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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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Tremblay R, Mehrjoo Y, Ahmed O, Simoneau A, McQuaid ME, Affar EB, Nislow C, Giaever G, Wurtele H. Persistent Acetylation of Histone H3 Lysine 56 Compromises the Activity of DNA Replication Origins. Mol Cell Biol 2023; 43:566-595. [PMID: 37811746 PMCID: PMC10791153 DOI: 10.1080/10985549.2023.2259739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
In Saccharomyces cerevisiae, newly synthesized histones H3 are acetylated on lysine 56 (H3 K56ac) by the Rtt109 acetyltransferase prior to their deposition on nascent DNA behind replication forks. Two deacetylases of the sirtuin family, Hst3 and Hst4, remove H3 K56ac from chromatin after S phase. hst3Δ hst4Δ cells present constitutive H3 K56ac, which sensitizes cells to replicative stress via unclear mechanisms. A chemogenomic screen revealed that DBF4 heterozygosity sensitizes cells to NAM-induced inhibition of sirtuins. DBF4 and CDC7 encode subunits of the Dbf4-dependent kinase (DDK), which activates origins of DNA replication during S phase. We show that (i) cells harboring the dbf4-1 or cdc7-4 hypomorphic alleles are sensitized to NAM, and that (ii) the sirtuins Sir2, Hst1, Hst3, and Hst4 promote DNA replication in cdc7-4 cells. We further demonstrate that Rif1, an inhibitor of DDK-dependent activation of origins, causes DNA damage and replication defects in NAM-treated cells and hst3Δ hst4Δ mutants. cdc7-4 hst3Δ hst4Δ cells are shown to display delayed initiation of DNA replication, which is not due to intra-S checkpoint activation but requires Rtt109-dependent H3 K56ac. Our results suggest that constitutive H3 K56ac sensitizes cells to replicative stress in part by negatively influencing the activation of origins of DNA replication.
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Affiliation(s)
- Roch Tremblay
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Yosra Mehrjoo
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Antoine Simoneau
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Mary E. McQuaid
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
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Barazandeh M, Kriti D, Nislow C, Giaever G. The cellular response to drug perturbation is limited: comparison of large-scale chemogenomic fitness signatures. BMC Genomics 2022; 23:197. [PMID: 35277135 PMCID: PMC8915488 DOI: 10.1186/s12864-022-08395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background Chemogenomic profiling is a powerful approach for understanding the genome-wide cellular response to small molecules. First developed in Saccharomyces cerevisiae, chemogenomic screens provide direct, unbiased identification of drug target candidates as well as genes required for drug resistance. While many laboratories have performed chemogenomic fitness assays, few have been assessed for reproducibility and accuracy. Here we analyze the two largest independent yeast chemogenomic datasets comprising over 35 million gene-drug interactions and more than 6000 unique chemogenomic profiles; the first from our own academic laboratory (HIPLAB) and the second from the Novartis Institute of Biomedical Research (NIBR). Results Despite substantial differences in experimental and analytical pipelines, the combined datasets revealed robust chemogenomic response signatures, characterized by gene signatures, enrichment for biological processes and mechanisms of drug action. We previously reported that the cellular response to small molecules is limited and can be described by a network of 45 chemogenomic signatures. In the present study, we show that the majority of these signatures (66%) are also found in the companion dataset, providing further support for their biological relevance as conserved systems-level, small molecule response systems. Conclusions Our results demonstrate the robustness of chemogenomic fitness profiling in yeast, while offering guidelines for performing other high-dimensional comparisons including parallel CRISPR screens in mammalian cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08395-x.
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Gaikani H, Smith AM, Lee AY, Giaever G, Nislow C. Systematic Prediction of Antifungal Drug Synergy by Chemogenomic Screening in Saccharomyces cerevisiae. Front Fungal Biol 2021; 2:683414. [PMID: 37744101 PMCID: PMC10512392 DOI: 10.3389/ffunb.2021.683414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/01/2021] [Indexed: 09/26/2023]
Abstract
Since the earliest days of using natural remedies, combining therapies for disease treatment has been standard practice. Combination treatments exhibit synergistic effects, broadly defined as a greater-than-additive effect of two or more therapeutic agents. Clinicians often use their experience and expertise to tailor such combinations to maximize the therapeutic effect. Although understanding and predicting biophysical underpinnings of synergy have benefitted from high-throughput screening and computational studies, one challenge is how to best design and analyze the results of synergy studies, especially because the number of possible combinations to test quickly becomes unmanageable. Nevertheless, the benefits of such studies are clear-by combining multiple drugs in the treatment of infectious disease and cancer, for instance, one can lessen host toxicity and simultaneously reduce the likelihood of resistance to treatment. This study introduces a new approach to characterize drug synergy, in which we extend the widely validated chemogenomic HIP-HOP assay to drug combinations; this assay involves parallel screening of comprehensive collections of barcoded deletion mutants. We identify a class of "combination-specific sensitive strains" that introduces mechanisms for the synergies we observe and further suggest focused follow-up studies.
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Affiliation(s)
- Hamid Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Andrew M. Smith
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, ON, Canada
| | - Anna Y. Lee
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, ON, Canada
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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Abstract
Using a validated yeast chemogenomic platform, we characterized the genome-wide effects of several pharmaceutical contaminants, including three N-nitrosamines (NDMA, NDEA and NMBA), two related compounds (DMF and 4NQO) and several of their metabolites. A collection of 4800 non-essential homozygous diploid yeast deletion strains were screened in parallel and the strain abundance was quantified by barcode sequencing. These data were used to rank deletion strains representing genes required for resistance to the compounds to delineate affected cellular pathways and to visualize the global cellular effects of these toxins in an easy-to-use searchable database. Our analysis of the N-nitrosamine screens uncovered genes (via their corresponding homozygous deletion mutants) involved in several evolutionarily conserved pathways, including: arginine biosynthesis, mitochondrial genome integrity, vacuolar protein sorting and DNA damage repair. To investigate why NDMA, NDEA and DMF caused fitness defects in strains lacking genes of the arginine pathway, we tested several N-nitrosamine metabolites (methylamine, ethylamine and formamide), and found they also affected arginine pathway mutants. Notably, each of these metabolites has the potential to produce ammonium ions during their biotransformation. We directly tested the role of ammonium ions in N-nitrosamine toxicity by treatment with ammonium sulfate and we found that ammonium sulfate also caused a growth defect in arginine pathway deletion strains. Formaldehyde, a metabolite produced from NDMA, methylamine and formamide, and which is known to cross-link free amines, perturbed deletion strains involved in chromatin remodeling and DNA repair pathways. Finally, co-administration of N-nitrosamines with ascorbic or ferulic acid did not relieve N-nitrosamine toxicity. In conclusion, we used parallel deletion mutant analysis to characterize the genes and pathways affected by exposure to N-nitrosamines and related compounds, and provide the data in an accessible, queryable database.
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Affiliation(s)
- Joseph Uche Ogbede
- Genome Science & Technology Graduate Program, University of British Columbia, Vancouver, Canada
| | - Guri Giaever
- Faculty of Pharmaceutical Science, University of British Columbia, Vancouver, Canada
| | - Corey Nislow
- Genome Science & Technology Graduate Program, University of British Columbia, Vancouver, Canada.
- Faculty of Pharmaceutical Science, University of British Columbia, Vancouver, Canada.
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Edouarzin E, Horn C, Paudyal A, Zhang C, Lu J, Tong Z, Giaever G, Nislow C, Veerapandian R, Hua DH, Vediyappan G. Broad-spectrum antifungal activities and mechanism of drimane sesquiterpenoids. Microb Cell 2020; 7:146-159. [PMID: 32548177 PMCID: PMC7278516 DOI: 10.15698/mic2020.06.719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eight drimane sesquiterpenoids including (-)-drimenol and (+)-albicanol were synthesized from (+)-sclareolide and evaluated for their antifungal activities. Three compounds, (-)-drimenol, (+)-albicanol, and (1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalene-1-carbaldehyde (4) showed strong activity against C. albicans. (-)-Drimenol, the strongest inhibitor of the three, (at concentrations of 8 – 64 µg/ml, causing 100% death of various fungi), acts not only against C. albicans in a fungicidal manner, but also inhibits other fungi such as Aspergillus, Cryptococcus, Pneumocystis, Blastomyces, Saksenaea and fluconazole resistant strains of C. albicans, C. glabrata, C. krusei, C. parapsilosis and C. auris. These observations suggest that drimenol is a broad-spectrum antifungal agent. At a high concentration (100 μg/ml) drimenol caused rupture of the fungal cell wall/membrane. In a nematode model of C. albicans infection, drimenol rescued the worms from C. albicans-mediated death, indicating drimenol is tolerable and bioactive in metazoans. Genome-wide fitness profiling assays of both S. cerevisiae (nonessential homozygous and essential heterozygous) and C. albicans (Tn-insertion mutants) collections revealed putative genes and pathways affected by drimenol. Using a C. albicans mutant spot assay, the Crk1 kinase associated gene products, Ret2, Cdc37, and orf19.759, orf19.1672, and orf19.4382 were revealed to be involved in drimenol's mechanism of action. The three orfs identified in this study are novel and appear to be linked with Crk1 function. Further, computational modeling results suggest possible modifications of the structure of drimenol, including the A ring, for improving the antifungal activity.
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Affiliation(s)
- Edruce Edouarzin
- Department of Chemistry, 1212 Mid Campus Drive North, Kansas State University, Manhattan, KS 66506 USA
| | - Connor Horn
- Division of Biology, 1717 Claflin Road, Kansas State University, Manhattan, KS 66506 USA
| | - Anuja Paudyal
- Division of Biology, 1717 Claflin Road, Kansas State University, Manhattan, KS 66506 USA
| | - Cunli Zhang
- Department of Chemistry, 1212 Mid Campus Drive North, Kansas State University, Manhattan, KS 66506 USA
| | - Jianyu Lu
- Department of Chemistry, 1212 Mid Campus Drive North, Kansas State University, Manhattan, KS 66506 USA
| | - Zongbo Tong
- Department of Chemistry, 1212 Mid Campus Drive North, Kansas State University, Manhattan, KS 66506 USA
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC Canada V6T 1Z3
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC Canada V6T 1Z3
| | - Raja Veerapandian
- Division of Biology, 1717 Claflin Road, Kansas State University, Manhattan, KS 66506 USA
| | - Duy H Hua
- Department of Chemistry, 1212 Mid Campus Drive North, Kansas State University, Manhattan, KS 66506 USA
| | - Govindsamy Vediyappan
- Division of Biology, 1717 Claflin Road, Kansas State University, Manhattan, KS 66506 USA
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7
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Abstract
Sulfur assimilation and the biosynthesis of methionine, cysteine and S-adenosylmethionine (SAM) are critical to life. As a cofactor, SAM is required for the activity of most methyltransferases (MTases) and as such has broad impact on diverse cellular processes. Assigning function to MTases remains a challenge however, as many MTases are partially redundant, they often have multiple cellular roles and these activities can be condition-dependent. To address these challenges, we performed a systematic synthetic genetic analysis of all pairwise MTase double mutations in normal and stress conditions (16°C, 37°C, and LiCl) resulting in an unbiased comprehensive overview of the complexity and plasticity of the methyltransferome. Based on this network, we performed biochemical analysis of members of the histone H3K4 COMPASS complex and the phospholipid methyltransferase OPI3 to reveal a new role for a phospholipid methyltransferase in mediating histone methylation (H3K4) which underscores a potential link between lipid homeostasis and histone methylation. Our findings provide a valuable resource to study methyltransferase function, the dynamics of the methyltransferome, genetic crosstalk between biological processes and the dynamics of the methyltransferome in response to cellular stress.
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Affiliation(s)
- Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Elena Lissina
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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8
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Nawrotek A, Benabdi S, Niyomchon S, Kryszke MH, Ginestier C, Cañeque T, Tepshi L, Mariani A, St Onge RP, Giaever G, Nislow C, Charafe-Jauffret E, Rodriguez R, Zeghouf M, Cherfils J. PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling. Nat Chem Biol 2019; 15:358-366. [PMID: 30742123 DOI: 10.1038/s41589-019-0228-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022]
Abstract
Peripheral membrane proteins orchestrate many physiological and pathological processes, making regulation of their activities by small molecules highly desirable. However, they are often refractory to classical competitive inhibition. Here, we demonstrate that potent and selective inhibition of peripheral membrane proteins can be achieved by small molecules that target protein-membrane interactions by a noncompetitive mechanism. We show that the small molecule Bragsin inhibits BRAG2-mediated Arf GTPase activation in vitro in a manner that requires a membrane. In cells, Bragsin affects the trans-Golgi network in a BRAG2- and Arf-dependent manner. The crystal structure of the BRAG2-Bragsin complex and structure-activity relationship analysis reveal that Bragsin binds at the interface between the PH domain of BRAG2 and the lipid bilayer to render BRAG2 unable to activate lipidated Arf. Finally, Bragsin affects tumorsphere formation in breast cancer cell lines. Bragsin thus pioneers a novel class of drugs that function by altering protein-membrane interactions without disruption.
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Affiliation(s)
- Agata Nawrotek
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Sarah Benabdi
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Supaporn Niyomchon
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Marie-Hélène Kryszke
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Christophe Ginestier
- Université Aix-Marseille, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Tatiana Cañeque
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Livia Tepshi
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France.,CNRS, Cachan, France
| | - Angelica Mariani
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Robert P St Onge
- Genome Technology Center, Stanford School of Medicine, Stanford, CA, USA
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Charafe-Jauffret
- Université Aix-Marseille, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Raphaël Rodriguez
- Institut Curie, PSL Research University, Chemical Cell Biology Group, Paris, France.,CNRS, Paris, France.,INSERM, Paris, France
| | - Mahel Zeghouf
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France. .,CNRS, Cachan, France.
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole normale supérieure Paris-Saclay, Cachan, France. .,CNRS, Cachan, France.
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9
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Acton E, Lee AHY, Zhao PJ, Flibotte S, Neira M, Sinha S, Chiang J, Flaherty P, Nislow C, Giaever G. Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress. Open Biol 2018; 7:rsob.160330. [PMID: 28592509 PMCID: PMC5493772 DOI: 10.1098/rsob.160330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/24/2017] [Indexed: 12/25/2022] Open
Abstract
The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, ‘prototrophic’ versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PBprot) or by backcrossing (Backcrossed, BCprot) to a wild-type strain. To systematically assess the impact of the auxotrophies, genome-wide fitness profiles of prototrophic and auxotrophic collections were compared across diverse drug and environmental conditions in 250 experiments. Our quantitative profiles uncovered broad impacts of genotype on phenotype for three deletion collections, and revealed genotypic and strain-construction-specific phenotypes. The PBprot collection exhibited fitness defects associated with plasmid maintenance, while BCprot fitness profiles were compromised due to strain loss from nutrient selection steps during strain construction. The repaired prototrophic versions of the YKO collection did not restore wild-type behaviour nor did they clarify gaps in gene annotation resulting from the auxotrophic background. To remove marker bias and expand the experimental scope of deletion libraries, construction of a bona fide prototrophic collection from a wild-type strain will be required.
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Affiliation(s)
- Erica Acton
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Genome Science and Technology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Huei-Yi Lee
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pei Jun Zhao
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Stephane Flibotte
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mauricio Neira
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sunita Sinha
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Chiang
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick Flaherty
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, USA
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Jeyaraju DV, Hurren R, Wang X, MacLean N, Gronda M, Shamas-Din A, Minden MD, Giaever G, Schimmer AD. A novel isoflavone, ME-344, targets the cytoskeleton in acute myeloid leukemia. Oncotarget 2018; 7:49777-49785. [PMID: 27391350 PMCID: PMC5226547 DOI: 10.18632/oncotarget.10446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/26/2016] [Indexed: 01/08/2023] Open
Abstract
The isoflavone ME-344 is a potent anti-cancer agent with preclinical and clinical efficacy in solid tumors. Yet, the mechanism of action of ME-344 has not been fully defined and the preclinical efficacy in leukemia has not been established. Therefore, we investigated the anti-leukemic properties and mechanism of action of ME-344. In a panel of 7 leukemia cell lines, ME-344 was cytotoxic with an IC50 in the range of 70–260 nM. In addition, ME-344 was cytotoxic to primary AML patient samples over normal hematopoietic cells. In an OCI-AML2 xenograft model, ME-344 reduced tumor growth by up to 95% of control without evidence of toxicity. Mechanistically, ME-344 increased mitochondrial ROS generation in leukemic cells. However, antioxidant treatment did not rescue cell death, suggesting that ME-344 had additional targets beyond the mitochondria. We demonstrated that ME-344 inhibited tubulin polymerization by interacting with tubulin near the colchicine-binding site. Furthermore, inhibition of tubulin polymerization was functionally important for ME-344 induced death. Finally, we showed that ME-344 synergizes with vinblastine in leukemia cells. Thus, our study demonstrates that ME-344 displays preclinical efficacy in leukemia through a mechanism at least partly related to targeting tubulin polymerization.
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Affiliation(s)
- Danny V Jeyaraju
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aisha Shamas-Din
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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11
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Hammond TG, Allen PL, Gunter MA, Chiang J, Giaever G, Nislow C, Birdsall HH. Physical Forces Modulate Oxidative Status and Stress Defense Meditated Metabolic Adaptation of Yeast Colonies: Spaceflight and Microgravity Simulations. Microgravity Sci Technol 2017; 30:195-208. [PMID: 31258252 PMCID: PMC6560652 DOI: 10.1007/s12217-017-9588-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/19/2017] [Indexed: 06/09/2023]
Abstract
Baker's yeast (Saccharomyces cerevisiae) has broad genetic homology to human cells. Although typically grown as 1-2mm diameter colonies under certain conditions yeast can form very large (10 + mm in diameter) or 'giant' colonies on agar. Giant yeast colonies have been used to study diverse biomedical processes such as cell survival, aging, and the response to cancer pharmacogenomics. Such colonies evolve dynamically into complex stratified structures that respond differentially to environmental cues. Ammonia production, gravity driven ammonia convection, and shear defense responses are key differentiation signals for cell death and reactive oxygen system pathways in these colonies. The response to these signals can be modulated by experimental interventions such as agar composition, gene deletion and application of pharmaceuticals. In this study we used physical factors including colony rotation and microgravity to modify ammonia convection and shear stress as environmental cues and observed differences in the responses of both ammonia dependent and stress response dependent pathways We found that the effects of random positioning are distinct from rotation. Furthermore, both true and simulated microgravity exacerbated both cellular redox responses and apoptosis. These changes were largely shear-response dependent but each model had a unique response signature as measured by shear stress genes and the promoter set which regulates them These physical techniques permitted a graded manipulation of both convection and ammonia signaling and are primed to substantially contribute to our understanding of the mechanisms of drug action, cell aging, and colony differentiation.
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Affiliation(s)
- Timothy G. Hammond
- Durham VA Medical Center, Medicine Service Line, 508 Fulton Street, Durham, NC 27705 USA
- Nephrology Division, Department of Medicine, Duke University School of Medicine, Durham, NC 27710 USA
- Space Policy Institute, Elliott School of International Affairs, George Washington University, Washington, DC 20052 USA
| | - Patricia L. Allen
- Durham VA Medical Center, Medicine Service Line, 508 Fulton Street, Durham, NC 27705 USA
| | | | - Jennifer Chiang
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Holly H. Birdsall
- Space Policy Institute, Elliott School of International Affairs, George Washington University, Washington, DC 20052 USA
- Department of Veterans Affairs, Veterans Healthcare Administration, Office of Research, Washington, DC 20420 USA
- Departments of Otorhinolaryngology, Immunology, and Psychiatry, Baylor College of Medicine, Houston, TX 77030 USA
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12
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Kwon Y, Chiang J, Tran G, Giaever G, Nislow C, Hahn BS, Kwak YS, Koo JC. Signaling pathways coordinating the alkaline pH response confer resistance to the hevein-type plant antimicrobial peptide Pn-AMP1 in Saccharomyces cerevisiae. Planta 2016; 244:1229-1240. [PMID: 27510723 DOI: 10.1007/s00425-016-2579-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/02/2016] [Indexed: 06/06/2023]
Abstract
Genome-wide screening of Saccharomyces cerevisiae revealed that signaling pathways related to the alkaline pH stress contribute to resistance to plant antimicrobial peptide, Pn-AMP1. Plant antimicrobial peptides (AMPs) are considered to be promising candidates for controlling phytopathogens. Pn-AMP1 is a hevein-type plant AMP that shows potent and broad-spectrum antifungal activity. Genome-wide chemogenomic screening was performed using heterozygous and homozygous diploid deletion pools of Saccharomyces cerevisiae as a chemogenetic model system to identify genes whose deletion conferred enhanced sensitivity to Pn-AMP1. This assay identified 44 deletion strains with fitness defects in the presence of Pn-AMP1. Strong fitness defects were observed in strains with deletions of genes encoding components of several pathways and complex known to participate in the adaptive response to alkaline pH stress, including the cell wall integrity (CWI), calcineurin/Crz1, Rim101, SNF1 pathways and endosomal sorting complex required for transport (ESCRT complex). Gene ontology (GO) enrichment analysis of these genes revealed that the most highly overrepresented GO term was "cellular response to alkaline pH". We found that 32 of the 44 deletion strains tested (72 %) showed significant growth defects compared with their wild type at alkaline pH. Furthermore, 9 deletion strains (20 %) exhibited enhanced sensitivity to Pn-AMP1 at ambient pH compared to acidic pH. Although several hundred plant AMPs have been reported, their modes of action remain largely uncharacterized. This study demonstrates that the signaling pathways that coordinate the adaptive response to alkaline pH also confer resistance to a hevein-type plant AMP in S. cerevisiae. Our findings have broad implications for the design of novel and potent antifungal agents.
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Affiliation(s)
- Youngho Kwon
- Division of Applied Life Science and IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jennifer Chiang
- University of British Columbia, Pharmaceutical Sciences, Vancouver, BC, Canada
| | - Grant Tran
- University of British Columbia, Pharmaceutical Sciences, Vancouver, BC, Canada
| | - Guri Giaever
- University of British Columbia, Pharmaceutical Sciences, Vancouver, BC, Canada
| | - Corey Nislow
- University of British Columbia, Pharmaceutical Sciences, Vancouver, BC, Canada
| | - Bum-Soo Hahn
- National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, 560-500, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science and IALS, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
| | - Ja-Choon Koo
- Division of Science Education and Institute of Science Education, Chonbuk National University, Jeonju, 761-756, Republic of Korea.
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13
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Kwon Y, Cha J, Chiang J, Tran G, Giaever G, Nislow C, Hur JS, Kwak YS. A chemogenomic approach to understand the antifungal action of Lichen-derived vulpinic acid. J Appl Microbiol 2016; 121:1580-1591. [DOI: 10.1111/jam.13300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/15/2016] [Accepted: 09/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Y. Kwon
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | - J. Cha
- Department of Plant Medicine and Institute of Agriculture & Life Science; Gyeongsang National University; Jinju Korea
| | - J. Chiang
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - G. Tran
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - G. Giaever
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - C. Nislow
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - J.-S. Hur
- Korean Lichen Research Institute; Suncheon National University; Suncheon Korea
| | - Y.-S. Kwak
- Department of Plant Medicine and Institute of Agriculture & Life Science; Gyeongsang National University; Jinju Korea
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14
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Williamson AE, Ylioja PM, Robertson MN, Antonova-Koch Y, Avery V, Baell JB, Batchu H, Batra S, Burrows JN, Bhattacharyya S, Calderon F, Charman SA, Clark J, Crespo B, Dean M, Debbert SL, Delves M, Dennis ASM, Deroose F, Duffy S, Fletcher S, Giaever G, Hallyburton I, Gamo FJ, Gebbia M, Guy RK, Hungerford Z, Kirk K, Lafuente-Monasterio M, Lee A, Meister S, Nislow C, Overington JP, Papadatos G, Patiny L, Pham J, Ralph S, Ruecker A, Ryan E, Southan C, Srivastava K, Swain C, Tarnowski M, Thomson P, Turner P, Wallace IM, Wells TC, White K, White L, Willis P, Winzeler EA, Wittlin S, Todd MH. Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles. ACS Cent Sci 2016; 2:687-701. [PMID: 27800551 PMCID: PMC5084075 DOI: 10.1021/acscentsci.6b00086] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 05/26/2023]
Abstract
The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.
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Affiliation(s)
- Alice E. Williamson
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul M. Ylioja
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Murray N. Robertson
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yevgeniya Antonova-Koch
- Department
of Pediatrics, Pharmacology & Drug Development, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vicky Avery
- Discovery Biology, Eskitis Institute for
Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Jonathan B. Baell
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Harikrishna Batchu
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Sanjay Batra
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Jeremy N. Burrows
- Medicines for Malaria Venture, PO Box
1826, 20 rte de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Soumya Bhattacharyya
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Felix Calderon
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Susan A. Charman
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Julie Clark
- Department of Chemical
Biology & Therapeutics, St. Jude Children’s
Research Hospital, MS 1000, Room E9050, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678, United States
| | - Benigno Crespo
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Matin Dean
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stefan L. Debbert
- Department of Chemistry, Lawrence University, 233 Steitz Science
Hall, 711 East Boldt Way, Appleton, Wisconsin 54911, United States
| | - Michael Delves
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K.
| | - Adelaide S. M. Dennis
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Frederik Deroose
- Asclepia Outsourcing Solutions, Damvalleistraat 49, B-9070 Destelbergen, Belgium
| | - Sandra Duffy
- Discovery Biology, Eskitis Institute for
Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Sabine Fletcher
- Discovery Biology, Eskitis Institute for
Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Guri Giaever
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Irene Hallyburton
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, University
of Dundee, Dundee, DD1 5EH, U.K.
| | - Francisco-Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - R. Kiplin Guy
- Department of Chemical
Biology & Therapeutics, St. Jude Children’s
Research Hospital, MS 1000, Room E9050, 262 Danny Thomas Place, Memphis, Tennessee 38105-3678, United States
| | - Zoe Hungerford
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kiaran Kirk
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Maria
J. Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Diseases of the Developing
World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Anna Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Stephan Meister
- Department
of Pediatrics, Pharmacology & Drug Development, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Corey Nislow
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - John P. Overington
- European Molecular
Biology Laboratory—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
| | - George Papadatos
- European Molecular
Biology Laboratory—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
| | - Luc Patiny
- Institute of Chemical Sciences and Engineering
(ISIC), Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - James Pham
- Department
of Biochemistry & Molecular Biology, Bio21 Molecular Science and
Biotechnology Institute, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Stuart
A. Ralph
- Department
of Biochemistry & Molecular Biology, Bio21 Molecular Science and
Biotechnology Institute, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrea Ruecker
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K.
| | - Eileen Ryan
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Christopher Southan
- IUPHAR/BPS Guide to PHARMACOLOGY, Centre for Integrative Physiology,
School of Biomedical Sciences, University
of Edinburgh, Edinburgh, EH8 9XD, U.K.
| | - Kumkum Srivastava
- CSIR-Central
Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Chris Swain
- Cambridge MedChem
Consulting, 8 Mangers
Lane, Duxford, Cambridge CB22 4RN, U.K.
| | - Matthew
J. Tarnowski
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Patrick Thomson
- School
of Chemistry, The University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, U.K.
| | - Peter Turner
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Iain M. Wallace
- European Molecular
Biology Laboratory—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K.
| | - Timothy
N. C. Wells
- Medicines for Malaria Venture, PO Box
1826, 20 rte de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Karen White
- Monash
Institute of Pharmaceutical Sciences, Monash
University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Laura White
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul Willis
- Medicines for Malaria Venture, PO Box
1826, 20 rte de Pre-Bois, 1215 Geneva 15, Switzerland
| | - Elizabeth A. Winzeler
- Department
of Pediatrics, Pharmacology & Drug Development, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
| | - Matthew H. Todd
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
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15
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Mathew MD, Mathew ND, Miller A, Simpson M, Au V, Garland S, Gestin M, Edgley ML, Flibotte S, Balgi A, Chiang J, Giaever G, Dean P, Tung A, Roberge M, Roskelley C, Forge T, Nislow C, Moerman D. Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity. PLoS Negl Trop Dis 2016; 10:e0005058. [PMID: 27755544 PMCID: PMC5068747 DOI: 10.1371/journal.pntd.0005058] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/20/2016] [Indexed: 12/03/2022] Open
Abstract
Background The lack of new anthelmintic agents is of growing concern because it affects human health and our food supply, as both livestock and plants are affected. Two principal factors contribute to this problem. First, nematode resistance to anthelmintic drugs is increasing worldwide and second, many effective nematicides pose environmental hazards. In this paper we address this problem by deploying a high throughput screening platform for anthelmintic drug discovery using the nematode Caenorhabditis elegans as a surrogate for infectious nematodes. This method offers the possibility of identifying new anthelmintics in a cost-effective and timely manner. Methods/Principal findings Using our high throughput screening platform we have identified 14 new potential anthelmintics by screening more than 26,000 compounds from the Chembridge and Maybridge chemical libraries. Using phylogenetic profiling we identified a subset of the 14 compounds as potential anthelmintics based on the relative sensitivity of C. elegans when compared to yeast and mammalian cells in culture. We showed that a subset of these compounds might employ mechanisms distinct from currently used anthelmintics by testing diverse drug resistant strains of C. elegans. One of these newly identified compounds targets mitochondrial complex II, and we used structural analysis of the target to suggest how differential binding of this compound may account for its different effects in nematodes versus mammalian cells. Conclusions/Significance The challenge of anthelmintic drug discovery is exacerbated by several factors; including, 1) the biochemical similarity between host and parasite genomes, 2) the geographic location of parasitic nematodes and 3) the rapid development of resistance. Accordingly, an approach that can screen large compound collections rapidly is required. C. elegans as a surrogate parasite offers the ability to screen compounds rapidly and, equally importantly, with specificity, thus reducing the potential toxicity of these compounds to the host and the environment. We believe this approach will help to replenish the pipeline of potential nematicides. With over two billion people infected and many billions of dollars of lost crops annually, nematode infections are a serious problem for human health and for agricultural production. While there are drugs to treat infections, many pockets of parasites have been identified worldwide that are developing immunity to the standard treatment regimen. In this study we describe a strategy using the model organism C. elegans as a surrogate parasite to identify several new chemical compounds that may offer additional treatments for infection. We demonstrate how to use our platform to identify compounds that are specific in their effect to nematodes and are not simply biocides. We also show through genetic and molecular analysis in this organism that we can quickly identify the mode of action of any new compound. Most critically, we show that a compound first identified in a free-living nematode, Caenorhabditis elegans, is also effective on a parasitic nematode, Meloidogyne hapla. With this result and considering the level of sequence conservation across much of the nematode phyla we believe our strategy can be more widely applied to find new anthelmintics.
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Affiliation(s)
- Mark D. Mathew
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Neal D. Mathew
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela Miller
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mike Simpson
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vinci Au
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Garland
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mark L. Edgley
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephane Flibotte
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aruna Balgi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Chiang
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pamela Dean
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Audrey Tung
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin Roskelley
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom Forge
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald Moerman
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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16
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Wong LH, Sinha S, Bergeron JR, Mellor JC, Giaever G, Flaherty P, Nislow C. Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions. PLoS Genet 2016; 12:e1006275. [PMID: 27588687 PMCID: PMC5010250 DOI: 10.1371/journal.pgen.1006275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/03/2016] [Indexed: 01/22/2023] Open
Abstract
The emergence and prevalence of drug resistance demands streamlined strategies to identify drug resistant variants in a fast, systematic and cost-effective way. Methods commonly used to understand and predict drug resistance rely on limited clinical studies from patients who are refractory to drugs or on laborious evolution experiments with poor coverage of the gene variants. Here, we report an integrative functional variomics methodology combining deep sequencing and a Bayesian statistical model to provide a comprehensive list of drug resistance alleles from complex variant populations. Dihydrofolate reductase, the target of methotrexate chemotherapy drug, was used as a model to identify functional mutant alleles correlated with methotrexate resistance. This systematic approach identified previously reported resistance mutations, as well as novel point mutations that were validated in vivo. Use of this systematic strategy as a routine diagnostics tool widens the scope of successful drug research and development. One of the most profound outcomes of fast, reliable genome sequencing is the ability to tailor drug therapy to an individual’s genotype. This ‘personalized’ or ‘precision medicine’ is the realization of a decades-long effort to maximize drug effect and limit unwanted side effects. An undesirable consequence of such targeted therapies, however, is the emergence of drug resistance. This outcome is the result of an evolutionary process where mutations in the drug target render the drug perturbation allow such mutant cells to proliferate. Because of the unbiased, and stochastic nature of the emergence of drug resistance, it is impossible to predict. We developed a test where hundreds of thousands of mutant cells are exposed to a drug simultaneously and those cells that modulate resistance survive. This method is innovative because it partners a high-throughput experimental protocol with a tailored statistical model to identify all mutations that modulate resistance. Finally, we used synthetic biology to re-create these mutations and demonstrate that they were, in fact, bona fide drug-resistant variants. These mutations were further extended and confirmed to also be resistant in the human orthologue. This combined biological-computational approach allows one to identify drug’s degree of resistance to both guide treatments and future drug discovery.
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Affiliation(s)
- Lai H. Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Sunita Sinha
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Julien R. Bergeron
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | | | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Patrick Flaherty
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail: (PF); (CN)
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- * E-mail: (PF); (CN)
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17
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Nislow C, Wong LH, Lee AHY, Giaever G. Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.top080945. [PMID: 27587784 DOI: 10.1101/pdb.top080945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Constructed by a consortium of 16 laboratories, the Saccharomyces genome-wide deletion collections have, for the past decade, provided a powerful, rapid, and inexpensive approach for functional profiling of the yeast genome. Loss-of-function deletion mutants were systematically created using a polymerase chain reaction (PCR)-based gene deletion strategy to generate a start-to-stop codon replacement of each open reading frame by homologous recombination. Each strain carries two molecular barcodes that serve as unique strain identifiers, enabling their growth to be analyzed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays or through the use of next-generation sequencing technologies. Functional profiling of the deletion collections, using either strain-by-strain or parallel assays, provides an unbiased approach to systematically survey the yeast genome. The Saccharomyces yeast deletion collections have proved immensely powerful in contributing to the understanding of gene function, including functional relationships between genes and genetic pathways in response to diverse genetic and environmental perturbations.
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Affiliation(s)
- Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lai Hong Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Amy Huei-Yi Lee
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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18
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Nislow C, Wong LH, Lee AHY, Giaever G. Functional Profiling Using the Saccharomyces Genome Deletion Project Collections. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.prot088039. [PMID: 27587776 DOI: 10.1101/pdb.prot088039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure.
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Affiliation(s)
- Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lai Hong Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Amy Huei-Yi Lee
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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19
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Suresh S, Schlecht U, Xu W, Miranda M, Davis RW, Nislow C, Giaever G, St Onge RP. Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.prot088054. [PMID: 27587778 DOI: 10.1101/pdb.prot088054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to be individually measured from a single pooled culture. The collection, and other resources that followed, has ushered in a new era in chemical biology, enabling unbiased and systematic identification of chemical-genetic interactions (CGIs) with remarkable ease. CGIs link bioactive compounds to biological processes, and hence can reveal the mechanism of action of growth-inhibitory compounds in vivo, including those of antifungal, antibiotic, and anticancer drugs. The chemogenomic profiling method described here measures the sensitivity induced in yeast heterozygous and homozygous deletion strains in the presence of a chemical inhibitor of growth (termed haploinsufficiency profiling and homozygous profiling, respectively, or HIPHOP). The protocol is both scalable and amenable to automation. After competitive growth of yeast knockout collection cultures, with and without chemical inhibitors, CGIs can be identified and quantified using either array- or sequencing-based approaches as described here.
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Affiliation(s)
- Sundari Suresh
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Weihong Xu
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Molly Miranda
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ronald W Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert P St Onge
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
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20
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Suresh S, Schlecht U, Xu W, Bray W, Miranda M, Davis RW, Nislow C, Giaever G, Lokey RS, St Onge RP. Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.top077701. [PMID: 27587783 DOI: 10.1101/pdb.top077701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical-genetic interactions (CGIs) describe a phenomenon where the effects of a chemical compound (i.e., a small molecule) on cell growth are dependent on a particular gene. CGIs can reveal important functional information about genes and can also be powerful indicators of a compound's mechanism of action. Mapping CGIs can lead to the discovery of new chemical probes, which, in contrast to genetic perturbations, operate at the level of the gene product (or pathway) and can be fast-acting, tunable, and reversible. The simple culture conditions required for yeast and its rapid growth, as well as the availability of a complete set of barcoded gene deletion strains, facilitate systematic mapping of CGIs in this organism. This process involves two basic steps: first, screening chemical libraries to identify bioactive compounds affecting growth and, second, measuring the effects of these compounds on genome-wide collections of mutant strains. Here, we introduce protocols for both steps that have great potential for the discovery and development of new small-molecule tools and medicines.
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Affiliation(s)
- Sundari Suresh
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Weihong Xu
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Walter Bray
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Molly Miranda
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Ronald W Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Robert P St Onge
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304
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21
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Simoneau A, Ricard É, Weber S, Hammond-Martel I, Wong LH, Sellam A, Giaever G, Nislow C, Raymond M, Wurtele H. Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress. Nucleic Acids Res 2016; 44:2706-26. [PMID: 26748095 PMCID: PMC4824096 DOI: 10.1093/nar/gkv1537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/24/2015] [Indexed: 12/13/2022] Open
Abstract
The Saccharomyces cerevisiae genome encodes five sirtuins (Sir2 and Hst1-4), which constitute a conserved family of NAD-dependent histone deacetylases. Cells lacking any individual sirtuin display mild growth and gene silencing defects. However, hst3Δ hst4Δ double mutants are exquisitely sensitive to genotoxins, and hst3Δ hst4Δ sir2Δmutants are inviable. Our published data also indicate that pharmacological inhibition of sirtuins prevents growth of several fungal pathogens, although the biological basis is unclear. Here, we present genome-wide fitness assays conducted with nicotinamide (NAM), a pan-sirtuin inhibitor. Our data indicate that NAM treatment causes yeast to solicit specific DNA damage response pathways for survival, and that NAM-induced growth defects are mainly attributable to inhibition of Hst3 and Hst4 and consequent elevation of histone H3 lysine 56 acetylation (H3K56ac). Our results further reveal that in the presence of constitutive H3K56ac, the Slx4 scaffolding protein and PP4 phosphatase complex play essential roles in preventing hyperactivation of the DNA damage-response kinase Rad53 in response to spontaneous DNA damage caused by reactive oxygen species. Overall, our data support the concept that chromosome-wide histone deacetylation by sirtuins is critical to mitigate growth defects caused by endogenous genotoxins.
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Affiliation(s)
- Antoine Simoneau
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Molecular biology program, Université de Montréal, P.O. Box 6128, Succursale Centre-ville, Montreal, H3C 3J7, Canada
| | - Étienne Ricard
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Molecular biology program, Université de Montréal, P.O. Box 6128, Succursale Centre-ville, Montreal, H3C 3J7, Canada
| | - Sandra Weber
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada
| | - Ian Hammond-Martel
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Molecular biology program, Université de Montréal, P.O. Box 6128, Succursale Centre-ville, Montreal, H3C 3J7, Canada
| | - Lai Hong Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Adnane Sellam
- Infectious Diseases Research Centre-CRI, CHU de Québec Research Center (CHUQ), Université Laval, Québec, G1V 4G2, Canada Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Québec, G1V 0A6, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Martine Raymond
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, H3C 3J7, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Department of Medicine, Université de Montréal, Montreal, H3T 1J4, Canada
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22
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Bernard D, Gebbia M, Prabha S, Gronda M, MacLean N, Wang X, Hurren R, Sukhai MA, Cho EE, Manolson MF, Datti A, Wrana J, Minden MD, Al-Awar R, Aman A, Nislow C, Giaever G, Schimmer AD. Select microtubule inhibitors increase lysosome acidity and promote lysosomal disruption in acute myeloid leukemia (AML) cells. Apoptosis 2016; 20:948-59. [PMID: 25832785 DOI: 10.1007/s10495-015-1123-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
To identify new biological vulnerabilities in acute myeloid leukemia, we screened a library of natural products for compounds cytotoxic to TEX leukemia cells. This screen identified the novel small molecule Deoxysappanone B 7,4' dimethyl ether (Deox B 7,4), which possessed nanomolar anti-leukemic activity. To determine the anti-leukemic mechanism of action of Deox B 7,4, we conducted a genome-wide screen in Saccharomyces cerevisiae and identified enrichment of genes related to mitotic cell cycle as well as vacuolar acidification, therefore pointing to microtubules and vacuolar (V)-ATPase as potential drug targets. Further investigations into the mechanisms of action of Deox B 7,4 and a related analogue revealed that these compounds were reversible microtubule inhibitors that bound near the colchicine site. In addition, Deox B 7,4 and its analogue increased lysosomal V-ATPase activity and lysosome acidity. The effects on microtubules and lysosomes were functionally important for the anti-leukemic effects of these drugs. The lysosomal effects were characteristic of select microtubule inhibitors as only the Deox compounds and nocodazole, but not colchicine, vinca alkaloids or paclitaxel, altered lysosome acidity and induced lysosomal disruption. Thus, our data highlight a new mechanism of action of select microtubule inhibitors on lysosomal function.
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Affiliation(s)
- Dannie Bernard
- Princess Margaret Cancer Centre, University Health Network, Rm 9-516, 610 University Ave, Toronto, ON, M5G 2M9, Canada
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23
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Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y, Kwon SK, Crüsemann M, Bok Lee Y, Kim JF, Giaever G, Nislow C, Moore BS, Thomashow LS, Weller DM, Kwak YS. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J 2016; 10:119-29. [PMID: 26057845 PMCID: PMC4681868 DOI: 10.1038/ismej.2015.95] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/26/2015] [Accepted: 05/03/2015] [Indexed: 01/21/2023]
Abstract
Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic's mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.
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Affiliation(s)
- Jae-Yul Cha
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Sangjo Han
- Bioinformatics Tech Lab, SK Telecom, Sungnam, Republic of Korea
| | - Hee-Jeon Hong
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hyunji Cho
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Daran Kim
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Youngho Kwon
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Max Crüsemann
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Yong Bok Lee
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - David M Weller
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - Youn-Sig Kwak
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
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24
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Burns AR, Luciani GM, Musso G, Bagg R, Yeo M, Zhang Y, Rajendran L, Glavin J, Hunter R, Redman E, Stasiuk S, Schertzberg M, Angus McQuibban G, Caffrey CR, Cutler SR, Tyers M, Giaever G, Nislow C, Fraser AG, MacRae CA, Gilleard J, Roy PJ. Caenorhabditis elegans is a useful model for anthelmintic discovery. Nat Commun 2015; 6:7485. [PMID: 26108372 PMCID: PMC4491176 DOI: 10.1038/ncomms8485] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Parasitic nematodes infect one quarter of the world's population and impact all humans through widespread infection of crops and livestock. Resistance to current anthelmintics has prompted the search for new drugs. Traditional screens that rely on parasitic worms are costly and labour intensive and target-based approaches have failed to yield novel anthelmintics. Here, we present our screen of 67,012 compounds to identify those that kill the non-parasitic nematode Caenorhabditis elegans. We then rescreen our hits in two parasitic nematode species and two vertebrate models (HEK293 cells and zebrafish), and identify 30 structurally distinct anthelmintic lead molecules. Genetic screens of 19 million C. elegans mutants reveal those nematicides for which the generation of resistance is and is not likely. We identify the target of one lead with nematode specificity and nanomolar potency as complex II of the electron transport chain. This work establishes C. elegans as an effective and cost-efficient model system for anthelmintic discovery.
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Affiliation(s)
- Andrew R. Burns
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Genna M. Luciani
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Gabriel Musso
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rachel Bagg
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - May Yeo
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Yuqian Zhang
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Luckshika Rajendran
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - John Glavin
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Robert Hunter
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4Z6
| | - Susan Stasiuk
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4Z6
| | - Michael Schertzberg
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - G. Angus McQuibban
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, University of California, San Francisco, California 94158, USA
| | - Sean R. Cutler
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada H3T 1J4
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Andy G. Fraser
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Calum A. MacRae
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4Z6
| | - Peter J. Roy
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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25
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Mor V, Rella A, Farnoud AM, Singh A, Munshi M, Bryan A, Naseem S, Konopka JB, Ojima I, Bullesbach E, Ashbaugh A, Linke MJ, Cushion M, Collins M, Ananthula HK, Sallans L, Desai PB, Wiederhold NP, Fothergill AW, Kirkpatrick WR, Patterson T, Wong LH, Sinha S, Giaever G, Nislow C, Flaherty P, Pan X, Cesar GV, de Melo Tavares P, Frases S, Miranda K, Rodrigues ML, Luberto C, Nimrichter L, Del Poeta M. Identification of a New Class of Antifungals Targeting the Synthesis of Fungal Sphingolipids. mBio 2015; 6:e00647. [PMID: 26106079 PMCID: PMC4479701 DOI: 10.1128/mbio.00647-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Recent estimates suggest that >300 million people are afflicted by serious fungal infections worldwide. Current antifungal drugs are static and toxic and/or have a narrow spectrum of activity. Thus, there is an urgent need for the development of new antifungal drugs. The fungal sphingolipid glucosylceramide (GlcCer) is critical in promoting virulence of a variety of human-pathogenic fungi. In this study, we screened a synthetic drug library for compounds that target the synthesis of fungal, but not mammalian, GlcCer and found two compounds [N'-(3-bromo-4-hydroxybenzylidene)-2-methylbenzohydrazide (BHBM) and its derivative, 3-bromo-N'-(3-bromo-4-hydroxybenzylidene) benzohydrazide (D0)] that were highly effective in vitro and in vivo against several pathogenic fungi. BHBM and D0 were well tolerated in animals and are highly synergistic or additive to current antifungals. BHBM and D0 significantly affected fungal cell morphology and resulted in the accumulation of intracellular vesicles. Deep-sequencing analysis of drug-resistant mutants revealed that four protein products, encoded by genes APL5, COS111, MKK1, and STE2, which are involved in vesicular transport and cell cycle progression, are targeted by BHBM. IMPORTANCE Fungal infections are a significant cause of morbidity and mortality worldwide. Current antifungal drugs suffer from various drawbacks, including toxicity, drug resistance, and narrow spectrum of activity. In this study, we have demonstrated that pharmaceutical inhibition of fungal glucosylceramide presents a new opportunity to treat cryptococcosis and various other fungal infections. In addition to being effective against pathogenic fungi, the compounds discovered in this study were well tolerated by animals and additive to current antifungals. These findings suggest that these drugs might pave the way for the development of a new class of antifungals.
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Affiliation(s)
- Visesato Mor
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Antonella Rella
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Amir M Farnoud
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Ashutosh Singh
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Mansa Munshi
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Arielle Bryan
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Shamoon Naseem
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - James B Konopka
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
| | - Iwao Ojima
- Department of Chemistry and Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, USA
| | - Erika Bullesbach
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Alan Ashbaugh
- Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | | | | | - Margaret Collins
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Larry Sallans
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Pankaj B Desai
- Department of Pharmaceutical Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Nathan P Wiederhold
- Department of Pathology, Fungus Testing Laboratory, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Annette W Fothergill
- Department of Pathology, Fungus Testing Laboratory, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - William R Kirkpatrick
- Division of Infectious Diseases, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Thomas Patterson
- Division of Infectious Diseases, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Lai Hong Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Colombia, Canada
| | - Sunita Sinha
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Colombia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Colombia, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Colombia, Canada
| | - Patrick Flaherty
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Xuewen Pan
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Gabriele Vargas Cesar
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia de Melo Tavares
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Susana Frases
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Leonardo Nimrichter
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA
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26
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Arnoldo A, Kittanakom S, Heisler LE, Mak AB, Shukalyuk AI, Torti D, Moffat J, Giaever G, Nislow C. A genome scale overexpression screen to reveal drug activity in human cells. Genome Med 2014; 6:32. [PMID: 24944581 PMCID: PMC4062067 DOI: 10.1186/gm549] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 04/22/2014] [Indexed: 02/08/2023] Open
Abstract
Target identification is a critical step in the lengthy and expensive process of drug development. Here, we describe a genome-wide screening platform that uses systematic overexpression of pooled human ORFs to understand drug mode-of-action and resistance mechanisms. We first calibrated our screen with the well-characterized drug methotrexate. We then identified new genes involved in the bioactivity of diverse drugs including antineoplastic agents and biologically active molecules. Finally, we focused on the transcription factor RHOXF2 whose overexpression conferred resistance to DNA damaging agents. This approach represents an orthogonal method for functional screening and, to our knowledge, has never been reported before.
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Affiliation(s)
- Anthony Arnoldo
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Banting and Best Department of Medical Research, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Saranya Kittanakom
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Banting and Best Department of Medical Research, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Lawrence E Heisler
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Banting and Best Department of Medical Research, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada ; Donnelly Sequencing Center, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Anthony B Mak
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Andrey I Shukalyuk
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 170 College Street, Toronto M5S 3E3, Canada
| | - Dax Torti
- Donnelly Sequencing Center, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Guri Giaever
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada ; Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada ; Department of Pharmaceutical Sciences, University of British Columbia, 6619-2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Corey Nislow
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada ; Banting and Best Department of Medical Research, University of Toronto, Toronto, M5S 3E1, Canada ; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada ; Donnelly Sequencing Center, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada ; Department of Pharmaceutical Sciences, University of British Columbia, 6619-2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
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27
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Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MKL, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science 2014; 344:208-11. [PMID: 24723613 DOI: 10.1126/science.1250217] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes.
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Affiliation(s)
- Anna Y Lee
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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28
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Cokol M, Weinstein ZB, Yilancioglu K, Tasan M, Doak A, Cansever D, Mutlu B, Li S, Rodriguez-Esteban R, Akhmedov M, Guvenek A, Cokol M, Cetiner S, Giaever G, Iossifov I, Nislow C, Shoichet B, Roth FP. Large-scale identification and analysis of suppressive drug interactions. Chem Biol 2014; 21:541-551. [PMID: 24704506 PMCID: PMC4281482 DOI: 10.1016/j.chembiol.2014.02.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/26/2014] [Accepted: 02/07/2014] [Indexed: 11/29/2022]
Abstract
One drug may suppress the effects of another. Although knowledge of drug suppression is vital to avoid efficacy-reducing drug interactions or discover countermeasures for chemical toxins, drug-drug suppression relationships have not been systematically mapped. Here, we analyze the growth response of Saccharomyces cerevisiae to anti-fungal compound ("drug") pairs. Among 440 ordered drug pairs, we identified 94 suppressive drug interactions. Using only pairs not selected on the basis of their suppression behavior, we provide an estimate of the prevalence of suppressive interactions between anti-fungal compounds as 17%. Analysis of the drug suppression network suggested that Bromopyruvate is a frequently suppressive drug and Staurosporine is a frequently suppressed drug. We investigated potential explanations for suppressive drug interactions, including chemogenomic analysis, coaggregation, and pH effects, allowing us to explain the interaction tendencies of Bromopyruvate.
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Affiliation(s)
- Murat Cokol
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; Nanotechnology Research and Application Center, Sabanci University, Istanbul 34956, Turkey.
| | - Zohar B Weinstein
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kaan Yilancioglu
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Murat Tasan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Allison Doak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Dilay Cansever
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Beste Mutlu
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Siyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Raul Rodriguez-Esteban
- Department of Computational Biology, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA
| | - Murodzhon Akhmedov
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Aysegul Guvenek
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Melike Cokol
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Selim Cetiner
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Guri Giaever
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Corey Nislow
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Brian Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, One Jimmy Fund Way, Boston, MA 02215, USA; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada; Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada.
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29
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Torres NP, Lee AY, Giaever G, Nislow C, Brown GW. A high-throughput yeast assay identifies synergistic drug combinations. Assay Drug Dev Technol 2014; 11:299-307. [PMID: 23772551 DOI: 10.1089/adt.2012.503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Drug combinations are commonly used in the treatment of a range of diseases such as cancer, AIDS, and bacterial infections. Such combinations are less likely to be thwarted by resistance, and they have the desirable potential to be synergistic. Synergistic combinations can have decreased toxicity if lower doses of the constituent agents can be used. Conversely, antagonistic combinations can lead to lower efficacy of a treatment. Unfortunately, practical limitations, including the large number of possible combinations to be tested and the importance of optimizing concentrations and order of addition, discourage systematic studies of compound combinations. To address these limitations, we present a platform to screen drug combinations at multiple concentrations with varying orders of addition in Saccharomyces cerevisiae, at high throughput. In a proof of principle, we screened all possible pairwise combinations of 11 DNA damaging agents and found that of the 66 combinations tested, six were synergistic and three were antagonistic. The strength of two-thirds of these combinations was dependent on the order in which the drugs were added to the cells. We further tested the synergistic and antagonistic combinations in two cancer cell lines and found the combination of mitomycin C and irinotecan to be synergistic in both cell lines. This pilot study demonstrates the utility of using yeast for screening large matrices of drug combinations, and it provides a means to prioritize drug combination tests in human cells. Finally, we underscore the importance of testing the order of addition for assessing drug combinations.
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Nile AH, Tripathi A, Yuan P, Mousley CJ, Suresh S, Wallace IM, Shah SD, Pohlhaus DT, Temple B, Nislow C, Giaever G, Tropsha A, Davis RW, St Onge RP, Bankaitis VA. PITPs as targets for selectively interfering with phosphoinositide signaling in cells. Nat Chem Biol 2014; 10:76-84. [PMID: 24292071 PMCID: PMC4059020 DOI: 10.1038/nchembio.1389] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 10/02/2013] [Indexed: 01/26/2023]
Abstract
Sec14-like phosphatidylinositol transfer proteins (PITPs) integrate diverse territories of intracellular lipid metabolism with stimulated phosphatidylinositol-4-phosphate production and are discriminating portals for interrogating phosphoinositide signaling. Yet, neither Sec14-like PITPs nor PITPs in general have been exploited as targets for chemical inhibition for such purposes. Herein, we validate what is to our knowledge the first small-molecule inhibitors (SMIs) of the yeast PITP Sec14. These SMIs are nitrophenyl(4-(2-methoxyphenyl)piperazin-1-yl)methanones (NPPMs) and are effective inhibitors in vitro and in vivo. We further establish that Sec14 is the sole essential NPPM target in yeast and that NPPMs exhibit exquisite targeting specificities for Sec14 (relative to related Sec14-like PITPs), propose a mechanism for how NPPMs exert their inhibitory effects and demonstrate that NPPMs exhibit exquisite pathway selectivity in inhibiting phosphoinositide signaling in cells. These data deliver proof of concept that PITP-directed SMIs offer new and generally applicable avenues for intervening with phosphoinositide signaling pathways with selectivities superior to those afforded by contemporary lipid kinase-directed strategies.
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Affiliation(s)
- Aaron H. Nile
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090 USA
| | - Ashutosh Tripathi
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7355 USA
| | - Peihua Yuan
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
| | - Carl J. Mousley
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
| | - Sundari Suresh
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Iain Michael Wallace
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Sweety D. Shah
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090 USA
| | - Denise Teotico Pohlhaus
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7355 USA
| | - Brenda Temple
- R. L. Juliano Structural Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260 USA
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences,, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences,, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7355 USA
| | - Ronald W. Davis
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Robert P. St Onge
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | - Vytas A. Bankaitis
- Department of Molecular & Cellular Medicine, Department of Biochemistry & Biophysics, Department of Chemistry, Texas A&M University, College Station, Texas 77843-1114 USA
- Department of Cell & Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090 USA
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31
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Lissina E, Weiss D, Young B, Rella A, Cheung-Ong K, Del Poeta M, Clarke SG, Giaever G, Nislow C. A novel small molecule methyltransferase is important for virulence in Candida albicans. ACS Chem Biol 2013; 8:2785-93. [PMID: 24083538 DOI: 10.1021/cb400607h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Candida albicans is an opportunistic pathogen capable of causing life-threatening infections in immunocompromised individuals. Despite its significant health impact, our understanding of C. albicans pathogenicity is limited, particularly at the molecular level. One of the largely understudied enzyme families in C. albicans are small molecule AdoMet-dependent methyltransferases (smMTases), which are important for maintenance of cellular homeostasis by clearing toxic chemicals, generating novel cellular intermediates, and regulating intra- and interspecies interactions. In this study, we demonstrated that C. albicans Crg1 (CaCrg1) is a bona fide smMTase that interacts with the toxin in vitro and in vivo. We report that CaCrg1 is important for virulence-related processes such as adhesion, hyphal elongation, and membrane trafficking. Biochemical and genetic analyses showed that CaCrg1 plays a role in the complex sphingolipid pathway: it binds to exogenous short-chain ceramides in vitro and interacts genetically with genes of glucosylceramide pathway, and the deletion of CaCRG1 leads to significant changes in the abundance of phytoceramides. Finally we found that this novel lipid-related smMTase is required for virulence in the waxmoth Galleria mellonella, a model of infection.
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Affiliation(s)
- Elena Lissina
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College St., Toronto, M5S 3E1, Canada
| | - David Weiss
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Brian Young
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Antonella Rella
- Department
of Molecular Genetics and Microbiology, Stony Brook University, 150 Life Sciences Building, Stony Brook, New York 11794-5222, United States
| | - Kahlin Cheung-Ong
- Department
of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College St., Toronto, M5S 3E1, Canada
| | - Maurizio Del Poeta
- Department
of Molecular Genetics and Microbiology, Stony Brook University, 150 Life Sciences Building, Stony Brook, New York 11794-5222, United States
| | - Steven G. Clarke
- Department
of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Guri Giaever
- Department
of Pharmaceutical Sciences, University of British Columbia, 2405
Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Corey Nislow
- Department
of Pharmaceutical Sciences, University of British Columbia, 2405
Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
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32
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Cheung-Ong K, Giaever G, Nislow C. DNA-damaging agents in cancer chemotherapy: serendipity and chemical biology. ACTA ACUST UNITED AC 2013; 20:648-59. [PMID: 23706631 DOI: 10.1016/j.chembiol.2013.04.007] [Citation(s) in RCA: 395] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/02/2013] [Accepted: 04/08/2013] [Indexed: 12/13/2022]
Abstract
DNA-damaging agents have a long history of use in cancer chemotherapy. The full extent of their cellular mechanisms, which is essential to balance efficacy and toxicity, is often unclear. In addition, the use of many anticancer drugs is limited by dose-limiting toxicities as well as the development of drug resistance. Novel anticancer compounds are continually being developed in the hopes of addressing these limitations; however, it is essential to be able to evaluate these compounds for their mechanisms of action. This review covers the current DNA-damaging agents used in the clinic, discusses their limitations, and describes the use of chemical genomics to uncover new information about the DNA damage response network and to evaluate novel DNA-damaging compounds.
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Affiliation(s)
- Kahlin Cheung-Ong
- Department of Molecular Genetics and the Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
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33
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Bernard D, Gebbia M, Prabha S, Gronda M, MacLean N, Wang X, Hurren R, Sukhai MA, Cho EE, Manolson MF, Datti A, Wrana J, Al-Awar R, Aman A, Nislow C, Giaever G, Schimmer AD. Abstract A299: Select microtubule inhibitors increase lysosome acidity and promote lysosomal disruption in acute myeloid leukemia (AML) cells. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-a299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
AML is a hematological malignancy for which the standard of care therapy has remained unchanged for almost 30 years. Novel therapeutic approaches are therefore urgently needed for the treatment of this heterogeneous disease. To identify new strategies for the treatment of AML, we screened a natural product library for compounds cytotoxic to AML cells and identified Deoxysappanone B 7,4’-dimethyl ether. Deoxysappanone B is a homoisoflavanoid compound extracted primarily from the dried heartwood of Caesalpinia sappan, a medicinal plant native to South-East Asia. However, anticancer activity of this compound has not been previously described and its molecular targets are largely unknown. In subsequent validation studies, Deoxysappanone B possessed anti-leukemic activity in 6 tested AML cell lines with nanomolar IC50s and was preferentially cytotoxic to primary AML cells and stem/progenitor cells over normal hematopoietic cells. To understand its mechanism of action, we performed chemo-genomic profiling of Deoxysappanone B in S. cerevisiae and identified enrichment of genes related to mitotic cell cycle as well as vacuolar acidification, therefore pointing to microtubules and lysosomes’ proton-pumping vacuolar (V)-ATPase as potential targets. We confirmed Deoxysappanone B's action as a microtubule inhibitor and localized its binding site near to that of colchicine via in-vitro tubulin polymerization and competitive binding assays. We also showed that Deoxysappanone B reversibly induces cell cycle arrest and cell death in a panel of AML cell lines as well as overcomes some mechanisms of resistance to vinca alkaloids. Validating the functional importance of tubulin as a target for Deoxysappanone B-mediated cell death, epidermoid carcinoma cells with a tubulin mutation were more resistant to Deoxysappanone B compared to their parental counterpart. In addition to inhibiting tubulin polymerization, Deoxysappanone B also increased lysosome acidity as measured by a V-ATPase enzymatic assay as well as staining with LysoSensor™ Yellow/Blue DND-160 and confocal microscopy. The sustained increase in lysosome acidity ultimately led to lysosomal disruption as evidenced by acridine orange staining. Supporting a tubulin-mediated effect on lysosomes, nocodazole, although not vinblastine, vincristine, paclitaxel or colchicine, produced a similar increase in lysosome acidity and lysosomal disruption. The effects on lysosomes were functionally relevant as pre-treatment with bafilomycin A1, a lysosomal V-ATPase inhibitor, partially abrogated the cytotoxic effect of Deoxysappanone B. Thus, our data provide insight into a novel mechanism of action of select microtubule inhibitors in the context of AML.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A299.
Citation Format: Dannie Bernard, Marinella Gebbia, Swayam Prabha, Marcela Gronda, Neil MacLean, Xiaoming Wang, Rose Hurren, Mahadeo A. Sukhai, Eunice E. Cho, Morris F. Manolson, Alessandro Datti, Jeffrey Wrana, Rima Al-Awar, Ahmed Aman, Corey Nislow, Guri Giaever, Aaron D. Schimmer. Select microtubule inhibitors increase lysosome acidity and promote lysosomal disruption in acute myeloid leukemia (AML) cells. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A299.
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Affiliation(s)
- Dannie Bernard
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marinella Gebbia
- 2Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Swayam Prabha
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marcela Gronda
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Neil MacLean
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xiaoming Wang
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rose Hurren
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mahadeo A. Sukhai
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Eunice E. Cho
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Morris F. Manolson
- 3Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Alessandro Datti
- 4Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeffrey Wrana
- 4Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rima Al-Awar
- 5Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ahmed Aman
- 5Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Corey Nislow
- 6Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- 6Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aaron D. Schimmer
- 1Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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34
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Srikumar T, Lewicki MC, Costanzo M, Tkach JM, van Bakel H, Tsui K, Johnson ES, Brown GW, Andrews BJ, Boone C, Giaever G, Nislow C, Raught B. Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. ACTA ACUST UNITED AC 2013; 201:145-63. [PMID: 23547032 PMCID: PMC3613684 DOI: 10.1083/jcb.201210019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multiple large-scale analyses in yeast implicate SUMO chain function in the
maintenance of higher-order chromatin structure and transcriptional repression
of environmental stress response genes. Like ubiquitin, the small ubiquitin-related modifier (SUMO) proteins can form
oligomeric “chains,” but the biological functions of these
superstructures are not well understood. Here, we created mutant yeast strains
unable to synthesize SUMO chains (smt3allR) and
subjected them to high-content microscopic screening, synthetic genetic array
(SGA) analysis, and high-density transcript profiling to perform the first
global analysis of SUMO chain function. This comprehensive assessment identified
144 proteins with altered localization or intensity in
smt3allR cells, 149 synthetic genetic
interactions, and 225 mRNA transcripts (primarily consisting of stress- and
nutrient-response genes) that displayed a >1.5-fold increase in
expression levels. This information-rich resource strongly implicates SUMO
chains in the regulation of chromatin. Indeed, using several different
approaches, we demonstrate that SUMO chains are required for the maintenance of
normal higher-order chromatin structure and transcriptional repression of
environmental stress response genes in budding yeast.
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Affiliation(s)
- Tharan Srikumar
- Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
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35
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Singh-Babak SD, Shekhar T, Smith AM, Giaever G, Nislow C, Cowen LE. A novel calcineurin-independent activity of cyclosporin A in Saccharomyces cerevisiae. Mol Biosyst 2013; 8:2575-84. [PMID: 22751784 DOI: 10.1039/c2mb25107h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fungi rely on regulatory networks to coordinate sensing of environmental stress with initiation of responses crucial for survival. Antifungal drugs are a specific type of environmental stress with broad clinical relevance. Small molecules with antifungal activity are ubiquitous in the environment, and are produced by a myriad of microbes in competitive natural communities. The echinocandins are fungal fermentation products and the most recently developed class of antifungals, with those in clinical use being semisynthetic derivatives that target the fungal cell wall by inhibiting 1,3-β-D-glucan synthase. Recent studies implicate the protein phosphatase calcineurin as a key regulator of cellular stress responses required for fungal survival of echinocandin-induced cell wall stress. Pharmacological inhibition of calcineurin can be achieved using the natural product and immunosuppressive drug cyclosporin A, which inhibits calcineurin by binding to the immunophilin Cpr1. This drug-protein complex inhibits the interaction between the regulatory and catalytic subunits of calcineurin, an interaction necessary for calcineurin function. Here, we report on potent activity of cyclosporin A when combined with the echinocandin micafungin against the model yeast Saccharomyces cerevisiae that is independent of its known mechanism of action of calcineurin inhibition. This calcineurin-independent synergy does not involve any of the 12 immunophilins known in yeast, individually or in combination, and is not mediated by any of the multidrug transporters encoded or controlled by YOR1, SNQ2, PDR5, PDR10, PDR11, YCF1, PDR15, ADP1, VMR1, NFT1, BPT1, YBT1, YNR070w, YOL075c, AUS1, PDR12, PDR1 and/or PDR3. Genome-wide haploinsufficiency profiling (HIP) and homozygous deletion profiling (HOP) strongly implicate the cell wall biosynthesis and integrity pathways as being central to the calcineurin-independent activity of cyclosporin A. Thus, systems level chemical genomic approaches implicate key cellular pathways in a novel mechanism of antifungal drug synergy.
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Affiliation(s)
- Sheena D Singh-Babak
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Medical Sciences Building, Room 4368, Toronto, Ontario M5S 1A8, Canada
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Sukhai MA, Prabha S, Hurren R, Rutledge AC, Lee AY, Sriskanthadevan S, Sun H, Wang X, Skrtic M, Seneviratne A, Cusimano M, Jhas B, Gronda M, MacLean N, Cho EE, Spagnuolo PA, Sharmeen S, Gebbia M, Urbanus M, Eppert K, Dissanayake D, Jonet A, Dassonville-Klimpt A, Li X, Datti A, Ohashi PS, Wrana J, Rogers I, Sonnet P, Ellis WY, Corey SJ, Eaves C, Minden MD, Wang JC, Dick JE, Nislow C, Giaever G, Schimmer AD. Lysosomal disruption preferentially targets acute myeloid leukemia cells and progenitors. J Clin Invest 2013; 123:315-28. [PMID: 23202731 PMCID: PMC3533286 DOI: 10.1172/jci64180] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 10/04/2012] [Indexed: 01/15/2023] Open
Abstract
Despite efforts to understand and treat acute myeloid leukemia (AML), there remains a need for more comprehensive therapies to prevent AML-associated relapses. To identify new therapeutic strategies for AML, we screened a library of on- and off-patent drugs and identified the antimalarial agent mefloquine as a compound that selectively kills AML cells and AML stem cells in a panel of leukemia cell lines and in mice. Using a yeast genome-wide functional screen for mefloquine sensitizers, we identified genes associated with the yeast vacuole, the homolog of the mammalian lysosome. Consistent with this, we determined that mefloquine disrupts lysosomes, directly permeabilizes the lysosome membrane, and releases cathepsins into the cytosol. Knockdown of the lysosomal membrane proteins LAMP1 and LAMP2 resulted in decreased cell viability, as did treatment of AML cells with known lysosome disrupters. Highlighting a potential therapeutic rationale for this strategy, leukemic cells had significantly larger lysosomes compared with normal cells, and leukemia-initiating cells overexpressed lysosomal biogenesis genes. These results demonstrate that lysosomal disruption preferentially targets AML cells and AML progenitor cells, providing a rationale for testing lysosomal disruption as a novel therapeutic strategy for AML.
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Affiliation(s)
- Mahadeo A. Sukhai
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Swayam Prabha
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rose Hurren
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Angela C. Rutledge
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anna Y. Lee
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shrivani Sriskanthadevan
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hong Sun
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Xiaoming Wang
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marko Skrtic
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ayesh Seneviratne
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Maria Cusimano
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Bozhena Jhas
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marcela Gronda
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Neil MacLean
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eunice E. Cho
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul A. Spagnuolo
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sumaiya Sharmeen
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Malene Urbanus
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kolja Eppert
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dilan Dissanayake
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alexia Jonet
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alexandra Dassonville-Klimpt
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Xiaoming Li
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alessandro Datti
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Pamela S. Ohashi
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jeff Wrana
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ian Rogers
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Pascal Sonnet
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - William Y. Ellis
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Seth J. Corey
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Connie Eaves
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mark D. Minden
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jean C.Y. Wang
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John E. Dick
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Guri Giaever
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- Princess Margaret Hospital/the Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
Campbell Family Institute for Breast Cancer Research, Toronto, Ontario, Canada.
Laboratoire des Glucides, CNRS FRE 3517, UFR de Pharmacie, Université de Picardie Jules Verne, 1, Amiens, France.
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
Department of Chemical Informatics, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Departments of Pediatrics and Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C. Chromatin is an ancient innovation conserved between Archaea and Eukarya. eLife 2012; 1:e00078. [PMID: 23240084 PMCID: PMC3510453 DOI: 10.7554/elife.00078] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 09/25/2012] [Indexed: 12/11/2022] Open
Abstract
The eukaryotic nucleosome is the fundamental unit of chromatin, comprising a protein octamer that wraps ∼147 bp of DNA and has essential roles in DNA compaction, replication and gene expression. Nucleosomes and chromatin have historically been considered to be unique to eukaryotes, yet studies of select archaea have identified homologs of histone proteins that assemble into tetrameric nucleosomes. Here we report the first archaeal genome-wide nucleosome occupancy map, as observed in the halophile Haloferax volcanii. Nucleosome occupancy was compared with gene expression by compiling a comprehensive transcriptome of Hfx. volcanii. We found that archaeal transcripts possess hallmarks of eukaryotic chromatin structure: nucleosome-depleted regions at transcriptional start sites and conserved -1 and +1 promoter nucleosomes. Our observations demonstrate that histones and chromatin architecture evolved before the divergence of Archaea and Eukarya, suggesting that the fundamental role of chromatin in the regulation of gene expression is ancient.DOI:http://dx.doi.org/10.7554/eLife.00078.001.
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Affiliation(s)
- Ron Ammar
- Department of Molecular Genetics , University of Toronto , Toronto , Canada ; Donnelly Centre , University of Toronto , Toronto , Canada
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Alfred SE, Surendra A, Le C, Lin K, Mok A, Wallace IM, Proctor M, Urbanus ML, Giaever G, Nislow C. A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis. Genome Biol 2012; 13:R105. [PMID: 23158586 PMCID: PMC3580497 DOI: 10.1186/gb-2012-13-11-r105] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/18/2012] [Indexed: 12/12/2022] Open
Abstract
Chemical biology, the interfacial discipline of using small molecules as probes to investigate biology, is a powerful approach of developing specific, rapidly acting tools that can be applied across organisms. The single-celled alga Chlamydomonas reinhardtii is an excellent model system because of its photosynthetic ability, cilia-related motility and simple genetics. We report the results of an automated fitness screen of 5,445 small molecules and subsequent assays on motility/phototaxis and photosynthesis. Cheminformatic analysis revealed active core structures and was used to construct a naïve Bayes model that successfully predicts algal bioactive compounds.
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Cheung-Ong K, Song KT, Ma Z, Shabtai D, Lee AY, Gallo D, Heisler LE, Brown GW, Bierbach U, Giaever G, Nislow C. Comparative chemogenomics to examine the mechanism of action of dna-targeted platinum-acridine anticancer agents. ACS Chem Biol 2012; 7:1892-901. [PMID: 22928710 DOI: 10.1021/cb300320d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Platinum-based drugs have been used to successfully treat diverse cancers for several decades. Cisplatin, the original compound of this class, cross-links DNA, resulting in cell cycle arrest and cell death via apoptosis. Cisplatin is effective against several tumor types, yet it exhibits toxic side effects and tumors often develop resistance. To mitigate these liabilities while maintaining potency, we generated a library of non-classical platinum-acridine hybrid agents and assessed their mechanisms of action using a validated genome-wide screening approach in Saccharomyces cerevisiae and in the distantly related yeast Schizosaccharomyces pombe. Chemogenomic profiles from both S. cerevisiae and S. pombe demonstrate that several of the platinum-acridines damage DNA differently than cisplatin based on their requirement for distinct modules of DNA repair.
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Affiliation(s)
| | | | - Zhidong Ma
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
27109, United States
| | | | | | | | | | | | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina
27109, United States
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40
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Shabtai D, Giaever G, Nislow C. An algorithm for chemical genomic profiling that minimizes batch effects: bucket evaluations. BMC Bioinformatics 2012; 13:245. [PMID: 23009392 PMCID: PMC3780717 DOI: 10.1186/1471-2105-13-245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 08/30/2012] [Indexed: 12/15/2022] Open
Abstract
Background Chemical genomics is an interdisciplinary field that combines small molecule perturbation with traditional genomics to understand gene function and to study the mode(s) of drug action. A benefit of chemical genomic screens is their breadth; each screen can capture the sensitivity of comprehensive collections of mutants or, in the case of mammalian cells, gene knock-downs, simultaneously. As with other large-scale experimental platforms, to compare and contrast such profiles, e.g. for clustering known compounds with uncharacterized compounds, a robust means to compare a large cohort of profiles is required. Existing methods for correlating different chemical profiles include diverse statistical discriminant analysis-based methods and specific gene filtering or normalization methods. Though powerful, none are ideal because they typically require one to define the disrupting effects, commonly known as batch effects, to detect true signal from experimental variation. These effects are not always known, and they can mask true biological differences. We present a method, Bucket Evaluations (BE) that surmounts many of these problems and is extensible to other datasets such as those obtained via gene expression profiling and which is platform independent. Results We designed an algorithm to analyse chemogenomic profiles to identify potential targets of known drugs and new chemical compounds. We used levelled rank comparisons to identify drugs/compounds with similar profiles that minimizes batch effects and avoids the requirement of pre-defining the disrupting effects. This algorithm was also tested on gene expression microarray data and high throughput sequencing chemogenomic screens and found the method is applicable to a variety of dataset types. Conclusions BE, along with various correlation methods on a collection of datasets proved to be highly accurate for locating similarity between experiments. BE is a non-parametric correlation approach, which is suitable for locating correlations in somewhat perturbed datasets such as chemical genomic profiles. We created software and a user interface for using BE, which is publically available.
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Affiliation(s)
- Daniel Shabtai
- Department of Cell and Systems Biology and the Donnelly Centre, University of Toronto, Toronto, ON, Canada
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Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmuller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C. Global Gene Deletion Analysis Exploring Yeast Filamentous Growth. Science 2012; 337:1353-6. [DOI: 10.1126/science.1224339] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Orij R, Urbanus ML, Vizeacoumar FJ, Giaever G, Boone C, Nislow C, Brul S, Smits GJ. Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae. Genome Biol 2012; 13:R80. [PMID: 23021432 PMCID: PMC3506951 DOI: 10.1186/gb-2012-13-9-r80] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 09/10/2012] [Accepted: 09/26/2012] [Indexed: 01/20/2023] Open
Abstract
Background Because protonation affects the properties of almost all molecules in cells, cytosolic pH (pHc) is usually assumed to be constant. In the model organism yeast, however, pHc changes in response to the presence of nutrients and varies during growth. Since small changes in pHc can lead to major changes in metabolism, signal transduction, and phenotype, we decided to analyze pHc control. Results Introducing a pH-sensitive reporter protein into the yeast deletion collection allowed quantitative genome-wide analysis of pHc in live, growing yeast cultures. pHc is robust towards gene deletion; no single gene mutation led to a pHc of more than 0.3 units lower than that of wild type. Correct pHc control required not only vacuolar proton pumps, but also strongly relied on mitochondrial function. Additionally, we identified a striking relationship between pHc and growth rate. Careful dissection of cause and consequence revealed that pHc quantitatively controls growth rate. Detailed analysis of the genetic basis of this control revealed that the adequate signaling of pHc depended on inositol polyphosphates, a set of relatively unknown signaling molecules with exquisitely pH sensitive properties. Conclusions While pHc is a very dynamic parameter in the normal life of yeast, genetically it is a tightly controlled cellular parameter. The coupling of pHc to growth rate is even more robust to genetic alteration. Changes in pHc control cell division rate in yeast, possibly as a signal. Such a signaling role of pHc is probable, and may be central in development and tumorigenesis.
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Affiliation(s)
- Rick Orij
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
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Jaime MDLA, Lopez-Llorca LV, Conesa A, Lee AY, Proctor M, Heisler LE, Gebbia M, Giaever G, Westwood JT, Nislow C. Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. BMC Genomics 2012; 13:267. [PMID: 22727066 PMCID: PMC3505485 DOI: 10.1186/1471-2164-13-267] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/25/2012] [Indexed: 12/30/2022] Open
Abstract
Background Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. Results Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP), and multicopy suppression (MSP) profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms), membrane functions (e.g. signalling, transport and targeting), membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. Conclusions Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and that when COS and Fluconazole are used in combination they act in a synergistic fashion. The gene targets of COS identified in this study indicate that COS’s mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens.
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Affiliation(s)
- Maria D L A Jaime
- Department of Cell and Systems Biology, University of Toronto, Mississauga, Ontario, Canada
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Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MKL, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Compound prioritization methods increase rates of chemical probe discovery in model organisms. ACTA ACUST UNITED AC 2012; 18:1273-83. [PMID: 22035796 DOI: 10.1016/j.chembiol.2011.07.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 06/29/2011] [Accepted: 07/15/2011] [Indexed: 11/30/2022]
Abstract
Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided.
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Affiliation(s)
- Iain M Wallace
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Blackman RK, Cheung-Ong K, Gebbia M, Proia DA, He S, Kepros J, Jonneaux A, Marchetti P, Kluza J, Rao PE, Wada Y, Giaever G, Nislow C. Mitochondrial electron transport is the cellular target of the oncology drug elesclomol. PLoS One 2012; 7:e29798. [PMID: 22253786 PMCID: PMC3256171 DOI: 10.1371/journal.pone.0029798] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 12/04/2011] [Indexed: 12/03/2022] Open
Abstract
Elesclomol is a first-in-class investigational drug currently undergoing clinical evaluation as a novel cancer therapeutic. The potent antitumor activity of the compound results from the elevation of reactive oxygen species (ROS) and oxidative stress to levels incompatible with cellular survival. However, the molecular target(s) and mechanism by which elesclomol generates ROS and subsequent cell death were previously undefined. The cellular cytotoxicity of elesclomol in the yeast S. cerevisiae appears to occur by a mechanism similar, if not identical, to that in cancer cells. Accordingly, here we used a powerful and validated technology only available in yeast that provides critical insights into the mechanism of action, targets and processes that are disrupted by drug treatment. Using this approach we show that elesclomol does not work through a specific cellular protein target. Instead, it targets a biologically coherent set of processes occurring in the mitochondrion. Specifically, the results indicate that elesclomol, driven by its redox chemistry, interacts with the electron transport chain (ETC) to generate high levels of ROS within the organelle and consequently cell death. Additional experiments in melanoma cells involving drug treatments or cells lacking ETC function confirm that the drug works similarly in human cancer cells. This deeper understanding of elesclomol's mode of action has important implications for the therapeutic application of the drug, including providing a rationale for biomarker-based stratification of patients likely to respond in the clinical setting.
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Affiliation(s)
- Ronald K. Blackman
- Synta Pharmaceuticals Corp., Lexington, Massachusetts, United States of America
| | - Kahlin Cheung-Ong
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - David A. Proia
- Synta Pharmaceuticals Corp., Lexington, Massachusetts, United States of America
| | - Suqin He
- Synta Pharmaceuticals Corp., Lexington, Massachusetts, United States of America
| | - Jane Kepros
- Synta Pharmaceuticals Corp., Lexington, Massachusetts, United States of America
| | - Aurelie Jonneaux
- UMR 837 – INSERM, Université de Lille II & CHRU LILLE, Lille, France
| | | | - Jerome Kluza
- UMR 837 – INSERM, Université de Lille II & CHRU LILLE, Lille, France
| | - Patricia E. Rao
- Synta Pharmaceuticals Corp., Lexington, Massachusetts, United States of America
| | - Yumiko Wada
- Synta Pharmaceuticals Corp., Lexington, Massachusetts, United States of America
| | - Guri Giaever
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Abstract
With the advent of next-generation sequencing (NGS) technology, methods previously developed for microarrays have been adapted for use by NGS. Here we describe in detail a protocol for Barcode analysis by sequencing (Bar-seq) to assess pooled competitive growth of individually barcoded yeast deletion mutants. This protocol has been optimized on two sequencing platforms: Illumina's Genome Analyzer IIx/HiSeq2000 and Life Technologies SOLiD3/5500. In addition, we provide guidelines for assessment of human knockdown cells using short-hairpin RNAs (shRNA) and an Illumina sequencing readout.
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Affiliation(s)
- Andrew M Smith
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
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Škrtić M, Sriskanthadevan S, Jhas B, Gebbia M, Wang X, Wang Z, Hurren R, Jitkova Y, Gronda M, Maclean N, Lai CK, Eberhard Y, Bartoszko J, Spagnuolo P, Rutledge AC, Datti A, Ketela T, Moffat J, Robinson BH, Cameron JH, Wrana J, Eaves CJ, Minden MD, Wang JC, Dick JE, Humphries K, Nislow C, Giaever G, Schimmer AD. Inhibition of mitochondrial translation as a therapeutic strategy for human acute myeloid leukemia. Cancer Cell 2011; 20:674-88. [PMID: 22094260 PMCID: PMC3221282 DOI: 10.1016/j.ccr.2011.10.015] [Citation(s) in RCA: 483] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/05/2011] [Accepted: 10/14/2011] [Indexed: 12/17/2022]
Abstract
To identify FDA-approved agents targeting leukemic cells, we performed a chemical screen on two human leukemic cell lines and identified the antimicrobial tigecycline. A genome-wide screen in yeast identified mitochondrial translation inhibition as the mechanism of tigecycline-mediated lethality. Tigecycline selectively killed leukemia stem and progenitor cells compared to their normal counterparts and also showed antileukemic activity in mouse models of human leukemia. ShRNA-mediated knockdown of EF-Tu mitochondrial translation factor in leukemic cells reproduced the antileukemia activity of tigecycline. These effects were derivative of mitochondrial biogenesis that, together with an increased basal oxygen consumption, proved to be enhanced in AML versus normal hematopoietic cells and were also important for their difference in tigecycline sensitivity.
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Affiliation(s)
- Marko Škrtić
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Shrivani Sriskanthadevan
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Bozhena Jhas
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Marinella Gebbia
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Xiaoming Wang
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Zezhou Wang
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Rose Hurren
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Yulia Jitkova
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Marcela Gronda
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Neil Maclean
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Courteney K. Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3 Canada
| | - Yanina Eberhard
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Justyna Bartoszko
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Paul Spagnuolo
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Angela C. Rutledge
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Alessandro Datti
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5 Canada
| | - Troy Ketela
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Jason Moffat
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Brian H. Robinson
- Genetics and Genome Biology, The Research Institute, The Hospital for Sick Children, Toronto, ON, M5G 1X8 Canada
| | - Jessie H. Cameron
- Genetics and Genome Biology, The Research Institute, The Hospital for Sick Children, Toronto, ON, M5G 1X8 Canada
| | - Jeffery Wrana
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5 Canada
| | - Connie J. Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3 Canada
| | - Mark D. Minden
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Jean C.Y. Wang
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
- Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, Ontario M5G 1L7, Canada
| | - John E. Dick
- Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, Ontario M5G 1L7, Canada
| | - Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3 Canada
| | - Corey Nislow
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Guri Giaever
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Aaron D. Schimmer
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
- To whom correspondence should be addressed: Aaron D. Schimmer, Princess Margaret Hospital, Rm 9-516, 610 University Ave, Toronto, ON, Canada M5G 2M9, Tel: 416-946-2838, Fax: 416-946-6546,
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48
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Berry DB, Guan Q, Hose J, Haroon S, Gebbia M, Heisler LE, Nislow C, Giaever G, Gasch AP. Multiple means to the same end: the genetic basis of acquired stress resistance in yeast. PLoS Genet 2011; 7:e1002353. [PMID: 22102822 PMCID: PMC3213159 DOI: 10.1371/journal.pgen.1002353] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 09/07/2011] [Indexed: 12/30/2022] Open
Abstract
In nature, stressful environments often occur in combination or close succession, and thus the ability to prepare for impending stress likely provides a significant fitness advantage. Organisms exposed to a mild dose of stress can become tolerant to what would otherwise be a lethal dose of subsequent stress; however, the mechanism of this acquired stress tolerance is poorly understood. To explore this, we exposed the yeast gene-deletion libraries, which interrogate all essential and non-essential genes, to successive stress treatments and identified genes necessary for acquiring subsequent stress resistance. Cells were exposed to one of three different mild stress pretreatments (salt, DTT, or heat shock) and then challenged with a severe dose of hydrogen peroxide (H2O2). Surprisingly, there was little overlap in the genes required for acquisition of H2O2 tolerance after different mild-stress pretreatments, revealing distinct mechanisms of surviving H2O2 in each case. Integrative network analysis of these results with respect to protein–protein interactions, synthetic–genetic interactions, and functional annotations identified many processes not previously linked to H2O2 tolerance. We tested and present several models that explain the lack of overlap in genes required for H2O2 tolerance after each of the three pretreatments. Together, this work shows that acquired tolerance to the same severe stress occurs by different mechanisms depending on prior cellular experiences, underscoring the context-dependent nature of stress tolerance. Cells experience stressful conditions in the real world that can threaten physiology. Therefore, organisms have evolved intricate defense systems to protect themselves against environmental stress. Many organisms can increase their stress tolerance at the first sign of a problem through a phenomenon called acquired stress resistance: when pre-exposed to a mild dose of one stress, cells can become super-tolerant to subsequent stresses that would kill unprepared cells. This response is observed in many organisms, from bacteria to plants to humans, and has application in human health and disease treatment; however, its mechanism remains poorly understood. We used yeast as a model to identify genes important for acquired resistance to severe oxidative stress after pretreatment with three different mild stresses (osmotic, heat, or reductive shock). Surprisingly, there was little overlap in the genes required to survive the same severe stress after each pretreatment. This reveals that the mechanism of acquiring tolerance to the same severe stress occurs through different routes depending on the mild stressor. We leveraged available datasets of physical and genetic interaction networks to address the mechanism and regulation of stress tolerance. We find that acquired stress resistance is a unique phenotype that can uncover new insights into stress biology.
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Affiliation(s)
- David B. Berry
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Qiaoning Guan
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Suraiya Haroon
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Marinella Gebbia
- Terrance Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada
| | - Lawrence E. Heisler
- Terrance Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada
| | - Corey Nislow
- Terrance Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Guri Giaever
- Terrance Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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49
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Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP. Systematic exploration of synergistic drug pairs. Mol Syst Biol 2011; 7:544. [PMID: 22068327 PMCID: PMC3261710 DOI: 10.1038/msb.2011.71] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 08/11/2011] [Indexed: 01/20/2023] Open
Abstract
Drug synergy allows a therapeutic effect to be achieved with lower doses of component drugs. Drug synergy can result when drugs target the products of genes that act in parallel pathways ('specific synergy'). Such cases of drug synergy should tend to correspond to synergistic genetic interaction between the corresponding target genes. Alternatively, 'promiscuous synergy' can arise when one drug non-specifically increases the effects of many other drugs, for example, by increased bioavailability. To assess the relative abundance of these drug synergy types, we examined 200 pairs of antifungal drugs in S. cerevisiae. We found 38 antifungal synergies, 37 of which were novel. While 14 cases of drug synergy corresponded to genetic interaction, 92% of the synergies we discovered involved only six frequently synergistic drugs. Although promiscuity of four drugs can be explained under the bioavailability model, the promiscuity of Tacrolimus and Pentamidine was completely unexpected. While many drug synergies correspond to genetic interactions, the majority of drug synergies appear to result from non-specific promiscuous synergy.
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Affiliation(s)
- Murat Cokol
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hon Nian Chua
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Murat Tasan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Beste Mutlu
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Zohar B Weinstein
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Yo Suzuki
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, San Diego, CA, USA
| | - Mehmet E Nergiz
- Department of Computer Engineering, Faculty of Engineering, Zirve University, Gaziantep, Turkey
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Anastasia Baryshnikova
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Guri Giaever
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frederick P Roth
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, USA
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50
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Lissina E, Young B, Urbanus ML, Guan XL, Lowenson J, Hoon S, Baryshnikova A, Riezman I, Michaut M, Riezman H, Cowen LE, Wenk MR, Clarke SG, Giaever G, Nislow C. A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis. PLoS Genet 2011; 7:e1002332. [PMID: 22028670 PMCID: PMC3197675 DOI: 10.1371/journal.pgen.1002332] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 08/19/2011] [Indexed: 11/24/2022] Open
Abstract
Using small molecule probes to understand gene function is an attractive approach that allows functional characterization of genes that are dispensable in standard laboratory conditions and provides insight into the mode of action of these compounds. Using chemogenomic assays we previously identified yeast Crg1, an uncharacterized SAM-dependent methyltransferase, as a novel interactor of the protein phosphatase inhibitor cantharidin. In this study we used a combinatorial approach that exploits contemporary high-throughput techniques available in Saccharomyces cerevisiae combined with rigorous biological follow-up to characterize the interaction of Crg1 with cantharidin. Biochemical analysis of this enzyme followed by a systematic analysis of the interactome and lipidome of CRG1 mutants revealed that Crg1, a stress-responsive SAM-dependent methyltransferase, methylates cantharidin in vitro. Chemogenomic assays uncovered that lipid-related processes are essential for cantharidin resistance in cells sensitized by deletion of the CRG1 gene. Lipidome-wide analysis of mutants further showed that cantharidin induces alterations in glycerophospholipid and sphingolipid abundance in a Crg1-dependent manner. We propose that Crg1 is a small molecule methyltransferase important for maintaining lipid homeostasis in response to drug perturbation. This approach demonstrates the value of combining chemical genomics with other systems-based methods for characterizing proteins and elucidating previously unknown mechanisms of action of small molecule inhibitors.
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Affiliation(s)
- Elena Lissina
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Brian Young
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Malene L. Urbanus
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Xue Li Guan
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jonathan Lowenson
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shawn Hoon
- Molecular Engineering Lab, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Anastasia Baryshnikova
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Isabelle Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Magali Michaut
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Markus R. Wenk
- Department of Biological Sciences, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Guri Giaever
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Pharmacy and Pharmaceutical Sciences, University of Toronto, Toronto, Canada
| | - Corey Nislow
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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