Acute Myeloid Leukemia Growth Research Articles

Abstract CT089: A phase 1 multi-center, open label, dose escalation study to evaluate the safety, pharmacokinetics (PK) and anti-tumor activity of T-1301, a novel small molecular multi-target kinase inhibitor, in patients with advanced solid tumors

Abstract Background: T-1301 is a novel small molecule multi-target kinase inhibitor, it also exhibited potent inhibitory activity against both wild type and mutant forms of various kinases, i.e., ABL1, FLT3, c-KIT, PDFGRA, RET, and TRKA. In in vitro studies, T-1301 effectively inhibited growth of acute myeloid leukemia (AML) as well as gastrointestinal stromal tumor (GIST) cells carrying mutations that are resistant to KIT-targeting tyrosine kinase inhibitors (TKIs) in clinical use. In animal studies, tumor regressions were observed in AML and GIST xenograft models, while growth inhibition were observed in various other types of solid tumor models. Method: This is an open label, multi-centered Phase 1 dose escalating study (NCT05156203). The primary objectives are to establish the maximal tolerated dose (MTD) and recommended Phase 2 dose (RP2D), and to assess the safety and tolerability of T-1301. The secondary objectives are to evaluate the pharmacokinetics (PK) and therapeutic response after receiving treatment. Eligible Patient should have histologically and cytologically confirmed advanced solid tumors (including lymphoma) with measurable or evaluable target lesion(s) per RICEST v1.1 and refractory to or without standard treatments, ECOG performance status 0-1, and adequate organ function. The dose escalation begins with accelerated titration and switch to the Bayesian Optimal Interval (BOIN) design when either one of the following events is observed in Cycle 1: the first instance of DLT, or any Grade 2 or higher drug-related adverse event (AE) in any patient. Then, at least 2 additional subjects are treated at the current dose level and the dose escalation will follow the Bayesian Optimal Interval (BOIN) design with cohorts of size 3-6.T-1301 is orally administered daily in a 28-day cycle (a 21-day consecutive dosing followed by a 7-day rest). The dosing schedule is once daily (QD) at the initial dose level and could be QD or twice daily starting with the second dose level according to the safety review committee (SRC) decision after reviewing the safety and PK data from each dose level. AEs are assessed according to CTCAE v5.0 and occurrence of dose limiting toxicity (DLT) is determined during the first cycle of treatment. The safety findings are reviewed by the SRC, which will determine the MTD and RP2D. Tumor response evaluation is performed after 2 cycles of treatment and assessed according to RECIST v1.1 criteria. For those who benefit from the study medication after 2 treatment cycles, intra-subject dose escalation for multiple times is allowed in extension study period. Patient recruitment began in December 2021 and is ongoing in Taiwan. Citation Format: Jen-Shi Chen, Ming-Huang Chen, Yi-Chang Liu, Wen-Chi Chou, Nai-Jung Chiang, Hui-Ching Wang, Ta-Sen Yeh, Shih-Feng Cho, Cheng-Hsu Wang, I-Fang Lee, Li-Tzong Chen. A phase 1 multi-center, open label, dose escalation study to evaluate the safety, pharmacokinetics (PK) and anti-tumor activity of T-1301, a novel small molecular multi-target kinase inhibitor, in patients with advanced solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT089.

Abstract 3297: Discovery and evaluation of GT19870, a GSPT1/Myc molecular glue drug (MGD) with oral bioavailability for targeting c-Myc and n-Myc-addictive blood cancer and solid tumors

Abstract c-Myc and n-Myc are oncogenic transcriptional factors driving tumor initiation, progression and poor prognosis in a variety of blood cancers and solid tumors, such as acute myeloid leukemia (AML), B-cell malignancies, castration resistance prostate cancer (mCRPC), small cell lung cancer and (SCLC) and neuroblastoma. Both c-Myc and n-Myc dysregulations have been directly linked to the poor clinical outcome in some of these cancers which are addictive to deregulated Myc proteins. Therefore, it is highly warranted to discover and develop novel therapeutical agents for targeting Myc-addictive cancers. GT19870 was discovered through a SAR effort for Myc degradation with improved bioavailability (F % 92.52) from GT19630, a GSPT1/Myc degrader series 1-4by using phenotypic screenings with c-Myc-addictive HL-60 AML cells and growth factor-dependent hematopoiesis progenitor TF-1 cells, followed by c-Myc ELISA and Western blot assays. GT19870 selectively inhibited the proliferation of HL60 cells with an IC50 of 2.6 nM as compared to an IC50 of 70.03 nM (26.5-fold selectivity) and effectively degraded c-Myc protein with an IC50 of 2.54 nM and IC90 <10 nM in HL-60 cells, as compared to an IC90>30 nM in CD3/CD28-stimulated PBMC assays. GT19870, as a MGD, was confirmed to selectively degrade GSPT1, a neo-substrate, by proteomic and Western Blot assays. Further, GT19870 was tested in SCLC, triple negative breast cancer (TNBC) and brain cancer cell panels, in which GT1987 was revealed potent anti-proliferation activities with an IC50<50 nM in 9 of 19 SCLC, 8 of 13 TNBC, and 7 of 24 brain cancer cell lines tested. Importantly GT19870 was also shown potent antitumor activities with IC50 of ≦5.4 nM in 8 of 8 SCLC patient derived organoids. Furthermore, GT19870 (salt form-GT19884) was demonstrated to induce target-engaged (c-Myc and n-Myc) tumor regression in AML, SCLC, mCRPC and neuroblastoma xenograft and PDX models with in a dose ranges of 3-12 mpk/qd/po. In brief, GT19870 is an oral MGD degrading GSPT1/c-Myc/n-Myc. This novel MGD has been demonstrated target-engaged antitumor activities in vitro and in vivo with selectivity of c-Myc degradation in c-Myc-addictive cancer cells as compared to growth factor-stimulated TF-1 cells and CD3/CD28 activated PBMC. GT19870 has been progressing IND enabling stage.

Integrative single-cell expression and functional studies unravels a sensitization to cytarabine-based chemotherapy through HIF pathway inhibition in AML leukemia stem cells.

Relapse remains a major challenge in the clinical management of acute myeloid leukemia (AML) and is driven by rare therapy-resistant leukemia stem cells (LSCs) that reside in specific bone marrow niches. Hypoxia signaling maintains cells in a quiescent and metabolically relaxed state, desensitizing them to chemotherapy. This suggests the hypothesis that hypoxia contributes to the chemoresistance of AML-LSCs and may represent a therapeutic target to sensitize AML-LSCs to chemotherapy. Here, we identify HIFhigh and HIFlow specific AML subgroups (inv(16)/t(8;21) and MLLr, respectively) and provide a comprehensive single-cell expression atlas of 119,000 AML cells and AML-LSCs in paired diagnostic-relapse samples from these molecular subgroups. The HIF/hypoxia pathway signature is attenuated in AML-LSCs compared with more differentiated AML cellsbut is more expressed than in healthy hematopoietic cells. Importantly, chemical inhibition of HIF cooperates with standard-of-care chemotherapy to impair AML growth and to substantially eliminate AML-LSCs in vitro and in vivo. These findings support the HIF pathway in the stem cell-driven drug resistance of AML and unravel avenues for combinatorial targeted and chemotherapy-based approaches to specifically eliminate AML-LSCs.

Harnessing upregulated E-selectin while enhancing SDF-1α sensing redirects infused NK cells to the AML-perturbed bone marrow

Increased bone marrow (BM) homing of NK cells is associated with positive outcome in patients with acute myeloid leukemia (AML) treated within adoptive NK cell transfer trials. While most efforts to further improve the efficacy focus on augmenting NK cell persistence and cytotoxicity, few address their ability to home to the tumor. Here, we decipher how AML growth alters the BM niche to impair NK cell infiltration and how insights can be utilized to resolve this issue. We show that AML development gradually impairs the BM homing capacity of infused NK cells, which was tightly linked to loss of SDF-1α in this environment. AML development also triggered up-regulation of E-selectin on BM endothelial cells. Given the poor E-selectin-binding capacity of NK cells, introduction of fucosyltransferase-7 (FUT7) to the NK cells per mRNA transfection resulted in potent E-selectin binding and stronger adhesion to E-selectin+ endothelial cells. Co-introduction of FUT7 and gain-of-function CXCR4 (CXCR4R334X) redirected NK cell homing to the BM of AML-bearing mice nearly to the levels in AML-free mice. This work shows how impaired NK cell homing caused by AML-induced microenvironmental changes can be overcome by genetic engineering. We speculate our insights can help further advance future NK cell immunotherapies.

AML Inhibits Lipid Uptake By the Liver through an HGF/c-MET Dependent Mechanism Which Results in an Increased Supply of Free Fatty Acid to the Tumor

Acute myeloid leukemia (AML) requires a high metabolic turnover to allow for constant expansion. We and others have previously shown that primary human AML blasts rely on fatty acid (FA)-oxidation for survival and proliferation. (Shafat MS, et al. 2017, Jones CL, et al. 2018). The liver plays a major role in carbohydrate, protein, amino acid, and lipid metabolism (Hodson L, and Gunn PJ. 2019). Given that AML is a FA dependent tumor, we have studied the interactions between AML and the liver, and specifically how these affect lipid metabolism, the availability of pro-tumoral FFA and ultimately the mechanism by which this supports AML growth. To understand the role of lipid metabolism we used two syngeneic models of AML (HOXA9/Meis1 or MN1). When engrafted with AML cells, mice body weight during the latter stages of disease. After sacrifice, the size of epididymal and inguinal fat pads were significantly reduced in mice with AML compared to controls. Mice with AML also had elevated free fatty acid (FFA) and reduced glucose in the plasma. We and others have shown that AML induces lipolysis of white adipose tissue for uptake by blasts and resulting in tumor expansion (Shafat MS, et al. 2017, Ye H, et al. 2016). Since the liver is the master regulator of available FA in the plasma, we isolated livers from AML engrafted mice. Transcriptomics revealed down-regulation of genes involved in FA uptake and metabolism. RT-qPCR of RNA isolated from liver samples confirmed these results showing down-regulation of FA transport proteins, (FABP1, SLC27A2, SLC27A5, and CD36) and FA metabolism genes (CPT1, ACADM, and HMGCS2). Furthermore, primary hepatocytes isolated and cultured with AML conditioned media showed a down-regulation of FA uptake and metabolism genes. These data support the hypothesis that AML secretes a factor that alters lipid metabolism in the liver. To discover the factor that AML secretes, and which regulates FA uptake and metabolism in the liver, a proteome profile of the serum from AML engrafted mice was compared to conditioned media from AML cultured cells. Pathway analysis revealed hepatocyte growth factor (HGF), IL-1B and Granulocyte colony stimulating factor (G-CSF) as possible key factors involved in liver FA metabolism (Jing Y, et al. 2019, Kaibori M, et al. 2002). In vitro gene expressions analysis of primary hepatocytes revealed that addition of HGF to the medium, but not Il-1b or G-CSF, inhibited expression of FA uptake genes. In addition, using Seahorse mitochondrial stress kit we confirmed that primary hepatocytes decreased FA oxidation when cultured with AML conditioned media or HGF. Next, we confirmed that AML derived HGF was responsible for inhibition of hepatocyte FA genes by using a neutralizing antibody to HGF which blocked the transcriptional changes previously observed in hepatocytes cultured in AML conditioned media. This showed that AML derived HGF downregulates hepatocyte FA uptake and metabolism. Finally, to determine the role of AML in the uptake of FA by hepatocytes, cultures of primary murine hepatocytes were pretreated with AML conditioned media or HGF with and without neutralizing antibody. A BODIPY conjugated long chain FA was then added to the culture. Images analysis showed hepatocytes had reduced lipid uptake in the presence of AML condition media or HGF, but this was restored with the addition of HGF neutralizing antibody. Here we report that AML inhibition of lipid uptake in the liver, through an HGF dependent mechanism, increases the availability of plasma FA and forms a fundamental part of the AML disease. Ongoing work to develop our understanding of how AML increases access to FA to aid proliferation, may aid in the development of new therapeutics to target liver metabolism in combination with other AML therapies.

TP-0184 inhibits FLT3/ACVR1 to overcome FLT3 inhibitor resistance and hinder AML growth synergistically with venetoclax.

We identified activin A receptor type I (ACVR1), a member of the TGF-β superfamily, as a factor favoring acute myeloid leukemia (AML) growth and a new potential therapeutic target. ACVR1 is overexpressed in FLT3-mutated AML and inhibition of ACVR1 expression sensitized AML cells to FLT3 inhibitors. We developed a novel ACVR1 inhibitor, TP-0184, which selectively caused growth arrest in FLT3-mutated AML cell lines. Molecular docking and in vitro kinase assays revealed that TP-0184 binds to both ACVR1 and FLT3 with high affinity and inhibits FLT3/ACVR1 downstream signaling. Treatment with TP-0184 or in combination with BCL2 inhibitor, venetoclax dramatically inhibited leukemia growth in FLT3-mutated AML cell lines and patient-derived xenograft models in a dose-dependent manner. These findings suggest that ACVR1 is a novel biomarker and plays a role in AML resistance to FLT3 inhibitors and that FLT3/ACVR1 dual inhibitor TP-0184 is a novel potential therapeutic tool for AML with FLT3 mutations.

CD74 + Leukemia-Associated Macrophages Supporess T Cell Immune Surveillance and Promote Leukemic Cell Growth in Acute Myeloid Leukemia

The bone marrow microenvironment plays a pivotal role in the recurrence of acute myeloid leukemia (AML). However, the exact mechanisms are not fully understood. Single-cell technologies have emerged as powerful tools for unraveling the immune microenvironment in leukemia. In this study, utilizing scRNA-seq on a cohort of 13 paired AML patients, we have unveiled a distinctive subcluster of tumor-associated macrophages (TAMs) linked to relapse leukemia. To explore the heterogeneity of the bone marrow microenvironment during the progression of AML, we conducted a scRNA-seq analysis on bone marrow cells obtained from 13 paired AML patients at the time of diagnosis (DX) and relapse (RE) (Figure 1A). Employing UMAP for dimensionality reduction, we detected multiple subclusters and observed a notable rise in the Macrophage CD74 cluster in all paired RE patients, suggesting a pivotal role of CD74+ TAMs in AML relapse (Figure 1B-C). Furthermore, CD274, FOS, TGFβ1, and CD163, recognized as markers of M2 macrophages, were significantly enriched in the CD74+ TAMs population (Figure 1D). Intriguingly, a higher proportion of CD74+ TAMs correlated with unfavorable outcomes in TCGA database (Figure 1E). Meanwhile, we found that the ligand macrophage migration inhibitory factor (MIF) of CD74 was associated with poor prognosis of AML (Figure 1F). To investigate the association of CD74+ TAMs with AML cells, Gene Set Variation Analysis (GSVA) was employed and revealed restrained pathways related to T cell function (Figure 2A). Through in vitro experiments on patient samples, we found that CD74+TAM can inhibit the proliferation of T cells and the secretion of IFN-γ. Further monoclonal antibody block experiments unveiled that this inhibitory effect might be attributed to the heightened expression of PD-L1, TGFβ1, and IL-10 by the macrophages (Figure 2B-C). In conclusion, we have substantiated the inhibitory role of CD74+ TAMs on T cells, which hampers their ability to engage in effective tumor killing. To elucidate the interplay between CD74+ TAMs and AML cells, we examined the gene expression profile of cytokines, noting a significant increase in the expression level of IL-6 within the CD74+ TAMs subclusters of the RE group (Figure 3A). Furthermore, upon co-culture with CD74+ TAMs, THP-1 cells exhibited notable activation of IL-6 related pathways (Figure 3B). The injection of CD74+ TAMs resulted in heightened AML initiation and poorer survival in patient-derived xenograft (PDX) model, which was reversed by blocking the IL-6-IL-6R axis (Figure 3C-D). These findings collectively confirm that IL-6 secreted by CD74+ TAMs fosters the malignancy and drug resistance of AML cells. Subsequently, MLL-AF9-induced AML mouse model was employed to explore the spatial interplay between CD74+ TAMs, AML cells and T cells. Immunofluorescence (IF) analysis of mouse bone marrow tissue revealed that after chemotherapy, the proximity between AML cells and CD74+ TAMs decreased (Figure 4A-B). Conversely, the presence of T cells surrounding CD74+ TAMs increased (Figure 4C-D). These findings indicate that CD74+ TAMs can inhibit T cell function and directly influence AML cells within the tumor microenvironment. In summary, our study revealed a notable rise in the proportion of TAMs expressing CD74 in relapsed AML patients. These CD74+ TAMs were found to facilitate leukemia progression while concurrently inhibiting T cell immune surveillance in the context of AML. Thus, our findings indicate that CD74+ TAMs represent a distinct type of macrophages associated with AML relapse.

A small molecule BCL6 inhibitor as chemosensitizers in acute myeloid leukemia

BCL6 is a transcriptional repressor that regulates multiple genes involved in immune cell differentiation, DNA damage repair, cell cycle, and apoptosis, and is a carcinogenic factor in acute myeloid leukemia (AML). AML is one of the four major types of leukemia with the 5-year survival rate of patients is less than 20% and chemotherapy resistance remains the major obstacle to the treatment failure of AML. We identified WK499, a small molecule compound that can bind to BCL6BTB structure. Treatment with WK499 hinders the interactions between BCL6 with its corepressor proteins, resulting in a remarkable change of BCL6 downstream genes and anti-proliferative effects in AML cells, and inducing cell cycle arrest and apoptosis. We verified that AraC and DOXo could induce BCL6 expression in AML cells, and found that WK499 had a synergistic effect when combined with chemotherapeutic drugs. We further proved that WK499 and AraC could achieve a better result of inhibiting the growth of AML in vivo. These findings indicate that WK499, a small molecule inhibitor of BCL6, not only inhibits the proliferation of AML, but also provides an effective therapeutic strategy for increasing AML sensitivity to chemotherapy.

TAK-981, a SUMOylation inhibitor, suppresses AML growth immune-independently.

Acute myeloid leukemia (AML) generally has an unsatisfactory prognosis despite the recent introduction of new regimens, including targeted agents and antibodies. To find a new druggable pathway, we performed integrated bioinformatic pathway screening on large OHSU and MILE AML databases, discovered the SUMOylation pathway, and validated it independently with an external data set (totaling 2959 AML and 642 normal sample data). The clinical relevance of SUMOylation in AML was supported by its core gene expression which is correlated with patient survival, European LeukemiaNet 2017 risk classification, and AML-relevant mutations. TAK-981, a first-in-class SUMOylation inhibitor currently under clinical trials for solid tumors, showed antileukemic effects with apoptosis induction, cell-cycle arrest, and induction of differentiation marker expression in leukemic cells. It exhibited potent nanomolar activity, often stronger than that of cytarabine, which is part of the standard of care. TAK-981's utility was further demonstrated in invivo mouse and human leukemia models as well as patient-derived primary AML cells. Our results also indicate direct and cancer cell-inherent anti-AML effects by TAK-981, different from the type 1 interferon and immune-dependent mechanism in a previous solid tumor study. Overall, we provide a proof-of-concept for SUMOylation as a new targetable pathway in AML and propose TAK-981 as a promising direct anti-AML agent. Our data should prompt studies on optimal combination strategies and transitions to clinical trials in AML.

Epichaperome inhibition targets TP53-mutant AML and AML stem/progenitor cells

AbstractTP53-mutant acute myeloid leukemia (AML) remains the ultimate therapeutic challenge. Epichaperomes, formed in malignant cells, consist of heat shock protein 90 (HSP90) and associated proteins that support the maturation, activity, and stability of oncogenic kinases and transcription factors including mutant p53. High-throughput drug screening identified HSP90 inhibitors as top hits in isogenic TP53–wild-type (WT) and -mutant AML cells. We detected epichaperomes in AML cells and stem/progenitor cells with TP53 mutations but not in healthy bone marrow (BM) cells. Hence, we investigated the therapeutic potential of specifically targeting epichaperomes with PU-H71 in TP53-mutant AML based on its preferred binding to HSP90 within epichaperomes. PU-H71 effectively suppressed cell intrinsic stress responses and killed AML cells, primarily by inducing apoptosis; targeted TP53-mutant stem/progenitor cells; and prolonged survival of TP53-mutant AML xenograft and patient-derived xenograft models, but it had minimal effects on healthy human BM CD34+ cells or on murine hematopoiesis. PU-H71 decreased MCL-1 and multiple signal proteins, increased proapoptotic Bcl-2-like protein 11 levels, and synergized with BCL-2 inhibitor venetoclax in TP53-mutant AML. Notably, PU-H71 effectively killed TP53-WT and -mutant cells in isogenic TP53-WT/TP53-R248W Molm13 cell mixtures, whereas MDM2 or BCL-2 inhibition only reduced TP53-WT but favored the outgrowth of TP53-mutant cells. Venetoclax enhanced the killing of both TP53-WT and -mutant cells by PU-H71 in a xenograft model. Our data suggest that epichaperome function is essential for TP53-mutant AML growth and survival and that its inhibition targets mutant AML and stem/progenitor cells, enhances venetoclax activity, and prevents the outgrowth of venetoclax-resistant TP53-mutant AML clones. These concepts warrant clinical evaluation.

Circadian clock protein Bmal1 accelerates acute myeloid leukemia by inhibiting ferroptosis through the EBF3/ALOX15 axis.

Acute myeloid leukemia (AML) is a major leukemia with high mortality. Ferroptosis is an important regulator of cancers. However, the role of ferroptosis and its regulatory mechanisms in AML remain largely unknown. In this study, we reported elevated brain and muscle ARNT-Like protein-1 (Bmal1) expression in AML patients and cell lines, and its upregulation indicated the poor survival of patients. The correlation analysis showed that Bmal1 expression was closely correlated with cytogenetics and the French-American-British subtypes, but was not correlated with age, gender and white blood cells. RSL3 reduced Bmal1 expression in HL-60 and NB4 cells. Malondialdehyde, total iron, Fe2+ , glutathione and lipid peroxidation were examined to evaluate ferroptosis. Overexpression of Bmal1 repressed RSL3-induced ferroptosis in AML cells. Bmal1 recruited Enhancer of zeste homolog 2 (EZH2) to the Early B cell factor 3 (EBF3) promoter and enhanced its methylation, thus suppressing EBF3 expression. Moreover, the knockdown of Bmal1 sensitized AML cells to RSL3-induced ferroptosis, and it was counteracted by EBF3 knockdown. Furthermore, EBF3 bound to the Arachidonate 15-pipoxygenase (ALOX15) promoter to enhance its expression, and overexpression of EBF3 enhanced RSL3-induced ferroptosis dependent on ALOX5. We established a subcutaneous AML xenograft tumor model and reported that knockdown of Bmal1 and overexpression of EBF3 restrained AML growth by promoting ALOX15-mediated ferroptosis in vivo. Collectively, Bmal1 inhibits RSL3-induced ferroptosis by promoting EZH2-mediated EBF3 methylation and suppressing the expression of EBF3 and ALOX15, thus accelerating AML.

Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia

The bone marrow (BM) is a complex microenvironment, coordinating the production of billions of blood cells every day. Despite its essential role and its relevance to hematopoietic diseases, this environment remains poorly characterized. Herewe present a high-resolution characterization of the niche in health and acute myeloid leukemia (AML) by establishing a single-cell gene expression database of 339,381 BM cells. We found significant changes in cell type proportions and gene expression in AML, indicating that the entire niche is disrupted. We then predicted interactions between hematopoietic stem and progenitor cells (HSPCs) and other BM cell types, revealing a remarkable expansion of predicted interactions in AML that promote HSPC-cell adhesion, immunosuppression, and cytokine signaling. In particular, predicted interactions involving transforming growth factor β1 (TGFB1) become widespread, and we show that this can driveAML cell quiescence invitro. Our results highlight potential mechanisms of enhanced AML-HSPC competitiveness and a skewed microenvironment, fostering AML growth.

A noncanonical enzymatic function of PIWIL4 maintains genomic integrity and leukemic growth in AML

AbstractRNA-binding proteins (RBPs) form a large and diverse class of factors, many members of which are overexpressed in hematologic malignancies. RBPs participate in various processes of messenger RNA (mRNA) metabolism and prevent harmful DNA:RNA hybrids or R-loops. Here, we report that PIWIL4, a germ stem cell–associated RBP belonging to the RNase H–like superfamily, is overexpressed in patients with acute myeloid leukemia (AML) and is essential for leukemic stem cell function and AML growth, but dispensable for healthy human hematopoietic stem cells. In AML cells, PIWIL4 binds to a small number of known piwi-interacting RNA. Instead, it largely interacts with mRNA annotated to protein-coding genic regions and enhancers that are enriched for genes associated with cancer and human myeloid progenitor gene signatures. PIWIL4 depletion in AML cells downregulates the human myeloid progenitor signature and leukemia stem cell (LSC)-associated genes and upregulates DNA damage signaling. We demonstrate that PIWIL4 is an R-loop resolving enzyme that prevents R-loop accumulation on a subset of AML and LSC-associated genes and maintains their expression. It also prevents DNA damage, replication stress, and activation of the ATR pathway in AML cells. PIWIL4 depletion potentiates sensitivity to pharmacological inhibition of the ATR pathway and creates a pharmacologically actionable dependency in AML cells.

KMT2D Deficiency Promotes Myeloid Leukemias which Is Vulnerable to Ribosome Biogenesis Inhibition.

KMT2C and KMT2D are the most frequently mutated epigenetic genes in human cancers. While KMT2C is identified as a tumor suppressor in acute myeloid leukemia (AML), the role of KMT2D remains unclear in this disease, though its loss promotes B cell lymphoma and various solid cancers. Here, it is reported that KMT2D is downregulated or mutated in AML and its deficiency, through shRNA knockdown or CRISPR/Cas9 editing, accelerates leukemogenesis in mice. Hematopoietic stem and progenitor cells and AML cells with Kmt2d loss have significantly enhanced ribosome biogenesis and consistently, enlarged nucleolus, increased rRNA and protein synthesis rates. Mechanistically, it is found that KMT2D deficiency leads to the activation of the mTOR pathway in both mouse and human AML cells. Kmt2d directly regulates the expression of Ddit4, a negative regulator of the mTOR pathway. Consistent with the abnormal ribosome biogenesis, it is shown that CX-5461, an inhibitor of RNA polymerase I, significantly restrains the growth of AML with Kmt2d loss in vivo and extends the survival of leukemic mice. These studies validate KMT2D as a de facto tumor suppressor in AML and reveal an unprecedented vulnerability to ribosome biogenesis inhibition.

Abstract 5166: Intratumoral delivery of mRNA encoding USP6 activates multiple immuno-stimulatory pathways simultaneously and inhibits local and distal tumor growth in murine models

Abstract Advances in immunotherapy have revolutionized cancer treatment, with patients with otherwise incurable disease having long-lasting responses. Unfortunately, deep remissions only occur in a select subset of patients. Cancer progression is common as many current immunotherapies only target one or two pathways, which can quickly lead to tumor resistance. Novel approaches that target several pathways concurrently are therefore needed to promote stronger responses in a wider patient population. Our group has recently discovered that the protein Ubiquitin-specific protease 6 (USP6) upregulates multiple, distinct immunostimulatory pathways. Tumor cell-specific expression of USP6 significantly increases CXCL9, CXCL10, and CCL5 chemokine production that enhances cytotoxic immune cell recruitment. Simultaneously, USP6 also upregulates several ligands and receptors that promote immune cell activation and killing of tumor cells such as CD112, MICA/B, ICAM1, and MHC Class I. In addition, USP6 increases the tumor cell’s sensitivity to immune-derived factors such as Type I and Type II interferons and TRAIL by raising the surface expression of their respective receptors. USP6 is hominid-specific and therefore requires xenografting human tumor cells into athymic, T-cell deficient nude mice. Despite the immunocompromised model, USP6 expression was found to increase immune cell recruitment to the tumor while repolarizing the immune microenvironment toward a more activated, tumor-suppressive state. Strikingly, immune cells in the peripheral blood were also affected with an increase in natural killer cell (NK) activation and a skewing of the myeloid population away from an immunosuppressive phenotype. Our group subsequently demonstrated that a USP6+ tumor was able to inhibit the growth of a USP6− distal tumor, with a concordant increase in NK, macrophage, and dendritic cell activation in the distal USP6− tumor. Given our data, we sought to translate USP6 into a novel immunotherapy. Delivery of mRNA encoding the USP6 protein recapitulates the immunostimulatory effects of USP6 in vitro. Intratumoral (I.T) injection of a lipid nanoparticle (LNP) encapsulating USP6 mRNA significantly inhibited Ewing sarcoma and acute myeloid leukemia growth in athymic mice, despite the model lacking a fully functional immune system. Moreover, I.T injection of USP6 mRNA LNPs inhibited the growth of a non-injected, distal tumor. Altogether, these data support that USP6 is a potentially powerful target and continued development of I.T USP6 mRNA LNPs as a novel immunotherapy. Citation Format: Ian Henrich, Margaret Billingsley, Kanika Jain, Laura Quick, Rob Young, Margaret Chou, Michael Mitchell. Intratumoral delivery of mRNA encoding USP6 activates multiple immuno-stimulatory pathways simultaneously and inhibits local and distal tumor growth in murine models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5166.

Abstract 3729: Targeting the writers of enhancers as a new therapeutic strategy in pediatric AML

Abstract Introduction: Children with acute myeloid leukemia (AML) urgently need new targeted therapeutics to improve their outcomes. Super-enhancers (SEs) are extensive chromatin regions denoted by abundant histone 3 lysine 27 acetylation (H3K27ac), which are associated with high-level expression of cell-identity genes, including oncogenes. SE-regulated genes have unique sensitivity to transcriptional inhibitors, allowing for cancer type-specific approaches. Thus, targeting CBP/EP300 (the highly homologous enzymes responsible for catalyzing H3K27 acetylation) may be a specific strategy to target lineage-specifying oncogenes in AML. However, to date, the high degree of homology between EP300 and CBP has limited chemical strategies to tissue-specific disruption. Gene editing studies have shown that CBP, and not EP300, is essential for maintaining normal hematopoiesis, while EP300 regulates AML growth and myeloid differentiation. We hypothesized that selectively targeting EP300 would suppress AML growth while sparing effects on normal myeloid differentiation. Methods: We studied publicly available expression and CRISPR screening databases for EP300 and CBP data in AML. We treated pediatric AML (pAML) cell lines and patient samples with the EP300/CBP HAT inhibitor A485 and the EP300-selective PROTAC [PROteolysis TArgeting Chimera]) JQAD1, and measured effects on cell growth by CellTiter-Glo, and apoptosis, differentiation, and cell cycle changes by flow cytometry. We treated pAML cells with compounds for 2 hours and performed mass spectrometry on HPLC-purified H3 proteins. Results: pAML patient samples have higher EP300 expression than normal bone marrow samples in the TARGET dataset, and AML cell lines have enhanced dependency on EP300 over CBP by CRISPR knockout analysis. Treatment of pAML cell lines with A485 slowed proliferation and induced apoptosis, cell cycle arrest, and differentiation. In contrast, equimolar concentrations of JQAD1 had more marked antileukemic effects in both pAML cell lines and primary samples. Immunoblotting analysis demonstrated reduced H3K27ac in pAML cells treated with both JQAD1 and A485, but EP300 degradation only with treatment with JQAD1, consistent with findings in other cancer models. Studies on the effects of EP300 degradation versus combined EP300/CBP inhibition on global and SE-regulated gene expression are ongoing. Middle-down mass spectrometry recapitulates decreased H3K27 acetylation with both agents. JQAD1 combined with the BCL2 inhibitor Venetoclax has a synergistic effect on cell line and patient sample growth, with coordinate induction of apoptosis and differentiation. A four-arm study of this combination in a pAML patient-derived xenograft model is ongoing. Conclusion: Selective degradation of EP300 using the PROTAC JQAD1 is a new strategy that demonstrates preclinical efficacy in pAML as a single agent and in combination with BCL2 inhibitors. Citation Format: Joanna S. Yi, Kevin Duong, Abiola Obawemimo, Tingjian Wang, Faith Joseph, Nicolas L. Young, Stephen Mack, Jun Qi, Adam Durbin. Targeting the writers of enhancers as a new therapeutic strategy in pediatric AML. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3729.

CircZBTB46 Protects Acute Myeloid Leukemia Cells from Ferroptotic Cell Death by Upregulating SCD.

Circular RNAs (circRNAs) have been shown to be closely linked to the tumorigenesis and treatment response of hematological malignancies. However, the biological functions and clinical implications of circRNAs in acute myeloid leukemia (AML) remain largely unknown. CircRNA microarray datasets were analyzed to screen differentially expressed circRNAs in AML patients. It was found that circZBTB46 was significantly upregulated in AML patients and AML cells. Moreover, the expression of circZBTB46 was associated with the stages of AML patients and showed high sensitivity and specificity for diagnosing AML. Silencing of circZBTB46 inhibited AML cell proliferation and induced cell cycle arrest. Importantly, the depletion of circZBTB46 notably increased ferroptosis and enhanced RSL3-induced ferroptosis in AML cells. Mechanistically, circZBTB46 upregulated the expression of stearoyl-CoA desaturase 1 (SCD) possibly by acting as a miRNA sponge. Finally, the circZBTB46 knockdown repressed the tumor growth of AML in vivo. In conclusion, circZBTB46 protects AML cells from ferroptosis and promotes the proliferation by upregulating SCD, thus suggesting that circZBTB46 may be a potential therapeutic target for AML.

Preclinical evaluation of the ROCK1 inhibitor, GSK269962A, in acute myeloid leukemia.

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy with high mortality that urgently requires new treatments. ROCK1 plays an essential role in regulating growth and survival in AML cells. In this study, we evaluated GSK269962A, a selective ROCK1 inhibitor, in preclinical models of AML. Compared with solid tumors, GSK269962A selectively inhibited cell growth and clonogenicity of AML cells. Furthermore, GSK269962A arrested AML cells in the G2 phase and induced apoptosis by regulating multiple cell cycle- and apoptosis-associated proteins. Strikingly, GSK269962A could eliminate leukemia cells from bone marrow, liver, and spleen in an animal model of AML and significantly prolong mouse survival. Mechanistically, GSK269962A could inhibit the growth of AML by blocking ROCK1/c-Raf/ERK signaling pathway. Notably, a correlation was found between the expression levels of ROCK1 protein and the sensitivity of GSK269962A in AML. These data highlight the potential role of ROCK1 as an attractive target for treating AML, as well as the potential of GSK269962A for use in clinical trials of AML.

The Role of Quiescence in Acute Myeloid Leukemia Growth

Acute myeloid leukemia (AML) is the most common leukemia in adults and its prognosis is usually poor. Despite the introduction of targeted treatments in recent years, AML remains a high-mortality disease with a 5-year survival of less than 30%. Emerging evidence suggest that therapy failure and leukemia relapse are due to the intra-tumoral genomic and biological heterogeneity. At biological level, AML is hierarchically organized with leukemia stem cells (LSCs) at the apex. LSCs are a rare cell sub-population with self-renewal capacity, responsible for leukemia initiation and maintenance. Standard AML therapies have limited effects on LSCs, mainly due to their property of exiting the cell cycle and enter quiescence. Preliminary data obtained in our group have shown that different leukemia-initiating oncogenes (NPMc+, PML-RARα and MLL-AF9) share the property of enforcing quiescence in pre-leukemic hematopoietic stem cells (HSCs), and that this is critical for the progression and maintenance of the leukemia clone. Underlying molecular mechanisms, however, are unknown. To this end, we have performed an in vivo reverse genetic screening to identify quiescence-related genes indispensable for leukemia growth. Among the identified hits, Socs2, Stat1 and Sytl4 silencing prevented AML outgrowth in vivo. Notably, Socs2 and Stat1 interference increased proliferation, prevented accumulation of quiescent blasts and induced apoptosis. Interestingly, Socs2 and Stat1 silencing exerted no effects on in vitro proliferation, cell cycle distribution or survival of AML blasts, suggesting that their effects are largely dependent on the in vivo leukemia context. Single-cell RNAseq (scRNAseq) analysis of Socs2-interfered blasts showed marked down-regulation of genes characterizing the dormant status of quiescent HSCs, suggesting that loss of quiescence in Socs2-interfered blasts is linked to the loss of their regenerative potential. Since dormancy and self-renewal potential in HSCs are antagonized by prolonged stress signals, we analyzed scRNAseq data for activation of the integrated stress response (ISR). Strikingly, Socs2-interfered cells showed aberrant activation of ATF4, UPR and autophagic transcriptional programs, which was evident in both proliferating and cell cycle restricted blasts, at variance with control blasts that showed increased ISR expression specifically in proliferating cells. Since elevated levels of UPR may act as danger signals and favor immune-mediated clearance in vivo, we analyzed immune-related signaling pathways. Consistently, Socs2-silenced blasts showed a dramatic down-regulation of specific immune check-point molecules, including CD24a, galectin 9 and VISTA, which are involved in the regulation of B cells, T cells, NK cells and macrophages. Based on these findings, we hypothesized that Socs2 regulates the resolution of stressful signals that eventually accumulate in hyper-proliferating AML blasts by allowing cells to enter quiescence and activate pathways of ISR resolution, including upregulation of immune check-point molecules. If blasts fail to enter quiescence, as in in the absence of Socs2 expression, cells maintain sustained ISR activation and downregulate immune check-point molecules, thus triggering immune-mediated cell death. Consistently, the anti-leukemic effect of Socs2-silencing was partially rescued upon propagation into immunocompromised mice. As well, macrophage depletion prolonged disease latency of Socs2-interfered blasts in immunocompetent mice. These findings provide preliminary evidence of the existence, in AML blasts, of an adaptive response to hyperproliferation that involves ISR activation, induction of quiescence and immune evasion. Targeting this adaptive response, as by Socs2 interference, may activate potent mechanisms of AML immune clearance.

Activin-like Kinase 2 (ALK2/ACVR1) Is a Resistance Factor and Therapeutic Vulnerability to FLT3 Inhibition in Acute Myeloid Leukemia

Background: FMS-like tyrosine kinase-3 (FLT3), a transmembrane receptor, is frequently mutated in acute myeloid leukemia (AML), and this is associated with poor prognosis. Although FLT3 inhibitors (FLT3i) have significantly improved overall survival, their clinical effectiveness is limited due to treatment resistance, and the molecular mechanism remains unknown. We previously reported that the bone morphogenetic protein (BMP) signaling pathway supports AML cell growth via osteogenic differentiation in mesenchymal stromal cells. However, the role of BMP in FLT3i resistance has not been studied. We hypothesized that BMP type-1 receptor (ALK2/ACVR1) is a resistance factor for FLT3i, and therefore targeting FLT3 and ACVR1 using a novel dual inhibitor, TP-0184, would overcome FLT3i resistance and sensitize AML cells to standard therapy. Methods: We assessed the association of ACVR1 expression with molecular mutations in AML by analyzing gene expression datasets (OHSU and TCGA). We also measured ACVR1 expression using qRT-PCR in FLT3-mutant AML cell lines (molm-13, molm-14, and MV4-11) treated with different doses of FLT3i (gilteritinib or midostaurin), as well as in peripheral blood mononuclear cells isolated from patients with FLT3-mutant AML treated with FLT3i. To determine the role of ACVR1 in FLT3i resistance, we knocked down ACVR1 in FLT3-mutant cells, treated them with various doses of FLT3i, and measured apoptosis using IncuCyte. We also measured the effect of TP-0184 on cell proliferation and the cell cycle in FLT3-wild-type (WT) and FLT3-mutant cells. To determine the mechanism of TP-0184-mediated cell cycle arrest, we measured the effect of TP-0184 on cell signaling pathways using Western blot analysis and RNA sequencing. We also performed human RTK kinase binding assay to understand the binding specificity of TP-0184 with 11 different FLT3 mutants. MTT assay was used to determine the synergistic effect of TP-0184 with cytarabine or venetoclax (BCL2 inhibitor). We investigated the effect of TP-0184 on AML growth in vivo using FLT3-mutant and FLT3-WT AML xenograft and patient-derived xenograft models. Results: Analysis of AML datasets showed that ACVR1 expression is upregulated in FLT3-mutant compared with FLT3-WT AML patient samples (p<0.01) and predicts poor overall survival (p=0.05). ACVR1 expression was also higher in FLT3-mutant than in FLT3-WT cell lines (p=0.039). Interestingly, ACVR1 expression was upregulated in patient samples of FLT3-mutant AML treated with gilteritinib (p=0.02) and FLT3-mutant cell lines treated with FLT3i in a dose- and time-dependent manner. Moreover, ACVR1 knockdown in FLT3-mutant cell lines sensitized AML cells to FLT3i 2- to 3-fold compared with scrambled control cells, suggesting that ACVR1 is a resistance factor in AML cells treated with FLT3i, and that targeting ACVR1 could sensitize AML cells to FLT3i. In FLT3-WT and FLT3-mutant AML cell lines treated with TP-0184, cell growth was significantly reduced in FLT3-mutant cells (IC50<25nM) but not in FLT3-WT cells. TP-0184 induced G1/G0 arrest in FLT3-mutant cells but had minimal or no effect in FLT3-WT cells, suggesting that TP-0184 overcomes ACVR1-mediated resistance in FLT3-mutant cells. Treatment with TP-0184 significantly inhibited multiple proteins downstream of FLT3, including STAT-5, ERK, PI3K, and mTOR pathways, and decreased in pSmad1/5 proteins downstream of ACVR1 in AML cells. These findings confirmed that TP-0184 inhibits both mutant FLT3 and ACVR1 in AML cells. Gene expression analysis revealed that TP-0184 significantly downregulated the serine biosynthesis pathway in FLT3-mutant cell lines. Moreover, molecular docking and kinase-binding studies confirmed that TP-0184 binds to FLT3 mutants with high affinity (KD=<5nM). Interestingly,TP-0184 with venetoclax or cytarabine showed a synergistic effect in FLT3-mutant cells (combination index 0.01; p<0.01). In vivo data also showed that TP-0184 inhibited AML growth and significantly prolonged survival in FLT3-mutant AML xenograft and patient-derived xenograft models (p<0.01). Conclusion: Our data indicate that ACVR1 causes resistance to FLT3 inhibitors. TP-0184, a dual inhibitor, targets mutant FLT3 and ACVR1 in AML cell lines. TP-0184 sensitizes AML cells with chemotherapy and venetoclax and inhibits AML growth in vivo.