1
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Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J. Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon 2023; 9:e12744. [PMID: 36597481 PMCID: PMC9800021 DOI: 10.1016/j.heliyon.2022.e12744] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.
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Affiliation(s)
- Katherine Chan
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Corresponding author
| | - Adrian Granda Farias
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Hunsang Lee
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Furkan Guvenc
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Patricia Mero
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Kevin R. Brown
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Henry Ward
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Kamaldeep Aulakh
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Audrey Astori
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Shahan Haider
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Edyta Marcon
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Ulrich Braunschweig
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Shuye Pu
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Andrea Habsid
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Amy Hin Yan Tong
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Natasha Christie-Holmes
- Combined Containment Level 3 Unit, Temerty Faculty of Medicine, University of Toronto Toronto, Ontario, Canada, M5S3E1
| | - Patrick Budylowski
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Ayoob Ghalami
- Office of Environmental Health & Safety, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario, Canada, M5S3E1,Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Finlay Maguire
- Department of Community Health and Epidemiology, Faculty of Medicine Dalhousie University, Halifax, Nova Scotia, Canada,Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jack Greenblatt
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Scott D. Gray-Owen
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Brian Raught
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Benjamin J. Blencowe
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Mikko Taipale
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Jason Moffat
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8,Institute for Biomedical Engineering, Rosebrugh Building, 164 College Street, Room 407, University of Toronto, Toronto, Ontario, Canada, M5S3G9,Corresponding author. Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
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2
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Gwynne WD, Suk Y, Custers S, Mikolajewicz N, Chan JK, Zador Z, Chafe SC, Zhai K, Escudero L, Zhang C, Zaslaver O, Chokshi C, Shaikh MV, Bakhshinyan D, Burns I, Chaudhry I, Nachmani O, Mobilio D, Maich WT, Mero P, Brown KR, Quaile AT, Venugopal C, Moffat J, Montenegro-Burke JR, Singh SK. Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma. Cancer Cell 2022; 40:1488-1502.e7. [PMID: 36368321 DOI: 10.1016/j.ccell.2022.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/09/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
MYC-driven medulloblastoma (MB) is an aggressive pediatric brain tumor characterized by therapy resistance and disease recurrence. Here, we integrated data from unbiased genetic screening and metabolomic profiling to identify multiple cancer-selective metabolic vulnerabilities in MYC-driven MB tumor cells, which are amenable to therapeutic targeting. Among these targets, dihydroorotate dehydrogenase (DHODH), an enzyme that catalyzes de novo pyrimidine biosynthesis, emerged as a favorable candidate for therapeutic targeting. Mechanistically, DHODH inhibition acts on target, leading to uridine metabolite scarcity and hyperlipidemia, accompanied by reduced protein O-GlcNAcylation and c-Myc degradation. Pyrimidine starvation evokes a metabolic stress response that leads to cell-cycle arrest and apoptosis. We further show that an orally available small-molecule DHODH inhibitor demonstrates potent mono-therapeutic efficacy against patient-derived MB xenografts in vivo. The reprogramming of pyrimidine metabolism in MYC-driven medulloblastoma represents an unappreciated therapeutic strategy and a potential new class of treatments with stronger cancer selectivity and fewer neurotoxic sequelae.
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Affiliation(s)
- William D Gwynne
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Yujin Suk
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Michael G DeGroote School of Medicine, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Stefan Custers
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Nicholas Mikolajewicz
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Jeremy K Chan
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zsolt Zador
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Shawn C Chafe
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Kui Zhai
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Laura Escudero
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Cunjie Zhang
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Olga Zaslaver
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chirayu Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Muhammad Vaseem Shaikh
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - David Bakhshinyan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Ian Burns
- Michael G DeGroote School of Medicine, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Iqra Chaudhry
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Omri Nachmani
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Daniel Mobilio
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - William T Maich
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Patricia Mero
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kevin R Brown
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Andrew T Quaile
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chitra Venugopal
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Jason Moffat
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J Rafael Montenegro-Burke
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Sheila K Singh
- Department of Surgery, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada.
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3
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Masud SN, Chandrashekhar M, Aregger M, Tan G, Zhang X, Mero P, Pirman DA, Zaslaver O, Smolen GA, Lin ZY, Wong CJ, Boone C, Gingras AC, Montenegro-Burke JR, Moffat J. Author Correction: Chemical genomics with pyrvinium identifies C1orf115 as a regulator of drug efflux. Nat Chem Biol 2022; 18:1162. [PMID: 36002506 DOI: 10.1038/s41589-022-01146-9] [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: 10/15/2022]
Affiliation(s)
- Sanna N Masud
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Megha Chandrashekhar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre, Toronto, ON, Canada.,Canadian Nuclear Laboratories, Chalk River, ON, Canada
| | - Michael Aregger
- Donnelly Centre, Toronto, ON, Canada.,Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | | | - Patricia Mero
- Donnelly Centre, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - David A Pirman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Gromoslaw A Smolen
- Agios Pharmaceuticals, Cambridge, MA, USA.,Celsius Therapeutics, Cambridge, MA, USA
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - J Rafael Montenegro-Burke
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Donnelly Centre, Toronto, ON, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada. .,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
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4
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Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, Yao Y, Mikolajewicz N, Ross C, Brown KR, Zid AA, Fan ZP, Hui S, Krall JA, Simons DM, Slater CJ, De Jesus V, Tang L, Singh R, Goldford JE, Martin S, Huang Q, Francis EA, Habsid A, Climie R, Tieu D, Wei J, Li R, Tong AHY, Aregger M, Chan KS, Han H, Wang X, Mero P, Brumell JH, Finelli A, Ailles L, Bader G, Smolen GA, Kingsbury GA, Hart T, Kung C, Moffat J. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature 2020; 586:120-126. [PMID: 32968282 DOI: 10.1038/s41586-020-2746-2] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 06/30/2020] [Indexed: 01/05/2023]
Abstract
The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood1-3. Here, to identify a phenotypically robust core set of genes and pathways that enable cancer cells to evade killing mediated by cytotoxic T lymphocytes (CTLs), we performed genome-wide CRISPR screens across a panel of genetically diverse mouse cancer cell lines that were cultured in the presence of CTLs. We identify a core set of 182 genes across these mouse cancer models, the individual perturbation of which increases either the sensitivity or the resistance of cancer cells to CTL-mediated toxicity. Systematic exploration of our dataset using genetic co-similarity reveals the hierarchical and coordinated manner in which genes and pathways act in cancer cells to orchestrate their evasion of CTLs, and shows that discrete functional modules that control the interferon response and tumour necrosis factor (TNF)-induced cytotoxicity are dominant sub-phenotypes. Our data establish a central role for genes that were previously identified as negative regulators of the type-II interferon response (for example, Ptpn2, Socs1 and Adar1) in mediating CTL evasion, and show that the lipid-droplet-related gene Fitm2 is required for maintaining cell fitness after exposure to interferon-γ (IFNγ). In addition, we identify the autophagy pathway as a conserved mediator of the evasion of CTLs by cancer cells, and show that this pathway is required to resist cytotoxicity induced by the cytokines IFNγ and TNF. Through the mapping of cytokine- and CTL-based genetic interactions, together with in vivo CRISPR screens, we show how the pleiotropic effects of autophagy control cancer-cell-intrinsic evasion of killing by CTLs and we highlight the importance of these effects within the tumour microenvironment. Collectively, these data expand our knowledge of the genetic circuits that are involved in the evasion of the immune system by cancer cells, and highlight genetic interactions that contribute to phenotypes associated with escape from killing by CTLs.
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Affiliation(s)
- Keith A Lawson
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Xiaoyu Zhang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Eiru Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rummy Akthar
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Yuxi Yao
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Catherine Ross
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Abdelrahman Abou Zid
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | | | - Shirley Hui
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | - Lujia Tang
- Agios Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | - Qian Huang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ryan Climie
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jiarun Wei
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ren Li
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine S Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Hong Han
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Xiaowei Wang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Mero
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurie Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gary Bader
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gromoslaw A Smolen
- Agios Pharmaceuticals, Cambridge, MA, USA.,Celsius Therapeutics, Cambridge, MA, USA
| | | | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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5
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Aregger M, Lawson KA, Billmann M, Costanzo M, Tong AHY, Chan K, Rahman M, Brown KR, Ross C, Usaj M, Nedyalkova L, Sizova O, Habsid A, Pawling J, Lin ZY, Abdouni H, Wong CJ, Weiss A, Mero P, Dennis JW, Gingras AC, Myers CL, Andrews BJ, Boone C, Moffat J. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Nat Metab 2020; 2:499-513. [PMID: 32694731 PMCID: PMC7566881 DOI: 10.1038/s42255-020-0211-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
The de novo synthesis of fatty acids has emerged as a therapeutic target for various diseases, including cancer. Because cancer cells are intrinsically buffered to combat metabolic stress, it is important to understand how cells may adapt to the loss of de novo fatty acid biosynthesis. Here, we use pooled genome-wide CRISPR screens to systematically map genetic interactions (GIs) in human HAP1 cells carrying a loss-of-function mutation in fatty acid synthase (FASN), whose product catalyses the formation of long-chain fatty acids. FASN-mutant cells show a strong dependence on lipid uptake that is reflected in negative GIs with genes involved in the LDL receptor pathway, vesicle trafficking and protein glycosylation. Further support for these functional relationships is derived from additional GI screens in query cell lines deficient in other genes involved in lipid metabolism, including LDLR, SREBF1, SREBF2 and ACACA. Our GI profiles also identify a potential role for the previously uncharacterized gene C12orf49 (which we call LUR1) in regulation of exogenous lipid uptake through modulation of SREBF2 signalling in response to lipid starvation. Overall, our data highlight the genetic determinants underlying the cellular adaptation associated with loss of de novo fatty acid synthesis and demonstrate the power of systematic GI mapping for uncovering metabolic buffering mechanisms in human cells.
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Affiliation(s)
- Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Corresponding authors: , , ,
| | - Keith A. Lawson
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Urology, Department of Surgery, University of Toronto
- Corresponding authors: , , ,
| | - Maximillian Billmann
- Department of Computer Science and Engineering, University of Minnesota – Twin Cities, Minneapolis, Minnestota, USA
- Corresponding authors: , , ,
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Amy H. Y. Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Mahfuzur Rahman
- Department of Computer Science and Engineering, University of Minnesota – Twin Cities, Minneapolis, Minnestota, USA
| | - Kevin R. Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Catherine Ross
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Nedyalkova
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Olga Sizova
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Judy Pawling
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Hala Abdouni
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Cassandra J. Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Mero
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - James W. Dennis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota – Twin Cities, Minneapolis, Minnestota, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota – Twin Cities, Minneapolis, Minnestota, USA
- Corresponding authors: , , ,
| | - Brenda J. Andrews
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Corresponding authors: , , ,
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Corresponding authors: , , ,
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Corresponding authors: , , ,
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6
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Cinà DP, Ketela T, Brown KR, Chandrashekhar M, Mero P, Li C, Onay T, Fu Y, Han Z, Saleem M, Moffat J, Quaggin SE. Forward genetic screen in human podocytes identifies diphthamide biosynthesis genes as regulators of adhesion. Am J Physiol Renal Physiol 2019; 317:F1593-F1604. [PMID: 31566424 PMCID: PMC6962514 DOI: 10.1152/ajprenal.00195.2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/30/2019] [Revised: 08/28/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023] Open
Abstract
Podocyte function is tightly linked to the complex organization of its cytoskeleton and adhesion to the underlying glomerular basement membrane. Adhesion of cultured podocytes to a variety of substrates is reported to correlate with podocyte health. To identify novel genes that are important for podocyte function, we designed an in vitro genetic screen based on podocyte adhesion to plates coated with either fibronectin or soluble Fms-like tyrosine kinase-1 (sFLT1)/Fc. A genome-scale pooled RNA interference screen on immortalized human podocytes identified 77 genes that increased adhesion to fibronectin, 101 genes that increased adhesion to sFLT1/Fc, and 44 genes that increased adhesion to both substrates when knocked down. Multiple shRNAs against diphthamide biosynthesis protein 1-4 (DPH1-DPH4) were top hits for increased adhesion. Immortalized human podocyte cells stably expressing these hairpins displayed increased adhesion to both substrates. We then used CRISPR-Cas9 to generate podocyte knockout cells for DPH1, DPH2, or DPH3, which also displayed increased adhesion to both fibronectin and sFLT1/Fc, as well as a spreading defect. Finally, we showed that Drosophila nephrocyte-specific knockdown of Dph1, Dph2, and Dph4 resulted in altered nephrocyte function. In summary, we report here a novel high-throughput method to identify genes important for podocyte function. Given the central role of podocyte adhesion as a marker of podocyte health, these data are a rich source of candidate regulators of glomerular disease.
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Affiliation(s)
- Davide P Cinà
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Troy Ketela
- Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Megha Chandrashekhar
- Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Mero
- Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Chengjin Li
- Tanenbaum-Lunenfeld Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Tuncer Onay
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yulong Fu
- Center for Genetic Medicine Research, Children's National Health System, Washington, District of Columbia
| | - Zhe Han
- Center for Genetic Medicine Research, Children's National Health System, Washington, District of Columbia
| | - Moin Saleem
- School of Clinical Sciences, Children's Renal Unit and Academic Renal Unit, University of Bristol, Bristol, United Kingdom
| | - Jason Moffat
- Donnelly Centre, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Susan E Quaggin
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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7
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Abstract
Genome editing using the CRISPR-Cas system has vastly advanced the ability to precisely edit the genomes of various organisms. In the context of mammalian cells, this technology represents a novel means to perform genome-wide genetic screens for functional genomics studies. Libraries of guide RNAs (sgRNA) targeting all open reading frames permit the facile generation of thousands of genetic perturbations in a single pool of cells that can be screened for specific phenotypes to implicate gene function and cellular processes in an unbiased and systematic way. CRISPR-Cas screens provide researchers with a simple, efficient, and inexpensive method to uncover the genetic blueprints for cellular phenotypes. Furthermore, differential analysis of screens performed in various cell lines and from different cancer types can identify genes that are contextually essential in tumor cells, revealing potential targets for specific anticancer therapies. Performing genome-wide screens in human cells can be daunting, as this involves the handling of tens of millions of cells and requires analysis of large sets of data. The details of these screens, such as cell line characterization, CRISPR library considerations, and understanding the limitations and capabilities of CRISPR technology during analysis, are often overlooked. Provided here is a detailed protocol for the successful performance of pooled genome-wide CRISPR-Cas9 based screens.
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Affiliation(s)
| | | | | | | | - Jason Moffat
- Donnelly Centre, University of Toronto; Department of Molecular Genetics, University of Toronto; Institute for Biomaterials and Biomedical Engineering, University of Toronto;
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8
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Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A, Habsid A, Sizova O, Nedyalkova L, Climie R, Tworzyanski L, Lawson K, Sartori MA, Alibeh S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, Usaj M, Billmann M, Rahman M, Constanzo M, Myers CL, Andrews BJ, Boone C, Durocher D, Moffat J. Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens. G3 (Bethesda) 2017; 7:2719-2727. [PMID: 28655737 PMCID: PMC5555476 DOI: 10.1534/g3.117.041277] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [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] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/12/2017] [Indexed: 12/26/2022]
Abstract
The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.
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Affiliation(s)
- Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | | | - Katie Chan
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | | | - Michael Aregger
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Nicole Hustedt
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Sahil Seth
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Avery Noonan
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Olga Sizova
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Ryan Climie
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Keith Lawson
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Sabriyeh Alibeh
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Sanna Masud
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Patricia Mero
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mahfuzur Rahman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
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9
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Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Mero P, Dirks P, Sidhu S, Roth FP, Rissland OS, Durocher D, Angers S, Moffat J. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell 2015. [PMID: 26627737 DOI: 10.1016/j.cell.2015.11.015.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.
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Affiliation(s)
- Traver Hart
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Megha Chandrashekhar
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Michael Aregger
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Zachary Steinhart
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Kevin R Brown
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Graham MacLeod
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Monika Mis
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Michal Zimmermann
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada
| | - Amelie Fradet-Turcotte
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada
| | - Song Sun
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-75123, Sweden; Department of Computer Science, University of Toronto, Toronto, ON M5G1X8, Canada
| | - Patricia Mero
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Peter Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G1X8, Canada
| | - Sachdev Sidhu
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Frederick P Roth
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G1X8, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olivia S Rissland
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G0A4, Canada
| | - Daniel Durocher
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Jason Moffat
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada.
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10
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Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Mero P, Dirks P, Sidhu S, Roth FP, Rissland OS, Durocher D, Angers S, Moffat J. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell 2015; 163:1515-26. [PMID: 26627737 DOI: 10.1016/j.cell.2015.11.015] [Citation(s) in RCA: 989] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/01/2015] [Accepted: 10/30/2015] [Indexed: 01/17/2023]
Abstract
The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.
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Affiliation(s)
- Traver Hart
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Megha Chandrashekhar
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Michael Aregger
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Zachary Steinhart
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Kevin R Brown
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Graham MacLeod
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Monika Mis
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Michal Zimmermann
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada
| | - Amelie Fradet-Turcotte
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada
| | - Song Sun
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-75123, Sweden; Department of Computer Science, University of Toronto, Toronto, ON M5G1X8, Canada
| | - Patricia Mero
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Peter Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G1X8, Canada
| | - Sachdev Sidhu
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Frederick P Roth
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G1X8, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olivia S Rissland
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G0A4, Canada
| | - Daniel Durocher
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S1A1, Canada
| | - Jason Moffat
- Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada.
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11
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Bona R, Piccioni D, Broda R, Mesto A, Mero P, Colombardo V, Conson M, Martinetti S. PS-074 Healthcare associated infections in Long-Term Care Facilities in Asti (Italy). Eur J Hosp Pharm 2014. [DOI: 10.1136/ejhpharm-2013-000436.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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12
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Colombardo V, Besso V, Bona R, Conson M, Nocera M, Sampietro M, Barbato I, Mero P, Piccioni D, Martinetti S. GRP-016 Analysis and Consumption of Innovative Antidiabetic Drugs in Piedmont Patients. Eur J Hosp Pharm 2013. [DOI: 10.1136/ejhpharm-2013-000276.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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13
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Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, Sircoulomb F, Medrano M, Fedyshyn Y, Koh JL, van Dyk D, Fedyshyn B, Luhova M, Brito GC, Vizeacoumar FJ, Vizeacoumar FS, Datti A, Kasimer D, Buzina A, Mero P, Misquitta C, Normand J, Haider M, Ketela T, Wrana JL, Rottapel R, Neel BG, Moffat J. Essential gene profiles in breast, pancreatic, and ovarian cancer cells. Cancer Discov 2012; 2:172-189. [PMID: 22585861 PMCID: PMC5057396 DOI: 10.1158/2159-8290.cd-11-0224] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [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] [Indexed: 12/16/2022]
Abstract
UNLABELLED Genomic analyses are yielding a host of new information on the multiple genetic abnormalities associated with specific types of cancer. A comprehensive description of cancer-associated genetic abnormalities can improve our ability to classify tumors into clinically relevant subgroups and, on occasion, identify mutant genes that drive the cancer phenotype ("drivers"). More often, though, the functional significance of cancer-associated mutations is difficult to discern. Genome-wide pooled short hairpin RNA (shRNA) screens enable global identification of the genes essential for cancer cell survival and proliferation, providing a "functional genomic" map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting ~16,000 genes and a newly developed, dynamic scoring approach, we identified essential gene profiles in 72 breast, pancreatic, and ovarian cancer cell lines. Integrating our results with current and future genomic data should facilitate the systematic identification of drivers, unanticipated synthetic lethal relationships, and functional vulnerabilities of these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types.
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Affiliation(s)
- Richard Marcotte
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Kevin R. Brown
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Fernando Suarez
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Azin Sayad
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Konstantina Karamboulas
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Paul M. Krzyzanowski
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Fabrice Sircoulomb
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Mauricio Medrano
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Yaroslav Fedyshyn
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Judice L.Y. Koh
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Dewald van Dyk
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Bodhana Fedyshyn
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Marianna Luhova
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | | | - Franco J. Vizeacoumar
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | | | - Alessandro Datti
- Samuel Lunenfeld Research Institute, Toronto, Canada
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Dahlia Kasimer
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Alla Buzina
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Patricia Mero
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Christine Misquitta
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Josee Normand
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Maliha Haider
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Troy Ketela
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Jeffrey L. Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Robert Rottapel
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Benjamin G. Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Jason Moffat
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Syam S, Mero P, Pham T, McIntosh CA, Bruhns P, Booth JW. Differential recruitment of activating and inhibitory Fc gamma RII during phagocytosis. J Immunol 2010; 184:2966-73. [PMID: 20154205 DOI: 10.4049/jimmunol.0900016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human myeloid cells express both activating and inhibitory receptors of the FcgammaRII family. FcgammaRIIA mediates processes associated with cell activation, including phagocytosis of IgG-opsonized particles, whereas coengagement of the inhibitory FcgammaRIIB downregulates such signaling. We analyzed the relative recruitment of these two receptors during phagocytosis of IgG-coated particles by ts20 Chinese hamster fibroblast cells cotransfected with both receptors carrying distinguishable fluorescent protein tags. We found that FcgammaRIIA is substantially enriched at sites of particle binding relative to its inhibitory counterpart, with a greater than 2-fold increase in the local ratio of activating to inhibitory receptor compared with that for the plasma membrane as a whole. Experiments with chimeric receptors revealed that the preferential enrichment of FcgammaRIIA results from differences between the extracellular domains of the receptors, and indicated that the lesser recruitment of FcgammaRIIB limits its ability to effectively inhibit FcgammaRIIA-mediated phagocytosis. Mutagenesis studies indicated that FcgammaRIIA residues leucine 132 and phenylalanine 160, which lie in IgG-binding regions of FcgammaRIIA and which differ in FcgammaRIIB, both contribute to the local relative enrichment of FcgammaRIIA by increasing its affinity for IgG1 relative to that of FcgammaRIIB. In human monocytes, engagement of approximately equal amounts of FcgammaRIIB was required to substantially inhibit FcgammaRIIA-mediated phagocytosis. These results demonstrate that differences in affinity for IgG between activating and inhibitory FcgammaR can result in substantial local changes in their relative concentrations during phagocytosis, with important functional consequences.
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Affiliation(s)
- Sujata Syam
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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Shaha SP, Tomic J, Shi Y, Pham T, Mero P, White D, He L, Baryza JL, Wender PA, Booth JW, Spaner DE. Prolonging microtubule dysruption enhances the immunogenicity of chronic lymphocytic leukaemia cells. Clin Exp Immunol 2009; 158:186-98. [PMID: 19737143 DOI: 10.1111/j.1365-2249.2009.04003.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cytotoxic chemotherapies do not usually mediate the expression of an immunogenic gene programme in tumours, despite activating many of the signalling pathways employed by highly immunogenic cells. Concomitant use of agents that modulate and complement stress-signalling pathways activated by chemotherapeutic agents may then enhance the immunogenicity of cancer cells, increase their susceptibility to T cell-mediated controls and lead to higher clinical remission rates. Consistent with this hypothesis, the microtubule inhibitor, vincristine, caused chronic lymphocytic leukaemia (CLL) cells to die rapidly, without increasing their immunogenicity. Protein kinase C (PKC) agonists (such as bryostatin) delayed the death of vincristine-treated CLL cells and made them highly immunogenic, with increased stimulatory abilities in mixed lymphocyte responses, production of proinflammatory cytokines, expression of co-stimulatory molecules and activation of c-Jun N-terminal kinase (JNK), p38 and nuclear factor kappa B (NF-kappaB) signalling pathways. This phenotype was similar to the result of activating CLL cells through Toll-like receptors (TLRs), which communicate 'danger' signals from infectious pathogens. Use of PKC agonists and microtubule inhibitors to mimic TLR-signalling, and increase the immunogenicity of CLL cells, has implications for the design of chemo-immunotherapeutic strategies.
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Affiliation(s)
- S P Shaha
- Division of Molecular and Cellular Biology, Research Institute, Sunnybrook Health Sciences Center, Toronto, Canada
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Mero P, Zhang CY, Huang ZY, Kim MK, Schreiber AD, Grinstein S, Booth JW. Phosphorylation-independent ubiquitylation and endocytosis of Fc gammaRIIA. J Biol Chem 2006; 281:33242-9. [PMID: 16959774 DOI: 10.1074/jbc.m605372200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [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: 11/06/2022] Open
Abstract
Endocytosis of the Fc receptor Fc gammaRIIA depends on a functional ubiquitin conjugation system, and the receptor becomes ubiquitylated upon ligand binding. Phosphorylation of tyrosines in Fc gammaRIIA by Src family kinases is thought to be the initiating event in its signaling. However, although the Src family kinase inhibitor PP1 inhibited both ligand-induced phosphorylation of Fc gammaRIIA and phagocytosis in ts20 cells expressing Fc gammaRIIA, it did not inhibit receptor ubiquitylation or endocytosis of soluble ligands. Conversely, genistein and the proteasomal inhibitor MG132 did not inhibit receptor phosphorylation but strongly inhibited both receptor ubiquitylation and endocytosis. A region of the receptor lying within the immunoreceptor tyrosine-based activation motif was found to be necessary for both ubiquitylation and endocytosis. Ubiquitylation occurs at the plasma membrane before internalization. Endocytosis of Fc gammaRIIA is dependent on clathrin but independent of the adaptor protein AP-2. These findings point to a novel mechanism for ubiquitylation and endocytosis of this immunoreceptor.
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Affiliation(s)
- Patricia Mero
- Molecular and Cellular Biology Research, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
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