Role In Acute Myeloid Leukemia Research Articles

In Silico Drug Repurposing Against PSMB8 as a Potential Target for Acute Myeloid Leukemia Treatment.

PSMB8 emerges as a prominent gene associated with cancer survival, yet its potential therapeutic role in acute myeloid leukemia (AML) remains unexplored within the existing literature. The principal aim of this study is to systematically screen an expansive library of molecular entities, curated from various databases to identify the prospective inhibitory agents with an affinity for PSMB8. A comprehensive assortment of molecular compounds obtained from the ZINC15 database was subjected to molecular docking simulations with PSMB8 by usingtheAutoDock tool in PyRx (version 0.9.9) to elucidate binding affinities. Following the docking simulations, a select subset of molecules underwent further investigation through comprehensive ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis employing AdmetSar and SwissADME tools. Finally, RMSD, RMSF, Rg, and H bond analyses were conducted via GROMACS to determine the best conformationally dynamic molecule that represents the candidate agent for the study. Following rigorous evaluation, Adozelesin, Fiduxosin, and Rimegepant have been singled out based on considerations encompassing bioavailability scores, compliance with filter criteria, and acute oral toxicity levels. Additionally, ligand interaction analysis indicates that Adozelesin and Fiduxosin exhibit an augmented propensity for hydrogen bond formation, a factor recognized for its facilitative role in protein-ligand interactions. After final analyses, we report that Fiduxosin may offera treatment possibility by reversing the low survival rates caused by PSMB8 high activation in AML. This study represents a strategic attempt to repurpose readily available pharmaceutical agents, potentially obviating the need for de novo drug development, and thereby offering promising avenues for therapeutic intervention in specific diseases.

Lysosome-related genes predict acute myeloid leukemia prognosis and response to immunotherapy.

Acute myeloid leukemia (AML) is a highly aggressive and pathogenic hematologic malignancy with consistently high mortality. Lysosomes are organelles involved in cell growth and metabolism that fuse to form specialized Auer rods in AML, and their role in AML has not been elucidated. This study aimed to identify AML subtypes centered on lysosome-related genes and to construct a prognostic model to guide individualized treatment of AML. Gene expression data and clinical data from AML patients were downloaded from two high-throughput sequencing platforms. The 191 lysosomal signature genes were obtained from the database MsigDB. Lysosomal clusters were identified by unsupervised consensus clustering. The differences in molecular expression, biological processes, and the immune microenvironment among lysosomal clusters were subsequently analyzed. Based on the molecular expression differences between lysosomal clusters, lysosomal-related genes affecting AML prognosis were screened by univariate cox regression and multivariate cox regression analyses. Algorithms for LASSO regression analyses were employed to construct prognostic models. The risk factor distribution, KM survival curve, was applied to evaluate the survival distribution of the model. Time-dependent ROC curves, nomograms and calibration curves were used to evaluate the predictive performance of the prognostic models. TIDE scores and drug sensitivity analyses were used to explore the implication of the model for AML treatment. Our study identified two lysosomal clusters, cluster1 has longer survival time and stronger immune infiltration compared to cluster2. The differences in biological processes between the two lysosomal clusters are mainly manifested in the lysosomes, vesicles, immune cell function, and apoptosis. The prognostic model consisting of six prognosis-related genes was constructed. The prognostic model showed good predictive performance in all three data sets. Patients in the low-risk group survived significantly longer than those in the high-risk group and had higher immune infiltration and stronger response to immunotherapy. Patients in the high-risk group showed greater sensitivity to cytarabine, imatinib, and bortezomib, but lower sensitivity to ATRA compared to low -risk patients. Our prognostic model based on lysosome-related genes can effectively predict the prognosis of AML patients and provide reference evidence for individualized immunotherapy and pharmacological chemotherapy for AML.

Increased Th17 and Treg levels in peripheral blood positively correlate with minimal residual disease in acute myeloid leukaemia.

Immune dysregulation plays a key role in acute myeloid leukemia (AML). We aimed to explore the correlation between T helper cell 17 (Th17) and the regulatory cells (Tregs) in the peripheral blood of patients with newly diagnosed (ND) AML and bone marrow blast cells, as well as minimal residual disease (MRD) before and after treatment. Changes in Th17 and Treg cells in the peripheral blood of 32 patients with ND AML were observed before and after induction chemotherapy with cytarabine for seven days and anthracycline for three days. The levels of inflammatory cytokines were measured using an enzyme-linked immunosorbent assay. Correlation analysis between bone marrow blast cells and Th17 and Treg cell frequencies was performed using the Pearson's correlation test. Frequencies of Th17 and Treg cells and MRD were assessed using flow cytometry. IL-6, IL-10, IL-17A, and GM-CSF levels gradually increased in patients with ND AML and CR and NR patients. The percentages of Th17 and Treg cells positively correlated with those of blast cells. In addition, the frequencies of Th17 and Treg cells in MRD-positive patients were higher than those in MRD-negative patients at the initial induction and after three months of chemotherapy. The frequencies of Tregs and Th17 cells positively correlated with MRD onset. Increased Th17 and Treg cell levels were positively correlated with onset of AML, poor remission, and MRD.

HSPA8 Chaperone Complex Drives Chaperone-Mediated Autophagy Regulation in Acute Promyelocytic Leukemia Cell Differentiation

Introduction: Acute myeloid leukemia (AML) is a cancer of the hematopoietic system characterized by hyperproliferation of undifferentiated cells of the myeloid lineage. While most of AML therapies are focused toward tumor debulking, all-trans retinoic acid (ATRA) induces neutrophil differentiation in the AML subtype acute promyelocytic leukemia (APL). Macroautophagy has been extensively investigated in the context of various cancers and is often dysregulated in AML where it can have context-dependent pro- or anti-leukemogenic effects. On the contrary, the implications of chaperone-mediated autophagy (CMA) on the pathophysiology of diseases are still being explored and its role in AML remains elusive. Methods: We took advantage of human AML primary samples and databases to analyze CMA gene expression and activity. Furthermore, we used ATRA-sensitive (NB4) and -resistant (NB4-R1) APL cells to further dissect a potential function for CMA in ATRA-mediated neutrophil differentiation. NB4-R1 cells are unique in that they do respond to retinoic acid transcriptionally but do not mature in response to retinoid signaling alone unless maturation is triggered by adding cyclic adenosine monophosphate. Results: Here, we report that CMA-related mRNA transcripts are significantly higher expressed in immature hematopoietic cells as compared to neutrophils, contrasting the macroautophagy gene expression patterns. Accordingly, lysosomal degradation of an mCherry-KFERQ CMA reporter decreases during ATRA-induced differentiation of APL cells. On the other hand, using NB4-R1 cells we found that macroautophagy flux primed ATRA-resistant NB4-R1 cells to differentiate upon ATRA treatment but reduced the association of lysosome-associated membrane protein type 2A (LAMP-2A) and heat shock protein family A (Hsp70) member 8 (HSPA8), necessary for complete neutrophil maturation. Accordingly, depletion of HSPA8 attenuated CMA activity and facilitated APL cell differentiation. In contrast, maintaining high CMA activity by ectopic expression of LAMP-2A impeded APL differentiation. Conclusion: Overall, our findings suggest that APL neutrophil differentiation requires CMA inactivation and that this pathway predominantly depends on HSPA8 and is possibly assisted by other co-chaperones.

High SEC61A1 expression predicts poor outcome of acute myeloid leukemia.

The malfunction of SEC61A1 has been linked to several types of cancers, but its role in acute myeloid leukemia (AML) remains poorly understood. In this study, we used a series of bioinformatics analysis techniques, including gene expression profiling and proteomic analysis. Our findings were subsequently validated through a series of in vitro experiments, such as SEC61A1 knockdown in cell lines and RT-qPCR. We discovered a significant up-regulation of SEC61A1 in AML patients compared to healthy controls. AML patients with elevated SEC61A1 expression exhibited reduced overall survival compared to those with lower expression. Moreover, SEC61A1 expression emerged as an independent risk factor for predicting the survival of AML patients undergoing allo-HSCT. Our analysis also revealed an association between high SEC61A1 expression and increased signaling pathways related to cell growth. Our study underscores the importance of SEC61A1 expression as a novel prognostic indicator for predicting survival among AML patients, while also identifying it as a promising therapeutic target.

CD7-positive leukemic blasts with DNMT3A mutations predict poor prognosis in patients with acute myeloid leukemia.

DNMT3A mutations can be detected in premalignant hematopoietic stem cells and are primarily associated with clonal hematopoiesis of indeterminate potential; however, current evidence does not support assigning them to a distinct European Leukemia Net (ELN) prognostic risk stratification. CD7 is a lymphoid antigen expressed on blasts in approximately 30% of acute myeloid leukemia (AML), and its role in AML remains unclear and depends on subgroup evaluation. This study investigated the prognostic value of DNMT3A mutation combined with CD7 expression in AML. We retrospectively analyzed the clinical data of 297 newly diagnosed non-M3 AML patients. According to the DNMT3A mutation and CD7 expression in AML cells, patients were divided into the DNMT3A-mutated/CD7-positive (CD7+), DNMT3A-mutated/CD7-negative (CD7-), DNMT3A-wild-type/CD7+, and DNMT3A-wild-type/CD7- groups. The DNMT3A-mutated/CD7+ group had lower complete remission rates and higher relapse rates. Importantly, these patients had significantly shorter overall survival (OS) and relapse-free survival (RFS). Furthermore, multivariate analysis showed that CD7+ with DNMT3A mutation was an independent risk factor for OS and RFS. CD7+ with DNMT3A mutation predicts a poor prognosis in AML patients, and the immunophenotype combined with molecular genetic markers can help to further refine the current risk stratification of AML.

BATF promotes extramedullary infiltration through TGF-β1/Smad/MMPs axis in acute myeloid leukemia.

Acute myeloid leukemia (AML) is one of the most prevalent types of leukemia and is challenging to cure for most patients. Basic Leucine Zipper ATF-Like Transcription Factor (BATF) has been reported to participate in the development and progression of numerous tumors. However, its role in AML is largely unknown. In this study, the expression and prognostic value of BATF were examined in AML. Our results demonstrated that BATF expression was upregulated in AML patients, which was significantly correlated with poor clinical characteristics and survival. Afterward, functional experiments were performed after knocking down or overexpressing BATF by transfecting small interfering RNAs and overexpression plasmids into AML cells. Our findings revealed that BATF promoted the migratory and invasive abilities of AML cells in vitro and in vivo. Moreover, the target genes of BATF were searched from databases to explore the binding of BATF to the target gene using ChIP and luciferase assays. Notably, our observations validated that BATF is bound to the promoter region of TGF-β1, which could transcriptionally enhance the expression of TGF-β1 and activate the TGF-β1/Smad/MMPs signaling pathway. In summary, our study established the aberrantly high expression of BATF and its pro-migratory function via the TGF-β1-Smad2/3-MMP2/9 axis in AML, which provides novel insights into extramedullary infiltration of AML.

Reactive oxygen species and its role in pathogenesis and resistance to therapy in acute myeloid leukemia.

Relapse following a short clinical response to therapy is the major challenge for the management of acute myeloid leukemia (AML) patients. Leukemic stem cells (LSC), as the source of relapse, have been investigated for their metabolic preferences and their alterations at the time of relapse. As LSC rely on oxidative phosphorylation (OXPHOS) for energy requirement, reactive oxygen species (ROS), as by-products of OXPHOS, have been investigated for their role in the effectiveness of the standard AML therapy. Increased levels of non-mitochondrial ROS, generated by nicotinamide adenine dinucleotide phosphate oxidase, in a subgroup of AML patients add to the complexity of studying ROS. Although there are various studies presenting the contribution of ROS to AML pathogenesis, resistance, and its inhibition or activation as a target, a model that can clearly explain its role in AML has not been conceptualized. This is due to the heterogeneity of AML, the dynamics of ROS production, which is influenced by factors such as the type of treatment, cell differentiation state, mitochondrial activity, and also the heterogeneous generation of non-mitochondrial ROS and limited available data on their interaction with the microenvironment. This review summarizes these challenges and the recent progress in this field.

Proteolysis Targeting Chimera Degraders of the METTL3-14 m6A-RNA Methyltransferase.

Methylation of adenine N6 (m6A) is the most frequent RNA modification. On mRNA, it is catalyzed by the METTL3-14 heterodimer complex, which plays a key role in acute myeloid leukemia (AML) and other types of blood cancers and solid tumors. Here, we disclose the first proteolysis targeting chimeras (PROTACs) for an epitranscriptomics protein. For designing the PROTACs, we made use of the crystal structure of the complex of METTL3-14 with a potent and selective small-molecule inhibitor (called UZH2). The optimization of the linker started from a desfluoro precursor of UZH2 whose synthesis is more efficient than that of UZH2. The first nine PROTAC molecules featured PEG- or alkyl-based linkers, but only the latter showed cell penetration. With this information in hand, we synthesized 26 PROTACs based on UZH2 and alkyl linkers of different lengths and rigidity. The formation of the ternary complex was validated by a FRET-based biochemical assay and an in vitro ubiquitination assay. The PROTACs 14, 20, 22, 24, and 30, featuring different linker types and lengths, showed 50% or higher degradation of METTL3 and/or METTL14 measured by Western blot in MOLM-13 cells. They also showed substantial degradation on three other AML cell lines and prostate cancer cell line PC3.

ZEB1 shapes AML immunological niches, suppressing CD8 T cell activity while fostering Th17 cell expansion

Acute myeloid leukemia (AML) progression is influenced by immune suppression induced by leukemia cells. ZEB1, a critical transcription factor in epithelial-to-mesenchymal transition, demonstrates immune regulatory functions in AML. Silencing ZEB1 in leukemic cells reduces engraftment and extramedullary disease in immune-competent mice, activating CD8T lymphocytes and limiting Th17 cell expansion. ZEB1 in AML cells directly promotes Th17 cell development that, in turn, creates a self-sustaining loop and a pro-invasive phenotype, favoring transforming growth factor β (TGF-β), interleukin-23 (IL-23), and SOCS2 gene transcription. In bone marrow biopsies from AML patients, immunohistochemistry shows a direct correlation between ZEB1 and Th17. Also, the analysis of ZEB1 expression in larger datasets identifies two distinct AML groups, ZEB1high and ZEB1low, each with specific immunological and molecular traits. ZEB1high patients exhibit increased IL-17, SOCS2, and TGF-β pathways and a negative association with overall survival. This unveils ZEB1's dual role in AML, entwining pro-tumoral and immune regulatory capacities in AML blasts.

Discovery of novel and potent CDK8 inhibitors for the treatment of acute myeloid leukaemia

It has been reported that CDK8 plays a key role in acute myeloid leukaemia. Here, a total of 40 compounds were rational designed and synthesised based on the previous SAR. Among them, compound 12 (3-(3-(furan-3-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl)benzamide) showed the most potent inhibiting activity against CDK8 with an IC50 value of 39.2 ± 6.3 nM and anti AML cell proliferation activity (molm-13 GC50 = 0.02 ± 0.01 μM, MV4-11 GC50 = 0.03 ± 0.01 μM). Mechanistic studies revealed that this compound 12 could inhibit the phosphorylation of STAT-1 and STAT-5. Importantly, compound 12 showed relative good bioavailability (F = 38.80%) and low toxicity in vivo. This study has great significance for the discovery of more efficient CDK8 inhibitors and the development of drugs for treating AML in the future.

RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9

BackgroundThe oncogenic protein HOXA9 plays a critical role in leukemia transformation and maintenance, and its aberrant expression is a hallmark of most aggressive acute leukemia. Although inhibiting the upstream regulators of HOXA9 has been proven as a significant therapeutic intervention, the comprehensive regulation network controlling HOXA9 expression in leukemia has not been systematically investigated.ResultsHere, we perform genome-wide CRISPR/Cas9 screening in the HOXA9-driven reporter acute leukemia cells. We identify a poorly characterized RNA-binding protein, RBM5, as the top candidate gene required to maintain leukemia cell fitness. RBM5 is highly overexpressed in acute myeloid leukemia (AML) patients compared to healthy individuals. RBM5 loss triggered by CRISPR knockout and shRNA knockdown significantly impairs leukemia maintenance in vitro and in vivo. Through domain CRISPR screening, we reveal that RBM5 functions through a noncanonical transcriptional regulation circuitry rather than RNA splicing, such an effect depending on DNA-binding domains. By integrative analysis and functional assays, we identify HOXA9 as the downstream target of RBM5. Ectopic expression of HOXA9 rescues impaired leukemia cell proliferation upon RBM5 loss. Importantly, acute protein degradation of RBM5 through auxin-inducible degron system immediately reduces HOXA9 transcription.ConclusionsWe identify RBM5 as a new upstream regulator of HOXA9 and reveal its essential role in controlling the survival of AML. These functional and molecular mechanisms further support RBM5 as a promising therapeutic target for myeloid leukemia treatment.

Mitochondrial regulation of GPX4 inhibition-mediated ferroptosis in acute myeloid leukemia.

Resistance to apoptosis in acute myeloid leukemia (AML) cells causes refractory or relapsed disease, associated with dismal clinical outcomes. Ferroptosis, a mode of non-apoptotic cell death triggered by iron-dependent lipid peroxidation, has been investigated as potential therapeutic modality against therapy-resistant cancers, but our knowledge of its role in AML is limited. We investigated ferroptosis in AML cells and identified its mitochondrial regulation as a therapeutic vulnerability. GPX4 knockdown induced ferroptosis in AML cells, accompanied with characteristic mitochondrial lipid peroxidation, exerting anti-AML effects in vitro and in vivo. Electron transport chains (ETC) are primary sources of coenzyme Q10 (CoQ) recycling for its function of anti-lipid peroxidation in mitochondria. We found that the mitochondria-specific CoQ potently inhibited GPX4 inhibition-mediated ferroptosis, suggesting that mitochondrial lipid redox regulates ferroptosis in AML cells. Consistently, Rho0 cells, which lack functional ETC, were more sensitive to GPX4 inhibition-mediated mitochondrial lipid peroxidation and ferroptosis than control cells. Furthermore, degradation of ETC through hyperactivation of a mitochondrial protease, caseinolytic protease P (ClpP), synergistically enhanced the anti-AML effects of GPX4 inhibition. Collectively, our findings indicate that in AML cells, GPX4 inhibition induces ferroptosis, which is regulated by mitochondrial lipid redox and ETC.

Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology

The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships among protein kinase sequence, structure, function, and disease in a human and machine-readable format. In this study, we have significantly expanded ProKinO by incorporating additional data on expression patterns and drug interactions. Furthermore, we have developed a completely new browser from the ground up to render the knowledge graph visible and interactive on the web. We have enriched ProKinO with new classes and relationships that capture information on kinase ligand binding sites, expression patterns, and functional features. These additions extend ProKinO’s capabilities as a discovery tool, enabling it to uncover novel insights about understudied members of the protein kinase family. We next demonstrate the application of ProKinO. Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinases in human cancers with abnormal expression in multiple cancers, including a previously unappreciated role in acute myeloid leukemia. We have identified recurrent oncogenic mutations in the PAK5 activation loop predicted to alter substrate binding and phosphorylation. Additionally, we have identified common ligand/drug binding residues in PAK family kinases, underscoring ProKinO’s potential application in drug discovery. The updated ontology browser and the addition of a web component, ProtVista, which enables interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling community. The updated ProKinO database is accessible at https://prokino.uga.edu.

Acute myeloid leukemia-derived bone marrow mesenchymal cells exhibit improved support for leukemic cell proliferation

IntroductionThe bone marrow (BM) microenvironment plays a significant role in acute myeloid leukemia (AML) genesis and there is evidence that BM mesenchymal stromal cells (BMMSCs) can support leukemia progenitor cell proliferation and survival and provide resistance to cytotoxic therapies. Hypothesis and methodNevertheless, currently unknown are the relevance of the spatial localization of AML cells relative to the BMMSCs and whether BMMSCs from patients with AML and healthy subjects have similar properties. To address these issues, we performed a differential gene expression analysis using RNA-sequencing data generated from healthy donors (HDs) and leukemic BMMSCs. ResultsThe Gene Set Enrichment Analysis (GSEA) revealed that leukemic BMMSCs were associated with the terms “positive regulation of cell cycle”, “angiogenesis” and “signaling by the estimated glomerular filtration rate (eGFR)”, whereas healthy donor (HD)-derived BMMSCs were associated with “programmed cell death in response to the reactive oxygen species (ROS)”, “negative regulation of the cytochrome C from the mitochondria” and “interferon signaling”. Next, we evaluated the mitochondrial superoxide production in AML cells in a co-culture layered model. The superoxide production was reduced in leukemic cells in close contact (adhered to the surface or beneath the cell layer) with BMMSCs, indicating lower oxidative stress. ConclusionTaken together, our results suggest that AML-derived BMMSCs are transcriptionally rewired and can reduce the metabolic stress of leukemic cells.

Presence of Recurrent Somatic Mutations in Mesenchymal Stromal Cell Fractions Isolated from Acute Myeloid Leukemia As an Evidence of Clonality

Introduction: Acute myeloid leukemia (AML) involves somatic mutations in hematopoietic stem cells (HSCs). Recent evidence suggests the bone marrow microenvironment, particularly mesenchymal stromal cells (MSCs), also influences AML development. Abnormalities in MSCs from AML patients have been observed (von der Heide et al., 2016), potentially impacting leukemia progression. This study aims to identify MSC somatic mutations and their consequences, further exploring their role in AML. Understanding MSCs' impact on the leukemic microenvironment may shed light on AML pathophysiology and guide targeted therapies, particularly benefiting patients with adverse risk disease. Methods: A total of 28 bone marrow cases were collected from AML patients with adverse risk, including those with complex karyotype, monosomy karyotype, chromosome 5/7/17 abnormalities, TP53 mutation, or relapsed/refractory AML. From these cases, 14 paired MSC and leukemic cell (LC) fractions were analyzed and are presented here. Magnetic bead sorting was used to isolate CD33+ LCs, while the plastic adherence method was employed for MSC culture. Following magnetic isolation, CD33- cells were plated in DMEM-LG with FBS and pen/strep, and MSC colonies formed within 48 hours. Contaminating cells were removed through media changes, and passaging was performed at 70-80% confluency. Flow cytometry at passage 3 characterized MSCs based on cell surface expression of CD105, CD73, and CD90, in accordance with the ISCT guideline. DNA and RNA were extracted from MSCs at passage 3 and subjected to whole exome sequencing (WES) using the Illumina platform, along with the LC fractions. WES aimed for 200X depth for the paired DNA samples. A standard bioinformatics pipeline was used for sequence alignment and variant calling, with variants requiring sufficient read depth (≥30x) and variant allele frequency in the case (>5%) and in the control (<5%). Synonymous variants were filtered out, and gene ontology and pathway enrichment analyses explored the biological significance and potential involvement in leukemogenesis of the identified mutations. Whole transcriptomics for gene expression analyses was also conducted for both MSC and LC fractions. Results: In 14 analyzed cases, a total of 548 somatic variants were identified in the MSC fraction, affecting 480 genes, including 518 nonsynonymous single nucleotide variants (SNVs), 7 stop-gain SNVs, 1 stoploss, 1 non-frameshift insertion, 2 frameshift deletions, 1 frameshift insertion, and 2 non-frameshift deletions, with 16 unknown variants. The average read depth was 75 (range: 15 - 887), and the average variant allele frequency was 50% (range: 11% - 90%). On average, 38 genes were mutated per MSC case, with 8 genes detected in at least 3 cases, 25 in exactly 2 cases, and 447 genes found in only one case. In the leukemic fraction, 686 somatic variants in 595 genes were identified, with an average read depth of approximately 75 (range: 10 - 2596) and an average variant allele frequency of 47% (range: 8% - 85%). On average, 48 mutations were detected per leukemic case, with 12 mutations found in at least 3 cases, 40 in 2 cases, and 543 in only one case. Among the 14 cases, 10 cases (71%) had mutations in known driver genes for AML ( FLT3, NPM1, IDH1, IDH2, DNMT3A, RUNX1, TP53) exclusively in the leukemic fraction. As seen in Figure 1., of the 480 genes mutated in the MSC fraction, 69 overlapped with the 595 genes mutated in the leukemic fraction, while 411 genes were uniquely mutated in the MSC fraction. Further analysis is ongoing, and pathway analysis will be conducted once the remaining 14 cases are processed. Conclusions: This study identifies distinct somatic mutations in AML patients' MSC and leukemic cell fractions, revealing genomic complexity and crosstalk impacting leukemia progression. Understanding the functional implications of these mutations is crucial for unraveling their roles in leukemogenesis and developing personalized therapeutic interventions targeting MSC somatic mutations.

HDAC Inhibitor Synergizes with GL-V9, a Derivative of Wogonin, to Suppress Acute Myeloid Leukemia By Downregulating ESPL1 and PLK4

Background Developing more effective non-chemotherapy options is emerging needed for acute myeloid leukemia (AML). GL-V9, a newly synthetic flavonoid derivative, exhibits anticancer activities with low toxicity as its nature features, however, the anti-leukemia effect and molecular mechanism against AML remain elusive. HDACs inhibitors are promising effective therapies for cancers. Chidamide (CS055/HBI-8000) is a benzamide histone deacetylase (HDAC) inhibitor that induces growth inhibition, cell cycle arrest, and apoptosis in MDS and AML. Here, we sought to determine the potential synergistic anti-leukemia effect of Chidamide combined with GL-V9 in AML. Methods Cell proliferation assays were measured by Cell Counting Kit-8(CCK-8) in AML cells; CalcuSyn was used for synergy analysis. Cell cycle and apoptosis were measured by flow cytometry analysis. Transcriptome was analyzed by RNA-seq in U937 cells treated with 10μM Chidamide and in MV4-11 treated with 4μM GL-V9. qPCR was utilized for gene expression; R2 genomics analysis and visualization application were used for comparison of the expression difference and the Kaplan-Meier overall survival analysis was conducted by the Gene Expression Profiling Interactive Analysis (GEPIA) platform. Results GL-V9 had a dose-dependent effect on cell proliferation arrest in U937 and MV4-11 cells. Chidamide significantly sensitized this effect of GL-V9 versus single-drug controls, and CalcuSyn analysis showed the synergistic effect of the combination (Fig.1A). The combination also significantly increased the % of apoptotic cells versus single-drug controls (p<0.0001) (Fig1.B). Chidamide induced G0/G1-phase arrest and GL-V9 induced G2/M arrest, whereas the combination significantly decreased the % of S-phase cells (Fig.1C). These data indicate that Chidamide+GL-V9 combination results in the synergistic effect on cell growth inhibition, apoptosis and cell cycle arrest in AML. Next, the drug-induced change of the global transcriptome was analyzed. The significantly different expression genes (DEGs) were identified upon GL-V9 treatment and Chidamide treatment versus vehicle control. 1663 DEGs are identified upon GL-V9 treatment and 3756 DEGs upon Chidamide, in which 1405 were intersected regulated (1231 genes changed in the same direction but 174 changed in the opposite (Fig.2AB). The overlapped DEGs are mainly enriched in cell cycle regulation, DNA repair, chromosome segregation, spindle organization, DNA damage, etc. (Fig2.C). ESPL1 and PLK4 are at the top of the overlapped down-regulated DEGs; and qPCR results confirmed their mRNA levels are significantly downregulated by GL-V9+Chidamide, GL-V9, and Chidamide versus the vehicle control (p<0.0001) (Fig. 2D). ESPL1 encoded protein, Separase is an enzyme resolving sister chromatid cohesion, and plays a pivotal role in cell division and oncogenesis. PLK4 (polo-like kinase 4) is a key regulator of centrosome duplication and the substrate of histone acetyltransferases, and PLK4 overexpression leads to centrosome amplification in human cancer and contributes to multipolar spindle assembly. Our results not only indicated that the combination exerts its anti-tumor effect through down-regulation of ESPL1 and PLK4 expression but also reveal their oncogenic roles in AML. Indeed, the mRNA levels of ESPL1 and PLK4 are significantly high expressed in AML patients versus normal BM controls, and ESPL1 high expression is correlated with poor prognosis (Log-rank p=0.0039) (Fig2.E). In addition, our data showed that the expression of the anti-apoptosis genes BCL2 and BCL2L1 are significantly decreased, and the early apoptosis indicators, Caspase-3 and Casepase-9 increased by the combination versus the single-drug controls in U937 cells (Fig2.F). The proposed mechanism model is summarized in Fig. 2G. Conclusion Our data indicate that HDAC inhibitor Chidamide significantly synergizes GL-V9-induced cell growth inhibition, apoptosis, and cell cycle arrest in AML, and the underlying mechanism by suppressing the expression of ESPL1 and PLK4, the key regulators of cell division and proliferation. Our results also provide a potential chemotherapy-free option for AML patients.

Optimal Therapeutic Strategies in Relapsed/Refractory AML with Prior Exposure to Venetoclax Based Therapy

Background: Acute myeloid leukemia (AML) is an aggressive hematological malignancy arising from immature myeloid progenitors with notoriously poor outcomes, particularly in the elderly. Venetoclax (Ven) plays an essential role in acute myeloid leukemia (AML) directed therapy as it is approved for frontline therapy in combination with azacitidine (Aza), decitabine (Dec), or low-dose cytarabine (LDAC) for patients aged 75 years and older, or those with significant comorbidities. However, venetoclax-based therapy is not curative, and the ideal salvage regimen is unclear in these patients. We performed a retrospective review that analyzed a single center's venetoclax-based regimens to identify rational subsequent lines of therapy after failing venetoclax. Methods: We conducted a retrospective review of adult patients at Roswell Park Comprehensive Cancer Center who had a confirmed AML diagnosis and received a venetoclax-based regimen as upfront therapy between January 2015-February 2023. Demographics, prior hematological disorders, ELN risk stratification, Eastern Cooperative Oncology Group (ECOG) performance status, treatment received in upfront vs relapsed/refractory settings, date of remission/relapse, disease-specific variables [molecular data, cytogenetics], and outcomes [duration of response, time to progression, MRD status, and overall survival] were collected. Of note, in patients who received upfront venetoclax regimen, the subsequent salvage therapy was grouped by targeted (Gliterinib, Enasidenib, Ivosidenib), low-intensity (single agent hypomethylating therapy, gemtuzumab, ozogamicin), or intensive groups (CLAG-M) and analysis was performed for progression-free survival (PFS). The patient demographics and clinical characteristics were summarized by group (i.e. response, regimens) using the Mann-Whitney U and Fisher's exact test. Survival functions were described by the Kaplan-Meier method and compared with the Log-rank test. Analyses were performed in SAS v9.4 (Cary, NC) at a significance level of 0.05. Results: The retrospective study analyzed 97 patients. In the upfront analysis, the median age was 73.4 years (range: 51.4-89.8) and 64 (66.0%) of the patients were male. 65 patients (67.0%) received Aza/Ven, 26 (26.8%) Dec/Ven, and 6 (6.2%) LDAC/Ven. Per ELN 2022 criteria, 13.3% of patients were stratified as favorable,12.2% as intermediate, and 74.4% as adverse risk. Of the adverse risk patients, 67/97 (69.1%) patients received Aza/Ven. Median survival time for all upfront induction regimens was 15.8 months (95% CI: 8.1-22.6), greatest median survival with Aza/Ven of 19.1 months (95% CI:10.4-23.6). Median PFS by all induction regimens was 8.9 months (95% CI: 5.0-13.9) with the greatest median PFS being Aza/Ven at 10.9 months (95% CI: 6.6-20.2); p=0.045). Overall, 29 out of 97 (29.9%) patients received salvage therapy. These included 19 (65.5%) males with 93.1% of patients being Caucasian. The majority of patients (81.5%) had adverse ELN risk stratification (Table 1). Total 1-year survival rate is 0.050 (0.31-0.67), with intensive 0.050 (0.16-0.67), low intensity 0.67 (0.35-0.86), targeted 0.39 (0.18-0.60). Total 3-year survival rate is 0.19 (0.06-0.38) with intensive 0.17 (0.02-0.46), low intensity 0.30 (0.08-0.56), and targeted 0.20 (0.05-0.41). Patients receiving subsequent salvage therapy after upfront venetoclax regimen showed the greatest PFS after receiving low-intensity therapy compared to targeted or intensive regimens with a median survival of 13.9 months (95% CI: 0.0-35.9); p<0.001) (Figure 1). Median survival after intensive therapy was 1.3 months (95% CI:0.5-3.9) and targeted therapy 5.8 months (95% CI: 2.8-10.0). Total OS 14.9 (95% CI: 6.1-22.7) with a low-intensity median survival of 22.7 months (95% CI:1.4-Not Reached (NR)). Conclusion: In this single-center retrospective review, it was found that a low-intensity salvage regimen after the upfront venetoclax regimen showed the greatest PFS compared to targeted or intensive regimens, however, there is no statistically significant difference in OS. Our study results were limited by a small sample size. Further studies are needed to clearly define the ideal salvage regimen for AML patients failing upfront venetoclax-based therapy.

EP0042, a Dual FLT3 and Aurora Kinase Inhibitor: Results from an Ongoing Phase I/IIa Dose-Finding/Dose Optimization Study in Patients with Relapsed/Refractory Acute Myeloid Leukemia

Background: EP0042 was developed as an orally bioavailable potent inhibitor of FLT3 and Aurora kinases. Aurora kinases play an important role in acute myeloid leukemia (AML) and have been implicated in the development of resistance to FLT3 inhibitors (Joshi S et al. Cancer Cell 2021;39:999-1014, 8). Dual inhibition of FLT3 and Aurora kinase has been shown to overcome acquired resistance to selective FLT3 inhibition both in vitro and in vivo (Moore A et al. Leukemia 2012;26:1462-70; Tariq M et al. Br J Cancer 2021;125:966-74). Preliminary data from this ongoing Phase 1 study of EP0042 in relapsed/refractory AML were presented previously (Taussig et al. Blood 2022:140(Supplement 1): 6222-6223). Here we present further data from the dose finding and dose optimisation cohorts from the study. Methods The primary objective of this phase I/IIa, multi-centre study is to investigate safety/tolerability and to establish both the MTD and optimal dose of EP0042 when used as monotherapy, or in combination with established standard treatments in patients with AML, myelodysplastic syndrome (MDS) or chronic myelomonocytic leukemia (CMML) who have relapsed on or are refractory to previous therapy. Secondary objectives include PK characterisation and assessment of anti-tumour activity. Results As of July 13 th 2023, 38 patients (17 f/21 m) were enrolled across 9 different cohorts. Median age 72 years, range 25-84. Patients presented with relapsed/refractory AML (34), CMML (1) or MDS (3). 9 patients had FLT3 mutated AML at the point of entry (All FLT3 ITD). Patients were administered doses ranging from 40mg to 170mg, QD or BID, with different schedules, across 7 cohorts (Table 1). One Cycle = 28 days. 150mg BID 28/28 days was identified as the MTD with 2 DLTs identified, Grade 3 somnolence and ataxia, and Grade 3 encephalopathy. Two dose optimisation cohorts (Table 1) were subsequently initiated to further optimise the potential RP2D. These cohorts are currently ongoing. The median number of prior treatments was 2 (range 1-6). 12 patients received a prior FLT3 inhibitor including midostaurin, gilteritinib or sorafenib and 8/12 patients received ≥2 prior FLT3 inhibitors. 3 patients received prior ASCT. The most common treatment-emergent adverse events (TEAEs) ≥20% were: diarrhea (54.1%), fatigue (54.1%), febrile neutropenia (51.4%), decreased appetite (43.2%), dyspnea (35.1%), somnolence (29.7%), constipation (27.0%), ataxia (27.0%) and nausea (24.3%). 23.3% of TEAEs were > grade 3. The most common treatment related AEs (TRAEs, all grades ≥10%) were decreased appetite (29.7%), somnolence (29.7%), ataxia (27.0%), fatigue (24.3%), diarrhea (13.5%), nausea (13.5%) and dizziness (16.2%). No treatment-related death has been reported across all cohorts. Most events were manageable by temporary dose reductions and or/short interruptions. All events of ataxia and somnolence were reversible after a short treatment interruption. Across all cohorts, 18 patients achieved stable disease (SD) as best response (median no. of cycles = 3, range 1-11). 1 patient continued treatment for 11 cycles (100mg BID, FLT3wt) and another for 8 cycles (140 mg BID, FLT3-ITD) with clinical benefit. 1 patient achieved a best response of CR MRD- (150mg BID, FLT3wt) with aCRi first detected at C6D1 (2% blast, down from 38% at screening and 80% at C3D1) and confirmed with CR MRD- at C7D1 by flow cytometry. Treatment is still ongoing at C10 and patient remains transfusion independent for 4 months. Evidence of peripheral blast response was observed in 5 patients, with complete disappearance of peripheral blasts compared to baseline after a median time of 2 months on treatment. Data from the ongoing dose optimisation cohorts will be presented at the congress. Conclusions This extended data set confirms thatEP0042 has acceptable tolerability and safety. Two patient cohorts are ongoing to establish the optimum continuous dose regimen to take forward. Promising evidence of clinical benefit has been observed including a durable CR MRD-. This remission in a patient with FLT3 wild type AML indicates that EP0042 may have broader activity in AML, beyond FLT3 mutated disease. Dose optimisation cohorts are continuing to identify the RP2D. Further cohorts are planned for evaluation of EP0042 in combination with standard of care therapies.

ALOX5AP is a new prognostic indicator in acute myeloid leukemia

BackgroundThe overexpression of ALOX5AP has been observed in many types of cancer and has been identified as an oncogene. However, its role in acute myeloid leukemia (AML) has not been extensively studied. This study aimed to identify the expression and methylation patterns of ALOX5AP in bone marrow (BM) samples of AML patients, and further explore its clinical significance.MethodsEighty-two de novo AML patients and 20 healthy donors were included in the study. Meanwhile, seven public datasets from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were included to confirm the alteration of ALOX5AP. Receiver operating characteristic (ROC) curve analysis was applied to determine the discriminative capacity of ALOX5AP expression to discriminate AML. The prognostic value of ALOX5AP was identified by the Kaplan–Meier method and log-rank test. It was further validated in four independent cohorts (n = 1186). Significantly different genes associated with ALOX5AP expression were subsequently compared by LinkedOmics, and Metascape database.ResultsThe level of ALOX5AP expression was significantly increased in bone marrow cells of AML patients compared with healthy donors (P < 0.05). ROC curve analysis suggested that ALOX5AP expression might be a potential biomarker to discriminate AML from controls. ALOX5AP overexpression was associated with decreased overall survival (OS) in AML according to the TCGA data (P = 0.006), which was validated by other four independent cohorts. DNA methylation levels of ALOX5AP were significantly lower in AML patients compared to normal samples (P < 0.05), as confirmed in the Diseasemeth database and the independent cohort GSE63409. ALOX5AP level was positively associated with genes with proleukemic effects such as PAX2, HOX family, SOX11, H19, and microRNAs that act as oncogenes in leukemia, such as miR125b, miR-93, miR-494, miR-193b, while anti-leukemia-related genes and tumor suppressor microRNAs such as miR-582, miR-9 family and miR-205 were negatively correlated.ConclusionALOX5AP overexpression, associated with its hypomethylation, predicts poorer prognosis in AML.