Patient-derived Acute Myeloid Leukemia Research Articles

Acute Myeloid Leukemia Cells Rely on the Glycolytic Enzyme PGK1 to Support Energy Production and Amino Acid Metabolism

Acute myeloid leukemia (AML) cells frequently display an increased dependence on glucose compared to healthy hematopoietic stem and progenitors (HSPCs). Furthermore, increased glucose metabolism is associated with worse outcomes in AML. However, the upstream regulators that drive glucose metabolism as well as how glucose is utilized in AML remains largely unknown. Here, we have discovered that the oncogenic transcription factor (TF), JUN supports AML, in part, by regulating glycolytic enzymes that utilize glucose to support both cellular energetics and amino acid metabolism. Having previously reported that certain aggressive AML sub-types depend on JUN, we next set out to identify JUN-regulated transcriptional programs that support AML. To do so, we engineered the human AML cell line, THP-1 to express either control (shNT) or JUN-targeting shRNAs and then performed RNA-seq on cells from each condition. Next, we carried out a functional enrichment analyses and discovered that genes encoding numerous enzymatic regulators of glycolysis were significantly down-regulated by JUN-inhibition. Using qPCR validation, we confirmed that JUN inhibition results in reduced mRNA expression of Hexokinase 1 & 2 (HK1 & HK2), Glucose-Phosphate Isomerase (GPI), Phosphofructose Kinase (PFKP), Aldolase A (ALDOA), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Phosphoglycerate Kinase (PGK1), Enolase 1 (ENO1) and Pyruvate Kinase Muscle (PKM). ChIP assays confirmed that JUN directly localizes to the promoters of each of these genes except for ALDOA and PKM. To assess whether the JUN-dependent changes in glycolytic gene expression translated to defects in the ability of AML cells to catabolize glucose, we performed a glycolysis stress test on shNT- and shJUN-expressing human AML cell lines (e.g. THP-1, NOMO-1 and MOLM-14). From this assessment, we found that JUN inhibition resulted in a complete loss of glucose catabolism in all cell lines tested. We postulated that JUN activates glycolytic gene expression to support AML and thus, inhibition of JUN-regulated glycolytic genes will impede leukemia cell function. To test this hypothesis, we generated shRNAs targeting each of the JUN-regulated glycolytic enzymes. We then engineered mouse leukemia cells expressing the human leukemogenic allele, MLL-AF9 - found in both childhood and adult AML - to express these shRNAs and then assessed their colony forming capacity (CFC) in cytokine-enriched semisolid culture. In parallel, we also assessed how knockdown of each glycolytic enzyme impacted the CFC of healthy HSPCs. Notably, we observed that inhibition of each enzyme significantly impaired the CFC of MLL-AF9 leukemia cells but that inhibition of Pfkp, Aldoa or Pgk1 did not impact the CFC of healthy HSPC, suggesting that these enzymes were selectively important for AML. We next evaluated how knockdown of Pfkp, Aldoa or Pgk1 impacted leukemia propagation in vivo. Interestingly, inhibition of Pfkp or Pgk1, but not Aldoa, significantly delayed the onset of MLL-AF9 driven leukemia in vivo. Moreover, we found that a chemical inhibitor of PGK1, CBR-470-1, reduces the CFC of patient-derived AML cells in vitro. Since Pgk1 had not previously been studied in AML, we focused our attention on the its role in leukemia cell metabolism. We thus performed untargeted metabolomics of shNT- and shPgk1-expressing mouse MLL-AF9 cells using hydrophilic liquid chromatography mass spectrometry (HILIC-MS). PGK1 utilizes ADP to convert 1,3-bisphosphoglycerate into 3-phosphoglycerate (3-PG) and ATP. 3-PG can subsequently be used to generate phosphoenolpyruvate (PEP) or in the de novo synthesis of serine (Ser). As expected, we found that Pgk1 inhibition resulted in a significant decrease in 3-PG, PEP and Ser. We also observed that Pgk1 inhibition resulted in the decrease of several tricarboxylic acid cycle (TCA) intermediates that support oxidative phosphorylation energy production. Surprisingly, we also found that Pgk1 inhibition resulted in a marked decrease in several amino acids, including Alanine, Arginine and Histidine. We are currently investigating whether the decrease in these amino acids mediated by Pgk1 inhibition is due to an impediment of their biosynthesis or their consumption in gluconeogenic pathways. Collectively, our studies identify JUN as a previously unrecognized regulator of AML cell metabolism and shed new into how glucose is catabolized in AML cells.

Orthogonal Proteogenomic Approaches Identify the Druggable PA2G4-MYC Axis in 3q26 AML

Despite next-generation technologies improved our understanding of the complexity of high-risk acute myeloid leukemia (AML), effective targeted therapies are delayed due to the prevalence of major oncogenic disease drivers such as RAS, RUNX1, TP53. In some cases, the integration of orthogonal omics led to the identification or repurposing of drugs for "undruggable" transcription factors (TFs), prospecting a benefit for patients with the most aggressive leukemia subtypes. Here, we sought to discover how to target the Ecotropic Viral Integration Site-1 gene (EVI1/MECOM), the most lethal oncogenic TF in AML carrying chromosome 3q26 abnormalities. To this end, we intersected phenotypic, gene expression-based and proteomic high-throughput approaches for small molecule and target identification. We screened a collection of 5294 compounds enriched for Food and Drug Administration (FDA) approved or bioactive drugs at 1 µM and identified those that caused more than 95% reduction of cell viability compared to vehicle control in MOLM1 and UCSD/AML1 cell lines carrying 3q26 rearrangments (EVI1high). We then selected a set of sentinel genes that defined an EVI1 "on" and "off" transcriptional signature based on the TF1 EVI1high cell line treated with an EVI1-directed siRNA or control, and used the Connectivity Map to identify inducers of an EVI1 "off" state. Histone deacetylase inhibitors (HDACi) scored as the top class of compounds able to repress leukemia proliferation by suppressing the EVI1 signature. We focused on the compounds with pan (AR-42, belinostat) or selective (entinostat) HDAC inhibitory properties. These molecules induced apoptosis and decreased the levels of EVI1 in AML cell lines and in primary EVI1high blast cells. Interestingly, the expression of EVI1 sensitizes cells to HDAC inhibition both in an inducible EVI1 cell model and in EVI1high compared to EVI1low AML cell lines. Primary EVI1high blasts were also more sensitive to HDAC inhibition compared to those from other AML subtypes, while equally resistant to chemotherapy agents. We translated these results in a "N-of-1" clinical trial proposing entinostat in association with azacytidine to patients with relapse/refractory 3q26 AML based on a compassionate use program for this regimen. Pharmacodynamic modulation of EVI1 was assessed at 6 hours (T6) after entinostat administration in patients and in matched patient-derived AML xenografts (PDLX). EVI1 expression markedly decreased in circulating blasts collected at T6 compared to T0 (before treatment), and EVI1 depletion paralleled clinical and hematologic improvements at follow-up evaluations. This effect was not observed in patients treated with cytarabine. Longitudinal single-cell RNA sequencing (scRNASeq) of bone marrow AML cells collected before and after patients' treatment cycle revealed an inhibitory effect on Myc target genes in the leukemic clone. This effect was also observed in cell lines treated with AR-42, belinostat and entinostat suggesting that different HDACi regulates the Evi1-Myc axis in 3q26 AML. Not surprisingly, HDACi mediated or genetic silencing of EVI1 led to a decrement of MYC in EVI1high AML models. To dissect the EVI1 co-transcriptional complex and explain for the modulation of Myc signaling in EVI1high AML, we performed rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME). Sixty-nine proteins co-immunoprecipitated with endogenous EVI1 both in cell lines and in 3q26 PDLX models. Eleven of these EVI1 interactors were targets of Myc signaling, including PA2G4, a RNA-binding protein that was markedly modulated by HDACi. Importantly, PA2G4 silencing or inhibition (WS6) depletes MYC at transcriptional and protein levels recapitulating the phenotypic effect seen with HDACi in EVI1high cell models. Consequently, WS6 treatment reduced the growth of AML cells in PDLX models in vivo by suppressing an EV1-MYC signature at single-cell leukemia level without inducing widespread toxicities. In contrast, PA2G4 overexpression rescued EVIhigh AML cell lines from the effects induced by HDACi inhibition. These data support the evidence that PA2G4 is a mediator of Evi1-Myc axis in AML. In conclusion, our work positions PA2G4 at the crosstalk of the Evi1-Myc leukemogenic signal for developing new therapeutics and, at this interesting time, urges upfront HDACi-based combination therapies in patients with 3q26 AML.

Streptavidin-Drug Conjugates Streamline Identification of Optimal Toxic Payloads for Antibody-Based Hematopoietic Stem Cell Transplantation Conditioning

INTRODUCTION: Allogeneic hematopoietic stem cell transplantation (allo-HSCT) provides the best and possibly only chance for cure for acute myeloid leukemia (AML). In preparation for allo-HSCT, patients undergo conditioning with chemotherapy and/or irradiation to deplete host hematopoietic stem cells (HSCs), suppress the host immune system, and destroy residual leukemia cells. However, conditioning associated toxicities impose a formidable barrier to patients undergoing this potentially curative therapy. Antibody-drug conjugates (ADCs) have emerged as a promising and potentially safer alternative for allo-HSCT conditioning by allowing targeted depletion of the host HSC niche. Previously, we used saporin-conjugated CD45- or cKit-ADCs as the backbone of a novel conditioning regimen which enabled engraftment between fully mismatched mice. However, saporin ADCs were nonmyeloablative and showed modest antitumor activity. We hypothesized that fully myeloablative ADCs capable of enhanced antileukemia activity could be produced using alternative toxic payloads to saporin. However, direct conjugation of multiple candidate payloads and/or antibodies is costly, time-consuming, and laborious. Here, we describe the production of a panel of streptavidin (SAv)-drug conjugates which allows efficient ADC generation from any biotinylated protein. This flexible platform enabled the rapid production of CD45-ADCs conjugated to multiple toxic payloads, facilitating in vitro screening of their ability to target HSCs and leukemia cells. METHODS: Azide-alkyne cycloaddition ("Click" chemistry) was used to covalently link SAv-azide (Protein Mods, Inc) with dibenzocyloocytne (DBCO)-coupled drug payloads (Levena Biopharma) (Fig. 1). We conjugated three toxic payloads to SAv for these studies: monomethyl auristatin E (MMAE), Duocarmycin SA (Duo), and PNU-159682 (PNU). All of these payloads contain cleavable valine-citrulline linkers for payload release following ADC internalization. For the conjugation reactions, SAv-azide was combined with DBCO-coupled payload and incubated 2 hours at 20oC, with 20% DMSO added as cosolvent. Free payload and DMSO were removed using size exclusion chromatography and dialysis. ADCs were freshly prepared before use by mixing SAv-drug conjugates in a 1:1 molar ratio for 15 minutes with biotinylated antibodies. For our initial studies, we evaluated murine anti-CD45.2 (Clone 104) and human anti-CD45 (Clones BC8 and HI30). Non-biotinylated antibodies combined with SAv-drug conjugates were used as negative controls. All ADCs were tested for cytotoxicity in vitro against 1) murine YAC-1 (mCD45.2+) and human Jurkat (mCD45.2-) cell lines using XTT viability assays, 2) primary HSCs from B6 mice using methylcellulose assays, and 3) AML1 primary murine leukemia cells (Dnmt3aR878H/+ and FLT3-ITD; provided by Dr. Tim Ley) using methylcellulose assays. IC50 values for each assay were derived with nonlinear regression of dose response data. RESULTS: Mouse CD45-Duo and CD45-PNU were highly effective at killing AML1 cells (IC50 values: 39.2pM and 61.1pM, respectively; Fig. 2), as well as B6 HSCs (IC50 values: 0.85nM and 0.13nM, respectively) in vitro. Notably, mouse CD45-MMAE was ineffective against YAC-1 cells, B6 HSCs, and AML1 cells, suggesting that MMAE is not an effective payload for ADC-based conditioning in the mouse. Importantly, nonbiotinylated antibodies mixed with SAv-drug conjugates were largely ineffective, indicating the need for the antibody to bind the SAv-drug conjugate to achieve specific toxicity. Preliminary studies using human CD45-MMAE and CD45-Duo demonstrated that while both payloads could yield ADCs able to kill Jurkat cells, ADCs made using human antibody clone BC8 were considerably more effective than ADCs made with clone HI30. CONCLUSIONS: Our novel SAv-drug conjugate successfully enabled rapid generation of ADCs with a number of potential toxic payloads. This system identified multiple effective candidate payloads for use in mouse and human ADCs for targeting HSCs and leukemia cells in vitro and in vivo. Our ongoing and future studies with this system are focused in three areas: 1) production and testing of mouse and human cKit ADCs, 2) using mouse ADCs to condition for murine HSCT and target AML1 cells in vivo, and 3) evaluating killing of human cord blood-derived HSCs and patient-derived AML cells with human ADCs. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

SYK Inhibitors, Entospletinib and Lanraplenib, Show Potent Anti-Leukemic Activity in Combination with Targeted Agents

Introduction: Spleen tyrosine kinase (SYK) acts as a key integrator of cellular signaling from surface contact and receptor tyrosine kinase receptors containing an immunoreceptor tyrosine-based activation motif (ITAM). In acute myeloid leukemia (AML), SYK serves as a relay to an oncogenic transcriptional regulatory network (TRN) linked to NPM1, HOXA9, and MEIS1 helping to suppress myeloid progenitor maturation and promote proliferation. The selective, oral SYK inhibitor, entospletinib (ENTO), has demonstrated clinical activity in HOXA9/MEIS1-driven AML with acceptable tolerability when combined with intensive induction chemotherapy. A global phase 3 trial (AGILITY, NCT05020665) is currently underway, evaluating the combination of ENTO with intensive induction/consolidation chemotherapy in patients with treatment-naive NPM1-mutated (NPM1m) AML with measurable residual disease as the primary endpoint. Lanraplenib (LANRA) is a next-generation SYK inhibitor with similar potency, enhanced selectivity, and more favorable pharmacologic properties that is currently being evaluated in combination with gilteritinib in patients with relapsed or refractory (R/R) FLT3-mutated AML (NCT05028751). Results: ENTO exhibits anti-proliferative activity in NPM1m AML with associated HOXA9/MEIS1 dysregulation in ex vivo drug sensitivity studies. We hypothesized that SYK inhibition could synergize with other targeted therapies to enhance anti-leukemic activity at different nodes in this pathway. To address this hypothesis, the FLT3 internal tandem duplication/MLL-rearranged cell lines, MOLM13 and MV411, were treated with increasing doses of either LANRA or ENTO in combination with a small molecule MLL-Menin inhibitor (SNDX5613). Synergistic anti-proliferative effects were observed across a broad range of concentrations. No combinatorial or single-agent SNDX5613 activity was seen in the KASUMI-1 AML cell line, which lacks an MLL rearrangement. Phenotypic studies using flow cytometry were performed to assess the mechanistic response for SYK inhibition with LANRA in combination with SNDX5613. LANRA was found to increase the percentage of CD11b-positive cells and mean fluorescence intensity, while SNDX5613 led to a marked increase in CD14. In contrast to either single agent, the combination triggered early apoptosis and cell death, suggesting a more complete blockade of the HOXA9/MEIS1 transcriptional program through synergistic inhibition by orthogonal mechanisms. Furthermore, treatment of leukemic cells with either ENTO or LANRA inhibited SYK auto-phosphorylation in a dose-dependent manner. We also explored the potential for synergistic activity with gilteritinib (FLT3 inhibitor) and venetoclax (BCL2 inhibitor) using patient-derived AML isolates ex vivo based on the potential for SYK signaling cross talk with FLT3 itself and survival pathways. We found strong synergistic anti-proliferative activity for the combination of LANRA with either gilteritinib or venetoclax. Patient-derived xenograft (PDX) studies also demonstrated deeper reductions in leukemic burden in the peripheral blood, liver, and bone marrow after 28 days of treatment. Follow-up PDX studies assessing overall survival and pharmacodynamic activity are ongoing using an optimized dosing regimen and schedule. Summary/Conclusion: SYK is a promising therapeutic target for genetically defined subsets of AML. Two highly selective SYK inhibitors are currently undergoing clinical testing in different but complementary clinical settings. Given its central role as a modulator of leukemogenic signaling, SYK inhibition has the potential to synergize with other targeted therapies in AML. In preclinical studies, LANRA-mediated SYK inhibition shows compelling anti-proliferative and pro-apoptotic activity in combination with gilteritinib, venetoclax, and SNDX5613 in genetically defined subsets of AML.

A Circulating Microbial Metabolite Drives the Clonal Expansion of Pre-Leukemic Cells

Inflammatory mediators, including cytokines and microbial ligands, are implicated in the development of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). A consequence of aging and various autoimmune and inflammatory conditions is loss of intestinal barrier integrity and translocation of microbial species and metabolites into circulation. More recent findings revealed that patients with inflammatory bowel disease (IBD) harbor mutant hematopoietic clones and often present with clinical manifestations of MDS/AML. Moreover, intestinal barrier dysfunction is commonly reported at diagnosis in patients with MDS and AML. These observations led us to speculate that microbial-derived signals may contribute to the expansion of pre-leukemic hematopoietic stem and progenitor cells (HSPCs) and development of myeloid malignancies. To determine if loss of intestinal barrier integrity contributes to the expansion of pre-leukemic DNMT3a-mutant HSPCs, we generated a model of IBD by inducing gut epithelial injury using dextran sulfate sodium (DSS). Upon gut epithelial injury, we observed a significant expansion of DNMT3a-mutant HSPCs, but not of wild-type (WT) HSPCs, in vivo. Unexpectedly, DNMT3a-mutant HSPCs do not exhibit a competitive advantage over WT cells in the absence of intestinal barrier dysfunction, such as following DSS or high-dose radiation. Fecal material from DSS-treated WT mice was sufficient to induce expansion of DNMT3a-mutant HSPCs and this expansion was prevented with broad-spectrum antibiotics. These findings indicate that the competitive advantage of DNMT3a-mutant HSPCs following gut epithelial injury was due to alterations in the microbiome. In parallel sequencing studies, we identified a significant enrichment of gram-negative bacterial phyla in stool samples from the IBD mouse model, IBD patients, and treatment-naive AML patients. All gram-negative bacteria uniquely generate a microbial intermediate, ADP-heptose, as part of the lipopolysaccharide biosynthesis pathway. ADP-heptose can enter the blood circulation and freely translocate into cells and activate the ALPK1-TIFA complex ("TIFAsome"). Alpha-protein kinase 1 (ALPK1) and tumor necrosis factor receptor-associated factor (TRAF)-interacting protein with an FHA domain (TIFA) are overexpressed in primary human MDS and AML HSPCs as compared to healthy donors and their expression is correlated with poor prognosis. Gram negative bacteria and corresponding ADP-heptose levels were also significantly increased in the plasma of individuals with intestinal barrier injury, such with IBD, MDS, or upon aging, as compared to young healthy individuals. The circulating levels of ADP-heptose from aged individuals and IBD or MDS patients were sufficient to induce the TIFAsome in leukemic cells. Moreover, administration of disease relevant levels of ADP-heptose resulted in expansion and enhanced function of mouse DNMT3a-mutant HSPCs and of human AML cell lines and primary MDS cells in vivo. Expansion of DNMT3a-mutant HSPCs and human MDS/AML cells was directly related to overexpression of ALPK1, as WT HSPCs or ALPK1-deficient AML cells did not respond to ADP-heptose. To gain deeper mechanistic insight, we examined global transcriptional and epigenetic changes in purified WT and DNTM3a-mutant HSCs treated with ADP-heptose. DNMT3a-mutant HSCs treated with ADP-heptose resulted in epigenetic changes and increased expression of gene programs related to non-canonical NF-kB, ERK/MAPK, cell cycle activation, cell survival, and stem cell function. Indeed, ADP-heptose caused increased cycling and self-renewal of DNMT3a-mutant HSPCs, but not WT HSPCs, via the TIFAsome in vitro and in vivo. Based on the enriched pathways in DNMT3a-mutant HSCs treated with ADP-heptose, we screened small molecule inhibitors of TIFAsome activation. We found that targeting UBE2N abrogated ADP-heptose-mediated signaling via the TIFAsome and expansion of patient-derived AML xenografts. In summary, we report that conditions leading to intestinal barrier dysfunction and circulating ADP-heptose from gram-negative bacteria induce expansion of pre-leukemic and MDS/AML cells via ALPK1-TIFA. Lastly, we provide a potential therapeutic strategy to prevent the competitive advantage of pre-leukemic cells prior to overt malignant transformation.

Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia.

Membrane lipids control the cellular activity of kinases containing the Src homology 2 (SH2) domain through direct lipid-SH2 domain interactions. Here we report development of new nonlipidic small molecule inhibitors of the lipid-SH2 domain interaction that block the cellular activity of their host proteins. As a pilot study, we evaluated the efficacy of lipid-SH2 domain interaction inhibitors for spleen tyrosine kinase (Syk), which is implicated in hematopoietic malignancies, including acute myeloid leukemia (AML). An optimized inhibitor (WC36) specifically and potently suppressed oncogenic activities of Syk in AML cell lines and patient-derived AML cells. Unlike ATP-competitive Syk inhibitors, WC36 was refractory to de novo and acquired drug resistance due to its ability to block not only the Syk kinase activity, but also its noncatalytic scaffolding function that is linked to drug resistance. Collectively, our study shows that targeting lipid-protein interaction is a powerful approach to developing new small molecule drugs.

Perillaldehyde is a new ferroptosis inducer with a relevant clinical potential for acute myeloid leukemia therapy

Ferroptosis induction is an emerging strategy to treat cancer and contrast the tricky issue of chemoresistance, which can arise towards apoptosis. This work elucidates the anticancer mechanisms evoked by perillaldehyde, a monoterpenoid isolated from Ammodaucus leucotrichus Coss. & Dur. We investigated and characterized its antileukemic potential in vitro, disclosing its ability to trigger ferroptosis. Specifically, perillaldehyde induced lipid peroxidation, decreased glutathione peroxidase 4 protein expression, and depleted intracellular glutathione on HL-60 promyelocytic leukemia cells. Besides, it stimulated the active secretion of ATP, one of the most crucial events in the induction of efficient anticancer response, prompting further studies to disclose its possible nature as an immunogenic cell death inducer. To preliminarily assess the clinical relevance of perillaldehyde, we tested its ability to induce cell death on patient-derived acute myeloid leukemia biopsies, recording a similar mechanism of action and potency compared to HL-60 cells. To round the study off, we tested its selectivity towards tumor cells and disclosed lower toxicity on normal cells compared to both HL-60 and acute myeloid leukemia biopsies. Altogether, these data depict a favorable risk-benefit profile for perillaldehyde and reveal its peculiar antileukemic potential, which qualifies this natural product to proceed further through the drug development pipeline.

Hsa_circ_0044907 promotes acute myeloid leukemia progression through upregulating oncogene KIT via sequestering miR-186-5p

ABSTRACT Background: It has been reported that circular RNA hsa_circ_0044907 (circ_0044907) expression is overtly elevated in acute myeloid leukemia (AML) patient-derived BMMCs. However, the effect of circ_0044907 on AML progression remains un-clarified. Methods: Expression of circ_0044907 in BM and AML cells were detected with real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Cell viability, proliferation, apoptosis, and cycle progression were determined by 3-(4,5-Dimethylthiazol-2-yl)−2,5-Diphenyltetrazolium Bromide (MTT), 5-ethynyl-2’-deoxyuridine (EDU), and flow cytometry assays. The regulatory mechanism of circ_0044907 was predicted by bioinformatics analysis and validated by dual-luciferase reporter, RNA pull-down, and RNA immunoprecipitation (RIP) assays. In vivo experiments were carried out to verify the function of circ_0044907. Results: Circ_0044907 was overexpressed in AML patient-derived BM and AML cells. Furthermore, circ_0044907 could distinguish AML patients from healthy controls, and high circ_0044907 expression in BM had a poor prognosis for AML patients, implying that circ_0044907 served as a diagnostic and prognostic indicator for AML. Functionally, circ_0044907 silencing reduced cell viability, restrained cell proliferation, arrested cell cycle progression, and induced cell apoptosis in AML cells in vitro. Furthermore, circ_0044907 knockdown decreased AML cell growth in xenograft mouse models. Mechanically, circ_0044907 sponged miR-186-5p to block the inhibiting effect of miR-186-5p on KIT. Silenced miR-186-5p expression weakened circ_0044907 knockdown mediated suppression on AML cell viability, proliferation, and cycle progression. Also, forced KIT expression weakened miR-186-5p upregulation mediated inhibition on AML cell viability, proliferation, and cycle progression. Conclusion: Circ_0044907 absorbed miR-186-5p to block the inhibiting impact of miR-186-5p on KIT, thus promoting AML progression.

Dietary methionine starvation impairs acute myeloid leukemia progression

AbstractTargeting altered tumor cell metabolism might provide an attractive opportunity for patients with acute myeloid leukemia (AML). An amino acid dropout screen on primary leukemic stem cells and progenitor populations revealed a number of amino acid dependencies, of which methionine was one of the strongest. By using various metabolite rescue experiments, nuclear magnetic resonance−based metabolite quantifications and 13C-tracing, polysomal profiling, and chromatin immunoprecipitation sequencing, we identified that methionine is used predominantly for protein translation and to provide methyl groups to histones via S-adenosylmethionine for epigenetic marking. H3K36me3 was consistently the most heavily impacted mark following loss of methionine. Methionine depletion also reduced total RNA levels, enhanced apoptosis, and induced a cell cycle block. Reactive oxygen species levels were not increased following methionine depletion, and replacement of methionine with glutathione or N-acetylcysteine could not rescue phenotypes, excluding a role for methionine in controlling redox balance control in AML. Although considered to be an essential amino acid, methionine can be recycled from homocysteine. We uncovered that this is primarily performed by the enzyme methionine synthase and only when methionine availability becomes limiting. In vivo, dietary methionine starvation was not only tolerated by mice, but also significantly delayed both cell line and patient-derived AML progression. Finally, we show that inhibition of the H3K36-specific methyltransferase SETD2 phenocopies much of the cytotoxic effects of methionine depletion, providing a more targeted therapeutic approach. In conclusion, we show that methionine depletion is a vulnerability in AML that can be exploited therapeutically, and we provide mechanistic insight into how cells metabolize and recycle methionine.

Targeting FLT3 with a new-generation antibody-drug conjugate in combination with kinase inhibitors for treatment of AML

AbstractFms-like tyrosine kinase 3 (FLT3) is often overexpressed or constitutively activated by internal tandem duplication (ITD) and tyrosine kinase domain (TKD) mutations in acute myeloid leukemia (AML). Despite the use of receptor tyrosine kinase inhibitors (TKI) in FLT3-ITD–positive AML, the prognosis of patients is still poor, and further improvement of therapy is required. Targeting FLT3 independent of mutations by antibody-drug conjugates (ADCs) is a promising strategy for AML therapy. Here, we report the development and preclinical characterization of a novel FLT3-targeting ADC, 20D9-ADC, which was generated by applying the innovative P5 conjugation technology. In vitro, 20D9-ADC mediated potent cytotoxicity to Ba/F3 cells expressing transgenic FLT3 or FLT3-ITD, to AML cell lines, and to FLT3-ITD–positive patient-derived xenograft AML cells. In vivo, 20D9-ADC treatment led to a significant tumor reduction and even durable complete remission in AML xenograft models. Furthermore, 20D9-ADC demonstrated no severe hematotoxicity in in vitro colony formation assays using concentrations that were cytotoxic in AML cell line treatment. The combination of 20D9-ADC with the TKI midostaurin showed strong synergy in vitro and in vivo, leading to reduction of aggressive AML cells below the detection limit. Our data indicate that targeting FLT3 with an advanced new-generation ADC is a promising and potent antileukemic strategy, especially when combined with FLT3-TKI in FLT3-ITD–positive AML.

NPM1-Mutated Patient-Derived AML Cells Are More Vulnerable to Rac1 Inhibition.

The prognosis of acute myeloid leukemia (AML) is poor, especially for the elderly population. Targeted therapy with small molecules may be a potential strategy to overcome chemoresistance and improve survival in AML. We investigated the inhibition of the signaling molecule ras-related C3 botulinum toxin substrate 1 (Rac1) in leukemia cells derived from 79 consecutive AML patients, using five Rac1 inhibitors: ZINC69391, ITX3, EHOP-016, 1A-116, and NSC23766. In vitro cell proliferation and apoptosis assays and the assessment of cytokine profiles in culture media were conducted. All five inhibitors had an antiproliferative effect; IC50 ranged from 3–24 µM. They induced significant apoptosis and necrosis compared to the untreated controls (p < 0.0001) at concentrations around IC40 and IC80. A high versus an intermediate or low antiproliferative effect was more common in NPM1-mutated (p = 0.002) and CD34-negative (p = 0.008) samples, and when NPM1 and FLT3 (p = 0.027) were combined. Presence of NPM1 mutation was associated with reduced viability after treatment with EHOP-016 (p = 0.014), ITX3 (p = 0.047), and NSC23766 (p = 0.003). Several cytokines crucial for leukemogenesis were reduced after culture, with the strongest effects observed for 1A-116 and NSC23766. Our findings suggest potent effects of Rac1 inhibition in primary AML cells and, interestingly, samples harboring NPM1 mutation seem more vulnerable.

Targeting MDM2 enhances antileukemia immunity after allogeneic transplantation via MHC-II and TRAIL-R1/2 upregulation

AbstractPatients with acute myeloid leukemia (AML) often achieve remission after allogeneic hematopoietic cell transplantation (allo-HCT) but subsequently die of relapse driven by leukemia cells resistant to elimination by allogeneic T cells based on decreased major histocompatibility complex II (MHC-II) expression and apoptosis resistance. Here we demonstrate that mouse-double-minute-2 (MDM2) inhibition can counteract immune evasion of AML. MDM2 inhibition induced MHC class I and II expression in murine and human AML cells. Using xenografts of human AML and syngeneic mouse models of leukemia, we show that MDM2 inhibition enhanced cytotoxicity against leukemia cells and improved survival. MDM2 inhibition also led to increases in tumor necrosis factor-related apoptosis-inducing ligand receptor-1 and -2 (TRAIL-R1/2) on leukemia cells and higher frequencies of CD8+CD27lowPD-1lowTIM-3low T cells, with features of cytotoxicity (perforin+CD107a+TRAIL+) and longevity (bcl-2+IL-7R+). CD8+ T cells isolated from leukemia-bearing MDM2 inhibitor-treated allo-HCT recipients exhibited higher glycolytic activity and enrichment for nucleotides and their precursors compared with vehicle control subjects. T cells isolated from MDM2 inhibitor-treated AML-bearing mice eradicated leukemia in secondary AML-bearing recipients. Mechanistically, the MDM2 inhibitor-mediated effects were p53-dependent because p53 knockdown abolished TRAIL-R1/2 and MHC-II upregulation, whereas p53 binding to TRAILR1/2 promotors increased upon MDM2 inhibition. The observations in the mouse models were complemented by data from human individuals. Patient-derived AML cells exhibited increased TRAIL-R1/2 and MHC-II expression on MDM2 inhibition. In summary, we identified a targetable vulnerability of AML cells to allogeneic T-cell–mediated cytotoxicity through the restoration of p53-dependent TRAIL-R1/2 and MHC-II production via MDM2 inhibition.

CKS1 inhibition depletes leukemic stem cells and protects healthy hematopoietic stem cells in acute myeloid leukemia.

Acute myeloid leukemia (AML) is an aggressive hematological disorder comprising a hierarchy of quiescent leukemic stem cells (LSCs) and proliferating blasts with limited self-renewal ability. AML has a dismal prognosis, with extremely low two-year survival rates in the poorest cytogenetic risk patients, primarily due to the failure of intensive chemotherapy protocols to deplete LSCs, and the significant toxicity towards healthy hematopoietic cells. Whilst much work has been done to identify genetic and epigenetic vulnerabilities in AML LSCs, little is known about protein homeostasis in drug resistance and relapse. By targeting the proteostatic regulator CKS1, we demonstrate a dual role for CKS1-dependent protein degradation in reducing AML blasts in vivo, and importantly depleting LSCs, whilst inhibition of CKS1 has the opposite effect on normal hematopoiesis, protecting normal hematopoietic stem cells from chemotherapeutic toxicity. Together these findings demonstrate CKS1-dependent proteostasis is a key vulnerability in malignant stem cell biology.

Engineered Nanoparticles as Potential Therapeutics for Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a malignancy associated with poor prognosis. Particularly, older patients suffer greatly from the standard chemotherapy and have a 5‐year survival of only 4%. Hence, new therapeutic agents with higher specificity and lower general cytotoxicity are urgently required.We have discovered that positively charged amino‐functionalized polystyrene nanoparticles (NP‐PS+) induce accumulation of acidic vesicular organelles with elevated pH and impaired processing of procathepsin B leading to mTOR inhibition, activation of autophagy, and induction of caspase‐dependent apoptosis in leukemia cells, but not in normal human macrophages. The antileukemic effect of NP‐PS+ was also preserved in vivo, where NP‐PS+ inhibited proliferation and induced apoptosis in leukemia xenografts grown on chick chorioallantoic membranes.Similar to polystyrene particles, amino‐functionalized gold nanoparticles (NP‐Au+) exhibited selective cytotoxicity towards AML cell lines as well as primary patient‐derived AML cells. Thus, NP‐Au+ particles induced cell death in primary human leukemia cells and reduced their colony‐forming potential, whereas normal hematopoietic cells remained unaffected by the treatment with NP‐Au+. NP‐Au+ targeted specifically the oxidative mitochondrial respiration, which is, different to normal hematopoietic cells, the main source of energy production in AML blasts and leukemic stem cells. Different to NP‐Au+, conventional chemotherapeutics such ascytarabine act in a cell cycle‐dependent manner and target only on proliferating AML blasts but not on quiescent leukemic stem cells. In agreement with the in vitro data, NP‐Au+ exhibited antileukemic efficacy against primary human AML xenografted into mice applied either as monotherapy or as a cytarabine combination regimen in the absence of detectable adverse events.Thus, this engineered nanomaterial that targets particularly resistant quiescent leukemic stem cells holds great promise as a novel nanotherapeutic for the treatment of acute myeloid leukemia independent of its cytogenetic profile.

TH1 cytokines induce senescence in AML

Cancer testis antigen PRAME is over-expressed in a variety of malignant cells but is not or minimally expressed in normal non-germ line cells. Adoptive transfer of PRAME-specific T cells is thus under investigation in clinical trials as an innovative therapeutic option for acute myeloid leukemia (AML). However, their senescence-inducing activity has not been studied. This study therefore examines senescence induction in AML cells by PRAME-specific TH1 cells. Analysis of cell cycle and marker expression demonstrate that the supernatants of antigen-stimulated PRAME-specific TH1 cells induce senescence in AML cell lines Kasumi and Nomo-1 through combinative IFN-γ and TNF-α. Additionally IFN-γ and TNF-α secreted by TCR-activated Vδ2+ or CMV-specific T cells can also drive these AML cell lines into terminal growth arrest. G1/0 arrest is also suggested in patient-derived AML by TH1 cytokines or supernatants from Zoledronate-stimulated or aCD3/aCD28-stimulated PBMCs. Thus, we show for the first time that senescence is induced in AML cells by combined IFN-γ and TNF-α, and that these cytokines can be derived either from TCR-engineered CD4+ T cells, or intriguingly from Virus-specific as well as innate Vδ2+ T cells responding to their cognate antigens, namely T-cell responses targeting an antigen that is NOT expressed by the leukemic cells.

Interleukin-4 treatment reduces leukemia burden in acute myeloid leukemia.

Interleukin-4 (IL-4) is a signature cytokine pivotal in Type 2helper T cell (Th2) immune response, particularly in allergy and hypersensitivity. Interestingly, IL-4 increases endogenous levels of prostaglandin D2 (PGD2 ) and its metabolites, Δ12 -prostaglandin J2 (Δ12 -PGJ2 ) and 15-deoxy-Δ12,14 -prostaglandin J2 (15d-PGJ2 ), collectively called cyclopentenone PGs (CyPGs). However, the therapeutic role of IL-4 in hematologic malignancies remains unclear. Here, we employed a murine model of acute myeloid leukemia (AML), where human MLL-AF9 fusion oncoprotein was expressed in hematopoietic progenitor cells, to test the effect of IL-4 treatment in vivo. Daily intraperitoneal treatment with IL-4 at 60µg/kg/d significantly alleviated the severity of AML, as seen by decreased leukemia-initiating cells (LICs). The effect of IL-4 was mediated, in part, by the enhanced expression of hematopoietic- PGD2 synthase (H-PGDS) to effect endogenous production of CyPGs, through autocrine and paracrine signaling mechanisms. Similar results were seen with patient-derived AML cells cultured ex vivo with IL-4. Use of GW9662, a peroxisome proliferator-activated receptor gamma (PPARγ) antagonist, suggested endogenous CyPGs-PPARγ axis mediated p53-dependent apoptosis of LICs by IL-4. Taken together, our results reveal a beneficial role of IL-4 treatment in AML suggesting a potential therapeutic regimen worthy of clinical trials in patients with AML.

Ceramide-induced integrated stress response overcomes Bcl-2 inhibitor resistance in acute myeloid leukemia

AbstractInducing cell death by the sphingolipid ceramide is a potential anticancer strategy, but the underlying mechanisms remain poorly defined. In this study, triggering an accumulation of ceramide in acute myeloid leukemia (AML) cells by inhibition of sphingosine kinase induced an apoptotic integrated stress response (ISR) through protein kinase R–mediated activation of the master transcription factor ATF4. This effect led to transcription of the BH3-only protein Noxa and degradation of the prosurvival Mcl-1 protein on which AML cells are highly dependent for survival. Targeting this novel ISR pathway, in combination with the Bcl-2 inhibitor venetoclax, synergistically killed primary AML blasts, including those with venetoclax-resistant mutations, as well as immunophenotypic leukemic stem cells, and reduced leukemic engraftment in patient-derived AML xenografts. Collectively, these findings provide mechanistic insight into the anticancer effects of ceramide and preclinical evidence for new approaches to augment Bcl-2 inhibition in the therapy of AML and other cancers with high Mcl-1 dependency.

The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation.

The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor (TF) and the cohesin loader NIPBL regulate enhancer-dependent gene activity. Using mass spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that the glucocorticoid (GC) receptor (GR) interacts with NIPBL and the cohesin complex at the chromatin level, promoting loop extrusion and long-range gene regulation. Real-time single-molecule experiments show that loss of cohesin markedly diminishes the concentration of TF molecules at specific nuclear confinement sites, increasing TF local concentration and promoting gene regulation. Last, patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to GCs, suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, resulting in poor response to GC treatment.

A novel IgG-based FLT3xCD3 bispecific antibody for the treatment of AML and B-ALL

BackgroundIn lymphoid malignancies, the introduction of chimeric antigen receptor T (CAR-T) cells and bispecific antibodies (bsAbs) has achieved remarkable clinical success. However, such immunotherapeutic strategies are not yet established for...

Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies.

Identification of cell phenotypic states within heterogeneous populations, along with elucidation of their switching dynamics, is a central challenge in modern biology. Conventional single-cell analysis methods typically provide only indirect, static phenotypic readouts. Transmitted light images, on the other hand, provide direct morphological readouts and can be acquired over time to provide a rich data source for dynamic cell phenotypic state identification. Here, we describe an end-to-end deep learning platform, UPSIDE (Unsupervised Phenotypic State IDEntification), for discovering cell states and their dynamics from transmitted light movies. UPSIDE uses the variational auto-encoder architecture to learn latent cell representations, which are then clustered for state identification, decoded for feature interpretation, and linked across movie frames for transition rate inference. Using UPSIDE, we identified distinct blood cell types in a heterogeneous dataset. We then analyzed movies of patient-derived acute myeloid leukemia cells, from which we identified stem-cell associated morphological states as well as the transition rates to and from these states. UPSIDE opens up the use of transmitted light movies for systematic exploration of cell state heterogeneity and dynamics in biology and medicine.