Driver Mutations In Acute Myeloid Leukemia Research Articles

Common Driver Mutations in AML: Biological Impact, Clinical Considerations, and Treatment Strategies.

Next-generation sequencing of samples from patients with acute myeloid leukemia (AML) has revealed several driver gene mutations in adult AML. However, unlike other cancers, AML is defined by relatively few mutations per patient, with a median of 4-5 depending on subtype. In this review, we will discuss the most common driver genes found in patients with AML and focus on the most clinically relevant ones that impact treatment strategies. The most common driver gene mutations in AML occur in NPM1 and FLT3, accounting for ~30% each. There are now targeted therapies being tested or already approved for these driver genes. Menin inhibitors, a novel targeted therapy that blocks the function of the menin protein, are in clinical trials for NPM1 driver gene mutant AML after relapse. A number of FLT3 inhibitors are now approved for FLT3 driver gene mutant AML in combination with chemotherapy in the frontline and also as single agent in relapse. Although mutations in IDH1/2 and TP53 only occur in around 10-20% of patients with AML each, they can affect the treatment strategy due to their association with prognosis and availability of targeted agents. While the impact of other driver gene mutations in AML is recognized, there is a lack of data on the actionable impact of those mutations.

Common Pathways for Acute Myeloid Leukemia Progression in Systemic Mastocytosis with Associated Hematologic Neoplasm

Background: Mastocytosis is a heterogenous disease of mast cell (MC) clonal proliferation with pathologic accumulation in organ systems such as but not limited to skin, bone marrow, gastrointestinal tract, liver and spleen. Mast cells are CD34+, CD117+ (stem cell factor, KIT) with greater than 90% of people with mastocytosis harboring KIT D816V activating mutations which allows for increased proliferation and accumulation of neoplastic mast cells leading to downstream mast cell activation and intolerable symptoms. Advanced systemic mastocytosis (advSM) is categorized into three major subtypes, aggressive SM, MC leukemia and SM with an associated hematologic neoplasm (SM-AHN). SM-AHN is the most common advSM subtype accounting for about 75% of advSM cases and typically includes myeloid neoplasms such as MDS, CMML, or MPN. In most pts with SM-AHN, clinical symptoms is driven by the MC component and the goal of treatment with KIT inhibitors is to decrease the MC burden, thus improving quality of life and overall survival (Nat Med refs), However, the median survival of SM-AHN remains poor at 2-3.5 years with many pts transforming to advanced myeloid neoplasms especially an acute myeloid leukemia (AML). The use of next generation sequencing has helped to prognosticate patients with AdvSM. Patients with advSM typically exhibit multiple somatic mutations other than KIT D816V We describe the molecular signature of patients with SM-AHN who transformed to AML. Commonly involved genes are TET2, SRSF2, ASXL1, RUNX1, and CBL with inferior OS and adverse clinical characteristic associated with SRSF2/ ASXL1/ RUNX1 (S/A/R). To better prognosticate, Jawhar and colleagues introduced the MARS score. This incorporated molecular findings in AdvSM to help estimate overall survival which identified 3 risk categories (low, intermediate, and high). The overall survival in low, intermediate and high were not reached, 4.3 years, and 1.9 respectively for patients with AdvSM. While mutational findings in the MARS score can help prognosticate overall survival in these patients, the molecular footprint of progression or transformation to acute myeloid leukemia has not been established. We describe the molecular signature of patients with SM-AHN who transformed to AML. Methods: We analyzed 10 pts with SM-AHN who transformed to AML from 2000-2022. Of those patients, 7 were found to have full next generation sequencing at the time of initial consultation and transformation. These data were collected and descriptive analysis was performed. Results: We identified 7 pts with SM-AHN who progressed to AML. At SM-AHN diagnosis all pts had at least 2 additional co-mutations with a maximum of 7 co-mutations along with KIT D817V. The most common co-mutations were splicing factor mutations ( SRSF2 and SF3B1), TET2, RASEZH2, CUX1 and CBL. Six of the seven received treatment for SM-AHN. These patients received treatment with multikinase inhibitors or hypomethylating agents. The acquired driver mutations were NPM1, FLT3-ITD, RUNX1, and RAS pathway. In patient 1, a new FLT3-ITD and RUNX1 was acquired with an increased VAF of a RAS pathway mutation ( PTPN1) which was originally present in the SM-AHN diagnosis. Patient 3 also developed a new RUNX1 mutation at AML transformation. Patients 4 and 5 had new NPM1 mutations and patients 6 and 7 had a new RAS pathway mutations . Patient 2 acquired new BCOR, RIT1 and CBL mutations. Upon transformation to AML, 5/7 patients had resolution or a decrease of greater than 10% of KIT D816V VAF. One of the seven had no change in KIT D816V VAF at the time of transformation, this was also the only patient to receive no prior therapy. Only 1/7 had a VAF increase of greater than 20% in KIT D817V at transformation. The MARS score was calculated at the time of diagnosis of SM-AHN which showed that only 4 of 7 had a high MARS score. Time from SM-AHN diagnosis to AML progression ranged from 4-31 months. Survival was calculated from time of SM-AHN diagnosis to death which ranged from 6-47 months. Conclusion: Acquisition of known AML driver mutations (RAS, RUNX1, NPM1, FLT3-ITD) are commonly found in SM-AHN patients at time of progression to AML. The MARS score calculated in our patients did not correlate with time to transition to AML.

FGF13 suppresses acute myeloid leukemia by regulating bone marrow niches.

Fibroblast growth factor 13 (FGF13) is aberrantly expressed in multiple cancer types, suggesting its essential role in tumorigenesis. Hence, we aimed to explore its definite role in the development of acute myeloid leukemia (AML) and emphasize its associations with bone marrow niches. Results showed that FGF13 was lowly expressed in patients with AML and that its elevated expression was related to prolonged overall survival (OS). Univariate and multivariate Cox regression analyses identified FGF13 as an independent prognostic factor. A prognostic nomogram integrating FGF13 and clinicopathologic variables was constructed to predict 1-, 3-, and 5-year OS. Gene mutation and functional analyses indicated that FGF13 was not associated with AML driver mutations but was related to bone marrow niches. As for immunity, FGF13 was remarkably associated with T cell count, immune checkpoint genes, and cytokines. In addition, FGF13 overexpression substantially inhibited the growth and significantly induced the early apoptosis of AML cells. The xenograft study indicated that FGF13 overexpression prolonged the survival of recipient mice. Overall, FGF13 could serve as an independent prognostic factor for AML, and it was closely related to the bone marrow microenvironment.

Proteomic and phosphoproteomic landscapes of acute myeloid leukemia

AbstractWe have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow–derived controls. After confirming data quality, we orthogonally validated several previously undescribed features of AML revealed by the proteomic data. We identified examples of posttranscriptionally regulated proteins both globally (ie, in all AML samples) and also in patients with recurrent AML driver mutations. For example, samples with IDH1/2 mutations displayed elevated levels of the 2-oxoglutarate–dependent histone demethylases KDM4A/B/C, despite no changes in messenger RNA levels for these genes; we confirmed this finding in vitro. In samples with NPMc mutations, we identified several nuclear importins with posttranscriptionally increased protein abundance and showed that they interact with NPMc but not wild-type NPM1. We identified 2 cell surface proteins (CD180 and MRC1/CD206) expressed on AML blasts of many patients (but not healthy CD34+ stem/progenitor cells) that could represent novel targets for immunologic therapies and confirmed these targets via flow cytometry. Finally, we detected nearly 30 000 phosphosites in these samples; globally, AML samples were associated with the abnormal phosphorylation of specific residues in PTPN11, STAT3, AKT1, and PRKCD. FLT3-TKD samples were associated with increased phosphorylation of activating tyrosines on the cytoplasmic Src-family tyrosine kinases FGR and HCK and related signaling proteins. PML-RARA–initiated AML samples displayed a unique phosphorylation signature, and TP53-mutant samples showed abundant phosphorylation of serine-183 on TP53 itself. This publicly available database will serve as a foundation for further investigations of protein dysregulation in AML pathogenesis.

Polyclonality Strongly Correlates with Biological Outcomes and Is Significantly Increased Following Improvements to the Phase 1/2 HGB-206 Protocol and Manufacturing of LentiGlobin for Sickle Cell Disease (SCD; bb1111) Gene Therapy (GT)

Polyclonality Strongly Correlates with Biological Outcomes and Is Significantly Increased Following Improvements to the Phase 1/2 HGB-206 Protocol and Manufacturing of LentiGlobin for Sickle Cell Disease (SCD; bb1111) Gene Therapy (GT)

Acute Myeloid Leukemia Classification System That Associates Normal Myeloid-Cell Subset Gene Signatures with Prognosis

Background: Acute Myeloid Leukemia (AML) represents a group of heterogeneous clonal disorders of hematopoietic progenitor cells that are driven by multiple genetic events that impair cell differentiation and apoptosis and invoke uncontrolled cell proliferation. Consequently, immature myeloid blasts rapidly accumulate in the bone marrow and block the generation of mature end stage cells, which eventually causes potentially fatal infections and hemorrhages. AML is characterized by extensive genetic and phenotypic heterogeneity, which currently is diagnostically classified based on blast morphology defined by the French-American-British (FAB) Cooperative Group, cytogenetic abnormalities, and improved knowledge of genomic and epigenomic alterations. However, this has not yet resulted in treatment progress. AML patients are still routinely treated with a standard first-line combinatorial chemotherapy regimen with an overall survival rate remaining below 20%. Therefore, there is an unmet need for novel methods to stratify patients into therapy-relevant subtypes.Concept and Aims: We hypothesize that phenotypic heterogeneity of AML is a consequence of dysregulated differentiation and that classification based on transcriptional reminiscence of cell of origin (COO) during AML transformation is of pathogenetic impact and therefore provide diagnostic and prognostic value. It is the aim of this project to generate and validate a COO classification system based on normal myeloid-cell-subset-associated gene signatures (MAGS) to stratify AML patients into therapy-relevant and prognostic subtypes.MAGS Generation: Based on gene expression profiles of publicly available sorted normal myeloid subpopulations, we generated a COO classifier including the CD34+/CD38- hematopoietic stem cells (HSC), CD34+/CD38+/CD45RA- megakaryocyte-erythroid progenitors (MEP), and CD34+/CD38+/CD45RA+ granulocytic-monocytic progenitors (GMP) using regularized multinomial regression with 3 discrete outcomes and the elastic net penalty. The regularization parameters were chosen by cross validation.Results: MAGS prediction accuracy was validated in an independent dataset (n = 38; accuracy = 0.79) of sorted normal myeloid subpopulations. The prognostic value of MAGS assignment was studied by survival analyses using the Kaplan Meier method, log-rank test statistics, and simple and multiple Cox proportional hazards regression analysis in 2 clinical cohorts (TCGA: n = 115; GSE6891: n = 431). MAGS assignment had significant prognostic associations with overall survival (Figure 1; Table 1A) revealing that the linage committed MAGS subtypes GMP and MEP showed superior prognosis compared to the undifferentiated AMLs captured by the MAGS HSC subtype. Furthermore, multiple Cox regression analysis with MAGS assignment (HSC, GMP, MEP), FAB score (M0-M6), cytogenetics (good, intermediate, poor), and age (dichotomized into <55 and ≥55) as independent explanatory variables showed that MAGS assignment provides independent prognostic information (Table 1B), indicating that the MAGS classification captures distinct pathogenetic and prognostic knowledge not already explained by the FAB- or cytogenetic classifications. Molecular characterization of MAGS subtypes by differential gene expression analysis, gene set enrichment analysis, and identification of subtype specific mutation patterns of well-documented AML driver mutations indicated a reduced proliferation rate as well as overrepresentation of EVI1 mutations associated with the poor responding HSC subtype.Conclusion: In accordance with our previous reports in malignant B-cell disorders, we have documented a novel classification system that associates normal myeloid progenitor subsets with AML subtypes of distinct pathogenetic and prognostic importance not already explained by the FAB- or cytogenetic classifications. Further pathogenetic studies are needed to develop a diagnostic platform using MAGS-assigned subtypes to improve disease management. [Display omitted] DisclosuresSeverinsen:ARIAD: Research Funding; Celgene: Research Funding; Novartis: Research Funding. El-Galaly:Roche: Other: Travel funding; Takeda: Other: Travel funding.

Somatic Mutations Drive Specific, but Reversible, Epigenetic Heterogeneity States in AML.

Epigenetic allele diversity is linked to inferior prognosis in acute myeloid leukemia (AML). However, the source of epiallele heterogeneity in AML is unknown. Herein we analyzed epiallele diversity in a genetically and clinically annotated AML cohort. Notably, AML driver mutations linked to transcription factors and favorable outcome are associated with epigenetic destabilization in a defined set of susceptible loci. In contrast, AML subtypes linked to inferior prognosis manifest greater abundance and highly stochastic epiallele patterning. We report an epiallele outcome classifier supporting the link between epigenetic diversity and treatment failure. Mouse models with TET2 or IDH2 mutations show that epiallele diversity is especially strongly induced by IDH mutations, precedes transformation to AML, and is enhanced by cooperation between somatic mutations. Furthermore, epiallele complexity was partially reversed by epigenetic therapies in AML driven by TET2/IDH2, suggesting that epigenetic therapy might function in part by reducing population complexity and fitness of AMLs. SIGNIFICANCE: We show for the first time that epigenetic clonality is directly linked to specific mutations and that epigenetic allele diversity precedes and potentially contributes to malignant transformation. Furthermore, epigenetic clonality is reversible with epigenetic therapy agents.This article is highlighted in the In This Issue feature, p. 1775.

SIRT7: an influence factor in healthy aging and the development of age-dependent myeloid stem-cell disorders

Molecular alterations within the hematopoietic system influence cellular longevity and development of age-related myeloid stem-cell disorders like acute myeloid leukemia (AML) and chronic myeloid leukemia (CML). A reduced SIRT7-expression in aged murine hematopoietic stem cells (HSC) resulted in reduced longevity and increased proliferation. In this study we investigated age-related changes of SIRT7-expression in healthy humans and relevant pathomechanisms in AML and CML. SIRT7-expression in leukocytes of healthy people decreased in an age-dependent manner. Low SIRT7 mRNA levels were also detected in AML and CML patients. With positive treatment response, SIRT7-expression increased, but showed reduction when patients progressed or relapsed. Pharmacologic inhibition of driver mutations in AML (FLT3-ITD) or CML (BCR-ABL) also restored SIRT7 levels in cell lines and patient samples. Furthermore, SIRT7-expression increased with time during PMA-mediated monocyte differentiation of THP-1 cells. SIRT7-overexpression in THP-1 cells resulted in increased expression of differentiation markers. BCR-ABL, FLT3-ITD, and differentiation-associated SIRT7-expression in general were positively regulated by C/EBPα, -β, and -ε binding to two different C/EBP-binding sites within the SIRT7 promoter. SIRT7 is important in human hematopoietic cell aging and longevity. It might act as tumor suppressor and could potentially serve as general biomarker for monitoring treatment response in myeloid stem-cell disorders.

Clonal competition within complex evolutionary hierarchies shapes AML over time

Clonal heterogeneity and evolution has major implications for disease progression and relapse in acute myeloid leukemia (AML). To model clonal dynamics in vivo, we serially transplanted 23 AML cases to immunodeficient mice and followed clonal composition for up to 15 months by whole-exome sequencing of 84 xenografts across two generations. We demonstrate vast changes in clonality that both progress and reverse over time, and define five patterns of clonal dynamics: Monoclonal, Stable, Loss, Expansion and Burst. We also show that subclonal expansion in vivo correlates with a more adverse prognosis. Furthermore, clonal expansion enabled detection of very rare clones with AML driver mutations that were undetectable by sequencing at diagnosis, demonstrating that the vast majority of AML cases harbor multiple clones already at diagnosis. Finally, the rise and fall of related clones enabled deconstruction of the complex evolutionary hierarchies of the clones that compete to shape AML over time.

High-Throughput Functional Ex-Vivo Drug Testing and Multi-Omics Profiling in Patients with Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is the most common leukemia in adults and the prognosis is dismal. The heterogeneity of driver mutations in AML from one patient to another is significant. Although new treatment targets and modalities have recently been introduced, a lack of therapies to cover the entire spectrum of molecularly distinct AML classes remains a challenge. Furthermore, often only a fraction of the patients carrying mutations actually respond to the drugs predicted to target such genomic subtypes in AML. Our question was if outcome can be improved by optimizing existing and emerging therapies? To address this, we applied direct functional drug testing ex vivo in patients with newly diagnosed AML, along with deep molecular profiling to identify new therapeutic and diagnostic opportunities for specific genetic subclasses. To date, 122 patient samples have been included in the study. We have collected AML patient mononuclear cells isolated from fresh bone marrow aspirates from the Karolinska University Hospital Huddinge and Uppsala University Hospital, or applied biobanked samples from the Swedish acute leukemia biobank. The cells from the patient are tested for 72h with up to 525 conventional and investigative oncology drugs in a 5-point concentration range to determine optimal treatment options. The test is based on bulk cell viability and the cells are cultured in bone marrow stroma-conditioned media. The data is compared to healthy bone marrow controls to filter out generally toxic drugs and combinations. Excess patient material is applied for multi-omics analysis, including genome sequencing, deep proteomic profiling, concentrations of soluble factors, bulk/single-cell RNA sequencing and mass cytometry. Our results indicate significant heterogeneity in functional drug responses across individual patients, even among those with the same founder mutations. We could identify potential targeted treatments for most patients based on the exvivo testing. For instance, patients that show resistance to the Bcl-2 inhibitor Venetoclax can be associated with a distinct drug sensitivity response pattern that includes drugs with different mechanisms of actions. Based on the clustering of drug response data in all clinical samples, we could identify groups of patients with similar global drug responses, and drugs with similar patterns of efficacy across all patients. Disclosures Lehmann: Pfizer: Membership on an entity's Board of Directors or advisory committees; Abbive: Membership on an entity's Board of Directors or advisory committees; TEVA: Consultancy, Membership on an entity's Board of Directors or advisory committees. Kallioniemi:Medisapiens: Other: Co-founder and stockholder; Sartar Therapeutics: Other: Co-founder and stockholder; Astra-Zeneca: Other: Joint Grant; Pelago: Other: Joint Grant; Takara: Other: Joint Grant; Abbot: Other: Licensing income.

The Impact of the Cellular Origin in Acute Myeloid Leukemia: Learning From Mouse Models.

Acute myeloid leukemia (AML) is a genetically heterogeneous disease driven by a limited number of cooperating mutations. There is a long-standing debate as to whether AML driver mutations occur in hematopoietic stem or in more committed progenitor cells. Here, we review how different mouse models, despite their inherent limitations, have functionally demonstrated that cellular origin plays a critical role in the biology of the disease, influencing clinical outcome. AML driven by potent oncogenes such as mixed lineage leukemia fusions often seem to emerge from committed myeloid progenitors whereas AML without any major cytogenetic abnormalities seem to develop from a combination of preleukemic initiating events arising in the hematopoietic stem cell pool. More refined mouse models may serve as experimental platforms to identify and validate novel targeted therapeutic strategies.

Single-Cell Atlas of Driver Mutations in Acute Myeloid Leukemia (AML)

Single-Cell Atlas of Driver Mutations in Acute Myeloid Leukemia (AML)

Therapy-Related Myeloid Neoplasms (tMN) Following Treatment of Acute Myeloid Leukemia (AML): Exome Sequencing Reveals the Presence of an Ancestral Clone Refractory to Chemotherapy

Therapy-Related Myeloid Neoplasms (tMN) Following Treatment of Acute Myeloid Leukemia (AML): Exome Sequencing Reveals the Presence of an Ancestral Clone Refractory to Chemotherapy

Evidence for Complete Mutation Clearance in Normal Karyotype AML Patients with Very Long (> 5 years) Remissions after Chemotherapy Alone

The fraction of patients with cytogenetically normal acute myeloid leukemia (AML) who have long (>5 years) first remissions after chemotherapy alone is estimated to be about 9.1% in young (<60 years) and 1.6% in older (>60 years) patients1; very few intermediate risk patients are therefore “cured” with chemotherapy alone. At this time, it is not yet clear whether these long remission patients are “living with disease”, or whether all AML cells have been eliminated. Many people in complete morphologic remission have evidence for persistence of their ancestral and/or founding clones within the first 2-3 years after treatment, but genomic studies of very long first remissions have not yet been described. To determine whether patients with very long first remissions with chemotherapy alone clear their mutations, or are living with persistent disease, we performed an analysis of the mutational landscape and mutation persistence of 8 cases of normal karyotype AML with remissions of >5 years, and who received standard “7+3” induction and high dose cytarabine consolidation (3 to 4 cycles) as their primary therapy. All patients were diagnosed and treated at Washington University in Saint Louis; patient characteristics are summarized in Table 1. The mean age of patients at initial diagnosis was 43.5 years (range 19-63), and the mean time of follow up in first remission is currently 92 months (7.6 years) (range 62-146 months). To the best of our knowledge, none of the patients has relapsed to date. In every case, the day +14 bone marrow demonstrated ablation, and the day +28 bone marrow showed complete morphologic remission.For each case, we defined the mutational landscape at presentation with enhanced exome sequencing (235x coverage of the entire exome, and ~1008x coverage of recurrently mutated AML genes, as defined in the TCGA AML study). Each case had one or more recognized AML driver mutations, with a mean of 44 (range 31-64) somatic exome mutations (Table 1). The mutational spectrum at diagnosis was not statistically different from larger cohorts of intermediate risk AML patients with standard outcomes: 2 cases had mutations in DNMT3A, 6 had NPMc, 4 had NRAS, 3 had FLT3, 2 had WT1, 2 had STAG2, 2 had SLC43A3, and 2 had PTPN11 mutations. We were able to create probes for 225 mutations (mean of 28 per case, range 17-41) for analysis on the Haloplex platform; we used this platform to perform deep, error-corrected sequencing in one or more remission samples obtained from the bone marrow or peripheral blood of each patient after more than 1 year of remission. The mean depth of Haloplex coverage for all variants for all 8 samples was 1607x (range: 102-12,538x). Importantly, each sample had at least one AML-specific mutation assayed with a coverage depth greater than 3500x, yielding a sensitivity to detect 1 cell in 1,750 (0.06%). In the remission samples, 7/8 patients demonstrated complete clearance of all mutations in all samples tested, strongly suggesting that all AML cells had been eliminated by standard induction and consolidation therapies. In one case (868442), we detected a persistent ancestral clone in morphologic remission samples, harboring DNMT3AR882H (VAF 10.19% in long remission) and IRS2D106Y mutations (VAF 12.82% in long remission). These data suggest that a small subset of normal karyotype AML patients treated with chemotherapy alone may able to completely eradicate all AML cells. Although the mechanism is not yet clear (increased susceptibility to chemotherapy, immunologic surveillance of neoantigens, etc.), these data suggest that some patients in long remissions after chemotherapy do not have persistent subclinical disease, nor do they retain ancestral clones that could potentially contribute to relapse. In ongoing studies, our aim is to define biomarkers that can be used to prospectively identify this subset of patients, so that they can avoid the risk of allotransplantation in first remission.Reference:Vasu, Sumithira et al., Blood Advances 2.13 (2018): 1645-1650. Web. 31 July. 2018. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.