1
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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. bioRxiv 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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2
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van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Sheykhkarimli D, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. Am J Hum Genet 2023; 110:1769-1786. [PMID: 37729906 PMCID: PMC10577081 DOI: 10.1016/j.ajhg.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Defects in hydroxymethylbilane synthase (HMBS) can cause acute intermittent porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ∼⅓ of clinical HMBS variants are missense variants, and most clinically reported HMBS missense variants are designated as "variants of uncertain significance" (VUSs). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino acid substitutions. The resulting variant effect maps generally agreed with biochemical expectations and provide further evidence that HMBS can function as a monomer. Additionally, the maps implicated specific residues as having roles in active site dynamics, which was further supported by molecular dynamics simulations. Most importantly, these maps can help discriminate pathogenic from benign HMBS variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.
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Affiliation(s)
- Warren van Loggerenberg
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | | | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Rayna Hamilton
- Advanced Academic Programs, Johns Hopkins University, Washington, DC 20036, USA
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada
| | | | - Sami Mustajoki
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Elena Pischik
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Elena Di Pierro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Unit of Medicine and Metabolic Diseases, 20122 Milano, Italy
| | - Michela Barbaro
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Ylva Floderus
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Caroline Schmitt
- Centre français des porphyries, hôpital Louis-Mourier, Assistance Publique-Hopitaux de Paris, 92701 Colombes, France; Centre de recherche sur l'inflammation, Université Paris Cité, UMR1149 INSERM, 75018 Paris, France
| | - Laurent Gouya
- Centre français des porphyries, hôpital Louis-Mourier, Assistance Publique-Hopitaux de Paris, 92701 Colombes, France; Centre de recherche sur l'inflammation, Université Paris Cité, UMR1149 INSERM, 75018 Paris, France
| | | | | | - Edith C H Friesema
- Porphyria Expertcenter Rotterdam, Center for Lysosomal and Metabolic Diseases, Department of Internal Medicine, Erasmus MC, 3015 Rotterdam, the Netherlands
| | - Raili Kauppinen
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Aasne K Aarsand
- Norwegian Porphyria Centre, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Garton
- Institute Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada.
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3
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Gersing S, Cagiada M, Gebbia M, Gjesing AP, Coté AG, Seesankar G, Li R, Tabet D, Weile J, Stein A, Gloyn AL, Hansen T, Roth FP, Lindorff-Larsen K, Hartmann-Petersen R. A comprehensive map of human glucokinase variant activity. Genome Biol 2023; 24:97. [PMID: 37101203 PMCID: PMC10131484 DOI: 10.1186/s13059-023-02935-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Glucokinase (GCK) regulates insulin secretion to maintain appropriate blood glucose levels. Sequence variants can alter GCK activity to cause hyperinsulinemic hypoglycemia or hyperglycemia associated with GCK-maturity-onset diabetes of the young (GCK-MODY), collectively affecting up to 10 million people worldwide. Patients with GCK-MODY are frequently misdiagnosed and treated unnecessarily. Genetic testing can prevent this but is hampered by the challenge of interpreting novel missense variants. RESULT Here, we exploit a multiplexed yeast complementation assay to measure both hyper- and hypoactive GCK variation, capturing 97% of all possible missense and nonsense variants. Activity scores correlate with in vitro catalytic efficiency, fasting glucose levels in carriers of GCK variants and with evolutionary conservation. Hypoactive variants are concentrated at buried positions, near the active site, and at a region of known importance for GCK conformational dynamics. Some hyperactive variants shift the conformational equilibrium towards the active state through a relative destabilization of the inactive conformation. CONCLUSION Our comprehensive assessment of GCK variant activity promises to facilitate variant interpretation and diagnosis, expand our mechanistic understanding of hyperactive variants, and inform development of therapeutics targeting GCK.
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Affiliation(s)
- Sarah Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Matteo Cagiada
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
| | - Anette P Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Atina G Coté
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
| | - Gireesh Seesankar
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
| | - Roujia Li
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada
| | - Daniel Tabet
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Anna L Gloyn
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada.
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
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4
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van Loggerenberg W, Sowlati-Hashjin S, Weile J, Hamilton R, Chawla A, Gebbia M, Kishore N, Frésard L, Mustajoki S, Pischik E, Di Pierro E, Barbaro M, Floderus Y, Schmitt C, Gouya L, Colavin A, Nussbaum R, Friesema ECH, Kauppinen R, To-Figueras J, Aarsand AK, Desnick RJ, Garton M, Roth FP. Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation. bioRxiv 2023:2023.02.06.527353. [PMID: 36798224 PMCID: PMC9934555 DOI: 10.1101/2023.02.06.527353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~⅓ of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.
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Affiliation(s)
- Warren van Loggerenberg
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Rayna Hamilton
- Advanced Academic Programs, Johns Hopkins University, Washington, DC, USA
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | | | - Sami Mustajoki
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Elena Pischik
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Elena Di Pierro
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Unit of Medicine and Metabolic Diseases, Milan, Italy
| | - Michela Barbaro
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ylva Floderus
- Porphyria Centre Sweden, Centre for Inherited Metabolic Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Schmitt
- Centre Français des Porphyries, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes and Centre de Recherche sur l’Inflammation, UMR1149 INSERM, Université Paris Cité, Paris, France
| | - Laurent Gouya
- Centre Français des Porphyries, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes and Centre de Recherche sur l’Inflammation, UMR1149 INSERM, Université Paris Cité, Paris, France
| | | | | | - Edith C. H. Friesema
- Porphyria Expertcenter Rotterdam, Center for Lysosomal and Metabolic Diseases, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Raili Kauppinen
- Research Program in Molecular Medicine, Biomedicum-Helsinki, University of Helsinki
| | - Jordi To-Figueras
- Biochemistry and Molecular Genetics Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Aasne K Aarsand
- Norwegian Porphyria Centre, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, ON, Canada
| | - Frederick P. Roth
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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5
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van Leeuwen J, Pons C, Tan G, Wang JZ, Hou J, Weile J, Gebbia M, Liang W, Shuteriqi E, Li Z, Lopes M, Ušaj M, Dos Santos Lopes A, van Lieshout N, Myers CL, Roth FP, Aloy P, Andrews BJ, Boone C. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol 2021; 16:e9828. [PMID: 32939983 PMCID: PMC7507402 DOI: 10.15252/msb.20209828] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 07/01/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Essential genes tend to be highly conserved across eukaryotes, but, in some cases, their critical roles can be bypassed through genetic rewiring. From a systematic analysis of 728 different essential yeast genes, we discovered that 124 (17%) were dispensable essential genes. Through whole-genome sequencing and detailed genetic analysis, we investigated the genetic interactions and genome alterations underlying bypass suppression. Dispensable essential genes often had paralogs, were enriched for genes encoding membrane-associated proteins, and were depleted for members of protein complexes. Functionally related genes frequently drove the bypass suppression interactions. These gene properties were predictive of essential gene dispensability and of specific suppressors among hundreds of genes on aneuploid chromosomes. Our findings identify yeast's core essential gene set and reveal that the properties of dispensable essential genes are conserved from yeast to human cells, correlating with human genes that display cell line-specific essentiality in the Cancer Dependency Map (DepMap) project.
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Affiliation(s)
- Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Guihong Tan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jason Zi Wang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jing Hou
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Wendy Liang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Zhijian Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Maykel Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Matej Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Andreia Dos Santos Lopes
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
| | - Natascha van Lieshout
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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6
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Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA. A reference map of the human binary protein interactome. Nature 2020; 580:402-408. [PMID: 32296183 PMCID: PMC7169983 DOI: 10.1038/s41586-020-2188-x] [Citation(s) in RCA: 548] [Impact Index Per Article: 137.0] [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: 04/19/2019] [Accepted: 02/14/2020] [Indexed: 12/14/2022]
Abstract
Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships1,2. Here, we present a human “all-by-all” reference interactome map of human binary protein interactions, or “HuRI”. With ~53,000 high-quality protein-protein interactions (PPIs), HuRI has approximately four times more such interactions than high-quality curated interactions from small-scale studies. Integrating HuRI with genome3, transcriptome4, and proteome5 data enables the study of cellular function within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying specific subcellular roles of PPIs. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms underlying tissue-specific phenotypes of Mendelian diseases. HuRI represents a systematic proteome-wide reference linking genomic variation to phenotypic outcomes.
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Affiliation(s)
- Katja Luck
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dae-Kyum Kim
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bridget E Begg
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wenting Bian
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ruth Brignall
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tiziana Cafarelli
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Francisco J Campos-Laborie
- Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.,Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Benoit Charloteaux
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dongsic Choi
- The Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Quebec, Canada
| | - Atina G Coté
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Meaghan Daley
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven Deimling
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Alice Desbuleux
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Molecular Biology of Diseases, Groupe Interdisciplinaire de Génomique Appliquée (GIGA) and Laboratory of Viral Interactomes, University of Liège, Liège, Belgium
| | - Amélie Dricot
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Madeleine F Hardy
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nishka Kishore
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jennifer J Knapp
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - István A Kovács
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Network Science Institute, Northeastern University, Boston, MA, USA.,Wigner Research Centre for Physics, Institute for Solid State Physics and Optics, Budapest, Hungary
| | - Irma Lemmens
- Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium.,Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Miles W Mee
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Joseph C Mellor
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada.,seqWell, Beverly, MA, USA
| | - Carl Pollis
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Aaron D Richardson
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sadie Schlabach
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bridget Teeking
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anupama Yadav
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mariana Babor
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Christian Bowman-Colin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Suet-Feung Chin
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Claudia Colabella
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy.,Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati" (IZSUM), Perugia, Italy
| | - Georges Coppin
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Molecular Biology of Diseases, Groupe Interdisciplinaire de Génomique Appliquée (GIGA) and Laboratory of Viral Interactomes, University of Liège, Liège, Belgium
| | - Cassandra D'Amata
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - David De Ridder
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steffi De Rouck
- Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium.,Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Miquel Duran-Frigola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Hanane Ennajdaoui
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Florian Goebels
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Liana Goehring
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anjali Gopal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Ghazal Haddad
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Elodie Hatchi
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Paris, France.,Université Paris Diderot, Paris, France
| | - Yoseph Kassa
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Serena Landini
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roujia Li
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Natascha van Lieshout
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Andrew MacWilliams
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dylan Markey
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joseph N Paulson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.,Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA, USA
| | - Sudharshan Rangarajan
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Rasla
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashyad Rayhan
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Thomas Rolland
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adriana San-Miguel
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dayag Sheykhkarimli
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eyal Simonovsky
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Murat Taşan
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Tejeda
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- Molecular Biology of Diseases, Groupe Interdisciplinaire de Génomique Appliquée (GIGA) and Laboratory of Viral Interactomes, University of Liège, Liège, Belgium
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Jochen Weile
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Yu Xia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Xinping Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Quan Zhong
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.,Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Suzanne Gaudet
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Janusz Rak
- The Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Quebec, Canada
| | - Jan Tavernier
- Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium.,Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Frederick P Roth
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA. .,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada. .,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. .,Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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7
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Celaj A, Gebbia M, Musa L, Cote AG, Snider J, Wong V, Ko M, Fong T, Bansal P, Mellor JC, Seesankar G, Nguyen M, Zhou S, Wang L, Kishore N, Stagljar I, Suzuki Y, Yachie N, Roth FP. Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network. Cell Syst 2019; 10:25-38.e10. [PMID: 31668799 PMCID: PMC6989212 DOI: 10.1016/j.cels.2019.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 05/07/2019] [Revised: 08/14/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022]
Abstract
Many traits are complex, depending non-additively on variant combinations. Even in model systems, such as the yeast S. cerevisiae, carrying out the high-order variant-combination testing needed to dissect complex traits remains a daunting challenge. Here, we describe “X-gene” genetic analysis (XGA), a strategy for engineering and profiling highly combinatorial gene perturbations. We demonstrate XGA on yeast ABC transporters by engineering 5,353 strains, each deleted for a random subset of 16 transporters, and profiling each strain’s resistance to 16 compounds. XGA yielded 85,648 genotype-to-resistance observations, revealing high-order genetic interactions for 13 of the 16 transporters studied. Neural networks yielded intuitive functional models and guided exploration of fluconazole resistance, which was influenced non-additively by five genes. Together, our results showed that highly combinatorial genetic perturbation can functionally dissect complex traits, supporting pursuit of analogous strategies in human cells and other model systems. Celaj et al. introduce “X-gene” genetic analysis (XGA), a strategy for modeling complex systems by engineering and profiling highly combinatorial genetic perturbations. They apply XGA to 16 yeast ABC transporters, revealing many high-order genetic interactions. Neural network models yielded intuitive functional models and illuminated an ABC transporter influence network, supporting application of XGA to other organisms and processes.
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Affiliation(s)
- Albi Celaj
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Louai Musa
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Atina G Cote
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Minjeong Ko
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | - Tiffany Fong
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul Bansal
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Joseph C Mellor
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gireesh Seesankar
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maria Nguyen
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shijie Zhou
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Liangxi Wang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
| | - Nishka Kishore
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Mediterranean Institute for Life Sciences, Split 21 000, Croatia
| | - Yo Suzuki
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Nozomu Yachie
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan; Department of Biological Sciences, School of Science, University of Tokyo, Tokyo 113-0033, Japan; Institute for Advanced Biosciences, Keio University, Yamagata 997-0035, Japan; PRESTO, Japan Science and Technology Agency, Tokyo 153-8904, Japan.
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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8
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Díaz-Mejía JJ, Celaj A, Mellor JC, Coté A, Balint A, Ho B, Bansal P, Shaeri F, Gebbia M, Weile J, Verby M, Karkhanina A, Zhang Y, Wong C, Rich J, Prendergast D, Gupta G, Öztürk S, Durocher D, Brown GW, Roth FP. Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics. Mol Syst Biol 2018; 14:e7985. [PMID: 29807908 PMCID: PMC5974512 DOI: 10.15252/msb.20177985] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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] [Indexed: 01/08/2023] Open
Abstract
Condition‐dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State‐of‐the‐art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double‐mutant strains, does not scale readily to multi‐condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG‐GI), by which double‐mutant strains generated via en masse “party” mating can also be monitored en masse for growth to detect genetic interactions. By using site‐specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG‐GI enables multiplexed quantitative tracking of double mutants via next‐generation sequencing. We applied BFG‐GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4‐nitroquinoline 1‐oxide (4NQO), bleomycin, zeocin, and three other DNA‐damaging environments. BFG‐GI recapitulated known genetic interactions and yielded new condition‐dependent genetic interactions. We validated and further explored a subnetwork of condition‐dependent genetic interactions involving MAG1,SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53.
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Affiliation(s)
- J Javier Díaz-Mejía
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Albi Celaj
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Joseph C Mellor
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Atina Coté
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Attila Balint
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Brandon Ho
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Pritpal Bansal
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Fatemeh Shaeri
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Marta Verby
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Anna Karkhanina
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - YiFan Zhang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Justin Rich
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - D'Arcy Prendergast
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Gaurav Gupta
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Sedide Öztürk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Daniel Durocher
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Grant W Brown
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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9
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Vigentini I, Gebbia M, Belotti A, Foschino R, Roth FP. CRISPR/Cas9 System as a Valuable Genome Editing Tool for Wine Yeasts with Application to Decrease Urea Production. Front Microbiol 2017; 8:2194. [PMID: 29163459 PMCID: PMC5678006 DOI: 10.3389/fmicb.2017.02194] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 07/24/2017] [Accepted: 10/25/2017] [Indexed: 11/16/2022] Open
Abstract
An extensive repertoire of molecular tools is available for genetic analysis in laboratory strains of S. cerevisiae. Although this has widely contributed to the interpretation of gene functionality within haploid laboratory isolates, the genetics of metabolism in commercially-relevant polyploid yeast strains is still poorly understood. Genetic engineering in industrial yeasts is undergoing major changes due to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) engineering approaches. Here we apply the CRISPR/Cas9 system to two commercial “starter” strains of S. cerevisiae (EC1118, AWRI796), eliminating the CAN1 arginine permease pathway to generate strains with reduced urea production (18.5 and 35.5% for EC1118 and AWRI796, respectively). In a wine-model environment based on two grape musts obtained from Chardonnay and Cabernet Sauvignon cultivars, both S. cerevisiae starter strains and CAN1 mutants completed the must fermentation in 8–12 days. However, recombinant strains carrying the can1 mutation failed to produce urea, suggesting that the genetic modification successfully impaired the arginine metabolism. In conclusion, the reduction of urea production in a wine-model environment confirms that the CRISPR/Cas9 system has been successfully established in S. cerevisiae wine yeasts.
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Affiliation(s)
- Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Alessandra Belotti
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Roberto Foschino
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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10
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van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C. Exploring genetic suppression interactions on a global scale. Science 2017; 354:354/6312/aag0839. [PMID: 27811238 DOI: 10.1126/science.aag0839] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 10/04/2016] [Indexed: 12/21/2022]
Abstract
Genetic suppression occurs when the phenotypic defects caused by a mutation in a particular gene are rescued by a mutation in a second gene. To explore the principles of genetic suppression, we examined both literature-curated and unbiased experimental data, involving systematic genetic mapping and whole-genome sequencing, to generate a large-scale suppression network among yeast genes. Most suppression pairs identified novel relationships among functionally related genes, providing new insights into the functional wiring diagram of the cell. In addition to suppressor mutations, we identified frequent secondary mutations,in a subset of genes, that likely cause a delay in the onset of stationary phase, which appears to promote their enrichment within a propagating population. These findings allow us to formulate and quantify general mechanisms of genetic suppression.
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Affiliation(s)
- Jolanda van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.,Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Joseph C Mellor
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Takafumi N Yamaguchi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Helena Friesen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - John Koschwanez
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Mojca Mattiazzi Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Maria Pechlaner
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Mehmet Takar
- Department of Biological Sciences, Vanderbilt University, 1161 21st Avenue South, Nashville, TN 37232, USA
| | - Matej Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Kerry Andrusiak
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Pritpal Bansal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Claire E Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jessica Cao
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Atina Cote
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Gene Horecka
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ira Horecka
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Elena Kuzmin
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Nicole Legro
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Wendy Liang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Natascha van Lieshout
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Margaret McNee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Fatemeh Shaeri
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Song Sun
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Lu Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Michael Yuen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrew Murray
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, 1161 21st Avenue South, Nashville, TN 37232, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. .,Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada. .,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada.,Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada. .,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada
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11
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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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12
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Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Mol Syst Biol 2016; 12:863. [PMID: 27107012 PMCID: PMC4848762 DOI: 10.15252/msb.20156660] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [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] [Indexed: 12/22/2022] Open
Abstract
High‐throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome‐scale interaction mapping. Here, we report Barcode Fusion Genetics‐Yeast Two‐Hybrid (BFG‐Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG‐Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein‐pair barcodes that can be quantified via next‐generation sequencing. We applied BFG‐Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG‐Y2H increases the efficiency of protein matrix screening, with quality that is on par with state‐of‐the‐art Y2H methods.
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Affiliation(s)
- Nozomu Yachie
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Synthetic Biology Division, Research Center for Advanced Science and Technology The University of Tokyo, Tokyo, Japan Institute for Advanced Bioscience, Keio University, Tsuruoka, Yamagata, Japan PRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Evangelia Petsalaki
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Joseph C Mellor
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN Institut Pasteur, Paris, France
| | - Marta Verby
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Sedide B Ozturk
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Siyang Li
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Atina G Cote
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Roberto Mosca
- Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Jennifer J Knapp
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Minjeong Ko
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Analyn Yu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Nidhi Sahni
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Song Yi
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Tanya Tyagi
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cassandra Wong
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Louai Musa
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Yi-Chun Liu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Pascal Braun
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Plant Systems Biology, Technische Universität München Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Aloy
- Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute Mt. Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Canadian Institute for Advanced Research, Toronto, ON, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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13
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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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14
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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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15
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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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16
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van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet 2013; 9:e1003479. [PMID: 23658529 PMCID: PMC3642058 DOI: 10.1371/journal.pgen.1003479] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [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: 09/12/2012] [Accepted: 03/12/2013] [Indexed: 11/30/2022] Open
Abstract
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology, and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors, including the CAF-1 complex, Spt10, and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning, and these data provide a valuable resource for future studies. The genome in eukaryotic cells is packaged into nucleosomes, which play critical roles in regulating where and when different genes are expressed. For example, nucleosomes can physically block access of transcription factor to sites on DNA or direct regulatory proteins to DNA. Consistent with these roles, nucleosomes assume a stereotypical pattern around genes: they are depleted at the promoter region that marks the start of genes and assume a regularly spaced array within genes. To identify factors involved in this organization, we generated high-resolution nucleosome and transcriptome maps for 50 loss-of-function mutants with known or suspected roles in nucleosome biology in budding yeast. We show that nucleosome organization is determined by the combined effects of many factors that often exert opposing forces on nucleosomes. We further demonstrate that specific nucleosomes can be positioned independently within genes and that repositioning of nucleosomes at the start of genes may affect expression of these genes in response to environmental stimuli. Data mining of this extensive resource allowed us to show that general transcription factors act as insulators at diverging promoters to prevent the formation of cryptic transcripts, and also revealed 36 novel transcripts regulated by the Tup1/Cyc8 complex.
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Affiliation(s)
- Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kyle Tsui
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Sanie Mnaimneh
- Department of Medical Research, Banting and Best, Toronto, Ontario, Canada
| | - Timothy R. Hughes
- Department of Medical Research, Banting and Best, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Department of Medical Research, Banting and Best, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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17
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Arndt KM, Piro AS, Mayekar MK, Tomson BN, Wier AD, VanDemark AP, Heisler LE, Gebbia M, Nislow C. The role of the Paf1 complex in controlling transcriptioncoupled histone modifications. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.324.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Adam D. Wier
- Biological SciencesUniversity of PittsburghPittsburghPA
| | | | - Lawrence E. Heisler
- Terrance Donnelly Centre and Banting & Best Department of Medical ResearchUniversity of TorontoTorontoONCanada
| | - Marinella Gebbia
- Terrance Donnelly Centre and Banting & Best Department of Medical ResearchUniversity of TorontoTorontoONCanada
| | - Corey Nislow
- Terrance Donnelly Centre and Banting & Best Department of Medical ResearchUniversity of TorontoTorontoONCanada
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18
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Tomson BN, Crisucci EM, Heisler L, Gebbia M, Nislow C, Arndt KM. Characterization of snoRNA 3’‐end formation in
Saccharomyces cerevisiae
reveals a broad role for the Paf1 complex and locus‐specific roles for histone post‐translational modifications. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.lb97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | - Karen M Arndt
- Biological SciencesUniversity of PittsburghPittsburghPA
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19
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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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21
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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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22
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Abstract
The basic unit of chromatin is double-stranded DNA wrapped around nucleosome core particles, the -classic "beads-on-a-string" described by Kornberg and colleagues. The history of chromatin studies has experienced many peaks, from the earliest studies by Miescher to the biochemical studies of the 1960s and 1970s, the appreciation for the influence of histone modifications in controlling gene expression in the 1990s to the genome-wide studies that began in 2006 and show no signs of abating with the introduction of next generation sequencing technologies. Genome-wide studies not only have provided a base line to understand relationships between chromatin structure and gene function but also have begun to provide new insights into chromatin remodelling. Here, we describe the use of genome-wide approaches to determining nucleosome occupancy in yeast.
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Affiliation(s)
- Kyle Tsui
- The Donnelly Centre for Biomolecular Research, University of Toronto, Toronto, ON, Canada
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23
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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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24
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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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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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Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. Nucleosome-coupled expression differences in closely-related species. BMC Genomics 2011; 12:466. [PMID: 21942931 PMCID: PMC3209474 DOI: 10.1186/1471-2164-12-466] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 09/26/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown. RESULTS We address this challenge by generating nucleosome positioning and cell cycle expression data for Saccharomyces bayanus and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, S. bayanus and S. cerevisiae. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs). CONCLUSIONS Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.
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Affiliation(s)
- Yuanfang Guan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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27
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Dinér P, Veide Vilg J, Kjellén J, Migdal I, Andersson T, Gebbia M, Giaever G, Nislow C, Hohmann S, Wysocki R, Tamás MJ, Grøtli M. Design, synthesis, and characterization of a highly effective Hog1 inhibitor: a powerful tool for analyzing MAP kinase signaling in yeast. PLoS One 2011; 6:e20012. [PMID: 21655328 PMCID: PMC3104989 DOI: 10.1371/journal.pone.0020012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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: 01/21/2011] [Accepted: 04/08/2011] [Indexed: 11/19/2022] Open
Abstract
The Saccharomyces cerevisiae High-Osmolarity Glycerol (HOG) pathway is a conserved mitogen-activated protein kinase (MAPK) signal transduction system that often serves as a model to analyze systems level properties of MAPK signaling. Hog1, the MAPK of the HOG-pathway, can be activated by various environmental cues and it controls transcription, translation, transport, and cell cycle adaptations in response to stress conditions. A powerful means to study signaling in living cells is to use kinase inhibitors; however, no inhibitor targeting wild-type Hog1 exists to date. Herein, we describe the design, synthesis, and biological application of small molecule inhibitors that are cell-permeable, fast-acting, and highly efficient against wild-type Hog1. These compounds are potent inhibitors of Hog1 kinase activity both in vitro and in vivo. Next, we use these novel inhibitors to pinpoint the time of Hog1 action during recovery from G(1) checkpoint arrest, providing further evidence for a specific role of Hog1 in regulating cell cycle resumption during arsenite stress. Hence, we describe a novel tool for chemical genetic analysis of MAPK signaling and provide novel insights into Hog1 action.
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Affiliation(s)
- Peter Dinér
- Medicinal Chemistry, Department of Chemistry, University of Gothenburg,
Göteborg, Sweden
| | - Jenny Veide Vilg
- Microbiology, Department of Cell and Molecular Biology, University of
Gothenburg, Göteborg, Sweden
| | - Jimmy Kjellén
- Microbiology, Department of Cell and Molecular Biology, University of
Gothenburg, Göteborg, Sweden
| | - Iwona Migdal
- Institute of Plant Biology, Department of Genetics and Cell Physiology,
University of Wroclaw, Wroclaw, Poland
| | - Terese Andersson
- Medicinal Chemistry, Department of Chemistry, University of Gothenburg,
Göteborg, Sweden
| | - Marinella Gebbia
- Department of Pharmaceutical Sciences, University of Toronto, Toronto,
Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of Toronto, Toronto,
Canada
| | - Corey Nislow
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
| | - Stefan Hohmann
- Microbiology, Department of Cell and Molecular Biology, University of
Gothenburg, Göteborg, Sweden
| | - Robert Wysocki
- Institute of Plant Biology, Department of Genetics and Cell Physiology,
University of Wroclaw, Wroclaw, Poland
| | - Markus J. Tamás
- Microbiology, Department of Cell and Molecular Biology, University of
Gothenburg, Göteborg, Sweden
| | - Morten Grøtli
- Medicinal Chemistry, Department of Chemistry, University of Gothenburg,
Göteborg, Sweden
- * E-mail:
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28
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Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 2009; 32:878-87. [PMID: 19111667 DOI: 10.1016/j.molcel.2008.11.020] [Citation(s) in RCA: 318] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/05/2008] [Accepted: 11/26/2008] [Indexed: 01/17/2023]
Abstract
The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes. One-third of the binding specificities have not been previously reported. Several binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially approximately 100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters.
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Affiliation(s)
- Gwenael Badis
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
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29
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Ericson E, Gebbia M, Heisler LE, Wildenhain J, Tyers M, Giaever G, Nislow C. Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet 2008; 4:e1000151. [PMID: 18688276 PMCID: PMC2483942 DOI: 10.1371/journal.pgen.1000151] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 07/02/2008] [Indexed: 11/19/2022] Open
Abstract
To better understand off-target effects of widely prescribed psychoactive drugs, we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a model system. Because the known human targets of these drugs do not exist in yeast, we could employ the yeast gene deletion collections and parallel fitness profiling to explore potential off-target effects in a genome-wide manner. Among 214 tested, documented psychoactive drugs, we identified 81 compounds that inhibited wild-type yeast growth and were thus selected for genome-wide fitness profiling. Many of these drugs had a propensity to affect multiple cellular functions. The sensitivity profiles of half of the analyzed drugs were enriched for core cellular processes such as secretion, protein folding, RNA processing, and chromatin structure. Interestingly, fluoxetine (Prozac) interfered with establishment of cell polarity, cyproheptadine (Periactin) targeted essential genes with chromatin-remodeling roles, while paroxetine (Paxil) interfered with essential RNA metabolism genes, suggesting potential secondary drug targets. We also found that the more recently developed atypical antipsychotic clozapine (Clozaril) had no fewer off-target effects in yeast than the typical antipsychotics haloperidol (Haldol) and pimozide (Orap). Our results suggest that model organism pharmacogenetic studies provide a rational foundation for understanding the off-target effects of clinically important psychoactive agents and suggest a rational means both for devising compound derivatives with fewer side effects and for tailoring drug treatment to individual patient genotypes.
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Affiliation(s)
- Elke Ericson
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Marinella Gebbia
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lawrence E. Heisler
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jan Wildenhain
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Mike Tyers
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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30
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Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 2007; 446:806-10. [PMID: 17314980 DOI: 10.1038/nature05649] [Citation(s) in RCA: 690] [Impact Index Per Article: 40.6] [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: 12/05/2007] [Accepted: 02/05/2007] [Indexed: 12/27/2022]
Abstract
Defining the functional relationships between proteins is critical for understanding virtually all aspects of cell biology. Large-scale identification of protein complexes has provided one important step towards this goal; however, even knowledge of the stoichiometry, affinity and lifetime of every protein-protein interaction would not reveal the functional relationships between and within such complexes. Genetic interactions can provide functional information that is largely invisible to protein-protein interaction data sets. Here we present an epistatic miniarray profile (E-MAP) consisting of quantitative pairwise measurements of the genetic interactions between 743 Saccharomyces cerevisiae genes involved in various aspects of chromosome biology (including DNA replication/repair, chromatid segregation and transcriptional regulation). This E-MAP reveals that physical interactions fall into two well-represented classes distinguished by whether or not the individual proteins act coherently to carry out a common function. Thus, genetic interaction data make it possible to dissect functionally multi-protein complexes, including Mediator, and to organize distinct protein complexes into pathways. In one pathway defined here, we show that Rtt109 is the founding member of a novel class of histone acetyltransferases responsible for Asf1-dependent acetylation of histone H3 on lysine 56. This modification, in turn, enables a ubiquitin ligase complex containing the cullin Rtt101 to ensure genomic integrity during DNA replication.
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Affiliation(s)
- Sean R Collins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
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31
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Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics 2006; 7:365. [PMID: 16872538 PMCID: PMC1557541 DOI: 10.1186/1471-2105-7-365] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 07/27/2006] [Indexed: 01/08/2023] Open
Abstract
Background Identification of protein interaction networks has received considerable attention in the post-genomic era. The currently available biochemical approaches used to detect protein-protein interactions are all time and labour intensive. Consequently there is a growing need for the development of computational tools that are capable of effectively identifying such interactions. Results Here we explain the development and implementation of a novel Protein-Protein Interaction Prediction Engine termed PIPE. This tool is capable of predicting protein-protein interactions for any target pair of the yeast Saccharomyces cerevisiae proteins from their primary structure and without the need for any additional information or predictions about the proteins. PIPE showed a sensitivity of 61% for detecting any yeast protein interaction with 89% specificity and an overall accuracy of 75%. This rate of success is comparable to those associated with the most commonly used biochemical techniques. Using PIPE, we identified a novel interaction between YGL227W (vid30) and YMR135C (gid8) yeast proteins. This lead us to the identification of a novel yeast complex that here we term vid30 complex (vid30c). The observed interaction was confirmed by tandem affinity purification (TAP tag), verifying the ability of PIPE to predict novel protein-protein interactions. We then used PIPE analysis to investigate the internal architecture of vid30c. It appeared from PIPE analysis that vid30c may consist of a core and a secondary component. Generation of yeast gene deletion strains combined with TAP tagging analysis indicated that the deletion of a member of the core component interfered with the formation of vid30c, however, deletion of a member of the secondary component had little effect (if any) on the formation of vid30c. Also, PIPE can be used to analyse yeast proteins for which TAP tagging fails, thereby allowing us to predict protein interactions that are not included in genome-wide yeast TAP tagging projects. Conclusion PIPE analysis can predict yeast protein-protein interactions. Also, PIPE analysis can be used to study the internal architecture of yeast protein complexes. The data also suggests that a finite set of short polypeptide signals seem to be responsible for the majority of the yeast protein-protein interactions.
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Affiliation(s)
- Sylvain Pitre
- School of Computer Science, Carleton University, Ottawa, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Canada
| | - Albert Chan
- Department of Mathematics and Computer Science, Fayetteville State University, Fayetteville, USA
| | - Jim Cheetham
- Department of Biology, Carleton University, Ottawa, Canada
| | - Alex Duong
- Department of Biology, Carleton University, Ottawa, Canada
| | - Andrew Emili
- Banting and Best Institute of Medical Research, Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada
| | - Marinella Gebbia
- Banting and Best Institute of Medical Research, Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada
| | - Jack Greenblatt
- Banting and Best Institute of Medical Research, Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada
| | | | - Nevan Krogan
- Banting and Best Institute of Medical Research, Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada
| | - Xuemei Luo
- School of Computer Science, Carleton University, Ottawa, Canada
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32
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Krogan NJ, Lam MHY, Fillingham J, Keogh MC, Gebbia M, Li J, Datta N, Cagney G, Buratowski S, Emili A, Greenblatt JF. Proteasome Involvement in the Repair of DNA Double-Strand Breaks. Mol Cell 2004; 16:1027-34. [PMID: 15610744 DOI: 10.1016/j.molcel.2004.11.033] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.4] [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: 06/01/2004] [Revised: 08/17/2004] [Accepted: 10/21/2004] [Indexed: 11/23/2022]
Abstract
Affinity purification of the yeast 19S proteasome revealed the presence of Sem1 as a subunit. Its human homolog, DSS1, was found likewise to copurify with the human 19S proteasome. DSS1 is known to associate with the tumor suppressor protein BRCA2 involved in repair of DNA double-strand breaks (DSBs). We demonstrate that Sem1 is required for efficient repair of an HO-generated yeast DSB using both homologous recombination (HR) and nonhomologous end joining (NHEJ) pathways. Deletion of SEM1 or genes encoding other nonessential 19S or 20S proteasome subunits also results in synthetic growth defects and hypersensitivity to genotoxins when combined with mutations in well-established DNA DSB repair genes. Chromatin immunoprecipitation showed that Sem1 is recruited along with the 19S and 20S proteasomes to a DSB in vivo, and this recruitment is dependent on components of both the HR and NHEJ repair pathways, suggesting a direct role of the proteasome in DSB repair.
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Affiliation(s)
- Nevan J Krogan
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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Purandare SM, Ware SM, Kwan KM, Gebbia M, Bassi MT, Deng JM, Vogel H, Behringer RR, Belmont JW, Casey B. A complex syndrome of left-right axis, central nervous system and axial skeleton defects in Zic3 mutant mice. Development 2002; 129:2293-302. [PMID: 11959836 DOI: 10.1242/dev.129.9.2293] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [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: 01/15/2023]
Abstract
X-linked heterotaxy (HTX1) is a rare developmental disorder characterized by disturbances in embryonic laterality and other midline developmental field defects. HTX1 results from mutations in ZIC3, a member of the GLI transcription factor superfamily. A targeted deletion of the murine Zic3 locus has been created to investigate its function and interactions with other molecular components of the left-right axis pathway. Embryonic lethality is seen in approximately 50% of null mice with an additional 30% lethality in the perinatal period. Null embryos have defects in turning, cardiac development and neural tube closure. Malformations in live born null mice include complex congenital heart defects, pulmonary reversal or isomerism, CNS defects and vertebral/rib anomalies. Investigation of nodal expression in Zic3-deficient mice indicates that, although nodal is initially expressed symmetrically in the node, there is failure to maintain expression and to shift to asymmetric expression. Subsequent nodal and Pitx2 expression in the lateral plate mesoderm in these mice is randomized, indicating that Zic3 acts upstream of these genes in the determination of left-right asymmetry. The phenotype of these mice correctly models the defects found in human HTX1 and indicates an important role for Zic3 in both left-right and axial patterning.
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Affiliation(s)
- Smita M Purandare
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
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Kosaki R, Gebbia M, Kosaki K, Lewin M, Bowers P, Towbin JA, Casey B. Left-right axis malformations associated with mutations in ACVR2B, the gene for human activin receptor type IIB. Am J Med Genet 1999; 82:70-6. [PMID: 9916847 DOI: 10.1002/(sici)1096-8628(19990101)82:1<70::aid-ajmg14>3.0.co;2-y] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Targeted disruption of the mouse activin receptor type IIB gene (Acvr2b) results in abnormal left-right (LR) axis development among Acvr2b-/- homozygotes [Oh and Li, 1997: Genes Dev 11:1812-1826]. The resulting malformations include atrial and ventricular septal defects, right-sided morphology of the left atrium and left lung, and spleen hypoplasia. Based on these results, we hypothesized that mutations in the type IIB activin receptor gene are associated with some cases of LR axis malformations in humans. We report here characterization of the ACVR2B genomic structure, analysis of ACVR2B splice variants, and screening for ACVR2B mutations among 112 sporadic and 14 familial cases of LR axis malformations. Two missense substitutions have been identified, one of which appears in two unrelated individuals. Neither of these nucleotide changes has been found in 200 control chromosomes. We conclude that ACVR2B mutations are present only rarely among human LR axis malformation cases.
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Affiliation(s)
- R Kosaki
- Department of Pathology, Baylor College of Medicine and Texas Children's Hospital, Houston 77030, USA
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35
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Gebbia M, Ferrero GB, Pilia G, Bassi MT, Aylsworth A, Penman-Splitt M, Bird LM, Bamforth JS, Burn J, Schlessinger D, Nelson DL, Casey B. X-linked situs abnormalities result from mutations in ZIC3. Nat Genet 1997; 17:305-8. [PMID: 9354794 DOI: 10.1038/ng1197-305] [Citation(s) in RCA: 280] [Impact Index Per Article: 10.4] [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] [Indexed: 02/05/2023]
Abstract
Vertebrates position unpaired organs of the chest and abdomen asymmetrically along the left-right (LR) body axis. Each structure comes to lie non-randomly with respect to the midline in an overall position designated situs solitus, exemplified in humans by placement of the heart, stomach and spleen consistently to the left. Aberrant LR axis development can lead to randomization of individual organ position (situs ambiguus) or to mirror-image reversal of all lateralized structures (situs inversus). Previously we mapped a locus for situs abnormalities in humans, HTX1, to Xq26.2 by linkage analysis in a single family (LR1) and by detection of a deletion in an unrelated situs ambiguus male (Family LR2; refs 2,3). From this chromosomal region we have positionally cloned ZIC3, a gene encoding a putative zinc-finger transcription factor. One frameshift, two missense and two nonsense mutations have been identified in familial and sporadic situs ambiguus. The frameshift allele is also associated with situs inversus among some heterozygous females, suggesting that ZIC3 functions in the earliest stages of LR-axis formation. ZIC3, which has not been previously implicated in vertebrate LR-axis development, is the first gene unequivocally associated with human situs abnormalities.
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Affiliation(s)
- M Gebbia
- Department of Pathology, Baylor College of Medicine, Houston, Texas 77030-3498, USA
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36
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Ferrero GB, Gebbia M, Pilia G, Witte D, Peier A, Hopkin RJ, Craigen WJ, Shaffer LG, Schlessinger D, Ballabio A, Casey B. A submicroscopic deletion in Xq26 associated with familial situs ambiguus. Am J Hum Genet 1997; 61:395-401. [PMID: 9311745 PMCID: PMC1715914 DOI: 10.1086/514857] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [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: 02/05/2023] Open
Abstract
Abnormal left-right-axis formation results in heterotaxy, a multiple-malformation syndrome often characterized by severe heart defects, splenic abnormalities, and gastrointestinal malrotation. Previously we had studied a large family in which a gene for heterotaxy, HTX1, was mapped to a 19-cM region in Xq24-q27.1. Further analysis of this family has revealed two recombinations that place HTX1 between DXS300 and DXS1062, an interval spanning approximately 1.3 Mb in Xq26.2. In order to provide independent confirmation of HTX1 localization, a PCR-based search for submicroscopic deletions in this region was performed in unrelated males with sporadic or familial heterotaxy. A cluster of sequence-tagged sites failed to amplify in an individual who also had a deceased, affected brother. FISH identified the mother as a carrier of the deletion, which arose as a new mutation from the maternal grandfather. The deletion interval spans 600-1,100 kb and lies wholly within the 1.3-Mb region identified by recombination. Discovery of this deletion supports localization of HTX1 to Xq26.2 and reveals the first molecular-genetic abnormality associated with human left-right-asymmetry defects.
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Affiliation(s)
- G B Ferrero
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
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37
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Abstract
BACKGROUND Heterotaxy results from failure to establish normal left/right asymmetry during embryonic development. Typical manifestations include complex heart defects and malpositioning of abdominal organs. Missense base substitutions clustered in a 150-base pair region of the gap-junction gene connexin43 (cx43) have been implicated in the pathogenesis of heterotaxy. METHODS AND RESULTS cx43 was studied in 38 cases of sporadic and familial heterotaxy. A 400-base pair region containing the previously reported mutation sites was amplified and directly sequenced in 19 patients. Nineteen additional patients were tested for restriction fragments predicted by two of the previously reported missense substitutions. No difference from normal control subjects was detected in any of the patients. CONCLUSIONS Randomly selected cases of heterotaxy are unlikely to be the result of mutations in cx43.
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Affiliation(s)
- M Gebbia
- Department of Pathology, Baylor College of Medicine, Houston, Tex 77030, USA
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38
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Mantegazza R, Gebbia M, Mora M, Barresi R, Bernasconi P, Baggi F, Cornelio F. Major histocompatibility complex class II molecule expression on muscle cells is regulated by differentiation: implications for the immunopathogenesis of muscle autoimmune diseases. J Neuroimmunol 1996; 68:53-60. [PMID: 8784260 DOI: 10.1016/0165-5728(96)00068-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Major histocompatibility complex (MHC) class II molecules are expressed on myoblasts after interferon-gamma (IFN-gamma) treatment, suggesting a muscle cell involvement in antigen presentation in inflammatory myopathies. However, they were not observed on normal or pathological myofibers. This discrepancy might be related to different responsiveness of developmentally differentiated muscle cells to IFN-gamma. Myoblasts expressed class II transcripts and proteins after IFN-gamma, while myotubes and innervated contracting muscle cells did not show staining for class II molecules. At all cell stages no loss of IFN-gamma receptor was detected indicating that myofiber maturation blocks their capacity to express MHC class II molecules. This suggests that completely differentiated myofibers cannot participate in class II restricted immunological reactions.
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MESH Headings
- Actins/genetics
- Antigens, CD/genetics
- Antigens, Differentiation, B-Lymphocyte/genetics
- Autoimmune Diseases/immunology
- Base Sequence
- Cell Differentiation/immunology
- Cell Fusion/immunology
- Cells, Cultured/chemistry
- Cells, Cultured/drug effects
- Cells, Cultured/immunology
- Gene Expression/immunology
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Humans
- Interferon-gamma/pharmacology
- Molecular Sequence Data
- Muscle Fibers, Skeletal/cytology
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/immunology
- Muscle, Skeletal/chemistry
- Muscle, Skeletal/cytology
- Muscle, Skeletal/immunology
- Muscular Diseases/immunology
- Myosins/genetics
- RNA, Messenger/immunology
- Receptors, Interferon/genetics
- Transcription, Genetic/immunology
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Affiliation(s)
- R Mantegazza
- Divisione Malattie Neuromuscolari, Istituto Nazionale Neurologico C. Besta (UNNCB), Milan, Italy.
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39
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Morandi L, Bernasconi P, Gebbia M, Mora M, Crosti F, Mantegazza R, Cornelio F. Lack of mRNA and dystrophin expression in DMD patients three months after myoblast transfer. Neuromuscul Disord 1995; 5:291-5. [PMID: 7580241 DOI: 10.1016/0960-8966(94)00070-p] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [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: 01/26/2023]
Abstract
We report our experience on myoblast transplantation in three Duchenne muscular dystrophy patients. Pure myoblasts (55 x 10(6) per patient) from HLA-matched donors, were injected into a tibialis anterior and the controlateral muscle was sham injected. Three months after transplantation, biopsies from the injected muscles were negative for dystrophin expression by immunocytochemistry. Reverse transcriptase-PCR (RT-PCR) failed to amplify any fragments of the deleted regions. This result confirms that myoblast transplantation is feasible, although the efficacy of this therapeutic approach is poor.
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Affiliation(s)
- L Morandi
- Department of Neuromuscular Diseases, Istituto Nazionale Neurologico C. Besta, Milan, Italy
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40
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Bassi MT, Schiaffino MV, Renieri A, De Nigris F, Galli L, Bruttini M, Gebbia M, Bergen AA, Lewis RA, Ballabio A. Cloning of the gene for ocular albinism type 1 from the distal short arm of the X chromosome. Nat Genet 1995; 10:13-9. [PMID: 7647783 DOI: 10.1038/ng0595-13] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.0] [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: 01/26/2023]
Abstract
Ocular albinism type 1 (OA1) is an X-linked disorder characterized by severe impairment of visual acuity, retinal hypopigmentation and the presence of macromelanosomes. We isolated a novel transcript from the OA1 critical region in Xp22.3-22.2 which is expressed at high levels in RNA samples from retina, including the retinal pigment epithelium, and from melanoma. This gene encodes a protein of 424 amino acids displaying several putative transmembrane domains and sharing no similarities with previously identified molecules. Five intragenic deletions and a 2 bp insertion resulting in a premature stop codon were identified from DNA analysis of patients with OA1, indicating that we have identified the OA1 gene.
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Affiliation(s)
- M T Bassi
- Department of Molecular Biology, University of Siena, Italy
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41
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Franco B, Meroni G, Parenti G, Levilliers J, Bernard L, Gebbia M, Cox L, Maroteaux P, Sheffield L, Rappold GA, Andria G, Petit C, Ballabio A. A cluster of sulfatase genes on Xp22.3: mutations in chondrodysplasia punctata (CDPX) and implications for warfarin embryopathy. Cell 1995; 81:15-25. [PMID: 7720070 DOI: 10.1016/0092-8674(95)90367-4] [Citation(s) in RCA: 201] [Impact Index Per Article: 6.9] [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: 01/26/2023]
Abstract
X-linked recessive chondrodysplasia punctata (CDPX) is a congenital defect of bone and cartilage development characterized by aberrant bone mineralization, severe underdevelopment of nasal cartilage, and distal phalangeal hypoplasia. A virtually identical phenotype is observed in the warfarin embryopathy, which is due to the teratogenic effects of coumarin derivatives during pregnancy. We have cloned the genomic region within Xp22.3 where the CDPX gene has been assigned and isolated three adjacent genes showing highly significant homology to the sulfatase gene family. Point mutations in one of these genes were identified in five patients with CDPX. Expression of this gene in COS cells resulted in a heat-labile arylsulfatase activity that is inhibited by warfarin. A deficiency of a heat-labile arylsulfatase activity was demonstrated in patients with deletions spanning the CDPX region. These data indicate that CDPX is caused by an inherited deficiency of a novel sulfatase and suggest that warfarin embryopathy might involve drug-induced inhibition of the same enzyme.
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Affiliation(s)
- B Franco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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42
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Mora M, Morandi L, Merlini L, Vita G, Baradello A, Barresi R, Di Blasi C, Blasevich F, Gebbia M, Daniel S. Fetus-like dystrophin expression and other cytoskeletal protein abnormalities in centronuclear myopathies. Muscle Nerve 1994; 17:1176-84. [PMID: 7935525 DOI: 10.1002/mus.880171008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [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: 01/27/2023]
Abstract
We have investigated supposed maturational arrest of muscle in centronuclear myopathies (CNMs) by characterizing the expression of dystrophin, other cytoskeletal proteins, and fetal myosin in the muscle fibers of 9 CNM patients (4 sporadic, 3 familial, 2 adult sporadic). Dystrophin and beta-spectrin localized intracytoplasmically in centrally nucleated fibers. Talin and vinculin were normally expressed. Desmin was radially organized in several fibers in all patients. Scattered vimentinpositive fibers were found in 3 cases. Six myotonic dystrophy cases and 4 inflammatory myopathy cases with regenerating fibers were also studied: dystrophin and the membrane cytoskeletal proteins were normally expressed in the former; and dystrophin, spectrin, and vinculin were reduced in the latter. Intracytoplasmic dystrophin is further evidence of maturational arrest in CNMs. Spectrin and dystrophin codistribute in these pathological conditions as in normal muscle. We conclude that the altered cytoskeletal network found in CNMs likely plays a pathogenetic role in these conditions.
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Affiliation(s)
- M Mora
- Department of Neuromuscular Diseases, Istituto Nazionale Neurologico C. Besta, Milano, Italy
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43
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Mora M, Morandi L, Piccinelli A, Gussoni E, Gebbia M, Blasevich F, Dworzak F, Cornelio F. Dystrophin abnormalities in Duchenne and Becker dystrophy carriers: correlation with cytoskeletal proteins and myosins. J Neurol 1993; 240:455-61. [PMID: 8263549 DOI: 10.1007/bf00874112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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: 01/29/2023]
Abstract
Characterization with a panel of six antibodies revealed abnormal dystrophin expression in 6 of 20 Duchenne muscular dystrophy (DMD) carriers examined, and in 5 of 12 Becker muscular dystrophy (BMD) carriers examined. The immunocytochemistry of muscle fibres was normal with five of the antibodies in two BMD carriers, but some muscle fibres were negative to the antibody directed against a portion of the dystrophin rod domain. Mosaicism was detected with all six antibodies in the other three BMD (but in only a small number of fibres) and in all DMD carriers muscles. Spectrin, vinculin and talin were immunolocalized in the same muscle specimens in order to assess membrane cytoskeletal integrity and to correlate their expression with that of dystrophin. These proteins, including vinculin, which was previously reported to be reduced in DMD patient muscles, were normally present on the surface of all dystrophin-deficient fibres. Muscle fibre types were characterized using monoclonal antibodies against fetal myosin and adult fast and adult slow myosin heavy chains. In both the DMD and BMD carriers, a significant reduction in type 2B fibres, as well as an increase in type 2C and fetal myosin-containing fibres was found - as has also been reported in DMD patients. Altered dystrophin expression was observed more frequently in type 2 than type 1 fibres. Dystrophin deficiency was found in a high percentage of type 2C fibres as well as in all fibres expressing fetal myosin; this suggests that dystrophin-deficient fibres are more susceptible to degeneration, leading to regeneration.
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Affiliation(s)
- M Mora
- Department of Neuromuscular Diseases, Carlo Besta Neurological Institute, Milan, Italy
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44
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Morandi L, Mora M, Bernasconi P, Mantegazza R, Gebbia M, Balestrini MR, Cornelio F. Very small dystrophin molecule in a family with a mild form of Becker dystrophy. Neuromuscul Disord 1993; 3:65-70. [PMID: 8329891 DOI: 10.1016/0960-8966(93)90043-j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The genetic defect in a family with a mild form of Becker dystrophy was characterized by immunocytochemical, immunoblot and genomic DNA analysis in two patients and a carrier. Immunocytochemical localization on muscle preparations with a series of antibodies against different regions of the dystrophin molecule showed normal dystrophin expression with all the antibodies except anti-30 kDa antiserum. In the carrier's muscle, mosaicism was observed only with the anti-30 kDa. Immunoblot analysis revealed a band of about 250 kDa in the patients' muscles and a double band of normal and of reduced weight protein in carrier muscle. In the patients Multiplex-PCR (M-PCR) and Southern blot revealed deletions from exon 13 to exon 41. The study confirms that very mild Becker muscular dystrophy can be associated with a large intragenic deletion from the dystrophin gene.
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Affiliation(s)
- L Morandi
- Department of Neuromuscular Diseases, Istituto Neurologico Carlo Besta, Milano, Italy
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45
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Abstract
Chronic exposure to manganese-laden dusts induces, in humans and lower primates, neurological disorders with clinicopathological features that resemble idiopathic Parkinson's disease. As many authors have suggested, manganese neurotoxicity could be related to the capability of this metal to increase catechol autoxidation in catecholaminergic neurons, therefore increasing the formation of toxic compounds such as peroxides, superoxides, free radicals, and semi-orthoquinones. Oxidative stresses and consequent neuronal damage could then occur if physiological scavenger mechanisms fail in their detoxifying action. We here report that manganese chloride weakly inhibits, in a dose-dependent way by a reversible competitive mechanism, human brain glutathione-S-transferases possibly suggesting that manganese intoxication could cause intraneuronal accumulation of cytotoxic compounds. We also report that both 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, a neurotoxin known to induce in man Parkinson-like syndromes, and one of its metabolites 1-methyl-4-phenylpyridinium failed to decrease glutathione-S-transferase activity.
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Affiliation(s)
- A Vescovi
- Lab. of Neuropharmacology, Neurological Institute C. Besta, Milan, Italy
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46
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Bussone G, Frediani F, Leone M, Gebbia M, Lamperti E, Boiardi A. Trh-Test In Cluster Headache. Cephalalgia 1987. [DOI: 10.1177/03331024870070s6137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- G. Bussone
- Centro Cefalee - Istituto Neurologico “C. Besta” Via Celoria, 11 20133 Milano
| | - F. Frediani
- Centro Cefalee - Istituto Neurologico “C. Besta” Via Celoria, 11 20133 Milano
| | - M. Leone
- Centro Cefalee - Istituto Neurologico “C. Besta” Via Celoria, 11 20133 Milano
| | - M. Gebbia
- Centro Cefalee - Istituto Neurologico “C. Besta” Via Celoria, 11 20133 Milano
| | - E. Lamperti
- Centro Cefalee - Istituto Neurologico “C. Besta” Via Celoria, 11 20133 Milano
| | - A. Boiardi
- Centro Cefalee - Istituto Neurologico “C. Besta” Via Celoria, 11 20133 Milano
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