Target In Leukemia Research Articles

Discovery of LWY713 as a potent and selective FLT3 PROTAC degrader with in vivo activity against acute myeloid leukemia

Fms-like tyrosine kinase 3 (FLT3) has been validated as a therapeutic target for acute myeloid leukemia (AML). While a number of FLT3 kinase inhibitors have been approved for AML treatment, the clinical data revealed that they cannot achieve complete and sustained suppression of FLT3 signaling at the tolerated dose. Here we report a series of new, potent and selective FLT3 proteolysis targeting chimera degraders. The optimal compound LWY713 potently induced the degradation of FLT3 with a DC50 value of 0.64 nM and a Dmax value of 94.8% in AML MV4-11 cells with FLT3-internal tandem duplication (ITD) mutation. Mechanistic studies demonstrated that LWY713 selectively induced FLT3 degradation in a cereblon- and proteasome-dependent manner. LWY713 potently inhibited FLT3 signaling, suppressed cell proliferation, and induced cell G0/G1-phase arrest and apoptosis in MV4-11 cells. Importantly, LWY713 displayed potent in vivo antitumor activity in MV4-11 xenograft models.

Mechanisms of Cytokine-Induced NK Cell Therapy: IL-12/15/18 Induce a Unique Transcriptional, Epigenetic, and Functional Human NK Cell Memory Program

NK cells are innate lymphoid cells critical for mediating anti-tumor responses and are being advanced as a cancer immunotherapy. While conventional (c) NK cell-based therapies have been explored in clinical trials, challenges related to cancer target recognition, in vivo persistence, and functionality result in limited activity. To overcome these challenges, NK cell memory programs have been investigated. Cytokine-induced memory-like (CIML or ML) NK cells are generated after brief activation with IL-12, IL-15, and IL-18, resulting in enhanced functionality, cytotoxicity, and in vivo persistence. ML NK cells have been advanced in multiple clinical trials for leukemia with promising results. Despite this translational progress, the underlying cellular dynamics and molecular mechanisms of ML reprogramming remain unclear. Elucidating these molecular programs may optimize NK therapeutics and reveal new translational strategies. We hypothesized that transcriptional and epigenetic mechanisms contribute to ML NK cell heterogeneity arising after IL-12/15/18 activation. To test this, NK cells from healthy donors were activated with IL-12/15/18 (to become ML) or IL-15 (to maintain cNK) and differentiated in vitro for 7 days (Fig 1, n=3-40 donors), followed by the assessment of their transcriptome (CITE-seq) and epigenome (ATAC-seq). CITE-seq clustering revealed unexpected heterogeneity with ~50% clustering with cNK cells (effector, effcNK) and ~50% forming a unique enriched ML cluster (eML). eML clusters were significantly increased in frequency in the IL-12/15/18 condition, compared to cNK (Mean±SEM=53±10.5% for IL-12/15/18, 6.2±1.1% for IL-15, p<0.0001) and discovered to expressed ENTPD1 (CD39). Based on CITE-seq, a flow cytometry strategy was developed to distinguish eML NK cells from effector cNK and cNK cells. Next, we identified eML NK cells 3-4 weeks after adoptive transfer of IL-12/15/18 activated donor NK cells across three different clinical trials (mean=13.3±1.9%, p<0.001). eML NK cells produced significantly more IFNg compared to cNK cells and effector cNK cells when stimulated with leukemia targets (Fig. 2, p<0.0001), and had enhanced cytotoxicity compared to cNK cells (EC50 of eML=0.862, EC50 of cNK=2.223, p<0.0001). Bulk ATAC-seq on flow-sorted populations revealed that eML NK cells have a distinct global epigenetic profile with >4,500 significant differentially accessible regions (DARs) compared to effcNK, while effcNK and cNK cells were epigenetically similar. Further, we interrogated which transcription factors are enriched in DARs of eML NK cells revealing TBOX and IRF family motifs. Within CITE-seq, the eML cluster was comprised of two subsets (eML-1 and eML-2). eML1 had increased expression of the transcription factors TCF7 and TOX2. In contrast, eML-2 had increased expression of IRF4 and PRDM1, as well as terminal exhaustion genes, including LAG3 and TIGIT (p<0.05). To evaluate eML-1 and eML-2 function, we performed CITE-seq after stimulation of eML NK cells with leukemia targets. eML-1 NK cells were the most functional, with significantly increased IFNG compared to eML-2, while eML-2 was hypofunctional and marked by high TOX expression (p<0.05). These findings suggest that optimizing strategies that lead to eML-1 differentiation may enhance the therapeutic activity of IL-12/15/18-induced ML NK cells. In summary, we identify heterogeneity following IL-12/15/18 activation of NK cells, resulting in multiple cellular fates. Further, these data identify an eML NK cell population with a distinct single-cell transcriptional and epigenetic program that directly manifests as enhanced NK cell functional response to leukemia.

CLL-1-Targeted Allogeneic CAR-T Cells Exhibit High on-Target Specificity and Potent Cytotoxicity in Preclinical Models of Acute Myeloid Leukemia

Background: CLL-1 is a compelling therapeutic target for acute myeloid leukemia (AML) as it is highly expressed on AML tumor cells and leukemic stem cells, but is not expressed on hematopoietic stem cells. An allogeneic anti-CLL-1 CAR-T cell therapy (CB-012) is in development for relapsed or refractory (r/r) AML. The CAR was generated with a fully human scFv targeting CLL-1 that was selected from a panel of scFvs. CB-012 was engineered with a next-generation Cas12a CRISPR hybrid RNA-DNA (chRDNA) genome-editing technology to leverage both checkpoint disruption and immune cloaking for potentially improved antitumor activity. Methods: Cas12a chRDNA guides were implemented to generate five genome edits in the manufacture of CB-012. A fully human anti-CLL-1 CAR transgene was site-specifically inserted into the TRAC gene, thereby eliminating TCR expression to reduce graft-versus-host disease. A B2M-HLA-E fusion transgene was inserted into the native B2M gene, preventing expression of all HLA class I antigens except HLA-E, to blunt both T and NK cell-mediated allograft rejection of the CAR-T cells. A knockout of the PDCD1 gene prevented PD-1 receptor expression and thus PD-L1 ligand binding to prolong antitumor activity. This multiplex genome-editing strategy was designed to enhance the antitumor activity of CB-012. In vitro and in vivo studies evaluated specificity for antigen binding, antigen-dependent activity, and preclinical safety assessments. Results: CB-012 CAR-T cells express a fully human anti-CLL-1 scFv-containing CAR construct and demonstrate potent antigen-dependent cytotoxic activity in human AML cell line co-cultures. In AML xenograft models, a single-dose administration of CB-012 CAR-T cells exerted robust tumor control, leading to significant prolongation of survival. Cell binding studies suggested that the anti-CLL-1 scFv does not exhibit tissue cross-reactivity when examined in the context of a collection of cell types representing vital tissues. In an unbiased cell surface protein microarray, the anti-CLL-1 scFv demonstrated specific interaction with human CLL-1, without detectable non-specific interactions. CB-012 CAR-T cells exhibited limited tissue infiltration and expansion in treatment naïve, immunocompromised mouse models. Conclusion: CB-012 demonstrated highly specific and potent CLL-1-targeted cytolytic activity in vitro and in vivo. Specificity of the anti-CLL-1 scFv was further demonstrated by screening in an unbiased protein-binding study and no adverse safety signals were observed in murine models. These data support advancing the development of CB-012 into a first-in-human clinical trial for patients with r/r AML.

RNA-Binding Protein RBM5 Plays an Essential Role in Acute Myeloid Leukemia By Activating the Oncogenic Protein HOXA9

Acute myeloid leukemia (AML) represents a type of malignant hematological disease that indicates poor outcomes in children and adults. HOXA9 overexpression is observed in 50-70% of human AML and positively correlates with poor patient outcomes. Leukemia subtypes with hallmark overexpression of HOXA9 include but are not limited to those carrying KMT2A gene rearrangements (KMT2A-r), NPM1c mutations, NUP98-fusions and EZH2 mutation. Accumulating genetic evidence also indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation, and loss of function of HOXA9 and downstream pathways consequently impaired leukemia maintenance. Although HOXA9 is not an ideal direct candidate for therapeutic interventions, uncovering the novel regulators of HOXA9 might elucidate the HOXA9 regulation mechanism that could be exploited to identify novel therapeutic targets in HOXA9-driven leukemias. In this study, we performed genome-wide CRISPR/Cas9 screens in the HOXA9-endogenous reporter acute leukemia cells and unbiasedly identified that candidate genes are significantly enriched in RNA binding and RNA splicing regulation. An RBP protein, RBM5, was among the top essential genes. Initially, RBM5 was reported as a tumor suppressor gene in lung cancer. Thus far, the function of the encoding protein RBM5 in blood cancer remained largely unknown. To further test how RBM5 expression might correlate with AML development, we analyzed the public RNA-seq data from the TCGA clinical cancer sample datasets, RBM5 is highly expressed in AML, indicating a plausible role in AML oncogenesis. Functional validation by two individual sgRNAs against different exons of RBM5 confirmed the selectively survival essential of RBM5 in AML cell lines. Ectopic expression of sgRNA-resistant RBM5 cDNA ultimately rescued the cellular phenotype upon RBM5 loss. We utilized an alternative loss-of-function approach, RNA interference (RNAi), to further examine the functional requirement of RBM5, Two independent shRNAs targeted RBM5 mRNA in three AML cells lines. RBM5 loss significantly impaired cell growth, reduced colony numbers and triggered notable myeloid differentiation. We further transplant MOLM13 cells targeted with shRBM5 into NSG mice, and observed that RBM5 shRNAs-treated animals lagged progressively more behind with much less splenomegaly and reduced leukemia cell infiltration in bone marrow, spleen, and peripheral blood compared to the wild-type control, suggesting that RBM5 is required for AML progression in vivo. More importantly, Suppression of RBM5 in primary AML cells significantly reduced colony numbers and induced myeloid differentiation, as demonstrated by the maturation markers CD11b and CD14. In addition, the domain dropout CRISPR screen revealed that the DNA-binding domain C2H2 is required for the gene function. Integrative analysis further suggested that HOXA9 promises the direct transcriptional target of RBM5 as demonstrated by functional rescue assay and HOXA9 partially restore the gene transcriptional defect in RBM5 null leukemia cells. In summary, our innovative research reported that a new RNA-binding protein, RBM5, is required for the survival of AML through non-canonical transcriptional regulation via a complex regulatory mechanism. These data support RBM5 as a promising AML therapeutic target in future studies.

A Phase II Study of Vibecotamab, a CD3-CD123 Bispecific T-Cell Engaging Antibody, for MDS or CMML after Hypomethylating Failure and in MRD-Positive AML

Background Leukemic stem cells have high expression of CD123 compared to normal hematopoietic stem cells and is therefore a therapeutic target in multiple leukemias including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and chronic myelomonocytic leukemia (CMML). Vibecotamab (formally XmAb14045) is a CD3-CD123 bispecific engaging antibody that has shown clinical activity in relapsed/refractory AML, particularly in low-blast disease. We therefore sought to evaluate vibecotamab in other low-blast states, including MDS or CMML after hypomethylating agent failure and MRD-positive AML. Methods In this two-arm, open-label, phase II study, adults with either MDS (IPSS-R intermediate or higher risk) or CMML (CMML-1 or CMML-2) after failure of hypomethylating agents or AML in first or second morphologic remission with detectable MRD at a level of ≥0.1% by flow cytometry were eligible. CD123 expression ≥20% on aberrant myeloid blasts was required for enrollment. Vibecotamab was given IV in a ramp-up dose schedule on days 1 (0.43µg/kg), 3 (0.75µg/kg), 5 (1.1µg/kg), and 8 (1.7µg/kg) in cycle 1, followed by weekly doses of vibecotamab at a dose of 1.7µg/kg. Patients (pts) received up to 4 cycles of vibecotamab in 28-day cycles. The primary endpoint of the MDS/CMML cohort was response rate (CR + mCR + PR + HI + clinical benefit) within 4 cycles. The primary endpoint of the AML MRD cohort was the MRD negativity rate within 4 cycles. Results Between May 2022 and July 2023, 23 pts were treated (11 MDS/CMML, 12 AML MRD). Baseline characteristics are shown in Table 1. In the MDS/CMML cohort, 7 pts (63%) had received two or more prior lines of therapy, 8 pts (73%) had prior venetoclax exposure, and 2 pts (18%) had prior hematopoietic stem cell transplant (HSCT). Six MDS pts (66%) were IPSS-R high or very high risk. In the AML cohort, 6 pts (50%) had received two or more lines of prior therapy, 11 pts (92%) had prior venetoclax exposure, and 5 pts (42%) had prior HSCT. Ten pts (83%) were ELN 2022 adverse risk. The baseline CD123 expression was 72% (range, 43%-99%) in the MDS/CMML cohort and 89% (range, 55%-99%) in the AML MRD cohort. The baseline MRD by flow cytometry in the AML MRD cohort was 1.1% (range, 0.1%-3.9%). Responses are shown in Table 2. In the MDS/CMML cohort, 7 pts responded (64%), with 6 pts (56%) achieving marrow complete remission (mCR) and 1 pt (9%) achieving hematologic improvement (HI) per International Working Group (IWG) 2006 criteria. Among the 9 MDS pts, 4 (44%) achieved mCR + HI (2 HI-N, 1 HI-P, and 1 HI-P + HI-N), and 1 (11%) achieved HI (HI-N + HI-P). Per revised IWG 2023 MDS response criteria, 5 of the 9 MDS pts (56%) achieved complete remission with limited count recovery (CR L). Two of 4 MDS pts (50%) with TP53 mutations achieved CR L. Both CMML pts achieved mCR, with one pt also achieving HI-N. Among 9 pts with baseline bone marrow blasts =>5% at trial enrollment, 6 (67%) achieved a mCR, with or without HI. Best response occurred after the first cycle in all pts. CD123 expression was not associated with likelihood of response. Of the 7 responders, 5 are in ongoing response (range 0.3-6.9 months), one died in CR L from non-hematologic complications (heart failure), and one relapsed 5 months after achieving CR L. Of the 12 pts in the AML MRD cohort, 3 (25%) achieved MRD negativity, all of which occurred after 1 cycle of vibecotamab. Among the 3 responders, all were ELN adverse risk and had prior venetoclax exposure, 2 had prior HSCT, and 1 had inv(3). The median MRD and CD123 expression in responders was 0.2% (range 0.1%-0.2%) and 98% (range 95%-99%) vs 1.8% (range 0.5%-3.9%) and 87% (range 66%-96%) in non-responders, respectively. At last follow-up, all 3 responders are still in MRD-negative remission (range 3.2-12.8 months). Vibecotamab was well-tolerated with no pts requiring dose reductions or being taken off study due to adverse events. Ten pts (44%) experienced grade 2 infusion reactions and 1 pt (4%) experienced a grade 3 infusion reaction. Myelosuppression was minimal, consistent with previous studies of vibecotamab. Conclusion Vibecotamab was safe and active in low-blast, high-risk myeloid diseases, with a response rate of 64% in MDS/CMML after HMA failure and 25% in MRD-positive AML. The clinical activity of vibecotamab, including in pts with prior venetoclax exposure and/or HSCT, and its lack of clinically significant myelosuppression provide rationale to combine it with other agents in AML, MDS, and CMML.

CRISPR-Cas9 Screening Identifies Therapeutic Targets for AML1-ETO Positive Leukemia

Objectives: Targeted therapy has achieved tremendous success in leukemia therapy over the past few decades, especially in those with fusion proteins, such as t(15;17) which generates PML-RARa and t(9;22) which generates BCR-ABL. However, effective targeted therapy for AML1-ETO-positive leukemia, which arises from one of the most frequent chromosomal translocations t(8;21), remains largely elusive. In this study, we performed CRISPR-Cas9 screening on the AML1-ETO-positive Kasumi-1 cell line using an AML-related sgRNA library to identify potential therapeutic targets that could restore normal differentiation in AML1-ETO-positive AML. Methods: To identify critical genes capable of reversing differentiation blockage in AML1-ETO-driven leukemogenesis, we constructed an AML1-related sgRNA library which focused genes and signaling pathways regulated by AML1-ETO. This sgRNA library consist of (1) coding genes of proteins interacting with AML1, (2) genes activated by AML1-ETO, and (3) genes downregulated upon knockdown of AML1-ETO as observed in CHIP-seq results. This sgRNA library comprises 4130 sgRNAs targeting 929 human genes (~4 sgRNA/gene), along with 100 control sgRNAs. CD13 high and CD13 low populations were collected by flow cytometry at 10th day post-transduction of sgRNA library. The enrichment of gRNAs between CD13 high and CD13 low group was analyzed using the MAGeCK program, and the candidate genes were identified based on the log2 fold change of sgRNA abundance. To make the screening results more reliable, we used CD11b as another screening marker to repeat aforementioned process. We further preformed single candidate gene knockout in Kasumi-1 and SKNO-1 cell line to validate the screening phenotype. The regulatory function of candidate gene in AML1-ETO positive leukemia was explored through various in vitro assays, including cell apoptosis, cell proliferation, morphological evaluation, flow cytometry analysis, quantitative real-time PCR (qPCR), and Western blot. Results: The gene set enriched in the CD13 high group is considered to be positive hit. Silence of these genes may reverse blockage of differentiation, making them potential therapeutic targets for AML1-ETO leukemia. Additionally, genes such as CBFB, MTA2, DOT1L, PRMT1, RUNX1 and KDM1A, which had been previously reported to promote myeloid differentiation when down-regulated, were also significantly enriched in the CD13 high group, these findings demonstrated the credibility of our screening strategy and results. Clathrin Heavy Chain (CLTC) emerged as one of the top-ranking genes in our study. CLTC is a crucial protein involved in the regulation of clathrin-mediated endocytosis, which plays a critical role in various cellular processes including cell signaling, proliferation, and differentiation. Expression of CD13 and CD16 were upregulated in CLTC knockout cells, further validating our screening results. Besides, morphological analysis displayed a more mature cell morphology with a decrease in nucleus-to-cytoplasm ratio and indented shaped nuclei, suggesting that repression of CLTC promotes terminal differentiation of AML blasts. Cell biology experiments indicated that knockout of CLTC remarkably inhibited the proliferation of Kasumi-1 and SKNO-1 cells, meanwhile, apoptosis of these cells was accelerated. Therefore, these results collectively suggested that the down-regulation of CLTC exhibited significant tumor-suppressive effect in AML1-ETO leukemia. Furthermore, Western blot and RT-qPCR analyses revealed that CLTC is highly expressed in AML1-ETO-positive leukemia, whereas its expression is downregulated upon deletion of AML1-ETO fusion protein. This suggested that CLTC might be regulated by AML1-ETO fusion protein and contribute to its oncogenic activity. Conclusions: Our results revealed a possible novel mechanism underlying the blockage of myeloid differentiation in AML1-ETO leukemia, and have identified CLTC as a promising therapeutic target for AML1-ETO-driven leukemogenesis.

Human ILC1s Target Leukemia Stem Cells and Control Development of AML

Acute myeloid leukemia (AML) is a devastating disease with a median 5-year survival of only 40-45% for patients younger than age 65 who are treated with standard chemotherapy. Although in some cases allogeneic stem cell transplantation has proven to be curative, the treatment-related mortality and the risk for disease relapse due to persistence of leukemia stem cells (LSCs) remains relatively high. Therefore, safer and more effective novel therapeutic approaches are needed to improve the clinical outcomes of patients with AML. Innate lymphoid cell (ILC) is critical in mediating immune responses and regulating tissue homeostasis and inflammation. We recently reported that mouse ILC1s contribute to the control of AML by eliminating LSCs and inhibiting their differentiation into myeloid blasts, and functional impairment of mouse ILC1s in AML leads to the outgrowth of LSCs and disease relapse (Li et al., Nature Immunology. 2022). However, the full role and mechanistic characterization of human ILC1s in anti-tumor responses to AML remains to be fully explored. Upon analysis of ILC1s in the blood of patients with AML at the onset of disease, we observed a highly significant reduction in the total ILC1s count among lineage-negative cells (Lin −, defined asdepletion of CD3, CD4, CD8, CD14, CD15, CD16, CD19, CD20, CD33, CD34, CD203c, FceRI, and CD56 positive cells) relative to healthy donors ( p = 0.031, n = 6 healthy donors; n = 4 patients with AML). Further, functional ILC1s positive for IFNγ and DNAM-1 were significantly reduced in the patients with AML compared to healthy donors. Analysis of 106 AML cases from the Cancer Genome Atlas (TCGA) showed that AML patients with a high ILC1 gene signature had a significantly prolonged overall survival compared to AML patients with a low ILC1 gene signature. By directly interacting with LSCs, human ILC1s can eliminate LSCs via the production of IFNγ. Through Wright-Giemsa staining, we observed that ILC1s blocked the differentiation of CD34 +CD38 − cells into macrophage-like leukemia-supporting cells, which were previously reported to support the growth of leukemic cells rather than inhibit them. Flow cytometry of these differentiated cells showed that some exhibited the tumor-promoting phenotype with expression of CD11b and CD206. These macrophage-like leukemia-supporting cells significantly decreased when co-cultured with ILC1s. This differentiation is at least partially dependent on TNF secreted by ILC1s. We also performed an in vivo transplantation experiment, in which human CD34 +CD38 − cells and human ILC1s were co-injected intravenously (i.v.) into NOD.Cg- Prkdc scid Il2rg tm1WjlTg (NSG-SGM3) mice that express human IL3, GM-CSF, and SCF to support the stable engraftment of myeloid lineages. Injection of human ILC1s from healthy individuals reduced the LSC engraftment into these mice and suppressed the progression of AML. This was evidenced by a significant decrease in the number of CD45 +CD33 + blast cells, CD34 +CD38 − LSCs, and significantly prolonged survival of the mice ( p = 0.0118, n = 5/group). These results were all in comparison to mice that did not receive an injection of ILC1s. Although ILC1s target LSCs, they have no toxicity on normal HSCs. For a therapeutic purpose, we were able to derive ILC1s from umbilical cord blood (UCB) CD34 + hematopoietic stem cells (HSCs) with over 700-fold expansion and the expanded ILC1s demonstrate authentic ILC1 phenotypes and functions. Moreover, arming the expanded ILC1s with a chimeric antigen receptor (CAR) targeting FLT3, which we previously constructed (Chen et al., Leukemia. 2017), enhanced their effector function. In conclusion, ILC1s in patients with AML are impaired, while a high expression of the ILC1 gene signature is associated with better overall survival. Human ILC1s can both eliminate LSCs via production of IFNγ and block LSC differentiation into tumor-promoting macrophage-like cells through TNF. These effects converge to limit leukemogenesis in vivo. The use of UCB CD34 + HSCs to generate ILC1s, especially after being engineered with a CAR, could allow for a readily available supply of ILC1s to be produced for human adoptive transfer studies. Our findings provide evidence that targeting human ILC1s may be a promising therapeutic approach for extending disease-free survival in patients with AML.

TP53 Deficiency in AML Confers Resistance to CAR T-Cells That Can be Overcome By Targeting the Cholesterol or Wnt Pathways

Introduction TP53-mutant acute myeloid leukemia (AML) and myelodysplastic neoplasms (MDS) are distinct clinicogenomic entities characterized by chemotherapy resistance and high relapse rates after allogeneic stem cell transplantation, and thus, represent an unmet clinical need. Chimeric antigen receptor (CAR) T-cell therapy might be a promising therapeutic option for TP53-mutant AML/MDS. However, the AML-intrinsic determinants of response to T-cell-based approaches in AML, in particular the impact of TP53-deficiency, are largely unknown. In the present study, we addressed the biologically and clinically highly relevant question as to whether, and, if so, how TP53 deficiency in AML cells might confer resistance to CAR T-cell therapy. Results We took advantage of recently developed, CRISPR/Cas9-engineered TP53 isogenic AML cell lines harboring TP53 null, missense, or wildtype alleles to exclude other potential genetic confounders of therapy resistance. Flow cytometry-based co-culture assays using these isogenic cell lines together with CAR T-cells targeting the common AML surface antigens CD33, CD371, CD123, and CD117, showed that AML cells harboring TP53 null or missense mutations were relatively resistant to CAR T-cells in vitro. CAR T-cells engaging TP53-deficient leukemia cells proliferated less, upregulated exhaustion markers, displayed increased trogocytosis, and were ultimately unable to control AML cell outgrowth. Live-cell imaging revealed a longer engagement time of CAR T-cells with TP53-deficient AML cells before killing occurred as judged by propidium iodide influx. Immunodeficient mice xenografted with TP53-deficient AML cells and treated with CAR T-cells exhibited significantly shortened survival compared to TP53-wildtype AML controls. Transcriptional profiling revealed that the cholesterol pathway was upregulated in TP53-deficient AML cells under CAR T-cell attack. Simultaneously, CAR T-cells engaging TP53-deficient AML demonstrated a downregulated Wnt pathway, in particular the master regulators of T-cell fate TCF7 and EOMES. Rational pharmacological targeting of either of these pathways, blocking by Simvastatin and activation by BIO-acetoxime, respectively, rescued TP53-deficient AML cell sensitivity to CAR T-cell-mediated killing in vitro. Discussion and Outlook Using a combination of in vitro co-incubation assays, live-cell imaging, gene expression profiling and a therapeutic in vivo model we could demonstrate that TP53 deficiency in AML cells confers relative resistance to CAR T-cell therapy and elucidate some of the underlying molecular mechanisms in leukemia target cells and CAR T-cells. We thus propose a model, in which the intrinsic apoptotic defect in TP53-deficient AML/MDS cells results in a longer duration of the cellular interaction between CAR T-cells and TP53-deficient AML/MDS cells. This longer temporal interaction eventually leads to reduced CAR T-cell proliferation and enhanced CAR T-cell exhaustion with an overall decrease in AML cell killing (figure 1). Furthermore, we identified the cholesterol pathway as a potential therapeutic vulnerability of TP53-deficient AML cells engaged by CAR T-cells, and the Wnt pathway as a promising avenue to enhance the efficacy of CAR T-cell therapy in TP53-deficient AML/MDS. Our data suggest that the combination of CAR T-cell therapies with pharmacological co-interventions - as exemplified in this study - may be a preferable strategy towards more efficacious and tolerable cellular therapies for patients with TP53-mutant myeloid neoplasms.

DAP10 Co-Stimulation Imparts Memory-like Features to CD5 Targeting Cord Blood Derived CAR-NK Cells

Relapsed/refractory T-cell malignancies have a particularly poor prognosis and novel therapies are direly needed. CD5 is a great candidate for adoptive cellular therapy to target T-cell malignancies since it is ubiquitously expressed on T cells with restricted expression on other hematopoietic cells. NK cells are an attractive platform for CAR engineering to target CD5 since, unlike T cells, they do not express CD5 on their surface, which eliminates the risk of fratricide. Another advantage of NK cells for CAR engineering is their safety profile; in contrast to T cells, they do not cause cytokine release syndrome (CRS) or immune effector cell-associated neurotoxicity syndrome (ICANS) and they are not associated with graft-versus-host disease (GVHD) in the allogeneic setting, opening the potential for a completely off-the-shelf cellular product to be used at point of care. Therefore, we sought to develop CD5 targeting CAR-NK cells for the treatment of T-cell malignancies. Multiple studies have demonstrated that the choice of co-stimulatory domain in CAR-T cells influences their function, persistence and metabolic profile. In the field of CAR-NK cells, the first constructs tested in the clinic have incorporated CD28, a T cell specific co-stimulatory domain, borrowing from the design of CAR-T cells. There is a sparsity of data regarding the impact of co-stimulatory domains on the proliferation, transcriptomic and proteomic profile, polyfunctionality, metabolism and fitness of CAR-NK cells. In this study, we aimed to do so, by comprehensively studying the impact of co-stimulatory domains including some that are more relevant for NK cell biology, namely DNAX-activating Protein 10 (DAP10), a major adaptor protein and the exclusive signaling intermediate of NKG2D in human NK cells, DNAX-activating Protein 12 (DAP12), an important adaptor molecule that associates with multiple activating receptors (e.g. NKG2C, NKp44, activating KIRs) and NKG2D, one of the most potent NK cytotoxicity receptors which is essential for anti-tumor immunity. Our results show that CD5 CAR-NK cells with DAP10 co-stimulatory domain show enhanced cytotoxicity against CD5+ T-cell leukemia targets even after multiple tumor rechallenges in an Incucyte live-cell imaging assay. They also show augmented polyfunctionality compared to CD5 CAR-NK cells with other co-stimulatory domains in an Isoplexis single-cell secretome assay. Moreover, DAP10 co-stimulation endowed CD5 CAR-NK cells with enhanced metabolic fitness as evidenced by increased oxidative phosphorylation compared to other co-stimulatory molecules. At the epigenetic level, CD5 CAR-NK cells with DAP10 co-stimulation interrogated by sc-ATACseq show enrichment in AP-1 complex and BATF transcription factors related to memory formation and exhaustion resistance. This translates to better in vivo performance as CD5 CAR-NK cells with DAP10 co-stimulatory domain significantly improve tumor control and survival in an NSG mouse model of CD5+ T-cell leukemia (CCRF-CEM) and show evidence of recall response following tumor rechallenge. In conclusion, our data show that DAP10 co-stimulation induces epigenetic reprogramming of CD5 CAR-NK cells leading to enhanced cellular fitness and memory formation ensuing better anti-tumor potential. Based on these preclinical data, a Phase I/II clinical trial evaluating the safety and efficacy of CD5 CAR-NK cells for the treatment of CD5+ malignancies is in preparation.

Discovery of a potent and selective CBP bromodomain inhibitor (Y08262) for treating acute myeloid leukemia

The bromodomain of CREB (cyclic-AMP response element binding protein) binding protein (CBP) is an epigenetic “reader” and plays a key role in transcriptional regulation. CBP bromodomain is considered to be a promising therapeutic target for acute myeloid leukemia (AML). Herein, we report the discovery of a series of 1-(indolizin-3-yl)ethan-1-one derivatives as potent, and selective CBP bromodomain inhibitors focused on improving cellular potency. One of the most promising compounds, 7e (Y08262), inhibits the CBP bromodomain at the nanomolar level (IC50 = 73.1 nM) with remarkable selectivity. In addition, the new inhibitor also displays potent inhibitory activities in AML cell lines. Collectively, this study provides a new lead compound for further validation of CBP bromodomain as a molecular target for AML drug development.

Therapeutic targeting in pediatric acute myeloid leukemia with aberrant HOX/MEIS1 expression

Despite advances in the clinical management of childhood acute myeloid leukemia (AML) during the last decades, outcome remains fatal in approximately one third of patients. Primary chemoresistance, relapse and acute and long-term toxicities to conventional myelosuppressive therapies still constitute significant challenges and emphasize the unmet need for effective targeted therapies. Years of scientific efforts have translated into extensive insights on the heterogeneous spectrum of genetics and oncogenic signaling pathways of AML and identified a subset of patients characterized by upregulation of HOXA and HOXB homeobox genes and myeloid ecotropic virus insertion site 1 (MEIS1). Aberrant HOXA/MEIS1 expression is associated with genotypes such as rearrangements in Histone-lysine N-methyltransferase 2A (KMT2A-r), nucleoporin 98 (NUP98-r) and mutated nucleophosmin (NPM1c) that are found in approximately one third of children with AML. AML with upregulated HOXA/MEIS1 shares a number of molecular vulnerabilities amenable to recently developed molecules targeting the assembly of protein complexes or transcriptional regulators. The interaction between the nuclear scaffold protein menin and KMT2A has gained particular interest and constitutes a molecular dependency for maintenance of the HOXA/MEIS1 transcription program. Menin inhibitors disrupt the menin-KMT2A complex in preclinical models of KMT2A-r, NUP98-r and NPM1c acute leukemias and its occupancy at target genes leading to leukemic cell differentiation and apoptosis. Early-phase clinical trials are either ongoing or in development and preliminary data suggests tolerable toxicities and encouraging efficacy of menin inhibitors in adults with relapsed or refractory KMT2A-r and NPM1c AML. The Pediatric Acute Leukemia/European Pediatric Acute Leukemia (PedAL/EUPAL) project is focused to advance and coordinate informative clinical trials with new agents and constitute an ideal framework for testing of menin inhibitors in pediatric study populations. Menin inhibitors in combination with standard chemotherapy or other targeting agents may enhance anti-leukemic effects and constitute rational treatment strategies for select genotypes of childhood AML, and provide enhanced safety to avoid differentiation syndrome. In this review, we discuss the pathophysiological mechanisms in KMT2A-r, NUP98-r and NPM1c AML, emerging molecules targeting the HOXA/MEIS1 transcription program with menin inhibitors as the most prominent examples and future therapeutic implications of these agents in childhood AML.

Excessive concentrations of kinase inhibitors in translational studies impede effective drug repurposing

Drug repositioning seeks to leverage existing clinical knowledge to identify alternative clinical settings for approved drugs. However, repositioning efforts fail to demonstrate improved success rates in late-stage clinical trials. Focusing on 11 approved kinase inhibitors that have been evaluated in 139 repositioning hypotheses, we use data mining to characterize the state of clinical repurposing. Then, using a simple experimental correction with human serum proteins in invitro pharmacodynamic assays, we develop a measurement of a drug's effective exposure. We show that this metric is remarkably predictive of clinical activity for a panel of five kinase inhibitors across 23 drug variant targets in leukemia. We then validate our model's performance in six other kinase inhibitors for two types of solid tumors: non-small cell lung cancer (NSCLC) and gastrointestinal stromal tumors (GISTs). Our approach presents a straightforward strategy to use existing clinical information and experimental systems to decrease the clinical failure rate in drug repurposing studies.

Uncovering NOTCH1 as a Promising Target in the Treatment of MLL-Rearranged Leukemia.

MLL rearrangement (MLLr) is responsible for the development of acute leukemias with poor outcomes. Therefore, new therapeutic approaches are urgently needed. The NOTCH1 pathway plays a critical role in the pathogenesis of many cancers including acute leukemia. Using a CRISPR/Cas9 MLL-AF4/-AF9 translocation model, the newly developed NOTCH1 inhibitor CAD204520 with less toxic side effects allowed us to unravel the impact of NOTCH1 as a pathogenic driver and potential therapeutic target in MLLr leukemia. RNA sequencing (RNA-seq) and RT-qPCR of our MLLr model and MLLr cell lines showed the NOTCH1 pathway was overexpressed and activated. Strikingly, we confirmed this elevated expression level in leukemia patients. We also demonstrated that CAD204520 treatment of MLLr cells significantly reduces NOTCH1 and its target genes as well as NOTCH1 receptor expression. This was not observed with a comparable cytarabine treatment, indicating the specificity of the small molecule. Accordingly, treatment with CAD204520 resulted in dose-dependent reduced proliferation and viability, increased apoptosis, and the induction of cell cycle arrest via the downregulation of MLL and NOTCH1 target genes. In conclusion, our findings uncover the oncogenic relevance of the NOTCH1 pathway in MLLr leukemia. Its inhibition leads to specific anti-leukemic effects and paves the way for further evaluation in clinical settings.

Z-ligustilide preferentially caused mitochondrial dysfunction in AML HL-60 cells by activating nuclear receptors NUR77 and NOR1

BackgroundNuclear receptors NUR77 and NOR1 were identified as critical targets in acute myeloid leukemia (AML) therapy. Previously, we showed that Z-ligustilide (Z-LIG) selectively targeted AML by restoring NUR77 and NOR1. However, its downstream mechanisms are yet to be elucidated.MethodsSRB staining assay was used to measure cell viability. Cell apoptosis, mitochondrial membrane potential and mitochondrial reactive oxygen species were analyzed using flow cytometry. The potential targets of Z-LIG in AML HL-60 cells were evaluated by RNA sequencing. Changes in RNA levels were measured using quantitative RT-qPCR and western blot analysis was used to detect the expression of proteins.ResultsZ-LIG preferentially induced mitochondrial dysfunction in HL-60 cells compared with 293T cells. Furthermore, RNA sequencing revealed that mitochondrial transcription and translation might be potential Z-LIG targets inhibiting HL-60 cells. NUR77/NOR1 overexpression significantly reduced the mitochondrial ATP and mitochondrial membrane potential and increased mitochondrial reactive oxygen species in HL-60 cells but not in 293T cells. Moreover, Z-LIG induced mitochondrial dysfunction by restoring NUR77 and NOR1 in HL-60 cells. Compared with HL-60 cells, the apoptosis-inducing activities of NUR77/NOR1 and Z-LIG were significantly reduced in HL-60 ρ0 cells depleted in mitochondrial DNA (mt-DNA). Moreover, NUR77/NOR1 and Z-LIG downregulated mitochondrial transcription and translation related proteins in HL-60 cells. Notably, Z-LIG remarkably reduced mitochondrial ATP in primary AML cells and showed anti-AML activity in mouse models of human AML.ConclusionsCollectively, our findings suggested that Z-LIG selectively induces mitochondrial dysfunction in AML HL-60 cells by restoring NUR77 and NOR1, a process associated with interference in mtDNA transcription.

Aldehyde Dehydrogenase Genes as Prospective Actionable Targets in Acute Myeloid Leukemia.

It has been previously shown that the aldehyde dehydrogenase (ALDH) family member ALDH1A1 has a significant association with acute myeloid leukemia (AML) patient risk group classification and that AML cells lacking ALDH1A1 expression can be readily killed via chemotherapy. In the past, however, a redundancy between the activities of subgroup members of the ALDH family has hampered the search for conclusive evidence to address the role of specific ALDH genes. Here, we describe the bioinformatics evaluation of all nineteen member genes of the ALDH family as prospective actionable targets for the development of methods aimed to improve AML treatment. We implicate ALDH1A1 in the development of recurrent AML, and we show that from the nineteen members of the ALDH family, ALDH1A1 and ALDH2 have the strongest association with AML patient risk group classification. Furthermore, we discover that the sum of the expression values for RNA from the genes, ALDH1A1 and ALDH2, has a stronger association with AML patient risk group classification and survival than either one gene alone does. In conclusion, we identify ALDH1A1 and ALDH2 as prospective actionable targets for the treatment of AML in high-risk patients. Substances that inhibit both enzymatic activities constitute potentially effective pharmaceutics.

Genomics and transcriptomic alterations of the glutamate receptors in acute myeloid leukemia.

Glutamine and glutamate have been widely explored as potential therapeutic targets in acute myeloid leukemia (AML). In addition to its bioenergetic role in leukemia cell proliferation, L-glutamate is a neurotransmitter that acts on glutamate receptors. However, the role of glutamate receptors in AML is largely understudied. Here, we comprehensively analyze the genomic and transcriptomic alterations of glutamate receptor genes in AML using publicly available data. We investigated the frequency of mutations in the glutamate receptor genes and whether an association exist between the presence of these mutations and clinical and molecular characteristics or patient's clinical outcome. We also assessed the dysregulation of glutamate receptor gene expression in AML with and without mutations and whether gene dysregulation is associated with clinical outcomes. We found that 29 (14.5%) of 200 patients with AML had a mutation in at least one glutamate receptor gene. The DNMT3A mutations were significantly more frequent in patients with mutations in at least one glutamate receptor gene compared with patients without mutations (13 of 29 [44.8%] vs. 41 of 171 [23.9%], p value: 0.02). Notably, patients with mutations in at least one glutamate receptor gene survived shorter than patients without mutations; however, the results did not reach statistical significance (overall survival: 15.5 vs. 19.0 months; p value: 0.10). Mutations in the glutamate receptor genes were not associated with changes in gene expression and the transcriptomic levels of glutamate receptor genes were not associated with clinical outcome.

Potential Candidate Genes for Therapeutic Targeting in Chronic Myeloid Leukemia: A Pilot Study.

Chronic myeloid leukemia (CML) is a prevalent hematological malignancy known for the presence of the Philadelphia chromosome and activation of the BCR-Abl kinase activity. Although tyrosine kinase inhibitors are widely used as the standard treatment, resistance remains a concern among certain patients. This study aimed to investigate the gene expression profile of a group of CML patients in comparison to a control group in order to identify novel candidate genes associated with the disease. Whole transcriptome sequencing was performed, and gene expression levels were validated using quantitative real-time PCR. Additionally, single nucleotide and insertion/deletion variants were analyzed in the selected candidate genes among 10 CML patients and 4 healthy control subjects. Analysis revealed a set of differentially expressed genes, whose up- or downregulation was further confirmed by qRT-PCR. Among the upregulated genes in the patient group were ribosomal protein like (RPL) members, specifically RPL9, RPL34, RPL36A, and RPL39, while downregulation was observed in CCDC170, LDB1, and SBF1 compared to the healthy subjects. Furthermore, gene variant studies identified novel genetic changes in these candidate genes, suggesting potential clinical significance in CML. This study highlights RPL9, RPL34, RPL36A, RPL39, CCDC170, LDB1, and SBF1 as potential targets in CML. Additionally, it underscores the importance of investigating these genes and their variants in larger cohort studies to assess their clinical significance in CML patients.

Vacuolar ATPase Is a Possible Therapeutic Target in Acute Myeloid Leukemia: Focus on Patient Heterogeneity and Treatment Toxicity.

Vacuolar ATPase (V-ATPase) is regarded as a possible target in cancer treatment. It is expressed in primary acute myeloid leukemia cells (AML), but the expression varies between patients and is highest for patients with a favorable prognosis after intensive chemotherapy. We therefore investigated the functional effects of two V-ATPase inhibitors (bafilomycin A1, concanamycin A) for primary AML cells derived from 80 consecutive patients. The V-ATPase inhibitors showed dose-dependent antiproliferative and proapoptotic effects that varied considerably between patients. A proteomic comparison of primary AML cells showing weak versus strong antiproliferative effects of V-ATPase inhibition showed a differential expression of proteins involved in intracellular transport/cytoskeleton functions, and an equivalent phosphoproteomic comparison showed a differential expression of proteins that regulate RNA processing/function together with increased activity of casein kinase 2. Patients with secondary AML, i.e., a heterogeneous subset with generally adverse prognosis and previous cytotoxic therapy, myeloproliferative neoplasia or myelodysplastic syndrome, were characterized by a strong antiproliferative effect of V-ATPase inhibition and also by a specific mRNA expression profile of V-ATPase interactome proteins. Furthermore, the V-ATPase inhibition altered the constitutive extracellular release of several soluble mediators (e.g., chemokines, interleukins, proteases, protease inhibitors), and increased mediator levels in the presence of AML-supporting bone marrow mesenchymal stem cells was then observed, especially for patients with secondary AML. Finally, animal studies suggested that the V-ATPase inhibitor bafilomycin had limited toxicity, even when combined with cytarabine. To conclude, V-ATPase inhibition has antileukemic effects in AML, but this effect varies between patients.

A Leukemic Target with a Thousand Faces: The Mitochondria.

In the era of personalized medicine greatly improved by molecular diagnosis and tailor-made therapies, the survival rate of acute myeloid leukemia (AML) at 5 years remains unfortunately low. Indeed, the high heterogeneity of AML clones with distinct metabolic and molecular profiles allows them to survive the chemotherapy-induced changes, thus leading to resistance, clonal evolution, and relapse. Moreover, leukemic stem cells (LSCs), the quiescent reservoir of residual disease, can persist for a long time and activate the recurrence of disease, supported by significant metabolic differences compared to AML blasts. All these points highlight the relevance to develop combination therapies, including metabolism inhibitors to improve treatment efficacy. In this review, we summarized the metabolic differences in AML blasts and LSCs, the molecular pathways related to mitochondria and metabolism are druggable and targeted in leukemia therapies, with a distinct interest for Venetoclax, which has revolutionized the therapeutic paradigms of several leukemia subtype, unfit for intensive treatment regimens.

A new hope for early T cell precursor acute lymphoblastic leukemia therapy based on STAT5+ leukemic stem cell targeting.

Leukemia stem cells are known to drive tumor progression, drug resistance, microenvironmental shift, and relapse, which would make them a perfect therapeutic target. However, their phenotypic and functional similarity to their normal counterparts leaves limited road maps for their selective elimination. Tremblay et al. recently unraveled the fundamental role of overactivated pSTAT5 as a functional marker of early T cell precursor acute lymphoblastic leukemia stem cells driving leukemic progression and highlighted its potential use as a therapeutic target to prevent fatal outcomes.