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Supplementary Figure 4 from Selective Inhibition of Histone Deacetylases Sensitizes Malignant Cells to Death Receptor Ligands

Supplementary Figure Legends 1-4 from Selective Inhibition of Histone Deacetylases Sensitizes Malignant Cells to Death Receptor Ligands

Supplementary Figure 2 from Selective Inhibition of Histone Deacetylases Sensitizes Malignant Cells to Death Receptor Ligands

Supplementary Figure 3 from Selective Inhibition of Histone Deacetylases Sensitizes Malignant Cells to Death Receptor Ligands

Normal epithelial cells undergo apoptosis upon detachment from the extracellular matrix, a process termed “anoikis.” However, malignant epithelial cells with metastatic potential resist anoikis and can survive in an anchorage-independent fashion. Molecules that sensitize resistant cells to anoikis will be useful chemical probes to understand this pathway. To identify novel anoikis sensitizers in anoikis-resistant PPC-1 prostate adenocarcinoma cells, a library of 2,000 off-patent drugs and natural products was screened for their ability to preferentially induce cell death in suspension over adherent culture conditions. This screen identified five members of the family of cardiac glycosides as anoikis sensitizers, including ouabain, peruvoside, digoxin, digitoxin, and strophanthidin. We conducted further studies with ouabain to discern the mechanism of cardiac glycoside-induced anoikis sensitization. Ouabain initiated anoikis through the mitochondrial pathway of caspase activation. In addition, ouabain sensitized cells to anoikis by inhibiting its known target, the Na+/K+ ATPase pump, and inducing hypoosmotic stress. Resistance to anoikis permits cancer cells to survive in the circulation and facilitates their metastasis to distant organs, so we tested the effects of Na+/K+ ATPase inhibition on distant tumor formation in mouse models. In these mouse models, ouabain inhibited tumor metastases but did not alter the growth of subcutaneous tumors. Thus, we have identified a novel mechanism to sensitize resistant cells to anoikis and decrease tumor metastasis. These results suggest a potential mechanism for the observed clinical reduction in metastasis and relapse in breast cancer patients who have undergone treatments with cardiac glycosides. [Cancer Res 2009;69(7):2739–47]

Supplementary Figure 3 from Inhibition of the Sodium Potassium Adenosine Triphosphatase Pump Sensitizes Cancer Cells to Anoikis and Prevents Distant Tumor Formation

Supplementary Figure 2 from Inhibition of the Sodium Potassium Adenosine Triphosphatase Pump Sensitizes Cancer Cells to Anoikis and Prevents Distant Tumor Formation

Supplementary Figure 1 from Inhibition of the Sodium Potassium Adenosine Triphosphatase Pump Sensitizes Cancer Cells to Anoikis and Prevents Distant Tumor Formation

The endocytic adaptor protein Numb acts as a tumor suppressor through downregulation of oncogenic pathways in multiple cancer types. The identification of splicing alterations giving rise to changes in Numb protein isoform expression indicate that Numb also has tumor promoting activity, though the underlying mechanisms are unknown. Here we report that NUMB exon 9 inclusion, which results in production of a protein isoform with an additional 49 amino acids, is a feature of multiple cancer types including all subtypes of breast cancer and correlates with worse progression-free survival. Specific deletion of exon 9-included Numb isoforms (Exon9in) from breast cancer cells reduced cell growth and prevents spontaneous lung metastasis in a mouse model. Quantitative proteome profiling showed that loss of Exon9in causes downregulation of membrane receptors and adhesion molecules, as well as proteins involved in extracellular matrix organization and the epithelial-mesenchymal transition (EMT) state. In addition, exon 9 deletion caused remodeling of the endocytic network, decreased ITGβ5 surface localization, cell spreading on vitronectin and downstream signaling to ERK and SRC. Together these observations suggest that Exon9in isoform expression disrupts the endocytic trafficking functions of Numb, resulting in increased surface expression of ITGβ5 as well as other plasma membrane proteins to promote cell adhesion, EMT, and tumor metastasis.

Deregulated alternative splicing of the endocytic adaptor NUMB resulting in high expression of Exon9in (exon 9-containing) isoforms has been reported in several cancer types. However, the role of Numb isoform expression in tumor progression and the underlying mechanisms remain elusive. Here, we report greater exon 9 inclusion in multiple cancer types including all subtypes of breast cancer, and correlation of higher exon 9 inclusion in patients with worse prognosis. Deletion of Exon9in in breast cancer cells leads to reduced cell growth and a significant decrease of lung metastasis in orthotopic xenograft experiments. Quantitative mass spectrometry revealed downregulation of proteins involved in EMT and ECM organization and remodeling of the endocytic protein network in cells lacking the Exon9in Numb isoforms. Exon 9 deletion also results in reduced surface levels of ITGβ5, and downstream signaling to ERK and SRC, consistent with enhance lysosomal targeting mediated by the remaining Exon9sk (exon 9 skipping) Numb isoforms.SIGNIFICANCEExpression of NUMB Exon9in protein isoforms correlate with worse progression free survival, particularly in breast cancer. Our findings also reveal that Exon9in isoforms promote breast cancer progression by relieving Numb mediated down regulation of integrins and implicate Numb alternative splicing as a progression factor in multiple cancer types.

CBL is a RING type E3 ubiquitin ligase that functions as a negative regulator of tyrosine kinase signaling and loss of CBL E3 function is implicated in several forms of leukemia. The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL and are required for CBL-dependent downregulation of antigen receptor, cytokine receptor, and receptor tyrosine kinase signaling. Despite the established role of SLAP/SLAP2 in regulating CBL activity, the nature of the interaction and the mechanisms involved are not known. To understand the molecular basis of the interaction between SLAP/SLAP2 and CBL, we solved the crystal structure of CBL tyrosine kinase binding domain (TKBD) in complex with SLAP2. The carboxy-terminal region of SLAP2 adopts an α-helical structure which binds in a cleft between the 4H, EF-hand, and SH2 domains of the TKBD. This SLAP2 binding site is remote from the canonical TKBD phospho-tyrosine peptide binding site but overlaps with a region important for stabilizing CBL in its autoinhibited conformation. In addition, binding of SLAP2 to CBL in vitro activates the ubiquitin ligase function of autoinhibited CBL. Disruption of the CBL/SLAP2 interface through mutagenesis demonstrated a role for this protein-protein interaction in regulation of CBL E3 ligase activity in cells. Our results reveal that SLAP2 binding to a regulatory cleft of the TKBD provides an alternative mechanism for activation of CBL ubiquitin ligase function.

On-patent and off-patent drugs with previously unrecognized anticancer activity could be rapidly repurposed for this new indication given their prior toxicity testing. To identify such compounds, we conducted chemical screens and identified the antihelmintic flubendazole. Flubendazole induced cell death in leukemia and myeloma cell lines and primary patient samples at nanomolar concentrations. Moreover, it delayed tumor growth in leukemia and myeloma xenografts without evidence of toxicity. Mechanistically, flubendazole inhibited tubulin polymerization by binding tubulin at a site distinct from vinblastine. In addition, cells resistant to vinblastine because of overexpression of P-glycoprotein remained fully sensitive to flubendazole, indicating that flubendazole can overcome some forms of vinblastine resistance. Given the different mechanisms of action, we evaluated the combination of flubendazole and vinblastine in vitro and in vivo. Flubendazole synergized with vinblastine to reduce the viability of OCI-AML2 cells. In addition, combinations of flubendazole with vinblastine or vincristine in a leukemia xenograft model delayed tumor growth more than either drug alone. Therefore, flubendazole is a novel microtubule inhibitor that displays preclinical activity in leukemia and myeloma.

Background Normal epithelial cells undergo anoikis, or apoptosis on loss of anchorage to the extracellular matrix, by initiating the death receptor pathway of caspase activation. However, malignant epithelial cells with metastatic potential resist anoikis and can survive in an anchorage-independent fashion. We hypothesized that c-Fas – associated death domain – like interleukin-1 – converting enzyme – like inhibitory protein (FLIP), an endogenous inhibitor of death receptor signaling, may suppress anoikis. Methods We assessed viability and apoptosis of PPC-1 prostate cancer cells cultured in adherent and suspension condi tions using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt and Annexin V staining assays. Expression of the death receptor Fas and activation of caspase 8 were measured using flow cytometry. Expression of Fas ligand was measured by reverse transcription – polymerase chain reaction. FLIP protein expression was measured by immunoblotting. Small-molecule inhibitors of FLIP (including the death receptor sensitizer 5809354) and small-interfering (si) RNA directed against FLIP were used to assess the effects of FLIP inhibition on anoikis of prostate cancer cells in vitro and in vivo. All statistical tests were two-sided. Results PPC-1 cells cultured in suspension resisted anoikis, despite increased expression of Fas (0 versus 8 hours, mean relative percent expression = 100% versus 135%, difference = 35%, 95% confidence interval [CI] = 10% to 61%; P = .02) and Fas L (0 versus 24 hours, mean relative percent expression = 100% versus 208%, difference = 108%, 95% CI = 18% to 197%; P = .02). Knockdown of FLIP expression by siRNA or treatment with 5809354 sensitized prostate cancer cells to anoikis (control siRNA versus FLIP siRNA at 10 nM, mean relative percent viability = 95% versus 51%, difference = 44%, 95% CI = 34% to 54%; P

A new class of selective FXIIIa inhibitors with a bicyclic [1,2,4]-thiadiazole pharmacophore is described. At 160 muM, compound 8 caused 50% reduction in fibrin gamma-chain cross-linking and suppressed the polymerization of alpha chains in platelet-depleted human plasma clots. Fibrinolysis rates in response to tissue plasminogen activator were directly proportional to the concentration of 8 in plasma at the time of clotting.

Evasion of death receptor ligand–induced apoptosis represents an important contributor to cancer development and progression. Therefore, molecules that restore sensitivity to death receptor stimuli would be important tools to better understand this biological pathway and potential leads for therapeutic adjuncts. Previously, the small-molecule 4-(4-chloro-2-methylphenoxy)-N-hydroxybutanamide (that we propose be named droxinostat) was identified as a chemical sensitizer to death receptor stimuli, decreasing the expression of the caspase-8 inhibitor FLIP. However, the direct targets of droxinostat were unknown. To better understand the mechanism of action of droxinostat and highlight new strategies to restore sensitivity to death receptor ligands, we analyzed changes in gene expression using the Connectivity Map after treating cells with droxinostat. Changes in gene expression after droxinostat treatment resembled changes observed after treatment with histone deacetylase (HDAC) inhibitors. Therefore, we examined the effects of droxinostat on HDAC activity and showed that it selectively inhibited HDAC3, HDAC6, and HDAC8 and that inhibition of these HDACs was functionally important for its ability to sensitize cells to death ligands. Thus, we have identified a selective HDAC inhibitor and showed that selective HDAC inhibition sensitizes cells to death ligands, thereby highlighting a new mechanism to overcome resistance to death receptor ligands. Mol Cancer Ther; 9(1); 246–56

Normal epithelial cells undergo apoptosis upon detachment from the extracellular matrix, a process termed “anoikis.” However, malignant epithelial cells with metastatic potential resist anoikis and can survive in an anchorage-independent fashion. Molecules that sensitize resistant cells to anoikis will be useful chemical probes to understand this pathway. To identify novel anoikis sensitizers in anoikis-resistant PPC-1 prostate adenocarcinoma cells, a library of 2,000 off-patent drugs and natural products was screened for their ability to preferentially induce cell death in suspension over adherent culture conditions. This screen identified five members of the family of cardiac glycosides as anoikis sensitizers, including ouabain, peruvoside, digoxin, digitoxin, and strophanthidin. We conducted further studies with ouabain to discern the mechanism of cardiac glycoside-induced anoikis sensitization. Ouabain initiated anoikis through the mitochondrial pathway of caspase activation. In addition, ouabain sensitized cells to anoikis by inhibiting its known target, the Na+/K+ ATPase pump, and inducing hypoosmotic stress. Resistance to anoikis permits cancer cells to survive in the circulation and facilitates their metastasis to distant organs, so we tested the effects of Na+/K+ ATPase inhibition on distant tumor formation in mouse models. In these mouse models, ouabain inhibited tumor metastases but did not alter the growth of subcutaneous tumors. Thus, we have identified a novel mechanism to sensitize resistant cells to anoikis and decrease tumor metastasis. These results suggest a potential mechanism for the observed clinical reduction in metastasis and relapse in breast cancer patients who have undergone treatments with cardiac glycosides. [Cancer Res 2009;69(7):2739–47]

Malignant epithelial cells with metastatic potential resist apoptosis that normally occurs upon loss of anchorage from the extracellular matrix, a process termed “anoikis.” Resistance to anoikis enables malignant cells to survive in an anchorage-independent manner, which leads to the formation of distant metastases. To understand the regulation of anoikis, we designed, automated, and conducted a high-throughput chemical screen for anoikis sensitizers. PPC-1 anoikis–resistant prostate cancer cells were seeded in hydrogel-coated ultralow binding plates for suspension conditions and standard tissue culture plates to promote adhesion. After seeding, cells were treated with aliquots from a library of previously characterized small molecules, and viability was assessed using the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt, assay. From this chemical screen, we identified anisomycin that induced apoptosis in suspension conditions, but was not toxic to these cells grown under adherent conditions. Anisomycin sensitized cells to anoikis by decreasing levels of the caspase-8 inhibitor FLIP and subsequently activating the death receptor pathway of caspase activation. Although anisomycin activated c-Jun-NH2-kinase and p38, these kinases were not functionally important for the effect of anisomycin on anoikis and FLIP. Rather, anisomycin decreased FLIP and sensitized cells to anoikis by inhibiting its protein synthesis. Finally, we showed that anisomycin decreased distal tumor formation in a mouse model of prostate cancer metastases. Thus, a novel chemical screen identified anisomycin as an anoikis sensitizer that acts by decreasing FLIP protein synthesis. Our results suggest that FLIP is a suppressor of anoikis and inhibiting FLIP protein synthesis may be a useful antimetastatic strategy. [Cancer Res 2007;67(17):8307–15]

Acquisition of resistance to anchorage dependant cell death, a process termed anoikis, is a requirement for cancer cell metastasis. However, the molecular determinants of anoikis resistance and sensitivity are poorly understood. To better understand resistance to anoikis we conducted a genome wide lentiviral shRNA screen to identify genes whose knockdown render RWPE-1 prostate cells resistant to anoikis. RWPE-1 cells are a non-malignant prostate cell line that undergo cell death upon detachment from extracellular matrix. To identify genetic regulators of anoikis, RWPE-1 cells were infected with a pooled lentiviral hairpin shRNA library with 54,021 hairpins targeting 11,255 genes. After infection, cells were cultured in suspension conditions for three weeks and an anoikis-resistant cell population was selected. From this population, genomic DNA was isolated and shRNA sequences were amplified and sequenced. Thirty four shRNA sequences reproducibly protected RWPE-1 cells from anoikis after culture under suspension conditions. We selected α/β hydrolase domain containing 4 (ABHD4) for further analysis as it conferred the greatest protection to anoikis in our screening assays. To validate the effects of ABHD4 knockdown on anoikis resistance, we infected RWPE-1 with 2 independent shRNA targeting ABHD4 or control sequences. We also over-expressed ABHD4 in wild type cells. Finally, we co-infected cells with ABDH4 cDNA and shRNA as a rescue experiment to demonstrate on-target activity. Target knockdown or over-expression after infection was confirmed by Q-RTPCR or immunoblotting. Using two independent shRNA, knockdown of ABHD4 inhibited anoikis as evidence by increased clonogenic growth compared to cells infected with control sequences. Demonstrating an on-target effect, rescue of ABHD4 expression returned levels of clonogenic growth to wild type levels. Finally, over-expression of ABHD4 increased sensitivity to anoikis and less clonogenic growth was observed in these cells compared to control cells. Resistance to anoikis after ABHD4 knockdown was associated with decreased cleavage of PARP and decreased activation of caspases-3, 8 and 9, but was independent in changes of FLIP expression. Interesting, resistance to anoikis after ABHD4 knockdown was independent of the known role of ABHD4 in the anandamide synthesis pathway and the generation of glycerophospho-N-acyl ethanolamines. Thus, reductions in the levels of ABHD4 confer resistance to anoikis while over-expression of the target enhances anoikis in the anoikis-sensitive cell line RWPE-1. As such, we have identified a novel genetic regulator of anoikis sensitivity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A22.

To identify known drugs with unrecognized anti-leukemia activity, we compiled a library of 500 on patent and off patent compounds, and screened it to identify compounds cytotoxic to leukemia cell lines. From this screen we identified Tigecycline, an antibiotic approved for the treatment of cutaneous and intra-abdominal infections. Tigecycline induced cell death in leukemia cell lines (LD50 3 to 8 μM, n = 6 cell lines) and primary Acute Myeloid Leukemia (AML) patient samples (LD50 5-10 μM, n = 7), preferentially over normal hematopoietic cells (10% cell death at 20 μM, n = 4) by MTS assays and Annexin V staining. Likewise, in colony formation assays, Tigecycline (5μM) reduced the clonogenic growth of primary AML patient samples (n = 4) by 95±1.5 %, demonstrating an effect on leukemia progenitor cells. In contrast, 5 μM of Tigecycline reduced the clonogenic growth of normal hematopoetic cells by 34± 5% (n = 5). Although Tigecycline is structurally related to tetracycline and minocycline, these drugs were not cytotoxic towards AML cell lines up to 25 μM. Thus, Tigecycline appears preferentially cytotoxic to leukemia cells at pharmacologically achievable concentrations. Given the anti-leukemic effects of Tigecycline in vitro, we evaluated the efficacy of Tigecycline as a potential anti-leukemic agent in vivo. Mice injected subcutaneously with OCI-AML2 leukemia cells were treated with Tigecycline 50 mg/kg i.p. daily. Compared to control, Tigecycline decreased tumour mass and volume without toxicity. We also assessed the effect of Tigecycline on primary AML stem cells defined by their ability to initiate leukemic engraftment in vivo. NOD-SCID mice were injected intra-femorally with primary AML cells. Two weeks after injection, mice were treated with Tigecycline 50 mg/kg i.p. daily for two weeks. After treatment, engraftment of human AML cells was measured by flow cytometry. Compared to control, Tigecycline decreased engraftment of AML cells without toxicity. Tigecycline binds and inhibits the bacterial 30S ribosome. Bacterial ribosomes are more homologous to mitochondrial ribosomes than cytosolic ribosomes, so we compared the effects of Tigecycline on mitochondrial and cytosolic protein synthesis. At times preceding the onset of cell death, Tigecycline decreased levels of the mitochondrial protein Cox-1. In contrast, it did not decrease the expression of cytosolic short half-life proteins Bcl-XL and XIAP, suggesting a preferential effect on mitochondrial protein synthesis. Thus, Tigecycline demonstrated preclinical activity through a mechanism related to mitochondrial protein synthesis inhibition. Moreover, Tigecycline appeared cytotoxic to leukemia stem cells over normal hematopoetic stem cells. Given its prior pharmacology and toxicology testing, Tigecycline could be rapidly repositioned for a new anti-leukemic indication. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4538.

Abstract 1017 Poster Board I-39 On patent and off-patent drugs with previously unrecognized anti-cancer activity, could be rapidly repurposed for this new indication given their prior toxicity testing. To identify such compounds, we compiled and screened a chemical library for potential anti-leukemia agents. From these screens, we identified the antihelmintic flubendazole that is currently used for the treatment of gastrointestinal and systemic parasites, but has not been evaluated for the treatment of malignancy. To explore its efficacy as an anti-cancer agent, leukemia and myeloma cell lines were treated with increasing concentrations of flubendazole. Seventy-two hours after incubation, cell viability was measured by the MTS assay. Flubendazole reduced cell viability with an LD50 ≤ 1 μM in 8/8 myeloma and 4/6 leukemia cell lines, a concentration that is pharmacologically achievable. Likewise, flubendazole reduced the clonogenic growth of primary AML samples at nanomolar concentrations. Cell death was confirmed by Trypan blue staining. Given the effects in leukemia and myeloma cells lines, we evaluated the effects of flubendazole in mouse models of leukemia and myeloma. Sublethally irradiated SCID mice were injected subcutaneously with OCI-AML2 leukemia or OPM2 myeloma cells. Mice were then treated intraperitoneally with flubendazole (20-50 mg/kg/day – doses more than 10-fold lower than the LD50) or buffer alone. Flubendazole decreased tumor weight and volume in both mouse models up to 5-fold compared to control without evidence of weight loss or gross organ toxicity. Mechanistically, flubendazole inhibited bovine-tubulin polymerization in cell-free assays and disrupted microtubule architecture in intact cells as visualized by confocal microscopy. We demonstrated that flubendazole bound tubulin at the colchicine binding site, a region distinct from where vinca-alkaloids bind. Flubendazole arrested cells in the G2 phase of the cell cycle and increased the number of multi-nucleated cells. We also demonstrated that cell death after flubendazole treatment was related to its ability to inhibit microtubule polymerization by using cell lines with tubulin mutations (gifts from Dr F. Loganzo, Wyeth, Pearl River, NY and Drs. S. Band Horwitz and C. Yang, Albert Einstein College of Medicine, Bronx, NY). Vinca-alkaloids are p-glycoprotein (Pgp) substrates and Pgp over-expression can limit the efficacy of these agents. Therefore, we tested the effects of Pgp over-expression on flubendazole's cytotoxicty. CEM-VBL cells over-expressing Pgp remained fully sensitive to flubendazole, but were over 1000-fold more resistant to vinblastine than wild type CEM cells. Therefore, flubendazole can overcome some forms of vinca-alkaloid resistance. Given that flubendazole binds tubulin at a site distinct from vinca-alkaloids, we evaluated the combination of flubendazole and vinblastine in vitro and in vivo. OCI-AML2 leukemia cells were treated with increasing concentrations of flubendazole and vinblastine. Flubendazole and vinblastine synergistically induced cell death with combination index (CI) values of 0.09, 0.017, 0.003 and 0.001 at the EC 50, 25, 10 and 5, respectively, where CI values Disclosures: Off Label Use: Flubendazole is used to treat gastrointestinal and systemic parasite infections.

Summary Cancer cells acquire pathological phenotypes through accumulation of mutations that perturb signaling networks. However, global analysis of these events is currently limited. Here, we identify six types of network-attacking mutations (NAMs), including changes in kinase and SH2 modulation, network rewiring, and the genesis and extinction of phosphorylation sites. We developed a computational platform (ReKINect) to identify NAMs and systematically interpreted the exomes and quantitative (phospho-)proteomes of five ovarian cancer cell lines and the global cancer genome repository. We identified and experimentally validated several NAMs, including PKCγ M501I and PKD1 D665N, which encode specificity switches analogous to the appearance of kinases de novo within the kinome. We discover mutant molecular logic gates, a drift toward phospho-threonine signaling, weakening of phosphorylation motifs, and kinase-inactivating hotspots in cancer. Our method pinpoints functional NAMs, scales with the complexity of cancer genomes and cell signaling, and may enhance our capability to therapeutically target tumor-specific networks., Graphical Abstract, Highlights • Mutations perturbing signaling networks are systematically classified and interpreted • Several such functional mutations are identified in cancer and experimentally validated • The results suggest that a single point mutant can have profound signaling effects • Systematic interpretation of genomic data may assist future precision-medicine efforts, A systematic classification of genomic variants in cancer reveals the many ways in which signaling networks can be perturbed, including rewiring and the creation or destruction of phosphorylation sites.