1101
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Liu J, Shui SL. Delivery methods for site-specific nucleases: Achieving the full potential of therapeutic gene editing. J Control Release 2016; 244:83-97. [PMID: 27865852 DOI: 10.1016/j.jconrel.2016.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/30/2016] [Accepted: 11/07/2016] [Indexed: 12/20/2022]
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1102
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Gaj T, Sirk SJ, Shui SL, Liu J. Genome-Editing Technologies: Principles and Applications. Cold Spring Harb Perspect Biol 2016; 8:a023754. [PMID: 27908936 PMCID: PMC5131771 DOI: 10.1101/cshperspect.a023754] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Targeted nucleases have provided researchers with the ability to manipulate virtually any genomic sequence, enabling the facile creation of isogenic cell lines and animal models for the study of human disease, and promoting exciting new possibilities for human gene therapy. Here we review three foundational technologies-clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs). We discuss the engineering advances that facilitated their development and highlight several achievements in genome engineering that were made possible by these tools. We also consider artificial transcription factors, illustrating how this technology can complement targeted nucleases for synthetic biology and gene therapy.
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Affiliation(s)
- Thomas Gaj
- Department of Bioengineering, University of California, Berkeley, California 94720
| | - Shannon J Sirk
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Sai-Lan Shui
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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1103
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Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P. An atlas of human kinase regulation. Mol Syst Biol 2016; 12:888. [PMID: 27909043 PMCID: PMC5199121 DOI: 10.15252/msb.20167295] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision‐making has been limited by the small number of simultaneously monitored phospho‐regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs. Co‐regulation along the conditions predicts kinase–complex and kinase–substrate associations. Additionally, the kinase regulation profile acts as a molecular fingerprint to identify related and opposing signaling states. Using this atlas, we identified essential mediators of stem cell differentiation, modulators of Salmonella infection, and new targets of AKT1. This provides a global view of human phosphorylation‐based signaling and the necessary context to better understand kinase‐driven decision‐making.
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Affiliation(s)
- David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Mindaugas Jonikas
- Quantitative Cell Biology Group, MRC Clinical Sciences Centre, Imperial College, London, UK
| | - Robert T Lawrence
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bachir El Debs
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joel Selkrig
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Silvia Dm Santos
- Quantitative Cell Biology Group, MRC Clinical Sciences Centre, Imperial College, London, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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1104
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Genome-wide CRISPR screens reveal a Wnt–FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors. Nat Med 2016; 23:60-68. [DOI: 10.1038/nm.4219] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/30/2016] [Indexed: 02/08/2023]
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1105
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Horak P, Fröhling S, Glimm H. Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls. ESMO Open 2016; 1:e000094. [PMID: 27933214 PMCID: PMC5133384 DOI: 10.1136/esmoopen-2016-000094] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach. The basic assumption of precision oncology is that molecular markers detected by NGS will predict response to targeted therapies independently from tumour histology. However, along with a ubiquitous availability of NGS, the complexity and heterogeneity at the individual patient level had to be acknowledged. Not only does the latter present challenges to clinical decision-making based on sequencing data, it is also an obstacle to the rational design of clinical trials. Novel tissue-agnostic trial designs were quickly developed to overcome these challenges. Results from some of these trials have recently demonstrated the feasibility and efficacy of this approach. On the other hand, there is an increasing amount of whole-exome and whole-genome NGS data which allows us to assess ever smaller differences between individual patients with cancer. In this review, we highlight different tumour sequencing strategies currently used for precision oncology, describe their individual strengths and weaknesses, and emphasise their feasibility in different clinical settings. Further, we evaluate the possibility of NGS implementation in current and future clinical trials, and point to the significance of NGS for translational research.
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Affiliation(s)
- Peter Horak
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stefan Fröhling
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Hanno Glimm
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
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1106
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The ribosome-engaged landscape of alternative splicing. Nat Struct Mol Biol 2016; 23:1117-1123. [PMID: 27820807 DOI: 10.1038/nsmb.3317] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) has revealed an enormous complexity of alternative splicing (AS) across diverse cell and tissue types. However, it is currently unknown to what extent repertoires of splice-variant transcripts are translated into protein products. Here, we surveyed AS events engaged by the ribosome. Notably, at least 75% of human exon-skipping events detected in transcripts with medium-to-high abundance in RNA-seq data were also detected in ribosome profiling data. Furthermore, relatively small subsets of functionally related splice variants are engaged by ribosomes at levels that do not reflect their absolute abundance, thus indicating a role for AS in modulating translational output. This mode of regulation is associated with control of the mammalian cell cycle. Our results thus suggest that a major fraction of splice variants is translated and that specific cellular functions including cell-cycle control are subject to AS-dependent modulation of translation output.
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1107
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Chen S, Sun H, Miao K, Deng CX. CRISPR-Cas9: from Genome Editing to Cancer Research. Int J Biol Sci 2016; 12:1427-1436. [PMID: 27994508 PMCID: PMC5166485 DOI: 10.7150/ijbs.17421] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer development is a multistep process triggered by innate and acquired mutations, which cause the functional abnormality and determine the initiation and progression of tumorigenesis. Gene editing is a widely used engineering tool for generating mutations that enhance tumorigenesis. The recent developed clustered regularly interspaced short palindromic repeats-CRISPR-associated 9 (CRISPR-Cas9) system renews the genome editing approach into a more convenient and efficient way. By rapidly introducing genetic modifications in cell lines, organs and animals, CRISPR-Cas9 system extends the gene editing into whole genome screening, both in loss-of-function and gain-of-function manners. Meanwhile, the system accelerates the establishment of animal cancer models, promoting in vivo studies for cancer research. Furthermore, CRISPR-Cas9 system is modified into diverse innovative tools for observing the dynamic bioprocesses in cancer studies, such as image tracing for targeted DNA, regulation of transcription activation or repression. Here, we view recent technical advances in the application of CRISPR-Cas9 system in cancer genetics, large-scale cancer driver gene hunting, animal cancer modeling and functional studies.
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Affiliation(s)
- Si Chen
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Heng Sun
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Kai Miao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
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1108
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Howard TP, Vazquez F, Tsherniak A, Hong AL, Rinne M, Aguirre AJ, Boehm JS, Hahn WC. Functional Genomic Characterization of Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 81:237-246. [PMID: 27815544 DOI: 10.1101/sqb.2016.81.031070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
International efforts to sequence cancer genomes now provide an overview of the major genetic alterations that occur in most human cancers. These studies have identified many highly recurrent alterations in specific cancer subtypes but have also identified mutations that occur at lower frequency and unstudied variants of known cancer-associated genes. To elucidate the function of such cancer alleles, we have developed several approaches to systematically interrogate genomic changes found in human tumors. In general, we have taken two complementary approaches. In the first approach, we focus on perturbing genes identified as mutated, amplified, or deleted by cancer genome annotation efforts, whereas in the second, we have taken an unbiased approach to identify genes that are essential for cancer cell proliferation or survival in cell lines that are extensively annotated to identify context-specific essential genes. These studies begin to allow us to define a cancer dependencies map.
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Affiliation(s)
- Thomas P Howard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Francisca Vazquez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Aviad Tsherniak
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Andrew L Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142.,Boston Children's Hospital, Boston, Massachusetts 02115
| | - Mik Rinne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Jesse S Boehm
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
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1109
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Zhu S, Wei W. Making better CRISPR libraries. eLife 2016; 5:e21863. [PMID: 27809196 PMCID: PMC5094850 DOI: 10.7554/elife.21863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 11/17/2022] Open
Abstract
A new algorithm improves the performance of CRISPR-based genetic screens in mammals.
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Affiliation(s)
- Shiyou Zhu
- Biodynamic Optical Imaging Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China
| | - Wensheng Wei
- Biodynamic Optical Imaging Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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1110
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Mullen PJ, Yu R, Longo J, Archer MC, Penn LZ. The interplay between cell signalling and the mevalonate pathway in cancer. Nat Rev Cancer 2016; 16:718-731. [PMID: 27562463 DOI: 10.1038/nrc.2016.76] [Citation(s) in RCA: 477] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mevalonate (MVA) pathway is an essential metabolic pathway that uses acetyl-CoA to produce sterols and isoprenoids that are integral to tumour growth and progression. In recent years, many oncogenic signalling pathways have been shown to increase the activity and/or the expression of MVA pathway enzymes. This Review summarizes recent advances and discusses unique opportunities for immediately targeting this metabolic vulnerability in cancer with agents that have been approved for other therapeutic uses, such as the statin family of drugs, to improve outcomes for cancer patients.
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Affiliation(s)
- Peter J Mullen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Rosemary Yu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Joseph Longo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Michael C Archer
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5G 1L7
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5S 3E2
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada M5G 1L7
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5G 1L7
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1111
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Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DYR, Seydoux G, Mohr SE, Zuber J, Perrimon N. Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 2016; 18:24-40. [PMID: 27795562 DOI: 10.1038/nrg.2016.118] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Our understanding of the genetic mechanisms that underlie biological processes has relied extensively on loss-of-function (LOF) analyses. LOF methods target DNA, RNA or protein to reduce or to ablate gene function. By analysing the phenotypes that are caused by these perturbations the wild-type function of genes can be elucidated. Although all LOF methods reduce gene activity, the choice of approach (for example, mutagenesis, CRISPR-based gene editing, RNA interference, morpholinos or pharmacological inhibition) can have a major effect on phenotypic outcomes. Interpretation of the LOF phenotype must take into account the biological process that is targeted by each method. The practicality and efficiency of LOF methods also vary considerably between model systems. We describe parameters for choosing the optimal combination of method and system, and for interpreting phenotypes within the constraints of each method.
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Affiliation(s)
- Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Matthew Gemberling
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering and the Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 43 Ludwigstrasse, Bad Nauheim 61231, Germany
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21218, USA.,Howard Hughes Medical Institute, 725 North Wolfe Street, Baltimore, Maryland 21218, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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1112
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Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol 2016; 34:1279-1286. [PMID: 27798563 DOI: 10.1038/nbt.3715] [Citation(s) in RCA: 320] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 09/30/2016] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9 screens have been widely adopted to analyze coding-gene functions, but high-throughput screening of non-coding elements using this method is more challenging because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. We report a high-throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We validated 9 of 51 lncRNA hits using CRISPR-Cas9-mediated genomic deletion, functional rescue, CRISPR activation or inhibition and gene-expression profiling. Our high-throughput pgRNA genome deletion method will enable rapid identification of functional mammalian non-coding elements.
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Affiliation(s)
- Shiyou Zhu
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| | - Wei Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jingze Liu
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China
| | - Chen-Hao Chen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Qi Liao
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Ping Xu
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Han Xu
- Broad Institute of MIT and Harvard, Cambridge Center, Cambridge, Massachusetts, USA
| | - Tengfei Xiao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Zhongzheng Cao
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jingyu Peng
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Pengfei Yuan
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaole Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wensheng Wei
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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1113
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Vaz B, Popovic M, Newman JA, Fielden J, Aitkenhead H, Halder S, Singh AN, Vendrell I, Fischer R, Torrecilla I, Drobnitzky N, Freire R, Amor DJ, Lockhart PJ, Kessler BM, McKenna GW, Gileadi O, Ramadan K. Metalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Repair. Mol Cell 2016; 64:704-719. [PMID: 27871366 PMCID: PMC5128727 DOI: 10.1016/j.molcel.2016.09.032] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/15/2016] [Accepted: 09/22/2016] [Indexed: 01/12/2023]
Abstract
The cytotoxicity of DNA-protein crosslinks (DPCs) is largely ascribed to their ability to block the progression of DNA replication. DPCs frequently occur in cells, either as a consequence of metabolism or exogenous agents, but the mechanism of DPC repair is not completely understood. Here, we characterize SPRTN as a specialized DNA-dependent and DNA replication-coupled metalloprotease for DPC repair. SPRTN cleaves various DNA binding substrates during S-phase progression and thus protects proliferative cells from DPC toxicity. Ruijs-Aalfs syndrome (RJALS) patient cells with monogenic and biallelic mutations in SPRTN are hypersensitive to DPC-inducing agents due to a defect in DNA replication fork progression and the inability to eliminate DPCs. We propose that SPRTN protease represents a specialized DNA replication-coupled DPC repair pathway essential for DNA replication progression and genome stability. Defective SPRTN-dependent clearance of DPCs is the molecular mechanism underlying RJALS, and DPCs are contributing to accelerated aging and cancer. DNA-protein crosslinks (DPCs) stall DNA replication and induce genomic instability SPARTAN (SPRTN) is a DNA replication-coupled metalloprotease which proteolyses DPCs SPRTN metalloprotease is a fundamental enzyme in DPC repair pathway Ruijs-Aalfs syndrome is caused by a defect in DPC repair due to mutations in SPRTN
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Affiliation(s)
- Bruno Vaz
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Marta Popovic
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Joseph A Newman
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - John Fielden
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Hazel Aitkenhead
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Swagata Halder
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Abhay Narayan Singh
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Iolanda Vendrell
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Neele Drobnitzky
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain
| | - David J Amor
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Gillies W McKenna
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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1114
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A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia. Cell Rep 2016. [PMID: 27760321 DOI: 10.1016/j.celrep.2016.09.079.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive cancer with a poor prognosis, for which mainstream treatments have not changed for decades. To identify additional therapeutic targets in AML, we optimize a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screening platform and use it to identify genetic vulnerabilities in AML cells. We identify 492 AML-specific cell-essential genes, including several established therapeutic targets such as DOT1L, BCL2, and MEN1, and many other genes including clinically actionable candidates. We validate selected genes using genetic and pharmacological inhibition, and chose KAT2A as a candidate for downstream study. KAT2A inhibition demonstrated anti-AML activity by inducing myeloid differentiation and apoptosis, and suppressed the growth of primary human AMLs of diverse genotypes while sparing normal hemopoietic stem-progenitor cells. Our results propose that KAT2A inhibition should be investigated as a therapeutic strategy in AML and provide a large number of genetic vulnerabilities of this leukemia that can be pursued in downstream studies.
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1115
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Ding S, Mooney N, Li B, Kelly MR, Feng N, Loktev AV, Sen A, Patton JT, Jackson PK, Greenberg HB. Comparative Proteomics Reveals Strain-Specific β-TrCP Degradation via Rotavirus NSP1 Hijacking a Host Cullin-3-Rbx1 Complex. PLoS Pathog 2016; 12:e1005929. [PMID: 27706223 PMCID: PMC5051689 DOI: 10.1371/journal.ppat.1005929] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/10/2016] [Indexed: 11/18/2022] Open
Abstract
Rotaviruses (RVs) are the leading cause of severe gastroenteritis in young children, accounting for half a million deaths annually worldwide. RV encodes non-structural protein 1 (NSP1), a well-characterized interferon (IFN) antagonist, which facilitates virus replication by mediating the degradation of host antiviral factors including IRF3 and β-TrCP. Here, we utilized six human and animal RV NSP1s as baits and performed tandem-affinity purification coupled with high-resolution mass spectrometry to comprehensively characterize NSP1-host protein interaction network. Multiple Cullin-RING ubiquitin ligase (CRL) complexes were identified. Importantly, inhibition of cullin-3 (Cul3) or RING-box protein 1 (Rbx1), by siRNA silencing or chemical perturbation, significantly impairs strain-specific NSP1-mediated β-TrCP degradation. Mechanistically, we demonstrate that NSP1 localizes to the Golgi with the host Cul3-Rbx1 CRL complex, which targets β-TrCP and NSP1 for co-destruction at the proteasome. Our study uncovers a novel mechanism that RV employs to promote β-TrCP turnover and provides molecular insights into virus-mediated innate immunity inhibition.
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Affiliation(s)
- Siyuan Ding
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Nancie Mooney
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Bin Li
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Marcus R. Kelly
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ningguo Feng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Alexander V. Loktev
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Adrish Sen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - John T. Patton
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Peter K. Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Harry B. Greenberg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
- * E-mail:
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1116
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Dhillon KK, Bajrami I, Taniguchi T, Lord CJ. Synthetic lethality: the road to novel therapies for breast cancer. Endocr Relat Cancer 2016; 23:T39-55. [PMID: 27528623 DOI: 10.1530/erc-16-0228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 12/12/2022]
Abstract
When the BRCA1 and BRCA2 tumour suppressor genes were identified in the early 1990s, the immediate implications of mapping, cloning and delineating the sequence of these genes were that individuals in families with a BRCA gene mutation could be tested for the presence of a mutation and their risk of developing cancer could be predicted. Over time though, the discovery of BRCA1 and BRCA2 has had a much greater influence than many might have imagined. In this review, we discuss how the discovery of BRCA1 and BRCA2 has not only provided an understanding of the molecular processes that drive tumourigenesis but also reignited an interest in therapeutically exploiting loss-of-function alterations in tumour suppressor genes.
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Affiliation(s)
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
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1117
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Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 2016; 354:769-773. [PMID: 27708057 DOI: 10.1126/science.aag2445] [Citation(s) in RCA: 444] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/21/2016] [Indexed: 11/03/2022]
Abstract
Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the seven enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer-promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.
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Affiliation(s)
- Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Rockwell Anyoha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Glen Munson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sharon R Grossman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Department of Biology, MIT, Cambridge, MA 02139, USA
| | | | - Michael Kane
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Computational and Systems Biology Program, MIT, Cambridge, MA 02139, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Department of Biology, MIT, Cambridge, MA 02139, USA
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1118
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Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC. Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers. Cell Syst 2016; 3:302-316.e4. [PMID: 27684187 PMCID: PMC5455996 DOI: 10.1016/j.cels.2016.09.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/11/2016] [Accepted: 09/02/2016] [Indexed: 12/20/2022]
Abstract
Genome-scale expression studies and comprehensive loss-of-function genetic screens have focused almost exclusively on the highest confidence candidate genes. Here, we describe a strategy for characterizing the lower confidence candidates identified by such approaches. We interrogated 177 genes that we classified as essential for the proliferation of cancer cells exhibiting constitutive β-catenin activity and integrated data for each of the candidates, derived from orthogonal short hairpin RNA (shRNA) knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated gene editing knockout screens, to yield 69 validated genes. We then characterized the relationships between sets of these genes using complementary assays: medium-throughput stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry, yielding 3,639 protein-protein interactions, and a CRISPR-mediated pairwise double knockout screen, yielding 375 combinations exhibiting greater- or lesser-than-additive phenotypic effects indicating genetic interactions. These studies identify previously unreported regulators of β-catenin, define functional networks required for the survival of β-catenin-active cancers, and provide an experimental strategy that may be applied to define other signaling networks.
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Affiliation(s)
- Joseph Rosenbluh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Johnathan Mercer
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Yashaswi Shrestha
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Rachel Oliver
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Pablo Tamayo
- Moores Cancer Center and School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Itay Tirosh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Ella Hartenian
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Heiko Horn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lola Fagbami
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jacob Jaffe
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Kasper Lage
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA.
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1119
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Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife 2016; 5:e19760. [PMID: 27661255 PMCID: PMC5094855 DOI: 10.7554/elife.19760] [Citation(s) in RCA: 570] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022] Open
Abstract
We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict highly effective single guide RNAs (sgRNAs) for targeting nuclease-dead Cas9-mediated transcriptional repression (CRISPRi) and activation (CRISPRa). We use this algorithm to design next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. A CRISPRi screen for essential genes in K562 cells demonstrates that the large majority of sgRNAs are highly active. We also find CRISPRi does not exhibit any detectable non-specific toxicity recently observed with CRISPR nuclease approaches. Precision-recall analysis shows that we detect over 90% of essential genes with minimal false positives using a compact 5 sgRNA/gene library. Our results establish CRISPRi and CRISPRa as premier tools for loss- or gain-of-function studies and provide a general strategy for identifying Cas9 target sites.
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Affiliation(s)
- Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Ryan A Pak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
| | - Yuwen Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Chong Yon Park
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, United states
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
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1120
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Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, The International Mouse Phenotyping Consortium, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KK, McKerlie C, Beaudet AL, Bucan M, Murray SA. High-throughput discovery of novel developmental phenotypes. Nature 2016; 537:508-514. [PMID: 27626380 PMCID: PMC5295821 DOI: 10.1038/nature19356] [Citation(s) in RCA: 874] [Impact Index Per Article: 97.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 08/10/2016] [Indexed: 12/29/2022]
Abstract
Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.
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Affiliation(s)
- Mary E. Dickinson
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Xiao Ji
- Genomics and Computational Biology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
| | - Lydia Teboul
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Michael D. Wong
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacqueline K. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Wolfgang J. Weninger
- Centre for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Henrik Westerberg
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Lynette Bower
- Mouse Biology Program, University of California, Davis
| | - James M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | | | - Francesco Chiani
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo, Itally
| | - Dave Clary
- Mouse Biology Program, University of California, Davis
| | - James Cleak
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | | | - Brendan Doe
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Helmut Fuchs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Antonella Galli
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Alessia Gambadoro
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo, Itally
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Shiying Guo
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Neil R. Horner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Chih-wei Hsu
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Sara J. Johnson
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Lance C. Keith
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California, Davis
| | - Thomas N. Lawson
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | - Manuel Mark
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Susan Marschall
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lauryl M.J. Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Edward Ryder
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kaitlin E. Samocha
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Mohammed Selloum
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Zsombor Szoke-Kovacs
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | | | | | - Ilinca Tudose
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Jonathan Warren
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Olivia Wendling
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - David B. West
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609
| | - Leeyean Wong
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | | | | | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | - Glauco P. Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo, Itally
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Monica J. Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Helen E. Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | | | | | - Martin Hrabe de Angelis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Yann Herault
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Tim Mohun
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - R. Mark Henkelman
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steve D.M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Maja Bucan
- Departments of Genetics and Psychiatry, Perlman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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1121
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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: 3.0] [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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1122
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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: 611] [Impact Index Per Article: 67.9] [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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1123
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Sidik SM, Huet D, Ganesan SM, Huynh MH, Wang T, Nasamu AS, Thiru P, Saeij JPJ, Carruthers VB, Niles JC, Lourido S. A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Cell 2016; 166:1423-1435.e12. [PMID: 27594426 PMCID: PMC5017925 DOI: 10.1016/j.cell.2016.08.019] [Citation(s) in RCA: 575] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 08/05/2016] [Indexed: 12/11/2022]
Abstract
Apicomplexan parasites are leading causes of human and livestock diseases such as malaria and toxoplasmosis, yet most of their genes remain uncharacterized. Here, we present the first genome-wide genetic screen of an apicomplexan. We adapted CRISPR/Cas9 to assess the contribution of each gene from the parasite Toxoplasma gondii during infection of human fibroblasts. Our analysis defines ∼200 previously uncharacterized, fitness-conferring genes unique to the phylum, from which 16 were investigated, revealing essential functions during infection of human cells. Secondary screens identify as an invasion factor the claudin-like apicomplexan microneme protein (CLAMP), which resembles mammalian tight-junction proteins and localizes to secretory organelles, making it critical to the initiation of infection. CLAMP is present throughout sequenced apicomplexan genomes and is essential during the asexual stages of the malaria parasite Plasmodium falciparum. These results provide broad-based functional information on T. gondii genes and will facilitate future approaches to expand the horizon of antiparasitic interventions.
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Affiliation(s)
- Saima M Sidik
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Diego Huet
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Suresh M Ganesan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - My-Hang Huynh
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Tim Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Armiyaw S Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jeroen P J Saeij
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA
| | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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1124
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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: 24] [Impact Index Per Article: 2.7] [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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1125
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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: 61] [Impact Index Per Article: 6.8] [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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1126
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Salzano FM. The role of natural selection in human evolution - insights from Latin America. Genet Mol Biol 2016; 39:302-11. [PMID: 27561111 PMCID: PMC5004836 DOI: 10.1590/1678-4685-gmb-2016-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/08/2016] [Indexed: 11/23/2022] Open
Abstract
A brief introduction considering Darwin's work, the evolutionary synthesis, and the
scientific biological field around the 1970s and subsequently, with the molecular
revolution, was followed by selected examples of recent investigations dealing with
the selection-drift controversy. The studies surveyed included the comparison between
essential genes in humans and mice, selection in Africa and Europe, and the possible
reasons why females in humans remain healthy and productive after menopause, in
contrast with what happens in the great apes. At the end, selected examples of
investigations performed in Latin America, related to the action of selection for
muscle performance, acetylation of xenobiotics, high altitude and tropical forest
adaptations were considered. Despite dissenting views, the influence of positive
selection in a considerable portion of the human genome cannot presently be
dismissed.
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Affiliation(s)
- Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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1127
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Tanabe S, Aoyagi K, Yokozaki H, Sasaki H. Regulation of CTNNB1 signaling in gastric cancer and stem cells. World J Gastrointest Oncol 2016; 8:592-598. [PMID: 27574551 PMCID: PMC4980649 DOI: 10.4251/wjgo.v8.i8.592] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/22/2016] [Accepted: 05/17/2016] [Indexed: 02/05/2023] Open
Abstract
Recent research has shown that the alteration of combinations in gene expression contributes to cellular phenotypic changes. Previously, it has been demonstrated that the combination of cadherin 1 and cadherin 2 expression can identify the diffuse-type and intestinal-type gastric cancers. Although the diffuse-type gastric cancer has been resistant to treatment, the precise mechanism and phenotypic involvement has not been revealed. It may be possible that stem cells transform into gastric cancer cells, possibly through the involvement of a molecule alteration and signaling mechanism. In this review article, we focus on the role of catenin beta 1 (CTNNB1 or β-catenin) and describe the regulation of CTNNB1 signaling in gastric cancer and stem cells.
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1128
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Borden KLB. The eukaryotic translation initiation factor eIF4E wears a "cap" for many occasions. ACTA ACUST UNITED AC 2016; 4:e1220899. [PMID: 28090419 PMCID: PMC5173310 DOI: 10.1080/21690731.2016.1220899] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/12/2016] [Accepted: 08/02/2016] [Indexed: 01/11/2023]
Abstract
The eukaryotic translation initiation factor eIF4E plays important roles in controlling the composition of the proteome. Indeed, dysregulation of eIF4E is associated with poor prognosis cancers. The traditional view has been that eIF4E acts solely in translation. However, over the last ∼25 years, eIF4E was found in the nucleus where it acts in mRNA export and in the last ∼10 years, eIF4E was found in cytoplasmic processing bodies (P-bodies) where it functions in mRNA sequestration and stability. The common biochemical thread for these activities is the ability of eIF4E to bind the 7-methylguanosine cap on the 5′ end of mRNAs. Recently, the possibility that eIF4E directly binds some mRNA elements independently of the cap has also been raised. Importantly, the effects of eIF4E are not genome-wide with a subset of transcripts targeted depending on the presence of specific mRNA elements and context-dependent regulatory factors. Indeed, eIF4E governs RNA regulons through co-regulating the expression of groups of transcripts acting in the same biochemical pathways. In addition, studies over the past ∼15 years indicate that there are multiple strategies that regulatory factors employ to modulate eIF4E activities in context-dependent manners. This perspective focuses on these new findings and incorporates them into a broader model for eIF4E function.
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Affiliation(s)
- Katherine L B Borden
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer (IRIC), Université de Montréal , Montreal, Québec, Canada
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1129
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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: 393] [Impact Index Per Article: 43.7] [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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1130
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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: 269] [Impact Index Per Article: 29.9] [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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1131
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McLysaght A, Hurst LD. Open questions in the study of de novo genes: what, how and why. Nat Rev Genet 2016; 17:567-78. [PMID: 27452112 DOI: 10.1038/nrg.2016.78] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes.
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Affiliation(s)
- Aoife McLysaght
- The Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK
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1132
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de Queiroz RM, Madan R, Chien J, Dias WB, Slawson C. Changes in O-Linked N-Acetylglucosamine (O-GlcNAc) Homeostasis Activate the p53 Pathway in Ovarian Cancer Cells. J Biol Chem 2016; 291:18897-914. [PMID: 27402830 DOI: 10.1074/jbc.m116.734533] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Indexed: 12/14/2022] Open
Abstract
O-GlcNAcylation is a dynamic post-translational modification consisting of the addition of a single N-acetylglucosamine sugar to serine and threonine residues in proteins by the enzyme O-linked β-N-acetylglucosamine transferase (OGT), whereas the enzyme O-GlcNAcase (OGA) removes the modification. In cancer, tumor samples present with altered O-GlcNAcylation; however, changes in O-GlcNAcylation are not consistent between tumor types. Interestingly, the tumor suppressor p53 is modified by O-GlcNAc, and most solid tumors contain mutations in p53 leading to the loss of p53 function. Because ovarian cancer has a high frequency of p53 mutation rates, we decided to investigate the relationship between O-GlcNAcylation and p53 function in ovarian cancer. We measured a significant decrease in O-GlcNAcylation of tumor tissue in an ovarian tumor microarray. Furthermore, O-GlcNAcylation was increased, and OGA protein and mRNA levels were decreased in ovarian tumor cell lines not expressing the protein p53. Treatment with the OGA inhibitor Thiamet-G (TMG), silencing of OGA, or overexpression of OGA and OGT led to p53 stabilization, increased nuclear localization, and increased protein and mRNA levels of p53 target genes. These data suggest that changes in O-GlcNAc homeostasis activate the p53 pathway. Combination treatment of the chemotherapeutic cisplatin with TMG decreased tumor cell growth and enhanced cell cycle arrest without impairing cytotoxicity. The effects of TMG on tumor cell growth were partially dependent on wild type p53 activation. In conclusion, changes in O-GlcNAc homeostasis activate the wild type p53 pathway in ovarian cancer cells, and OGA inhibition has the potential as an adjuvant treatment for ovarian carcinoma.
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Affiliation(s)
- Rafaela Muniz de Queiroz
- From the Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-902RJ, Brazil
| | - Rashna Madan
- Division of Hematology/Oncology, Department of Pathology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | | | - Wagner Barbosa Dias
- From the Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-902RJ, Brazil,
| | - Chad Slawson
- the Departments of Biochemistry and Molecular Biology and
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1133
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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: 2.4] [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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1134
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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: 1158] [Impact Index Per Article: 128.7] [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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1135
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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: 16] [Impact Index Per Article: 1.8] [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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1136
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Altpeter F, Springer NM, Bartley LE, Blechl AE, Brutnell TP, Citovsky V, Conrad LJ, Gelvin SB, Jackson DP, Kausch AP, Lemaux PG, Medford JI, Orozco-Cárdenas ML, Tricoli DM, Van Eck J, Voytas DF, Walbot V, Wang K, Zhang ZJ, Stewart CN. Advancing Crop Transformation in the Era of Genome Editing. THE PLANT CELL 2016; 28:1510-20. [PMID: 27335450 PMCID: PMC4981132 DOI: 10.1105/tpc.16.00196] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/14/2016] [Indexed: 05/17/2023]
Abstract
Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.
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Affiliation(s)
- Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, University of Florida, IFAS, Gainesville, Florida 32611
| | - Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Ann E Blechl
- U.S. Department of Agriculture-Agriculture Research Service, Western Regional Research Center, Albany, California 94710
| | - Thomas P Brutnell
- Enterprise Institute for Renewable Fuels, Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794
| | - Liza J Conrad
- Natural Sciences Collegium, Eckerd College, St. Petersburg, Florida 33711
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - David P Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Albert P Kausch
- Department of Cellular and Molecular Biology, University of Rhode Island, Kingston, Rhode Island 02881
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - June I Medford
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | | | - David M Tricoli
- Plant Transformation Facility, University of California, Davis, California 95616
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York 14853
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305
| | - Kan Wang
- Department of Agronomy and Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996
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1137
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Balchin D, Hayer-Hartl M, Hartl FU. In vivo aspects of protein folding and quality control. Science 2016; 353:aac4354. [DOI: 10.1126/science.aac4354] [Citation(s) in RCA: 832] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Most proteins must fold into unique three-dimensional structures to perform their biological functions. In the crowded cellular environment, newly synthesized proteins are at risk of misfolding and forming toxic aggregate species. To ensure efficient folding, different classes of molecular chaperones receive the nascent protein chain emerging from the ribosome and guide it along a productive folding pathway. Because proteins are structurally dynamic, constant surveillance of the proteome by an integrated network of chaperones and protein degradation machineries is required to maintain protein homeostasis (proteostasis). The capacity of this proteostasis network declines during aging, facilitating neurodegeneration and other chronic diseases associated with protein aggregation. Understanding the proteostasis network holds the promise of identifying targets for pharmacological intervention in these pathologies.
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1138
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DeJesus R, Moretti F, McAllister G, Wang Z, Bergman P, Liu S, Frias E, Alford J, Reece-Hoyes JS, Lindeman A, Kelliher J, Russ C, Knehr J, Carbone W, Beibel M, Roma G, Ng A, Tallarico JA, Porter JA, Xavier RJ, Mickanin C, Murphy LO, Hoffman GR, Nyfeler B. Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62. eLife 2016; 5. [PMID: 27351204 PMCID: PMC4924995 DOI: 10.7554/elife.17290] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
SQSTM1 is an adaptor protein that integrates multiple cellular signaling pathways and whose expression is tightly regulated at the transcriptional and post-translational level. Here, we describe a forward genetic screening paradigm exploiting CRISPR-mediated genome editing coupled to a cell selection step by FACS to identify regulators of SQSTM1. Through systematic comparison of pooled libraries, we show that CRISPR is superior to RNAi in identifying known SQSTM1 modulators. A genome-wide CRISPR screen exposed MTOR signalling and the entire macroautophagy machinery as key regulators of SQSTM1 and identified several novel modulators including HNRNPM, SLC39A14, SRRD, PGK1 and the ufmylation cascade. We show that ufmylation regulates SQSTM1 by eliciting a cell type-specific ER stress response which induces SQSTM1 expression and results in its accumulation in the cytosol. This study validates pooled CRISPR screening as a powerful method to map the repertoire of cellular pathways that regulate the fate of an individual target protein. DOI:http://dx.doi.org/10.7554/eLife.17290.001
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Affiliation(s)
- Rowena DeJesus
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Francesca Moretti
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Gregory McAllister
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Zuncai Wang
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Phil Bergman
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Shanming Liu
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Elizabeth Frias
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - John Alford
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - John S Reece-Hoyes
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Alicia Lindeman
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Jennifer Kelliher
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Carsten Russ
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Judith Knehr
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Walter Carbone
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Martin Beibel
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Aylwin Ng
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - John A Tallarico
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Jeffery A Porter
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Craig Mickanin
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Leon O Murphy
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Gregory R Hoffman
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Beat Nyfeler
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
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1139
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Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens. Nat Commun 2016; 7:11786. [PMID: 27283361 PMCID: PMC4906395 DOI: 10.1038/ncomms11786] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/28/2016] [Indexed: 12/22/2022] Open
Abstract
The application of forward genetic screens to cultured human cells represents a powerful method to study gene function. The repurposing of the bacterial CRISPR/Cas9 system provides an effective method to disrupt gene function in mammalian cells, and has been applied to genome-wide screens. Here, we compare the efficacy of genome-wide CRISPR/Cas9-mediated forward genetic screens versus gene-trap mutagenesis screens in haploid human cells, which represent the existing 'gold standard' method. This head-to-head comparison aimed to identify genes required for the endoplasmic reticulum-associated degradation (ERAD) of MHC class I molecules. The two approaches show high concordance (>70%), successfully identifying the majority of the known components of the canonical glycoprotein ERAD pathway. Both screens also identify a role for the uncharacterized gene TXNDC11, which we show encodes an EDEM2/3-associated disulphide reductase. Genome-wide CRISPR/Cas9-mediated screens together with haploid genetic screens provide a powerful addition to the forward genetic toolbox.
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1140
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Purifying selection shapes the coincident SNP distribution of primate coding sequences. Sci Rep 2016; 6:27272. [PMID: 27255481 PMCID: PMC4891680 DOI: 10.1038/srep27272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/17/2016] [Indexed: 12/13/2022] Open
Abstract
Genome-wide analysis has observed an excess of coincident single nucleotide polymorphisms (coSNPs) at human-chimpanzee orthologous positions, and suggested that this is due to cryptic variation in the mutation rate. While this phenomenon primarily corresponds with non-coding coSNPs, the situation in coding sequences remains unclear. Here we calculate the observed-to-expected ratio of coSNPs (coSNPO/E) to estimate the prevalence of human-chimpanzee coSNPs, and show that the excess of coSNPs is also present in coding regions. Intriguingly, coSNPO/E is much higher at zero-fold than at nonzero-fold degenerate sites; such a difference is due to an elevation of coSNPO/E at zero-fold degenerate sites, rather than a reduction at nonzero-fold degenerate ones. These trends are independent of chimpanzee subpopulation, population size, or sequencing techniques; and hold in broad generality across primates. We find that this discrepancy cannot fully explained by sequence contexts, shared ancestral polymorphisms, SNP density, and recombination rate, and that coSNPO/E in coding sequences is significantly influenced by purifying selection. We also show that selection and mutation rate affect coSNPO/E independently, and coSNPs tend to be less damaging and more correlated with human diseases than non-coSNPs. These suggest that coSNPs may represent a “signature” during primate protein evolution.
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1141
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Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA. A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. Cell 2016; 165:1493-1506. [PMID: 27238023 PMCID: PMC4894308 DOI: 10.1016/j.cell.2016.05.003] [Citation(s) in RCA: 513] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/28/2016] [Accepted: 04/20/2016] [Indexed: 12/28/2022]
Abstract
Essential gene functions underpin the core reactions required for cell viability, but their contributions and relationships are poorly studied in vivo. Using CRISPR interference, we created knockdowns of every essential gene in Bacillus subtilis and probed their phenotypes. Our high-confidence essential gene network, established using chemical genomics, showed extensive interconnections among distantly related processes and identified modes of action for uncharacterized antibiotics. Importantly, mild knockdown of essential gene functions significantly reduced stationary-phase survival without affecting maximal growth rate, suggesting that essential protein levels are set to maximize outgrowth from stationary phase. Finally, high-throughput microscopy indicated that cell morphology is relatively insensitive to mild knockdown but profoundly affected by depletion of gene function, revealing intimate connections between cell growth and shape. Our results provide a framework for systematic investigation of essential gene functions in vivo broadly applicable to diverse microorganisms and amenable to comparative analysis.
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Affiliation(s)
- Jason M Peters
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Tomasz L Czarny
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Matthew H Larson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Spencer Wong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John S Hawkins
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Candy H S Lu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Marta
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anthony L Shiver
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Evan H Whitehead
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; UCSF Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; School of Medicine, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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1142
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Maeda T. Regulation of hematopoietic development by ZBTB transcription factors. Int J Hematol 2016; 104:310-23. [PMID: 27250345 DOI: 10.1007/s12185-016-2035-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/26/2016] [Accepted: 05/26/2016] [Indexed: 12/19/2022]
Abstract
Hematopoietic development is governed by the coordinated expression of lineage- and differentiation stage-specific genes. Transcription factors play major roles in this process and their perturbation may underlie hematologic and immunologic disorders. Nearly 1900 transcription factors are encoded in the human genome: of these, 49 BTB (for broad-complex, tram-track and bric à brac)-zinc finger transcription factors referred to as ZBTB or POK proteins have been identified. ZBTB proteins, including BCL6, PLZF, ThPOK and LRF, exhibit a broad spectrum of functions in normal and malignant hematopoiesis. This review summarizes developmental and molecular functions of ZBTB proteins relevant to hematology.
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Affiliation(s)
- Takahiro Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, One Blackfan Circle, Boston, MA, 02115, USA.
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1143
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Lauschke VM, Ingelman-Sundberg M. Requirements for comprehensive pharmacogenetic genotyping platforms. Pharmacogenomics 2016; 17:917-24. [PMID: 27248710 DOI: 10.2217/pgs-2016-0023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recent research highlighted the large extent of rare variants in pharmacogenes and, on this basis, it was estimated that rare variants account for 30-40% of the functional variability in pharmacogenes. It has been proposed that comprehensive next-generation sequencing (NGS)-based sequencing of pharmacogenes could soon be a cost-effective methodology for clinical routine genotyping. Yet, multiple challenges on technical, interpretative and ethical levels need to be overcome to enable the reasonable dissemination of comprehensive pharmacogenetic genotyping, that includes rare genetic variation, into clinical practice. We argue that current pre-emptive pharmacogenetic testing cannot be based on comprehensive approaches but needs to be restricted to validated variants. Rather, comprehensive strategies should only be used for retrospective analyses of patients exhibiting unanticipated drug responses. Thereby, subsequent to computational analyses and functional validations, emerging variants with confirmed functional relevance can be incorporated into candidate genotyping strategies, thus refining and enhancing future pre-emptive genetic testing.
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Affiliation(s)
- Volker M Lauschke
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden
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1144
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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: 4.3] [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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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: 298] [Impact Index Per Article: 33.1] [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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Sdelci S, Lardeau CH, Tallant C, Klepsch F, Klaiber B, Bennett J, Rathert P, Schuster M, Penz T, Fedorov O, Superti-Furga G, Bock C, Zuber J, Huber KVM, Knapp S, Müller S, Kubicek S. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nat Chem Biol 2016; 12:504-10. [PMID: 27159579 DOI: 10.1038/nchembio.2080] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/18/2016] [Indexed: 12/14/2022]
Abstract
Bromodomain-containing proteins of the BET family recognize histone lysine acetylation and mediate transcriptional activation of target genes such as the MYC oncogene. Pharmacological inhibitors of BET domains promise therapeutic benefits in a variety of cancers. We performed a high-diversity chemical compound screen for agents capable of modulating BRD4-dependent heterochromatization of a generic reporter in human cells. In addition to known and new compounds targeting BRD4, we identified small molecules that mimic BRD4 inhibition without direct engagement. One such compound was a potent inhibitor of the second bromodomain of TAF1. Using this inhibitor, we discovered that TAF1 synergizes with BRD4 to control proliferation of cancer cells, making TAF1 an attractive epigenetic target in cancers driven by MYC.
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Affiliation(s)
- Sara Sdelci
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Charles-Hugues Lardeau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Freya Klepsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Björn Klaiber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Philipp Rathert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.,Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Johann Wolfgang Goethe-University, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Abstract
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
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1149
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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: 176] [Impact Index Per Article: 19.6] [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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