AbstractAcute Myeloid Leukemia Research Articles

Abstract 2064: Unveiling the correlation between gemtuzumab-ozogamicin efficacy and CD33+ expression in AML primary samples using the novel AML vitroscreen

Abstract Acute myeloid leukemia (AML) poses a significant therapeutic challenge, with a rising incidence in recent times. This clonal hematopoietic disorder of progenitor and stem cells exhibits aggressive behavior, and despite initial remission, recurrence is common1. The conventional shift from chemotherapy to monoclonal antibodies and antibody-drug conjugates (ADCs) has been hindered by the absence of AML-specific antigens. Notably, CD33, expressed strongly in 80-90% of AML cells, has become a target for gemtuzumab-ozogamicin (Mylotarg), the sole FDA approved ADC for AML treatment2. While advancements in understanding AML molecular mechanisms have influenced clinical approaches, the lack of clinically representative models hinders therapeutic progress. Existing models, both in vivo and ex vivo, struggle to capture the heterogeneity and complexity of AML3. Addressing this, we present our proprietary assay, Champions AML VitroScreen®4, designed for testing therapeutic candidates in primary AML samples. Our diverse bank of deeply characterized AML samples encompasses multiple subtypes, allowing evaluation of therapeutic responses through cell viability, proliferation, and clonal composition analyses. To validate our novel assay, we employed the VitroScreen platform to test Mylotarg across various AML subtypes, considering CD33 expression levels. By assessing more than 20 AML models, we determined the IC50 for Mylotarg and observed dose-dependent responses, where sensitivity to the drugh correlated with CD33 expression. Through multiple endpoints, including viability, proliferation, apoptosis, and phenotyping, we categorized primary AML models as responders, low responders, or resistant, establishing a strong positive correlation between Mylotarg sensitivity and CD33 expression. Our innovative approach, utilizing deeply characterized AML patient samples in the AML VitroScreen® platform, facilitates high-throughput drug testing. This system, serving as an ideal clinical translational setting in preclinical research, holds promise for developing tailored therapeutic strategies. Ultimately, this approach could significantly impact patient outcomes by offering improved strategies for both primary and recurrent AML cases. Citation Format: Mara Gilardi, Garima Kaushik, Brandon Walling, Paolo Schiavini, Stefano Cairo, Marianna Zipeto. Unveiling the correlation between gemtuzumab-ozogamicin efficacy and CD33+ expression in AML primary samples using the novel AML vitroscreen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2064.

Abstract 7397: Application of state transition theory for predicting responses of acute myeloid leukemia to chemotherapy

Abstract Acute Myeloid Leukemia (AML) is aggressive cancer that initiates in the bone marrow (BM) and circulates in the peripheral blood (PB). The AML initiation and progressions are complex disease evolution associated with gene mutations and chromosomal abnormalities that change expression profiles of downstream genes characterizing functional networks of leukemic cells. We previously reported the application of the state-transition theory to characterize AML disease progression by modeling transcriptome changes during AML progression as a dynamic system that undergoes state-transition in an AML state-space characterized by an AML potential. Here, we investigate the impact of treatment on transcriptome state-transition and examine the hypothesis that treatment dynamically alters the AML potential. We use the Cbfb-MYH11 (CM) knock-in AML mouse model and a ”5+3” chemotherapy regimen to model the impact of current standard of care for newly diagnosed AML. CM leukemic mice were treated with a combination of cytarabine (Ara-C; 50mg/kg/day; 5 days) and Daunorubicin (DNR; 1.5mg/kg/day; 3 days) after detection of overt leukemia, defined by > 20% leukemia blast (cKit+) detected by flow cytometry in the PB. Time-series samples of peripheral blood mononuclear cell (PBMC) (n=174) were collected weekly before, during, and following “5+3” chemotherapy and subjected to RNA sequencing. All samples were mapped to the AML state-space constructed based on time-sequential RNA-seq collected over the course of CM AML development. Based on the state-transition model, all 10 treated AML mice achieved partial response to chemotherapy with a mean time to relapse (return to leukemia state) of 5 weeks confirming the anti-leukemia effects of treatment by the blast percentages (ckit%). We used the state-transition treatment model to study the dynamics of chemotherapy on the AML potential using state-space trajectories before, during, and after “5+3” chemotherapy. Dynamic changes of concentrations of Ara-C and DNR in the CM mouse model during ”5+3” chemotherapy were modeled by drug doses, half-life, and Heaviside step function. The drug effects were introduced to the AML potential as anti-leukemic treatment forces. Several treatment protocols were examined to find combinations of drug doses and timing that showed the longest survival rates. The model predicted that sequential doses reducing 50% of the original “5+3” chemotherapy dose would produce the longest survival rate. The model suggests that controlling the state-space trajectories in the healthy state with reduced doses will provide the most effective outcomes from “5+3” chemotherapy. Citation Format: Lisa Uechi, Yu-Hsuan Fu, David E. Frankhouser, Lianjun Zhang, Ying-Chieh Chen, Denis O'Meally, Sergio Branciamore, Jihyun Irizarry, Bin Zhang, Guido Marcucci, Ya-Huei Kuo, Russell C. Rockne. Application of state transition theory for predicting responses of acute myeloid leukemia to chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7397.

Abstract 7468: Development of a high complexity flow cytometry panel to assess minimum residual disease in acute myeloid leukemia

Abstract Acute Myeloid Leukemia (AML) is a highly heterogeneous disease with a diverse range of abnormal myeloid subpopulations resulting in challenges in clinical diagnosis and treatment. Many methods such as flow cytometry are used to provide precise information for risk stratification and treatment methods. Flow cytometry utilizes the expression patterns of cellular markers to characterize the high diversity in AML subpopulations with high sensitivity and specificity. This coupled with rapid analysis timelines allows for flow cytometry to be an excellent tool for the identification of AML lineage and progression through both phenotypic analysis and difference from normal. As AML lineage and disease progression are predictors of residual disease and relapse; the need for effective and accurate characterization of AML populations is critical. Here, Champions Oncology has developed a high-complexity 18-color flow cytometry panel to identify AML subpopulations at high resolution. We have characterized AML samples to evaluate the expression of phenotypic markers and their heterogeneity. Utilizing primary AML samples, we have evaluated the stability of AML subpopulations to understand how delayed analysis, such as what is seen in clinical trials, may impact marker expression and observed key populations were stable for up to 72 hours after collection. In addition to stability, understanding the lower limits of detection is critical for AML patients, particularly for minimum residual disease and relapse screening. The use of a flow cytometric panel again provides an excellent tool for these tests due to the single cell nature that allows for the interrogation of individual populations with primary AML subpopulations detected at a range of 10−3 to 10−4. Finally, with hundreds of never-passaged AML models characterized and cryopreserved by both flow cytometry and sequencing at Champions Oncology, we investigated how the cryopreservation processes impacted the expression of AML subpopulations. We have observed similar expression and detection of AML populations following cryopreservation indicating that these models can be utilized as an excellent tool for further studies. Collectively, our data indicates that the panel developed at Champions Oncology provides robust data analysis of AML subpopulations and can be an excellent tool for the tracking of AML disease progression in the clinic. Citation Format: Jessica Pearl, Elena Bruni, Haoting Hsu, Brandon Walling, Karin Abarca-Heidemann. Development of a high complexity flow cytometry panel to assess minimum residual disease in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7468.

Abstract 4740: Acid ceramidase inhibition enhances venetoclax sensitivity in preclinical models of acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) is an aggressive hematologic malignancy in urgent need of improved therapeutic strategies. AML blasts frequently rely on the anti-apoptotic protein, Bcl-2, for survival. The specific Bcl-2 inhibitor, venetoclax (VEN), is FDA-approved in combination with low-dose cytarabine (LDAC) or azacitidine for patients unfit for intensive induction chemotherapy. Unfortunately, responses are transient due to upregulation of compensatory survival proteins (e.g., Bcl-xL or Mcl-1) or resistance characterized by reprogrammed mitochondrial bioenergetics. Our research aims to improve current AML treatments and understanding of AML pathogenesis by targeting dysregulated sphingolipid metabolism. Ceramides are tumor-suppressor sphingolipids that mediate therapy-induced cell death. Sphingolipid dysregulation that results in decreased ceramide content and/or enhanced ceramide catabolism is an emerging AML hallmark. We’ve previously shown that acid ceramidase (AC), a ceramide catabolizing lysosomal enzyme, is overexpressed in AML and contributes to drug resistance. Here, we demonstrated that AC inhibition enhanced VEN cytotoxicity. Combining the AC inhibitor/ceramide analog, SACLAC, with VEN resulted in synergistic lethality in multiple AML cell lines in cell viability and apoptosis assays. Genetic inhibition of AC also improved VEN cytotoxicity. The SACLAC+VEN combination achieved Bliss scores (SynergyFinder 2.0) between 22 and 32 in cell lines, which indicate a highly synergistic combination. SACLAC+VEN efficacy was comparable to the FDA-approved combination of VEN+LDAC when tested in 67 primary AML patient samples. Pharmacological inhibition of AC also increased the efficacy of the VEN+LDAC combination. Mechanistically, the observed synergistic lethality was independent of changes to Bcl-2, Mcl-1, and Bcl-xL protein levels. Combined AC and Bcl-2 inhibition resulted in synergistic ceramide accumulation, integrated stress response (ISR) activation, and caspase-dependent apoptosis characterized by impaired mitochondrial function. Pretreatment with the pan-caspase inhibitor, zVAD-FMK, or ISR inhibitor, ISRIB, significantly rescued cell death. Ongoing studies aim to further characterize mitochondrial impairment and ISR activation induced by inhibiting AC and Bcl-2. Taken together, these results detail the first report of ISR activation and mitochondrial defects elicited by combined AC and Bcl-2 inhibition as contributory to cytotoxic impact (mechanism) and warrant additional studies of AC inhibitors with frontline AML therapeutics. Citation Format: Johnson Ung, Su-Fern Tan, Jeremy J. Shaw, Todd E. Fox, Maansi Taori, David F. Claxton, Kelsey H. Fisher-Wellman, Myles C. Cabot, David J. Feith, Thomas P. Loughran. Acid ceramidase inhibition enhances venetoclax sensitivity in preclinical models of acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4740.

Abstract 6564: SOS1 inhibitor treatment improves response to Venetoclax in acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. First-line treatment of AML patients consists primarily of chemotherapy, sometimes combined with a targeted therapy. However, elderly patients unfit for chemotherapy receive venetoclax, a BCL2 inhibitor, combined with azacitadine or decitabine. While responses in these patients are high (50-70%, with median OS of 10-17 months), around 30-50% of them do not respond and most relapse within 1-10 years. Increased MAPK pathway activity or low frequency RAS pathway mutations have been identified as key mediators of resistance to standard-of-care targeted therapies for AML, including venetoclax. Here, we found that in DepMap whole-genome CRISPR screens, leukemia cell lines, including AML, show a particular dependency on SOS1. A subsequent PRISM screen with a selective inhibitor of SOS1 confirmed these results. To validate these results in vitro, we treated 7 AML cell lines showing strongest dependency on SOS1 based on DepMap and PRISM screens, with SOS1i or a SHP2 inhibitor. We found that in 4 of 7 cell lines treatment with SOS1i or SHP2i strongly impaired proliferation. In 3 of 4 responding cell lines, the anti-proliferative effect with either SOS1i or SHP2i was stronger than azacytidine single agent treatment. We next treated 29 primary ex vivo cultures of AML with SOS1i and found that the treatment induced strong or intermediate anti-proliferative effect in 21 of 29 models (72%). In two AML PDX models, treatment with SOS1i as a single agent resulted in approximately 25% reduction of human CD45+ AML blast cells in both models. Venetoclax treatment led to approximately 75% decrease in AML blasts, while the combined venetoclax and SOS1i treatment resulted in near complete eradication of the disease. Annexin V staining of AML monoblasts demonstrated that this decrease was due to an increase in apoptosis in the combination groups. In summary, we demonstrate that SOS1 inhibitor treatment may be used to improve responses to venetoclax in AML patients. Citation Format: Kaja Kostyrko, Melanie Hinkel, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Daniel Gerlach, Irene Waizenegger. SOS1 inhibitor treatment improves response to Venetoclax in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6564.

Abstract 1703: SMARCA2/4 degraders relieve the differentiation block in AML via changes in chromatin looping and accessibility

Abstract Acute Myeloid Leukemia (AML) is characterized by the unfettered proliferation and poor differentiation of myeloid cells causing reduced survival. The mammalian BAF complexes (also known as SWI/SNF) are important regulators of MYC and the cell cycle. There are three BAF complexes (cBAF, ncBAF and pBAF) that share several subunits. SMARCA2 and 4 are mutually exclusive ATPase subunits within the BAF complexes that use ATP hydrolysis and helicase activity to remodel chromatin via nucleosome sliding and removal. PBRM1 is a SMARCA4 associated factor present in pBAF. The association of SMARCA4 with regulatory elements of transcription factors makes it an intriguing target for AML. To evaluate the role of SMARC2/4 in AML, we analyzed RNA transcripts from highly purified primary AML initiating populations and control samples. Sorted leukemia stem cells (Lin-ve, CD34+, CD38-) overexpressed SMARCA2/4 when compared to healthy cells. A novel and highly selective SMARCA2/4 and PBRM1 PROTAC degrading agent AU-15330 was used to investigate the therapeutic effectiveness of targeting BAF complexes as well as the role of SMARCA2/4 in leukemic pathogenesis. Our data demonstrate that AU-15330 effectively degrades SMARCA2/4 and PBRM1 in human leukemia cell lines with varying mutational profiles; MV4-11 was the most sensitive cell line. When evaluating healthy CD34+ HSPCs as well as patient derived AML cells in colony assays, AU-15330 treatment increased differentiation in patient AML samples with minimal effects on healthy CD34+ cells. A xenograft of patient derived AML cells in irradiated mice was performed to determine the requirement of SMARCA2/4 in leukemia stem cell maintenance. Mice treated with AU-15330 had greater myeloid differentiation, fewer human cells in their bone marrows and reduced leukemia stem cell activity, seen in secondary transplants. To understand the underlying mechanism of how SMARCA2/4 and PBRM1 promote leukemic pathogenesis, we used a multi-omic analysis of transcription and chromatin dynamics in MV4-11 cells: ATAC-seq and RNA-seq identified downregulated genes with decreased accessibility, PRO-seq determined early transcriptional changes and HiChIP showed changes in enhancer promoter loops with SMARC2/4 degradation. Several leukemia related transcription factors as well as inflammatory genes were identified from these analyses as possible targets of the BAF complexes in the context of AML. Finally, to determine the effect of SMARCA2/4 degradation on pBAF association with chromatin, single cell imaging was performed of U2OS cells with HALO-tagged PBRM1 treated with the degrader or DMSO. pBAF in the degrader treated cells improved engagement with target chromatin however, a decrease in the stability of the complex binding to the nucleosome when compared to DMSO treated cells was shown. Taken together, these studies will determine the role of SMARCA2/4 in leukemia disease. Citation Format: Sarah Aminov, Kith Pradhan, Srabani Sahu, Shanisha Gordon-Mitchell, Emma Rabinovich, Ariel Fromowitz, Joyeeta Chakraborty, Srinivas Aluri, Rongbao Zhao, Nayem Haque, Milagros Carbajal, Aditi Shastri, Ulrich Steidl, Susanta Samajdarr, Akhil Kumar, Murali Ramachandra, Robert A. Coleman, Kristy Stengel, Amit K. Verma. SMARCA2/4 degraders relieve the differentiation block in AML via changes in chromatin looping and accessibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1703.

Abstract 6869: Paired single-cell B-cell transcriptomics and receptor sequencing reveal activation states and clonal signatures that characterize B cell immunity in acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) is the second most common adult leukemia with a five-year survival rate around 30%. For decades, AML treatment has centered around intensive chemotherapy frequently followed by allogeneic stem cell transplant (Allo-SCT). The power of Allo-SCT to induce lasting remission has been attributed to a potent graft-versus-leukemia effect and has inspired efforts to stimulate host immunity against AML via immune checkpoint blockade (ICB). Thus far, these studies have yielded mixed results. While tumor-infiltrating T-cells have long been the focus of immunotherapy investigations, a growing body of data points to a central role of B-cells in mediating anti-tumor immunity, and a comprehensive assessment of B lymphocytes within the AML immune microenvironment has never been carried out with single cell clonal resolution. We performed paired single-cell transcriptomic and B cell receptor (BCR) analysis on 52 bone marrow aspirate samples. These samples included 6 from healthy bone marrow donors (normal), 24 from newly diagnosed AML patients (NewlyDx), and 22 from 8 relapsed or refractory AML patients (RelRef), who underwent assessment both before and after ICB with azacitidine/nivolumab. We first used transcriptomic data to delineate canonical B-cell subpopulations and observed a reduction in nascent B cells and an expansion of differentiated B cells in AML patients (RelRef>NewlyDx). Overlaying BCR sequencing and clonotypic analysis revealed clonal expansion, low clonotypic diversity, and extensive somatic hypermutation in the RelRef samples, suggesting antigen-driven affinity maturation within the tumor microenvironment. Furthermore, we identified robust AP-1 expression (a marker of activation) in B-cells from NewlyDx patients and a marked loss of AP-1 in RelRef patients, suggesting that B-cell exhaustion may be a key immunologic feature of AML relapse. Importantly, we observed that AP-1 activity is restored and that specific B-cell clones expand after ICB, but only among patients who clinically respond to ICB. In line with these observations, we also noted the clonal expansion of AML-associated plasma cells and loss of clonotypic diversity among ICB clinical responders, pointing to an antitumor role for these clones. Finally, we characterized atypical memory B cells which demonstrate high antigen presentation activity, close interaction with AML cells and are associated with unfavorable clinical outcomes, suggesting that they play a direct role in aiding AML survival and immune escape. Collectively, our findings establish the dynamic landscape of AML-associated B-cells while identifying specific B-cell subpopulations and B-cell-AML interactions that may be targeted by the next generation of AML-directed immunotherapies. Citation Format: Shengnan Guo, Gopi S. Mohan, Bofei Wang, Tianhao Li, Naval Daver, Yuting Zhao, Patrick K. Reville, Dapeng Hao, Hussein A. Abbas. Paired single-cell B-cell transcriptomics and receptor sequencing reveal activation states and clonal signatures that characterize B cell immunity in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6869.

Abstract 7218: Venetoclax triggers apoptosis and augments the effectiveness of doxorubicin against acute myeloid leukemia cells

Abstract Acute myeloid leukemia (AML) is a hematologic malignancy characterized by the clonal proliferation of immature blast cells in the peripheral blood and bone marrow. AML is the second most common type of childhood leukemia, and 50% to 60% of relapses occur within the first year of diagnosis. Chemotherapy side effects and resistance are becoming major clinical issues. Although anthracyclines are one of the most commonly used induction regimens for children with AML in the United States, clinicians avoid them due to adverse effects and clinical resistance issues. To address this clinical issue, we are looking for a novel AML approach to boost the usage of anthracyclines. Since Bcl-2 protein overexpression in AML is related to uncontrolled growth, poor prognosis, and chemoresistance. Multiple clinical trials have suggested combining venetoclax (a selective Bcl-2 inhibitor) with well-established medicines to boost efficacy and overcome resistance. We suggest that inhibiting Bcl-2 is a feasible strategy for increasing the use of anthracycline medicines. We proposed combining doxorubicin and venetoclax as an alternative approach for AML patients. In a panel of three AML cell lines, Kusami-1, U937, and THP-1, our western blot revealed that Kusami-1 had the highest expression of Bcl-2 proteins. Surprisingly, venetoclax causes Kusami-1 cell death and increases the efficacy of doxorubicin in a dose-dependent manner, suggesting that utilizing a lower clinical standard dose may avoid major adverse effects such as cardiotoxicity. Furthermore, the Annexin V Apoptosis Detection Kit indicated that venetoclax coupled with doxorubicin synergistically promoted total apoptosis in Kusami-1 cells. The combination medication shown promising and synergistic in vitro anti-leukemic action against AML cell lines and represents a potentially viable treatment option for AML patients. Future research will use the combination approach in AML cell lines, as well as in patient samples and in vivo experiments. Citation Format: Osama Aloudat, Omar S. Al Odat, Tulin Budak-Alpdogan, Subash Jonnalagadda, Yong Chen, Manoj Pandey. Venetoclax triggers apoptosis and augments the effectiveness of doxorubicin against acute myeloid leukemia cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7218.

Abstract 4947: Uncovering the molecular basis for clinically relevant sphingolipidomic subtypes in acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) has been extensively studied at the genomic level, resulting in various genomic classifications. Despite the progress, three key challenges remain: 1) a significant proportion of patients lack identified genomic features, 2) a discrepancy exists between genomic risk classification and clinical outcomes, and 3) many mutated targets remain non-druggable. There is an urgent need for an enhanced AML risk classification that goes beyond genomic aberrations to guide effective therapeutics. Recent research, including our own, has increasingly linked AML pathogenesis and therapeutic resistance with dysfunctional sphingolipid metabolism, a family of bioactive molecules crucial for cellular functions. In a recent manuscript, we identified two robust sphingolipidomic clusters in AML, characterized by reciprocal abundances of hexosylceramide (Hex) and sphingomyelin (SM) species (HexloSMhi, HexhiSMlo). These clusters correlate with latent transcriptional states and stratify patient groups in multiple independent datasets such as TCGA, and BeatAML, with the HexloSMhi cluster representing a high-risk subgroup associated with poor clinical outcomes. These findings underscore the role of sphingolipids in refining AML risk assessment and creating avenues for discovery and therapeutic intervention. However, the signaling states driving these sphingolipidomic clusters and the mechanisms elevating risk in the HexloSMhi cluster require further investigation. To identify regulatory genes for the AML subtypes, we constructed gene regulatory networks using differentially expressed genes. Focusing on the high-risk subtype, we identified highly connected genes ranked by connectivity, including KDM1A, GSK3β, LCK, and STAT5A. We found that higher STAT5A abundances in the HexloSMhi subtype, particularly correlated with pro-survival Bcl-xL proteins. Furthermore, we identified STAT5 protein abundance as a key variable associated with drug sensitivity from pharmacological screening with sphingolipid pathway inhibitors and AML therapeutics 30 AML cell lines and patient samples. This is encouraging as STAT5 is druggable as evidenced in the NIH-Pharos druggable genome database, and several small-molecule inhibitors are currently in clinical trials. Analysis of gene expression data suggest that STAT5 inhibition, through genetic or pharmacological means, downregulates cell cycle-related genes and significantly alters sphingolipid gene expression. Recent work by others indicates that sphingolipid-catalyzing enzymes regulate STAT5 activity in leukemias, with ceramides acting as a second messenger in cells. Taken together, this suggests a possibility of a positive feedback loop between sphingolipid homeostasis and activity of STAT5; the details of this interaction require further investigation. Citation Format: B Bishal Paudel, Su-Fern Tan, Johnson Ung, David Claxton, David J. Feith, Thomas P. Loughran, Kevin A. Janes. Uncovering the molecular basis for clinically relevant sphingolipidomic subtypes in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4947.

Abstract 1327: Affinity tuning anti-CD123 chimeric antigen receptor natural killer cell therapy to treat acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) is a highly prevalent blood and bone marrow cancer characterized by the uncontrolled growth of abnormal myeloblasts. Current treatments for AML often result in systemic toxicities for patients, many of whom will still experience relapse. There is thus an unmet need to develop safer and more effective therapies targeting AML. Chimeric antigen receptor (CAR) T cells, which are engineered to express a cancer-targeting extracellular antibody single-chain variable fragment (scFv) linked to an intracellular T cell-activating domain, have shown promise in treating B cell leukemias, but their success has been limited in myeloid leukemias. This is due in part to the lack of AML-specific target antigens. Moreover, impaired T cell function, a hallmark of AML, is also problematic when relying on autologous T cell activation upon reinfusion. We overcame the limitations of CAR T therapy in AML by developing CAR-expressing natural killer (NK) cells targeting CD123. While present on both healthy and AML cells, CD123 is expressed at >10-fold higher levels on malignant cells. Furthermore, use of NK allows use of fully functional allogeneic cells from healthy donors, since NK cells do not induce graft-versus-host-disease. To optimize the tumor cell selectivity of CAR NK cells, we employed the yeast display directed evolution platform to isolate anti-CD123 scFvs with varying affinities and are identifying and characterizing clones that maximize the interaction with CD123high AML cells over healthy CD123low cells, as determined by binding, cytotoxicity, cytokine secretion, and intracellular signaling studies. Collectively, our efforts introduce a new paradigm for engineered cell therapeutics with significant promise for AML treatment. Citation Format: Monika Kizerwetter, Huilin Yang, Ruyan Rahnama, Challice Bonifant, Jamie Spangler. Affinity tuning anti-CD123 chimeric antigen receptor natural killer cell therapy to treat acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1327.

Abstract 7224: Investigation of the efficacy of duocarmycin SA in combination with FDA approved drugs in acute myeloid leukemia cells in vitro

Abstract Acute myeloid leukemia (AML) is a hematological malignancy that is characterized by the arrest of hematopoietic stem cell differentiation, clonal expansion of myeloid hematopoietic precursors and poor patient survival outcomes. Despite therapeutic advancements, the prognosis of AML patients remains poor and improving patient survival outcomes continues to be a challenge. Therefore, the objective of this study was to investigate the efficacy of Duocarmycin SA (DSA- an antitumor antibiotic that induces DNA alkylation) in combination with FDA approved drugs currently used in the treatment of AML. In this study, DSA was evaluated in combination with doxorubicin (an anthracycline that disrupts topoisomerase II mediated DNA repair) or etoposide (a topoisomerase II inhibitor used to treat relapsed/refractory AML) in human AML cells in vitro. We hypothesized that DSA in combination with doxorubicin or etoposide would exhibit synergistic effects by improving the efficacy of both doxorubicin and etoposide in AML cells. The human AML cell lines (Molm-14 and HL60) were used for all studies. The phenotype of the cells was confirmed by flow cytometry and the IC50 of the drugs were determined using the MTT assay. Our results showed that the AML cells were CD45+, CD33+, CD13+ and CD4+. The IC50 of DSA alone for Molm-14 cells and HL60 cells were 11.12 pM and 114.8 pM, respectively. DSA alone induced DNA double-stranded breaks, significantly decreased the production of colonies and significantly increased apoptosis in AML cells in a dose-dependent manner. The IC50 of doxorubicin alone and etoposide alone was 68.6 nM and 129.7 nM, respectively. DSA in combination with the FDA approved AML drugs showed increased cytotoxic efficacy by observable decreases in AML cell viability. In summary, 1) picomolar concentrations of DSA alone was sufficient to significantly reduce AML cell viability; 2) DSA in combination with doxorubicin or etoposide significantly reduced AML cell viability and reduced the IC50 concentration of doxorubicin and etoposide. Thus, highlighting the therapeutic potential of using DSA in combination with doxorubicin or etoposide as a drug combination strategy to improve AML patient survival outcomes by decreasing the concentration of drugs necessary to treat patients and reducing off-target toxicity. Citation Format: William A. Chen, Diego Aguilar, Leena So, Yasmeen Jawhar, Nhi Nguyen, Natalie Drew, Terry G. Williams, Carlos A. Casiano, Sinisa Dovat, Kristopher Boyle, Olivia L. Francis-Boyle. Investigation of the efficacy of duocarmycin SA in combination with FDA approved drugs in acute myeloid leukemia cells in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7224.

Abstract 7227: Isatin analogs potentiate the cytotoxicity of venetoclax in acute myeloid leukemia cells

Abstract Acute Myeloid Leukemia (AML) is a rare but common hematological malignancy in children and adults. AML is a highly heterogeneous disease caused by the acquisition of several mutations affecting multiple cellular processes, thus requiring concomitant targeting of key survival nodes to treat effectively. As current first-line therapies for AML suffer with poor outcomes, drug resistance, and high relapse rates, there is an immediate need for new combinatorial therapies that are both safe and effective. Venetoclax (VEN), a selective inhibitor of antiapoptotic protein B-cell lymphoma-2 (BCL2), has been FDA-approved for treating adult AML and displayed potential in pediatric leukemia treatment. However, the activation of an antiapoptotic BCL2 family member, Myeloid Cell Leukemia 1 (MCL1), is often a primary mechanism of resistance to VEN therapy. Our group has developed Isatin analogs (ISA) that exhibited diverse biological activities, including anti-cancer activities alone or in combination with standard agents. ISA demonstrated anti-leukemic activity by targeting leukemic stem cells (LSCs) with high aldehyde dehydrogenase (ALDH) activity. In this study, we demonstrate ISA induces apoptosis by downregulating antiapoptotic MCL1 levels in pediatric and adult AML cell lines. Based on the inhibitory effects of Isatin analogs on key signaling pathways (PI3K/AKT, STAT3) and MCL1, we combined ISA with a BCL2 inhibitor, VEN, for effective AML treatment. The combination of ISA with VEN exhibited synergetic cytotoxicity in naïve (MOLM-13, MV4-11) and VEN-resistant (HL-60, OCI-AML3, U937, and KG-1) human AML cell lines by bliss analysis. ISA also showed significant synergetic cytotoxicity in combination with ABT-737, a BH3 mimetic inhibitor of Bcl-xL, Bcl-2, and Bcl-w. Combinatorial treatment of AML cell lines with sub-lethal doses of ISA and VEN showed a significant increase in cellular apoptosis as indicated by the levels of annexin V measured by flow cytometry. Immunoblotting analysis after co-treatment with ISA and VEN showed downregulation of MCL1 levels along with alteration of other key apoptosis regulators in both VEN-sensitive (MV4-11) and inherently VEN-resistant (U937) AML cell lines. Current and future studies will primarily focus on further exploiting the molecular mechanism of action for the combinatorial approach. Furthermore, our aim will be to demonstrate activity in primary patient cells along with preclinical efficacy in AML animal models. To summarize, in vitro findings showed synergetic cooperation between ISA and VEN in combination for effective induction of apoptosis and anti-leukemic activity in AML cells that are sensitive and resistant to VEN. Citation Format: Upendarrao Golla, Satyam Patel, Jeremy Hengst, Charyguly Annageldiyev, Joseph Schramm, Shantu Amin, Dhimant Desai, David Claxton, Sinisa Dovat, Arati Sharma. Isatin analogs potentiate the cytotoxicity of venetoclax in acute myeloid leukemia cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7227.

Abstract 7354: Proteogenomic and metabolomic characterization of acute myeloid leukemia

Abstract Acute myeloid leukemia (AML) is a blood malignancy of poor prognosis with marked heterogeneity. To elucidate the underlying mechanisms that drive AML as part of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) effort, we performed comprehensive genomics, transcriptomics, proteomics including multiple post-translational modifications (phosphorylation, acetylation, and glycosylation), metabolomics, and lipidomics characterization of 173 treatment-naïve AML patients. Applying the similarity network fusion method on both transcriptomics and proteomics data, we identified 8 proteogenomic clusters. These clusters recapitulate specific recurrent mutations and established clinical subtypes available within the cohort. We used single-cell RNAseq data as a reference to perform immune component analysis for collected bulk samples. The result reveals that our proteogenomic clustering also captures the variations of AML differentiation hierarchies including CD14+ monocyte-like and GMP-like AML. To assess the complex disease nature of AML, we performed functional analysis for each cluster to reveal interplay between multiple genomic aberrations such as NPM1, FLT3-ITD, DNMT3A mutations, complex chromosomal alterations, and the leukemia cell differentiation. Importantly, the multi-omics analysis performed not only connects previously identified molecular drivers and cell differentiation variations within AML, but also links them with observed cancer metabolomic reprogramming with their drug response implications. Moreover, our study also identified site-specific post-translational modifications previously not known in AML, highlighting the valuable insights and clinical relevance of these newly identified clusters. Citation Format: Alec Chu, Yi Hsiao, Yamei Deng, Chenwei Wang, Jennifer Kyle, Yongchao Dou, James C. Pino, Camilo Posso, Leanne Henry, Lijun Chen, Ginny Xiaohe Li, Tung-Shing Mamie Lih, Yifat Geffen, Fengchao Yu, Li Ding, Gil Omenn, Chandan Kumar, Saravana M. Dhanasekaran, Elie Traer, Jeffrey W. Tyner, Hui Zhang, Tao Liu, Sara Gosline, Bing Zhang, Arul Chinnaiyan, Alexey I. Nesvizhskii, Marcin Cieslik, The CPTAC Consortium. Proteogenomic and metabolomic characterization of acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7354.

Abstract 4664: Therapeutic targeting of TP53-mutated acute myeloid leukemia by inhibiting cell cycle checkpoint

Abstract Acute myeloid leukemia (AML) is a hematological malignancy characterized by various somatic mutations leading to abnormal proliferation and differentiation of hematopoietic cells. Mutations on the TP53 gene occur in 5% to 10% of patients with de novo AML, with higher frequency in patients with relapsed and refractory (R/R) AML. Patients with TP53-mutated AML typically exhibit a poor response to conventional induction therapy and have a short overall survival (OS) rate, with a median duration of 5-9 months. Although various target agents have been developed for the treatment of AML, treatment options for TP53-mutated AML remain limited. Here, we have discovered a novel drug combination that can enhance the efficacy of the conventional therapeutic regimen for TP53-mutated AML patients. For in vitro analysis, we used the human AML cell line Kasumi-1(AML-M2), which harbors a homozygous TP53 R248Q mutation. We treated kasumi-1 cells with a combination of cytarabine and Idarubicin to produce drug tolerant persisters (DTPs) which is a minor population that survived the drug treatment. The Kasumi-1 DTPs displayed temporal G2/M phase cell cycle arrest and significant resistance to further repeated drug treatment. To discover drug candidates targeting TP53-mutated DTPs, we first examined the differentially expressed genes (DEGs) of TP53-mutated AML patients using patients’ RNA expression data deposited in the cancer genome atlas (TCGA) database. Using selected DEGs, drug candidates potentially affecting TP53-mutated AML cells were extracted from the connectivity map (CMap build 02) database. In addition, through a literature search, drugs with the ability to reactivate mutant p53, drugs that directly target mutant p53, synthetic lethal partners with mutant p53, and drugs that target leukemia stem cells were selected as candidate groups. As a result, we selected 46 drug candidates that would be effective for TP53-mutated AML through in silico analysis and therapy strategies targeting p53. Using in vitro cytotoxicity assay, we screened 46 candidate compounds at multiple doses and confirmed several drugs that effectively eliminate DTPs. The drug screening showed that cell cycle checkpoint inhibitors not only resulted in a significant reduction of G2/M phase arrested cells but also induction of apoptotic cells at the subG1 phase. Furthermore, the zero interaction potency (ZIP) model of SynergyFinder (https://synergyfinder.fimm.fi) analysis showed that cell cycle checkpoint inhibitors synergistically enhanced the cytotoxic effect of cytarabine on Kasumi-1 DTPs. Collectively, this study suggests that novel combination treatment of cell cycle checkpoint inhibitors with conventional drugs selectively inhibits TP53-mutated AML DTPs. Citation Format: Daehyeon Gwak, Dongchan Kim, Heejun Jang, Jun Liu, Suji Min, Ja Min Byun, Youngil Koh, Junshik Hong, Sung-soo Yoon, Dong-Yeop Shin, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea, Republic of. Therapeutic targeting of TP53-mutated acute myeloid leukemia by inhibiting cell cycle checkpoint [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4664.

Abstract 5228: Engineering CD123-targeting vδ1-enriched γδT cells with enhanced preclinical efficacy and safety profile

Abstract Acute myeloid leukemia (AML) is an aggressive hematological malignancy that, despite advances in treatment, has an overall 5-year survival rate of less than 30%. There is an urgent unmet need for new and effective therapies for AML. Chimeric antigen receptor (CAR)-modified cell therapies are emerging as promising options. However, the selection of suitable antigens is challenging, due to the heterogeneous expression of potential antigen targets in AML. Most antigens, such as CD123, are expressed on both leukemic cells and normal hematopoietic stem and progenitor cells. In addition, conventional autologous or allogeneic T cell therapies present many limitations, such as cytokine release syndrome (CRS) and graft-vs-host disease (GvHD). We therefore evaluated CD123-targeting CAR designs in vδ1-enriched γδT cells, an innate immune cell platform that is inherently non-MHC restricted, has low risks of CRS and GvHD, and is capable of discriminating between malignant and healthy cells in preclinical models. We engineered vδ1-enriched γδT cells from peripheral blood of healthy individuals to express various CD123-targeting CAR constructs. The CD123-targeting CAR-engineered vδ1-enriched γδT cells expressed high levels of natural cytotoxicity receptors, suggesting capability to target innate receptor ligands on AML cell surface. CD123-targeting CAR-expressing vδ1-enriched γδT cells demonstrated enhanced cytotoxicity in vitro against multiple AML cell lines, in both short-term co-culture and repeated antigen stimulation assays. CD123-targeting CAR-expressing vδ1-enriched γδT cells also showed enhanced efficacy and survival in vivo against mouse models of human AML. Interestingly, attenuation of CAR activity via novel designs preserved the inherent selectivity of vδ1-enriched γδT cells against AML cells relative to normal hematopoietic stem or progenitor cells, which also express CD123. Together, our results demonstrated through rational CAR designing and engineering in vδ1-enriched γδT cells, an allogeneic cell therapy targeting CD123 can be generated with selective cytotoxicity against AML cells while sparing normal hematopoietic stem cells. Such product designs have the potential to be a transformative therapeutic option for a broad population of AML patients. Citation Format: Mei Rosa Ng, Sarah L. Hayward, Di Zhang, Gary Gu, Bri Paulhus, Donjeta Gjuka, Collin Crowley, Sophie McLaughlin, Anya Lublinsky, Angel Mathew, Evans Berreondo Giron, Doanh Mai, Madisen Lee, Megha Wal, Rebecca Alade, Andre Simoes, Robin Lytle, James Gavin, Shira Cramer, Zhong-hua Yan, Taylor Hickman, Rashmi Choudhary, Cori Abikoff, Yana Wang, Istvan Kovacs, Nandhu M. Sobhana, Lan Cao. Engineering CD123-targeting vδ1-enriched γδT cells with enhanced preclinical efficacy and safety profile [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5228.

Abstract 479: Enhanced payload delivery for acute myeloid leukemia treatment through CD37-targeting DNA nanobots

Abstract Acute Myeloid Leukemia (AML) treatment faces considerable challenges, in particular the delivery of therapeutics with sufficient potency and specificity. Traditional Antibody-Drug Conjugates (ADCs) offer a strategic approach to cancer therapy by combining the targeting capabilities of monoclonal antibodies with the cell-killing effect of cytotoxic drugs. However, the limitations in drug-to-antibody ratio (DAR) and the challenges in controlling the release kinetics have often hindered their therapeutic window suggesting novel approaches are necessary. Our approach integrates DNA nanobot technology to facilitate targeted delivery of anthracycline agents directly to CD37-expressing leukemic cells. CD37, a tetraspanin superfamily antigen, has shown promise as a target for AML due to its selective expression on immune cells and favorable internalization properties. By harnessing DNA origami assembly techniques, we developed a customizable platform capable of accommodating a significantly higher payload of chemotherapeutic agents than traditional ADCs. This increased payload potential, paired with the precision targeting of CD37, presents a potent therapeutic strategy with the possibility of reduced systemic toxicity. Here we present preclinical evidence demonstrating targeted delivery of our DNA nanobot drug delivery device and anthracycline payload to CD37+ AML target cells in vitro. In addition, we show targeted efficacy in vitro and in vivo of our anthracycline-loaded DNA nanobot-enabled delivery system, which significantly outperformed free anthracycline in AML target cells. Collectively, our findings suggest an improvement in the therapeutic index of anthracycline and antimitotic agents as well as the ability to combine multiple drug pathways in a single delivery device. The implications of this work extend beyond AML, offering a versatile platform that could revolutionize ADC chemistry and targeted drug delivery. We propose that our DNA nanobot delivery system signifies a pivotal advancement in the field of targeted cancer therapy, with the potential to overcome longstanding barriers in the treatment of AML and potentially other malignancies. Citation Format: Nicholas Vantangoli, Patrick D. Halley, Jeffrey R. Spitzner, John C. Byrd, Karilyn T. Larkin, Carlos E. Castro, Christopher R. Lucas. Enhanced payload delivery for acute myeloid leukemia treatment through CD37-targeting DNA nanobots [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 479.

Abstract 2262: Genomic profiling of leukemic cell lines, responders vs. non-responders to Narazaciclib (HX301 or ON123300), a novel kinase inhibitor with activity against CSF1R and FLT3

Abstract Acute myeloid leukemia (AML) is an aggressive myeloid leukemia with global annual mortality ~150,000. While standard of care (SOC) of the 1st -line treatment being mainly induction chemotherapy, available targeted therapies cover rather limited patients carrying specific driver mutations (IDH mutations and FLT3-ITR). We previously reported a novel kinase inhibitor, Narazaciclib with strong anti-CSF1R activity (IC50 0.7nM) as well as anti-FLT3 (IC50 7nM), and also thus anti-AML activity for certain AML experimental models, as shown in vitro and in vivo (AACR Annual Meeeting, 2023). In the present study, we assessed the impact of HX301 on the in vitro proliferations of a panel of leukemic cell lines (n = 54), including a panel of AML cell lines (n = 33), that have been parallelly genomic-profiled by whole-exome sequencing and whole-transcriptome sequencing. We then set out to analyze the proliferation data and the genomic data, in attempt to elucidate genes and pathways that may be associated with the treatment responses. The biomarker analysis has been performed on gene expression, mutation and copy number variation levels, and the data been presented using common methodologies, including principal component analysis, differential expression analysis, correlation analysis, Gene Ontology enrichment analysis, gene set variation analysis, somatic gene mutation analysis, and copy number variation analysis, etc. Some of the observations have been made: 1) differential expression analysis on all leukemic cell lines shows that 254 genes have been positively associated with the responders; while expression of 191 genes are negatively correlated with AUC, i.e. positively associated with response, as revealed by Spearman correlation analysis; 2) Gene Ontology enrichment analysis revealed these response related genes are mostly involved in myeloid leukocyte activation and defense response; 3) all FLT3-ITD AML lines are responders, presumably due to the FLT3i activity of HX301; 4) CSF1R expression levels seem not correlated to drug responses; 5) pathway analysis on non FLT3-ITD AML lines reveals that STAT5 activation downstream of FLT3 signaling, IL7 pathway and NFKB pathway are significantly associated with better response. Finally, we are also attempted to use statistics learning to reveal genes, as a potential predictive biomarker, that may be correlated to drug response. Citation Format: Jia Xue, Tao Yang, Hang Ke, Sheng Guos, Henry Qixiang Li. Genomic profiling of leukemic cell lines, responders vs. non-responders to Narazaciclib (HX301 or ON123300), a novel kinase inhibitor with activity against CSF1R and FLT3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2262.

Abstract 272: Novel role for eIF4E in homing of acute myeloid leukemia cells

Abstract Acute myeloid leukemia (AML) remains with dismal outcomes, mostly attributed to the inability of therapies to eliminate leukemia stem cells (LSCs) leading to relapse. LSCs home to the bone marrow (BM) niche where they maintain their quiescence state once in contact with mesenchymal stromal cells (MSCs). Therefore, understanding what controls AML-niche interactions could lead to therapeutic approaches that can prevent relapse. First, we implemented a novel 3D in vitro system to mimic human AML-niche interactions. This 3D structure consists of a spheroid formed with BM-MSCs (HS5 cell line), recreating a hypoxic microenvironment. When AML cells (MM6 cell line) are added to the spheroid in a 1:1 proportion, AML cells migrate to the spheroid. After 24 hours, 0.18% of the AML cells home/colonize the spheroid (n=8). Next, we assessed the cell cycle status of AML cells in co-culture with the spheroid and compare to those in liquid culture or placed on a MSC monolayer (2D). We found that cells upon contact with MSCs increased their quiescence, 18.63% G0 in 2D and significantly higher in 3D conditions (25.03%; p=0.0048). It is also important to point out that colonizing cells have a lower proliferate capacity than non-colonizing cells after 7 days of co-culture (p=0.0286). This quiescence feature suggests a stem-like behavior of cells homing to the spheroid. Eukaryotic translation initiation factor 4E (eIF4E) has been found altered in AML. While the capacity of eIF4E to increase cell migration and growth has been shown in solid cancers, the mechanism of eIF4E to accelerate AML progression remains unknown. Thus, we hypothesized that eIF4E may play a role in homing of AML cells to the niche. To this end, we used CRISPR to deplete eIF4E in MM6 cells and found that CRISPR 4E cells have significantly decreased homing capacity to the spheroid compared with control cells (p=0.0065). Importantly, we found a lower percentage of CRISPR 4E cells underwent quiescence after co-culture with MSCs (2D or 3D) (p<0.0001). We corroborated observations using xenograft mice. After 20 hours of intravenous injection, we observed a higher percentage of AML cells in the blood of the mice injected with CRISPR 4E cells compared with control cells (p=0.0286), suggesting that CRISPR 4E cells are not able to effectively exit from peripheral blood to home to their niche. Altogether, we stablished a novel in vitro 3D model that mimics stem cell features of the AML-BM niche. We demonstrated that the depletion of eIF4E in AML cells decreases their homing and prevents them from acquiring niche-induced quiescence. Citation Format: Leandro M. Martinez, Eloisi Caldas Lopes, Mayumi Sugita, Jadwiga Gasiorek, Kata Alilovic, Katherine L. Borden, Monica L. Guzman. Novel role for eIF4E in homing of acute myeloid leukemia cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 272.

Abstract 3115: Systematic analysis of gene mutations and therapeutic efficacy via ex vivo hematological vitroscreen platform

Abstract Acute myeloid leukemia (AML) is a common hematological malignancy found in adult patients, and FMS-like tyrosine kinase 3 gene (FLT3) mutation occurs in about 30% of patients. In 2019, a phase 3 clinical trial suggested that gilteritinib treatment resulted in significantly longer survival than salvage chemotherapy in relapsed or refractory FLT3-mutated AML patients. Targeting FLT3-mutants in AML has become one of the important therapeutic strategies in this decade. The ex vivo hematological VitroScreen platform provides a powerful tool to evaluate the performance of FLT3 inhibitors and other test articles. With Champions Oncology’s primary hematological repository (https://www.championsoncology.com/hematological-vitroscreen) and proprietary LUMIN Bioinformatics platform, we classified models based on patient responses, clinical annotation, NGS data, and cell surface markers. In this Ex vivo study, we tested gilteritinib in 30 AML patients, and 8 of models were identified as FLT-3 mutants’ carrier. Fold changes of cell viability after gilteritinib treatment were assessed based on quantitation of the ATP present. FLT3-mutants models showed significantly higher sensitivity to gilteritinib than FLT3-WT models (IC50, 132.56 nM vs. 234.16nM) in a 6-day assay. Only 25% of models in the FLT3-mutants group had higher IC50 than the average of all AML models (n=28, IC50 = 204.05 nM), compared to 53% in the FLT3-WT group. Our preclinical data highly match the observations in previous clinical trials, which suggest that VitroScreen is a reliable high throughput tool for drug development of drug resistant cancers. Citation Format: Fu-Ju Chou, Stefano Cairo, Mara Gilardi, Abhay Andar, Karin Abarca-Heidemann, Maria Mancini. Systematic analysis of gene mutations and therapeutic efficacy via ex vivo hematological vitroscreen platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3115.

Abstract 4413: Identifying genome-wide histone profiles in patient derived models of AML for predictive biomarker development

Abstract Acute myeloid leukemia (AML) is a complex disease with highly individualized treatment plans for patients. Mostly these are based on genetic and phenotypic markers of the disease, but the patient’s overall condition is playing a significant role as well. To develop innovative drugs for a broad patient cohort, it is essential to understand the biological implications of these differences and to model them preclinically. In this study, we are assessing the utility of EpiCypher’s CUT&Tag-FFPE platform to characterize the epigenome of AML PDX samples. CUT&Tag-FFPE is an epigenome profiling assay that is compatible with Formalin-Fixed Paraffin-Embedded (FFPE) samples, enabling robust genome-wide profiling of histone modifications from limited clinical samples. We derived PDX model LEXFAM 2799 (NPM1 wt; FLT3 wt, t(8;21)) and LEXFAM 2966 (NPM1 mut; FLT3 wt) from treatment naïve patients and established in immunocompromised NSG mice. LEXFAM 2799 is a fast-growing model with passaging times of 33 days, whereas LEXFAM 2966 displays a passaging time of 140 days. We next treated with Standard of Care (SoC) agents Decitabine, Cytarabine and all-trans-retinoic acid (ATRA): LEXF 2966 was highly sensitive towards Decitabine leading to complete remission. Cytarabine induced a partial remission and ATRA had only minor effect on tumor growth. In contrast LEXFAM 2799 was resistant towards treatment with ATRA and showed only partial remission under treatment with Cytarabine or Decitabine. Using the CUT&Tag-FFPE platform we are analyzing FFPE slides from the above mentioned two AML PDX models to investigate differences in the genome-wide histone profile that relate to the different growth behavior as well as sensitivity towards SoC treatment. The goal of these studies is to identify tumor model specific profiles that correlated specifically with the sensitivity towards the hypomethylating agent Decitabine. In addition, we plan to analyze additional untreated as well as treated AML PD models to validate the identified signatures confirming them as predictive biomarkers for sensitivity towards current standard of care and prospectively as well innovative compounds. Citation Format: Alysha Simmons, Eva Oswald, Georg Kuales, Michael Keogh, Vishnu U. Kumary, Eva Brill, Martis W. Cowles, Bryan Venters, Julia B. Schueler. Identifying genome-wide histone profiles in patient derived models of AML for predictive biomarker development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4413.