Human Acute Lymphoblastic Leukemia Cells Research Articles

Development and evaluation of novel artemisinin-isatin hybrids with potential anti-leukemic cytotoxicity.

Twenty-one novel ester tethered artemisinin-isatin hybrids were designed, synthesized and screened against human myeloid leukemia cell lines (K562 and K562/ADR), human acute lymphoblastic leukemia cell line (CCRF-CEM) as well as normal human peripheral blood mononuclear cells (PBMCs) for their cytotoxicity by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The structure-activity relationships (SARs) were also discussed to facilitate further rational design of more effective candidates. The preliminary results showed that most of the ester tethered artemisinin-isatin hybrids (IC50: 0.32-29.35 µM) exhibited promising activity against CCRF-CEM cells, and some of them (IC50: 1.23-49.84 µM) were also active against K562 and K562/ADR human myeloid leukemia cell lines. Among them, hybrid 7d (IC50: 0.32, 2.67 and 1.23 µM) not only possessed profound activity against the three tested leukemia cell lines and excellent safety and selectivity profiles, but also showed promising pharmacokinetic properties. Accordingly, hybrid 7d could be considered as a potential lead molecule for the development of novel anti-leukemic agents with minimal untoward events to normal human cells.

Epigenetic Fine Mapping and Functional Dissection of Inherited Non-Coding Variation Impacting the Pharmacogenomics of Acute Lymphoblastic Leukemia Treatment

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer. Despite cure rates exceeding 90%, relapsed ALL is the 5th most common pediatric cancer. Although chemotherapeutic drug resistance remains the primary cause of treatment failure and relapse, it remains unclear to what extent non-coding inherited DNA sequence variants impact gene regulatory programs that contribute to differences in chemotherapeutic drug resistance and clinical outcome in childhood ALL. To address this knowledge gap we performed epigenetic fine mapping on inherited non-coding DNA sequence variants associated with ex vivo resistance to six antileukemic agents (dexamethasone, prednisolone, l-asparaginase, vincristine, 6-mercaptopurine and 6-thioguanine) in primary ALL cells from pediatric patients and inherited non-coding DNA sequence variants associated with clinical outcome (persistence of minimal residual disease and relapse) in pediatric patient cohorts using chromatin accessibility data from over 130 primary ALL cells, ALL cell lines and ALL xenografts. This analysis fine mapped over 1700 variants (sentinel variants and variants in high linkage disequilibrium; r2>0.8) to cis-regulatory elements in the ALL genome. To comprehensively dissect the functional effects of these fine mapped variants on gene regulatory activity we performed massively parallel reporter assays (MPRAs) in 10 human ALL cell lines of both B- and T-cell lineages. MPRAs utilized 23 DNA barcodes per variant allele and tested variants at bidirectional promoters using both sequence orientations. In total, 98,168 oligonucleotides each containing 175-bp of genomic sequence centered on each variant allele and a unique 10-bp barcode sequence were evaluated for gene regulatory activity. MPRA identified 558 variants with significant and concordant allele-specific activities in three or more ALL cell lines. Expression quantitative trait loci (eQTL) mapping and HiChIP three-dimensional promoter loop profiling identified candidate target genes for a subset of functional variants. We additionally evaluated the functional effects of top ranked variants using luciferase reporter assays and CRISPR/Cas9 genome editing. These variants were associated with the expression of B3GNT5, CACUL1, HERC1, KDM4C and VRK3. Notably, two of these functional variants (rs10411204 and rs1247117) impacted transcription factor (TF) consensus DNA motifs for AP-1 family TFs and PU.1. Collectively, these data suggest that many inherited non-coding variants associated with pharmacogenomic traits in childhood ALL have significant gene regulatory effects. Importantly, the identification of chemotherapeutic drug resistance-associated molecular pathways perturbed by inherited non-coding variants can improve our ability to circumvent drug resistance with novel therapeutic approaches.

Genetic and Epigenetic Cis-Regulatory Disruptions Impacting the Canonical Wnt Signaling Repressor TLE1 Gene Promote Glucocorticoid Resistance in Childhood Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer and despite improved survival rates, more children die of ALL than any other cancer. Glucocorticoids (GCs) are a mainstay of contemporary, multi-drug chemotherapy in the treatment of childhood ALL. Resistance to GCs is predictive of ALL relapse and poor clinical outcomes, and therefore represents a major hurdle limiting further improvements in survival rates. While advances have been made in identifying genes implicated in GC resistance, there remains an insufficient understanding of the impact of cis-regulatory disruptions in GC resistance. This is particularly relevant for GCs, which function through the activation of the glucocorticoid receptor (GR) nuclear receptor transcription factor. To better understand the role of cis-regulatory disruptions in GC resistance we comprehensively mapped the dynamic gene regulatory response to GCs in two human ALL cell lines using functional genomic (RNA-seq, ChIP-seq, ATAC-seq and HiChIP) and massively parallel reporter (ATAC-STARR-seq) assays at multiple time points within a 24-hour window. In total, over 100 independent datasets were generated and integrated. We identified thousands of GR binding sites and GC-responsive changes to chromatin state, including the formation of over 250 GC-responsive super-enhancers and depletion of AP-1 bound cis-regulatory elements implicated in cell proliferation and anti-apoptotic processes. Our results further show that GR mediates gene regulatory effects in ALL cells at GC-responsive chromatin sites through long-range looping interactions with GC-responsive gene promoters. Notably, GC-responsive chromatin sites were also enriched for functionally active cis-regulatory elements. By integrating our GC response maps with inherited DNA sequence variants and differentially accessible chromatin sites associated with GC resistance in primary ALL cells from patients enrolled on St. Jude clinical trials, we identified two GR-bound cis-regulatory elements at the canonical Wnt signaling repressor TLE1 gene locus that were genetically or epigenetically disrupted in GC-resistant patient samples. Functional evaluation of these two GR binding sites using CRISPR genome or CRISPR interference epigenome editing validated their impact on GC resistance and TLE1 gene expression. To better understand the relationship between GC signaling and canonical Wnt signaling, we further performed TOP-flash luciferase reporter assays, cellular drug viability assays and transcriptomic drug response profiling which identified mutual antagonism between these two signaling pathways. Collectively, these data uncovered genetic and epigenetic cis-regulatory disruptions of canonical Wnt signaling as a novel mechanism impacting GC resistance in childhood ALL and further suggest that therapeutic inhibition of canonical Wnt signaling could improve GC sensitivity in patients with resistant disease.

Polymeric CXCR4 Inhibitors Exhibit Novel Anti-Leukemic Effects

Acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) are common leukemias with a mortality rate estimated to be greater than 50%. This dismal outcome is in part due to current therapeutics. Intensive remission therapy is difficult for patients to tolerate and despite good complete remission rates, is not curative for all patients. In relapse/refractory status, there are even fewer effective therapeutics. There is a strong need for more effective, less toxic therapeutics. The surface receptor CXCR4 has become a recent target of interest, as it is highly expressed on leukemia cells and, via its canonical ligand CXCL12, enables cells to evade chemotherapeutics by localizing them to the protective bone marrow niche. The small molecule inhibitor AMD3100 (plerixafor) disrupts this localization by blocking the CXCL12:CXCR4 interaction and is being investigated for its ability to mobilize leukemia cells to the peripheral blood. Thus, AMD3100 acts as a chemosensitizer, but by itself, AMD3100 does not have anti-leukemic effects. It has been recently shown that CXCR4 has additional non-canonical activities outside of CXCL12 that are vital for leukemia survival and maintenance. Genetic knock out of Cxcr4 in an AML model decreases survival and increases differentiation in a CXCL12 independent manner. This implies that CXCR4 has previously unrecognized activities in leukemia and that inhibitors capable of blocking both CXCR4's canonical and non-canonical activities would more effective therapeutics. We developed a class of polymeric CXCR4 inhibitors (PAMDs) via Michael-type addition of AMD3100 and focused on one analog PAMD-Ch17, which contains additional cholesterol modifications. PAMD-Ch17 was originally designed to delivery siRNAs, but we surprisingly found it had anti-leukemic effects on its own. PAMD-Ch17, but not AMD3100, induces cytotoxicity and promotes differentiation of mouse AML cells in vitro. In colony assays, treatment with PAMD-Ch17 causes a statistically significant decrease in leukemia colony growth while treatment with AMD3100 was indistinguishable from the control. Across a panel of seven human AML and ALL cell lines, PAMD-Ch17 inhibited metabolic activity, a proxy for viability, at the nanomolar doses whereas AMD3100 had no effect even at the highest micromolar dose. As we predict that PAMD-Ch17 is acting through CXCR4, we compared cell surface expression of the receptor to PAMD-Ch17 sensitivity for each cell line. We found that PAMD-Ch17 IC50 was moderately negatively correlated with CXCR4 expression (r= -0.69), suggesting PAMD-CH17 mediates at least some of its effects through CXCR4. To further address the mechanisms of PAMD-Ch17's activity, we cultured Jurkat T-ALL cells with AMD3100 or PAMD-Ch17 at the same dose for 24 hours and stained using the 12G5 CXCR4 monoclonal antibody, which is known to compete with AMD3100 and CXC12. We found that AMD3100 caused a statistically significant decrease in 12G5 staining as compared to control treated cells, but PAMD-Ch17 induced a complete loss of 12G5 staining that was statistically significant as compared to both control and AMD3100 treated cells. PAMD-Ch17, but not AMD3100, also caused a moderate, but significantly decrease in staining with another antibody against the N-terminus of CXCR4, a region not predicted to be affected by AMD3100 or CXCL12. These results indicate that PAMD-Ch17 more effectively blocks the epitope recognized by the 12G5 antibody but may also interact other domains of CXCR4 or decrease its cell surface expression. We also developed a line of PAMD-CH17 resistant Jurkat cells. The resistant cells have an IC50 of at least 2-fold greater than naïve Jurkat cells. Interestingly, the resistant cells are not recognized by the 12G5 monoclonal antibody but are stained by the N-terminus antibody. These results imply that the CXCR4 expressed on resistant cells has an altered conformation that may less effectively bind PAMD-Ch17. Collectively, these data suggest that PAMD-Ch17 more effectively inhibits CXCR4 leading to its novel anti-leukemic effects and support the development of PAMDs for the treatment of leukemia.

Novel bioactive hybrid Celecoxib-HDAC Inhibitor, induces apoptosis in human acute lymphoblastic leukemia cells

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. Here, we exploited the synergy between histone deacetylase inhibitors (HDACi) and cyclooxygenase 2 (COX-2) inhibitors by generating and testing a series of hybrid Celecoxib-HDAC inhibitors (selenium-containing analogues of Celecoxib) on ALL cells, of which compound 11 exhibited significant inducement to kill NALM6 cells with an average IC50 of 9.95 ± 0.44 μM compared with control Celecoxib at 28.58 ± 1.44 μM and inhibited NALM6 cells growth via the inhibition of the cell cycle in G2 phase. Furthermore, compound 11 induced apoptosis by activating PARP cleavage. Taken together, compound 11 possessed the potential to be developed further as a chemotherapeutic agent for ALL.

Amelioration of human acute lymphoblastic leukemia (ALL) cells by ZnO-TiO2-Chitosan-Amygdalin nanocomposites

The present study aims to study the cytotoxicity of ZnO-TiO 2 -Chitosan-Amygdalin nanocomposites (ZnO-TiO 2 -Chitosan-Amygdalin) on T lymphoblast cancer cells (MOLT-4). In a study, nanocomposites containing 2.5 to 15 µg/ml MTT were screened for their anticancer activity. Its anticancer properties were significantly higher than those of other nanocomposites with an IC 50 value of 10.34 µg/ml. We studied the mechanism of action for cytotoxic cell death by fluorescence microscopy using Acridine Orange/EtBr (AO/EtBr) and Rhodamine 123 staining procedures. Using DCFH-DA, ZnO-TiO 2 -Chitosan-Amygdalin nanocomposites were analyzed to determine ROS production. The change in apoptotic protein expression for the 24 h following treatment with MOLT-4 cells for Caspase-3, 8, and 9. Nanocomposites containing ZnO-TiO 2 -Chitosan-Amygdalin increased the number of early and late apoptotic cells in MOLT-4 cells. ZnO-TiO 2 -Chitosan-Amygdalin nanocomposites also enhanced mitochondrial apoptosis through Caspase cascade signaling. MOLT-4 cells phosphorylated Caspase cascade in response to ZnO-TiO 2 -Chitosan-Amygdalin nanocomposites. Compared to the control group, the cancer cells treated with ZnO-TiO 2 -Chitosan-Amygdalin nanocomposites significantly arrest the proliferation and induces cleavage of pro-apoptotic proteins which leads to apoptotic cell death. Accordingly, ZnO-TiO 2 -Chitosan-Amygdalin nanocomposites might be effective against T lymphoblast cancer.

Integrating Activity-Guided Strategy and Fingerprint Analysis to Target Potent Cytotoxic Brefeldin A from a Fungal Library of the Medicinal Mangrove Acanthus ilicifolius.

Mangrove-associated fungi are rich sources of novel and bioactive compounds. A total of 102 fungal strains were isolated from the medicinal mangrove Acanthus ilicifolius collected from the South China Sea. Eighty-four independent culturable isolates were identified using a combination of morphological characteristics and internal transcribed spacer (ITS) sequence analyses, of which thirty-seven strains were selected for phylogenetic analysis. The identified fungi belonged to 22 genera within seven taxonomic orders of one phyla, of which four genera Verticillium, Neocosmospora, Valsa, and Pyrenochaeta were first isolated from mangroves. The cytotoxic activity of organic extracts from 55 identified fungi was evaluated against human lung cancer cell lines (A-549), human cervical carcinoma cell lines (HeLa), human hepatoma cells (HepG2), and human acute lymphoblastic leukemia cell lines (Jurkat). The crude extracts of 31 fungi (56.4%) displayed strong cytotoxicity at the concentration of 50 μg/mL. Furthermore, the fungus Penicillium sp. (HS-N-27) still showed strong cytotoxic activity at the concentration of 25 µg/mL. Integrating cytotoxic activity-guided strategy and fingerprint analysis, a well-known natural Golgi-disruptor and Arf-GEFs inhibitor, brefeldin A, was isolated from the target active strain HS-N-27. It displayed potential activity against A549, HeLa and HepG2 cell lines with the IC50 values of 101.2, 171.9 and 239.1 nM, respectively. Therefore, combining activity-guided strategy with fingerprint analysis as a discovery tool will be implemented as a systematic strategy for quick discovery of active compounds.

Fut7 Promotes Adhesion and Invasion of Acute Lymphoblastic Leukemia Cells through the Integrin/Fak/Akt Pathway.

Purpose To investigate the role and mechanism of N-fucosyltransferase VII (FUT7) in acute lymphoblastic leukemia (ALL). Methods Bone marrow tissues were collected from patients with ALL and children with immune thrombocytopenic purpura (control) hospitalized in our hospital during the same period. Then, the FUT7 expression in bone marrow tissues was detected by qRT-PCR and western blotting. Human ALL cell strain Jurkat was cultured, and after knockdown or overexpression of FUT7, cell proliferation, apoptosis, adhesion and invasion were examined by MTT assay, flow cytometry, fibronectin adhesion assay and transwell, respectively; the protein expression level of integrin α5, integrin β1, p-FAK, and p-AKT was tested by western blotting. Results The FUT7 expression was up-regulated in bone marrow cells of ALL patients. After knockdown of FUT7, the proliferation, adhesion and migration ability of ALL cells were significantly reduced, and apoptosis was increased, while the overexpression of FUT7 obtained the opposite results. Moreover, the overexpression of FUT7 also promoted the protein expression of integrin α5, integrin β1, p-FAK, p-AKT. Conclusion FUT7 can promote the adhesion and invasion of ALL cells by activating the integrin/FAK/AKT pathway.

Effective RNAi in leukemia cells is enhanced by spermine-modified pullulan combined with desloratadine

RNA interference is a very useful tool for clinical treatment as well as mechanistic studies of leukemia. However, leukemia cells are known as hard-to-transfected by non-virus carriers. The low capacity of endocytosis and lysosomal escape of synthetic carriers are two obstacles for successful RNAi in leukemia cells. In this work, we established a universal powerful strategy for mediating effective RNAi in different types of leukemia cells by sequentially using spermine-modified pullulan (PS) as siRNA carrier and desloratadine (DL) to promote the lysosomal escape. It was shown that the complex of PS and siRNA could be largely internalized by human T-cell acute lymphoblastic leukemia cells, acute myeloid leukemia cells and chronic myeloid leukemia cells in serum-containing media, and the internalized complex was able to escape from the lysosomes by the aid of DL, resulting in effective RNAi against the key genes for the different leukemia cells.

The Cooperative Anti-Neoplastic Activity of Polyphenolic Phytochemicals on Human T-Cell Acute Lymphoblastic Leukemia Cell Line MOLT-4 In Vitro.

Acute lymphoblastic leukemia (ALL) is the most common hematological malignancy affecting pediatric patients. ALL treatment regimens with cytostatics manifest substantial toxicity and have reached the maximum of well-tolerated doses. One potential approach for improving treatment efficiency could be supplementation of the current regimen with naturally occurring phytochemicals with anti-cancer properties. Nutraceuticals such as quercetin, curcumin, resveratrol, and genistein have been studied in anti-cancer therapy, but their application is limited by their low bioavailability. However, their cooperative activity could potentially increase their efficiency at low, bioavailable doses. We studied their cooperative effect on the viability of a human ALL MOLT-4 cell line in vitro at the concentration considered to be in the bioavailable range in vivo. To analyze their potential side effect on the viability of non-tumor cells, we evaluated their toxicity on a normal human foreskin fibroblast cell line (BJ). In both cell lines, we also measured specific indicators of cell death, changes in cell membrane permeability (CMP), and mitochondrial membrane potential (MMP). Even at a low bioavailable concentration, genistein and curcumin decreased MOLT-4 viability, and their combination had a significant interactive effect. While resveratrol and quercetin did not affect MOLT-4 viability, together they enhanced the effect of the genistein/curcumin mix, significantly inhibiting MOLT-4 population growth in vitro. Moreover, the analyzed phytochemicals and their combinations did not affect the BJ cell line. In both cell lines, they induced a decrease in MMP and correlating CMP changes, but in non-tumor cells, both metabolic activity and cell membrane continuity were restored in time. (4) Conclusions: The results indicate that the interactive activity of analyzed phytochemicals can induce an anti-cancer effect on ALL cells without a significant effect on non-tumor cells. It implies that the application of the combinations of phytochemicals an anti-cancer treatment supplement could be worth further investigation regardless of their low bioavailability.

CD19/BAFF-R dual-targeted CAR T cells for the treatment of mixed antigen-negative variants of acute lymphoblastic leukemia.

Chimeric antigen receptor (CAR) T cells targeting CD19 mediate potent anti-tumor effects in B cell malignancies including acute lymphoblastic leukemia (ALL), but antigen loss remains the major cause of treatment failure. To mitigate antigen escape and potentially improve durability of remission, we developed a dual-targeting approach using an optimized, bispecific CAR construct that targets both CD19 and BAFF-R. CD19-BAFF-R dual CAR T cells exhibited antigen-specific cytokine release, degranulation and cytotoxicity against both CD19−/− and BAFF-R−/− variant human ALL cells in vitro. Immunodeficient mice engrafted with mixed CD19−/− and BAFF-R−/− variant ALL cells and treated with a single dose of CD19-BAFF-R dual CAR T cells experienced complete eradication of both CD19−/− and BAFF-R−/− ALL variants, while mice treated with monospecific CD19 or BAFF-R CAR T cells succumbed to outgrowths of CD19-/BAFF-R+ or CD19+/BAFF-R- tumors, respectively. Further, CD19-BAFF-R dual CAR T cells showed prolonged in vivo persistence, raising the possibility that these cells may have potential to promote durable remissions. Together, our data support clinical translation of BAFF-R/CD19 dual CAR T cells to treat ALL.

Characterization of a novel glucocorticoid-resistant human B-cell acute lymphoblastic leukemia cell line, with AMPK, mTOR and fatty acid synthesis pathway inhibition

BackgroundAcquired glucocorticoid (GC) resistance remains the main obstacle in acute lymphoblastic leukemia (ALL) therapy. The aim of the present study was to establish a novel GC-resistant B-ALL cell line and investigate its biological characteristics.MethodsA cell culture technique was used to establish the GC-resistant cell line from the parental cell, NALM-6. Molecular and cellular biological techniques including flow cytometry, MTT assay, western blotting, DNA fingerprinting analysis and whole transcriptome sequencing (WTS) were used to characterize the GC-resistant cell lines. Nude mice were used for xenograft studies.ResultsThe GC-resistant cell line, NALM-6/HDR, was established by culturing NALM-6 cells under hypoxia for 5 weeks with a single dexamethasone (Dex) treatment. We subcloned the NALM-6/HDR cell lines, and got 6 monoclone Dex-resistant cell lines, NALM-6/HDR-C1, C3, C4, C5, C6 and C9 with resistance index (RI) ranging from 20,000–50,000. NALM-6/HDR and its monoclone cell line, NALM-6/HDR-C5, exhibited moderate (RI 5–15) to high resistance (RI > 20) to Ara-c; low or no cross-resistance to L-Asp, VCR, DNR, and MTX (RI < 5). STR analysis confirmed that NALM-6/HDR and NALM-6/H were all derived from NALM-6. All these cells derived from NALM-6 showed similar morphology, growth curves, immunophenotype, chromosomal karyotype and tumorigenicity. WTS analysis revealed that the main metabolic differences between NALM-6 or NALM-6/H (GC-sensitive) and NALM-6/HDR (GC-resistant) were lipid and carbohydrates metabolism. Western blotting analysis showed that NALM-6/HDR cells had a low expression of GR and p-GR. Moreover, AMPK, mTORC1, glycolysis and de novo fatty acid synthesis (FAS) pathway were inhibited in NALM-6/HDR when compared with NALM-6.ConclusionsNALM-6/HDR cell line may represent a subtype of B-ALL cells in patients who acquired GC and Ara-c resistance during the treatment. These patients may get little benefit from the available therapy target of AMPK, mTORC1, glycolysis and FAS pathway.

Mapping the Glucocorticoid Gene Regulatory Network and Alterations That Contribute to Steroid Resistance in Childhood Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer and despite improved survival rates, relapsed ALL is still among the most common causes of cancer death in children. Although changes in the expression of specific genes have been linked to chemotherapeutic resistance, relatively little is understood of the pharmacogenomic impact of the noncoding, cis-regulatory landscape governing gene regulation. Glucocorticoids (GCs; i.e. steroids) are a mainstay of contemporary, multi-drug chemotherapy in ALL, and GC resistance is predictive of both relapse and poor clinical outcome in ALL. Because GCs function through activation of glucocorticoid receptor (GR), a nuclear receptor transcription factor that interacts directly with cis-regulatory elements, unveiling the glucocorticoid gene regulatory network (GC-GRN) in leukemia cells is crucial to understanding not only the biological mechanism of apoptosis, but also illuminating gene regulatory mechanisms contributing to GC resistance. To test the hypothesis that alterations to the GC-GRN are important contributors to steroid resistance in ALL, we comprehensively mapped cellular responses to GCs in human ALL cell lines using >100 independent functional genomic datasets. This comprehensive approach uncovered thousands of genes and cis-regulatory elements that were responsive to GCs, and further identified >38,000 high-confidence glucocorticoid response elements (GREs) in the ALL genome. A closer examination of these data revealed GR binding profiles that were consistent with the long-range flexible billboard model of gene regulation. By further integrating our results with genetic and epigenetic data in primary ALL cells from patients enrolled on St. Jude clinical trials, we identified 45 DNA sequence variants associated with ex vivo GC resistance that map to GREs and functionally validated an associated variant within the TLE1 gene locus. We also uncovered 1929 accessible chromatin sites (FDR<0.1) in primary ALL cells that were associated with ex vivo GC resistance, and these GC-resistance accessible chromatin sites were highly enriched at GREs determined from ALL cell lines (p<2.2x10 -16). High-throughput pharmacogenomic CRISPRi screening in human ALL cell lines with a library of >10,000 sgRNAs targeting >1000 GR binding events at putative GC-resistance accessible chromatin sites identified a subset of GR binding sites implicated in GC resistance. Overall, these data indicate that GCs initiate pervasive, genome-wide effects on the leukemia epigenome and transcriptome, and that genetic and epigenetic alterations to GREs are mechanisms contributing to GC resistance in childhood ALL. DisclosuresPui: Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Novartis: Other: Data Monitoring Committee. Evans: Princess Máxima Center for Pediatric Oncology, Scientific Advisory Board, Chair: Membership on an entity's Board of Directors or advisory committees; BioSkryb, Inc.: Membership on an entity's Board of Directors or advisory committees; St. Jude Children's Research Hospital, Emeritus Member (began Jan 2021): Ended employment in the past 24 months.

Small Molecule Inhibition of PDE6D-RAS Interaction Suppresses the Growth of Acute Lymphoblastic Leukemia Cell Lines

Small Molecule Inhibition of PDE6D-RAS Interaction Suppresses the Growth of Acute Lymphoblastic Leukemia Cell Lines

Identification of Patient-Specific Anti-Apoptotic Molecules As Therapeutic Targets in Poor Prognosis Acute Lymphoblastic Leukemia (ALL)

Relapse and refractory ALL shows dismal prognosis despite recent progress in intensive chemotherapy and development of molecular targeting agents. In this study, we aimed to identify vulnerabilities in genetically-diverse ALL and to find additional therapeutic targets in Philadelphia chromosome-positive (Ph+) ALL and chronic myeloid myeloid leukemia (CML) to overcome BCR-ABL tyrosine kinase inhibitor (TKI) resistance.To this end, we performed in vitro drug screening using 23 human ALL samples (9 Ph+ ALL, 5 MLL-ALL, 1 ALL with ETV-RUNX1, 5 B-ALL, not otherwise specified and 4 T-ALL), 10 CML samples and eight mixed phenotype acute leukemia (MPAL) samples (four B-Myeloid and four T-Myeloid). Based on our recent findings in AML (Hashimoto, Saito et al., Nature Cancer 2021), we treated leukemia-engrafting cells with small molecules targeting anti-apoptotic molecules (BCL-2, MCL-1 or BIRC) or molecules associated with cell division (AURKB) in addition to tyrosine kinase inhibitors.Among these compounds, BIRC inhibitor and venetoclax exhibited great efficacy. Responsiveness to each compound was: 28 of 41 for BIRC inhibitor (68.3%), 24 of 40 for venetoclax (60%), 11 of 37 for MCL-1 inhibitor (29.7%) and 4 of 37 for AURKB inhibitor (10.8%). We found differential sensitivity between T-ALL/MPAL T-myeloid and CML. Seven out of eight T-ALL and MPAL T-myeloid samples were highly sensitive to venetoclax (87.5%), while nine out of 10 CML samples were responsive to BIRC inhibition (90%). On the other hand, among Ph+ ALL/MPAL and Ph- B-ALL/MPAL B-myeloid samples, sensitivities to BIRC inhibitor and venetoclax were variable.To identify determinants of sensitivity to compounds, we examined the relation between mutational profile and in vitro leukemia elimination through targeted DNA sequencing for 79 lymphoid and myeloid malignancy-associated somatic mutations. Consistent with our previous study, CBL-mutated leukemia showed higher sensitivity to BIRC inhibitor (four of five cases) compared with venetoclax (two of five cases). Among genes related to RAS signaling pathway, KRAS mutations were most frequent (n=6). While five of six KRAS-mutated cases were BIRC inhibitor sensitive (83.3%), three of six cases were sensitive to venetoclax (50%). For cases with mutations in BCR-ABL1 kinase domain, the sensitivity to BIRC inhibitor and venetoclax was variable.Finally, we went on to setup in vivo experiments to elucidate if targeting the patient-specific vulnerabilities resulted in potent therapeutic efficacy against patient leukemic cells. We created patient-derived xenograft (PDX) models of 5 Ph+ ALL/MPAL, 2 Ph- B-ALL/MPAL, 2 T-ALL/MPAL and 2 CML cases. For Ph+ ALL/MPAL and CML, BIRC inhibitor and/or venetoclax combined with dexamethasone (DEX) and TKI achieved effective in vivo elimination of leukemic cells as predicted by in vitro experiments. Combination therapy showed almost complete elimination of Ph+ leukemic cells even in the presence of T315I mutation. For Ph- B-ALL/MPAL and T-ALL/MPAL, preliminary in vivo experiments showed additional inhibition of BIRC and BCL-2 resulted in more profound reduction of leukemic cells in BM compared with DEX alone (Combination: 2.1% [0.25-8] of hCD45+ leukemic cells, n=13 vs. DEX alone: 67.2% [59-76.5], n=11, median [IQR], p<0.001).We found targeting anti-apoptotic molecules in combination with DEX and/or TKI eradicated human genetically-diverse ALL, MPAL and CML cells both in vitro and in vivo. Inhibition of BIRC and BCL-2 overcame glucocorticoid resistance of Ph- ALL. Altogether, our results may offer precision medicine approach and contribute to improvement of clinical outcome in treatment-resistant ALL, CML and MPAL. DisclosuresUchida: Sumitomo Dainippon Pharma Co., Ltd.: Honoraria; Otsuka Pharmaceutical Co., Ltd.: Honoraria; Astellas Pharma Inc.: Honoraria; Chugai Pharmaceutical Co., Ltd.: Honoraria; Novartis Pharma Inc.: Honoraria. Harigae: Ono pharma: Honoraria, Other: Subsidies or Donations; Astellas Pharma: Other: Subsidies or Donations; Kyowakirin: Other: Subsidies or Donations; Janssen Pharma: Honoraria; Chugai Pharma: Honoraria; Novartis Pharma: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria.

Targeted Isolation of a Cytotoxic Cyclic Hexadepsipeptide from the Mesophotic Zone Sponge-Associated Fungus Cymostachys sp. NBUF082.

LC-MS/MS-based molecular networking facilitated the targeted isolation of a new cyclic hexadepsipeptide, cymodepsipeptide (1), and two known analogues, RF–2691A (2) and RF–2691B (3), from the fungus Cymostachys sp. NBUF082 that was derived from a mesophotic zone Aaptos sponge collected near Apo Island. The constitution and configuration of 1 was elucidated through 1D and 2D NMR-spectroscopy, high resolution mass-spectrometry, and chemical degradations including Marfey’s analysis and chiral HPLC. It was observed that 1 was moderately cytotoxic against CCRF-CEM human acute lymphocytic leukemia cells in vitro with the IC50 value of 9.2 ± 1.1 μM.

Schlafen 11 expression in human acute leukemia cells with gain-of-function mutations in the interferon-JAK signaling pathway

SummarySchlafen11 (SLFN11) is referred to as interferon (IFN)-inducible. Based on cancer genomic databases, we identified human acute myeloid and lymphoblastic leukemia cells with gain-of-function mutations in the Janus kinase (JAK) family as exhibiting high SLFN11 expression. In these cells, the clinical JAK inhibitors cerdulatinib, ruxolitinib, and tofacitinib reduced SLFN11 expression, but IFN did not further induce SLFN11 despite phosphorylated STAT1. We provide evidence that suppression of SLFN11 by JAK inhibitors is caused by inactivation of the non-canonical IFN pathway controlled by AKT and ERK. Accordingly, the AKT and ERK inhibitors MK-2206 and SCH77284 suppressed SLFN11 expression. Both also suppressed the E26 transformation-specific (ETS)-family genes ETS-1 and FLI-1 that act as transcription factors for SLFN11. Moreover, SLFN11 expression was inhibited by the ETS inhibitor TK216. Our study reveals that SLFN11 expression is regulated via the JAK, AKT and ERK, and ETS axis. Pharmacological suppression of SLFN11 warrants future studies.

Improved pharmacokinetic and pharmacodynamic profile of a novel PEGylated native Erwinia chrysanthemi L-Asparaginase

SummaryIntroduction. Erwinase® (native Erwinia chrysanthemi L-Asparaginase (nErA)) is an approved second-line treatment for acute lymphoblastic leukaemia (ALL) in children and adolescents, who develop hypersensitivity or neutralising antibodies to E.coli derived L-Asparaginases (ASNases). However, nErA has a short in vivo half-life requiring frequent dosing schedules in patients. In this study, nErA was covalently conjugated to PEG molecules with the aim of extending its half-life in vivo. Methods. Firstly, efficacy of this novel product PEG-nErA was investigated on human ALL cell lines (Jurkat, CCRF-CEM and CCRF-HSB2), in vitro. Secondly, its pharmacokinetic (PK) and pharmacodynamic (PD) characteristics were determined, in vivo (12 rats in each group). Results. It was found that the specific activity (U/mg of enzyme) and the kinetic constant (KM) of nErA remained unaltered post PEGylation. PEG-nErA was shown to have similar cytotoxicity to nErA (IC50: 0.06–0.17 U/mL) on human ALL cell lines, in vitro. Further, when compared to nErA, PEG-nErA showed a significantly improved half-life in vivo, which meant that L-Asparagine (Asn) levels in plasma remained depleted for up to 25 days with a four-fold lower dose (100 U/kg) compared with 72 h for nErA at 400 U/kg dose. Conclusion. Overall, this next generation product PEG-nErA (with improved PK and PD characteristics compared to nErA) would bring a significant advantage to the therapeutic needs of ALL patients and should be further explored in clinical trials.

Co-culture model of B-cell acute lymphoblastic leukemia recapitulates a transcription signature of chemotherapy-refractory minimal residual disease

B-cell acute lymphoblastic leukemia (ALL) is characterized by accumulation of immature hematopoietic cells in the bone marrow, a well-established sanctuary site for leukemic cell survival during treatment. While standard of care treatment results in remission in most patients, a small population of patients will relapse, due to the presence of minimal residual disease (MRD) consisting of dormant, chemotherapy-resistant tumor cells. To interrogate this clinically relevant population of treatment refractory cells, we developed an in vitro cell model in which human ALL cells are grown in co-culture with human derived bone marrow stromal cells or osteoblasts. Within this co-culture, tumor cells are found in suspension, lightly attached to the top of the adherent cells, or buried under the adherent cells in a population that is phase dim (PD) by light microscopy. PD cells are dormant and chemotherapy-resistant, consistent with the population of cells that underlies MRD. In the current study, we characterized the transcriptional signature of PD cells by RNA-Seq, and these data were compared to a published expression data set derived from human MRD B-cell ALL patients. Our comparative analyses revealed that the PD cell population is markedly similar to the MRD expression patterns from the primary cells isolated from patients. We further identified genes and key signaling pathways that are common between the PD tumor cells from co-culture and patient derived MRD cells as potential therapeutic targets for future studies.

Abstract LB153: Emergence of a hyper-proliferative phenotype in TET2 edited human CAR T cells

Abstract The chance integration of a lentiviral chimeric antigen receptor (CAR) vector in a TET2 allele led to the expansion of a dominant CAR T cell clone, which coincided with tumor clearance in a chronic lymphocytic leukemia (CLL) patient (Fraietta et. al. Nature 2018). This observation raised the possibility of treating patients with few TET2-edited CAR T cells rather than hundreds of millions of CAR T cells as is currently done in most CAR therapies. In a pre-clinical murine model of human acute lymphoblastic leukemia (ALL), we evaluated the functional implications of TET2 loss in human T cells engineered to express different CARs. We assessed the effect of TET2 disruption on anti-tumor CAR T cell efficacy by treating immune deficient mice bearing human ALL cell line, NALM6, with limiting dose of either TET2 edited (CRISPR/Cas9) or unedited CAR T cells. We employed the two most widely used second generation CD19-specific CAR encompassing the costimulatory domain of either CD28 (Rv-1928z) or 4-1BB (Rv-19BBz). TET2 editing enhanced the anti-tumor efficacy of Rv-19BBz CAR T cells but not Rv-1928z CAR T cells. This enhanced efficacy in TET2 edited Rv-19BBz was associated with increased early cell numbers and a higher fraction of central memory CAR T cells, consistent with the clinical case report by Fraietta et al. who observed a dominant clonal expansion with a lentiviral vector-encoded 4-1BB costimulated CAR. In contrast, TET2 editing in Rv-1928z CAR T cells did not enhance their proliferation or increased their memory phenotype. Rv-1928z CAR T cells have a stronger induction of effector differentiation than Rv-19BBz CAR T cells. This led us to hypothesize that TET2 editing cannot limit the induction of effector differentiation in Rv-1928z CAR T cells but enhanced the early expansion and memory phenotype of Rv-19BBz CAR T cells. We have previously shown that 1928z driven by the TRAC promoter (TRAC-1928z) and Rv-1928z co-expressing the 4-1BB ligand (Rv-1928z-41BBL) can limit the induction of effector differentiation as compared to Rv-1928z. Disruption of TET2 enhanced the anti-tumor efficacy of both these CAR T cells and promoted acquisition of early central memory phenotype. However, TET2 edited CAR T cells, over time, attain a hyper-proliferative phenotype while maintaining a central memory profile by flow cytometry phenotyping. The frequency at which T cells achieve this phenotype depends on the CAR receptor. Functional studies reveal that these cells have highly compromised effector function. Transcriptional profiling show enrichment in gene signatures related to T cell leukemia/lymphoma with sustained upregulation of cell cycle associated factors that could not be explained by frequently observed point mutations and occasional chromosomal aberrations. These observations support a model wherein signals emanating from CARs and loss of TET2 establish sustained proliferation with loss of effector function. Citation Format: Nayan Jain, Zeguo Zhao, Archana Iyer, Michael Lopez, Judith Feucht, Richard Koche, Julie Yang, Yingqian Zhan, Michel Sadelain. Emergence of a hyper-proliferative phenotype in TET2 edited human CAR T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB153.