1001
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Kiessling MK, Schuierer S, Stertz S, Beibel M, Bergling S, Knehr J, Carbone W, de Vallière C, Tchinda J, Bouwmeester T, Seuwen K, Rogler G, Roma G. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics 2016; 17:723. [PMID: 27613601 PMCID: PMC5016932 DOI: 10.1186/s12864-016-3042-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular processes; however discovering novel lineage-specific genetic dependencies from the many hits still remains a challenge. RESULTS To assess whether CRISPR-Cas9 dropout screens can help identify cancer dependencies, we screened two human cancer cell lines carrying known and distinct oncogenic mutations using a genome-wide sgRNA library. We found that the gRNA targeting the driver mutation EGFR was one of the highest-ranking candidates in the EGFR-mutant HCC-827 lung adenocarcinoma cell line. Likewise, sgRNAs for NRAS and MAP2K1 (MEK1), a downstream kinase of mutant NRAS, were identified among the top hits in the NRAS-mutant neuroblastoma cell line CHP-212. Depletion of these genes targeted by the sgRNAs strongly correlated with the sensitivity to specific kinase inhibitors of the EGFR or RAS pathway in cell viability assays. In addition, we describe other dependencies such as TBK1 in HCC-827 cells and TRIB2 in CHP-212 cells which merit further investigation. CONCLUSIONS We show that genome-wide CRISPR dropout screens are suitable for the identification of oncogenic drivers and other essential genes.
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Affiliation(s)
- Michael K. Kiessling
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Cheryl de Vallière
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Joelle Tchinda
- Department of Oncology, Children University Hospital Zürich, Zürich, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Klaus Seuwen
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
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1002
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Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat Biotechnol 2016; 34:933-941. [DOI: 10.1038/nbt.3659] [Citation(s) in RCA: 577] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 07/31/2016] [Indexed: 02/06/2023]
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1003
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Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA. O-GlcNAcase Is an RNA Polymerase II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1β. J Biol Chem 2016; 291:22703-22713. [PMID: 27601472 DOI: 10.1074/jbc.m116.751420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/29/2016] [Indexed: 12/24/2022] Open
Abstract
We describe here the identification and functional characterization of the enzyme O-GlcNAcase (OGA) as an RNA polymerase II elongation factor. Using in vitro transcription elongation assays, we show that OGA activity is required for elongation in a crude nuclear extract system, whereas in a purified system devoid of OGA the addition of rOGA inhibited elongation. Furthermore, OGA is physically associated with the known RNA polymerase II (pol II) pausing/elongation factors SPT5 and TRIM28-KAP1-TIF1β, and a purified OGA-SPT5-TIF1β complex has elongation properties. Lastly, ChIP-seq experiments show that OGA maps to the transcriptional start site/5' ends of genes, showing considerable overlap with RNA pol II, SPT5, TRIM28-KAP1-TIF1β, and O-GlcNAc itself. These data all point to OGA as a component of the RNA pol II elongation machinery regulating elongation genome-wide. Our results add a novel and unexpected dimension to the regulation of elongation by the insertion of O-GlcNAc cycling into the pol II elongation regulatory dynamics.
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Affiliation(s)
- Melissa Resto
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Bong-Hyun Kim
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Alfonso G Fernandez
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Brian J Abraham
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, and.,Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Keji Zhao
- Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Brian A Lewis
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893,
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1004
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Duffy S, Fam HK, Wang YK, Styles EB, Kim JH, Ang JS, Singh T, Larionov V, Shah SP, Andrews B, Boerkoel CF, Hieter P. Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. Proc Natl Acad Sci U S A 2016; 113:9967-76. [PMID: 27551064 PMCID: PMC5018746 DOI: 10.1073/pnas.1611839113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Somatic copy number amplification and gene overexpression are common features of many cancers. To determine the role of gene overexpression on chromosome instability (CIN), we performed genome-wide screens in the budding yeast for yeast genes that cause CIN when overexpressed, a phenotype we refer to as dosage CIN (dCIN), and identified 245 dCIN genes. This catalog of genes reveals human orthologs known to be recurrently overexpressed and/or amplified in tumors. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells. Rhabdomyosarcoma lines with elevated human Tdp1 levels also exhibit CIN that can be partially rescued by siRNA-mediated knockdown of TDP1 Overexpression of dCIN genes represents a genetic vulnerability that could be leveraged for selective killing of cancer cells through targeting of an unlinked synthetic dosage lethal (SDL) partner. Using SDL screens in yeast, we identified a set of genes that when deleted specifically kill cells with high levels of Tdp1. One gene was the histone deacetylase RPD3, for which there are known inhibitors. Both HT1080 cells overexpressing hTDP1 and rhabdomyosarcoma cells with elevated levels of hTdp1 were more sensitive to histone deacetylase inhibitors valproic acid (VPA) and trichostatin A (TSA), recapitulating the SDL interaction in human cells and suggesting VPA and TSA as potential therapeutic agents for tumors with elevated levels of hTdp1. The catalog of dCIN genes presented here provides a candidate list to identify genes that cause CIN when overexpressed in cancer, which can then be leveraged through SDL to selectively target tumors.
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Affiliation(s)
- Supipi Duffy
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Hok Khim Fam
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Yi Kan Wang
- BC Cancer Agency, Vancouver, BC, Canada V5Z 4E6
| | - Erin B Styles
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Jung-Hyun Kim
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - J Sidney Ang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Tejomayee Singh
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Vladimir Larionov
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | | | - Brenda Andrews
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1
| | - Cornelius F Boerkoel
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;
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1005
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Miles LA, Garippa RJ, Poirier JT. Design, execution, and analysis of pooled in vitro CRISPR/Cas9 screens. FEBS J 2016; 283:3170-80. [PMID: 27250066 DOI: 10.1111/febs.13770] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022]
Abstract
The recently described clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology has proven to be an exquisitely powerful and invaluable method of genetic manipulation and/or modification. As such, many researchers have realized the potential of using the CRISPR/Cas9 system as a novel screening method for the identification of important proteins in biological processes and have designed short guide RNA libraries for an in vitro screening. The seminal papers describing these libraries offer valuable information regarding methods for generating the short guide RNA libraries, creating cell lines containing these libraries, and specific details regarding the screening workflow. However, certain considerations are often overlooked that may be important when planning and performing a screen, including which CRISPR library to use and how to best analyze the resulting screen data. In this review, we offer suggestions to answer some of these questions that are not covered as deeply in the papers describing the available CRISPR libraries for an in vitro screening.
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Affiliation(s)
- Linde A Miles
- Pharmacology Graduate Training Program, Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Ralph J Garippa
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - John T Poirier
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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1006
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Mohr SE, Hu Y, Ewen‐Campen B, Housden BE, Viswanatha R, Perrimon N. CRISPR guide RNA design for research applications. FEBS J 2016; 283:3232-8. [PMID: 27276584 PMCID: PMC5014588 DOI: 10.1111/febs.13777] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/24/2016] [Accepted: 06/07/2016] [Indexed: 12/23/2022]
Abstract
The rapid rise of CRISPR as a technology for genome engineering and related research applications has created a need for algorithms and associated online tools that facilitate design of on-target and effective guide RNAs (gRNAs). Here, we review the state of the art in CRISPR gRNA design for research applications of the CRISPR-Cas9 system, including knockout, activation, and inhibition. Notably, achieving good gRNA design is not solely dependent on innovations in CRISPR technology. Good design and design tools also rely on availability of high-quality genome sequence and gene annotations, as well as on availability of accumulated data regarding off-targets and effectiveness metrics.
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Affiliation(s)
- Stephanie E. Mohr
- Drosophila RNAi Screening CenterHarvard Medical SchoolBostonMAUSA
- Department of GeneticsHarvard Medical SchoolBostonMAUSA
| | - Yanhui Hu
- Drosophila RNAi Screening CenterHarvard Medical SchoolBostonMAUSA
- Department of GeneticsHarvard Medical SchoolBostonMAUSA
| | | | | | | | - Norbert Perrimon
- Drosophila RNAi Screening CenterHarvard Medical SchoolBostonMAUSA
- Department of GeneticsHarvard Medical SchoolBostonMAUSA
- Howard Hughes Medical InstituteBostonMAUSA
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1007
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Cross BCS, Lawo S, Archer CR, Hunt JR, Yarker JL, Riccombeni A, Little AS, McCarthy NJ, Moore JD. Increasing the performance of pooled CRISPR-Cas9 drop-out screening. Sci Rep 2016; 6:31782. [PMID: 27545104 PMCID: PMC4992892 DOI: 10.1038/srep31782] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/27/2016] [Indexed: 11/23/2022] Open
Abstract
Components of the type II CRISPR-Cas complex in bacteria have been used successfully in eukaryotic cells to facilitate rapid and accurate cell line engineering, animal model generation and functional genomic screens. Such developments are providing new opportunities for drug target identification and validation, particularly with the application of pooled genetic screening. As CRISPR-Cas is a relatively new genetic screening tool, it is important to assess its functionality in a number of different cell lines and to analyse potential improvements that might increase the sensitivity of a given screen. To examine critical aspects of screening quality, we constructed ultra-complex libraries containing sgRNA sequences targeting a collection of essential genes. We examined the performance of screening in both haploid and hypotriploid cell lines, using two alternative guide design algorithms and two tracrRNA variants in a time-resolved analysis. Our data indicate that a simple adaptation of the tracrRNA substantially improves the robustness of guide loss during a screen. This modification minimises the requirement for high numbers of sgRNAs targeting each gene, increasing hit scoring and creating a powerful new platform for successful screening.
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Affiliation(s)
- Benedict C. S. Cross
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Steffen Lawo
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Caroline R. Archer
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Jessica R. Hunt
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Joanne L. Yarker
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Alessandro Riccombeni
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Annette S. Little
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Nicola J. McCarthy
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Jonathan D. Moore
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
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1008
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Mutlu N, Kumar A. Mapping paths: new approaches to dissect eukaryotic signaling circuitry. F1000Res 2016; 5. [PMID: 27540473 PMCID: PMC4965690 DOI: 10.12688/f1000research.8818.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic cells are precisely “wired” to coordinate changes in external and intracellular signals with corresponding adjustments in the output of complex and often interconnected signaling pathways. These pathways are critical in understanding cellular growth and function, and several experimental trends are emerging with applicability toward more fully describing the composition and topology of eukaryotic signaling networks. In particular, recent studies have implemented CRISPR/Cas-based screens in mouse and human cell lines for genes involved in various cell growth and disease phenotypes. Proteomic methods using mass spectrometry have enabled quantitative and dynamic profiling of protein interactions, revealing previously undiscovered complexes and allele-specific protein interactions. Methods for the single-cell study of protein localization and gene expression have been integrated with computational analyses to provide insight into cell signaling in yeast and metazoans. In this review, we present an overview of exemplary studies using the above approaches, relevant for the analysis of cell signaling and indeed, more broadly, for many modern biological applications.
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Affiliation(s)
- Nebibe Mutlu
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anuj Kumar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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1009
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Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, Kost-Alimova M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC. Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting. Cancer Discov 2016; 6:914-29. [PMID: 27260156 PMCID: PMC4972686 DOI: 10.1158/2159-8290.cd-16-0154] [Citation(s) in RCA: 371] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/31/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell-cycle arrest. By examining single-guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR/Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR/Cas9 elicits a gene-independent antiproliferative cell response. This effect has important practical implications for the interpretation of CRISPR/Cas9 screening data and confounds the use of this technology for the identification of essential genes in amplified regions. SIGNIFICANCE We found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells. These observations have practical implications for using CRISPR/Cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies. Cancer Discov; 6(8); 914-29. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Munoz et al., p. 900This article is highlighted in the In This Issue feature, p. 803.
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Affiliation(s)
- Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Robin M Meyers
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Barbara A Weir
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Francisca Vazquez
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Cheng-Zhong Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Uri Ben-David
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - April Cook
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Mihir B Doshi
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Stanley Gill
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Han Xu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Levi D Ali
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Guozhi Jiang
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sasha Pantel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Coyin Oh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gregory Kryukov
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Levi A Garraway
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Kimberly Stegmaier
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Boston Children's Hospital, Boston, Massachusetts
| | - Charles W Roberts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts. St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Todd R Golub
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Harvard Medical School, Boston, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts.
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1010
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Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD, Golji J, Ruddy DA, Yu K, McAllister G, DeWeck A, Abramowski D, Wan J, Shirley MD, Neshat SY, Rakiec D, de Beaumont R, Weber O, Kauffmann A, McDonald ER, Keen N, Hofmann F, Sellers WR, Schmelzle T, Stegmeier F, Schlabach MR. CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions. Cancer Discov 2016; 6:900-13. [PMID: 27260157 DOI: 10.1158/2159-8290.cd-16-0178] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/27/2016] [Indexed: 11/16/2022]
Abstract
UNLABELLED CRISPR/Cas9 has emerged as a powerful new tool to systematically probe gene function. We compared the performance of CRISPR to RNAi-based loss-of-function screens for the identification of cancer dependencies across multiple cancer cell lines. CRISPR dropout screens consistently identified more lethal genes than RNAi, implying that the identification of many cellular dependencies may require full gene inactivation. However, in two aneuploid cancer models, we found that all genes within highly amplified regions, including nonexpressed genes, scored as lethal by CRISPR, revealing an unanticipated class of false-positive hits. In addition, using a CRISPR tiling screen, we found that sgRNAs targeting essential domains generate the strongest lethality phenotypes and thus provide a strategy to rapidly define the protein domains required for cancer dependence. Collectively, these findings not only demonstrate the utility of CRISPR screens in the identification of cancer-essential genes, but also reveal the need to carefully control for false-positive results in chromosomally unstable cancer lines. SIGNIFICANCE We show in this study that CRISPR-based screens have a significantly lower false-negative rate compared with RNAi-based screens, but have specific liabilities particularly in the interrogation of regions of genome amplification. Therefore, this study provides critical insights for applying CRISPR-based screens toward the systematic identification of new cancer targets. Cancer Discov; 6(8); 900-13. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Aguirre et al., p. 914This article is highlighted in the In This Issue feature, p. 803.
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Affiliation(s)
- Diana M Munoz
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Pamela J Cassiani
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Li Li
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Eric Billy
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Joshua M Korn
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Michael D Jones
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Javad Golji
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Kristine Yu
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Gregory McAllister
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Antoine DeWeck
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dorothee Abramowski
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jessica Wan
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Matthew D Shirley
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Sarah Y Neshat
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Daniel Rakiec
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Rosalie de Beaumont
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Odile Weber
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Audrey Kauffmann
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - E Robert McDonald
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Nicholas Keen
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Francesco Hofmann
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - William R Sellers
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Tobias Schmelzle
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Frank Stegmeier
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Michael R Schlabach
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
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1011
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Dunn NR, Tolwinski NS. Ptk7 and Mcc, Unfancied Components in Non-Canonical Wnt Signaling and Cancer. Cancers (Basel) 2016; 8:cancers8070068. [PMID: 27438854 PMCID: PMC4963810 DOI: 10.3390/cancers8070068] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/29/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022] Open
Abstract
Human development uses a remarkably small number of signal transduction pathways to organize vastly complicated tissues. These pathways are commonly associated with disease in adults if activated inappropriately. One such signaling pathway, Wnt, solves the too few pathways conundrum by having many alternate pathways within the Wnt network. The main or "canonical" Wnt pathway has been studied in great detail, and among its numerous downstream components, several have been identified as drug targets that have led to cancer treatments currently in clinical trials. In contrast, the non-canonical Wnt pathways are less well characterized, and few if any possible drug targets exist to tackle cancers caused by dysregulation of these Wnt offshoots. In this review, we focus on two molecules-Protein Tyrosine Kinase 7 (Ptk7) and Mutated in Colorectal Cancer (Mcc)-that do not fit perfectly into the non-canonical pathways described to date and whose roles in cancer are ill defined. We will summarize work from our laboratories as well as many others revealing unexpected links between these two proteins and Wnt signaling both in cancer progression and during vertebrate and invertebrate embryonic development. We propose that future studies focused on delineating the signaling machinery downstream of Ptk7 and Mcc will provide new, hitherto unanticipated drug targets to combat cancer metastasis.
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Affiliation(s)
- Norris Ray Dunn
- Agency for Science Technology and Research (A*STAR) Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore.
| | - Nicholas S Tolwinski
- Division of Science, Yale-NUS College, Singapore 138610, Singapore.
- Department of Biological Sciences, Centre for Translational Medicine, NUS Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Level 10 South, 10-02M, Singapore 117599, Singapore.
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1012
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The Hidden Complexity of Mendelian Traits across Natural Yeast Populations. Cell Rep 2016; 16:1106-1114. [PMID: 27396326 DOI: 10.1016/j.celrep.2016.06.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/15/2016] [Accepted: 06/10/2016] [Indexed: 11/21/2022] Open
Abstract
Mendelian traits are considered to be at the lower end of the complexity spectrum of heritable phenotypes. However, more than a century after the rediscovery of Mendel's law, the global landscape of monogenic variants, as well as their effects and inheritance patterns within natural populations, is still not well understood. Using the yeast Saccharomyces cerevisiae, we performed a species-wide survey of Mendelian traits across a large population of isolates. We generated offspring from 41 unique parental pairs and analyzed 1,105 cross/trait combinations. We found that 8.9% of the cases were Mendelian. Further tracing of causal variants revealed background-specific expressivity and modified inheritances, gradually transitioning from Mendelian to complex traits in 30% of the cases. In fact, when taking into account the natural population diversity, the hidden complexity of traits could be substantial, confounding phenotypic predictability even for simple Mendelian traits.
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1013
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Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 2016; 17:148. [PMID: 27380939 PMCID: PMC4934014 DOI: 10.1186/s13059-016-1012-2] [Citation(s) in RCA: 1054] [Impact Index Per Article: 131.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. RESULTS We conduct the first independent evaluation of CRISPR/Cas9 predictions. To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. We also evaluate on-target efficiency prediction algorithms against available datasets. The correlation between the predictions and the guide activity varied considerably, especially for zebrafish. Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. We further demonstrate that the best predictions can significantly reduce the time spent on guide screening. CONCLUSIONS To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here.
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Affiliation(s)
- Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Kai Schönig
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, 68159, Germany
| | - Hélène Eckert
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, Cedex, 05 75248, France
| | - Alexis Eschstruth
- CNRS UMR 7622, INSERM U1156, Sorbonne Université Paris 06, Paris, France
| | | | | | | | - Alena Shkumatava
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, Cedex, 05 75248, France
| | | | - Jim Kent
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | | | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, Paris, France.
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1014
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McDade JR, Waxmonsky NC, Swanson LE, Fan M. Practical Considerations for Using Pooled Lentiviral CRISPR Libraries. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2016; 115:31.5.1-31.5.13. [PMID: 27366891 DOI: 10.1002/cpmb.8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CRISPR/Cas9 technology is ideally suited for genome-wide screening applications due to the ease of generating guide RNAs (gRNAs) and the versatility of Cas9 or Cas9 derivatives to knockout, repress, or activate expression of target genes. Several pooled lentiviral CRISPR libraries have been developed and are now publicly available, but while using CRISPR/Cas9 for genetic experiments has become widely adopted, genome-wide screening experiments remain technically challenging. This review covers the basics of CRISPR/Cas9, describes several publicly available CRISPR libraries, and provides a general protocol for conducting genome-wide screening experiments using CRISPR/Cas9. © 2016 by John Wiley & Sons, Inc.
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1015
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Park J, Kim JS, Bae S. Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9. Bioinformatics 2016; 32:2017-23. [PMID: 27153724 PMCID: PMC4920116 DOI: 10.1093/bioinformatics/btw103] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/02/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION CRISPR-derived RNA guided endonucleases (RGENs) have been widely used for both gene knockout and knock-in at the level of single or multiple genes. RGENs are now available for forward genetic screens at genome scale, but single guide RNA (sgRNA) selection at this scale is difficult. RESULTS We develop an online tool, Cas-Database, a genome-wide gRNA library design tool for Cas9 nucleases from Streptococcus pyogenes (SpCas9). With an easy-to-use web interface, Cas-Database allows users to select optimal target sequences simply by changing the filtering conditions. Furthermore, it provides a powerful way to select multiple optimal target sequences from thousands of genes at once for the creation of a genome-wide library. Cas-Database also provides a web application programming interface (web API) for advanced bioinformatics users. AVAILABILITY AND IMPLEMENTATION Free access at http://www.rgenome.net/cas-database/ CONTACT sangsubae@hanyang.ac.kr or jskim01@snu.ac.kr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jeongbin Park
- Department of Chemistry, Hanyang University, Seoul 133-791, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul 151-747, South Korea Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 133-791, South Korea Institute for Materials Design, Hanyang University, Seoul 133-791, South Korea
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1016
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Haeussler M, Concordet JP. Genome Editing with CRISPR-Cas9: Can It Get Any Better? J Genet Genomics 2016; 43:239-50. [PMID: 27210042 PMCID: PMC5708852 DOI: 10.1016/j.jgg.2016.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/13/2016] [Accepted: 04/23/2016] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo. At the same time, the on-target activity of thousands of guides has been determined. These data have led to numerous online tools that facilitate the selection of guide RNAs in target sequences. It appears that for most basic research applications, cleavage activity can be maximized and off-targets minimized by carefully choosing guide RNAs based on computational predictions. Moreover, recent studies of Cas proteins have further improved the flexibility and precision of the CRISPR-Cas toolkit for genome editing. Inspired by the crystal structure of the complex of sgRNA-SpCas9 bound to target DNA, several variants of SpCas9 have recently been engineered, either with novel protospacer adjacent motifs (PAMs) or with drastically reduced off-targets. Novel Cas9 and Cas9-like proteins called Cpf1 have also been characterized from other bacteria and will benefit from the insights obtained from SpCas9. Genome editing with CRISPR-Cas9 may also progress with better understanding and control of cellular DNA repair pathways activated after Cas9-induced DNA cleavage.
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Affiliation(s)
- Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, 1156 High Street, University of California, Santa Cruz, CA 95064, USA
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, Inserm U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005 Paris, France.
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1017
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Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat Biotechnol 2016; 34:634-6. [PMID: 27159373 PMCID: PMC4900911 DOI: 10.1038/nbt.3567] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/11/2016] [Indexed: 12/11/2022]
Abstract
We compare the ability of shRNA and CRISPR/Cas9 screens to identify essential genes in the human chronic myelogenous leukemia cell line K562. We find that the precision of the two libraries in detecting essential genes is similar and that combining data from both screens improves performance. Notably, results from the two screens show little correlation, which can be partially explained by identification of distinct essential biological processes with each technology.
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1018
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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] [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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1019
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Hart T, Moffat J. BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics 2016; 17:164. [PMID: 27083490 PMCID: PMC4833918 DOI: 10.1186/s12859-016-1015-8] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/06/2016] [Indexed: 12/03/2022] Open
Abstract
Background The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. Results We offer BAGEL (Bayesian Analysis of Gene EssentiaLity), a supervised learning method for analyzing gene knockout screens. Coupled with gold-standard reference sets of essential and nonessential genes, BAGEL offers significantly greater sensitivity than current methods, while computational optimizations reduce runtime by an order of magnitude. Conclusions Using BAGEL, we identify ~2000 fitness genes in pooled library knockout screens in human cell lines at 5 % FDR, a major advance over competing platforms. BAGEL shows high sensitivity and specificity even across screens performed by different labs using different libraries and reagents.
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Affiliation(s)
- Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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1020
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Kim JJ, Lipatova Z, Segev N. TRAPP Complexes in Secretion and Autophagy. Front Cell Dev Biol 2016; 4:20. [PMID: 27066478 PMCID: PMC4811894 DOI: 10.3389/fcell.2016.00020] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/04/2016] [Indexed: 12/13/2022] Open
Abstract
TRAPP is a highly conserved modular multi-subunit protein complex. Originally identified as a “transport protein particle” with a role in endoplasmic reticulum-to-Golgi transport, its multiple subunits and their conservation from yeast to humans were characterized in the late 1990s. TRAPP attracted attention when it was shown to act as a Ypt/Rab GTPase nucleotide exchanger, GEF, in the 2000s. Currently, three TRAPP complexes are known in yeast, I, II, and III, and they regulate two different intracellular trafficking pathways: secretion and autophagy. Core TRAPP contains four small subunits that self assemble to a stable complex, which has a GEF activity on Ypt1. Another small subunit, Trs20/Sedlin, is an adaptor required for the association of core TRAPP with larger subunits to form TRAPP II and TRAPP III. Whereas the molecular structure of the core TRAPP complex is resolved, the architecture of the larger TRAPP complexes, including their existence as dimers and multimers, is less clear. In addition to its Ypt/Rab GEF activity, and thereby an indirect role in vesicle tethering through Ypt/Rabs, a direct role for TRAPP as a vesicle tether has been suggested. This idea is based on TRAPP interactions with vesicle coat components. While much of the basic information about TRAPP complexes comes from yeast, mutations in TRAPP subunits were connected to human disease. In this review we will summarize new information about TRAPP complexes, highlight new insights about their function and discuss current controversies and future perspectives.
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Affiliation(s)
- Jane J Kim
- Department of Biological Sciences, University of Illinois at Chicago Chicago, IL, USA
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago Chicago, IL, USA
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1021
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Natsume T, Kiyomitsu T, Saga Y, Kanemaki MT. Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors. Cell Rep 2016; 15:210-218. [PMID: 27052166 DOI: 10.1016/j.celrep.2016.03.001] [Citation(s) in RCA: 389] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/28/2016] [Accepted: 02/24/2016] [Indexed: 01/31/2023] Open
Abstract
Studying the role of essential proteins is dependent upon a method for rapid inactivation, in order to study the immediate phenotypic consequences. Auxin-inducible degron (AID) technology allows rapid depletion of proteins in animal cells and fungi, but its application to human cells has been limited by the difficulties of tagging endogenous proteins. We have developed a simple and scalable CRISPR/Cas-based method to tag endogenous proteins in human HCT116 and mouse embryonic stem (ES) cells by using donor constructs that harbor synthetic short homology arms. Using a combination of AID tagging with CRISPR/Cas, we have generated conditional alleles of essential nuclear and cytoplasmic proteins in HCT116 cells, which can then be depleted very rapidly after the addition of auxin to the culture medium. This approach should greatly facilitate the functional analysis of essential proteins, particularly those of previously unknown function.
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Affiliation(s)
- Toyoaki Natsume
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Tomomi Kiyomitsu
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yumiko Saga
- Division of Mammalian Development, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masato T Kanemaki
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
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1022
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Affiliation(s)
- Charles Boone
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
| | - Brenda J Andrews
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
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1023
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1024
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