effect on the proliferation of both wild-type and NPM1-mutant AML cells. The inhibitory effect on OCI-AML3 cells was stronger, compared to OCI-AML2 cells. Flow cytometry showed that NSC348884 could significantly induce AML cell apoptosis and had a stronger proapoptotic effect on OCI-AML3 cells. NSC348884 had inhibitory and proapoptotic effects on both wild-type and NPM1-mutated AML cells. The effect of NSC348884 on AML cells, carrying NPM1 mutation was significantly stronger.

Randomized phase-III study of low-dose cytarabine and etoposide + /− all-trans retinoic acid in older unfit patients with NPM1-mutated acute myeloid leukemia

The aim of this randomized clinical trial was to evaluate the impact of all-trans retinoic acid (ATRA) in combination with non-intensive chemotherapy in older unfit patients (> 60 years) with newly diagnosed NPM1-mutated acute myeloid leukemia. Patients were randomized (1:1) to low-dose chemotherapy with or without open-label ATRA 45 mg/m2, days 8–28; the dose of ATRA was reduced to 45 mg/m2, days 8–10 and 15 mg/m2, days 11–28 after 75 patients due to toxicity. Up to 6 cycles of cytarabine 20 mg/day s.c., bid, days 1–7 and etoposide 100 mg/day, p.o. or i.v., days 1–3 with (ATRA) or without ATRA (CONTROL) were intended. The primary endpoint was overall survival (OS). Between May 2011 and September 2016, 144 patients (median age, 77 years; range, 64–92 years) were randomized (72, CONTROL; 72, ATRA). Baseline characteristics were balanced between the two study arms. The median number of treatment cycles was 2 in ATRA and 2.5 in CONTROL. OS was significantly shorter in the ATRA compared to the CONTROL arm (p = 0.023; median OS: 5 months versus 9.2 months, 2-years OS rate: 7% versus 10%, respectively). Rates of CR/CRi were not different between treatment arms; infections were more common in ATRA beyond treatment cycle one. The addition of ATRA to low-dose cytarabine plus etoposide in an older, unfit patient population was not beneficial, but rather led to an inferior outcome.The clinical trial is registered at clinicaltrialsregister.eu (EudraCT Number: 2010-023409-37, first posted 14/12/2010).

Secondary-type mutations do not impact outcome in NPM1-mutated acute myeloid leukemia – implications for the European LeukemiaNet risk classification

Secondary-type mutations do not impact outcome in NPM1-mutated acute myeloid leukemia – implications for the European LeukemiaNet risk classification