Small-molecule targeting of translation initiation for cancer therapy

Translation initiation plays a critical role in the regulation of cell growth and tumorigenesis. We report here that inhibiting translation initiation through induction of eIF2α phosphorylation by small-molecular-weight compounds restricts the availability of the eIF2·GTP·Met-tRNAi ternary complex and abrogates the proliferation of cancer cells in vitro and tumor growth in vivo. Restricting the availability of the ternary complex preferentially down-regulates the expression of growth-promoting proteins and up-regulates the expression of ER stress response genes in cancer cells as well as in tumors excised from either animal models of human cancer or cancer patients. These findings provide the first direct evidence for translational control of gene-specific expression by small molecules in vivo and indicate that translation initiation factors are bona fide targets for development of mechanism-specific anti-cancer agents

Chemical Genetics Identify eIF2α Kinase Heme Regulated Inhibitor as Anti-Cancer Target

Translation initiation plays a critical role in cellular homeostasis, proliferation, differentiation and malignant transformation. Consistently, increasing the abundance of the eIF2·GTP·Met-tRNAi translation initiation complex transforms normal cells and contributes to cancer initiation and the severity of some anemia. The chemical modifiers of the eIF2·GTP·Met-tRNAi ternary complex are therefore invaluable tools for studying its role in the pathobiology of human disorders and for determining if this complex can be pharmacologically targeted for therapeutic purposes. Using a cell based assay, we identified N,N’-diarylureas as novel inhibitors of the ternary complex abundance. Direct functional-genetics and biochemical evidence demonstrated that the N,N’-diarylureas activate heme regulated inhibitor kinase, thereby phosphorylate eIF2α and reduce abundance of the ternary complex. Using tumor cell proliferation in vitro and tumor growth in vivo as paradigms, we demonstrate that N,N’-diarylureas are potent and specific tools for studying the role eIF2·GTP·Met-tRNAi ternary complex in the pathobiology of human disorders

Reporter enzyme inhibitor study to aid assembly of orthogonal reporter gene assays

Abstract: Reporter gene assays (RGAs) are commonly used to measure biological pathway modulation by small molecules. Understanding how such compounds interact with the reporter enzyme is critical to accurately interpret RGA results. To improve our understanding of reporter enzymes and develop optimal RGA systems, we investigated eight reporter enzymes differing in brightness, emission spectrum, stability, and substrate requirements. These included common reporter enzymes such as firefly luciferase (Photinus pyralis), Renilla reniformis luciferase and β-lactamase as well as mutated forms of R. reniformis luciferase emitting either blue- or green-shifted luminescence, a red-light emitting form of Luciola cruciata firefly luciferase, a mutated form of Gaussia princeps luciferase, and a propriety luciferase termed “NanoLuc” derived from the luminescent sea shrimp Oplophorus gracilirostris. To determine hit rates and structure-activity-relationships, we screened a collection of 42,460 PubChem compounds at 10µM using purified enzyme preparations. We then compared hit rates and chemotypes of confirmed actives for each enzyme. The hit rates ranged from <0.1% for β-lactamase to as high as 10% for mutated forms of Renilla luciferase. Related luciferases such as Renilla luciferase mutants showed high degrees of inhibitor overlap ranging from 40-70%, while unrelated luciferases such as firefly luciferases, GLuc, and NanoLuc showed <10% overlap. Examination of representative inhibitors in cell-based assays revealed that inhibitor-based-enzyme stabilization can lead to rises in bioluminescent signal for firefly luciferase, Renilla luciferase, and NanoLuc, with shorter half-life reporters showing increased activation responses. From this study we suggest strategies to improve the construction and interpretation of assays employing these enzymes

Chemical genetics identify eIF2α kinase heme-regulated inhibitor as an anticancer target

Translation initiation plays a critical role in cellular homeostasis, proliferation, differentiation and malignant transformation. Consistently, increasing the abundance of the eIF2–GTP–tRNAi Met translation initiation complex transforms normal cells and contributes to cancer initiation and the severity of some anemias. The chemical modifiers of the eIF2–GTP–tRNAi Met ternary complex are therefore invaluable tools for studying its role in the pathobiology of human disorders and for determining whether this complex can be pharmacologically targeted for therapeutic purposes. Using a cell-based assay, we identified N,N9-diarylureas as unique inhibitors of ternary complex accumulation. Direct functional-genetic and biochemical evidence demonstrated that the N,N9-diarylureas activate heme-regulated inhibitor kinase, thereby phosphorylating eIF2a and reducing the abundance of the ternary complex. Using tumor cell proliferation in vitro and tumor growth in vivo as paradigms, we demonstrate that N,N9-diarylureas are potent and specific tools for studying the role of eIF2–GTP–tRNAi Met ternary complex in the pathobiology of human disorders.</p

Jenkins-CI, an open source continuous integration system, as a scientific data and image processing platform.

Image based screening assays generate large volumes of heterogeneous data, requiring a plethora of computational tools for processing and analysis. Building robust, scalable workflows for such applications is a major undertaking; requiring collaboration between scientists and engineers with their own specialized area of expertise. Jenkins-CI, is an open source continuous integration system, which has been used to build an analysis platform for processing high content screening results (HCS). The availability of over 800 plugins for Jenkins-CI enables numerous standard computing tasks and allows the robust integration of specialized applications designed high throughput screening. CellProfiler is an open source resource that has become one of the preferred tools for the analysis and quantification of biological images. Jenkins-CI has made it possible to configure CellProfiler for high performance, parallel processing on Linux clusters deployed at two distant locations. This ability to deploy, at scale, and to parallelize the use of CellProfiler greatly facilitates its use in high throughput screening applications. The Jenkins-CI platform described here is accessible via an internet web interface facilitating sharing, annotating and reuse of protocols and results. Image processing pipelines developed using the CellProfiler desktop client can be deployed and shared through a centralized Jenkins repository. Centralized monitoring of the system allows operational issues to be quickly identified, facilitating user support. Limitations in the user interface of Jenkins were addressed using plugins from the Jenkins-CI community. Examples showing how Jenkins-CI can be used to run CellProfiler for the analysis of HCS assays is presented

SMOOT libraries and phage-induced directed evolution of Cas9 to engineer reduced off-target activity.

RNA-guided endonucleases such as Cas9 provide efficient on-target genome editing in cells but may also cleave at off-target loci throughout the genome. Engineered variants of Streptococcus pyogenes Cas9 (SpCas9) have been developed to globally reduce off-target activity, but individual off-targets may remain, or on-target activity may be compromised. In order to evolve against activity at specific off-targets while maintaining strong on-target editing, we developed a novel M13 bacteriophage-mediated selection method. Using this method, sequential rounds of positive and negative selection are used to identify mutations to Cas9 that enhance or diminish editing activity at particular genomic sequences. We also introduce scanning mutagenesis of oligo-directed targets (SMOOT), a comprehensive mutagenesis method to create highly diverse libraries of Cas9 variants that can be challenged with phage-based selection. Our platform identifies novel SpCas9 mutants which mitigate cleavage against off-targets both in biochemical assays and in T-cells while maintaining higher on-target activity than previously described variants. We describe an evolved variant, S. pyogenes Adapted to Reduce Target Ambiguity Cas9 (SpartaCas), composed of the most enriched mutations, each of unknown function. This evolved Cas9 mutant reduces off-target cleavage while preserving efficient editing at multiple therapeutically relevant targets. Directed evolution of Cas9 using our system demonstrates an improved structure-independent methodology to effectively engineer nuclease activity

Rescue screens with secreted proteins reveal compensatory potential of receptor tyrosine kinases in driving cancer growth

Oncogenic alterations of kinases are a frequent cause of cancer growth. Accordingly, inhibition of such “driver” kinases is a clinically proven anti-cancer therapeutic approach. While initial responses to kinase inhibitors can be significant, the emergence of resistance often limits therapeutic benefit. Resistance mechanisms that have been discovered in relapse samples include mutations in the drug target or activation of alternative pathways to bypass dependence on the original target. In the case of kinases, bypass can occur through activation of an alternative growth-promoting kinase that compensates for inhibition of the original driver kinase. Several known oncogenic kinases belong to the family of receptor tyrosine kinases (RTK). Besides genetic alterations like mutation, gene amplification, or translocation, RTK activation also occurs by stimulation with its cognate ligands. Such RTK activation can be autocrine or paracrine, depending on whether the ligands are produced by the tumors themselves or originate from surrounding cells in the tumor microenvironment. Here, we systematically assessed the potential of secreted proteins to induce resistance to kinase inhibitors in cellular screens. To this end a cDNA library encoding 3482 secreted proteins was transfected into a producer cell line. Supernatants were then transferred to several RTK-dependent cancer cell lines that were concomitantly treated with a corresponding kinase inhibitor in order to determine which supernatants could prevent growth inhibition. Using cancer cells originally dependent on either MET, FGFR2, or FGFR3, we observed a bypass of dependence through ligand-mediated activation of alternative RTKs. Our findings indicate a broad and versatile potential for RTKs from the HER and FGFR families as well as MET to compensate for loss of each other. We further provide evidence that combined inhibition of simultaneously active RTKs can lead to added anti-cancer effect

Reporter Enzyme Inhibitor Study To Aid Assembly of Orthogonal Reporter Gene Assays

Reporter gene assays (RGAs) are commonly used to measure biological pathway modulation by small molecules. Understanding how such compounds interact with the reporter enzyme is critical to accurately interpret RGA results. To improve our understanding of reporter enzymes and to develop optimal RGA systems, we investigated eight reporter enzymes differing in brightness, emission spectrum, stability, and substrate requirements. These included common reporter enzymes such as firefly luciferase (<i>Photinus pyralis</i>), <i>Renilla reniformis</i> luciferase, and β-lactamase, as well as mutated forms of <i>R. reniformis</i> luciferase emitting either blue- or green-shifted luminescence, a red-light emitting form of <i>Luciola cruciata</i> firefly luciferase, a mutated form of <i>Gaussia princeps</i> luciferase, and a proprietary luciferase termed “NanoLuc” derived from the luminescent sea shrimp <i>Oplophorus gracilirostris</i>. To determine hit rates and structure–activity relationships, we screened a collection of 42,460 PubChem compounds at 10 μM using purified enzyme preparations. We then compared hit rates and chemotypes of actives for each enzyme. The hit rates ranged from <0.1% for β-lactamase to as high as 10% for mutated forms of <i>Renilla</i> luciferase. Related luciferases such as <i>Renilla</i> luciferase mutants showed high degrees of inhibitor overlap (40–70%), while unrelated luciferases such as firefly luciferases, <i>Gaussia</i> luciferase, and NanoLuc showed <10% overlap. Examination of representative inhibitors in cell-based assays revealed that inhibitor-based enzyme stabilization can lead to increases in bioluminescent signal for firefly luciferase, <i>Renilla</i> luciferase, and NanoLuc, with shorter half-life reporters showing increased activation responses. From this study we suggest strategies to improve the construction and interpretation of assays employing these reporter enzymes

Reporter Enzyme Inhibitor Study To Aid Assembly of Orthogonal Reporter Gene Assays

Reporter gene assays (RGAs) are commonly used to measure biological pathway modulation by small molecules. Understanding how such compounds interact with the reporter enzyme is critical to accurately interpret RGA results. To improve our understanding of reporter enzymes and to develop optimal RGA systems, we investigated eight reporter enzymes differing in brightness, emission spectrum, stability, and substrate requirements. These included common reporter enzymes such as firefly luciferase (<i>Photinus pyralis</i>), <i>Renilla reniformis</i> luciferase, and β-lactamase, as well as mutated forms of <i>R. reniformis</i> luciferase emitting either blue- or green-shifted luminescence, a red-light emitting form of <i>Luciola cruciata</i> firefly luciferase, a mutated form of <i>Gaussia princeps</i> luciferase, and a proprietary luciferase termed “NanoLuc” derived from the luminescent sea shrimp <i>Oplophorus gracilirostris</i>. To determine hit rates and structure–activity relationships, we screened a collection of 42,460 PubChem compounds at 10 μM using purified enzyme preparations. We then compared hit rates and chemotypes of actives for each enzyme. The hit rates ranged from <0.1% for β-lactamase to as high as 10% for mutated forms of <i>Renilla</i> luciferase. Related luciferases such as <i>Renilla</i> luciferase mutants showed high degrees of inhibitor overlap (40–70%), while unrelated luciferases such as firefly luciferases, <i>Gaussia</i> luciferase, and NanoLuc showed <10% overlap. Examination of representative inhibitors in cell-based assays revealed that inhibitor-based enzyme stabilization can lead to increases in bioluminescent signal for firefly luciferase, <i>Renilla</i> luciferase, and NanoLuc, with shorter half-life reporters showing increased activation responses. From this study we suggest strategies to improve the construction and interpretation of assays employing these reporter enzymes

Target identification for a Hedgehog pathway inhibitor reveals the receptor GPR39

Hedgehog (Hh) signaling determines cell fate during development and can drive tumorigenesis. We performed a screen for new compounds that can impinge on Hh signaling downstream of Smoothened (Smo). A series of cyclohexyl-methyl aminopyrimidine chemotype compounds ('CMAPs') were identified that could block pathway signaling in a Smo-independent manner. In addition to inhibiting Hh signaling, the compounds generated inositol phosphates through an unknown GPCR. Correlation of GPCR mRNA expression levels with compound activity across cell lines suggested the target to be the orphan receptor GPR39. RNA interference or cDNA overexpression of GPR39 demonstrated that the receptor is necessary for compound activity. We propose a model in which CMAPs activate GPR39, which signals to the Gli transcription factors and blocks signaling. In addition to the discovery of GPR39 as a new target that impinges on Hh signaling, we report on small-molecule modulators of the receptor that will enable in vitro interrogation of GPR39 signaling in different cellular contexts.© 2014 Nature America, Inc. All rights reserved