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Glucocorticoids (GCs), including dexamethasone (dex), are a central component of combination chemotherapy for childhood B-cell precursor acute lymphoblastic leukemia (B-ALL). GCs work by activating the GC receptor (GR), a ligand-induced transcription factor, which in turn regulates genes that induce leukemic cell death. Which GR-regulated genes are required for GC cytotoxicity, which pathways affect their regulation, and how resistance arises are not well understood. Here, we systematically integrate the transcriptional response of B-ALL to GCs with a next-generation short hairpin RNA screen to identify GC-regulated "effector" genes that contribute to cell death, as well as genes that affect the sensitivity of B-ALL cells to dex. This analysis reveals a pervasive role for GCs in suppression of B-cell development genes that is linked to therapeutic response. Inhibition of phosphatidylinositol 3-kinase δ (PI3Kδ), a linchpin in the pre-B-cell receptor and interleukin 7 receptor signaling pathways critical to B-cell development (with CAL-101 [idelalisib]), interrupts a double-negative feedback loop, enhancing GC-regulated transcription to synergistically kill even highly resistant B-ALL with diverse genetic backgrounds. This work not only identifies numerous opportunities for enhanced lymphoid-specific combination chemotherapies that have the potential to overcome treatment resistance, but is also a valuable resource for understanding GC biology and the mechanistic details of GR-regulated transcription.

Introduction Acute myeloid leukemia (AML) is a malignancy of myeloid progenitor cells that leads to the accumulation of immature blasts in the blood and bone marrow. While the 5-year relative survival rate has increased from 6.4% to 28.7% in the last 40 years, death rates have remained steady at 3-4%. Less toxic, more effective targeted treatments are needed to improve outcomes for patients with AML. Previous studies identified cAMP response element-binding protein (CREB) as a potential therapeutic target for AML therapy. CREB is overexpressed in AML and is associated with poor prognosis. We identified a small molecule, XX-650-23, that inhibits interaction between CREB and its co-activator, CREB Binding Protein. However, XX-650-23 does not have optimal physical chemical properties for clinical application in humans. Niclosamide, an FDA approved anthelmintic drug, shares structural similarity with XX-650-23, and suppresses the proliferation of AML cells in vitro and in vivo by inhibiting CREB-dependent signaling. The aim of this study is to define the molecular pathways that mediate the effects of niclosamide in AML cells. This will allow for more precise selection of patient populations for treatment, identify potential sources of niclosamide resistance and reveal combination therapies that make use of the distinct pathways targeted. Methods To identify genetic factors modulating cellular sensitivity to niclosamide treatment, we performed a CRISPR/Cas9 library screen in the presence or absence of niclosamide. HL60 cells expressing Cas9 were infected with a custom sgRNA lentivirus library of 220 genes from a previous genome-wide shRNA screen. After puromycin selection, HL60 cells expressing pooled sgRNAs were grown in either niclosamide or 0.1% DMSO for 20 days. Genomic DNA was extracted from control and niclosamide-treated cells. Frequency of sgRNA were measured by next generation sequencing and analyzed using the Cas9 high-throughput maximum likelihood estimator (casTLE) algorithm. Results Sixty-five gene hits were found to be significant (p≤0.05). Of the top 220 hits from the previous genome-wide shRNA screen, 26 were identified as positive hits (p ≤0.05) in the CRISPR/Cas9 knock out screen. The CRISPR screen identified genes enriched in a number of pathways including programmed cell death, nucleotide biosynthesis, mitochondrial processes and canonical glycolysis, as measured by gene ontology term analysis. Numerous gene deletions conferred resistance to niclosamide treatment. Genes DHODH (score= 123; effect= 2.9) and HSPA9 (score= 144; effect = 2.5), involved in nucleotide biosynthesis and mitochondrial processes, were significantly enriched in the surviving population. Perturbation of known metabolic pathways sensitized AML cells to niclosamide, including ATP synthase F1 subunit beta (ATP5B) (score= 316; effect= -5.1), hexokinase 2 (HK2) (score= 312; effect= -5.4), phosphofructokinase (PFKP) (score= 195; effect= -1.9) and mitochondrial phosphate carrier protein (SLC25A3) (score= 271; effect= -7.8). SLC25A3 and ATP5B play a role in oxidative phosphorylation and mitochondrial proton transmembrane transport, whereas HK2 and PFKP are key to glycolysis, suggesting that niclosamide's mechanism of action is dependent on energy metabolism. Furthermore, we found that disruption of Bcl-2 (BCL2) was sensitizing to niclosamide treatment (score= 129; effect= -4.7). To confirm the sensitizing effect of Bcl-2 inhibition on niclosamide treatment, HL60 cells were treated with niclosamide and Bc1-2 inhibitor venetoclax. Pretreatment of HL60 cells with niclosamide led to significantly decreased cell viability upon venetoclax treatment (p Overall, our study identified genes with strong signatures for cell death, nucleotide biosynthesis, mitochondrial function and metabolic processes. Compounds inhibiting genes identified in this screen could be combined with niclosamide for synergistic effect. Targets overrepresented in the surviving population represent sources of resistance to niclosamide therapy. This study provides insight into mechanisms of action and resistance in AML cells treated with niclosamide and novel targets for combination therapy. Disclosures No relevant conflicts of interest to declare. OffLabel Disclosure: Niclosamide is an anthelmintic, FDA approved to treat tapeworm infections.

CREB (cAMP Response Element Binding protein) is a transcription factor that is overexpressed in primary Acute Myeloid Leukemia (AML) cells and is associated with a decreased event-free survival and increased risk of relapse. We previously demonstrated that CREB overexpression increases leukemia cell growth and survival. Transgenic mice overexpressing CREB in myeloid cells develop a myeloproliferative neoplasm and myelodysplasia. CREB knockdown inhibits AML cell proliferation but not normal hematopoietic stem cell activity in vivo. To demonstrate the feasibility of targeting CREB for treatment for AML, we recently described a small molecule inhibitor of CREB, N-(4-cyanophenyl)-3-hydroxy-2-naphthamide (XX-650-23), which is a compound originally based on naphthol AS-E phosphate first identified as an inhibitor of CREB interaction with its coactivator, CBP (CREB Binding Protein). To identify a lead candidate with improved potency and physicochemical properties, we performed structure-activity relationships (SAR) studies for a series of salicylamides derived from naphthol AS-E phosphate. Development of this series led to the identification of the anthelmintic niclosamide as a potent agent that suppresses cell viability of five AML cell lines (IC50= 280 nM (HL60), 340 nM (KG1), 420 nM (MOLM13), 560 nM (MV411), 360 nM (U937), without a significant decrease in colony forming activity of normal bone marrow cells up to 10 μM (18- to 36-fold therapeutic window). Niclosamide binds CBP with a KD of 22.3 nM by Surface Plasmon Resonance (Biacore) analysis. To determine whether niclosamide specifically inhibits CREB-mediated gene expression in cells, luciferase reporter gene activity under the control of a promoter containing two CRE elements was measured after treatment of niclosamide for 6 hours. Niclosamide inhibited CREB-driven luciferase activity in HL60 cells with an IC50 of 1.09 μM. We also examined the efficacy of niclosamide in an AML patient-derived xenograft (PDX) mouse model. Niclosamide significantly inhibited the progression of AML in mice injected with primary AML cells. The percentage of circulating AML cells in the peripheral blood (%), vehicle vs. niclosamide treatment 5 weeks after engraftment were 28.75 ± 3.507 vs. 0.5363 ± 0.2744 (n=8, p< 0.001, mean ± SEM). In Kaplan Meier analysis, the median survival of PDX mice was 41 days vs. 51.5 days (p = 0.0015, log-rank test). To characterize the cellular effects of niclosamide, we analyzed the DNA profile, apoptosis, DNA-damage, cell cycle regulators, and other signaling molecules using flow cytometry. Niclosamide treatment increased DNA-damaged and apoptosis populations during the G1/S cell cycle phase, which also showed reduced phosphorylated CREB levels. To examine the functional requirement of CREB, we determined the effects of CREB knockdown in HL60 cells treated with niclosamide. CREB knockdown protected HL60 cells from niclosamide treatment-mediated cytotoxic effects (IC50=670 nM for CREB knockdown vs. 200 nM for vector control cells). Furthermore, combination treatment of niclosamide with XX-650-23 in HL60 cells showed an additive antiproliferative effect, suggesting that niclosamide and XX-650-23 regulate the same targets or pathways to inhibit viability of AML cells. To further identify genes that confer resistance or sensitivity to niclosamide, we performed a functional shRNA screen using subsets of whole genomic shRNA libraries (apoptosis, motility, other cancer; 35154 elements). We identified 53 genes, including tumor necrosis factor receptor superfamily members, which when knocked downed conferred resistance to niclosamide at a 10% false discovery rate. Taken together, our results demonstrate that niclosamide is a potential drug to treat AML by inducing DNA-damage, apoptosis and cell cycle arrest through the inhibition of CREB-dependent pathways in AML cells. Disclosures No relevant conflicts of interest to declare.

Although the treatment and prognosis of patients with pediatric acute lymphoblastic leukemia (ALL) have improved during the last decades, there is still a clinical need for more effective/selective and less toxic therapies. To address this, we have interrogated various signaling pathways in human ALL cells and mouse strains that express E2A-PBX1, which is present in 5-7% of pediatric ALL. Phospho-flow analysis revealed basal hyper-phosphorylation levels of PLCγ2 in mouse E2A-PBX1 leukemias, consistent with hyper-activation of upstream signaling pathways. Efficient shRNA-mediated depletion of PLCγ2 reduced colony formation of mouse E2A-PBX1+ leukemias in vitro and increased disease-free survival after secondary bone marrow transplantation in vivo. Furthermore, PLCγ2-depleted human ALL cell lines including E2A-PBX1+ cells, showed reduced proliferation. These data suggest a pathogenic role of hyperactivated PLCγ2 in pre-B-ALL. Bioinformatics analysis of E2A-PBX1 target genes in human ALLs revealed an enrichment of B- and T-cell activation pathways, which include the SRC-family kinase LCK and the cytoplasmic kinase ZAP70, upstream of PLCγ2. Comparative analyses of global transcriptional profiles in human primary and mouse leukemias and preleukemias induced by the E2A-PBX1 oncogene identified the signaling kinase ZAP70 as one of the earliest and most consistently up-regulated genes in E2A-PBX1 leukemias. Using a candidate gene approach, we identified LCK with increased expression levels in E2A-PBX1 leukemia cells compared to normal B-cell progenitors. Mouse and human E2A-PBX1 leukemia cells were dependent on the E2A-PBX1 target genes ZAP70 and LCK for proliferation and survival as confirmed by shRNA knock-down experiments. Hence, efficient depletion of these genes resulted in a decrease of phosphorylated PLCγ2, suggesting therapeutic targets in E2A-PBX1 leukemias. Combined suppression of ZAP70 and LCK using double-shRNA experiments showed an additive effect on inhibition of cell proliferation and decrease of phosphorylated PLCγ2. These results provide a rationale for combination therapy to block this hyper-activated signaling pathway at different levels. Several small molecule inhibitors were evaluated for their effects on PLCγ2 upstream pathways in E2A-PBX1 leukemia cells. SRC-family kinase inhibitors including dasatinib were most effective in reducing phosphorylation of PLCγ2 and inhibiting cell proliferation. Furthermore, dasatinib showed promising preclinical efficacy in vitro in colony forming assays and in vivo after secondary bone marrow transplantation of leukemias. In summary, our studies demonstrate that the proliferation and survival of E2A-PBX1 leukemias are dependent on PLCγ2 and upstream signaling pathways, which are suitable for pharmacological inhibition. Disclosures No relevant conflicts of interest to declare.

There is a critical need for new agents with novel therapeutic targets and improved safety profiles in high-risk acute lymphoblastic leukemia (ALL), which is a significant cause of morbidity and mortality in pediatric and adult populations. Phenotypic high-throughput chemical screens allow for discovery of small molecules that modulate complex phenotypes and provide lead compounds for novel therapies; however, identification of their mechanistically relevant targets remains a major experimental challenge. We applied a chemical genetics approach involving sequential unbiased high-throughput chemical and ultra-complex, genome-scale shRNA screens to address this challenge and identify novel agents in ALL. A cell-based phenotypic high-throughput chemical screen of 115,000 compounds identified 640 compounds that inhibited growth of one or both ALL cell lines with high-risk Mixed Lineage Leukemia (MLL) genetic abnormalities, but did not inhibit the growth of a cell line lacking MLL rearrangement. The most potent and selective 64 were tested on an expanded panel of eight human B-ALL cell lines to identify lead compound STF-118804. STF-118804 inhibited the growth of most B-ALL cell lines with high potency demonstrating IC50 values in the low nanomolar range. Leukemic samples from five pediatric ALL patients were also sensitive to STF-118804 in the low nanomolar range. STF-118804 displayed 5–10 fold more potency against most leukemias in comparison to cycling human (lineage-negative cord blood) and murine (c-kit+ bone marrow) progenitor cells, demonstrating a therapeutic index. STF-118804 displays distinctive cytotoxicity by inducing apoptosis without causing a phase-specific cell cycle arrest. To discover the molecular target of STF-118804, a functional genomic screen was performed to identify shRNAs that conferred sensitivity or resistance to STF-118804, utilizing an ultra-complex (∼25 shRNAs per gene) library targeting in total ∼9300 human genes and 1000s of negative control shRNAs. NAMPT was the most statistically significant gene to confer sensitivity to STF-118804, suggesting that STF-118804 functioned as a NAMPT inhibitor. NAMPT encodes nicotinamide phosphoribosyl transferase, a rate-limiting enzyme in the biosynthesis of nicotinamide adenine dinucleotide (NAD+), a crucial cofactor in many biochemical processes. STF-118804 was confirmed as a novel class of NAMPT inhibitor through metabolic rescue, enzymatic, and genetic studies. STF-118804 displayed strong inhibitory activity in in vitro NAMPT enzymatic assays. Over-expression of wild-type or mutant NAMPT in cells indicated that STF-118804 cytotoxicity is a result of its ability to inhibit NAMPT, and that STF-118804 does not have significant off-target effects on cell viability. The potential efficacy of STF-118804 in vivo was assessed in an orthotopic xenograft model of ALL. Sublethally irradiated immunodeficient mice were transplanted with human ALL cells engineered to constitutively express firefly luciferase. Dosing of STF-118804 was initiated two weeks post-transplant when ALL cells had engrafted and bioluminescent signal was detectable. Mice treated with STF-118804 showed regression of leukemia by bioimaging and significantly extended survival. The leukemia initiating cell (LIC) frequency in STF-118804 treated mice was significantly lower (∼8 fold) than vehicle treated mice, showing that STF-118804 was effective in reducing LICs. In summary, tandem high-throughput screening identified a highly-specific, potent, and structurally novel small molecule inhibitor of NAMPT that is active in ALL. Tandem high throughput screening using chemical and ultra-complex shRNA libraries provides a rapid chemical genetics approach for seamless progression from small molecule lead identification to target discovery and validation. Disclosures: No relevant conflicts of interest to declare.