Survival Of Acute Myeloid Leukemia Cells Research Articles

Microenvironment matters: In vitro 3D bone marrow niches differentially modulate survival, phenotype and drug responses of acute myeloid leukemia (AML) cells

Acute myeloid leukemia (AML) is a deadly form of leukemia with ineffective traditional treatment and frequent chemoresistance-associated relapse. Personalized drug screening holds promise in identifying optimal regimen, nevertheless, primary AML cells undergo spontaneous apoptosis during cultures, invalidating the drug screening results. Here, we reconstitute a 3D osteogenic niche (3DON) mimicking that in bone marrow to support primary AML cell survival and phenotype maintenance in cultures. Specifically, 3DON derived from osteogenically differentiated mesenchymal stem cells (MSC) from healthy and AML donors are co-cultured with primary AML cells. The AML cells under the AML_3DON niche showed enhanced viability, reduced apoptosis and maintained CD33+ CD34−phenotype, associating with elevated secretion of anti-apoptotic cytokines in the AML_3DON niche. Moreover, AML cells under the AML_3DON niche exhibited low sensitivity to two FDA-approved chemotherapeutic drugs, further suggesting the physiological resemblance of the AML_3DON niche. Most interestingly, AML cells co-cultured with the healthy_3DON niche are highly sensitive to the same sample drugs. This study demonstrates the differential responses of AML cells towards leukemic and healthy bone marrow niches, suggesting the impact of native cancer cell niche in drug screening, and the potential of re-engineering healthy bone marrow niche in AML patients as chemotherapeutic adjuvants overcoming chemoresistance, respectively.

Dotting out AML by targeting Fibrillarin.

Dysregulated biomolecular condensates, formed through multivalent interactions among proteins and nucleic acids have been recently identified to drive tumorigenesis. In acute myeloid leukemia (AML), condensates driven by RNA-binding proteins (RBPs) alter transcriptional networks. Yang and colleagues performed a CRISPR screen and identified Fibrillarin (FBL) as a new driver in AML leukemogenesis. FBL depletion caused cell cycle arrest and death in AML cells, with minimal impact on normal cells. FBL's phase separation domains are essential for pre-rRNA processing, influencing AML cell survival by regulating ribosome biogenesis and the translation of oncogenic proteins like MYC. Therapeutically, the chemotherapeutic agent CGX-635 targets FBL, inducing its aggregation, impairing pre-rRNA processing, and reducing AML cell survival. This highlights FBL's phase separation as a therapeutic vulnerability in AML. These findings suggest that targeting the phase separation properties of RBPs could offer a novel and effective strategy for AML treatment. Further research into condensate dynamics in cancer and development of condensate-modulating drugs holds significant promise for future cancer therapies.

Preclinical efficacy of BRG1/BRM ATPase inhibitor in B lymphoblastic leukemia.

10030 Background: Acute lymphoblastic leukemia (ALL) is the most common blood cancer in children and young adults. While ALL has a high cure rate, approximately 20% of patients who initially respond to treatment relapse and prognosis post relapse remains poor. New therapeutic treatments are needed to reduce relapse rates in B-ALL pediatric patients and to minimize the toxic side effects seen with current therapies. We and others have previously shown that BRG1/BRM ATPase inhibitors have efficacy in targeting acute myeloid leukemia (AML) and one, FHD-286, is currently being evaluated for its use in AML in an ongoing clinical trial (NCT04891757). BRG1 and BRM are the ATP-dependent catalytic subunits of the SWI/SNF chromatin remodeling complex which has a critical role in controlling gene expression, cell growth and survival of AML cells. Our prior work revealed that BRG1/BRM ATPase inhibition leads to selective transient reduction of normal B cells. Further, data from Depmap also nominates SMARCA4, the gene encoding BRG1, as a dependency in B-ALL cell lines, leading us to hypothesize that BRG1/BRM inhibition may be an effective therapy for B-ALL. Methods: We treated B-ALL cell lines with varying genetic lesions ( KMT2A-rearranged: RS4;11, KOPN-8, SEM; ETV6::RUNX1 fusion: REH and DUX4-rearranged: Nalm6) with dose titrations of FHD-286 and measured cell growth over the course of six days. In addition, at 48- and 72-hours post-treatment, we assayed cells for viability, cell cycle kinetics, and apoptosis induction via flow cytometry to provide insight into FHD-286’s mechanism of action in B-ALL. Results: We found that FHD-286 treatment resulted in decreased cell growth in a dose-dependent manner across all B-ALL cell lines. While all cell lines were displayed reduced proliferation at nanomolar doses, sensitivity varied. Nalm6, REH and SEM cells were the most sensitive with low nanomolar IC50s (2-7nM). In contrast, two of the KMT2Ar B-ALL lines, RS4;11 and KOPN-8, required higher doses to achieve growth inhibition (40-70nM). To better understand the mechanism by which FHD-286 is affecting cell growth, we evaluate whether FHD-286 is targeting cell growth through the apoptotic pathway or through cell cycle arrest. Our preliminary data indicates cell growth inhibition is only slightly attributable to cell cycle arrest and apoptosis induction, leading us to explore terminal differentiation as a mechanism of slowed proliferation. Conclusions: Our results show FHD-286 can strongly inhibit B-ALL cell growth in vitro, indicating FHD-286 as a potential therapeutic agent to treat B-ALL. In vivo validation is ongoing. Further directions include defining the effect of FHD-286 on chromatin remodeling, gene expression, and exploring efficacy in combination therapy, which has been shown to increase FHD-286 efficacy against AML. Our data may ultimately justify inclusion of B-ALL patients in clinical studies of BRG1/BRM inhibitors.

SMS121, a new inhibitor of CD36, impairs fatty acid uptake and viability of acute myeloid leukemia

Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and the second most common among children. AML is characterized by aberrant proliferation of myeloid blasts in the bone marrow and impaired normal hematopoiesis. Despite the introduction of new drugs and allogeneic bone marrow transplantation, patients have poor overall survival rate with relapse as the major challenge, driving the demand for new therapeutic strategies. AML patients with high expression of the very long/long chain fatty acid transporter CD36 have poorer survival and very long chain fatty acid metabolism is critical for AML cell survival. Here we show that fatty acids are transferred from human primary adipocytes to AML cells upon co-culturing. A drug-like small molecule (SMS121) was identified by receptor-based virtual screening and experimentally demonstrated to target the lipid uptake protein CD36. SMS121 reduced the uptake of fatty acid into AML cells that could be reversed by addition of free fatty acids and caused decreased cell viability. The data presented here serves as a framework for the development of CD36 inhibitors to be used as future therapeutics against AML.

Single cell and bulk RNA expression analyses identify enhanced hexosamine biosynthetic pathway and O-GlcNAcylation in acute myeloid leukemia blasts and stem cells.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults with an overall poor prognosis and high relapse rate. Multiple factors including genetic abnormalities, differentiation defects and altered cellular metabolism contribute to AML development and progression. Though the roles of oxidative phosphorylation and glycolysis are defined in AML, the role of the hexosamine biosynthetic pathway (HBP), which regulates the O-GlcNAcylation of cytoplasmic and nuclear proteins, remains poorly defined. We studied the expression of the key enzymes involved in the HBP in AML blasts and stem cells by RNA sequencing at the single-cell and bulk level. We performed flow cytometry to study OGT protein expression and global O-GlcNAcylation. We studied the functional effects of inhibiting O-GlcNAcylation on transcriptional activation in AML cells by Western blotting and real time PCR and on cell cycle by flow cytometry. We found higher expression levels of the key enzymes in the HBP in AML as compared to healthy donors in whole blood. We observed elevated O-GlcNAc Transferase (OGT) and O-GlcNAcase (OGA) expression in AML stem and bulk cells as compared to normal hematopoietic stem and progenitor cells (HSPCs). We also found that both AML bulk cells and stem cells show significantly enhanced OGT protein expression and global O-GlcNAcylation as compared to normal HSPCs, validating our in silico findings. Gene set analysis showed substantial enrichment of the NF-κB pathway in AML cells expressing high OGT levels. Inhibition of O-GlcNAcylation decreased NF-κB nuclear translocation and the expression of selected NF-κB-dependent genes controlling cell cycle. It also blocked cell cycle progression suggesting a link between enhanced O-GlcNAcylation and NF-κB activation in AML cell survival and proliferation. Our study suggests the HBP may prove a potential target, alone or in combination with other therapeutic approaches, to impact both AML blasts and stem cells. Moreover, as insufficient targeting of AML stem cells by traditional chemotherapy is thought to lead to relapse, blocking HBP and O-GlcNAcylation in AML stem cells may represent a novel promising target to control relapse.

Abstract 3231: Pharmacological inhibition of the m6A RNA reader, YTHDC1, as a novel approach to targeting biomolecular condensates in cancer

Abstract Epigenetic dysregulation is a hallmark of cancer, and tumors have evolved complex mechanisms to fine-tune oncogenic gene expression. In acute myeloid leukemia (AML), one such regulatory mechanism involves post transcriptional modification of RNAs. The most abundant post transcriptional modification is methylation of adenosine at the N6 position (m6A). This modification is catalyzed by the m6A “writer”, METTL3 and METTL14 complex, and is removed by “erasers” such as FTO and ALKBH5. m6A RNAs can regulate a variety of cellular processes which can impact tumor phenotypes, including RNA stability, splicing, and nuclear export; and METTL3 catalytic inhibitors are currently in clinical development for AML and other cancers (NCT05584111).The m6A “reader”, YTHDC1, has been recognized as a critical contributor to the proliferation and survival of AML cells. As the primary nuclear m6A reader, YTHDC1 localizes with m6A marked RNAs in phase-separated assemblies, termed biomolecular condensates, helping to maintain the stability of oncogenic transcripts such as MYC. Here, we have employed our proprietary microfluidics based screening platform (termed PhaseScanTM) to identify modulators of YTHDC1 biomolecular condensates. Evaluation of early screening hits helped identify that disruption of the interaction between YTHDC1 and m6A RNA is a functionally relevant mechanism of action (MoA) that results in dissolution of YTHDC1 condensates. Using computational and knowledge based approaches, we have identified other structurally distinct inhibitors that occupy the RNA binding pocket of YTHDC1 and disrupt its interaction with m6A RNA at nanomolar potencies. These compounds disrupt cellular YTHDC1 condensates, suppress oncogenic gene expression, and result in anti proliferative and pro-differentiation phenotypes in AML cell lines. Compounds are selective for YTHDC1 over other YTH family members and are also selective in dissolving YTHDC1 condensates over other nuclear and cytosolic condensate systems. Our optimized chemical matter has suitable ADME properties to support in vivo studies. Thus, targeting YTHDC1 biomolecular condensates represents a novel approach to the treatment of AML. Citation Format: Richard C. Centore, Mark Charles, Mansi Arora, Yiwen Chen, Matthew Watson, Charlotte Kelley, Magdalena Czekalska, Marius Rebmann, Mahmoud Ghandi, Jerome Cattin, Nagakumar Bharatham, Prathima Radhakrishnan, Alex Howarth, Gale Rudlaff, William E. Arter, Seema Qamar, Kadi Saar, Douglas Williamson, Andrew Seeber, Tuomas Knowles, Shilpi Arora. Pharmacological inhibition of the m6A RNA reader, YTHDC1, as a novel approach to targeting biomolecular condensates in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3231.

The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9.

The bromodomain-containing protein BRD9 is essential for AML cell viability, but it is unclear whether this requirement is due to the protein's role as an epigenetic reader. We inhibited this activity and identified altered gene-distal chromatin regulation and transcription consistent with a more mature myeloid cell state.

Abstract A049: Investigation of FHD-609, a potent degrader of BRD9, in preclinical models of acute myeloid leukemia (AML)

Abstract Acute myeloid leukemia (AML) is a complex disease with multiple sub-types, each characterized by unique clinical and molecular features, driving the need to develop targeted therapies which exploit specific vulnerabilities. Bromodomain-containing protein 9 (BRD9) is a component of the ncBAF chromatin remodeling complex, and has been recently indicated as a strong dependency in AML (Weisberg et al 2022). It has been shown that inhibitors of BRD9 induce growth inhibition and expression of apoptotic makers in AML cell lines (Hohmann et al 2016; Zhou et al 2021). It has also been reported that BRD9 is critical to AML cell survival through the maintenance of STAT5 signaling (Del Gaudio et al 2019). Herein, we profile the in vitro anti-proliferative effects of FHD-609, a potent and selective degrader of BRD9, in a panel of 40 AML cell lines representative of a broad range of AML sub-types. We observed that FHD-609 was effective at inhibiting the growth of a subset of AML cell lines, consistent with previous reports in the literature. We further investigated whether treatment of AML cell lines with FHD-609 would induce changes in cell cycle, and found an increase in G1 in the same subset of cell lines that showed cell growth inhibition. Furthermore, treatment with FHD-609 induced apoptosis in these cell lines. To identify the mechanisms of action of FHD-609 in AML, as well as potential predictive biomarkers for AML sensitivity to FHD-609, we performed a range of mechanistic studies including ATACseq, ChIPseq and RNAseq in AML cells treated with FHD-609. We observed significant changes in the chromatin landscape in sensitive AML cell lines, and negligible changes in insensitive cell lines. Further bioinformatics analysis identified a possible biomarker strategy that correlates with the sensitivity of AML cell lines to FHD-609 in vitro. To confirm whether this biomarker strategy would successfully predict response in vivo, we dosed AML CDX and PDX models with FHD-609 based on the biomarker selection strategy. We observed a strong anti-tumor effect in AML CDX models and significantly extended survival of the mice in the AML PDX models. In summary, we have shown that FHD-609 demonstrates strong anti-tumor efficacy in a subtype of AML and have identified a possible biomarker strategy to predict response. Citation Format: Claudia Dominici, David Mayhew, Ammar Adam, Flore Uzan, Victoria Garbitt-Amaral, Oliver Mikse, Brandon Antonakos, Hafiz Ahmad, Salonee Parikh, Mei Yun Lin, Gabriel Sandoval, David Lahr, Hsin-Jung Wu, Mengni Xu, Sean Brennan, Luis M. M. Soares, Jordana Muwanguzi, Huawei Chen, Zhaoxia Yang, Jason T Lowe, Matt Netherton, Laura Zawadzke, Johannes Voigt, Liyue Huang, Sabine Ruppel, Ho Man Chan, Ryan Kruger, David S Milan, Scott Innis, Qianhe Zhou, Steven F Bellon. Investigation of FHD-609, a potent degrader of BRD9, in preclinical models of acute myeloid leukemia (AML) [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A049.

Cephalochromin-Induced Mitochondrial Damage Overcomes Venetoclax-Resistance in Acute Myeloid Leukemia Models

The combination of the BCL2 inhibitor venetoclax (VEN) with hypomethylating agents (e.g. azacytidine, AZA) significantly increased complete remission (CR) rates and prolonged overall survival of adults with Acute Myeloid Leukemia (AML) who were ineligible to intensive chemotherapy. However, VEN+AZA is not a curative treatment and resistance to VEN and/or relapses are common. Therefore, the search for new agents able to improve the depth and duration of CR or to overcome VEN resistance are needed. Cephalochromin (CPC), a natural compound easily obtained from Comospora vilior, emerges as a potential candidate. Here, we initially accessed the effects of CPC and VEN monotherapies regarding the cell survival of a large panel of AML cell lines (n=12), covering the main different molecular profiles observed in AML patients. Each cell model exhibited a degree of sensitivity to each drug, with no correlation between the sensitivity for both compounds across the cell models. IC 50 values for CPC ranged from 0.45 to >20 µM, while VEN IC 50 values ranged from <0.001 to 17.5 µM upon 72 h of treatment. To evaluate the cytotoxic effects of CPC in healthy cells, we treated human peripheral blood mononuclear cells from 4 healthy donors, which revealed IC50 values ranging from 3.7 to 8.8 µM at 72 h, suggesting a potential feasible therapeutic window. To evaluate the potential combination effects of CPC + VEN in AML, we performed combination experiments in AML models, chosen based on their VEN sensitivity (Kasumi-1 and U937 cells as partially resistant and OCI-AML3 displaying higher VEN resistance). Combination effects in all AML models revealed an significant improvement on the performance of VEN when combined to CPC, even in low doses of both compounds. We next evaluated the molecular mechanisms associated with the effects of CPC on cell proliferation and survival. Clonogenic assays revealed that CPC treatment was associated with decreased stemness capacity, in a concentration-dependent manner. Cell cycle analysis on CPC-treated cells revealed a progressive increase in sub-G1 cells population, suggesting apoptosis induction in a dose-dependent manner, which was further corroborated by increased Annexin-V levels on treated cells. The effects of CPC regarding the apoptosis induction were more evident in Kasumi-1 cells when compared with U937 and OCI-AML3 cells. In OCI-AML3 cells (which display the highest MCL1 expression across the different AML models), combination of low concentrations of VEN (1 µM) and CPC (1.8 µM) showed an apoptosis induction in 95% of the cells. Similarly, the combination CPC + VEN resulted in higher levels of apoptosis induction in U937 (monocytic leukemia; VEN 2.5 + CPC 2.5 µM) and Kasumi-1 ( TP53 R248Q mutant; VEN 0.6 + CPC 2.5 µM) cells. Metabolic analysis of CPC treated cells revealed extensive mitochondrial damage associated with reduction in the mitochondria mass. Proteomic analysis showed increase PARP1 cleavage (apoptosis) and γH2AX (DNA damage) levels upon CPC treatment in all evaluated models, whereas MCL1 was reduced in Kasumi-1 cells. Moreover, SQSTM1/p62 levels were reduced in U937 and Kasumi-1 cells, suggesting induction of autophagy as a mechanism of response to CPC in these cells. Finally, these findings were confirmed in a cohort of ex vivo treated AML samples (n=10) treated with CPC and VEN alone or in combination, where the combination of VEN 0.1 + CPC 2.5 µM displayed strong synergistic effect when compared to the monotherapies. Treatment with CPC reduced the mitochondrial membrane potential, suggesting the disturbance on the mitochondrial metabolism as one of the key phenomena associated with the efficiency of the CPC+VEN combination therapy. In summary, by using multiple cellular models, we demonstrated that CPC treatment was able to decrease cell viability and survival of AML cells, while it spares healthy counterparts. We uncovered the potential combination effects of CPC with VEN in leukemic models of resistance to VEN. Mechanistically, CPC treatment induced impaired mitochondrial metabolism, DNA damage and decreased the expression of proteins related with VEN-resistance in AML, possibly explaining the synergic effects observed between VEN and CPC.

Histone Methyltranferase SETD8 Stimulates Proliferation and Anti-Apoptotic Effect in Acute Myeloid Leukemia through Epigenetically Upregulation of CXCR4

Acute myeloid leukemia (AML) is the most common type of leukemia., characterized by the rapid and uncontrolled growth of abnormal cells. Epigenetic modifications control gene expression without affecting its DNA sequence. H4K20me1 is the mono-methylation occurring on lysine 20 of histone H4, acting as an epigenetic mark that promotes gene expression. SETD8 is responsible for catalyzing the mono-methylation of lysine 20 on histone H4. While SETD8's role and mechanisms have been studied in various types of cancer, its function in AML remains unclear. This study is based on the screening of a small molecule compound library, which identified the inhibitor UNC0379 targeting the histone methyltransferase SETD8, showing clear inhibitory effects on three non-M3 AML cell lines. Bioinformatical analysis revealed elevated SETD8 expression in AML patients compared to normal individuals and higher SETD8 expression corresponded with lower overall survival rates (OS). Further investigations using AML cell lines and normal peripheral blood mononuclear cells (PBMCs) demonstrated that SETD8 knockdown or UNC0379 intervention inhibited cell proliferation and increased apoptosis in AML cells, while PBMC cells remained unaffected. In an AML model constructed with C1498 cell injection in C57BL/6J mice, we observed that SETD8 knockdown and treatment with UNC0379 inhibited tumor formation and infiltration. To elucidate the molecular mechanism of SETD8's impact on AML, we conducted transcriptome sequencing on SETD8 knockdown AML cells and found significantly decreased mRNA expression of CXCR4, which was further validated at the protein level. Also, BeatAML and TCGA datasets demonstrated a positive correlation between SETD8 and CXCR4 mRNA expression. These phenomena motivated us to clarify the regulation relationship between SETD8 and CXCR4. CXCR4 is a crucial membrane receptor. After stimulation, it promotes AML cell proliferation and survival. CHIP experiments in SETD8 knockdown cells revealed reduced H4K20me1 enrichment in the CXCR4 promoter region. Subsequent rescue experiments demonstrated that overexpressing CXCR4 or using its corresponding agonist SDF-1alpha in SETD8 knockdown cells moderately restored cell proliferation and reduced apoptosis. In summary, we discovered that SETD8 promotes CXCR4 transcriptional activation through catalyzing the H4K20me1 mark, thereby influencing AML cell proliferation and apoptosis. SETD8 presents a promising therapeutic target through genetic or pharmacological intervention.

Differentiation of Acute Myeloid Leukemia Cells upon Pharmacological Inhibition of LSD1 Requires Its N-Terminal Intrinsically Disordered Region

Lysine-specific histone demethylase 1 (LSD1/KDM1A) governs hematopoiesis by regulating hematopoietic stem cell renewal and proper differentiation. Additionally, LSD1 is required for the maintenance of acute myeloid leukemia (AML) cells and has emerged as a key therapeutic target. Prior work from our group and others have revealed that the LSD1 demethylase activity is not required for AML proliferation. Instead, the interaction between LSD1 and GFI1/GFI1B is necessary to sustain AML cell survival. Thus, beyond its canonical demethylase activity, LSD1 has nonenzymatic, transcription factor (TF)-specific scaffolding functions critical for its function. Most LSD1 inhibitors function by blocking protein-protein interactions between LSD1 and TFs, even though they were originally designed as enzyme inhibitors. While studies indicate that LSD1 has important scaffolding functions, how LSD1 can coordinate with TFs to control gene expression programs is not well understood. Here, we used CRISPR-suppressor scanning to identify regions of LSD1 outside the active site that when mutated can lead to resistance to the covalent LSD1 inhibitor, GSK-LSD1. The understudied N-terminal intrinsically disordered region (IDR) of LSD1 was among the most enriched regions. To explore this further, we generated clonal AML cell lines harboring in-frame deletions within the IDR. These IDR-mutant cell lines were drug resistant and failed to differentiate upon GSK-LSD1 treatment. Moreover, knockdown of endogenous LSD1 followed by overexpression of LSD1 IDR-mutants rescued growth in the presence of GSK-LSD1, confirming that a fully functional IDR is necessary for differentiation. We performed LSD1 co-immunoprecipitation followed by mass spectrometry in wild-type and IDR-mutant cells to measure changes in LSD1 interactors upon GSK-LSD1 treatment. GSK-LSD1 treatment disrupted the LSD1-GFI1B interaction in both wild-type and mutant cells at comparable levels. Since GSK-LSD1 still induces dissociation of the mutant complex but has minimal effect on proliferation, our results suggest that the IDR-mutant cells no longer require GFI1B. In support, knockout of GFI1B inhibited growth of wild-type but not IDR-mutant cells. Strikingly, GSK-LSD1 treatment promoted LSD1's interaction with several master regulator TFs in hematopoiesis, including C/EBPα, PU.1, and RUNX1. Notably, C/EBPα was the most up-regulated interactor in both cell lines, with modest enrichment in IDR-mutant over wild-type. Using live-cell imaging assays, we found that deletions within the LSD1 IDR enhance association with these TFs. These results suggest that GSK-LSD1 reprograms LSD1-TF interactions, disrupting LSD1-GFI1B to induce LSD1-C/EBPα association, and that the IDR mutations alters this LSD1 redistribution to other TF partners. LSD1 is known to silence gene enhancers during differentiation in a process termed “enhancer decommissioning”. The mechanisms by which LSD1 occupies and controls enhancers remain elusive. To test if the LSD1 IDR regulates enhancer elements, we profiled LSD1 and H3K27ac using ChIP-seq in wild-type and IDR-mutant cells upon GSK-LSD1 treatment. Upon GSK-LSD1 treatment, disruption of LSD1-GFI1B binding was accompanied by increased LSD1 levels at other TF and H3K27ac sites, supporting the notion that loss of LSD1-GFI1B interaction induces LSD1 redistribution to other TF partner sites. A concomitant increase in H3K27ac levels was observed across LSD1 sites co-bound by C/EBPα, PU.1, or RUNX1 in wild-type cells. By contrast, in IDR-mutant cells, increases in H3K27ac levels were blocked at these sites upon GSK-LSD1 treatment, suggesting that full enhancer activation is impaired by mutations in the IDR, potentially due to altered association with master regulator TFs. This points to a function of LSD1 IDR in controlling enhancer activation for differentiation. Collectively, our study reveals a role for IDR in regulating LSD1-TF interactions, controlling enhancer activation that is necessary for AML cell differentiation. These data provide deep functional and mechanistic insights into the role of LSD1 IDR and offer important considerations for pharmacological targeting of protein-protein interactions.

An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions.

Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.

PD-1/PD-L1 Interaction Regulates BCL2, KI67, BAX, and CASP3, Altering Proliferation, Survival, and Apoptosis in Acute Myeloid Leukemia

Programmed death ligand‑1 (PD‑L1) is a pivotal inhibitory checkpoint ligand known to induce T-cell exhaustion via interaction with the programmed death‑1 (PD‑1) receptor. Beyond this, PD-L1’s intrinsic signaling pathways within cancer cells warrant further exploration. This study aims to elucidate the effect of PD-L1 stimulation on the proliferation, survival, and apoptosis of acute myeloid leukemia (AML) cell lines.
 Two human AML cell lines, HL-60 and THP-1 were cultured and treated with phorbol 12-myristate 13-acetate (PMA) to induce PD-L1overexpression. Post-treatment PD-L1 expression was confirmed via flow cytometry. Subsequently, cell surface PD-L1 was stimulated using a recombinant PD-1, 24 hours post-PMA treatment. The expression alterations in pivotal genes including BCL2, MKI67, BAX, and CASP3 were monitored using quantitative real-time polymerase chain reaction 24 and 48 hours post-treatment. Additionally, annexin-V through flow cytometry.
 Findings reveal that PD-L1 stimulation augments AML cell proliferation and survival by enhancing MKI67 and BCL2 expressions while concurrently inhibiting cell apoptosis due to decreased BAX and CASP3 expression following PD-L1 stimulation. Notably, stimulated cells expressed exhibited reduced annexin-V compared to control cells.
 This study underscores that PD-L1 stimulation fosters AML cell proliferation and survival while impeding cell apoptosis. The results hold potential implications for targeting PD-L1 in AML treatment strategies.

Loss of CCAAT‐Enhancer Binding Protein Delta Promotes Acute Myeloid Leukemia Cell Proliferation and Survival By Upregulating Cyclin D1 Expression

Despite improvements in the treatment options, acute myeloid leukemia (AML) remains a fatal malignancy with an estimated 5-year relative survival rate of 31.7%. There is continued need for identification of new disease drivers to develop novel therapeutic options and improve clinical outcomes. Dysregulated transcriptional landscapes are associated with disease pathogenesis and treatment responses. To identify new disease drivers of AML, we analyzed RNA-Seq data from 59 patient-matched diagnosis and relapse (PAML) specimens (study cohort). A set of five differentially expressed genes (DEGs; STAT4, XRCC2, USP3, CEBPD, RBM47) with concordant changes in expression between diagnosis and relapse (Figure 1A) were selected for study using the following criteria: (a) concordant differential expression (DESeq2: log2FC > |1.2| and q < 0.05) in at least 25% of the relapsed patients in the study cohort (b) concordant differential expression in independent datasets of RNA-Seq without any experimental validation, and (c) high cancer driver potential based on their molecular function. Binding analysis for regulation of transcription (BART) on DEGs between normal CD34 + cells, diagnosis and relapsed AML patient specimens suggested that CEBPD could function as a transcriptional regulator of a subset of the DEGs. We hypothesized that dysregulated expression of these genes promotes AML disease progression. To examine their role in AML, we altered their expression in AML cell line models and measured changes in AML cell phenotypes. Of these genes, CRISPR-mediated knockdown of the transcription factor CCAAT/enhancer-binding protein delta (CEBPD) enhanced AML cell proliferation, self-renewal capacity, and survival of the relapsed AML cell line OCI-AML5. CEBPD knockdown also conferred OCI-AML5 resistance to cytarabine - a common chemotherapy drug used for AML treatment. Short hairpin RNA (shRNA)-mediated knockdown of CEBPD in OCI-AML5 validated these results. CRISPR-mediated upregulation of CEBPD expression induced monocyte/macrophage differentiation marker CD14 expression and enhanced apoptosis rates in OCI-AML5 cells. CEBPD upregulation also induced differentiation in the diagnosis AML cell line OCI-AML2. Survival analyses showed that lower expression of CEBPD was significantly associated with poor survival in pediatric AML patients, and there was a trend of lower CEBPD expression associating with worse survival in adult AML patients (UCSC Xena browser). These results altogether suggest that CEBPD plays a tumor suppressor role in AML. Gene set enrichment analyses (GSEA) on RNA-Seq data revealed significant positive enrichment of cell proliferation pathways upon CEBPD knockdown in OCI-AML5 cells as well as in a subset of the PAML patients with downregulated CEBPD expression at relapse. Differential gene expression and GSEA analyses altogether suggested upregulated cyclin D1 as one of the downstream drivers of enhanced growth of AML cells with repressed CEBPD expression (Figure 1B). RT-qPCR and Western Blot experiments confirmed upregulation of CCND1 expression in CEBPD knockdown OCI-AML5 and OCI-AML2 cells. Next, we sought to understand the molecular mechanisms repressing CEBPD expression during AML disease progression. We found an inverse association between CEBPD and DNMT3 methyltransferases mRNA expression in PAML and independent datasets. Treatment with the hypomethylating agent azacitidine upregulated CEBPD mRNA expression in multiple AML cell lines including OCI-AML5 and OCI-AML2, suggesting that hypermethylation represses CEBPD gene expression in these AML cells. Integrative analysis of gene expression with DNA methylation at the CEBPD promoter identified hypermethylation of multiple CpGs within the binding region of the transcription factor Sp1 in a subset of patients with CEBPD downregulation. CpG methylation has been shown to interfere with Sp1 binding at the CEBPD promoter. Since Sp1 binding promotes CEBPD transcription, hypermethylation at these sites may repress CEBPD expression during AML disease progression. Our study suggests that CEBPD can function as tumor suppressor in AML. Results suggest a role for DNA methylation in repressing CEBPD expression during AML disease progression. Furthermore, we show that CEBPD repression promotes AML cells' growth potentially via inducing the expression of the cell cycle driver CCND1.

Translational Control of FLT3-Mutated AML Cell Survival

Acute Myeloid Leukemia (AML) is the most common acute leukemia in adults with a five-year survival rate of ~30%. Approximately 30% of AML patients harbor an internal tandem duplication (ITD) mutation in the FMS related receptor tyrosine kinase 3 (FLT3) gene, which is an indicator of poor overall survival and a high relapse rate. These mutations cause constitutive activation of the FLT3 receptor, which amplify proliferation and survival signaling that supports leukemia progression and chemotherapy resistance. Although FLT3 inhibitors (FLT3i) improve median survival by a couple of months, and they have reduced toxicity relative to conventional chemotherapy in clinical trials, patients eventually acquire resistance and relapse. Clinical trials have revealed that AML blasts in the bone marrow (BM) were not effectively eliminated compared to AML blasts in peripheral blood, suggesting a protective role of the BM microenvironment that counteracts FLT3i therapy. A clear understanding of FLT3-mutated AML biology and how it is influenced by the microenvironment is imperative for developing new molecular approaches for improving efficacy of FLT3i-based therapies. We have discovered that BM stromal cell mediated regulation of Ataxia Telangiectasia Mutated (ATM) promotes Mammalian Target of Rapamycin Complex 1 (mTORC1) activity despite FLT3 inhibition, which maintains translation of oxidative phosphorylation genes that are critical for AML cell survival upon treatment with FLT3i [PMID: 36259537]. Key findings show that FLT3i inhibits mTOR and mTOR-dependent translation leading to cell death. However, in the presence of BM stromal factors, survival is restored upon FLT3i by regulating ATM/mTOR-dependent translation of essential phosphorylation genes to overcome FLT3i. Moreover, we demonstrated that the combination of FLT3i and mTORC1 inhibition (mTORC1i) synergistically kills human FLT3-mutated AML cells in vitro and substantially reduces tumor burden and prevents relapse in mouse models of FLT3-mutated AML. Further studies measuring translation in FLT3-mutated AML cells revealed that there are at least two different translation pathways dictated by FLT3. One of these pathways is mTOR-dependent, as expected, and the other is mTOR-independent. Additional studies have sought to characterize FLT3-controlled translation, independent of mTOR, and its importance for FLT3-mutated AML cell survival. Although highly sensitized to FLT3i, we observed that ATM/mTOR-deficient cells maintain near-normal translation and survival. Additionally, mounting evidence suggests that there are other kinases, such as CDK1, GSK3β, and p38, that drive mTOR-independent translation by phosphorylating 4E-BP1. With this knowledge, we took an unbiased approach and used O-Propargyl Puromycin (OPP)-translation assays to assess the impact of inhibitors against these kinases on translation activity in FLT3-mutated AML cell lines. This approach revealed CDK1 as a critical regulator of translation downstream of FLT3. Interestingly, myeloid progenitors reprogram to an mTOR-independent translational program requiring phosphorylation of 4E-BP1 by CDK1 [PMID: 32386556], which could be relevant for myeloid leukemias. Further corroborating my findings, RNA sequencing data suggest that FLT3 positively regulates CDK1 expression/activity, suggesting a downstream position in parallel with mTOR. In conclusion, we have uncovered a FLT3-controlled translation pathway that promotes FLT3-mutated AML cell survival independent of mTOR. Further characterization of this pathway could help predict mechanisms of resistance to FLT3 and mTOR inhibitors in AML and could identify new targets to promote more durable remissions in patients.

Downregulation of stromal syntenin sustains AMLdevelopment.

The crosstalk between cancer and stromal cells plays a critical role in tumor progression. Syntenin is a small scaffold protein involved in the regulation of intercellular communication that is emerging as a target for cancer therapy. Here, we show that certain aggressive forms of acute myeloid leukemia (AML) reduce the expression of syntenin in bone marrow stromal cells (BMSC). Stromal syntenin deficiency, in turn, generates a pro-tumoral microenvironment. From serial transplantations in mice and co-culture experiments, we conclude that syntenin-deficient BMSC stimulate AML aggressiveness by promoting AML cell survival and protein synthesis. This pro-tumoral activity is supported by increased expression of endoglin, a classical marker of BMSC, which in trans stimulates AML translational activity. In short, our study reveals a vicious signaling loop potentially at the heart of AML-stroma crosstalk and unsuspected tumor-suppressive effects of syntenin that need to beconsidered during systemic targeting of syntenin in cancer therapy.

Constitutively Synergistic Multiagent Drug Formulations Targeting MERTK, FLT3, and BCL-2 for Treatment of AML.

Although high-dose, multiagent chemotherapy has improved leukemia survival rates, treatment outcomes remain poor in high-risk subsets, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) in infants. The development of new, more effective therapies for these patients is therefore an urgent, unmet clinical need. The dual MERTK/FLT3 inhibitor MRX-2843 and BCL-2 family protein inhibitors were screened in high-throughput against a panel of AML and MLL-rearranged precursor B-cell ALL (infant ALL) cell lines. A neural network model was built to correlate ratiometric drug synergy and target gene expression. Drugs were loaded into liposomal nanocarriers to assess primary AML cell responses. MRX-2843 synergized with venetoclax to reduce AML cell density in vitro. A neural network classifier based on drug exposure and target gene expression predicted drug synergy and growth inhibition in AML with high accuracy. Combination monovalent liposomal drug formulations delivered defined drug ratios intracellularly and recapitulated synergistic drug activity. The magnitude and frequency of synergistic responses were both maintained and improved following drug formulation in a genotypically diverse set of primary AML bone marrow specimens. We developed a nanoscale combination drug formulation that exploits ectopic expression of MERTK tyrosine kinase and dependency on BCL-2 family proteins for leukemia cell survival in pediatric AML and infant ALL cells. We demonstrate ratiometric drug delivery and synergistic cell killing in AML, a result achieved by a systematic, generalizable approach of combination drug screening and nanoscale formulation that may be extended to other drug pairs or diseases in the future.

CircSLC25A13 acts as a ceRNA to regulate AML progression via miR-616-3p/ADCY2 axis.

Circular RNAs (circRNAs), a type of endogenous noncoding RNA (ncRNA), exert vital roles in leukemia progression and are promising prognostic factors. Here, we report a novel circRNA, circSLC25A13 (hsa_circ_0081188), which was increased in acute myeloid leukemia (AML) patients with poor overall survival (OS) comparing to patients with good prognosis. Knockdown of circSLC25A13 in AML cells inhibited proliferation and increased cell apoptosis in vitro and in vivo. Enhanced circSLC25A13 expression promoted the survival of AML cells. Mechanistically, circSLC25A13 played as a microRNA sponge of miR-616-3p, which inhibited the expression of adenylate cyclase 2 (ADCY2). Downregulation of miR-616-3p and overexpression of ADCY2 partially rescued circSLC25A13 deficient induced cell growth arrest. In summary, through competitive absorption of miR-616-3p and thereby upregulating ADCY2 expression, circSLC25A13 promoted AML progression. Moreover, circSLC25A13 may represent a potential novel biomarker for the prognosis of AML and offer a potential therapeutic target for AML treatment.

Deubiquitinase USP9X stabilizes RNA m6A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival

Post-translational modifications including protein ubiquitination regulate a plethora of cellular processes in distinct manners. RNA N6-methyladenosine is the most abundant post-transcriptional modification on mammalian mRNAs and plays important roles in various physiological and pathological conditions including hematologic malignancies. We previously determined that the RNA N6-methyladenosine eraser ALKBH5 is necessary for the maintenance of acute myeloid leukemia (AML) stem cell function, but the post-translational modifications involved in ALKBH5 regulation remain elusive. Here, we show that deubiquitinase ubiquitin-specific peptidase 9X (USP9X) stabilizes ALKBH5 and promotes AML cell survival. Through the use of mass spectrometry as an unbiased approach, we identify USP9X and confirm that it directly binds to ALKBH5. USP9X stabilizes ALKBH5 by removing the K48-linked polyubiquitin chain at K57. Using human myeloid leukemia cells and a murine AML model, we find that genetic knockdown or pharmaceutical inhibition of USP9X inhibits leukemia cell proliferation, induces apoptosis, and delays AML development. Ectopic expression of ALKBH5 partially mediates the function of USP9X in AML. Overall, this study uncovers deubiquitinase USP9X as a key for stabilizing ALKBH5 expression and reveals the important role of USP9X in AML, which provides a promising therapeutic strategy for AML treatment in the clinic.

CRIP1 supports the growth and migration of AML-M5 subtype cells by activating Wnt/β-catenin pathway

Acute myeloid leukemia (AML) is a clinically and molecularly heterogeneous hematopoietic disorder. To effectively eradicate AML, it is urgent to develop new therapeutic approaches and identify novel molecular targets. In silico analysis indicated that the expression of cysteine-rich intestinal protein 1 (CRIP1) was significantly elevated in AML cells and correlated with worse overall survival of the AML patients. However, its specific roles in AML remain elusive. Here we demonstrated that CRIP1 acted as a key oncogene to support AML cell survival and migration. Using a loss-of-function analysis, we found that CRIP1 silencing in U937 and THP1 cells by lentivirus-mediated shRNAs resulted in a decrease in cell growth, migration and colony formation, and an increase in chemosensitivity to Ara-C. CRIP1 silencing induced cell apoptosis and G1/S transition arrest. Mechanically, CRIP1 silencing caused inactivation of Wnt/β-catenin pathway through upregulating axin1 protein. The Wnt/β-catenin agonist SKL2001 markedly rescued the cell growth and migration defect induced by CRIP1 silencing. Our findings reveals that CRIP1 may contribute to AML-M5 pathogenesis and represent a novel target for AML-M5 treatment.