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The basic helix-loop-helix transcription factor NeuroD1 has been implicated in the neurogenesis and early differentiation of pancreatic endocrine cells. However, its function in relation to cancer has been poorly examined. In this study, we found that NeuroD1 is involved in the tumorigenesis of neuroblastoma. NeuroD1 was strongly expressed in a hyperplastic region comprising neuroblasts in the celiac sympathetic ganglion of 2-week-old MYCN transgenic (Tg) mice and was consistently expressed in the subsequently generated neuroblastoma tissue. NeuroD1 knockdown by short hairpin RNA (shRNA) resulted in motility inhibition of the human neuroblastoma cell lines, and this effect was reversed by shRNA-resistant NeuroD1. The motility inhibition by NeuroD1 knockdown was associated with induction of Slit2 expression, and knockdown of Slit2 could restore cell motility. Consistent with this finding, shRNA-resistant NeuroD1 suppressed Slit2 expression. NeuroD1 directly bound to the first and second E-box of the Slit2 promoter region. Moreover, we found that the growth of tumor spheres, established from neuroblastoma cell lines in MYCN Tg mice, was suppressed by NeuroD1 suppression. The functions identified for NeuroD1 in cell motility and tumor sphere growth may suggest a link between NeuroD1 and the tumorigenesis of neuroblastoma. Indeed, tumor formation of tumor sphere–derived cells was significantly suppressed by NeuroD1 knockdown. These data are relevant to the clinical features of human neuroblastoma: high NeuroD1 expression was closely associated with poor prognosis. Our findings establish the critical role of the neuronal differentiation factor NeuroD1 in neuroblastoma as well as its functional relationship with the neuronal repellent factor Slit2. Cancer Res; 71(8); 2938–48. ©2011 AACR.

Supplementary Methods, Tables 1-2, Figures 1-4 from The Neuronal Differentiation Factor NeuroD1 Downregulates the Neuronal Repellent Factor Slit2 Expression and Promotes Cell Motility and Tumor Formation of Neuroblastoma

Pi-class glutathione S-transferase (GSTP1) is highly expressed in a wide variety of human cancer tissues compared to the corresponding normal counterpart. Therefore, GSTP1 is a potential target enzyme for overcoming resistance to chemotherapeutic agents or visualizing specific lesions such as cancer. Here, we present orange and red fluorescence-emitting probes selective for GSTP1. Carbofluorescein and TokyoMagenta fluorophores were modified with a previously described GSTP1-selective chromogenic compound to generate orange and red fluorescence probes, respectively. Of these probes, Ps-CF, the orange fluorescence-emitting probe, was confirmed to be highly specific for detecting GSTP1 exogenously or endogenously expressed in various cancer cells. Additionally, it was demonstrated that Ps-CF is applicable for the simultaneous detection of GSTP1 and another cancer-associated enzyme by using a green fluorescence emitting γ-glutamyl transpeptidase (GGT) probe. In conclusion, the fluorescent probes developed in this study enable the simultaneous detection of multiple tumour markers such as GSTP1 with other cancer-associated enzymes by concurrently using spectrally distinguished fluorescent probes, potentially broadening the scope of cancer detection.

Pi-class glutathione S-transferase (GSTP1) is a detoxification enzyme that is highly expressed in various types of cancer cells and is a promising target for cancer imaging and therapy. Ps-TAc, an acetylated derivative of the GSTP1-specific fluorogenic substrate Ps-TG, is attracting attention as an effective GSTP1 fluorescent probe, and has been successfully used to visualize intracellular GSTP1 activity. Ps-TAc is a prodrug type fluorescent probe in which the phenolic hydroxyl group of Ps-TG is acetylated and thus is susceptible to nonspecific hydrolysis, potentially compromising its ability to detect GSTP1 activity. Here, we describe the development of a highly selective fluorogenic GSTP1 substrate that is membrane permeable and does not involve esterification and show its application to live-cell imaging and FACS analysis. We designed and synthesized several compounds with benzylsulfone substituents instead of the mesyl group of Ps-TG and tested their fluorescence activation by GSTP1 catalysis in vitro and in cellulo. Of the test compounds, Ps-TG3 was the most suitable for the visualization of intracellular GSTP1 activity because the signal from living cells increased significantly when MK-571, an inhibitor of multidrug resistance proteins (MRPs), was simultaneously loaded. The results obtained by co-loading Ps-TG3 and MK571 into GSTP1-nonexpressing cells suggest that Ps-TG3 can be a substrate for MRPs. The usefulness of Ps-TG3 was demonstrated by fluorescence imaging of several cancer cell cultures and FACS analysis of lymphoma cells. The results presented here suggest that Ps-TG3, in combination with MK571, is useful for visualizing and detecting intracellular GSTP1 activity in cancer cells that highly express GSTP1.

Glutathione S-transferase π (GSTP1-1 ) is overexpressed in many types of cancer and is involved in drug resistance. Therefore, GSTP1-1 is an important target in cancer therapy, and many GST inhibitors have been reported. We had previously developed an irreversible inhibitor, GS-ESF, as an effective GST inhibitor; however, its cellular permeability was too low for it to be used in inhibiting intracellular GST. We have now developed new irreversible inhibitors by introducing sulfonyl fluoride (SF) into chloronitrobenzene (CNB). The mechanism of action was revealed to be that CNBSF first reacts with glutathione (GSH) through an aromatic substitution in the cell, then the sulfonyl group on the GSH conjugate with CNBSF reacts with Tyr108 of GST to form a sulfonyl ester bond. Our new inhibitor irreversible inhibited GSTP1-1 both in vitro and in cellulo with a long duration of action.

Malignant mesothelioma (MM) frequently exhibits Hippo signaling pathway inactivation (HPI) mainly due to NF2 and/or LATS2 mutations, which leads to the activation of YAP transcriptional co-activator. Here, we show antitumor effects of statin on MM cells with HPI, through the interplay of the mevalonate and Hippo signaling pathways. Statin attenuated proliferation and migration of MM cells harboring NF2 mutation by accelerating YAP phosphorylation/inactivation. CD44 expression was decreased by statin, in parallel with YAP phosphorylation/inactivation. Importantly, we discovered that YAP/TEAD activated CD44 transcription by binding to the CD44 promoter at TEAD-binding sites. On the other hand, CD44 regulated Merlin phosphorylation according to cell density and sequentially promoted YAP transcriptional co-activator, suggesting that CD44 plays two pivotal functional roles as an upstream suppressor of the Hippo pathway and one of downstream targets regulated by YAP/TEAD. Moreover, the YAP/CD44 axis conferred cancer stem cell (CSC)-like properties in MM cells leading to chemoresistance, which was blocked by statin. Together, our findings suggest that YAP mediates CD44 up-regulation at the transcriptional level, conferring CSC-like properties in MM cells, and statin represents a potential therapeutic option against MM by inactivating YAP.

We herein report the first covalent G-site-binding inhibitor for GST, GS-ESF (1), which irreversibly inhibited the GSTP1-1 function. LC-MS/MS and X-ray structure analyses of the covalently linked GST-inhibitor complex suggested that 1 reacted with Tyr108 of GSTP1-1. The mechanism of covalent bond formation was discussed based on MD simulation results.

Glutathione S-transferase π (GSTP

Malignant mesothelioma (MM) shows inactivation of the BRCA1-associated protein 1 (BAP1) gene. In this study, we found BAP1 mutations in 5 (26%) of the 19 cell lines that we established from Japanese MM patients, and examined functional differences between the WT and mutant BAP1. First, we studied the subcellular localization of BAP1, demonstrating that the WT primarily resides in the nucleus and that the mutant BAP1 is found in the cytoplasm of the cells. Transduction of the WT BAP1 vector into MM cells with homozygous deletion at the BAP1 3′ side resulted in both inhibition of cell proliferation and anchorage-independent cell growth, whereas BAP1 mutants of a missense or C-terminal truncated form showed impaired growth inhibitory effects. Next, we studied how BAP1 is involved in MM cell survival after irradiation (IR), which causes DNA damage. After IR, we found that both WT and mutant BAP1 were similarly phosphorylated and phospho-BAP1 localized mainly in the nucleus. Interestingly, BRCA1 proteins were decreased in the MM cells with BAP1 deletion, and transduction of the mutants as well as WT BAP1 increased BRCA1 proteins, suggesting that BAP1 may promote DNA repair partly through stabilizing BRCA1. Furthermore, using the MM cells with BAP1 deletion, we found that WT BAP1, and even a missense mutant, conferred a higher survival rate after IR compared to the control vector. Our results suggested that, whereas WT BAP1 suppresses MM cell proliferation and restores cell survival after IR damage, some mutant BAP1 may also moderately retain these functions.

In eukaryotes, the cyclin-dependent kinase Cdk1p (Cdc2p) plays a central role in entry into and progression through nuclear division during mitosis and meiosis. Cdk1p is activated during meiotic nuclear divisions by dephosphorylation of its tyrosine-15 residue. The phosphorylation status of this residue is largely determined by the Wee1p kinase and the Cdc25p phosphatase. In fission yeast, the forkhead-type transcription factor Mei4p is essential for entry into the first meiotic nuclear division. We recently identified cdc25(+) as an essential target of Mei4p in the control of entry into meiosis I. Here, we show that wee1(+) is another important target of Mei4p in the control of entry into meiosis I. Mei4p bound to the upstream region of wee1(+) in vivo and in vitro and inhibited expression of wee1(+), whereas Mei4p positively regulated expression of the adjacent pseudogene. Overexpression of Mei4p inhibited expression of wee1(+) and induced that of the pseudogene. Conversely, deletion of Mei4p did not decrease expression of wee1(+) but inhibited that of the pseudogene. In addition, deletion of Mei4p-binding regions delayed repression of wee1(+) expression as well as induction of expression of the pseudogene. These results suggest that repression of wee1(+) expression is primarily owing to Mei4p-mediated transcriptional interference.

Acute myeloid leukemia (AML) cells highly depend on oxidative phosphorylation (OxPhos) to satisfy their heightened demands for energy, and the complex I OxPhos inhibitor IACS-010759 (Molina, Nat. Med. 2018) is currently in Phase 1 clinical trial in AML. In this study, we investigated how the bone marrow (BM) microenvironment affects the response to OxPhos inhibition in AML. To characterize the molecular mechanisms of sensitivity to OxPhos inhibition, we performed Cap Analysis of Gene Expression analysis (CAGE) on 31 genetically diverse primary AML samples (20 were defined as sensitive and 11 as resistant to IACS-010759; cut off >3.0 fold annexin V(+) by 100 nM IACS-010759/DMSO at 72 hours). CAGE identified higher expression of transcription start sites (TSS) for 17 genes in IACS-010759 resistant AML samples compared to sensitive (fold change >2.0, FDR < 0.05, EdgeR), which were related to cell adhesion, integrin and/or Rho GTPase family genes that modulate intracellular actin dynamics. We next investigated the interactions between IACS-010759 sensitive OCI-AML3 cells and BM-derived mesenchymal stem cells (MSC). Under conditions mimicking the BM microenvironment, IACS-010759 upregulated the pathways of focal adhesion and ECM-receptor interaction in OCI-AML3 cells (KEGG analysis based on CAGE). In turn, MSC co-culture increased oxygen consumption by AML, induced generation of mitochondrial ROS (control 4.4% vs IACS 44.4%), increased mtDNA (2-fold by q-PCR) and upregulation of mitochondrial proteins VDAC and cytochrome C, translating into dampened growth-inhibitory effects of IACS-010759. We further demonstrated that OCI-AML3 cells adhering to MSCs were fully protected from IACS-010759 induced apoptosis (IACS-induced specific apoptosis: non-adherent cells 16.2% ± 1.6% vs adherent cells 1.6% ± 0.7%, p=0.008, 30nM, 72hours). Similarly, adherent cells were fully protected from apoptosis induced by combination of IACS and AraC. These findings indicate that direct interactions with MSC trigger compensatory activation of mitochondrial respiration, increase in mitochondrial mass and resistance to OxPhos inhibition in AML. We next hypothesized that the trafficking of mitochondria from BM stroma cells to AML cells could represent a putative mechanism of an acquired resistance to OxPhos inhibition. To visualize mitochondria, OCI-AML3 and MSC were stably transfected with mitochondria-targeted PDHA1-GFP and -dsRed, respectively. We discovered that IACS-010759 induced transfer of MSC-derived mitochondria to OCI-AML3 cells (% of GFP/dsRed double-positive OCI-AML, control 4.1 ± 1.7 vs IACS 26.2 ± 13.4, p=0.002) via tunneling nanotubes (TNTs) detected by confocal and electron microscopy (Fig.1). Mitochondria transfer was only observed in the direct contact but not in the transwell co-cultures, and was abrogated by ICAM-1 neutralizing antibody and TNT blockade with Cytochalasin B. Likewise, combination of IACS with AraC increased mitochondrial transfer. We further found that IACS-010759 induced autophagy in OCI-AML3 cells co-cultured with MSC, as noted by increased conversion of LC3-I to LC3-II, which was further enhanced by the lysosome inhibitor Bafilomycin. Additionally, we observed autophagosome formation enwrapping MSC-derived mitochondria (Fig.1F), along with the degradation of an outer mitochondrial membrane protein Tom20. Finally, IACS-010759-induced transfer of mtDNA in BM-resident AML cells was confirmed in vivo in humanized AML PDX models (n=2). Daily oral treatment of mice harboring human AML with IACS-010759 (5.0 mg/kg/day, 21 days) increased the ratio of murine/human mtDNA in human AML cells isolated from BM, in 5 days on/2 days off PDX models tested (2.1 ± 0.3 fold, n=2). In conclusion, the findings of this study indicate an important role of mitochondria trafficking from BM stromal cells to AML cells in a compensatory adaptation to OxPhos inhibition in BM microenvironment. We propose that blocking of mitochondrial transfer could enhance the anti-AML efficacy of OxPhos targeting agents. Disclosures Zhang: The University of Texas M.D.Anderson Cancer Center: Employment. Kuruvilla:The University of Texas M.D.Anderson Cancer Center: Employment. Andreeff:BiolineRx: Membership on an entity's Board of Directors or advisory committees; Breast Cancer Research Foundation: Research Funding; Oncolyze: Equity Ownership; Oncoceutics: Equity Ownership; Senti Bio: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Eutropics: Equity Ownership; Reata: Equity Ownership; Aptose: Equity Ownership; 6 Dimensions Capital: Consultancy; Daiichi Sankyo, Inc.: Consultancy, Patents & Royalties: Patents licensed, royalty bearing, Research Funding; Jazz Pharmaceuticals: Consultancy; Celgene: Consultancy; Amgen: Consultancy; AstaZeneca: Consultancy; CPRIT: Research Funding; NIH/NCI: Research Funding; Center for Drug Research & Development: Membership on an entity's Board of Directors or advisory committees; Cancer UK: Membership on an entity's Board of Directors or advisory committees; NCI-CTEP: Membership on an entity's Board of Directors or advisory committees; German Research Council: Membership on an entity's Board of Directors or advisory committees; Leukemia Lymphoma Society: Membership on an entity's Board of Directors or advisory committees; NCI-RDCRN (Rare Disease Cliln Network): Membership on an entity's Board of Directors or advisory committees; CLL Foundation: Membership on an entity's Board of Directors or advisory committees. Konopleva:Astra Zeneca: Research Funding; Agios: Research Funding; Eli Lilly: Research Funding; AbbVie: Consultancy, Honoraria, Research Funding; Cellectis: Research Funding; Amgen: Consultancy, Honoraria; F. Hoffman La-Roche: Consultancy, Honoraria, Research Funding; Genentech: Honoraria, Research Funding; Ascentage: Research Funding; Kisoji: Consultancy, Honoraria; Reata Pharmaceuticals: Equity Ownership, Patents & Royalties; Ablynx: Research Funding; Forty-Seven: Consultancy, Honoraria; Calithera: Research Funding; Stemline Therapeutics: Consultancy, Honoraria, Research Funding.

Genetic mutations in FLT3 (fms-like tyrosine kinase-3) play an important role in the pathogenesis of acute myeloid leukemia (AML). FLT3 internal tandem duplications (FLT3-ITD) occur in approximately 25% of all AML cases and various tyrosine kinase inhibitors (TKIs) targeting FLT3-ITD such as quizartinib, crenolanib, and gilteritinib have been developed. Although these selective FLT3 inhibitors were thought to be promising, their effects turned out to be temporary due to the rapid development of resistance associated with clonal switching. Acquired FLT3 point mutations at D835 in the activation loop of tyrosine kinase domain are often accountable for clonal switching at least for Type II TKIs. In addition, adjunct mutations in other genes are also found to be associated with TKI resistance. To investigate the underlying molecular mechanism of this secondary, mutation-driven acquired resistance, we first analyzed co-occurring mutations in the leukemia cells obtained from 26 AML patients with FLT3-ITD (n=14) or FLT3-ITD/D835 dual (n=12) mutations, and performed cap analysis of gene expression (CAGE) sequencing, which identifies and quantifies the 5' ends of capped mRNA transcripts (transcription start sites) and allows investigating promoter structures necessary for gene expression. Patients with FLT3-ITD/D835 harbored a higher number of co-mutations such as ASXL1 and RUNX1 compared to AML with FLT3-ITD (FLT3-ITD/D835: 2.83 ± 0.52, FLT3-ITD: 0.49 ± 0.13, p To recapitulate the observations obtained with primary human AML samples, we generated MV4;11 cells with acquired FLT3-ITD/D835 mutations (MV4;11-QR cells) by culturing FLT3-ITD MV4;11 leukemia cells in the presence of quizartinib (1.5 nM), a selective FLT3 inhibitor, for 6 months. While quizartinib (0.2 nM) suppressed the proliferation of 50% of the parental MV4;11 at 72 hours, much higher concentrations of quizartinib (10 nM) was required to suppress the proliferation of MV4;11-QR cells. Quantitative RT-PCR and immunoblot analysis revealed that MV4;11-QR cells expressed higher transcript and protein levels of BCL2A1 than MV4;11 parental cells, while BCL2 levels were similar in both cells and MCL1 and BCLxL expression were lower in the MV4;11-QR than in the parental cells. Next, to investigate the molecular properties of AML cells bearing FLT3-ITD or FLT3-ITD/D835 without other co-mutations, we created Ba/F3 cells stably expressing FLT3-ITD or FLT3-ITD/D835. Of notes, the FLT3-ITD/D835 Ba/F3 cells expressed markedly higher BCL2 transcript and protein levels with lower expression of BCLxL than in FLT3-ITD Ba/F3 cells. No significant difference of MCL1 expression was observed. The sensitivity to quizartinib was massively decreased in the FLT3-ITD/D835 Ba/F3 cells (IC50: FLT3-ITD/D835 >1000nM vs. FLT3-ITD, 0.8nM, at 48h). Finally, we examined the efficacy of the BCL-2 specific inhibitor venetoclax in FLT3-ITD/D835 dual mutated cells with or without upregulation of BCL2 or BCL2A1, the latter shown to confer resistance to venetoclax by sequestering released BIM (Esteve-Arenys, Oncogene. 2018). As expected, venetoclax caused more profound cell growth inhibition and apoptosis induction in BCL2 upregulated FLT3-ITD/D835 Ba/F3 compared to FLT3-ITD Ba/F3 cells (IC50: FLT3-ITD/D835 301nM vs. FLT3-ITD >1000 nM, 96 h). However, FLT3-ITD/D835 bearing MV4;11-QR cells with upregulated BCL2A1 were less sensitive to venetoclax than MV4;11 parental cells (IC50: MV4;11-QR, 149nM vs. MV4;11, 33 nM, 72 h). In conclusion, these results demonstrate that acquisition of D835 mutation in FLT3-ITD mutated AML is often accompanied with multiple co-occurring genetic mutations, and depends on anti-apoptotic BCL-2 associated pro-survival mechanisms. BCL2A1 upregulation might be involved in pathogenesis of acquired drug resistance of FLT3-ITD/D835 dual mutant AML cells, and is a promising new target in FLT3-ITD/D835 refractory AML with complex mutations. Disclosures Carter: Amgen: Research Funding; AstraZeneca: Research Funding; Ascentage: Research Funding. Shah:Bristol-Myers Squibb: Research Funding. Konopleva:Genentech: Honoraria, Research Funding; Ascentage: Research Funding; Kisoji: Consultancy, Honoraria; Reata Pharmaceuticals: Equity Ownership, Patents & Royalties; Ablynx: Research Funding; Astra Zeneca: Research Funding; Agios: Research Funding; Calithera: Research Funding; Stemline Therapeutics: Consultancy, Honoraria, Research Funding; Forty-Seven: Consultancy, Honoraria; Eli Lilly: Research Funding; AbbVie: Consultancy, Honoraria, Research Funding; Cellectis: Research Funding; Amgen: Consultancy, Honoraria; F. Hoffman La-Roche: Consultancy, Honoraria, Research Funding. Andreeff:Daiichi Sankyo, Inc.: Consultancy, Patents & Royalties: Patents licensed, royalty bearing, Research Funding; Jazz Pharmaceuticals: Consultancy; Celgene: Consultancy; Amgen: Consultancy; AstaZeneca: Consultancy; 6 Dimensions Capital: Consultancy; Reata: Equity Ownership; Aptose: Equity Ownership; Eutropics: Equity Ownership; Senti Bio: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Oncoceutics: Equity Ownership; Oncolyze: Equity Ownership; Breast Cancer Research Foundation: Research Funding; CPRIT: Research Funding; NIH/NCI: Research Funding; Center for Drug Research & Development: Membership on an entity's Board of Directors or advisory committees; Cancer UK: Membership on an entity's Board of Directors or advisory committees; NCI-CTEP: Membership on an entity's Board of Directors or advisory committees; German Research Council: Membership on an entity's Board of Directors or advisory committees; Leukemia Lymphoma Society: Membership on an entity's Board of Directors or advisory committees; NCI-RDCRN (Rare Disease Cliln Network): Membership on an entity's Board of Directors or advisory committees; CLL Foundation: Membership on an entity's Board of Directors or advisory committees; BiolineRx: Membership on an entity's Board of Directors or advisory committees.

Motivation: Although several methods exist to relate high-dimensional gene expression data to various clinical phenotypes, finding combinations of features in such input remains a challenge, particularly when fitting complex statistical models such as those used for survival studies. Results: Our proposed method builds on existing ‘regularization path-following’ techniques to produce regression models that can extract arbitrarily complex patterns of input features (such as gene combinations) from large-scale data that relate to a known clinical outcome. Through the use of the data’s structure and itemset mining techniques, we are able to avoid combinatorial complexity issues typically encountered with such methods, and our algorithm performs in similar orders of duration as single-variable versions. Applied to data from various clinical studies of cancer patient survival time, our method was able to produce a number of promising gene-interaction candidates whose tumour-related roles appear confirmed by literature. Availability: An R implementation of the algorithm described in this article can be found at https://github.com/david-duverle/regularisation-path-following Contact: dave.duverle@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Shugoshin 1 (SGO1) is required for accurate chromosome segregation during mitosis and meiosis; however, its other functions, especially at interphase, are not clearly understood. Here, we found that downregulation of SGO1 caused a synergistic phenotype in cells overexpressing MYCN. Downregulation of SGO1 impaired proliferation and induced DNA damage followed by a senescence-like phenotype only in MYCN-overexpressing neuroblastoma cells. In these cells, SGO1 knockdown induced DNA damage, even during interphase and this effect was independent of cohesin. Furthermore, MYCN-promoted SGO1 transcription and SGO1 expression tended to be higher in MYCN- or MYC-overexpressing cancers. Together, these findings indicate that SGO1 plays a role in the DNA damage response in interphase. Therefore, we propose that SGO1 represents a potential molecular target for treatment of MYCN-amplified neuroblastoma.

Internal tandem duplications (ITD) in the juxtamembrane domain of FMS-like tyrosine kinase 3 (FLT3) cause ligand-independent constitutive activation of FLT3 kinase and its downstream signaling. FLT3-ITD mutations confer poor prognosis with high relapse rates in AML patients. FLT3-targeted therapies using tyrosine kinase inhibitors (TKIs) often induce additional point mutations within the tyrosine kinase domains (FLT3-TKD mutations), most commonly found at D835 activation loop. Additional FLT3-TKD mutations that cause secondary resistance emerge in at least 20% of patients with TKI treatment. To elucidate the alterations of transcriptome signatures of FLT3-ITD and TKD double mutations in AML, we performed cap analysis of gene expression (CAGE) sequencing for 26 primary AML samples (14 with FLT3-ITD, 12 with FLT3-ITD/D835). CAGE detects and quantifies the specific transcriptional start site (TSS) transcripts, which enables high-throughput gene expression profiling and promoter usage analysis. Altered transcription of TSS in FLT3-ITD/D835 AML samples were detected by comparison with TSS in FLT3-ITD samples, and upregulation of 310 TSS and downregulation of 22 TSS were mapped (FDR < 0.05, EdgeR). Based on Gene Ontology (GO) analysis, up-regulated genes were enriched in "apoptotic process", "intracellular signal transduction" and "immune system development", including pro-survival BCL2A1 and drug resistance related S100A8 and PRKCH. To validate these transcriptional changes, we utilized isogenic paired Ba/F3 cells transfected with FLT3-ITD or FLT3-ITD/D835. CAGE detected upregulation of 1945 TSS and downregulation of 1470 TSS in FLT3-ITD/D835 compared to FLT3-ITD cells (FDR < 0.05). TSS transcriptions of Bcl-2, Prkca, NF-κB1, Myc, and Cdkn1a (p21) were upregulated in FLT3-ITD/D835 cells. GO analysis consistently highlighted higher activation of NF-κB signaling and its downstream Bcl-2 in FLT3-ITD/D835 than in FLT3-ITD cells both for primary AML samples and Ba/F3 cells. To determine a correlation between activated promoters and transcription factors in FLT3-ITD/D835 cells, we performed an unbiased search for enriched sequence motifs using HOMER software. HOMER revealed that the promoter 4 of BCL2A1 contained a common motif of transcription factor STAT6, known to associate with NF-κB and cooperatively bound to their respective promoter elements. Ingenuity Pathway Analysis also highlighted higher activation of STAT6 in FLT3-ITD/D835 AML cells compared to FLT3-ITD. Immunoblot analysis confirmed higher expression of Bcl-2, c-Myc, p27, and lower expression of Bcl-xL and Mcl-1 in FLT3-ITD/D835 Ba/F3 compared to FLT3-ITD Ba/F3 cells. FLT3-ITD and FLT3-ITD/D835 cells showed similar expression level of Bax and Bid. We found that FLT3-ITD/D835 Ba/F3 cells proliferated slower than FLT3-ITD cells (growth rate; FLT3-ITD/D835 9.8±2.4 fold, FLT3-ITD 19.8±1.2 fold, p=0.003, 48 h) with G0/G1 accumulation (FLT3-ITD/D835 61.5±10.1%, FLT3-ITD 31.3±11.2%, p Finally, we hypothesized that targeting Bcl-2 may effectively overcome the acquired resistance of FLT3-ITD/D835 cells. Venetoclax (ABT-199/GDC-0199), a clinically available Bcl-2 selective inhibitor, as single agent was not capable of eliminating FLT3-ITD AML due to altered activation of FLT3 downstream signaling and Mcl-1 upregulation. FLT3-ITD/D835 cells showed higher expression of the Bcl-2 gene and/protein and were less dependent on FLT3 signaling compared to FLT3-ITD cells (Tabe, ASH 2017). As expected, venetoclax caused more profound cell growth inhibition and apoptosis induction in FLT3-ITD/D835 Ba/F3 than in FLT3-ITD Ba/F3 cells (IC50 2.98 μM vs 13.9 μM, ED50 28.8 μM vs 173 μM, 48 h). In conclusion, we identified Bcl-2 transcriptional activation as a novel mechanism by which the acquired D835 mutation in FLT3-ITD AML cells facilitates anti-apoptotic network activation and confers TKI resistance. Bcl-2 inhibition by venetoclax represents a putative therapeutic strategy in FLT3-ITD/TDK double-mutated AML cells. Disclosures Shah: Bristol-Myers Squibb: Research Funding; ARIAD: Research Funding. Konopleva:Stemline Therapeutics: Research Funding. Andreeff:AstraZeneca: Research Funding.

FMS-like tyrosine kinase 3 with internal tandem duplication (FLT3-ITD), the most frequent mutation in acute myeloid leukemia (AML), results in the constitutive ligand-independent activation of FLT3 receptor downstream signaling. FLT3-targeted therapies using tyrosine kinase inhibitors (TKIs) demonstrate single agent activity in these patients but long-term efficacy is limited by emerging resistance in part due to acquired point mutations in the tyrosine kinase domains (TKD) of the FLT3 gene, most commonly found at D835 within the activation loop. Exportin 1 (XPO1) mediates the nucleo-cytoplasmic transport, and is overexpressed in AML cells with FLT3-ITD mutations (Kojima, Blood, 2013). We have reported that the clinically available XPO1 inhibitor selinexor effectively inhibits cell proliferation in both FLT3-ITD and FLT3-ITD/D835 mutated cells through upregulation of TP53 and blockade of c-Myc signaling (Tabe, ASH, 2017). In this study, we aimed at developing novel mechanism-based combination therapies for TKI-resistant FLT3-ITD cells with acquired TKD mutation. First we investigated the transcriptional changes associated with XPO1 and FLT3 inhibition in FLT3-ITD and FLT3-ITD/D835 mutated cells. We utilized paired isogenic FLT3-ITD or FLT3-ITD/D835Y transfected Ba/F3 cell lines and performed the cap analysis of gene expression (CAGE) that identifies and quantifies gene expression at the transcription start sites (TSS). FLT3-ITD cells are sensitive and FLT3-ITD/D835 cells are resistant to FLT3 inhibitor quizartinib. CAGE detected the shared upregulation of 3833 TSS genes induced by selinexor in FLT3-ITD and FLT3-ITD/D835 cells (FDR Based on these findings, we focused on Bcl-2 as a novel therapeutic target in FLT3-ITD/D835 cells, and investigated the anti-leukemia efficacy of combined inhibition of Bcl-2 and XPO1. We utilized the clinically available selective Bcl-2 inhibitor venetoclax and observed synergistic anti-proliferative and pro-apoptotic effects of venetoclax and selinexor in FLT3-ITD/D835 (Combination Index, CI: 0.39 and 0.45). Simultaneous inhibition of Bcl-2 by venetoclax and FLT3 by quizartinib showed no synergistic or additive effects in FLT3-ITD/D835 cells. Western blot analysis showed that the combination of venetoclax / selinexor reduced Bcl-2 and Mcl-1 in FLT3-ITD/D835 cells, and activated cleaved caspase3. In FLT3-ITD cells, the venetoclax / selinexor combination induced only small decrease of Bcl-2, did not change Mcl-1 and Bcl-xL, and increased cleaved caspase3. These changes were not observed in wt-FLT3 transfected Ba/F3 cells. Collectively, CAGE analysis of transcription start sites identified the primary mechanism underlying the synergistic activity of concomitant inhibition of Bcl-2 and XPO1 in FLT3-ITD/D835 cells as related to the regulation of Bcl-2, Mcl-1, Bcl-xL and c-Myc. These findings suggest that Bcl-2 inhibition by venetoclax combined with XPO1 inhibition by selinexor could be developed into a promising therapeutic strategy for TKI-resistant AML patients with FLT3-ITD and secondary acquired TKD mutations. Disclosures Konopleva: Stemline Therapeutics: Research Funding. Andreeff:AstraZeneca: Research Funding.

Acute myeloid leukemia (AML) cells are highly dependent on oxidative phosphorylation (OxPhos) for survival and continually adapt to fluctuations in nutrient and oxygen availability in the bone marrow (BM) microenvironment. The first-in-class OxPhos inhibitor IACS-010759 (Molina, Nat. Medicine 2018) is currently in Phase 1 clinical trial in AML. To identify biomarkers of sensitivity or resistance to OxPhos inhibition, we performed Cap Analysis of Gene Expression analysis (CAGE) in primary AML samples (11 sensitive and 3 resistant to IACS-010759) and 6 AML cell lines (OCI-AML3, MOLM13, THP-1, U937, MV4;11, HL60). CAGE identified 41 gene transcripts that were significantly higher in IACS-010759 resistant primary AML samples than in sensitive samples (fold change >3.0, FDR We next studied OxPhos inhibition under conditions mimicking BM microenvironment, by co-culturing AML cells with healthy BM-derived mesenchymal stem cells (MSC). Anti-proliferative effects of IACS-010759 were reduced by co-culture with MSC (IC50 0.01nM vs 2.1nM OCI-AML3, 65.4nM vs >10µM MOLM13). MSC co-culture increased OCR and glycoPER, and IACS-010759 decreased OCR / increased glycoPER in both cell lines. To determine the mechanism of resistance to IACS-010759 under MSC co-culture conditions, we studied the mitochondrial exchange between AML cells and MSC. We observed the bidirectional mitochondrial transfer between MSCs and AML cells. Using AML and MSC cells stably infected with mitochondria-targeted PDHA1 (GFP in AML, dsRed in MSC) to visualize the mitochondria, we found that IACS-010759 treatment facilitated transfer of AML-derived mitochondria into the adhered MSCs (24h), and MSC-derived mitochondria transferred to floating AML cells (48-72h) along with formation of tunneling nanotubes (TNTs) of AML cells, in sensitive OCI-AML3 cells (PDHA1-GFP/DsRed double positive %, control vs IACS; 9.0% vs 23.3 %). Mitochondria transfer from MSCs to AML cells was minimally observed in MOLM13 cells with elevated basal OxPhos (4.0% vs 5.0%). We next investigated IACS-010759-induced metabolic changes in AML cells interacting with bone marrow (BM) stromal cells. Capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS) metabolite analysis further detected that IACS-010759 suppressed multiple anaplerotic amino acids in OCI-AML3 cells including glutamine and glutamic acid, which was reversed by MSC co-culture along with increase in intra-autophagosomal LC3-II in OCI-AML3 cells. These findings were not observed in MOLM13. Microenvironment-induced activation of glutamine metabolism and autophagy-associated amino acid metabolism could be additional compensatory mechanisms in response to OxPhos inhibition by IACS-010759 in BM microenvironment. Taken together, basal metabolic energetic capacity including elevated OxPhos and high compensatory glycolysis confer the AML-intrinsic resistance to IACS-010759, which can be reversed by simultaneous glycolysis inhibition. BM microenvironment facilitates secondary resistance to OxPhos inhibition through modulation of amino acid metabolism and direct mitochondrial transfer. Inhibition of these processes could enhance the anti-AML efficacy of OxPhos inhibition. Disclosures Andreeff: AstraZeneca: Research Funding. Konopleva:Stemline Therapeutics: Research Funding.

Members of the forkhead-box (Fox) family of transcription factors are present in many eukaryotes. More than 100 such proteins that share homology in the winged-helix DNA-binding domain have been identified in higher eukaryotes. This family of transcription factors is implicated in the regulation of a variety of cellular processes, including the cell cycle, apoptosis, DNA repair, stress resistance and metabolism. A subfamily of Fox proteins are required to activate expression of the genes encoding B-type cyclins, Cdc25 and Polo-like kinase (Plk) during the mitotic cell cycle and meiosis in organisms from yeast to mammals. These proteins are activators of cyclin-dependent kinase 1 (Cdk1). Cdk1 and Plk phosphorylate Fox and its associated proteins at different sites, resulting in activation or repression of Fox transcriptional activity, depending on the target genes. In addition to their documented transcriptional functions, Fox proteins are involved in the regulation of pre-mRNA processing, at least in yeast. In this review, we will focus on the role of Fox proteins in the fission yeast Schizosaccharomyces pombe and budding yeast Saccharomyces cerevisiae, in addition to the role of FoxM1 in mammals in the cell cycle and in pre-mRNA processing, as revealed in recent studies.

The kinase Cdc2p is a central regulator of entry into and progression through nuclear division during mitosis and meiosis in eukaryotes. Cdc2p is activated at the onset of mitosis by dephosphorylation on tyrosine-15, the phosphorylation status of which is determined mainly by the kinase Wee1p and the phosphatase Cdc25p. In fission yeast, the forkhead-type transcription factor Mei4p is required for expression of many genes during meiosis, with mei4 mutant cells arresting before meiosis I. The mechanism of cell cycle arrest in mei4 cells has remained unknown, however. We now show that cdc25 + is an important target of Mei4p in control of entry into meiosis I. Forced dephosphorylation of Cdc2p on tyrosine-15 thus induced meiosis I in mei4 mutant cells without a delay, although no spores were formed. We propose that Mei4p acts as a rate-limiting regulator of meiosis I by activating cdc25 + transcription in coordination with other meiotic events.

Neuroblastoma (NB) is a childhood malignant tumor that arises from precursor cells of the sympathetic nervous system. Spontaneous regression is a phenomenon unique to NBs and is caused by differentiation of tumor cells. PES1 is a multifunctional protein with roles in both neural development and ribosome biogenesis. Various kinds of models have revealed the significance of PES1 in neurodevelopment. However, the roles of PES1 in NB tumorigenesis and differentiation have remained unknown. Here we show that NB cases with MYCN amplification and clinically unfavorable stage (INSS stage 4) express higher levels of PES1. High PES1 expression was associated with worse overall and relapse-free survival. In NB cell lines, PES1 knockdown suppressed tumor cell growth and induced apoptosis. This growth inhibition was associated with the expression of NB differentiation markers. However, when the differentiation of NB cell lines was induced by the use of all-trans retinoic acid, there was a corresponding decrease in PES1 expression. Pes1 expression of tumorspheres originated from MYCN transgenic mice also diminished after the induction of differentiation with growth factors. We also reanalyzed the distribution of PES1 in the nucleolus. PES1 was localized in the dense fibrillar component, but not in the granular component of nucleoli. After treatment with the DNA-damaging agent camptothecin, this distribution was dramatically changed to diffuse nucleoplasmic. These data suggest that PES1 is a marker of NB outcome, that it regulates NB cell proliferation, and is associated with NB differentiation.

The basic helix-loop-helix transcription factor NeuroD1 has been implicated in the neurogenesis and early differentiation of pancreatic endocrine cells. However, its function in relation to cancer has been poorly examined. In this study, we found that NeuroD1 is involved in the tumorigenesis of neuroblastoma. NeuroD1 was strongly expressed in a hyperplastic region comprising neuroblasts in the celiac sympathetic ganglion of 2-week-old MYCN transgenic (Tg) mice and was consistently expressed in the subsequently generated neuroblastoma tissue. NeuroD1 knockdown by short hairpin RNA (shRNA) resulted in motility inhibition of the human neuroblastoma cell lines, and this effect was reversed by shRNA-resistant NeuroD1. The motility inhibition by NeuroD1 knockdown was associated with induction of Slit2 expression, and knockdown of Slit2 could restore cell motility. Consistent with this finding, shRNA-resistant NeuroD1 suppressed Slit2 expression. NeuroD1 directly bound to the first and second E-box of the Slit2 promoter region. Moreover, we found that the growth of tumor spheres, established from neuroblastoma cell lines in MYCN Tg mice, was suppressed by NeuroD1 suppression. The functions identified for NeuroD1 in cell motility and tumor sphere growth may suggest a link between NeuroD1 and the tumorigenesis of neuroblastoma. Indeed, tumor formation of tumor sphere–derived cells was significantly suppressed by NeuroD1 knockdown. These data are relevant to the clinical features of human neuroblastoma: high NeuroD1 expression was closely associated with poor prognosis. Our findings establish the critical role of the neuronal differentiation factor NeuroD1 in neuroblastoma as well as its functional relationship with the neuronal repellent factor Slit2. Cancer Res; 71(8); 2938–48. ©2011 AACR.

The spindle checkpoint is a surveillance mechanism that ensures the fidelity of chromosome segregation in mitosis. Here we show that fission yeast casein kinase II (CK2) is required for this checkpoint function. In the CK2 mutants mitosis occurs in the presence of a spindle defect, and the spindle checkpoint protein Mad2p fails to localize to unattached kinetochores. The CK2 mutants are sensitive to the microtubule depolymerising drug thiabendazole, which is counteracted by ectopic expression of mad2+. The level of Mad2p is low in the CK2 mutants. These results suggest that CK2 has a role in the spindle checkpoint by regulating Mad2p.

In most eukaryotes, cyclin-dependent kinases (Cdks) play a central role in control of cell-cycle progression. Cdks are inactivated from the end of mitosis to the start of the next cell cycle as well as during sexual differentiation. The forkhead-type transcription factor Fkh2p is required for the periodic expression of many genes and for efficient mating in the fission yeast Schizosaccharomyces pombe. However, the mechanism responsible for coordination of cell-cycle progression with sexual differentiation is still unknown. We now show that Fkh2p is phosphorylated by Cdc2p (Cdk1) and that phosphorylation of Fkh2p on T314 or S462 by this Cdk blocks mating in S. pombe by preventing the induction of ste11+ transcription, which is required for the onset of sexual development. We propose that functional interaction between Cdks and forkhead transcription factors may link the mitotic cell cycle and sexual differentiation.