Acute Myeloid Leukemia Bone Marrow Research Articles

High STAT4 expression correlates with poor prognosis in acute myeloid leukemia and facilitates disease progression by upregulating VEGFA expression.

The aim of our study is to explore the mechanism of transcription-4 (STAT4) in acute myeloid leukemia (AML). STAT4 level in AML bone marrow samples/cells was analyzed using bioinformatics and quantitative real-time PCR. The correlation between high STAT4 expression and the prognosis of AML patients was analyzed. The viability, apoptosis, and angiogenesis of AML cells were detected. The levels of STAT4, vascular endothelial growth factor A (VEGFA), and apoptosis-related proteins (Bcl-2 and Bax) in transfected AML cells were examined. STAT4 level was upregulated in AML. STAT4 silencing decreased the viability and angiogenesis, yet increased the apoptosis of AML cells, while overexpressed STAT4 did conversely. VEGFA silencing counteracted the impacts of overexpressed STAT4 upon promoting viability and angiogenesis as well as repressing the apoptosis of AML cells. High STAT4 expression was correlated with poor prognosis of AML patients and facilitated disease progression via upregulating VEGFA expression.

Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing.

Acute myeloid leukemia (AML) is a complex and heterogeneous group of aggressive hematopoietic stem cell disease. The presence of diverse and functionally distinct populations of leukemia cells within the same patient's bone marrow or blood poses a significant challenge in diagnosing and treating AML. A substantial proportion of AML patients demonstrate resistance to induction chemotherapy and a grim prognosis upon relapse. The rapid advance in next generation sequencing technologies, such as single-cell RNA-sequencing (scRNA-seq), has revolutionized our understanding of AML pathogenesis by enabling high-resolution interrogation of the cellular heterogeneity in the AML ecosystem, and their transcriptional signatures at a single-cell level. New studies have successfully characterized the inextricably intertwined interactions among AML cells, immune cells and bone marrow microenvironment and their contributions to the AML development, therapeutic resistance and relapse. These findings have deepened and broadened our understanding the complexity and heterogeneity of AML, which are difficult to detect with bulk RNA-seq. This review encapsulates the burgeoning body of knowledge generated through scRNA-seq, providing the novel insights and discoveries it has unveiled in AML biology. Furthermore, we discuss the potential implications of scRNA-seq in therapeutic opportunities, focusing on immunotherapy. Finally, we highlight the current limitations and future direction of scRNA-seq in the field.

Rhein exerts anti-multidrug resistance in acute myeloid leukemia via targeting FTO to inhibit AKT/mTOR.

Chemotherapy failure and resistance are the leading causes of mortality in patients with acute myeloid leukemia (AML). However, the role of m6A demethylase FTO and its inhibitor rhein in AML and AML drug resistance is unclear. Therefore, this study aimed to investigate the antileukemic effect of rhein on AML and explore its potential mechanisms underlying drug resistance. Bone marrow fluid was collected to assess FTO expression in AML. The Cell Counting Kit 8 reagent was used to assess cell viability. Migration assays were conducted to assess the cell migration capacity. Flow cytometry was used to determine the apoptotic effects of rhein and western blot analysis was used to detect protein expression. Online SynergyFinder software was used to calculate the drug synergy scores. The in-vivo antileukemic effect of rhein was assessed in an AML xenograft mouse model. We analyzed different types of AML bone marrow specimens to confirm that FTO is overexpressed in AML, particularly in cases of multidrug resistance. Subsequently, we conducted in-vivo and in-vitro investigations to explore the pharmacological activity and mechanism of rhein in AML and AML with multidrug resistance. The findings demonstrated that rhein effectively suppressed the proliferation and migration of AML cells in a time- and dose-dependent manner and induced apoptosis. Rhein targets FTO, inhibits the AKT/mTOR pathway, and exhibits synergistic antitumor effects when combined with azacitidine. This study elucidates the significant role of FTO and its inhibitor rhein in AML and AML with multidrug resistance, providing new insights for overcoming multidrug resistance in AML.

Epigenetic control over the cell-intrinsic immune response antagonizes self-renewal in acute myeloid leukemia

AbstractEpigenetic modulation of the cell-intrinsic immune response holds promise as a therapeutic approach for leukemia. However, current strategies designed for transcriptional activation of endogenous transposons and subsequent interferon type-I (IFN-I) response, show limited clinical efficacy. Histone lysine methylation is an epigenetic signature in IFN-I response associated with suppression of IFN-I and IFN-stimulated genes, suggesting histone demethylation as key mechanism of reactivation. In this study, we unveil the histone demethylase PHF8 as a direct initiator and regulator of cell-intrinsic immune response in acute myeloid leukemia (AML). Site-specific phosphorylation of PHF8 orchestrates epigenetic changes that upregulate cytosolic RNA sensors, particularly the TRIM25-RIG-I-IFIT5 axis, thereby triggering the cellular IFN-I response-differentiation-apoptosis network. This signaling cascade largely counteracts differentiation block and growth of human AML cells across various disease subtypes in vitro and in vivo. Through proteome analysis of over 200 primary AML bone marrow samples, we identify a distinct PHF8/IFN-I signature in half of the patient population, without significant associations with known clinically or genetically defined AML subgroups. This profile was absent in healthy CD34+ hematopoietic progenitor cells, suggesting therapeutic applicability in a large fraction of patients with AML. Pharmacological support of PHF8 phosphorylation significantly impairs the growth in samples from patients with primary AML. These findings provide novel opportunities for harnessing the cell-intrinsic immune response in the development of immunotherapeutic strategies against AML.

Abstract P29: Zotatifin, the eukaryotic translation initiation factor 4A (eIF4A) inhibitor, synergizes with Venetoclax to inhibit acute myeloid leukemia cell growth

Abstract New targeted therapies such as the selective and potent BCL-2 inhibitor Venetoclax have revolutionized the treatment of acute myeloid leukemia (AML). However, due to the cellular heterogeneity of the disease, drug-resistant cell types often emerge and drive relapse. We found that the eukaryotic translation initiation factor 4A (EIF4A) is highly expressed in multiple primitive AML cell types compared to their healthy counterparts, suggesting its potential as a therapeutic target. By unwinding complex structures in the 5’ UTR of transcripts, eIF4A promotes the translation of oncogene transcripts. A first-in-class drug, Zotatifin, inhibits the helicase activity of eIF4A and curtails tumor growth in receptor tyrosine kinase-driven tumors. Zotatifin is currently being evaluated in phase 1/2 trials across multiple solid tumors (NCT04092673). However, its effectiveness in blood cancers such as AML remains unexplored, and it is unknown whether Zotatifin may work synergistically with Venetoclax. Here, we treated AML cell lines in vitro and primary healthy or AML bone marrow ex vivo with Zotatifin or Venetoclax alone and in combination, and demonstrate synergistic killing of AML cells by the combination therapy (ZIP synergy score = 57.0 in MOLM-13, 19.3 in MV4-11, P < 0.0001). Mechanistically, we show that Zotatifin decreases eIF4A and AKT expression, and its combination with Venetoclax drives increased BAK and cleaved BAK expression, as well as increased cleavage of MCL-1 and BCL-2, consistent with drug synergy by convergence on the apoptotic pathway. In pilot colony-forming unit (CFU) assays, we found the combination to be tolerable in healthy CD34+ human hematopoietic stem and progenitor cells (HSPCs). To test drug efficacy in vivo, we generated a patient-derived xenograft (PDX) AML model from a patient who experienced relapse with complex cytogenetics, FLT3 and NPM1 mutations. Only the combination of Zotatifin and Venetoclax but not monotherapies effectively suppressed tumor burden as assessed by human CD45 engraftment in the peripheral blood. Further, the combination of Zotatifin and Venetoclax significantly prolonged survival of xenografted mice (median survival after treatment: vehicle 11 days, Venetoclax 13 days, Zotatifin 15 days, combination 42 days, P = 0.0002). Together, our data indicates that Zotatifin is synergistic with Venetoclax and may represent an effective treatment option for patients who are either primary refractory or have developed resistance to existing Venetoclax-containing regimens. Citation Format: Yoke Seng Lee, Jonathan Good, Noha Awais, Benjamin Eschle, Jenny Noel, Jean Acosta, Erica DePasquale, David Cucchi, Prafulla Gokhale, Fadi Najm, Peter van Galen. Zotatifin, the eukaryotic translation initiation factor 4A (eIF4A) inhibitor, synergizes with Venetoclax to inhibit acute myeloid leukemia cell growth [abstract]. In: Proceedings of the Blood Cancer Discovery Symposium; 2024 Mar 4-6; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(2_Suppl):Abstract nr P29.

Comprehensive analysis of m6A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing

N6 adenosine methylation (m6A), one of the most prevalent internal modifications on mammalian RNAs, regulates RNA transcription, stabilization, and splicing. Growing evidence has focused on the functional role of m6A regulators on acute myeloid leukemia (AML). However, the global m6A levels after azacytidine (AZA) plus venetoclax (VEN) treatment in AML patients remain unclear. In our present study, bone marrow (BM) sample pairs (including pre-treatment [AML] and post-treatment [complete remission (CR)] samples) were harvested from three AML patients who had achieved CR after AZA plus VEN treatment for Nanopore direct RNA sequencing. Notably, the amount of m6A sites and the m6A levels in CR BMs was significantly lower than those in the AML BMs. Such a significant reduction in the m6A levels was also detected in AZA-treated HL-60 cells. Thirteen genes with decreased m6A and expression levels were identified, among which three genes (HPRT1, SNRPC, and ANP32B) were closely related to the prognosis of AML. Finally, we speculated the mechanism via which m6A modifications affected the mRNA stability of these three genes. In conclusion, we illustrated for the first time the global landscape of m6A levels in AZA plus VEN treated AML (CR) patients and revealed that AZA had a significant demethylation effect at the RNA level in AML patients. In addition, we identified new biomarkers for AZA plus VEN-treated AML via Nanopore sequencing technology in RNA epigenetics.

Bone marrow macrophages are involved in the ineffective hematopoiesis of myelodysplastic syndromes.

Myelodysplastic syndromes (MDS) are a group of heterogeneous myeloid clonal disorders characterized by ineffective hematopoiesis. Accumulating evidence has shown that macrophages (MΦs) are important components in the regulation of tumor progression and hematopoietic stem cells (HSCs). However, the roles of bone marrow (BM) MΦsin regulating normal and malignant hematopoiesis in different clinical stages of MDS are largely unknown. Age-paired patients with lower-risk MDS (N = 15), higher-risk MDS (N = 15), de novo acute myeloid leukemia (AML) (N = 15), and healthy donors (HDs) (N = 15) were enrolled. Flow cytometry analysis showed increased pro-inflammatory monocyte subsets and a decreased classically activated (M1) MΦs/alternatively activated (M2) MΦs ratio in the BM of patients with higher-risk MDS compared to lower-risk MDS. BM MФs from patients with higher-risk MDS and AML showed impaired phagocytosis activity but increased migration compared with lower-risk MDS group. AML BM MΦs showed markedly higher S100A8/A9 levels than lower-risk MDS BM MΦs. More importantly, coculture experiments suggested that the HSC supporting abilities of BM MΦs from patients with higher-risk MDS decreased, whereas the malignant cell supporting abilities increased compared with lower-risk MDS. Gene Ontology enrichment comparing BM MΦs from lower-risk MDS and higher-risk MDS for genes was involved in hematopoiesis- and immunity-related pathways. Our results suggest that BM MΦs are involved in ineffective hematopoiesis in patients with MDS, which indicates that repairing aberrant BM MΦs may represent a promising therapeutic approach for patients with MDS.

Self-Supporting Human Acute Myeloid Leukemia (AML) Bone Marrow Organoids Established from Patient-Derived Xenografts Mimic the Human AML Microenvironment, with Distinct Cytokine Kinetics Correlating with Dynamic Cell Proliferation and Metabolic Shifts

Hallmarks of acute myeloid leukemia (AML) include (1) formation of a self-supporting and self-regulating tumor microenvironment (TME) in the bone marrow (BM) rendering pathological niches that orchestrate retention, proliferation and survival of AML blasts, and (2) a dynamic metabolism that promotes therapy resistance and disease progression. Efforts to understand AML biology and enhance current therapies are hampered by the paucity of state-of-the-art human models that can recreate the three-dimensional (3D) BM TME and recapitulate the heterogeneity, complexity, dynamics, and metabolic shifts observed in human disease. Previously, we described the development of the first long-term self-propagating serum- and cytokine-free human BM organoid generated from an AML patient-derived xenograft (PDX) that captured metabolic shifts during AML progression. Here, we characterize the dynamic changes observed in the self-constituted TME with respect to AML proliferation, metabolism, and upon reconstitution of secondary organoids. BM was collected from NSG mice engrafted with human primary AML cells (PDX-AML model) or naïve control mice and seeded into polyurethane scaffolds in serum- and cytokine-free medium at 4e6 cells per scaffold, optimized previously. Scaffolds were recharged with autologous PDX-AML BM on day (D) 13 and cultured until D70. Organoids were assessed for (1) inter- and intra-scaffold AML kinetics, (2) the TME, (3) metabolic composition and (4) propagation into secondary organoids. AML cell kinetics from organoid culture supernatants reflected those of scaffold-extracted populations (n=3). CD33 +CD44 + AML cells expanded and/or were maintained from 7% (D0) to >10% (D70), being >15% at most culture timepoints. Confocal microscopy revealed reconstitution of typical AML-TME niche interactions within organoids, including expression of fibronectin, VCAM-1 and N-Cadherin, and formation of proliferative niches composed of AML cells with heterogeneous Osteopontin- and Osterix-expressing support cells. Human AML-supportive cytokines were consistently observed in organoid supernatants (N=3), with SDF-1, IL-1α, IL-8, GM-CSF, FGF-2 and Osteopontin present throughout the culture; some cytokines had biphasic kinetics with factors critical for TME formation present early (e.g. Osteopontin, GM-CSF), and those required for AML proliferation dominant later (e.g. FLT3L, IL-8), coinciding also with metabolic shifts during culture. Despite the absence of IL-6, single molecule RNA fluorescence in situ hybridization confirmed IL-6 expression by niche-resident AML blasts suggesting autocrine signaling networks beyond those identified in supernatants. Cells from D70 organoids were able to re-establish secondary organoids (n=2) which also exhibited long-term (D70) AML maintenance (>11% blasts), and regenerated the AML TME. Previously, we identified 3 culture stages defined by metabolic shifts: 1) pre/early recharge (D4-D19), (2) intermediate (D25-D40) and, (3) late (from D55) where organoids exhibited highest proliferation. To further characterize these shifts, intracellular metabolites were extracted from organoids (n=5) at D10, D25, D40, D55 and D70, analyzed with gas-chromatography mass spectrometry (GC-MS) and evaluated through unsupervised hierarchical clustering and multivariate analysis. Significance Analysis of Microarrays (SAM) analysis demonstrated dysregulation of alanine, serine, isoleucine, glycolate, hexanoic acid and glycolysis when comparing stage 1 with stage 2, and in isoleucine, leucine, serine, succinate and tryptophan metabolism when comparing stage 2 with stage 3. When proliferative and non-proliferative timepoints were compared, amino acid and glycolysis-driven metabolic switches were identified, typical of AML metabolism. We have characterized a long-term 3D human AML BM biomimicry in serum- and cytokine-free conditions with a self-organizing TME that recapitulates many features of AML BM, including robust human AML cell maintenance within niches, cytokine and metabolic kinetics to support different phases of progression, and the ability to propagate into secondary organoids. This dynamic, physiologically-relevant ex vivo platform can enable studies in human AML pathogenesis/progression and is poised to test novel therapeutics directed towards AML cells, the TME and metabolic targets.

Dysregulation of Immune Regulators in AML Bone Marrow Promotes Dysfunction of CD8 + T Cells

Background: Acute myeloid leukemia (AML) originates in the bone marrow, evading immune recognition and destruction. The bone marrow microenvironment (BME), comprising diverse immune cells and regulators, profoundly influences AML development. However, the impact of immune regulators in the BME, particularly on T-cell anti-AML immunity, remains inadequately understood. Therefore, evaluating the impact of immune regulators in the AML bone marrow microenvironment on T cell dysfunction is of paramount importance and necessity. M ethod : Bone marrow blood samples were obtained from pediatric AML patients at diagnosis and age-matched healthy individuals considered as hematopoietic stem cell transplantation (HSCT) donors after written informed consent. By centrifuging at 2000-3000rpm for 10min, we obtained the supernatant as plasma and stored it in a -80°C refrigerator. After using proteomics to identify the expression of 180 immune regulatory factors in plasma samples, we performed GO and KEGG functional enrichment analysis. After density gradient centrifugation, we isolated bone marrow mononuclear cells (BMMNCs) and immediately identified frequencies of T cell populations and expression levels of functional markers by flow cytometry when they were fresh. Moreover, the co-culture model of CD8 +T cells and THP-1 cell line was used to evaluate the anti-AML effector function of T cells. CD8 +T cells in BMMNCs were sorted by FACS and then subjected to whole transcriptome sequencing and in vitro experiments. After using the TRRUST and KnockTF databases for transcription factor prediction analysis, we selected phospho-flow cytometry to detect and verify the association between the level of phosphorylation of transcription factors and the function of CD8 +T cells. The data were analyzed using R software. Results: Using proteomics techniques, we uncovered a substantial presence of immune-suppressive regulatory factors in AML bone marrow plasma. Interestingly, the canonical NF-κB pathway, mediated by immune regulators and vital for immune regulation in BME, displayed significant downregulation, implying T-cell dysfunction. In our investigation, we identified dysfunctional CD8 +T cells in the primary AML bone marrow, characterized by heightened expression of co-inhibitory receptors and pro-dysfunctional transcription factors, as well as significantly decreased anti-AML effector function. Transcriptome sequencing further linked AML CD8 +T cell dysfunction to reduced transcriptional activity of NF-κB p65 in the canonical NF-κB signaling pathway. Intriguingly, in vitro inhibition of NF-κB p65 and its phosphorylation led to elevated expression of exhaustion markers, such as PD-1, LAG-3, and TIM-3 on primary CD8 +T cells. Most notably, the stimulation of the canonical NF-κB signaling pathway effectively restored activation and effector function-related pathways in dysfunctional AML CD8 +T cells. Conclusion: Immune regulators in the bone marrow microenvironment play a vital role in maintaining dysfunctional AML CD8 +T cells. These findings provide a novel strategy to investigate the potential mechanisms and interventions for T-cell dysfunction.

Spatial Technologies Reveal the Immune Landscape of Pediatric Acute Myeloid Leukemia

Pediatric acute myeloid leukemia (AML) is a cancer with a particularly low mutational burden in comparison to other pediatric and adult cancers and therefore, thought to be a poor candidate for T cell-engaging immunotherapies (Gröbner et al., 2018; Pfister et al., 2022). However, little is known about the composition and function of T cells in the bone marrow (BM) of pediatric AML patients. Insight into the frequency and function of BM T cells in children with AML is relevant for naturally occurring AML immune defenses, as well as for T cell-engaging immunotherapies (Koedijk et al., 2021). Here, we performed a multidimensional characterization of the tumor immune microenvironment in children with newly diagnosed AML. We obtained 82 formalin-fixed and paraffin-embedded (FFPE) diagnostic bone biopsies from a representative cohort of pediatric patients with treatment-naïve de novo AML (N=72) and from age- and sex-matched pediatric patients with treatment-naïve early-stage rhabdomyosarcoma without malignant BM infiltration (non-leukemic controls, N=10). We employed immunohistochemistry (IHC) alongside immune-related gene expression profiling (NanoString PanCancer IO 360 TM Panel) and spatial transcriptomics (NanoString GeoMx TM Whole Transcriptome Atlas). Moreover, we acquired an additional dataset of pre-treatment immune-related gene expression profiling obtained from the BM of 30 flotetuzumab-treated (CD3 x CD123 bispecific antibody) refractory/relapsed (R/R) adult AML patients (NCT02152956; Vadakekolathu et al., 2020) for TIDE-based immune deconvolution (Jiang et al., 2018). Using IHC, we identified (a trend towards) a decreased abundance of the overall number of T cells ( P=0.09) and CD8 + T cells ( P=0.011; Panel A) in the BM of pediatric AML patients in comparison to non-leukemic controls, respectively. Notably, the extent of overall T cell and CD8 + T cell infiltration could differ up to 180-fold between individual AML patients. In general, this difference in T cell infiltration was not associated with the abundance of leukemic blasts or patient's cytogenetic alterations. Nevertheless, children with complex karyotype AML had higher numbers of BM T cells compared to children with normal karyotype AML ( P=0.03).Using differential gene expression analysis, we identified genes related to T cell-attracting chemokines, cytotoxicity, and immune checkpoints to be significantly upregulated in T cell-infiltrated- compared to T cell-depleted samples. Moreover, the ratio of anti- to pro-inflammatory macrophages (M2/M1-ratio) was significantly lower in T cell-infiltrated- compared to T cell-depleted pediatric AML samples ( P<0.001). Interestingly, this M2/M1-ratio was also significantly lower in R/R adults that responded to flotetuzumab immunotherapy in comparison to non-responders ( P<0.001). In fact, this M2/M1-ratio outperformed several other known predictors of response to flotetuzumab immunotherapy (AUROC: 0.852 (95% CI: 0.71-0.99), P=0.001; Jiang et al., 2018; Ayers et al., 2017). In addition, IHC revealed that 9 immune-infiltrated samples, including 6 KMT2A-rearranged AML samples, harbored large networks of T- and B cells (representative image of B cell-networks shown in panel B). Using spatial transcriptomics, we dissected the composition of these lymphoid aggregates and revealed localized anti-tumor immunity in the BM of AML. In comparison to tumor areas, these aggregates showed a higher abundance of activated cytotoxic T cells ( P<0.001), memory B cells ( P<0.001), and plasma cells ( P<0.001), suggesting the presence of tertiary lymphoid structure-like (TLS-like) aggregates in the BM of AML. In conclusion, we identified a subset of pediatric AML patients with relatively high T cell infiltration and a relatively low abundance of anti-inflammatory macrophages in the BM at diagnosis. Furthermore, we found that the BM M2/M1-ratio may be informative of response to T-cell engaging immunotherapies in adult AML, which needs to be validated in pediatric AML. Lastly, for the first time, we identified TLS-like aggregates in the BM of AML patients, which have been associated with immunotherapy response in many cancers (Schumacher & Thommen, 2022). Additional studies to further characterize the function and relevance of these lymphoid aggregates are ongoing.

Predicting Molecular Alterations from Blast Morphology of Acute Myeloid Leukemia Bone Marrow Aspirate Smears Using Machine Learning

Introduction Acute Myeloid Leukemia (AML) has enormous molecular and cytogenetic heterogeneity. Evaluation of bone marrow morphology is essential in the diagnosis of AML, however, it requires significant training and there is wide inter-observer variability. Genomic testing has been progressively relied on for AML classification, ultimately helping to dictate prognosis and guide clinical management. However, genomic testing, if performed, can be subject to prolonged turnaround times and lacks clinical penetration in low-resource settings. To overcome these challenges, we aimed to evaluate the feasibility of predicting clinically relevant genomic alterations from bone marrow cell morphology using a machine learning approach. Methods We scanned 799 Wright-stained bone marrow aspirate smear slides, made for routine patient care, for subjects diagnosed with AML. These subjects were linked to clinical data, including pertinent cytogenetic/molecular alterations and subclassified as cases with mutated Nucleophosmin 1 ( NPM1), those with TP53 mutations and those with myelodysplastic-related changes (AML-MRC). Whole slide images were screened for containing spicules and blasts, and were analyzed to detect 180 million cells (blasts and non-blasts) excluding hemodilute and particle regions. We developed a multi-instance model to predict patient molecular subtype by repeatedly sampling 512 cells from each slide and using these to train a classifier that weights cells with morphology relevant to subtype. We also trained a model to predict NPM1 and TP53 mutations independently, as well as other frequent variants reported to impact blast morphology. Results Performance in predicting NPM1/TP53/AML-MRC subtype was moderate (0.80 AUROC). Performance of the single-gene model varied, with NPM1 having the highest performance (0.85 AUROC) followed by IDH (0.80 AUROC), FLT3 (0.79 AUROC) and TP53 (0.62 AUROC). Conclusions This study provides promising preliminary results for prediction of genetic alterations in AML in a large-scale single-institution dataset. Interestingly, this method did not rely on the classification of individual cells, avoiding the need for manually collecting annotations to train a blast cell classifier. Future work will evaluate the morphology of cells attended by the multi-instance model, and explore the value of enriching sampled cells with blasts using cell classification methods.

Novel CD123xCD3 Bispecific Igm Antibody, Igm-2537, Potently Induces T-Cell Mediated Cytotoxicity of Acute Myeloid Leukemia Cells In Vivo and in Vitro with Minimal Cytokine Release

Introduction: New therapeutics are needed for the effective treatment of acute myeloid leukemia (AML), as standard chemotherapeutics are poorly tolerated and ~50% of patients relapse primarily due to the incomplete elimination of leukemia stem cells (LSCs). CD123, the IL-3Rα chain, is highly expressed on leukemic blasts and LSCs, and is further increased in patients with poor prognostic factors. Bispecific T-cell engager (TCE) antibodies and CAR-T cells targeting CD123 have shown promising clinical efficacy in AML patients, but cytokine release syndrome limits their therapeutic window and remains a major safety concern. IGM-2537 is a novel pentameric IgM bispecific TCE antibody engineered with ten anti-CD123 binding sites, and an anti-CD3ε single chain Fv domain fused to the joining chain to engage T-cells. Here, we report that IGM-2537 not only potently induces T-cell mediated cytolytic killing of AML cells in vitro and in vivo but also demonstrates minimal cytokine release, and little to no effect on normal hematopoietic progenitor cells and human vascular endothelial cells (HUVECs) with in vitro and ex vivo studies. Additionally, an improved tolerability, excellent pharmacodynamic (PD) response and lower cytokine release was observed with a cynomolgus cross-reactive IgM TCE in monkeys. Materials and Methods:Surface plasma resonance (SPR), cell membrane protein array, and alanine scanning were utilized to characterize human CD123 binding affinity, specificity and epitope mapping, respectively. T-cell dependent cellular cytotoxicity (TDCC) assays were employed to evaluate the potency of IGM-2537 target cytotoxicity, T cell activation and cytokine release. Ex vivo AML colony formation assays were used to assess the activity on AML blasts. Human MV-4-11 and MOLM-13 xenograft tumor models in humanized NSG dKO mice were utilized to determine in vivo anti-tumor activity of IGM-2537. Healthy human PBMCs and bone marrow (BM) samples as well as HUVECs were used in ex vivo assays to address potential safety concerns of IGM-2537 mediated effects on hematopoietic progenitor cells and HUVECs, respectively. Lastly, to confirm that a CD123 directed IgM-based TCE molecule can potentially provide better safety profile in vivo, a cynomolgus-cross reactive IgM TCE comparator was assessed in monkeys for tolerability and PK/PD responses. Results and Conclusions: IGM-2537 bound with high affinity and avidity to CD123. In vitro, IGM-2537 engaged both CD123 and CD3 to induce potent T-cell activation and T-cell mediated cytotoxicity of CD123 + AML cells, and autologous CD123 + basophils and plasmacytoid dendritic cells (pDCs). Though IGM-2537 demonstrated comparable maximal killing activity to a comparator IgG TCE, IGM-2537 demonstrated minimal cytokine release. In ex vivo patient-derived AML or normal BM colony formation assays, IGM-2537 eliminated AML colony forming cells at physiologically relevant effector/target (E/T) ratios but had little or no effect on normal hematopoietic progenitors. In addition, IGM-2537 demonstrated no cytotoxicity against HUVECs regardless of their CD123 expression at basal levels or at maximal levels upregulated by TNF-a and IFN-g, in contrast to a comparator IgG TCE. In vivo, IGM-2537 completely inhibited tumor growth in two AML xenograft tumor models, a subcutaneous MV-4-11 model, and a systemic MOLM-13 model in humanized NSG dKO mice. To further evaluate the potency and safety of the CD123xCD3 IgM bispecific TCE format in vivo, a cynomolgus cross-reactive CD123xCD3 IgM bispecific TCE was evaluated for tolerability and PD responses in cynomolgus monkeys using single doses. All animals tolerated the cross-reactive bispecific IgM TCE well at doses up to 10 mg/kg (the maximal dose level evaluated), a dose 100-fold greater than published doses of a comparator IgG TCE. Complete depletion of CD123 + basophils and substantial reductions of pDCs were seen in blood and BM with minimal to no cytokine induction. In summary, IGM-2537 demonstrated potent in vitro and in vivo T-cell mediated cytotoxicity of AML cell lines with minimal cytokine induction. The encouraging preclinical safety profiles were further supported by little/no effect on normal hematopoietic progenitor cells and HUVECs. These preclinical data support the clinical development of IGM-2537 for the treatment of AML and other hematological malignancies.

Integrated Methylation and Transcriptional Landscape and Evolution of Pediatric AML

Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy associated with poor outcomes despite intensive therapies. The genomic landscape of pediatric AML has been well characterized and has led to translational benefits, such as improved relapse predication and effective targeted therapies for a subset of individuals (e.g., FLT3-ITD AML). Despite these advances, the majority of patients continue to receive therapeutic interventions that have not changed in three decades. This underscores the need to advance our understanding of AML biology beyond genomic alterations (e.g., somatic mutations). Here, we present the largest (N = 858 patients) integrative analysis of pediatric AML paired transcriptomes and methylomes to date, performed at diagnosis for patients enrolled on Children's Oncology Group clinical trials AAML0531 (NCT00372593) or AAML1031 (NCT01371981). We also analyzed N = 400 and 253 corresponding transcriptomes and methylomes at relapse, respectively. Additionally, we performed comprehensive mutation and fusion calling from NGS data and integrated clinical covariates and outcomes. This robust dataset allowed us to uncover how pediatric AML epigenetics are perturbed from normal hematopoiesis, characterize the evolution of transcriptional and methylation changes from leukemia diagnosis to relapse, and identify more accurate relapse prediction models for pediatric AML. We initially performed unbiased hierarchical clustering on CpG sites that are differentially methylated between AML and normal bone marrow to identify distinct AML-restricted methylation (ARM) signatures. This analysis demonstrated that that these ARM clusters were enriched in specific cytomolecular subtypes of pediatric AML. Specifically, we identified methylation signatures that recapitulated their adult counterparts (e.g., IDH1/2, DNMT3A, WT1) and pediatric specific methylation signatures that clustered with RUNX1::RUNX1T1, CBFB::MYH11, KMT2A-rearrangement, NUP98::NSD1, NUP98::KDM5A, and CEBPA mutant AML. Next, we investigated the transcriptional and methylation signatures for the relapsed cases and compared them to diagnosis. We demonstrated that relapsed transcriptional and methylation signatures clustered within their cytomolecular subtype counterparts at diagnosis (i.e., AMLs at relapse more closely resemble AMLs at diagnosis with the same underlying gene fusion than other relapsed AMLs) ( Fig. 1A). However, analyzing our data in the context of these cytomolecular subtypes, we found that leukemias uniformly acquired a more stem-like state at relapse. We focused our biomarker discovery efforts on KMT2A-rearranged AMLs since (as a cohort) these patients have an intermediate risk of relapse and existing molecular biomarkers (e.g., KMT2A fusion partner and measurable residual disease detection) result in only modest improvements in relapse prediction. First, we found that CpG islands associated with CD34 and HOXA gene expression were frequently (but variably) hypermethylated, which was also associated with downregulation of CD34 and HOXA gene expression and favorable survival outcomes. Next, we performed non-negative matrix factorization on diagnosis and relapsed KMT2A-rearranged AMLs and identified a novel gene set associated with relapse and poor outcomes. These three distinct methylation-transcriptional findings (i.e., CD34, HOXA, and relapsed signatures) were subsequently transformed into a novel methylation-transcription biomarker score (MTBS) using machine learning algorithms (i.e., LASSO Cox regression). We used KMT2A-rearranged AML patients from AAML1031 as our training cohort (N = 129) to generate a MTBS that was able to distinguish KMT2A-rearranged cases with disparate outcomes. This algorithm was validated in an independent cohort from AAML0531 (N = 28) ( Fig. 1B). Additional methylation-transcriptional biomarker discovery efforts for pediatric AML are underway. Since pediatric AML is associated with a low mutational burden, understanding leukemia-specific transcriptional and epigenetic alterations is of utmost importance. Our study demonstrates the translational promise offered by deep functional genomic characterization of pediatric AML and we believe that further interrogation may provide additional novel insights into leukemia initiation, relapse prediction, and novel treatment approaches.

Navtemadlin, a Novel MDM2 Inhibitor, Potentiated Venetoclax-Induced Antitumor Efficacy in TP53 Wild-Type Acute Myeloid Leukemia (AML)

Introduction: The tumor suppressor p53 ( TP53) maintains genomic integrity, and nearly 50% of cancers are characterized by a loss or mutation in the TP53 gene. Murine double minute 2 (MDM2) negatively regulates p53 expression and promotes oncogenesis in TP53 wild-type ( TP53 WT) tumors. Navtemadlin (nvtm) is a potent, selective, orally available MDM2 inhibitor that overcomes MDM2 dysregulation by restoring p53 activity and inducing apoptosis in TP53 WT tumors. AML is a heterogeneous hematological malignancy resulting from the transformation of stem cells and is characterized by poor therapy response. Thus, combination therapies are required to avoid tumor escape mechanisms, such as alterations in apoptotic machinery and metabolism. Venetoclax (ven), a BCL-2 inhibitor, is a promising therapy in AML. Overexpression of anti-apoptotic members of the BCL-2 family, including myeloid cell leukemia-1 (MCL-1) limits ven response, thus requiring MCL-1 inhibitors to further improve sensitivity. A proof-of-concept study with idasanutlin (idasa), a first-generation MDM2 inhibitor and ven demonstrated manageable safety and encouraging efficacy in relapsed/refractory AML patients (Daver et al. Blood 2023). Here, we present a preclinical evaluation of nvtm alone and in combination with ven in the setting of TP53 WT AML, with a focus on metabolic pathways, pro-survival signaling, and bone marrow (BM) niche. Methods: AML-derived cell line, MOLM-13 ( TP53 WT, FLT3-ITD) was cultured alone, with HS5 AML stromal cells or with cytokines. Cultures were treated with DMSO, nvtm (0.1-1.5 μM), or ven (0.5 μM) for short-term (4-8 hrs) or long-term (48-72 hrs) and analyzed for changes in cell cycle progression, viability, clonogenicity potential, and metabolism (glycolysis and mitochondrial oxidative phosphorylation by analyzing extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) respectively). Primary AML BM mononuclear cells (MNCs) were cultured in cytokine support media. Results: In MOLM-13 cells, short-termnvtm (0.5 µM) treatment rapidly restored p53 expression and phosphorylation, with greater efficacy than idasa. Long-term treatment significantly induced apoptosis in a dose-dependent manner from 0.25 μM (p<0.01) with 80% cytotoxicity at 0.75 μM (p<0.001). Cell cycle analysis at 48 hr showed that nvtm significantly arrested cells in the sub-G0-G1 phase. Clonogenicity potential was significantly lowered in nvtm-treated cells. Metabolic alterations in the Mito Stress and Glycostress tests showed nvtm significantly lowered EACR, OCR, and mitochondrial membrane potential, as compared to idasa. We next evaluated the effects of nvtm in ven-treated MOLM-13 cells. Combination treatment significantly lowered the metabolism, cell viability, and clonogenicity potential of MOLM-13 cells, compared to nvtm or ven treatment. Immunoblotting analysis revealed a reduction in key anti-apoptosis proteins (BCL-2, MCL-1, PARP). Strikingly, nvtm downregulated ven-induced MCL-1 expression in a dose-dependent manner. Culturing MOLM-13 cells in HS5-conditioned media, transwells overlying HS5 cells, or with HS5 cells increased MOLM-13 cell resistance to nvtm. However, in HS5 co-cultures, a combination of nvtm and ven strongly re-sensitized MOLM-13 cells for apoptosis. Nvtm also significantly blocked the cytoprotective effects of AML-relevant cytokines (IL-6, SCF, FLT3 ligand, TPO, and GM-SCF). In cultures of primary AML BM-MNCs (n=11), nvtm alone at clinically relevant concentrations reduced viability (14-40%), and a combination nvtm and ven significantly enhanced AML cytotoxicity (30-52%). Conclusions: Nvtm, a potent second-generation MDM2 inhibitor, rapidly restored p53 function, induced apoptosis in p53 WT AML MOLM-13 by impeding cell cycle, viability, clonogenicity potential, and reducing both glycolysis and oxidative phosphorylation. Nvtm combined with ven significantly enhanced these effects. Importantly, this combination blocked stromal cell-mediated (contact and soluble factors) cytoprotection. These encouraging results provide a mechanistic basis for the evaluation of this combination in vivo and as a therapeutic strategy to overcome documented ven resistance mechanisms in TP53 WT AML patients.

Primary Acute Myeloid Leukemia Cells Trigger Distinct Activation Patterns in Expanded NK Cells

Increasing efforts are devoted to implement immunotherapies for the treatment of acute myeloid leukemia (AML). Recently, natural killer (NK) cell-based immunotherapy has shown initial encouraging results. However, which patients are most likely to benefit from NK cell-based treatments remains poorly understood. Here, we investigate the responses of NK cells to ex vivo co-cultures with 55 primary AML samples using single-cell transcriptomics. We identify a subgroup of AML patients eliciting strong responses in NK cells and define the molecular programs in NK cells and other microenvironmental cell types triggered by diverse AML cells. We performed functional single-cell immune profiling on co-cultures of primary expanded NK cells and 55 bone marrow (BM) samples from AML patients at diagnosis. We used NK cells expanded using irradiated K562-41BB-L-mbIL-21 feeder cells, resulting in a product commonly used in clinical trials. All expanded NK cells were from one single healthy donor displaying an HLA-C1C2 allotype.We investigated NK cell-treated and untreated cultures through multiplexed single-cell RNA sequencing (scRNA-seq) to dissect adaptive changes in both NK and AML BM cells upon their interaction. In total, we investigated 121 samples through scRNA-seq: 11 monocultures of expanded NK cells, 55 AML BM cells and 55 co-cultures of AML BM cells and expanded NK cells. scRNA-seq yielded 95,715 high quality cells (791 cells per sample on average), including 31,882 NK cells (483 cells per sample on average) and 63,833 AML BM cells (580 cells per sample on average). Unsupervised clustering of the cells revealed distinct clusters separating expanded NK cells from AML cells (Fig. 1a). We studied the sensitivity of leukemic cells to NK cytotoxicity using high-throughput flow cytometry. We further integrated the results with genetic and clinical data of the AML patients to characterize the mechanisms of action driving the transcriptomic responses and leukemic cell susceptibility to NK cell killing. After 24 h co-culture, scRNA-seq revealed that AML BM cells induced distinct gene expression states in the NK cells. The observed tumor-induced NK states were predominantly enriched in co-cultured samples and not found in NK cell monocultures which mostly consisted of resting-state NK cells. Across the co-cultures, half of the AML samples triggered at least 30% of NK cells to change from resting to tumor-induced states (Fig. 1b). Out of the 28 AML samples causing the strongest NK cell induction, 54% primarily triggered a type I interferon (IFN) signature, characterised by expression of genes encoding MX1, OAS1, and IRF7. In contrast, the other 46% mainly induced an activated phenotype, including expression of TNFRSF18 ( GITR), TNFRSF9 ( 4-1BB), TIGIT and HAVCR2 ( TIM-3). Killer cell immunoglobulin-like receptors-HLA ligand mismatchesare well known causes of NK alloreactivity. Thus, we explored whether HLA-C matched (C1C2, n=24) and mismatched (C1C1 or C2C2, n=28) AML samples influenced NK cell responses. Interestingly, no significant difference in the NK cell induction states was observed between matched and mismatched samples (Mann-Whitney p = 0.57). NK cell treatment also induced responses in the patients' own T cells. Both CD4+ and CD8+ T cells upregulated IFN-ɣ and type I IFN genes upon co-culture. The type I IFN signature in CD8+ T cells was mainly found in AML samples triggering strong NK cell induction. CD8+ T cells also upregulated cytotoxicity genes including FASLG and TNFSF10 (TRAIL), along with inhibitory molecules such as LAG3, suggesting that NK cells can promote effector functions of T cells. Our results suggest that AML BM cells from different patients trigger a heterogeneous response in expanded NK cells. Only in half of the cases, the leukemic BM cells induced substantial activation of NK cells. The observed variation in NK states was not determined by HLA-C allotypes, suggesting that other tumor cell features are responsible for the responses. This underscores the importance of understanding the molecular drivers of tumor and NK cell interaction. Our data additionally show that NK cell-based immunotherapy may be able to promote the functionality of the patient's own T cells, demonstrating how our ex vivo modeling approach can help to refine the mechanism of action of immunotherapies. Our work paves the way for identifying subgroups of AML patients responding to NK cell-based immunotherapies.

Genome-Wide Methylome and Transcriptome Profiling of Acute Myeloid Leukemia Derived Bone Marrow Mesenchymal Cells Identify Age Group Specific Biological Pathway Dysregulation in the Bone Marrow Microenvironment of AML

Adult patients with acute myeloid leukemia (AML) have a proportionate increase in mortality from their disease and therapy as age increases. In great part, this mortality is due to disease relapse that occurs at a higher rate irrespective of genetic assigned risk. While intensification of therapy in patients with favorable genomics such as core-binding-factor AML (CBF-AML) has yielded a high proportion of long-term remission and potential cure, this benefit has been less frequently observed in patients with AML age 60 and older despite receipt of similar therapy. Moreover, even less benefit has been observed in patients with unfavorable genomics such when bearing a complex karyotype (karyotype with ≥ 3 chromosome abnormalities). Reasons for this unfavorable outcome among older patients is unknown. We hypothesized that tumor-induced aging in cells of bone marrow microenvironment, specifically, in bone marrow mesenchymal stromal cells (BMSCs) plays a significant role in AML survival and progression in older compared to younger patients and that the difference in prognosis may depend on specific aging induced changes in the BMSCs. We expanded BMSCs under physiologic hypoxic conditions (91% nitrogen, 4% oxygen and 5% CO 2) to mimic the bone marrow microenvironment, isolated DNA and RNA from early passaged cells and performed methylation analysis using 850k Illumina DNAmehtylation arrays and gene expression analysis using mRNAseq. We used the Horvath Skin and Blood clock to calculate epigenetic age (DNA methylation age). We determined differentially expressed genes with increasing epigenetic or chronological age in the different AML genetic risk groups (n=9 CBF-AML, n=11 CK-AML and n=7 Normal donor BMSC) as well as in older (>60) and younger (<60) AML-BMSCs, and performed Gene Set Enrichment Analysis (GSEA) for the Hallmarks as well as aging and senescence related genesets (n=33 genesets). We found that BMSCs derived from AML bone marrow cells are more age accelerated than normal donor BMSCs. Our GSEA analysis revealed enrichment for age-associated gene networks that reflected hallmarks of aging, including mitochondrial dysfunction, inflammation, and cellular senescence. Specifically, we observed a positive enrichment for the SenMayo gene signature ( Saul et al. 2022, Nature Communications) and a negative enrichment of proliferation and mitotic gene sets with increasing epigenetic and chronological age (padj<0.05). Gene sets that are related to inhibition of adipogenesis were positively enriched in the CBF-AML BMSCs compared to the CK-AML BMSCs. Our integrated analysis revealed novel observations regarding the cellular changes that occur in the AML stromal microenvironment with increasing age. Most interestingly, our findings suggest that AML derived BMSCs have increased epigenetic age compared to normal donor BMSCs. Additional experiments are ongoing to functionally validate the findings predicted by the enrichment analysis. Our study is the first to suggest an increased epigenetic age in the stromal bone marrow microenvironment of older AML patients.

Dissecting Subtype-Specific Tumor-Time Interactions and Underlying Hidden Drivers in Pediatric Acute Myeloid Leukemia Via Single-Cell Multi-Omics

Introduction: Pediatric acute myeloid leukemia (AML) is a heterogeneous hematological malignancy characterized by various chromosomal abnormalities and somatic mutations. Investigating the origin of tumorigenesis and deciphering the complex interplay between AML cells and their surrounding tumor immune microenvironment (TIME) is crucial to understand the underlying mechanisms driving disease progression and response to therapy. Recent advancements in single-cell multi-omics technologies enabled us to characterize the transcriptional (GEX) and epigenetic (ATAC) landscapes of both tumors and TIMEs. Leveraging our in-house algorithm, scMINER (single-cell Mutual Information-based Network Engineering Ranger, Ding et al., 2023), this study aims to build a comprehensive cell type atlas in diverse pediatric AML bone marrow samples and construct intra- and inter-cellular networks, enabling the identification of hidden drivers that shape subtype-specific AML-TIME interactions. Methods: Using CD45 and CD33 as selective markers by flow cytometry, we have successfully isolated blasts and enriched for T cell and B cell populations for 10X single-cell multiome profiling across AML molecular subtypes, including UBTF-TD (n=1), NPM1 (n=1), and KMT2A rearrangement (n=1). We interrogated the GEX data using scMINER, including two key steps: (i) mutual information-based clustering analysis (MICA) and (ii) mutual information-based network inference engine (MINIE). MICA characterizes the intrinsic nonlinear similarity of gene expression distributions among cells, enabling a high resolution of clusters. MINIE reverse-engineers cluster-specific intracellular gene networks and infers protein activity of transcription factors (TF) or signaling factors (SIG) drivers based on the expression of its predicted regulon targets in the corresponding cluster. The activity profiles overcome the dropout effects of single-cell RNA-seq data and reflect protein activities across all cells. ArchR is used to analyze ATAC data. CellChat is used to construct and evaluate intercellular networks. Results: AML cells from three samples were divided into four major clusters, and we labeled them as NPM1, KMT2A, UBTF_one, and UBTF_two based on sample subtypes (Fig.1A). MICA managed to obtain distinct AML cell sub-clusters. Comparison with single-cell profiles of normal hematopoietic cells and annotation with marker genes revealed their correspondence with different myeloid developmental stages. Notably, the KMT2A cluster shared a high similarity in cell type proportion with the UBTF_two cluster, and the NPM1 cluster is closer to the UBTF_one cluster. This result demonstrated significant tumor heterogeneity within and across AML molecular subtypes. With the help of intracellular gene networks generated by MINIE, we identified multiple subtype-specific hidden drivers by differential activity analysis. For example, KMT2A and UBTF_two clusters exhibited elevated SAMHD1 levels, consistent with previous GSE data (Zhang et al., 2022). Chromatin accessibility analysis of ATAC data showed increased peaks near SAMHD1 in KMT2A and UBTF_two clusters, further supporting this observation. IRF8 showed a similar expression pattern to SAMHD1, suggesting its context-dependent role across AML subtypes. Accurate annotation of myeloid and immune cells greatly enriches the preciseness of the AML and TIME interaction patterns, which vary across AML molecular subtypes (Fig.1B). Interestingly, cells originated from KMT2A cluster exhibited similar interaction patterns to UBTF_two, while NPM1 and UBTF_one were grouped. This result indicated that different AML molecular subtypes may partially utilize the same mechanisms of tumor-TIME interaction, resulting in similar tumor phenotypes. Conclusions: Accurate clustering and well-defined annotation of myeloid and immune cells enabled us to build a comprehensive cell type atlas in AML samples. The subtype-specific network and the following analysis identified candidate hidden drivers that possibly contribute to the heterogeneity of tumor populations. AML subtypes sharing the same hidden drivers have similar cell type proportions and interaction patterns with TIMEs. This observation implies that AML subtypes share cell type-specific dependencies, which can be therapeutic targets to overcome the refractoriness posed by tumor heterogeneity.

Encouraging Efficacy Observed in Bexmab Study: A Phase 1/2 Study to Assess Safety and Efficacy of Bexmarilimab in Combination with Standard of Care in Myeloid Malignancies

Background Clever-1 (common lymphatic endothelial and vascular endothelial receptor-1) constitutes a novel macrophage checkpoint. The receptor contributes to immune tolerance by antigen clearing and T cell inhibition. In multiple models, tumor growth is significantly reduced when Clever-1 function is inhibited. Expression of Clever-1 on bone marrow (BM) cells is a prognostic factor for poor outcome in acute myeloid leukemia (AML) and suppression of Clever-1 signaling inhibits leukemia cell growth. Bexmarilimab (BEX), a humanized IgG4 monoclonal antibody, binds Clever-1 resulting in increased antigen presentation, secretion of proinflammatory cytokines and activation of T cells. Clever-1 is highly expressed on leukemic blasts and monocytes of AML and myelodysplastic syndrome (MDS) patients. Treatment of AML bone marrow cells with BEX alone or in combination with azacitidine/venetoclax results in enhanced antigen presentation capacity and increased activation markers on effector T cells with synergistic effect on cell death. Also, BEX treatment alone lowers blast metabolic fitness via interference with mitochondrial oxidation. The ongoing BEXMAB clinical study investigates safety and efficacy of BEX combined with standard of care (SoC) in patients with myeloid malignancies (NCT05428969). Method This is a Ph1/2 study, investigating BEX combined with azacitidine (doublet) in patients with higher risk MDS frontline or hypomethylating agent (HMA)-failed, and relapsed/refractory (r/r) AML patients. BEX is dosed Q1W in 28-day cycles until disease progression or intolerable toxicity. SoC azacitidine is administered as per label. During Ph1, BEX doses were escalated from 1.0 mg/kg to 6.0 mg/kg (Bayesian optimal interval [BOIN] design). BM was analyzed at the end of Cycle 1 and 3 followed by every three cycles. Ph2 will start with a dose optimization per malignancy followed by a dose expansion for efficacy evaluation (2-Stage design). Results Here we report data from the dose finding Ph1 of the doublet. As of 25 July 2023, 22 patients have been enrolled in the doublet (MDS n=5; MDS HMA failed n=5; r/r AML n=12). Baseline characteristics are shown in Table 1. 8/10 MDS/MDS HMA-failed patients were of high to very high risk based on rIPSS; of the r/r AML 7/12 patients had adverse risk based on ELN 2017. The median number of prior therapies for the MDS HMA-failed patients was 1 (range 1-2). The median number of prior therapies for the r/r AML patients was 2 (range 1-4) with all patients having failed prior HMA-containing therapies and 7/12 having received prior HMA plus venetoclax. The majority of observed adverse events (AE) were Grade 1-2 and no dose limiting toxicities have been reported. As of 25 July 2023, a total of 10 BEX related AEs have been reported (8% of all treatment emergent AEs) with four of these events of ≥ Grade 3, two being immune related (capillary leak syndrome and hemophagocytic lymphohistiocytosis). Sustained target engagement of soluble Clever-1 of up to 75% compared to baseline was seen at all tested dose levels in patient blood. Activity of BEX in patient BM was demonstrated using receptor binding assays with BEX treatment resulting in decreased blast Clever-1 expression at all dose levels of the doublet cohort. Increased immune activation as measured using HLA expression and T/NK cell numbers in patient BM was observed after BEX treatment across indications. Up to 2-3-fold increase of CD8 T and NK cells in the BM of BEX treated patients was observed. Preliminary efficacy shows objective responses in 8/15 evaluable patients across all tested BEX doses. Four were observed in patients with prior HMA-failure and four patients stayed on treatment > 6 months. Clinical activity for frontline MDS was seen as one complete remission (CR), marrow CR (mCR) and hematologic improvement for platelets (HI-P); for MDS with HMA failure as one CR, mCR and partial remission (PR); for r/r AML as two incomplete CRs (CRi). Based on accumulating data, responses are observed between end Cycle 1 and end Cycle 4 for all BEX doses. Conclusion Combining BEX plus azacitidine is well-tolerated and shows efficacy across indications. Additional clinical and pharmacodynamic data of the completed Ph1 of the study will be presented during the meeting. Ph2 of BEX plus azacitidine will open in the 2 nd half of 2023 in HMA-failed r/r AML and/or higher risk MDS patients.

Elucidating Single-Cell Transcriptional Differences of the MLL Subtype in Pediatric Acute Myeloid Leukemia Using Machine Learning and Gene Regulatory Analysis

Introduction: The prognosis for highly heterogeneous pediatric acute myeloid leukemia (AML), classified into eight major subtypes, varies considerably. Common pediatric AML abnormalities include the ones involving mixed lineage leukemia (MLL) gene rearrangements, RUNX1/RUNX1T1 (RUNX1) fusion, and chromosome 16 (inv(16)) inversion. MLL has the worst prognosis (5-year OS: 47%) while RUNX1 and inv(16) have much better prognoses (5-year OS: 91% and 87% respectively) ( von Neuhoff et al., 2010). Using single-cell profiling, our group had developed gene signatures to discriminate between these three subtypes, with the identified genes in the MLL signature correlating with a worse prognosis ( Krishnan et al., 2022). Here, to further improve the robustness of the blast-associated signatures, we employed a machine learning model and included more healthy control samples. Revealing differences between these subtypes' immune microenvironments (IME) is critical for identifying the cellular/molecular drivers of the poorer prognosis associated with the MLL subtype. To identify subtype-specific differences in genes/pathways, we performed an in-depth analysis of the blasts and IME. Methods: We analyzed single-cell transcriptome data from pediatric AML bone marrow (BM) samples collected at diagnosis (MLL, n=4; RUNX1, n=4; inv(16), n=3) and healthy BM samples (n=9) ( Bailur et al., 2020; Caron et al., 2020). Quality control and filtering yielded >63,000 cells. The 7-gene signature from Thomas et al. (2020) was used to distinguish leukemic blasts from non-blast cells. Differential expression (DE) analysis was conducted using Wilcoxon's test between the three subtypes' blast cells and healthy myeloid cells (>50% subtype-blasts expression, <20% other samples' expression). The most differentially expressed genes (Log2FC>0.6, p<1e-5) were used to derive the subtype-specific gene signatures, and they were then further refined by considering only the genes that were also differentially expressed (p<1e-5) in the TARGET-AML bulk RNA-seq dataset ( McNeer et al., 2019). These signatures were validated by training a machine-learning-based LightGBM classifier ( Ke et al., 2017) on the gene expression levels in additional TARGET bulk RNA-seq data to differentiate between the three subtypes by themselves as well as other AML and healthy samples. Cell communication and gene regulatory analysis were performed using the CellChat ( Jin et al., 2021) and pySCENIC ( Aibar et al., 2017) tools respectively. Results: Our analysis confirmed overexpression of the previously reported SOCS2, KCNE5 and TRPM4 genes in MLL leukemic blasts and identified new markers including LAMP5, LTC4S and HOXA9. HOXA9 is a transcription factor that has been shown to result in a poorer prognosis for patients suffering from AML ( Collins et al., 2015). CAV1 was found to be overexpressed in RUNX1-subtype blasts in addition to the POU4F1, NPW and TRH genes found previously. The inv(16) blast signature comprised of the AUTS2, PAM, ST18, SPARC and TSC22D1 genes. The LightGBM classifier trained on these signatures exhibited an overall AUROC test score of 0.9996 when discriminating between just the three subtypes and 0.9651 when other AML subtypes and healthy controls were considered as well (Fig. 1A). In the T-cell compartment of the IME, MLL patients not only had a significantly (p<1e-5) lower proportion of CD8+ Naïve T-cells than any of the other subtypes but also had a significantly (p=0.026) smaller overall proportion of CD8+ T-cells (Fig. 1B). Gene regulatory analysis revealed that MLL leukemic blasts had significantly (p<2e-16) enriched activity of the SPI-B transcription factor (TF), known to suppress CD8+ T-cell proliferation in various cancers ( Huang et al., 2021). Additionally, cell communication analysis revealed significantly (p<0.01) less communication involving the LCK pathway within CD8+ Naïve T-cells, a pathway known to play a key role in proliferation ( Seddon et al., 2000) Conclusions: This study evaluated the differences between the MLL, RUNX1, and inv(16) AML subtypes at the single-cell level, discovered gene signatures that effectively discriminate between the three subtypes as well as other AML and healthy samples, and revealed that the poorer prognosis of the MLL subtype may be attributable to dysregulation of CD8+ T-cell proliferation caused by abnormalities in the SPI-B TF and the LCK signaling pathway.

Sting Activation in Bone Marrow Macrophages Targets AML Blasts for Phagocytosis in an ICAM-1 Dependent Mechanism

The initiation and proliferation of acute myeloid leukaemia (AML) is in part regulated by the bone marrow microenvironment. Previous work by our group has shown that the stimulator of interferon genes (STING) pathway is activated in macrophages in the AML bone marrow microenvironment (Moore et al., 2022) . We found that AML-derived mitochondrial damage-associated molecular patterns were processed by bone marrow macrophages (BMMs) via LC3-associated phagocytosis (LAP). Furthermore, activation of STING resulted in a suppression of AML growth through an LAP dependent mechanism. Here we have investigated how the activation of STING in bone marrow macrophages increases macrophage phagocytic activity and in turn supresses the growth of AML. To understand the role of STING activation in bone marrow derived macrophages (BMDMs) in AML we used various STING agonists including DMXAA, 2'3'-cGAMP, and CpG oligonucleotides. We showed STING activation was induced through these agonists by measuring the upregulation of STING related genes ( Gbp2, Irf7 and Ifit3). We demonstrated that STING activation caused increased phagocytic clearance of live MN1 cells (mouse AML cell line) in an in vitro phagocytosis assay. In order to investigate how STING activation increases the phagocytic clearance of AML cells by BMDMs, we used three complementary methods. First, we performed a receptor tyrosine kinase array to measure the phosphorylation of mouse kinases following STING activation. Second, we investigated the transcriptomic changes resulting from STING activation with mRNA-sequencing. Third, after combining these results we identified an upregulation of key phagocytic pathways that specifically led us to focus on the adhesion molecules, in particular ICAM-1. Further investigation using an anti-ICAM-1 blocking antibody showed a reduction in the phagocytic potential of the BMDMs demonstrating the role of ICAM-1 in the phagocytic clearance of AML. Next, we activated human macrophages (derived from peripheral blood monocytes collected from healthy donors with approval of the East of England - Cambridgeshire and Hertfordshire Research Ethics Committee and the UK Health Research Authority, IRAS Project ID 33753) through STING which depleted AML in vitro confirming the results obtained using the mouse system. To investigate the in vivo significance of these findings, we treated C57Bl/6 animals with DMXAA and observed a significantly decreased tumour burden and increased survival following engraftment with MN1 cells. Cytotoxic T cell activity and number in the bone marrow was unchanged by STING activation in this model. In summary, we have shown that the activation of STING in bone marrow macrophages directly supresses the growth and proliferation of AML by stimulating the phagocytic activity of the macrophages, and the clearance of the leukaemic cells.