801
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Gong X, Du J, Parsons SH, Merzoug FF, Webster Y, Iversen PW, Chio LC, Van Horn RD, Lin X, Blosser W, Han B, Jin S, Yao S, Bian H, Ficklin C, Fan L, Kapoor A, Antonysamy S, Mc Nulty AM, Froning K, Manglicmot D, Pustilnik A, Weichert K, Wasserman SR, Dowless M, Marugán C, Baquero C, Lallena MJ, Eastman SW, Hui YH, Dieter MZ, Doman T, Chu S, Qian HR, Ye XS, Barda DA, Plowman GD, Reinhard C, Campbell RM, Henry JR, Buchanan SG. Aurora A Kinase Inhibition Is Synthetic Lethal with Loss of the RB1 Tumor Suppressor Gene. Cancer Discov 2018; 9:248-263. [PMID: 30373917 DOI: 10.1158/2159-8290.cd-18-0469] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/26/2018] [Accepted: 10/24/2018] [Indexed: 01/09/2023]
Abstract
Loss-of-function mutations in the retinoblastoma gene RB1 are common in several treatment-refractory cancers such as small-cell lung cancer and triple-negative breast cancer. To identify drugs synthetic lethal with RB1 mutation (RB1 mut), we tested 36 cell-cycle inhibitors using a cancer cell panel profiling approach optimized to discern cytotoxic from cytostatic effects. Inhibitors of the Aurora kinases AURKA and AURKB showed the strongest RB1 association in this assay. LY3295668, an AURKA inhibitor with over 1,000-fold selectivity versus AURKB, is distinguished by minimal toxicity to bone marrow cells at concentrations active against RB1 mut cancer cells and leads to durable regression of RB1 mut tumor xenografts at exposures that are well tolerated in rodents. Genetic suppression screens identified enforcers of the spindle-assembly checkpoint (SAC) as essential for LY3295668 cytotoxicity in RB1-deficient cancers and suggest a model in which a primed SAC creates a unique dependency on AURKA for mitotic exit and survival. SIGNIFICANCE: The identification of a synthetic lethal interaction between RB1 and AURKA inhibition, and the discovery of a drug that can be dosed continuously to achieve uninterrupted inhibition of AURKA kinase activity without myelosuppression, suggest a new approach for the treatment of RB1-deficient malignancies, including patients progressing on CDK4/6 inhibitors.See related commentary by Dick and Li, p. 169.This article is highlighted in the In This Issue feature, p. 151.
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Affiliation(s)
| | - Jian Du
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | - Yue Webster
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | | | - Xi Lin
- Eli Lilly and Company, Indianapolis, Indiana
| | | | - Bomie Han
- Eli Lilly and Company, Indianapolis, Indiana
| | | | - Sufang Yao
- Eli Lilly and Company, Indianapolis, Indiana
| | - Huimin Bian
- Eli Lilly and Company, Indianapolis, Indiana
| | | | - Li Fan
- Eli Lilly and Company, Indianapolis, Indiana
| | | | - Stephen Antonysamy
- Eli Lilly and Company, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, San Diego, California
| | | | - Karen Froning
- Eli Lilly and Company, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, San Diego, California
| | - Danalyn Manglicmot
- Eli Lilly and Company, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, San Diego, California
| | - Anna Pustilnik
- Eli Lilly and Company, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, San Diego, California
| | - Kenneth Weichert
- Eli Lilly and Company, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, San Diego, California
| | - Stephen R Wasserman
- Eli Lilly and Company, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois
| | | | - Carlos Marugán
- Eli Lilly and Company, Lilly Research Laboratories, Avenida de la Industria, Alcobendas, Spain
| | - Carmen Baquero
- Eli Lilly and Company, Lilly Research Laboratories, Avenida de la Industria, Alcobendas, Spain
| | - María José Lallena
- Eli Lilly and Company, Lilly Research Laboratories, Avenida de la Industria, Alcobendas, Spain
| | - Scott W Eastman
- Eli Lilly and Company, Alexandria Center for Life Sciences, New York, New York
| | - Yu-Hua Hui
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | - Shaoyou Chu
- Eli Lilly and Company, Indianapolis, Indiana
| | | | - Xiang S Ye
- Eli Lilly and Company, Indianapolis, Indiana
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802
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Zhang H, Pan H, Zhou C, Wei Y, Ying W, Li S, Wang G, Li C, Ren Y, Li G, Ding X, Sun Y, Li GL, Song L, Li Y, Yang H, Liu Z. Simultaneous zygotic inactivation of multiple genes in mouse through CRISPR/Cas9-mediated base editing. Development 2018; 145:dev.168906. [PMID: 30275281 DOI: 10.1242/dev.168906] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/19/2018] [Indexed: 12/31/2022]
Abstract
In vivo genetic mutation has become a powerful tool for dissecting gene function; however, multi-gene interaction and the compensatory mechanisms involved can make findings from single mutations, at best difficult to interpret, and, at worst, misleading. Hence, it is necessary to establish an efficient way to disrupt multiple genes simultaneously. CRISPR/Cas9-mediated base editing disrupts gene function by converting a protein-coding sequence into a stop codon; this is referred to as CRISPR-stop. Its application in generating zygotic mutations has not been well explored yet. Here, we first performed a proof-of-principle test by disrupting Atoh1, a gene crucial for auditory hair cell generation. Next, we individually mutated vGlut3 (Slc17a8), otoferlin (Otof) and prestin (Slc26a5), three genes needed for normal hearing function. Finally, we successfully disrupted vGlut3, Otof and prestin simultaneously. Our results show that CRISPR-stop can efficiently generate single or triple homozygous F0 mouse mutants, bypassing laborious mouse breeding. We believe that CRISPR-stop is a powerful method that will pave the way for high-throughput screening of mouse developmental and functional genes, matching the efficiency of methods available for model organisms such as Drosophila.
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Affiliation(s)
- He Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Pan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Guangxi University, Nanning 530004, Guangxi, China
| | - Changyang Zhou
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wei
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenqin Ying
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuting Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangqin Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yifei Ren
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gen Li
- Department of Otolaryngology, Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai 200011, China
| | - Xu Ding
- Department of Otolaryngology, Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai 200011, China
| | - Yidi Sun
- University of Chinese Academy of Sciences, Beijing 100049, China.,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Geng-Lin Li
- Department of Otolaryngology, Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai 200011, China.,Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Lei Song
- Department of Otolaryngology, Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai 200011, China
| | - Yixue Li
- University of Chinese Academy of Sciences, Beijing 100049, China.,Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200032, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai 200032, China
| | - Hui Yang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiyong Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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803
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Szlachta K, Kuscu C, Tufan T, Adair SJ, Shang S, Michaels AD, Mullen MG, Fischer NL, Yang J, Liu L, Trivedi P, Stelow EB, Stukenberg PT, Parsons JT, Bauer TW, Adli M. CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response. Nat Commun 2018; 9:4275. [PMID: 30323222 PMCID: PMC6189038 DOI: 10.1038/s41467-018-06676-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022] Open
Abstract
Predicting the response and identifying additional targets that will improve the efficacy of chemotherapy is a major goal in cancer research. Through large-scale in vivo and in vitro CRISPR knockout screens in pancreatic ductal adenocarcinoma cells, we identified genes whose genetic deletion or pharmacologic inhibition synergistically increase the cytotoxicity of MEK signaling inhibitors. Furthermore, we show that CRISPR viability scores combined with basal gene expression levels could model global cellular responses to the drug treatment. We develop drug response evaluation by in vivo CRISPR screening (DREBIC) method and validated its efficacy using large-scale experimental data from independent experiments. Comparative analyses demonstrate that DREBIC predicts drug response in cancer cells from a wide range of tissues with high accuracy and identifies therapeutic vulnerabilities of cancer-causing mutations to MEK inhibitors in various cancer types. Predicting the response to chemotherapy is a major goal of cancer research. Here the authors use CRISPR knockout screens in pancreatic ductal adenocarcinoma cells to identify deletions synergistic with MEK inhibitors.
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Affiliation(s)
- Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Cem Kuscu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Turan Tufan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Sara J Adair
- Department of Surgery, University of Virginia School of Medicine, 1215 Lee St, Charlottesville, VA, 22908, USA
| | - Stephen Shang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Alex D Michaels
- Department of Surgery, University of Virginia School of Medicine, 1215 Lee St, Charlottesville, VA, 22908, USA
| | - Matthew G Mullen
- Department of Surgery, University of Virginia School of Medicine, 1215 Lee St, Charlottesville, VA, 22908, USA
| | - Natasha Lopes Fischer
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Jiekun Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Limin Liu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Prasad Trivedi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Edward B Stelow
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, 1215 Lee St, Charlottesville, VA, 22908, USA
| | - P Todd Stukenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - J Thomas Parsons
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA
| | - Todd W Bauer
- Department of Surgery, University of Virginia School of Medicine, 1215 Lee St, Charlottesville, VA, 22908, USA
| | - Mazhar Adli
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall, Charlottesville, VA, 22908, USA.
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804
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Daley TP, Lin Z, Lin X, Liu Y, Wong WH, Qi LS. CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. Genome Biol 2018; 19:159. [PMID: 30296940 PMCID: PMC6176515 DOI: 10.1186/s13059-018-1538-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/11/2018] [Indexed: 11/10/2022] Open
Abstract
Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare off-target effects. We present a method, CRISPhieRmix, that resolves these issues by using a hierarchical mixture model with a broad-tailed null distribution. We show that CRISPhieRmix allows for more accurate and powerful inferences in large-scale pooled CRISPRi/a screens. We discuss key issues in the analysis and design of screens, particularly the number of guides needed for faithful full discovery.
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Affiliation(s)
- Timothy P. Daley
- Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305 USA
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
| | - Zhixiang Lin
- Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305 USA
- Present Address: Department of Statistics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Xueqiu Lin
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305 USA
- Department of Biomedical Data Science, Stanford University, 1265 Welch Road, Stanford, 94305 USA
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
- Department of Chemical and Systems Biology, Stanford University, 443 Via Ortega, Stanford, 94305 USA
- ChEM-H Institute, Stanford University, 443 Via Ortega, Stanford, 94305 USA
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805
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Pemovska T, Bigenzahn JW, Superti-Furga G. Recent advances in combinatorial drug screening and synergy scoring. Curr Opin Pharmacol 2018; 42:102-110. [PMID: 30193150 PMCID: PMC6219891 DOI: 10.1016/j.coph.2018.07.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022]
Abstract
Treatment of complex diseases such as cancer, cardiovascular disease, diabetes or neurological disorders frequently warrants the utilization of drug combinations for therapeutic intervention. In fact, the most successful example is the current standard of care for HIV patients. However, identification of successful drug cocktails is not a simple task and is hampered by lack of standardization in terminology, experimental protocols and models as well as data analysis. Here we discuss the most recent developments in combinatorial drug screening by covering technological advancements in screening strategies, cellular model systems as well as novel drug classes. We believe the research progress being made provides promising basis to build on and identify, develop and optimize efficacious clinically relevant combinatorial drug treatments.
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Affiliation(s)
- Tea Pemovska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17A, 1090 Vienna, Austria.
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806
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Menasche BL, Crisman L, Gulbranson DR, Davis EM, Yu H, Shen J. Fluorescence Activated Cell Sorting (FACS) in Genome-Wide Genetic Screening of Membrane Trafficking. ACTA ACUST UNITED AC 2018; 82:e68. [PMID: 30265447 DOI: 10.1002/cpcb.68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
About one-third of cellular proteins in eukaryotic cells are localized to membrane-enclosed organelles in the endomembrane system. Trafficking of these membrane proteins (including soluble lumenal proteins) among the organelles is mediated by small sac-like vesicles. Vesicle-mediated membrane trafficking regulates a broad range of biological processes, many of which are still poorly understood at the molecular level. A powerful approach to dissect a vesicle-mediated membrane trafficking pathway is unbiased genome-wide genetic screening, which only recently became possible in mammalian cells with the isolation of haploid human cell lines and the development of CRISPR-Cas9 genome editing. Here, we describe a FACS-based method to select populations of live mutant cells based on the surface levels of endogenous proteins or engineered reporters. Collection of these mutant populations enables subsequent deep sequencing and bioinformatics analysis to identify genes that regulate the trafficking pathway. This method can be readily adapted to genetically dissect a broad range of mammalian membrane trafficking processes using haploid genetics or CRISPR-Cas9 screens. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Bridget L Menasche
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Lauren Crisman
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Daniel R Gulbranson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Eric M Davis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Haijia Yu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingshi Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
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807
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Lone BA, Karna SKL, Ahmad F, Shahi N, Pokharel YR. CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering. GENETICS RESEARCH INTERNATIONAL 2018; 2018:3797214. [PMID: 30319822 PMCID: PMC6167567 DOI: 10.1155/2018/3797214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/19/2018] [Indexed: 12/26/2022]
Abstract
Microbes use diverse defence strategies that allow them to withstand exposure to a variety of genome invaders such as bacteriophages and plasmids. One such defence strategy is the use of RNA guided endonuclease called CRISPR-associated (Cas) 9 protein. The Cas9 protein, derived from type II CRISPR/Cas system, has been adapted as a versatile tool for genome targeting and engineering due to its simplicity and high efficiency over the earlier tools such as ZFNs and TALENs. With recent advancements, CRISPR/Cas9 technology has emerged as a revolutionary tool for modulating the genome in living cells and inspires innovative translational applications in different fields. In this paper we review the developments and its potential uses in the CRISPR/Cas9 technology as well as recent advancements in genome engineering using CRISPR/Cas9.
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Affiliation(s)
- Bilal Ahmad Lone
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Shibendra Kumar Lal Karna
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Faiz Ahmad
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Nerina Shahi
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Yuba Raj Pokharel
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
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808
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Peng H, Zheng Y, Blumenstein M, Tao D, Li J. CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling. Bioinformatics 2018; 34:3069-3077. [PMID: 29672669 DOI: 10.1093/bioinformatics/bty298] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/12/2018] [Indexed: 12/26/2022] Open
Abstract
Motivation CRISPR/Cas9 system is a widely used genome editing tool. A prediction problem of great interests for this system is: how to select optimal single-guide RNAs (sgRNAs), such that its cleavage efficiency is high meanwhile the off-target effect is low. Results This work proposed a two-step averaging method (TSAM) for the regression of cleavage efficiencies of a set of sgRNAs by averaging the predicted efficiency scores of a boosting algorithm and those by a support vector machine (SVM). We also proposed to use profiled Markov properties as novel features to capture the global characteristics of sgRNAs. These new features are combined with the outstanding features ranked by the boosting algorithm for the training of the SVM regressor. TSAM improved the mean Spearman correlation coefficiencies comparing with the state-of-the-art performance on benchmark datasets containing thousands of human, mouse and zebrafish sgRNAs. Our method can be also converted to make binary distinctions between efficient and inefficient sgRNAs with superior performance to the existing methods. The analysis reveals that highly efficient sgRNAs have lower melting temperature at the middle of the spacer, cut at 5'-end closer parts of the genome and contain more 'A' but less 'G' comparing with inefficient ones. Comprehensive further analysis also demonstrates that our tool can predict an sgRNA's cutting efficiency with consistently good performance no matter it is expressed from an U6 promoter in cells or from a T7 promoter in vitro. Availability and implementation Online tool is available at http://www.aai-bioinfo.com/CRISPR/. Python and Matlab source codes are freely available at https://github.com/penn-hui/TSAM. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hui Peng
- Faculty of Engineering and Information Technology, Advanced Analytics Institute, University of Technology Sydney, Broadway, NSW, Australia
| | - Yi Zheng
- Faculty of Engineering and Information Technology, Advanced Analytics Institute, University of Technology Sydney, Broadway, NSW, Australia
| | - Michael Blumenstein
- Faculty of Engineering and Information Technology, Advanced Analytics Institute, University of Technology Sydney, Broadway, NSW, Australia
| | - Dacheng Tao
- Faculty of Engineering and Information Technologies, School of Information Technologies, University of Sydney, Darlington, NSW, Australia
| | - Jinyan Li
- Faculty of Engineering and Information Technology, Advanced Analytics Institute, University of Technology Sydney, Broadway, NSW, Australia
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809
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Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. J Mol Biol 2018; 430:2900-2912. [PMID: 29932943 PMCID: PMC6097899 DOI: 10.1016/j.jmb.2018.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/10/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022]
Abstract
Synthetic lethal interactions, in which the simultaneous loss of function of two genes produces a lethal phenotype, are being explored as a means to therapeutically exploit cancer-specific vulnerabilities and expand the scope of precision oncology. Currently, three Food and Drug Administration-approved drugs work by targeting the synthetic lethal interaction between BRCA1/2 and PARP. This review examines additional efforts to discover networks of synthetic lethal interactions and discusses both challenges and opportunities regarding the translation of new synthetic lethal interactions into the clinic.
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Affiliation(s)
- John Paul Shen
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative, USA.
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative, USA
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810
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Duan C, Huan Q, Chen X, Wu S, Carey LB, He X, Qian W. Reduced intrinsic DNA curvature leads to increased mutation rate. Genome Biol 2018; 19:132. [PMID: 30217230 PMCID: PMC6138893 DOI: 10.1186/s13059-018-1525-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis. RESULTS Here, we use a combination of synthetic genes and sequences of thousands of isolated yeast colonies to show that intrinsic DNA curvature is a major cis determinant of mutation rate. Mutation rate negatively correlates with DNA curvature within genes, and a 10% decrease in curvature results in a 70% increase in mutation rate. Consistently, both yeast and humans accumulate mutations in regions with small curvature. We further show that this effect is due to differences in the intrinsic mutation rate, likely due to differences in mutagen sensitivity and not due to differences in the local activity of DNA repair. CONCLUSIONS Our study establishes a framework for understanding the cis properties of DNA sequence in modulating the local mutation rate and identifies a novel causal source of non-uniform mutation rates across the genome.
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Affiliation(s)
- Chaorui Duan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoshu Chen
- Human Genome Research Institute and Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shaohuan Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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811
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Adhikari H, Counter CM. Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability. Nat Commun 2018; 9:3646. [PMID: 30194290 PMCID: PMC6128905 DOI: 10.1038/s41467-018-05692-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 07/19/2018] [Indexed: 02/07/2023] Open
Abstract
In human cancers, oncogenic mutations commonly occur in the RAS genes KRAS, NRAS, or HRAS, but there are no clinical RAS inhibitors. Mutations are more prevalent in KRAS, possibly suggesting a unique oncogenic activity mediated by KRAS-specific interaction partners, which might be targeted. Here, we determine the specific protein interactomes of each RAS isoform by BirA proximity-dependent biotin identification. The combined interactomes are screened by CRISPR-Cas9 loss-of-function assays for proteins required for oncogenic KRAS-dependent, NRAS-dependent, or HRAS-dependent proliferation and censored for druggable proteins. Using this strategy, we identify phosphatidylinositol phosphate kinase PIP5K1A as a KRAS-specific interactor and show that PIP5K1A binds to a unique region in KRAS. Furthermore, PIP5K1A depletion specifically reduces oncogenic KRAS signaling and proliferation, and sensitizes pancreatic cancer cell lines to a MAPK inhibitor. These results suggest PIP5K1A as a potential target in KRAS signaling for the treatment of KRAS-mutant cancers. RAS isoforms are frequently mutated in cancer but their inhibition remains challenging. By comparing the protein interactomes of the highly similar isoforms HRAS, NRAS and KRAS, the authors here identify PIP5K1A as a KRAS-specific interactor and a target to inhibit KRAS-driven cell growth.
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Affiliation(s)
- Hema Adhikari
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, DUMC-3813, Durham, NC, 27713, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, DUMC-3813, Durham, NC, 27713, USA. .,Department of Radiation Oncology, Duke University Medical Center, DUMC-3813, Durham, NC, 27713, USA.
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812
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Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Blood 2018; 132:2375-2388. [PMID: 30181176 DOI: 10.1182/blood-2017-09-804401] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
Genomic studies have recently identified RPS15 as a new driver gene in aggressive and chemorefractory cases of chronic lymphocytic leukemia (CLL). RPS15 encodes a ribosomal protein whose conserved C-terminal domain extends into the decoding center of the ribosome. We demonstrate that mutations in highly conserved residues of this domain affect protein stability, by increasing its ubiquitin-mediated degradation, and cell-proliferation rates. On the other hand, we show that mutated RPS15 can be loaded into the ribosomes, directly impacting on global protein synthesis and/or translational fidelity in a mutation-specific manner. Quantitative mass spectrometry analyses suggest that RPS15 variants may induce additional alterations in the translational machinery, as well as a metabolic shift at the proteome level in HEK293T and MEC-1 cells. These results indicate that CLL-related RPS15 mutations might act following patterns known for other ribosomal diseases, likely switching from a hypo- to a hyperproliferative phenotype driven by mutated ribosomes. In this scenario, loss of translational fidelity causing altered cell proteostasis can be proposed as a new molecular mechanism involved in CLL pathobiology.
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813
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Stoeger T, Gerlach M, Morimoto RI, Nunes Amaral LA. Large-scale investigation of the reasons why potentially important genes are ignored. PLoS Biol 2018; 16:e2006643. [PMID: 30226837 PMCID: PMC6143198 DOI: 10.1371/journal.pbio.2006643] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/10/2018] [Indexed: 01/04/2023] Open
Abstract
Biomedical research has been previously reported to primarily focus on a minority of all known genes. Here, we demonstrate that these differences in attention can be explained, to a large extent, exclusively from a small set of identifiable chemical, physical, and biological properties of genes. Together with knowledge about homologous genes from model organisms, these features allow us to accurately predict the number of publications on individual human genes, the year of their first report, the levels of funding awarded by the National Institutes of Health (NIH), and the development of drugs against disease-associated genes. By explicitly identifying the reasons for gene-specific bias and performing a meta-analysis of existing computational and experimental knowledge bases, we describe gene-specific strategies for the identification of important but hitherto ignored genes that can open novel directions for future investigation.
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Affiliation(s)
- Thomas Stoeger
- Center for Genetic Medicine, Northwestern University, Chicago, United States of America
- Northwestern Institute on Complex Systems (NICO), Northwestern University, Evanston, United States of America
| | - Martin Gerlach
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, United States of America
| | - Richard I. Morimoto
- Department of Molecular Bioscience, Northwestern University, Evanston, United States of America
| | - Luís A. Nunes Amaral
- Northwestern Institute on Complex Systems (NICO), Northwestern University, Evanston, United States of America
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, United States of America
- Department of Molecular Bioscience, Northwestern University, Evanston, United States of America
- Department of Physics and Astronomy, Northwestern University, Evanston, United States of America
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814
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Godini R, Fallahi H. Shortening the list of essential genes in the human genome by network analysis. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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815
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Sydor AM, Coyaud E, Rovelli C, Laurent E, Liu H, Raught B, Mennella V. PPP1R35 is a novel centrosomal protein that regulates centriole length in concert with the microcephaly protein RTTN. eLife 2018; 7:37846. [PMID: 30168418 PMCID: PMC6141234 DOI: 10.7554/elife.37846] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
Centrosome structure, function, and number are finely regulated at the cellular level to ensure normal mammalian development. Here, we characterize PPP1R35 as a novel bona fide centrosomal protein and demonstrate that it is critical for centriole elongation. Using quantitative super-resolution microscopy mapping and live-cell imaging we show that PPP1R35 is a resident centrosomal protein located in the proximal lumen above the cartwheel, a region of the centriole that has eluded detailed characterization. Loss of PPP1R35 function results in decreased centrosome number and shortened centrioles that lack centriolar distal and microtubule wall associated proteins required for centriole elongation. We further demonstrate that PPP1R35 acts downstream of, and forms a complex with, RTTN, a microcephaly protein required for distal centriole elongation. Altogether, our study identifies a novel step in the centriole elongation pathway centered on PPP1R35 and elucidates downstream partners of the microcephaly protein RTTN.
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Affiliation(s)
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Cristina Rovelli
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Helen Liu
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Vito Mennella
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Biochemistry, University of Toronto, Ontario, Canada
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816
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Schuster A, Erasimus H, Fritah S, Nazarov PV, van Dyck E, Niclou SP, Golebiewska A. RNAi/CRISPR Screens: from a Pool to a Valid Hit. Trends Biotechnol 2018; 37:38-55. [PMID: 30177380 DOI: 10.1016/j.tibtech.2018.08.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
Abstract
High-throughput genetic screens interfering with gene expression are invaluable tools to identify gene function and phenotype-to-genotype interactions. Implementing such screens in the laboratory is challenging, and the choice between currently available technologies based on RNAi and CRISPR/Cas9 (CRISPR-associated protein 9) is not trivial. Identifying reliable candidate hits requires a streamlined experimental setup adjusted to the specific biological question. Here, we provide a critical assessment of the various RNAi/CRISPR approaches to pooled screens and discuss their advantages and pitfalls. We specify a set of best practices for key parameters enabling a reproducible screen and provide a detailed overview of analysis methods and repositories for identifying the best candidate gene hits.
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Affiliation(s)
- Anne Schuster
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Hélène Erasimus
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Petr V Nazarov
- Genomics and Proteomics Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Eric van Dyck
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg; KG Jebsen Brain Tumour Research Center, Department of Biomedicine, University of Bergen, Bergen, Norway; Co-senior authors.
| | - Anna Golebiewska
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg; Co-senior authors.
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817
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Findlay S, Heath J, Luo VM, Malina A, Morin T, Coulombe Y, Djerir B, Li Z, Samiei A, Simo-Cheyou E, Karam M, Bagci H, Rahat D, Grapton D, Lavoie EG, Dove C, Khaled H, Kuasne H, Mann KK, Klein KO, Greenwood CM, Tabach Y, Park M, Côté JF, Masson JY, Maréchal A, Orthwein A. SHLD2/FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice. EMBO J 2018; 37:embj.2018100158. [PMID: 30154076 PMCID: PMC6138439 DOI: 10.15252/embj.2018100158] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by two major pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). DNA repair pathway choice is governed by the opposing activities of 53BP1, in complex with its effectors RIF1 and REV7, and BRCA1. However, it remains unknown how the 53BP1/RIF1/REV7 complex stimulates NHEJ and restricts HR to the S/G2 phases of the cell cycle. Using a mass spectrometry (MS)-based approach, we identify 11 high-confidence REV7 interactors and elucidate the role of SHLD2 (previously annotated as FAM35A and RINN2) as an effector of REV7 in the NHEJ pathway. FAM35A depletion impairs NHEJ-mediated DNA repair and compromises antibody diversification by class switch recombination (CSR) in B cells. FAM35A accumulates at DSBs in a 53BP1-, RIF1-, and REV7-dependent manner and antagonizes HR by limiting DNA end resection. In fact, FAM35A is part of a larger complex composed of REV7 and SHLD1 (previously annotated as C20orf196 and RINN3), which promotes NHEJ and limits HR Together, these results establish SHLD2 as a novel effector of REV7 in controlling the decision-making process during DSB repair.
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Affiliation(s)
- Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - John Heath
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Vincent M Luo
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Abba Malina
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Théo Morin
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Yan Coulombe
- Genome Stability Laboratory, CHU de Québec Research Center, Quebec City, QC, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Billel Djerir
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Zhigang Li
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada
| | - Arash Samiei
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Estelle Simo-Cheyou
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Martin Karam
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Halil Bagci
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Damien Grapton
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada
| | - Elise G Lavoie
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada
| | - Christian Dove
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Husam Khaled
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Koren K Mann
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Kathleen Oros Klein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada
| | - Celia M Greenwood
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, MGill University, Montreal, QC, Canada
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Morag Park
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Jean-Francois Côté
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada.,Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.,Département de Médecine (Programmes de Biologie Moléculaire), Université de Montréal, Montreal, QC, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Quebec City, QC, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | | | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montreal, QC, Canada .,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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818
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Ramkumar P, Kampmann M. CRISPR-based genetic interaction maps inform therapeutic strategies in cancer. Transl Cancer Res 2018; 7:S61-S67. [PMID: 30148072 DOI: 10.21037/tcr.2018.01.02] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Poornima Ramkumar
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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819
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Pyatnitskiy MA, Karpov DS, Moshkovskii SA. [Searching for essential genes in cancer genomes]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:303-314. [PMID: 30135277 DOI: 10.18097/pbmc20186404303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The concept of essential genes, whose loss of functionality leads to cell death, is one of the fundamental concepts of genetics and is important for fundamental and applied research. This field is particularly promising in relation to oncology, since the search for genetic vulnerabilities of cancer cells allows us to identify new potential targets for antitumor therapy. The modern biotechnology capacities allow carrying out large-scale projects for sequencing somatic mutations in tumors, as well as directly interfering the genetic apparatus of cancer cells. They provided accumulation of a considerable body of knowledge about genetic variants and corresponding phenotypic manifestations in tumors. In the near future this knowledge will find application in clinical practice. This review describes the main experimental and computational approaches to the search for essential genes, concentrating on the application of these methods in the field of molecular oncology.
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Affiliation(s)
- M A Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow, Russia; Higher School of Economics, Moscow, Russia
| | - D S Karpov
- Institute of Biomedical Chemistry, Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - S A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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820
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Bachas C, Hodzic J, van der Mijn JC, Stoepker C, Verheul HMW, Wolthuis RMF, Felley-Bosco E, van Wieringen WN, van Beusechem VW, Brakenhoff RH, de Menezes RX. Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection. BMC Bioinformatics 2018; 19:301. [PMID: 30126372 PMCID: PMC6102854 DOI: 10.1186/s12859-018-2306-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background Reproducibility of hits from independent CRISPR or siRNA screens is poor. This is partly due to data normalization primarily addressing technical variability within independent screens, and not the technical differences between them. Results We present “rscreenorm”, a method that standardizes the functional data ranges between screens using assay controls, and subsequently performs a piecewise-linear normalization to make data distributions across all screens comparable. In simulation studies, rscreenorm reduces false positives. Using two multiple-cell lines siRNA screens, rscreenorm increased reproducibility between 27 and 62% for hits, and up to 5-fold for non-hits. Using publicly available CRISPR-Cas screen data, application of commonly used median centering yields merely 34% of overlapping hits, in contrast with rscreenorm yielding 84% of overlapping hits. Furthermore, rscreenorm yielded at most 8% discordant results, whilst median-centering yielded as much as 55%. Conclusions Rscreenorm yields more consistent results and keeps false positive rates under control, improving reproducibility of genetic screens data analysis from multiple cell lines. Electronic supplementary material The online version of this article (10.1186/s12859-018-2306-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Costa Bachas
- Department of Otolaryngology - Head and Neck Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands
| | - Jasmina Hodzic
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Johannes C van der Mijn
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Chantal Stoepker
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Rob M F Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, Amsterdam, 1081, HV, The Netherlands
| | | | - Wessel N van Wieringen
- Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands.,Department of Mathematics, VU University, Amsterdam, The Netherlands
| | - Victor W van Beusechem
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Ruud H Brakenhoff
- Department of Otolaryngology - Head and Neck Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, 1081, HV, The Netherlands
| | - Renée X de Menezes
- Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands.
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821
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Manzano M, Patil A, Waldrop A, Dave SS, Behdad A, Gottwein E. Gene essentiality landscape and druggable oncogenic dependencies in herpesviral primary effusion lymphoma. Nat Commun 2018; 9:3263. [PMID: 30111820 PMCID: PMC6093911 DOI: 10.1038/s41467-018-05506-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus. Our understanding of PEL is poor and therefore treatment strategies are lacking. To address this need, we conducted genome-wide CRISPR/Cas9 knockout screens in eight PEL cell lines. Integration with data from unrelated cancers identifies 210 genes as PEL-specific oncogenic dependencies. Genetic requirements of PEL cell lines are largely independent of Epstein-Barr virus co-infection. Genes of the NF-κB pathway are individually non-essential. Instead, we demonstrate requirements for IRF4 and MDM2. PEL cell lines depend on cellular cyclin D2 and c-FLIP despite expression of viral homologs. Moreover, PEL cell lines are addicted to high levels of MCL1 expression, which are also evident in PEL tumors. Strong dependencies on cyclin D2 and MCL1 render PEL cell lines highly sensitive to palbociclib and S63845. In summary, this work comprehensively identifies genetic dependencies in PEL cell lines and identifies novel strategies for therapeutic intervention.
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Affiliation(s)
- Mark Manzano
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ajinkya Patil
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Alexander Waldrop
- Duke Cancer Institute and Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Sandeep S Dave
- Duke Cancer Institute and Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Amir Behdad
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Eva Gottwein
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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822
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Nakagawa M, Shaffer AL, Ceribelli M, Zhang M, Wright G, Huang DW, Xiao W, Powell J, Petrus MN, Yang Y, Phelan JD, Kohlhammer H, Dubois SP, Yoo HM, Bachy E, Webster DE, Yang Y, Xu W, Yu X, Zhao H, Bryant BR, Shimono J, Ishio T, Maeda M, Green PL, Waldmann TA, Staudt LM. Targeting the HTLV-I-Regulated BATF3/IRF4 Transcriptional Network in Adult T Cell Leukemia/Lymphoma. Cancer Cell 2018; 34:286-297.e10. [PMID: 30057145 PMCID: PMC8078141 DOI: 10.1016/j.ccell.2018.06.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 04/25/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022]
Abstract
Adult T cell leukemia/lymphoma (ATLL) is a frequently incurable disease associated with the human lymphotropic virus type I (HTLV-I). RNAi screening of ATLL lines revealed that their proliferation depends on BATF3 and IRF4, which cooperatively drive ATLL-specific gene expression. HBZ, the only HTLV-I encoded transcription factor that is expressed in all ATLL cases, binds to an ATLL-specific BATF3 super-enhancer and thereby regulates the expression of BATF3 and its downstream targets, including MYC. Inhibitors of bromodomain-and-extra-terminal-domain (BET) chromatin proteins collapsed the transcriptional network directed by HBZ and BATF3, and were consequently toxic for ATLL cell lines, patient samples, and xenografts. Our study demonstrates that the HTLV-I oncogenic retrovirus exploits a regulatory module that can be attacked therapeutically with BET inhibitors.
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Affiliation(s)
- Masao Nakagawa
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Arthur L Shaffer
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michele Ceribelli
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Division of Pre-Clinical Innovation, NCATS, NIH, Bethesda, MD 20892, USA
| | - Meili Zhang
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - George Wright
- Biometric Research Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Wenming Xiao
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Division of Bioinformatics and Biostatistics, NCTR/FDA, Jefferson, AR 72079, USA
| | - John Powell
- Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael N Petrus
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yibin Yang
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Holger Kohlhammer
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sigrid P Dubois
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hee Min Yoo
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Emmanuel Bachy
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel E Webster
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yandan Yang
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Weihong Xu
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xin Yu
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Zhao
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Bonita R Bryant
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Joji Shimono
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Takashi Ishio
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Michiyuki Maeda
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Patrick L Green
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas A Waldmann
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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823
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Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting. BMC Genomics 2018; 19:604. [PMID: 30103702 PMCID: PMC6088408 DOI: 10.1186/s12864-018-4989-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 07/31/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome editing by CRISPR-Cas9 technology allows large-scale screening of gene essentiality in cancer. A confounding factor when interpreting CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes within copy number amplified regions of the genome. We have developed the computational tool CRISPRcleanR which is capable of identifying and correcting gene-independent responses to CRISPR-Cas9 targeting. CRISPRcleanR uses an unsupervised approach based on the segmentation of single-guide RNA fold change values across the genome, without making any assumption about the copy number status of the targeted genes. RESULTS Applying our method to existing and newly generated genome-wide essentiality profiles from 15 cancer cell lines, we demonstrate that CRISPRcleanR reduces false positives when calling essential genes, correcting biases within and outside of amplified regions, while maintaining true positive rates. Established cancer dependencies and essentiality signals of amplified cancer driver genes are detectable post-correction. CRISPRcleanR reports sgRNA fold changes and normalised read counts, is therefore compatible with downstream analysis tools, and works with multiple sgRNA libraries. CONCLUSIONS CRISPRcleanR is a versatile open-source tool for the analysis of CRISPR-Cas9 knockout screens to identify essential genes.
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Affiliation(s)
- Francesco Iorio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. .,Wellcome Sanger Institute, Cambridge, UK. .,Open Targets, Cambridge, UK.
| | - Fiona M Behan
- Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK.,Faculty of Medicine, Joint Research Center for Computational Biomedicine Aachen, RWTH Aachen University, Aachen, Germany.,Open Targets, Cambridge, UK.,Present address: Faculty of Medicine, Institute for Computational Biomedicine, Bioquant, Heidelberg University, Heidelberg, Germany
| | | | - Mathew J Garnett
- Wellcome Sanger Institute, Cambridge, UK. .,Open Targets, Cambridge, UK.
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824
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Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas. Hum Genet 2018; 137:665-678. [PMID: 30073413 PMCID: PMC6153521 DOI: 10.1007/s00439-018-1916-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022]
Abstract
Given the constantly improving cost and speed of genome sequencing, it is reasonable to expect that personal genomes will soon be known for many millions of humans. This stands in stark contrast with our limited ability to interpret the sequence variants which we find. Although it is, perhaps, easiest to interpret variants in coding regions, knowledge of functional impact is unknown for the vast majority of missense variants. While many computational approaches can predict the impact of coding variants, they are given a little weight in the current guidelines for interpreting clinical variants. Laboratory assays produce comparatively more trustworthy results, but until recently did not scale to the space of all possible mutations. The development of deep mutational scanning and other multiplexed assays of variant effect has now brought feasibility of this endeavour within view. Here, we review progress in this field over the last decade, break down the different approaches into their components, and compare methodological differences.
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825
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Noordermeer SM, Adam S, Setiaputra D, Barazas M, Pettitt SJ, Ling AK, Olivieri M, Álvarez-Quilón A, Moatti N, Zimmermann M, Annunziato S, Krastev DB, Song F, Brandsma I, Frankum J, Brough R, Sherker A, Landry S, Szilard RK, Munro MM, McEwan A, Goullet de Rugy T, Lin ZY, Hart T, Moffat J, Gingras AC, Martin A, van Attikum H, Jonkers J, Lord CJ, Rottenberg S, Durocher D. The shieldin complex mediates 53BP1-dependent DNA repair. Nature 2018; 560:117-121. [PMID: 30022168 PMCID: PMC6141009 DOI: 10.1038/s41586-018-0340-7] [Citation(s) in RCA: 409] [Impact Index Per Article: 68.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023]
Abstract
53BP1 is a chromatin-binding protein that regulates the repair of DNA double-strand breaks by suppressing the nucleolytic resection of DNA termini1,2. This function of 53BP1 requires interactions with PTIP3 and RIF14-9, the latter of which recruits REV7 (also known as MAD2L2) to break sites10,11. How 53BP1-pathway proteins shield DNA ends is currently unknown, but there are two models that provide the best potential explanation of their action. In one model the 53BP1 complex strengthens the nucleosomal barrier to end-resection nucleases12,13, and in the other 53BP1 recruits effector proteins with end-protection activity. Here we identify a 53BP1 effector complex, shieldin, that includes C20orf196 (also known as SHLD1), FAM35A (SHLD2), CTC-534A2.2 (SHLD3) and REV7. Shieldin localizes to double-strand-break sites in a 53BP1- and RIF1-dependent manner, and its SHLD2 subunit binds to single-stranded DNA via OB-fold domains that are analogous to those of RPA1 and POT1. Loss of shieldin impairs non-homologous end-joining, leads to defective immunoglobulin class switching and causes hyper-resection. Mutations in genes that encode shieldin subunits also cause resistance to poly(ADP-ribose) polymerase inhibition in BRCA1-deficient cells and tumours, owing to restoration of homologous recombination. Finally, we show that binding of single-stranded DNA by SHLD2 is critical for shieldin function, consistent with a model in which shieldin protects DNA ends to mediate 53BP1-dependent DNA repair.
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Affiliation(s)
- Sylvie M Noordermeer
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marco Barazas
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alexanda K Ling
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michele Olivieri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Nathalie Moatti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Michal Zimmermann
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Stefano Annunziato
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Inger Brandsma
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Alana Sherker
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sébastien Landry
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rachel K Szilard
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Meagan M Munro
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrea McEwan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Théo Goullet de Rugy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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826
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Aguirre AJ, Hahn WC. Synthetic Lethal Vulnerabilities in KRAS-Mutant Cancers. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031518. [PMID: 29101114 DOI: 10.1101/cshperspect.a031518] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
KRAS is the most commonly mutated oncogene in human cancer. Most KRAS-mutant cancers depend on sustained expression and signaling of KRAS, thus making it a high-priority therapeutic target. Unfortunately, development of direct small molecule inhibitors of KRAS function has been challenging. An alternative therapeutic strategy for KRAS-mutant malignancies involves targeting codependent vulnerabilities or synthetic lethal partners that are preferentially essential in the setting of oncogenic KRAS. KRAS activates numerous effector pathways that mediate proliferation and survival signals. Moreover, cancer cells must cope with substantial oncogenic stress conferred by mutant KRAS. These oncogenic signaling pathways and compensatory coping mechanisms of KRAS-mutant cancer cells form the basis for synthetic lethal interactions. Here, we review the compendium of previously identified codependencies in KRAS-mutant cancers, including the results of numerous functional genetic screens aimed at identifying KRAS synthetic lethal targets. Importantly, many of these vulnerabilities may represent tractable therapeutic opportunities.
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Affiliation(s)
- Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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827
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Mathews ES, Odom John AR. Tackling resistance: emerging antimalarials and new parasite targets in the era of elimination. F1000Res 2018; 7. [PMID: 30135714 PMCID: PMC6073090 DOI: 10.12688/f1000research.14874.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Malaria remains a significant contributor to global human mortality, and roughly half the world’s population is at risk for infection with
Plasmodium spp. parasites. Aggressive control measures have reduced the global prevalence of malaria significantly over the past decade. However, resistance to available antimalarials continues to spread, including resistance to the widely used artemisinin-based combination therapies. Novel antimalarial compounds and therapeutic targets are greatly needed. This review will briefly discuss several promising current antimalarial development projects, including artefenomel, ferroquine, cipargamin, SJ733, KAF156, MMV048, and tafenoquine. In addition, we describe recent large-scale genetic and resistance screens that have been instrumental in target discovery. Finally, we highlight new antimalarial targets, which include essential transporters and proteases. These emerging antimalarial compounds and therapeutic targets have the potential to overcome multi-drug resistance in ongoing efforts toward malaria elimination.
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Affiliation(s)
- Emily S Mathews
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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828
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Xiao T, Li W, Wang X, Xu H, Yang J, Wu Q, Huang Y, Geradts J, Jiang P, Fei T, Chi D, Zang C, Liao Q, Rennhack J, Andrechek E, Li N, Detre S, Dowsett M, Jeselsohn RM, Liu XS, Brown M. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Proc Natl Acad Sci U S A 2018; 115:7869-7878. [PMID: 29987050 PMCID: PMC6077722 DOI: 10.1073/pnas.1722617115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Endocrine therapy resistance invariably develops in advanced estrogen receptor-positive (ER+) breast cancer, but the underlying mechanisms are largely unknown. We have identified C-terminal SRC kinase (CSK) as a critical node in a previously unappreciated negative feedback loop that limits the efficacy of current ER-targeted therapies. Estrogen directly drives CSK expression in ER+ breast cancer. At low CSK levels, as is the case in patients with ER+ breast cancer resistant to endocrine therapy and with the poorest outcomes, the p21 protein-activated kinase 2 (PAK2) becomes activated and drives estrogen-independent growth. PAK2 overexpression is also associated with endocrine therapy resistance and worse clinical outcome, and the combination of a PAK2 inhibitor with an ER antagonist synergistically suppressed breast tumor growth. Clinical approaches to endocrine therapy-resistant breast cancer must overcome the loss of this estrogen-induced negative feedback loop that normally constrains the growth of ER+ tumors.
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Affiliation(s)
- Tengfei Xiao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Wei Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC 20010
- Department of Genomics and Precision Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20010
| | - Xiaoqing Wang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Han Xu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Jixin Yang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
- Department of Vascular and Endocrine Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Qiu Wu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Joseph Geradts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Peng Jiang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Teng Fei
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - David Chi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Chongzhi Zang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Qi Liao
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jonathan Rennhack
- Department of Physiology, Michigan State University, East Lansing, MI 48864
| | - Eran Andrechek
- Department of Physiology, Michigan State University, East Lansing, MI 48864
| | - Nanlin Li
- Department of Vascular and Endocrine Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Simone Detre
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Mitchell Dowsett
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Rinath M Jeselsohn
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215;
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215;
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
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829
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Explaining cancer type specific mutations with transcriptomic and epigenomic features in normal tissues. Sci Rep 2018; 8:11456. [PMID: 30061703 PMCID: PMC6065413 DOI: 10.1038/s41598-018-29861-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022] Open
Abstract
Most cancer driver genes are involved in generic cellular processes such as DNA repair, cell proliferation and cell adhesion, yet their mutations are often confined to specific cancer types. To resolve this paradox, we explained mutation frequencies of selected genes across tumor types with four features in the corresponding normal tissues from cancer-free subjects: mRNA expression and chromatin accessibility of mutated genes, mRNA expressions of their neighbors in curated pathways and the protein-protein interaction network. Encouragingly, these transcriptomic/epigenomic features in normal tissues were closely associated with mutational/functional characteristics in tumors. First, chromatin accessibility was a necessary but not sufficient condition for frequent mutations. Second, variations of mutation frequencies in selected genes across tissue types were significantly associated with all four features. Third, the genes possessing significant associations between mutation frequency variations and pathway gene expression were enriched with documented cancer genes. We further proposed a novel bivariate gene set enrichment analysis and confirmed that the pathway gene expression was the dominant factor in cancer gene enrichment. These findings shed lights on the functional roles of genes in normal tissues in shaping the mutational landscape during tumor genome evolution.
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830
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VanderSluis B, Costanzo M, Billmann M, Ward HN, Myers CL, Andrews BJ, Boone C. Integrating genetic and protein-protein interaction networks maps a functional wiring diagram of a cell. Curr Opin Microbiol 2018; 45:170-179. [PMID: 30059827 DOI: 10.1016/j.mib.2018.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 01/01/2023]
Abstract
Systematic experimental approaches have led to construction of comprehensive genetic and protein-protein interaction networks for the budding yeast, Saccharomyces cerevisiae. Genetic interactions capture functional relationships between genes using phenotypic readouts, while protein-protein interactions identify physical connections between gene products. These complementary, and largely non-overlapping, networks provide a global view of the functional architecture of a cell, revealing general organizing principles, many of which appear to be evolutionarily conserved. Here, we focus on insights derived from the integration of large-scale genetic and protein-protein interaction networks, highlighting principles that apply to both unicellular and more complex systems, including human cells. Network integration reveals fundamental connections involving key functional modules of eukaryotic cells, defining a core network of cellular function, which could be elaborated to explore cell-type specificity in metazoans.
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Affiliation(s)
- Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Henry N Ward
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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831
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Dhir A, Dhir S, Borowski LS, Jimenez L, Teitell M, Rötig A, Crow YJ, Rice GI, Duffy D, Tamby C, Nojima T, Munnich A, Schiff M, de Almeida CR, Rehwinkel J, Dziembowski A, Szczesny RJ, Proudfoot NJ. Mitochondrial double-stranded RNA triggers antiviral signalling in humans. Nature 2018; 560:238-242. [PMID: 30046113 DOI: 10.1038/s41586-018-0363-0] [Citation(s) in RCA: 380] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/06/2018] [Indexed: 11/09/2022]
Abstract
Mitochondria are descendants of endosymbiotic bacteria and retain essential prokaryotic features such as a compact circular genome. Consequently, in mammals, mitochondrial DNA is subjected to bidirectional transcription that generates overlapping transcripts, which are capable of forming long double-stranded RNA structures1,2. However, to our knowledge, mitochondrial double-stranded RNA has not been previously characterized in vivo. Here we describe the presence of a highly unstable native mitochondrial double-stranded RNA species at single-cell level and identify key roles for the degradosome components mitochondrial RNA helicase SUV3 and polynucleotide phosphorylase PNPase in restricting the levels of mitochondrial double-stranded RNA. Loss of either enzyme results in massive accumulation of mitochondrial double-stranded RNA that escapes into the cytoplasm in a PNPase-dependent manner. This process engages an MDA5-driven antiviral signalling pathway that triggers a type I interferon response. Consistent with these data, patients carrying hypomorphic mutations in the gene PNPT1, which encodes PNPase, display mitochondrial double-stranded RNA accumulation coupled with upregulation of interferon-stimulated genes and other markers of immune activation. The localization of PNPase to the mitochondrial inter-membrane space and matrix suggests that it has a dual role in preventing the formation and release of mitochondrial double-stranded RNA into the cytoplasm. This in turn prevents the activation of potent innate immune defence mechanisms that have evolved to protect vertebrates against microbial and viral attack.
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Affiliation(s)
- Ashish Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Laura Jimenez
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael Teitell
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Agnès Rötig
- INSERM UMR1163, Institut Imagine, Paris, France
| | - Yanick J Crow
- INSERM UMR1163, Institut Imagine, Paris, France.,Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France.,Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Gillian I Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Darragh Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France.,INSERM U1223, Paris, France
| | | | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | | | | | - Jan Rehwinkel
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland. .,Faculty of Biology, University of Warsaw, Warsaw, Poland.
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832
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Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Bronner IF, Casandra D, Mayho M, Brown J, Li S, Swanson J, Rayner JC, Jiang RHY, Adams JH. Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science 2018; 360:360/6388/eaap7847. [PMID: 29724925 DOI: 10.1126/science.aap7847] [Citation(s) in RCA: 552] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022]
Abstract
Severe malaria is caused by the apicomplexan parasite Plasmodium falciparum. Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of P. falciparum in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 Plasmodium-conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity.
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Affiliation(s)
- Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Deborah Casandra
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Matthew Mayho
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jacqueline Brown
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Suzanne Li
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Justin Swanson
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK.
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
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833
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Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA. Mapping the Genetic Landscape of Human Cells. Cell 2018; 174:953-967.e22. [PMID: 30033366 DOI: 10.1016/j.cell.2018.06.010] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/08/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022]
Abstract
Seminal yeast studies have established the value of comprehensively mapping genetic interactions (GIs) for inferring gene function. Efforts in human cells using focused gene sets underscore the utility of this approach, but the feasibility of generating large-scale, diverse human GI maps remains unresolved. We developed a CRISPR interference platform for large-scale quantitative mapping of human GIs. We systematically perturbed 222,784 gene pairs in two cancer cell lines. The resultant maps cluster functionally related genes, assigning function to poorly characterized genes, including TMEM261, a new electron transport chain component. Individual GIs pinpoint unexpected relationships between pathways, exemplified by a specific cholesterol biosynthesis intermediate whose accumulation induces deoxynucleotide depletion, causing replicative DNA damage and a synthetic-lethal interaction with the ATR/9-1-1 DNA repair pathway. Our map provides a broad resource, establishes GI maps as a high-resolution tool for dissecting gene function, and serves as a blueprint for mapping the genetic landscape of human cells.
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Affiliation(s)
- Max A Horlbeck
- 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, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albert Xu
- 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, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Min Wang
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Neal K Bennett
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Chong Y Park
- Innovative Genomics Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Derek Bogdanoff
- Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Britt Adamson
- 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, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric D Chow
- Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Tim R Peterson
- Department of Internal Medicine, Division of Bone and Mineral Diseases, and Department of Genetics, Institute for Public Health, Washington University School of Medicine, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, 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, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Luke A Gilbert
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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834
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Natsume T, Kanemaki MT. Conditional Degrons for Controlling Protein Expression at the Protein Level. Annu Rev Genet 2018; 51:83-102. [PMID: 29178817 DOI: 10.1146/annurev-genet-120116-024656] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
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835
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CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature 2018; 559:285-289. [PMID: 29973717 PMCID: PMC6071917 DOI: 10.1038/s41586-018-0291-z] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 06/07/2018] [Indexed: 12/18/2022]
Abstract
The observation that BRCA1- and BRCA2-deficient cells are sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors spurred their development into cancer therapies that target homologous recombination (HR) deficiency1. The cytotoxicity of PARP inhibitors depends on PARP trapping, the formation of non-covalent protein-DNA adducts composed of inhibited PARP1 bound to DNA lesions of unclear origins1–4. To address the nature of such lesions and the cellular consequences of PARP trapping, we undertook three CRISPR screens to identify genes and pathways that mediate cellular resistance to olaparib, a clinically approved PARP inhibitor1. Here were present a high-confidence set of 73 genes whose mutation causes increased PARP inhibitor sensitivity. In addition to an expected enrichment for HR-related genes, we discovered that mutation in all three genes encoding RNase H2 sensitized cells to PARP inhibition. We establish that the underlying cause of the PARP inhibitor hypersensitivity of RNase H2-deficient cells is impaired ribonucleotide excision repair (RER)5. Embedded ribonucleotides, abundant in the genome of RER-deficient cells, are substrates for topoisomerase 1 cleavage, resulting in PARP-trapping lesions that impede DNA replication and endanger genome integrity. We conclude that genomic ribonucleotides are a hitherto unappreciated source of PARP-trapping DNA lesions, and that the frequent deletion of RNASEH2B in metastatic prostate cancer and chronic lymphocytic leukemia could provide an opportunity to exploit these findings therapeutically.
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836
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de Weck A, Golji J, Jones MD, Korn JM, Billy E, McDonald ER, Schmelzle T, Bitter H, Kauffmann A. Correction of copy number induced false positives in CRISPR screens. PLoS Comput Biol 2018; 14:e1006279. [PMID: 30024886 PMCID: PMC6067744 DOI: 10.1371/journal.pcbi.1006279] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 07/31/2018] [Accepted: 06/07/2018] [Indexed: 01/10/2023] Open
Abstract
Cell autonomous cancer dependencies are now routinely identified using CRISPR loss-of-function viability screens. However, a bias exists that makes it difficult to assess the true essentiality of genes located in amplicons, since the entire amplified region can exhibit lethal scores. These false-positive hits can either be discarded from further analysis, which in cancer models can represent a significant number of hits, or methods can be developed to rescue the true-positives within amplified regions. We propose two methods to rescue true positive hits in amplified regions by correcting for this copy number artefact. The Local Drop Out (LDO) method uses the relative lethality scores within genomic regions to assess true essentiality and does not require additional orthogonal data (e.g. copy number value). LDO is meant to be used in screens covering a dense region of the genome (e.g. a whole chromosome or the whole genome). The General Additive Model (GAM) method models the screening data as a function of the known copy number values and removes the systematic effect from the measured lethality. GAM does not require the same density as LDO, but does require prior knowledge of the copy number values. Both methods have been developed with single sample experiments in mind so that the correction can be applied even in smaller screens. Here we demonstrate the efficacy of both methods at removing the copy number effect and rescuing hits from some of the amplified regions. We estimate a 70-80% decrease of false positive hits with either method in regions of high copy number compared to no correction.
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Affiliation(s)
- Antoine de Weck
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Javad Golji
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Michael D. Jones
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Joshua M. Korn
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | - Eric Billy
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - E. Robert McDonald
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
| | | | - Hans Bitter
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States of America
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837
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Ihry RJ, Worringer KA, Salick MR, Frias E, Ho D, Theriault K, Kommineni S, Chen J, Sondey M, Ye C, Randhawa R, Kulkarni T, Yang Z, McAllister G, Russ C, Reece-Hoyes J, Forrester W, Hoffman GR, Dolmetsch R, Kaykas A. p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med 2018; 24:939-946. [PMID: 29892062 DOI: 10.1038/s41591-018-0050-6] [Citation(s) in RCA: 638] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/28/2018] [Indexed: 12/13/2022]
Abstract
CRISPR/Cas9 has revolutionized our ability to engineer genomes and conduct genome-wide screens in human cells1-3. Whereas some cell types are amenable to genome engineering, genomes of human pluripotent stem cells (hPSCs) have been difficult to engineer, with reduced efficiencies relative to tumour cell lines or mouse embryonic stem cells3-13. Here, using hPSC lines with stable integration of Cas9 or transient delivery of Cas9-ribonucleoproteins (RNPs), we achieved an average insertion or deletion (indel) efficiency greater than 80%. This high efficiency of indel generation revealed that double-strand breaks (DSBs) induced by Cas9 are toxic and kill most hPSCs. In previous studies, the toxicity of Cas9 in hPSCs was less apparent because of low transfection efficiency and subsequently low DSB induction3. The toxic response to DSBs was P53/TP53-dependent, such that the efficiency of precise genome engineering in hPSCs with a wild-type P53 gene was severely reduced. Our results indicate that Cas9 toxicity creates an obstacle to the high-throughput use of CRISPR/Cas9 for genome engineering and screening in hPSCs. Moreover, as hPSCs can acquire P53 mutations14, cell replacement therapies using CRISPR/Cas9-enginereed hPSCs should proceed with caution, and such engineered hPSCs should be monitored for P53 function.
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Affiliation(s)
- Robert J Ihry
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Max R Salick
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Elizabeth Frias
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Kraig Theriault
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Julie Chen
- Department of Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Ranjit Randhawa
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Tripti Kulkarni
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Zinger Yang
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory McAllister
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Carsten Russ
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - John Reece-Hoyes
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - William Forrester
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory R Hoffman
- Department of Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ricardo Dolmetsch
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ajamete Kaykas
- Department of Neuroscience, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
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838
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Kurata JS, Lin RJ. MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs. RNA (NEW YORK, N.Y.) 2018; 24:966-981. [PMID: 29720387 PMCID: PMC6004052 DOI: 10.1261/rna.066282.118] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional gene regulators that play important roles in the control of cell fitness, differentiation, and development. The CRISPR-Cas9 gene-editing system is composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA) and directs DNA cleavage at a predetermined site. Several CRISPR-Cas9 libraries have been constructed for genome-scale knockout screens of protein function; however, few libraries have included miRNA genes. Here we constructed a miRNA-focused CRISPR-Cas9 library that targets 1594 (85%) annotated human miRNA stem-loops. The sgRNAs in our LX-miR library are designed to have high on-target and low off-target activity, and each miRNA is targeted by four to five sgRNAs. We used this sgRNA library to screen for miRNAs that affect cell fitness of HeLa or NCI-N87 cells by monitoring the change in frequency of each sgRNA over time. By considering the expression in the tested cells and the dysregulation of the miRNAs in cancer specimens, we identified five HeLa pro-fitness and cervical cancer up-regulated miRNAs (miR-31-5p, miR-92b-3p, miR-146b-5p, miR-151a-3p, and miR-194-5p). Similarly, we identified six NCI-N87 pro-fitness and gastric cancer up-regulated miRNAs (miR-95-3p, miR-181a-5p, miR-188-5p, miR-196b-5p, miR-584-5p, and miR-1304-3p), as well as three anti-fitness and down-regulated miRNAs (let-7a-3p, miR-100-5p, and miR-149-5p). Some of those miRNAs are known to be oncogenic or tumor-suppressive, but others are novel. Taken together, the LX-miR library is useful for genome-wide unbiased screening to identify miRNAs important for cellular fitness and likely to be useful for other functional screens.
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Affiliation(s)
- Jessica S Kurata
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences of the City of Hope, Duarte, California 91010, USA
| | - Ren-Jang Lin
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences of the City of Hope, Duarte, California 91010, USA
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839
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CK1α and IRF4 are essential and independent effectors of immunomodulatory drugs in primary effusion lymphoma. Blood 2018; 132:577-586. [PMID: 29954751 DOI: 10.1182/blood-2018-01-828418] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Primary effusion lymphoma (PEL) is an aggressive cancer with few treatment options. The immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide have recently been shown to kill PEL cell lines, and lenalidomide is in clinical trials against PEL. IMiDs bind to the CRL4CRBN E3 ubiquitin ligase complex, leading to the acquisition of the Ikaros family zinc finger proteins 1 and 3 (IKZF1 and IKZF3), casein kinase 1 α (CK1α), and zinc finger protein 91 (ZFP91) as neosubstrates. IMiDs are effective against multiple myeloma because of degradation of IKZF1 and IKZF3 and the consequent loss of interferon regulatory factor 4 (IRF4) and MYC expression. Lenalidomide is also effective in chromosome 5q deletion-associated myelodysplastic syndrome as a result of degradation of CK1α. An essential IKZF1-IRF4-MYC axis has recently been proposed to underlie the toxicity of IMiDs in PEL. Here, we further investigate IMiD effectors in PEL cell lines, based on genome-wide CRISPR/Cas9 screens for essential human genes. These screens and extensive validation experiments show that, of the 4 neosubstrates, only CK1α is essential for the survival of PEL cell lines. In contrast, IKZF1 and IKZF3 are dispensable, individually or in combination. IRF4 was critical in all 8 PEL cell lines tested, and surprisingly, IMiDs triggered downregulation of IRF4 expression independently of both IKZF1 and IKZF3. Reexpression of CK1α and/or IRF4 partially rescued PEL cell lines from IMiD-mediated toxicity. In conclusion, IMiD toxicity in PEL cell lines is independent of IKZF1 and IKZF3 but proceeds through degradation of the neosubstrate CK1α and downregulation of IRF4.
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840
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Chuai G, Ma H, Yan J, Chen M, Hong N, Xue D, Zhou C, Zhu C, Chen K, Duan B, Gu F, Qu S, Huang D, Wei J, Liu Q. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biol 2018; 19:80. [PMID: 29945655 PMCID: PMC6020378 DOI: 10.1186/s13059-018-1459-4] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized design of sgRNAs with high sensitivity and specificity. Here we present DeepCRISPR, a comprehensive computational platform to unify sgRNA on-target and off-target site prediction into one framework with deep learning, surpassing available state-of-the-art in silico tools. In addition, DeepCRISPR fully automates the identification of sequence and epigenetic features that may affect sgRNA knockout efficacy in a data-driven manner. DeepCRISPR is available at http://www.deepcrispr.net/ .
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Affiliation(s)
- Guohui Chuai
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jifang Yan
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Ming Chen
- R&D Information, Innovation Center China, AstraZeneca, 199 Liangjing Road, Shanghai, 201203, China
| | - Nanfang Hong
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Dongyu Xue
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Chi Zhou
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Chenyu Zhu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Ke Chen
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Bin Duan
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Feng Gu
- State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Sheng Qu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Deshuang Huang
- Machine Learning & Systems Biology Lab, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, China.
| | - Jia Wei
- R&D Information, Innovation Center China, AstraZeneca, 199 Liangjing Road, Shanghai, 201203, China.
| | - Qi Liu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 20009, China.
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China.
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841
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Phelan JD, Young RM, Webster DE, Roulland S, Wright GW, Kasbekar M, Shaffer AL, Ceribelli M, Wang JQ, Schmitz R, Nakagawa M, Bachy E, Huang DW, Ji Y, Chen L, Yang Y, Zhao H, Yu X, Xu W, Palisoc MM, Valadez RR, Davies-Hill T, Wilson WH, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Rodriguez FJ, Estephan F, Holdhoff M, Kruhlak MJ, Hewitt SM, Thomas CJ, Pittaluga S, Oellerich T, Staudt LM. A multiprotein supercomplex controlling oncogenic signalling in lymphoma. Nature 2018; 560:387-391. [PMID: 29925955 PMCID: PMC6201842 DOI: 10.1038/s41586-018-0290-0] [Citation(s) in RCA: 252] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/13/2018] [Indexed: 12/11/2022]
Abstract
B cell receptor (BCR) signalling has emerged as a therapeutic target in B cell lymphomas, but inhibiting this pathway in diffuse large B cell lymphoma (DLBCL) has benefited only a subset of patients1. Gene expression profiling identified two major subtypes of DLBCL, known as germinal centre B cell-like and activated B cell-like (ABC)2,3, that show poor outcomes after immunochemotherapy in ABC. Autoantigens drive BCR-dependent activation of NF-κB in ABC DLBCL through a kinase signalling cascade of SYK, BTK and PKCβ to promote the assembly of the CARD11-BCL10-MALT1 adaptor complex, which recruits and activates IκB kinase4-6. Genome sequencing revealed gain-of-function mutations that target the CD79A and CD79B BCR subunits and the Toll-like receptor signalling adaptor MYD885,7, with MYD88(L265P) being the most prevalent isoform. In a clinical trial, the BTK inhibitor ibrutinib produced responses in 37% of cases of ABC1. The most striking response rate (80%) was observed in tumours with both CD79B and MYD88(L265P) mutations, but how these mutations cooperate to promote dependence on BCR signalling remains unclear. Here we used genome-wide CRISPR-Cas9 screening and functional proteomics to determine the molecular basis of exceptional clinical responses to ibrutinib. We discovered a new mode of oncogenic BCR signalling in ibrutinib-responsive cell lines and biopsies, coordinated by a multiprotein supercomplex formed by MYD88, TLR9 and the BCR (hereafter termed the My-T-BCR supercomplex). The My-T-BCR supercomplex co-localizes with mTOR on endolysosomes, where it drives pro-survival NF-κB and mTOR signalling. Inhibitors of BCR and mTOR signalling cooperatively decreased the formation and function of the My-T-BCR supercomplex, providing mechanistic insight into their synergistic toxicity for My-T-BCR+ DLBCL cells. My-T-BCR supercomplexes characterized ibrutinib-responsive malignancies and distinguished ibrutinib responders from non-responders. Our data provide a framework for the rational design of oncogenic signalling inhibitors in molecularly defined subsets of DLBCL.
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Affiliation(s)
- James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryan M Young
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel E Webster
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sandrine Roulland
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Monica Kasbekar
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arthur L Shaffer
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michele Ceribelli
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Gaithersburg, MD, USA
| | - James Q Wang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Roland Schmitz
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Masao Nakagawa
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emmanuel Bachy
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yanlong Ji
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Gaithersburg, MD, USA
| | - Yandan Yang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Zhao
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xin Yu
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weihong Xu
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maryknoll M Palisoc
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Racquel R Valadez
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Theresa Davies-Hill
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wing C Chan
- Departments of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Elaine S Jaffe
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Randy D Gascoyne
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Elias Campo
- Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute for Clinical Pharmacology, Stuttgart, Germany
| | - Jan Delabie
- University Health Network, Laboratory Medicine Program, Toronto General Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fayez Estephan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthias Holdhoff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Craig J Thomas
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Gaithersburg, MD, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Oellerich
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. .,Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany. .,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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842
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LDHA in Neuroblastoma Is Associated with Poor Outcome and Its Depletion Decreases Neuroblastoma Growth Independent of Aerobic Glycolysis. Clin Cancer Res 2018; 24:5772-5783. [DOI: 10.1158/1078-0432.ccr-17-2578] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022]
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843
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RIOK1 kinase activity is required for cell survival irrespective of MTAP status. Oncotarget 2018; 9:28625-28637. [PMID: 29983885 PMCID: PMC6033344 DOI: 10.18632/oncotarget.25586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/19/2018] [Indexed: 01/03/2023] Open
Abstract
Genotype specific vulnerabilities of cancer cells constitute a promising strategy for the development of new therapeutics. Deletions of non-essential genes in tumors can generate unique vulnerabilities which could be exploited therapeutically. The MTAP gene is recurrently deleted in human cancers because of its chromosomal proximity to the tumor suppressor gene CDKN2A. Recent studies have uncovered an increased dependency of MTAP-deleted cancer cells on the function of a PRMT5 containing complex, including WDR77, PRMT5 and the kinase RIOK1. As RIOK1 kinase activity constitutes a potential therapeutic target, we wanted to test if MTAP deletion confers increased sensitivity to RIOK1 inhibition. Using CRISPR/Cas9-mediated genome engineering we generated analog sensitive alleles of RIOK1 in isogenic cell lines differing only by MTAP status. While we were able to independently confirm an increased dependency of MTAP-deleted cells on PRMT5, we did not detect a differential requirement for RIOK1 kinase activity between MTAP-proficient and deficient cells. Our results reveal that the kinase activity of RIOK1 is required for the survival of cancer cell lines irrespective of their MTAP status and cast doubt on the therapeutic exploitability of RIOK1 in the context of MTAP-deleted cancers.
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844
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Lampert F, Stafa D, Goga A, Soste MV, Gilberto S, Olieric N, Picotti P, Stoffel M, Peter M. The multi-subunit GID/CTLH E3 ubiquitin ligase promotes cell proliferation and targets the transcription factor Hbp1 for degradation. eLife 2018; 7:35528. [PMID: 29911972 PMCID: PMC6037477 DOI: 10.7554/elife.35528] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/16/2018] [Indexed: 12/17/2022] Open
Abstract
In yeast, the glucose-induced degradation-deficient (GID) E3 ligase selectively degrades superfluous gluconeogenic enzymes. Here, we identified all subunits of the mammalian GID/CTLH complex and provide a comprehensive map of its hierarchical organization and step-wise assembly. Biochemical reconstitution demonstrates that the mammalian complex possesses inherent E3 ubiquitin ligase activity, using Ube2H as its cognate E2. Deletions of multiple GID subunits compromise cell proliferation, and this defect is accompanied by deregulation of critical cell cycle markers such as the retinoblastoma (Rb) tumor suppressor, phospho-Histone H3 and Cyclin A. We identify the negative regulator of pro-proliferative genes Hbp1 as a bonafide GID/CTLH proteolytic substrate. Indeed, Hbp1 accumulates in cells lacking GID/CTLH activity, and Hbp1 physically interacts and is ubiquitinated in vitro by reconstituted GID/CTLH complexes. Our biochemical and cellular analysis thus demonstrates that the GID/CTLH complex prevents cell cycle exit in G1, at least in part by degrading Hbp1.
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Affiliation(s)
| | - Diana Stafa
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Algera Goga
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | | | | | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
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845
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Sharma S, Bartholdson SJ, Couch ACM, Yusa K, Wright GJ. Genome-scale identification of cellular pathways required for cell surface recognition. Genome Res 2018; 28:1372-1382. [PMID: 29914970 PMCID: PMC6120632 DOI: 10.1101/gr.231183.117] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 06/15/2018] [Indexed: 02/07/2023]
Abstract
Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challenges by using a genome-scale, cell-based genetic screening approach using CRISPR gene knockout technology to identify cellular pathways required for specific cell surface recognition events. By using high-affinity monoclonal antibodies and low-affinity ligands, we determined the necessary screening parameters, including the importance of establishing binding contributions from the glycocalyx, that permitted the unequivocal identification of genes encoding directly interacting membrane-embedded receptors with high statistical confidence. Importantly, we show that this genome-wide screening approach additionally identified receptor-specific pathways that are required for functional display of receptors on the cell surface that included chaperones, enzymes that add post-translational modifications, trafficking proteins, and transcription factors. Finally, we demonstrate the utility of the approach by identifying IGF2R (insulin like growth factor 2 receptor) as a binding partner for the R2 subunit of GABAB receptors. We show that this interaction is direct and is critically dependent on mannose-6-phosphate, providing a mechanism for the internalization and regulation of GABAB receptor signaling. We conclude that this single approach can reveal both the molecular nature and the genetic pathways required for functional cell surface display of receptors recognized by antibodies, secreted proteins, and membrane-embedded ligands without the need to make any prior assumptions regarding their biochemical properties.
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Affiliation(s)
- Sumana Sharma
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - S Josefin Bartholdson
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Amalie C M Couch
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Kosuke Yusa
- Stem Cell Genetics Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
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846
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Genetic Network Complexity Shapes Background-Dependent Phenotypic Expression. Trends Genet 2018; 34:578-586. [PMID: 29903533 DOI: 10.1016/j.tig.2018.05.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/09/2018] [Accepted: 05/17/2018] [Indexed: 11/22/2022]
Abstract
The phenotypic consequences of a given mutation can vary across individuals. This so-called background effect is widely observed, from mutant fitness of loss-of-function variants in model organisms to variable disease penetrance and expressivity in humans; however, the underlying genetic basis often remains unclear. Taking insights gained from recent large-scale surveys of genetic interaction and suppression analyses in yeast, we propose that the genetic network context for a given mutation may shape its propensity of exhibiting background-dependent phenotypes. We argue that further efforts in systematically mapping the genetic interaction networks beyond yeast will provide not only key insights into the functional properties of genes, but also a better understanding of the background effects and the (un)predictability of traits in a broader context.
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847
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Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. CONSERV GENET 2018; 19:995-1005. [PMID: 30100824 PMCID: PMC6061128 DOI: 10.1007/s10592-018-1072-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - K. C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA 95618 USA
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Patrick T. Reilly
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
| | - Michelle Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - the IMPC consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
- Mouse Biology Program, University of California, Davis, CA 95618 USA
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
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848
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Skucha A, Ebner J, Schmöllerl J, Roth M, Eder T, César-Razquin A, Stukalov A, Vittori S, Muhar M, Lu B, Aichinger M, Jude J, Müller AC, Győrffy B, Vakoc CR, Valent P, Bennett KL, Zuber J, Superti-Furga G, Grebien F. MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. Nat Commun 2018; 9:1983. [PMID: 29777171 PMCID: PMC5959866 DOI: 10.1038/s41467-018-04329-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
MLL-fusions represent a large group of leukemia drivers, whose diversity originates from the vast molecular heterogeneity of C-terminal fusion partners of MLL. While studies of selected MLL-fusions have revealed critical molecular pathways, unifying mechanisms across all MLL-fusions remain poorly understood. We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. Functional investigation of 128 conserved MLL-fusion-interactors identifies a specific role for the lysine methyltransferase SETD2 in MLL-leukemia. SETD2 loss causes growth arrest and differentiation of AML cells, and leads to increased DNA damage. In addition to its role in H3K36 tri-methylation, SETD2 is required to maintain high H3K79 di-methylation and MLL-AF9-binding to critical target genes, such as Hoxa9. SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. These results uncover a dependency for SETD2 during MLL-leukemogenesis, revealing a novel actionable vulnerability in this disease.
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Affiliation(s)
- Anna Skucha
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | - Jessica Ebner
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | | | - Mareike Roth
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Thomas Eder
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria
| | - Adrián César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Sarah Vittori
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Matthias Muhar
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Bin Lu
- Cold Spring Harbor Larboratory, Cold Spring Harbor, 11724, NY, USA
| | - Martin Aichinger
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Second Department of Pediatrics, Semmelweis University, Budapest, 1094, Hungary
| | | | - Peter Valent
- Department of Internal Medicine I. Division of Hematology and Hemostaseology, Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, 1090, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna, 1030, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, 1090, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Vienna, 1090, Austria.
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, 1210, Austria.
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849
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Dai Z, Mentch SJ, Gao X, Nichenametla SN, Locasale JW. Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width. Nat Commun 2018; 9:1955. [PMID: 29769529 PMCID: PMC5955993 DOI: 10.1038/s41467-018-04426-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/27/2018] [Indexed: 01/07/2023] Open
Abstract
Nutrition and metabolism are known to influence chromatin biology and epigenetics through post-translational modifications, yet how this interaction influences genomic architecture and connects to gene expression is unknown. Here we consider, as a model, the metabolically-driven dynamics of H3K4me3, a histone methylation mark that is known to encode information about active transcription, cell identity, and tumor suppression. We analyze the genome-wide changes in H3K4me3 and gene expression in response to alterations in methionine availability in both normal mouse physiology and human cancer cells. Surprisingly, we find that the location of H3K4me3 peaks is largely preserved under methionine restriction, while the response of H3K4me3 peak width encodes almost all aspects of H3K4me3 biology including changes in expression levels, and the presence of cell identity and cancer-associated genes. These findings may reveal general principles for how nutrient availability modulates specific aspects of chromatin dynamics to mediate biological function.
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Affiliation(s)
- Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Samantha J Mentch
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xia Gao
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | | | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Molecular Physiology Institute, Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
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Pan J, Meyers RM, Michel BC, Mashtalir N, Sizemore AE, Wells JN, Cassel SH, Vazquez F, Weir BA, Hahn WC, Marsh JA, Tsherniak A, Kadoch C. Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. Cell Syst 2018; 6:555-568.e7. [PMID: 29778836 DOI: 10.1016/j.cels.2018.04.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/03/2018] [Accepted: 04/24/2018] [Indexed: 11/15/2022]
Abstract
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex. Finally, by integrating functional networks with large protein-protein interaction networks, we discovered novel protein complexes involving recently evolved genes of unknown function. Taken together, these findings demonstrate the utility of genetic perturbation screens alone, and in combination with large-scale biophysical data, to enhance our understanding of mammalian protein complexes in normal and disease states.
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Affiliation(s)
- Joshua Pan
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Robin M Meyers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Brittany C Michel
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nazar Mashtalir
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Ann E Sizemore
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Seth H Cassel
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA; Medical Scientist Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Cigall Kadoch
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA.
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