Human Acute Myeloid Leukemia Stem Research Articles

TMIGD2 is an orchestrator and therapeutic target on human acute myeloid leukemia stem cells

Acute myeloid leukemia (AML) is initiated and sustained by a hierarchy of leukemia stem cells (LSCs), and elimination of this cell population is required for curative therapies. Here we show that transmembrane and immunoglobulin domain containing 2 (TMIGD2), a recently discovered co-stimulatory immune receptor, is aberrantly expressed by human AML cells, and can be used to identify and enrich functional LSCs. We demonstrate that TMIGD2 is required for the development and maintenance of AML and self-renewal of LSCs but is not essential for normal hematopoiesis. Mechanistically, TMIGD2 promotes proliferation, blocks myeloid differentiation and increases cell-cycle of AML cells via an ERK1/2-p90RSK-CREB signaling axis. Targeting TMIGD2 signaling with anti-TMIGD2 monoclonal antibodies attenuates LSC self-renewal and reduces leukemia burden in AML patient-derived xenograft models but has negligible effect on normal hematopoietic stem/progenitor cells. Thus, our studies reveal the function of TMIGD2 in LSCs and provide a promising therapeutic strategy for AML.

Purine Metabolism Modulates Leukemia Stem Cell Maintenance in MLL-Rearranged Acute Leukemia

Acute myeloid leukemia (AML) represents the most prevalent hematopoietic malignancy driven by leukemia stem cells (LSCs) and remains challenging to treat in adult patients. MLL rearrangement results in a genetically unique subtype of AML characterized by chromosomal translocations involving the MLL gene and over 80 fusion partners, including AF9 as one of the most common partners. The oncogenic MLL fusion proteins interact with multiple transcription and chromatin regulators, such as Menin, to induce leukemogenic stem cell gene programs and transform hematopoietic stem and progenitor cells. Although significant progress has been made in understanding the metabolic dysregulation in acute leukemia, such as alterations in glycolysis, energetic metabolism, amino acid metabolism, and fatty acid metabolism, the metabolic factors that modulate MLL fusion oncogenic transcriptional activity in AML remain incompletely elucidated. To identify novel metabolic vulnerabilities in MLL-rearranged AML, we performed a whole genome CRISPR dropout screen and profiled the metabolites of murine LSCs of MLL-AF9 murine model. This analysis revealed the purine biosynthesis pathway is essential for MLL-rearranged leukemia and that MLL-rearranged LSCs are enriched in metabolites of the purine biosynthesis pathway. Isotypoe incorporation experiments using [U- 13C]glucose demonstrated a high purine biosynthetic rate in the LSCs compared to bulk leukemia cells. Accordingly, human acute myeloid leukemia stem cells express high levels of the purine biosynthetic genes. Furthermore, we found that MYC, a well-known downstream target of MLL-AF9, mediates the enhanced purine synthesis in LSCs. These results demonstrate enhanced purine biosynthetic pathways in LSCs. We utilized genetic and pharmacological (mycophenolate mofetil, MMF, a purine biosynthesis inhibitor of IMPDH) approaches to target the enhanced purine metabolism and found inhibition of the purine synthesis pathway promotes myeloid differentiation of both murine and human LSCs. Metabolomics analysis reveals a remarkable reduction of purine metabolites. Supplementing the LSCs with guanosine, an intermediate metabolite of the purine biosynthesis pathway, substantially rescued the differentiation. Importantly, treatment of MLL-AF9-driven murine leukemia mice with MMF impaired LSCs function, prolonged leukemia survival, and reduced leukemia burden in the peripheral blood and bone marrow, while causing minimal effects on normal hematopoiesis. These results demonstrate the reliance on enhanced purine metabolism in LSCs maintenance. Previous work has shown that the purine biosynthesis pathway is essential for rRNA transcription in the nucleolus, which could be inhibited by CX-5461. To verify the essentiality of the rRNA transcription in MLL-rearranged LSCs, we treated MLL-AF9-induced murine LSCs cells with CX-5461 and found CX-5461 promotes myeloid differentiation of LSCs. Moreover, we found that the myeloid differentiation induced by MMF or CX-5461 is associated with reduced chromatin occupancy of the MLL-AF9 complex, especially Menin, and downregulated expression of MLL-AF9 target genes, such as Meis1, Hoxa9 and Myc, suggesting a regulatory role of nucleolar rRNA transcription on MLL-AF9 oncogenic gene expression program. We are currently focusing on the synergistic effects of targeting purine metabolism and Menin inhibition on AML suppression. Altogether, our findings reveal that purine metabolism maintains nucleolar rRNA transcription homeostasis to modulate MLL fusion complex-induced leukemogenic transcriptional activity in LSCs. The enhanced purine metabolism emerges as a crucial dependency for LSCs, providing potential targets for novel therapeutic strategies in treating MLL-rearranged leukemia.

Single Cell Correlation Analysis: A Novel Method to Analyze Single Cell RNA Sequencing Data Identifies a Self-Renewing Subpopulation of Human Acute Myeloid Leukemia Stem Cells

Introduction Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy. Despite early response to standard chemotherapy, 60-70% of patients relapse with treatment resistant disease and die of relapsed disease. Leukemia stem cells (LSCs), the subpopulation of leukemia cells with self-renewal capacity, can recapitulate leukemia to cause relapse. Ongoing work to define therapeutic targets that can block self-renewal would prevent relapse and disease progression in AML. Prior work has established that LSCs express a distinct gene expression profile. We sought to define the gene expression profile of self-renewal at the single-cell level because a precise understanding of the transcriptional basis for self-renewal could provide more effective therapeutic targets. Our group previously demonstrated that activated NRAS (NRAS G12V) mediates self-renewal in the LSC-enriched subpopulation of AML in the Mll-AF9/NRAS G12V mouse model of AML (Sachs 2014). Single cell RNA-sequencing (scRNA-seq) of the LSC-enriched subpopulation identified three distinct transcriptional profiles. Two genes that encode cell surface markers, Cd36 and Cd69, delineate these distinct profiles. Using in vivo leukemia engraftment assays, we found that only the CD36 -CD69 + LSC subgroup repopulates leukemia while the CD36 +CD69 - LSC subgroup does not, demonstrating that self-renewal capacity is limited to the CD36 -CD69 + subset of the LSC-enriched compartment (Sachs 2020). In contrast, the CD36 +CD69 - LSCs were highly proliferative while the CD36 -CD69 + LSCs were poorly proliferative. These experiments show that self-renewal and rapid proliferation are mutually exclusive features of LSCs, as has previously been shown in normal hematopoietic stem cells (Li 2013). Methods and Results We investigated whether primary human AML stem cells express the murine-derived single-cell self-renewal and proliferation gene expression profiles at the single-cell level. Current computational methods to compare single-cell gene expression profiles use arbitrary similarity scores and do not assess the statistical significance of their findings. Therefore, we developed a new computational method called Single cell Correlation Analysis (SCA). SCA is designed to quantitate the expression of a predefined profile in single-cell RNA sequencing data. The quantification of the expression profiles is assessed on a per-cell basis in an unsupervised manner, meaning that SCA does not rely on any pre-sorting or classification of the query cells. The significance of the quantitative metric (i.e. level of expression) is determined by permutation-based false discovery rate testing. SCA can therefore identify cells that express a profile of interest within a single-cell RNA sequencing dataset and incorporates a measure of statistical significance to that assignment. We used SCA to analyze scRNA-seq data from primary human AML samples. We used data from two samples sequenced by our group and previously published data from 16 samples (van Galen 2019). SCA identified cells that express the murine single-cell self-renewal profile in every sample (0.32-11.5%; FDR < 0.25). We sorted two primary human AML samples to isolate LSCs (CD34 +CD38 -) prior to single-cell capture and sequencing. SCA identified cells that express murine LSC self-renewal profile in both of these samples as well (8.9-11.3%; FDR < 0.25). Furthermore, with these analyses, we found that the single-cell profiles of self-renewal and proliferation were mutually exclusive in human LSCs, as they are in murine LSCs and normal HSCs. We performed gene set enrichment analysis (GSEA) and confirmed that the human cells that express the murine single cell self-renewal profile are enriched in previously reported LSC self-renewal gene expression profiles. Conclusion We present SCA, a novel computational method designed to quantitatively assess single-cell transcriptional datasets and evaluate the statistical significance of its results. Using this method, we demonstrate that primary human AML samples express the single-cell profiles of self-renewal that we previously validated experimentally. SCA-based identification of human self-renewing cells will allow us to interrogate novel transcriptional features of these cells in future studies.

Human acute myeloid leukemia stem cells: evolution of concept.

The history of human acute myeloid leukemia stem cells (AMLSCs) began in a seminal study performed by Lapidot and Dick, proving that only CD34+CD38- human primary acute myeloid leukemia (AML) cells can repopulate in severe combined immunodeficient mice. The concept of leukemic stem cells (LSCs) has impeded a huge change in the treatment strategy against AML from killing proliferating leukemic cells to eradicating quiescent/dormant LSCs. As next-generation sequencing technologies have developed, multiple and recurrent genetic mutations have been discovered in large cohorts of patients with AML, and the updated understanding of leukemogenesis has improved the old concept of LSC to a revised version of a serial developmental model of LSC; that is, pre-LSCs are generated as seeds by the first hit on epigenetic regulators, and then, leukemia-initiating LSCs emerge from seeds by the second hits on genes involved in transcription and signaling. Dreams for universal and targetable AMLSC biomarker sparing healthy hematopoietic stem cells have weakened after the confrontation of significant heterogeneity of AMLSCs from genomic and immunophenotypic viewpoints. However, there is still hope for effective targets for AMLSCs since there is evidence that grouped gene signatures, such as 17-gene LSC score, and common epigenetic signatures, such as HOXA clusters, independent of various gene mutations, exist. Recently, the LSC niche in the bone marrow has been actively investigated and has expanded our knowledge of the physiology and vulnerability of AMLSCs. Presently, an applicable treatment that always works in AMLSCs is lacking. However, we will find a way, we always have.

Exploring new molecules that regulate hematopoietic stem cells and early stages of lymphoid hematopoiesis: the functional significance of ESAM and SATB1

Hematopoietic stem cells (HSCs) possess multilineage differentiation capability, which sustains the production of blood and immune cells throughout life. However, the precise mechanisms by which HSCs initiate differentiation toward a particular lineage and the factors that attenuate their lymphopoietic potential with aging are yet to be elucidated. Our group has investigated this issue for over two decades. We initially developed a method for segregating early lymphoid progenitors from HSCs and identified two molecules: endothelial cell-selective adhesion molecule (ESAM), highly expressed in HSCs, and special AT-rich sequence binding protein 1 (SATB1), expressed in early lymphoid progenitors. ESAM marks HSCs across species, including humans. In addition to its significance in stress-induced hematopoiesis, ESAM is also useful in identifying features of human acute myeloid leukemia stem cells. Further, we determined the role of SATB1 in the early HSC differentiation processes toward the lymphoid lineage. Remarkably, SATB1 expression in HSCs significantly decreased with aging, whereas its exogenous induction in aged HSCs rejuvenated their lymphopoietic potential. Furthermore, SATB1-expressing HSCs demonstrated robust lymphopoietic and long-term reconstituting capability, whereas HSCs without SATB1 skewed toward the myeloid lineage. Thus, our continuing research has revealed the significance of ESAM and SATB1 in the fundamental biology of HSCs.

Single-Cell Transcriptional Profiling of Acute Myeloid Leukemia Identifies Prognostic Transcriptional Profiles at Diagnosis

Acute myeloid leukemia (AML) is a lethal cancer with a survival of less than 50%. Standard cytotoxic therapies frequently induce complete remission, but patients frequently relapse and die of their disease. Leukemia stem cells (LSCs) are the leukemia cells with self-renewal potential and ability to recapitulate the disease. In hematopoietic stem cells, the mechanisms of proliferation are distinct from self-renewal (Li et al. Nature 2013). Consequently, targeting proliferation may explain the failure of traditional chemotherapy to target LSCs and eradicate AML. Our goal is define the molecular mechanisms that allow AML to relapse. We previously showed that activated NRAS (NRASG12V) facilitates self-renewal in the LSC-enriched subpopulation of a mouse model of AML (Mll-AF9 / NRASG12V, Sachs et al. Blood 2014, Kim et al. Blood 2009). We hypothesize that understanding the NRAS-activated pathways required for self-renewal at the single-cell level can be used to identify clinically relevant features of human AML.We used single-cell RNA sequencing to identify the self-renewing cells among the LSC-enriched subgroup in this model (Mac1LowKit+Sca1+, “MKS”). We identified three discrete transcriptional profiles among the LSC-enriched subpopulation and found that that two of these profiles (Profile 1 and Profile 2) are NRASG12V-dependent. These two profiles can be differentiated by CD36 and CD69 expression. We sorted the MKS LSCs based on CD36 and CD69 expression. Sorted LSC subsets were transplanted into recipient mice to compare their ability to transfer leukemia as a measure of their self-renewal capacity. We found that MKS-CD36-CD69+ cells (consistent with Profile 1) rapidly transferred leukemia with high penetrance in 20 of 22 mice. In contrast, MKS-CD36+CD69- cells (Profile 2) failed transfer leukemia in most mice; only 2 of 25 of these mice developed AML (p < 0.004).In our previous work, we demonstrated that the NRASG12V-activated self-renewal gene expression profile that we identified in our murine model was expressed in human AML, suggesting that the gene expression behavior of LSCs from this model may recapitulate the gene expression behavior of human LSCs (Sachs et al. Blood 2014). We used our murine single-cell self-renewal transcriptional profile to define a 96-gene panel consisting of 88 genes from this profile and 8 housekeeping genes. We sorted primary, diagnostic human AML cells for leukemia stem and progenitor cells (CD34+CD38-) and performed single-cell qPCR on these cells using our 96-gene panel. We found that a subset of these human LSCs preferentially expresses Profile 1, the self-renewal gene expression profile that we identified in our murine model, and another subset preferentially expresses Profile 2 (the profile associated with no leukemia-reconstituting capacity).Next, we investigated whether CD36 and CD69 delineate clinically relevant transcriptional subgroups in human AML. We used previously published, clinically annotated gene expression datasets of human AML that include associated survival outcomes data (TCGA, GSE12417 (Metzeler et al. Blood 2008), and GSE6891 (Verhaak et al. Haematologica 2009)). Gene Cluster Expression Summary Score (GCESS, Scott et al. under review) analysis identified gene clusters associated with CD69 and CD36 in our murine single-cell dataset. We found that the CD36 and CD69-associated clusters are conserved in the human transcriptional datasets. More importantly, patients that express either the CD69 or the CD36-associated gene expression profile suffer from shorter survival times in these three, independent human transcriptional datasets.In these experiments, we use a murine model of AML to define the LSC self-renewal gene expression profile at the single-cell level and functionally validate this profile in vivo . Analogous to the murine model, a subset of human AML stem and progenitor cells expresses this LSC self-renewal gene expression profile at the single-cell level. Finally, we found that the gene expression profiles we identified in our murine single-cell data are associated with poor outcomes in human AML indicating that our single-cell gene expression analyses can be used to identify prognostic patient subgroups. These findings suggest that these gene expression profiles can be used to identify functional transcriptional modules associated with poor outcome in human AML. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

JAK/STAT Inhibition Targets TP53 altered Primary Human Acute Myeloid Leukemia Stem Cells

In acute myeloid leukemia (AML), the impact of genetic drivers on response to therapy and long-term survival has been well characterized. AML with complex cytogenetics and TP53 alterations (TP53Alt) is a poor-risk AML subtype that is largely insensitive to chemotherapy, modern targeted agents, and hematopoietic stem cell transplant leading to survival rates 0-10% at 1 year. In contrast, AML with favorable risk molecular features is highly sensitive to chemotherapy and confers survival rates of 50-70%. AML with intermediate risk molecular features can be responsive to chemotherapy and can be cured with hematopoietic stem cell transplant leading to overall survival rates of 30-60%. Leukemia stem cells (LSCs), the cells that recapitulate and propagate leukemia, are central to leukemia progression and relapse. Given the differences in chemo-sensitivity and clinical behavior of genetic subgroups of AML, we asked whether LSCs from poor risk AMLs exhibit distinct signaling activation profiles. We assembled a panel of 23 primary human AML samples with intermediate- and poor- risk genetics and used CyTOF (mass cytometry) to quantitatively measure the levels of immunophenotypic proteins and intracellular signaling molecules in each sample, at the single-cell level. We gated on CD34+CD123+CD3-CD19- cells (LSCs) and measured the level of intracellular signaling molecules within the LSCs of each sample. Notably, the intracellular signaling activation state of LSCs from each AML subtype was distinct; NFkB, pERK, p4EBP1, and pSTAT3 were uniquely upregulated in complex cytogenetics and TP53Alt LSCs, relative to LSCs from intermediate risk AML, suggesting that these signaling pathways may be important for LSC function in this AML subtype. Given that TP53Alt independently confer treatment resistance in AML, we focused on this genetic subgroup. We compared the gene expression profiles of TP53Alt and TP53-wild-type AML samples from the BEAT AML dataset (Tyner et al. Nature 2018) and found that the gene expression profiles of TP53Alt samples are enriched for gene sets representing JAK/STAT signaling, consistent with our CyTOF data, which identified activation of STAT3 in TP53Alt LSCs. A recent drug screen in AML demonstrated that a JAK1/2 kinase inhibitor, AZD1480, can reduce the in vitro viability of TP53-deleted AML cell lines (Nechiporuk et al. Ca Discovery 2019), but these effects were not tested in primary AML samples or on LSCs. Since LSCs confer treatment resistance, we investigated the effect of the AZD1480 on the LSC population in TP53Alt primary human AML samples. AZD1480 treatment abolished all colony formation in primary human TP53Alt AML samples (n=7, 6 replicates per sample, p&amp;lt;0.01). Treatment of these samples in liquid cultures led to a 50% reduction in LSC frequency. We used CyTOF to profile the intracellular signaling states of in vitro treated samples and found that AZD1480 attenuated pSTAT3, pSTAT5, p4EBP1, and NFkB in the LSCs of these samples. The mTOR/4EBp1 and NF༆B pathways have been implicated as drivers of self-renewal and LSC function in AML. Our data suggest that JAK/STAT inhibition may target these pathways in TP53Alt LSCs. These data demonstrate the unique signaling states of TP53Alt LSCs, relative to other LSCs, and show that inhibition of the JAK/STAT pathway specifically targets LSCs within human TP53Alt AML. Figure Disclosures No relevant conflicts of interest to declare.

The Novel Dihydroorotate Dehydrogenase (DHODH) Inhibitor PTC299 Inhibit De Novo Pyrimidine Synthesis with Broad Anti-Leukemic Activity Against Acute Myeloid Leukemia

Introduction: Acute myeloid leukemia (AML) is characterized by both aberrant proliferation and differentiation arrest at hematopoietic progenitor stages 1,2. AML relies upon de novo nucleotide synthesis to meet a dynamic metabolic landscape and to provide a sufficient supply of nucleotides and other macromolecules 3,4. Hence, we hypothesized that inhibition of de novo nucleotide synthesis would lead to depletion of the nucleotide pool and pyrimidine starvation in leukemic cells compared to their non-malignant counterparts and impact proliferative and differentiation inhibition pathways. PTC299 is an inhibitor of dihydroorotate dehydrogenase (DHODH), a rate limiting enzyme for de novo pyrimidine nucleotide synthesis that is currently in a clinical trial for the treatment of AML. Aim: We investigated the pre-clinical activity of PTC299 against AML in primary AML blasts and cytarabine-resistant cell lines. To confirm that PTC299 effects are due to inhibition of de novo pyrimidine nucleotide synthesis for leukemic growth, we specifically tested the impact of uridine and orotate rescue. In addition, a comprehensive analysis of alteration of metabolic signaling in PI3K/AKT pathways, apoptotic signatures and DNA damage responses were analyzed by Mass cytometry based proteomic analysis (CyTOF) and immunoblotting. The potential clinical relevance of DHODH inhibition was confirmed in an AML-PDX model. Results: The IC50s for all tested cell lines (at 3 day) and primary blasts (at 5-7 day) were in a very low nanomolar range: OCI-AML3 -4.43 nM, HL60 -59.7 nM and primary samples -18-90 nM. Treatment of AML in cytarabine-resistant cells demonstrated that PTC299 induced apoptosis, differentiation, and reduced proliferation with corresponding increase in Annexin V and CD14 positive cells (Fig.1). PTC299-induced apoptosis and inhibition of proliferation was rescued by uridine and orotate. To gain more mechanistic insights, we used an immunoblotting and mass cytometry (CyTOF) based approach to analyze changes in apoptotic and cell signaling proteins in OCI-AML3 cells. Apoptotic pathways were induced (cleaved PARP, cleaved Caspase-3) and DNA damage responses (TP53, γH2AX) and the PI3/AKT pathway were downregulated in response to PTC299. In isogenic cell lines, p53-wildtype cells were sustained and an increased DNA damage response with corresponding increase in apoptosis in comparison to p53-deficient cells was shown. (Fig.2) In a PDX mouse model of human AML, PTC299 treatment improved survival compared to mice treated with vehicle (median survival 40 days vs. 30 days, P=0.0002) (Fig.3). This corresponded with a reduction in the bone marrow burden of leukemia with increased expression of differentiation markers in mice treated with PTC299 (Fig.3). Conclusion: PTC299 is a novel dihydroorotate dehydrogenase (DHODH) inhibitor that triggers differentiation, apoptosis and/or inhibition of proliferation in AML and is being tested in a clinical trials for the treatment of acute myeloid malignancies. Reference: 1. Thomas D, Majeti R. Biology and relevance of human acute myeloid leukemia stem cells. Blood 2017; 129(12): 1577-1585. e-pub ahead of print 2017/02/06; doi: 10.1182/blood-2016-10-696054 2. Quek L, Otto GW, Garnett C, Lhermitte L, Karamitros D, Stoilova B et al. Genetically distinct leukemic stem cells in human CD34- acute myeloid leukemia are arrested at a hemopoietic precursor-like stage. The Journal of experimental medicine 2016; 213(8): 1513-1535. e-pub ahead of print 2016/07/06; doi: 10.1084/jem.20151775 3. Villa E, Ali ES, Sahu U, Ben-Sahra I. Cancer Cells Tune the Signaling Pathways to Empower de Novo Synthesis of Nucleotides. Cancers (Basel) 2019; 11(5). e-pub ahead of print 2019/05/22; doi: 10.3390/cancers11050688 4. DeBerardinis RJ, Chandel NS. Fundamentals of cancer metabolism. Sci Adv 2016; 2(5): e1600200. e-pub ahead of print 2016/07/08; doi: 10.1126/sciadv.1600200 Disclosures Weetall: PTC Therapeutic: Current Employment. Sheedy:PTC therapeutics: Current Employment. Ray:PTC Therapeutics Inc.: Current Employment. Konopleva:Genentech: Consultancy, Research Funding; Rafael Pharmaceutical: Research Funding; Ablynx: Research Funding; Ascentage: Research Funding; Agios: Research Funding; Kisoji: Consultancy; Eli Lilly: Research Funding; AstraZeneca: Research Funding; Reata Pharmaceutical Inc.;: Patents &amp; Royalties: patents and royalties with patent US 7,795,305 B2 on CDDO-compounds and combination therapies, licensed to Reata Pharmaceutical; AbbVie: Consultancy, Research Funding; Calithera: Research Funding; Cellectis: Research Funding; Amgen: Consultancy; Stemline Therapeutics: Consultancy, Research Funding; Forty-Seven: Consultancy, Research Funding; F. Hoffmann La-Roche: Consultancy, Research Funding; Sanofi: Research Funding. Andreeff:Amgen: Research Funding; Daiichi-Sankyo; Jazz Pharmaceuticals; Celgene; Amgen; AstraZeneca; 6 Dimensions Capital: Consultancy; Daiichi-Sankyo; Breast Cancer Research Foundation; CPRIT; NIH/NCI; Amgen; AstraZeneca: Research Funding; Centre for Drug Research &amp; Development; Cancer UK; NCI-CTEP; German Research Council; Leukemia Lymphoma Foundation (LLS); NCI-RDCRN (Rare Disease Clin Network); CLL Founcdation; BioLineRx; SentiBio; Aptose Biosciences, Inc: Membership on an entity's Board of Directors or advisory committees. Borthakur:BioLine Rx: Consultancy; BioTherix: Consultancy; Nkarta Therapeutics: Consultancy; Treadwell Therapeutics: Consultancy; Xbiotech USA: Research Funding; Polaris: Research Funding; AstraZeneca: Research Funding; BMS: Research Funding; BioLine Rx: Research Funding; Cyclacel: Research Funding; GSK: Research Funding; Jannsen: Research Funding; Abbvie: Research Funding; Novartis: Research Funding; Incyte: Research Funding; PTC Therapeutics: Research Funding; FTC Therapeutics: Consultancy; Curio Science LLC: Consultancy; PTC Therapeutics: Consultancy; Argenx: Consultancy; Oncoceutics: Research Funding.

Diminished AHR Signaling Drives Human Acute Myeloid Leukemia Stem Cell Maintenance.

Eliminating leukemic stem cells (LSC) is a sought after therapeutic paradigm for the treatment of acute myeloid leukemia (AML). While repression of aryl hydrocarbon receptor (AHR) signaling has been shown to promote short-term maintenance of primitive AML cells in culture, no work to date has examined whether altered AHR signaling plays a pathologic role in human AML or whether it contributes at all to endogenous LSC function. Here, we show AHR signaling is repressed in human AML blasts and preferentially downregulated in LSC-enriched populations within leukemias. A core set of AHR targets are uniquely repressed in LSCs across diverse genetic AML subtypes. In vitro and in vivo administration of the specific AHR agonist FICZ significantly impaired leukemic growth, promoted differentiation, and repressed self-renewal. Furthermore, LSCs suppressed a set of FICZ-responsive AHR target genes that function as tumor suppressors and promoters of differentiation. FICZ stimulation did not impair normal hematopoietic stem and progenitor (HSPC) function, and failed to upregulate a prominent LSC-specific AHR target in HSPCs, suggesting that differential mechanisms govern FICZ-induced AHR signaling manifestations in HSCs versus LSCs. Altogether, this work highlights AHR signaling suppression as a key LSC-regulating control mechanism and provides proof of concept in a preclinical model that FICZ-mediated AHR pathway activation enacts unique transcriptional programs in AML that identify it as a novel chemotherapeutic approach to selectively target human LSCs. SIGNIFICANCE: The AHR pathway is suppressed in leukemic stem cells (LSC), therefore activating AHR signaling is a potential therapeutic option to target LSCs and to treat acute myeloid leukemia.

Sirpαfc Treatment Targets Human Acute Myeloid Leukemia Stem Cells

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy and is the most common type of acute leukemia in adults. Although a majority of patients achieve remission following cytotoxic chemotherapy, most will relapse and ultimately die. Therapy resistance and relapse are driven by leukemia stem cells (LSC). Evidence of genetic and functional heterogeneity in the LSC compartment underscores the importance of developing therapeutic strategies that will target all subclones effectively. We previously showed that LSCs in AML depend on CD47-SIRPα interaction to evade immune surveillance (Theocharides et al, JEM 2012). CD47 acts as a "do not eat me" signal that binds to the inhibitory receptor SIRPα on macrophages and masks cancer cells from macrophage-mediated phagocytosis. TTI-621 (Trillium Therapeutics Inc., Ontario, Canada) is a human SIRPαFc protein formed by fusing the IgV doman of human SIRPα to a human IgG1-Fc moiety; it is designed to bind CD47 on leukemia cells and disrupt its interaction with SIRPα on host macrophages. Our previous studies in AML cell lines and a small number of primary AML samples demonstrated increased phagocytosis in vitro and decreased engraftment in xenotransplant models following SIRPαFc treatment (Theocharides et al, JEM 2012, Petrova et al, Clin Cancer Res 2017). Here, we tested the efficacy of TTI-621 against a broad panel of primary AML samples in xenotransplantation models to determine efficacy and response rates in this heterogeneous disease. Bulk cells obtained from the peripheral blood of 30 AML patients representing a broad range of cytogenetic and molecular subtypes were transplanted intrafemorally into sublethally-irradiated NSG mice. After a 2-week engraftment period, mice were treated with either SIRPαFc or control IgG by intraperitoneal injection 3×/week for 4 weeks, following which leukemic engraftment was determined by flow cytometry. In all but 1 sample, a significant reduction in AML engraftment was seen in SIRPαFc-treated mice compared to controls. For 23 samples defined as good responders, SIRPαFc treatment resulted in 91% (range 53-100%, p&lt;0.0001) and 98% (range 88-100%, p&lt;0.0001) reduction of leukemic engraftment in the injected femur and in non-injected bones, respectively, compared to controls. Six samples demonstrated a lesser response that was largely observed in the non-injected bones, with relative reduction of 69% (range 43-93%, p=0.03); these samples were defined as partial responders. The majority of samples from patients with unfavorable features such as age &gt;60, adverse cytogenetic risk, and secondary AML, as well as samples obtained from relapsed/resistant patients, were classified as good responders. Notably, 20 of 23 good responders had a high LSC17 score, which we have shown is associated with poor initial therapy response and short survival following standard treatments (Ng et al, Nature 2016). To determine whether SIRPαFc treatment killed LSCs, we transplanted leukemia cells harvested from primary treated mice into untreated secondary recipients at limiting dilution. For four independent samples, including three partial responders and the one non-responder, we observed a significantly lower LSC frequency (3.9-10.3 fold, p=0.002-0.024) in mice transplanted with SIRPαFc-treated cells compared to controls, indicating that SIRPαFc treatment reduced LSC numbers in primary mice, despite partial or no reduction of bulk disease. Our data demonstrate that SIRPαFc effectively targets LSCs in a human AML xenotransplantion model with high response rates across a heterogeneous cohort of primary AML samples, including samples with unfavorable risk features. SIRPαFc may be most effective in the remission setting as maintenance therapy for patients with detectable residual disease, to eradicate residual LSCs and prevent relapse. Disclosures Jin: Trillium Therapeutics: Other: licensing agreement. Wong:Trillium Therapetuics: Employment. Uger:Trillium Therapetuics: Employment. Minden:Trillium Therapetuics: Other: licensing agreement. Danska:Trillium Therapeutics: Other: licensing agreement, Research Funding. Wang:Pfizer AG Switzerland: Honoraria, Other: Travel and accommodation; Pfizer International: Honoraria, Other: Travel and accommodation; Trilium therapeutics: Other: licensing agreement, Research Funding; NanoString: Other: Travel and accommodation.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

IGFBP7 Induces Differentiation and Loss of Survival of Human Acute Myeloid Leukemia Stem Cells without Affecting Normal Hematopoiesis

Leukemic stem cells (LSCs) are thought to be the major cause of the recurrence of acute myeloid leukemia (AML) due to their potential for self-renewal. To identify therapeutic strategies targeting LSCs, while sparing healthy hematopoietic stem cells (HSCs), we performed gene expression profiling of LSCs, HSCs, and leukemic progenitors all residing within the same AML bone marrow and identified insulin-like growth factor-binding protein 7 (IGFBP7) as differentially expressed. Low IGFBP7 is a feature of LSCs and is associated with reduced chemotherapy sensitivity. Enhancing IGFBP7 by overexpression or addition of recombinant human IGFBP7 (rhIGFBP7) resulted in differentiation, inhibition of cell survival, and increased chemotherapy sensitivity of primary AML cells. Adding rhIGFBP7 reduced leukemic stem and/or progenitor survival and reversed a stem-like gene signature, but it had no influence on normal hematopoietic stem cell survival. Our data suggest a potential clinical utility of the addition of rhIGFBP7 to current chemotherapy regimens to decrease AML relapse rates.

Inhibition of Nicotinamide Phosphoribosyltransferase (NAMPT) Activity Selectively Targets Human Acute Myeloid Leukemia Stem Cells

Acute myeloid leukemia (AML) is an aggressive malignancy of the bone marrow associated with poor clinical outcomes. Conventional chemotherapies are effective in debulking the leukemic burden in most AML patients. However, a small population of disease-sustaining leukemic stem cells (LSCs) frequently persists and contributes to relapsed disease. Novel therapies that eradicate LSCs have the potential to improve clinical outcomes in AML.To discover novel anti-LSC agents, we performed a high-throughput flow cytometry-based drug screen of 1,220 compounds against a primary AML sample (8227). This sample harbors distinct subsets defined by CD34 and CD38 expression, and LSC activity assayed by xenotransplantation is restricted to the CD34+CD38- fraction. Through this screen, we identified compounds that selectively depleted the CD34+CD38- fraction including four structurally-unrelated NAMPT inhibitors (FK866, STF-118804, GMX1778, and KPT-9274). These inhibitors also depleted the LSC-enriched CD34+CD38- fraction in two other primary AML samples, indicating that the effect was not unique to 8227 cells. To further evaluate their impact on LSCs in 8227, we measured the expression of 104 genes that were previously found to be differentially expressed between LSC+ and LSC- cell fractions isolated from patient samples. Treatment with NAMPT inhibitors reduced the correlation between the measured LSC gene signature and the LSC+ reference profile, providing additional evidence for their anti-LSC activity.To determine whether the selective loss of CD34+CD38- cells was due to cell death or differentiation, we sorted subsets of 8227 cells based on CD34 and CD38 expression and treated each fraction with FK866. NAMPT inhibition preferentially triggered apoptosis as measured by Annexin V staining in the CD34+CD38- and CD34+CD38+ fractions over the CD34- fraction. We did not observe significant changes in the expression of CD34, CD38, or other myeloid differentiation markers (CD14 and CD15) in the remaining viable cells.Our subsequent mechanistic studies focused on KPT-9274 because it is the furthest along in clinical development. NAMPT is the rate-limiting enzyme in the NAD+ salvage pathway that converts nicotinamide (NAM) to nicotinamide mononucleotide (NMN), a direct NAD+ precursor. To confirm a decrease in intracellular NAD+ with KPT-9274 treatment, we introduced expression of genetically-encoded biosensors for measuring NAD+ levels in different cellular compartments in an AML cell line. KPT-9274 treatment for 15 hours lowered the free NAD+ pool in the cytosol and mitochondria but not in nucleus. To determine whether the drop in NAD+ was necessary for the effects of KPT-9274 on LSCs, we supplemented the primary AML samples with nicotinamide riboside (NR) which can be directly converted to NMN, thereby bypassing the requirement for NAMPT activity to generate NAD+. The addition of NR completely rescued the effects of KPT-9274 on the CD34+CD38- fraction. Niacin can also generate NAD+ through an alternative pathway that depends on nicotinic acid phosphoribosyltransferase (NAPRT). However, niacin supplementation failed to rescue the effects of NAMPT inhibition which correlated with the lack of NAPRT expression in LSC-enriched CD34+CD38- cells.Next, we studied the effects of KPT-9274 on normal CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from human cord blood. Although HSPCs were sensitive to the pro-apoptotic effects of KPT-9274, their survival was fully rescued by both NR and niacin. The rescue by niacin correlated with a higher expression of NAPRT in HSPCs. As the blood concentration of niacin is ~1,000 fold higher than that of NR, KPT-9274 is predicted to have a favorable therapeutic window in vivo. To demonstrate its in vivo activity, we treated immunodeficient NOD/SCID/IL2Rγ-null (NSG) mice engrafted with a luciferase-tagged AML cell line (OCI-AML3) with KPT-9274 at a dose of 150 or 250 mg/kg/day or vehicle control for 50 consecutive days by oral administration. KPT-9274 treatment significantly lowered leukemia burden and prolonged survival in both dosing cohorts.In summary, our results indicate that NAMPT inhibition represents an effective approach to target human LSCs through reduction in intracellular NAD+ levels and induction of apoptosis. Our data provide the preclinical rationale for investigating the use of KPT-9274 in AML clinical trials. DisclosuresChan:Genentech: Research Funding; Celgene: Research Funding; AbbVie: Research Funding.

AML Cells Express Exclusively the Long Isoform of LEF1 and Are Highly Vulnerable to Blockage of LEF1-β-Catenin Binding

Despite progress in the understanding of the biology of acute myeloid leukemia (AML) in recent years, mortality of the disease is still high. One reason for this is drug resistance of leukemic stem cells (LSCs), which are responsible for leukemic growth and relapse. Thus, there is great interest in understanding factors driving LSCs and in key differences between normal hematopoietic stem cells (HSC) and their leukemic counterparts. LEF1 acts via the canonical Wnt pathway by interacting with β-catenin (long isoform). Of note, a natural isoform of Lef1 is expressed in hematopoiesis, which lacks the β-catenin binding domain at the N-terminus and whose function is not well defined in normal and leukemic hematopoiesis (short isoform). Here we demonstrate in a cohort of 111 AML primary patient samples with normal karyotype, that exclusively the long isoform of LEF1 is expressed. These analyses were extended to functionally validated LSC populations, using the NSG xenograft model, and confirmed the highly predominant expression of the long isoform of LEF1 and the virtual lack of expression of the short isoform. This stood in clear contrast to normal HSCs: in highly purified CD34-/CD38-/CD93high HSCs, categorized as most immature human quiescent HSC population, as well as CD34+/CD49f+/CD90+ and CD34+/CD49f+/CD90- human HSCs, no expression of the long isoform could be detected with an exclusive expression of the short isoform of LEF1. In multipotent progenitors MPPs (CD34+/CD49f-/CD90- ) there was a shift towards expression of both isoforms. Thus, LSCs show an inverse expression pattern of LEF1 isoforms compared to their normal counterparts. To understand the function of the long versus short isoform, we cloned the murine long isoform and the Lef1 isoform lacking the ß-catenin binding domain at the N-terminus into retroviral expression vectors and transduced primary murine bone marrow cells. In line with our observation of the exclusive expression of the long isoform of LEF1 in human AML stem cells, we previously showed that expression of the long isoform induces AML in transplanted mice (Petropoulos et al., JEM 2008). In contrast, expression of the short isoform did not have any major effect at the level of repopulating stem cells as determined by quantifying CRU frequency in limit dilution transplantation assays. Furthermore, ChiP-Seq analyses showed predominant binding of the short isoform on genes associate re-entry of HSCs into quiescence such as like CD81 and Wnt5a, in line with our observation of exclusive expression of the short isoform in the human CD34-/CD38-/CD93high HSC population. Based on the observation that AML cells exclusively express the long isoform, which acts via β-catenin binding, we hypothesized that AML cells would be particularly vulnerable to drugs blocking the binding of LEF1-β-catenin binding. The small molecule inhibitors Cercosporin and Calphostin C (100nM), previously shown to block LEF1-β-catenin binding in CLL cells, reduced colony growth of the AML cell line THP1 by 100 % (p<0,0001) and impaired engraftment in NSG mice (26d control vs 32d Cercosporin 100nM, p=0,0013, and 53d Calphostin C, p= 0,0022). In contrast, normal CD34+ cord blood cells were much less vulnerable to these compounds (0,2% reduction of CFC growth with Cercosporin, 8% reduction in Calphostin C, not significant). Taken together, these data point to distinct LEF1 isoform expression in AML, thereby creating high vulnerability towards blockage of LEF1-β-catenin binding and forming a potentially targetable Achilles' heel at the level of leukemic stem cells. DisclosuresMetzeler:Novartis: Consultancy; Celgene: Consultancy, Research Funding. Buske:Roche: Honoraria, Research Funding; Bayer: Research Funding; Janssen: Honoraria, Research Funding.

Inhibition of Amino Acid Metabolism Selectively Targets Human Leukemia Stem Cells

In this study we interrogated the metabolome of human acute myeloid leukemia (AML) stem cells to elucidate properties relevant to therapeutic intervention. We demonstrate that amino acid uptake, steady-state levels, and catabolism are all elevated in the leukemia stem cell (LSC) population. Furthermore, LSCs isolated from de novo AML patients are uniquely reliant on amino acid metabolism for oxidative phosphorylation and survival. Pharmacological inhibition of amino acid metabolism reduces oxidative phosphorylation and induces cell death. In contrast, LSCs obtained from relapsed AML patients are not reliant on amino acid metabolism due to their ability to compensate through increased fatty acid metabolism. These findings indicate that clinically relevant eradication of LSCs can be achieved with drugs that target LSC metabolic vulnerabilities.

AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells.

Leukemia stem cells (LSCs) are thought to drive the genesis of acute myeloid leukemia (AML) as well as relapse following chemotherapy. Because of their unique biology, developing effective methods to eradicate LSCs has been a significant challenge. In the present study, we demonstrate that intrinsic overexpression of the mitochondrial dynamics regulator FIS1 mediates mitophagy activity that is essential for primitive AML cells. Depletion of FIS1 attenuates mitophagy and leads to inactivation of GSK3, myeloid differentiation, cell cycle arrest, and a profound loss of LSC self-renewal potential. Further, we report that the central metabolic stress regulator AMPK is also intrinsically activated in LSC populations and is upstream of FIS1. Inhibition of AMPK signaling recapitulates the biological effect of FIS1 loss. These data suggest a model in which LSCs co-opt AMPK/FIS1-mediated mitophagy as a means to maintain stem cell properties that may be otherwise compromised by the stresses induced by oncogenic transformation.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

PHYTOCHEMICAL AND CYTOTOXIC INVESTIGATIONS OF THE HEARTWOOD OF CAESALPINIA SAPPAN LINN

Objective: The purpose of this study was to identify the chemical constituents in the dichloromethane extract by gas chromatography–mass spectrometry (GC–MS) analysis and evaluate the cytotoxic effects on leukemia cells of isolated compounds from Caesalpinia sappan Linn.Methods: Dichloromethane extract obtained from the heartwood of C. sappan was investigated by GC–MS and column chromatography. Cytotoxic effects on leukemia cells of the isolated compounds were examined using MTT assay.Results: The GC–MS analysis of dichloromethane extract from C. sappan revealed the presence of 14 compounds. Linoleic acid and β-sitosterol were found to be the major compounds presenting in 14% and 13%, respectively. The separation of the dichloromethane extract led to the isolation of brazilin (1) as a major compound, together with lupeol (2), and a mixture of β-sitosterol (3), and stigmasterol (4). Their structures were elucidated based on spectroscopic methods. Brazilin (1) showed a cytotoxic effect on human acute myeloid leukemia cell (KG1) and human acute myeloid leukemia stem cell (KG1a) with inhibitory concentration at 50% growth (IC50) values of 13.30 ± 0.49 and 12.24 ± 1.08 μg/ml, respectively. Conclusion: Many groups of phytochemical compounds in the dichloromethane extract of C. sappan were detected by GC–MS analysis. Some of them have been reported to possess various biological activities. Moreover, brazilin (1) isolated compound from C. sappan shows cytotoxicity on leukemia cells, which could be a potential anticancer property.

MiR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells

SummaryTo investigate miRNA function in human acute myeloid leukemia (AML) stem cells (LSC), we generated a prognostic LSC-associated miRNA signature derived from functionally validated subpopulations of AML samples. For one signature miRNA, miR-126, high bioactivity aggregated all in vivo patient sample LSC activity into a single sorted population, tightly coupling miR-126 expression to LSC function. Through functional studies, miR-126 was found to restrain cell cycle progression, prevent differentiation, and increase self-renewal of primary LSC in vivo. Compared with prior results showing miR-126 regulation of normal hematopoietic stem cell (HSC) cycling, these functional stem effects are opposite between LSC and HSC. Combined transcriptome and proteome analysis demonstrates that miR-126 targets the PI3K/AKT/MTOR signaling pathway, preserving LSC quiescence and promoting chemotherapy resistance.

In Vivo Response to Cytarabine Chemotherapy Uncovers the Role of the Oxidative and Energetic Metabolism in the Chemoresistance of Human Primary AML Stem Cells

Resistant cells to conventional chemotherapy - which targets DNA synthesis - are thought to be rare and enriched in quiescent leukemic stem cells (LSCs) in acute myeloid leukemia (AML). In order to develop an improved understanding of chemotherapy resistance in AML, we analyzed the response to cytarabine (Ara-C) in our xenograft model with 20 primary AML patient specimens from two clinical sites. After demonstrating AML engraftment, mice are treated with Ara-C given IP daily for 5 days as a single agent at 60 mg/kg daily, which correlates with human dosing. In all mice treated with this regimen, there was a 4- to 46-fold cytoreductive effect at 1 week post-treatment. While in vivo Ara-C treatment induces changes in CD34pos CD38pos/neg phenotypes of 50% of AML-engrafted mice, this treatment does not induce any significant changes in cell cycle distribution and does not enrich in G0 quiescent cells in AML-engrafted mice. Surprisingly we observed that Ara-C induces a decrease or no change in the frequency of SL-ICs (control, 1:2,500-21,900 versus Ara-C, 1:4,500-34,200), suggesting that Ara-C would not spare LSCs in vivo and equally kills both cycling and quiescent cells. Furthermore, transcriptomic analysis of Ara-C residual leukemic cells (RLCs) from three different patient-derived xenografts confirmed that RLCs are not enriched in stem cell marker genes at 1 week post-treatment. However, our gene signature of the in vivo AML resistance is enriched in genes involved in inflammatory, immune and stress response. When tested in three independent AML cohorts (Verhaak et al. 2009; TGCA, 2011; Metzeler et al. 2011), this signature is associated with an unfavorable prognosis in patients treated with intensive chemotherapy. Finally we have shown that RLCs are PIMOpos cells with both high ROS content and active mitochondrial mass and membrane potential in AraC-treated xenografted mice compared to control mice. Accordingly, AML cells exhibiting high OXPHOS energetic phenotype are resistant to Ara-C chemotherapy in vivo while low OXPHOS AML cells are sensitive to AraC in NSG mice. Altogether these results suggest a novel model of cytarabine chemotherapy resistance in AML based on the oxidative and mitochondrial energy metabolism in vivo. DisclosuresNo relevant conflicts of interest to declare.